- GCR_STDERR - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GCR_STDERR_BUFFERSIZE - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GCR_STDOUT - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GCR_STDOUT_BUFFERSIZE - Static variable in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- generatedValue(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
-
- generateLaneInfo(String, int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
-
Generates lane info with the given parameters.
- generateRunInfo(String, String, String, String, String, String, String, String, String, int, int, boolean, String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
-
Generates a RunInfo object with the given parameters.
- generateRunnerLine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob
-
- generateRunnerLine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- generateSampleInfo(String, String, String, String, String, String, String, String, String, int, String, String, String, String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
-
Generates a sample info object given the fields, and prompts for null fields if the interactive flag is on.
- generateWorkflowXml(AbstractWorkflowDataModel, String, String, Path, boolean, File, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowXmlGenerator
-
generate a dax file from the object model
- GenericCommandRunner - Class in net.sourceforge.seqware.pipeline.modules
-
This is a very simple module that takes a few options on the command line and then passes the rest of the arguments to whatever command
is specified.
- GenericCommandRunner() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
- GenericMetadataSaver - Class in net.sourceforge.seqware.pipeline.modules
-
Deprecated.
Deprecating this in favour of Metadata(plugin) and the new CLI
- GenericMetadataSaver() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
-
Deprecated.
- GEO_REACTION_ID_ATTR_TAG - Static variable in class net.sourceforge.seqware.common.model.Sample
-
The presence of this attribute is used to identify that the sample is a library
- get(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
-
get.
- get(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
-
get.
- get(File) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
-
get.
- get(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
-
get.
- get(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
-
get.
- get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
-
get.
- get(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
-
get.
- get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
-
get.
- get(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
-
get.
- get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
-
get.
- get(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
-
get.
- get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
-
get.
- get(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
-
get.
- get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
-
get.
- get() - Static method in class net.sourceforge.seqware.common.factory.DBAccess
-
- get(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
- get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
- get() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
- get() - Static method in enum net.sourceforge.seqware.webservice.resources.TomcatVersion
-
- get_description() - Method in class io.seqware.pipeline.plugins.FileProvenanceQueryTool
-
- get_description() - Method in class io.seqware.pipeline.plugins.sanity.SanityCheck
-
get_description.
- get_description() - Method in class io.seqware.pipeline.plugins.UserSettingsPlugin
-
get_description.
- get_description() - Method in class io.seqware.pipeline.plugins.WorkflowLauncher
-
- get_description() - Method in class io.seqware.pipeline.plugins.WorkflowLifecycle
-
- get_description() - Method in class io.seqware.pipeline.plugins.WorkflowRelauncher
-
- get_description() - Method in class io.seqware.pipeline.plugins.WorkflowRescheduler
-
- get_description() - Method in class io.seqware.pipeline.plugins.WorkflowScheduler
-
- get_description() - Method in class io.seqware.pipeline.plugins.WorkflowWatcher
-
- get_description() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.deletion.DeletionDB
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.fileprovenance.FileProvenanceReporter
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
-
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
get_description.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
-
Generates a short description of the plugin, preferably one line.
- get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
-
Generates a short description of the plugin, preferably one line.
- get_galaxy_xml() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Output Galaxy definition files so you can use this module with Galaxy.
- get_syntax() - Method in class io.seqware.pipeline.plugins.UserSettingsPlugin
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Generates a "help" message for the user of the module.
- get_syntax() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
-
Generates a "help" message for the user of the module.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
Generates a "help" message for the user of the module.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
-
Deprecated.
Generates a "help" message for the user of the module.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
get_syntax.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
-
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Generates a "help" message for the user of the plugin.
- get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Generates a "help" message for the user of the plugin.
- get_workflow_info(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
get_workflow_info.
- get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
get_workflow_info.
- get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
get_workflow_info.
- get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
get_workflow_info.
- get_workflow_run_accession(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
get_workflow_run_accession.
- get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
get_workflow_run_accession.
- get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
get_workflow_run_accession.
- get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
get_workflow_run_accession.
- get_workflow_run_id(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
get_workflow_run_id.
- get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
get_workflow_run_id.
- get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
get_workflow_run_id.
- get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
get_workflow_run_id.
- getAbstract1() - Method in class io.seqware.webservice.generated.model.Study
-
- getAbstractStr() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field abstractStr.
- getAccession() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- getAccession() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- getAccession() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getAccession() - Method in class io.seqware.webservice.generated.model.Organism
-
- getAccession() - Method in class io.seqware.webservice.generated.model.Study
-
- getAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field accession.
- getAccession() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field accession.
- getAccession() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field accession.
- getAccessionByActionExternalID(String) - Static method in class io.seqware.WorkflowRuns
-
Extremely extremely expensive! Converts between sge id and determines the workflow run accession that it corresponds to.
- getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob
-
- getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob
-
- getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getActive() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field active.
- getActive() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field active.
- getAdapters() - Method in class io.seqware.webservice.generated.model.Sample
-
- getAdapters() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field adapters.
- getAdapterSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getAdapterSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field adapterSpec.
- getAddedSurcharge() - Method in class io.seqware.webservice.generated.model.Expense
-
- getAddedSurcharge() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field addedSurcharge.
- getAdminModelClass() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- getAdminModelClass() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- getAgent() - Method in class io.seqware.webservice.generated.model.Expense
-
- getAgent() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field agent.
- getAlgo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
get the job algorithm
- getAlgorithm() - Method in class io.seqware.webservice.generated.model.Processing
-
- getAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field algorithm.
- getAlgorithm() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field algorithm.
- getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field algorithm.
- getAlgorithm() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
-
getAlgorithm.
- getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
-
Getter for the field algorithm.
- getAlias() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Ius
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Lane
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Sample
-
- getAlias() - Method in class io.seqware.webservice.generated.model.Study
-
- getAlias() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field alias.
- getAlias() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field alias.
- getAlias() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field alias.
- getAlias() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field alias.
- getAlign() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getAll() - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
-
getAll.
- getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
-
getAll.
- getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
-
getAll.
- getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
-
getAll.
- getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
-
getAll.
- getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
-
getAll.
- getAllHtml(Lane, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getAllHtml.
- getAllHtml(IUS, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getAllHtml.
- getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getAllHtml.
- getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getAllHtml.
- getAllHtml(IUS, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getAllHtml.
- getAllHtml(Study, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllHtml(Experiment, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllHtml(Sample, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllHtml(Lane, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getAllHtml.
- getAllInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field allInputFiles.
- getAllItems() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field allItems.
- getAllProcessing() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getAllProcessing.
- getAllProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
-
getAllProcessings.
- getAllRuns() - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.
- getAllSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Get all selected Files, the files are organized by the name of the parameter (key) and a list of files selected (value) via a hash.
- getAllSequencerRuns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get all of the sequencer runs in the DB.
- getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getAllSequencerRuns.
- getAllStudies() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getAllStudies.
- getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getAllStudies.
- getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getAllStudies.
- getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getAllStudies.
- getAnalysisWorkflowHtml(WorkflowRun, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getAnalysisWorkflowHtml.
- getAncestorWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getAnnotations() - Method in interface net.sourceforge.seqware.common.model.Annotatable
-
Get the annotations for this model
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.Experiment
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.File
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.IUS
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.Processing
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.Sample
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.Study
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.Workflow
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getAnnotations() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getAnnotations() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getAnnotations() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
Set arbitrary key-value annotations on jobs.
- getAnnotations() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
Set arbitrary key-value annotations on provisioned files.
- getAnonymizedName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getAnonymizedName() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field anonymizedName.
- getApplication() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
- getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
- getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
-
Getter for the field arguments.
- getAssayType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of assayType
- getAsText() - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
-
getAsText.
- getAttribute(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
getAttribute.
- getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
-
Getter for the field attribute.
- getAttributes() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field attributes.
- getBarcode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of barcode
- getBaseCaller() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getBaseCaller() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getBaseCaller() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field baseCaller.
- getBaseCoord() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getBaseCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field baseCoord.
- getBaseDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field baseDir.
- getBaseIniFile() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getBaseIniFile() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field baseIniFile.
- getBatchSize() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieBashJob
-
- getBatchSize() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.BatchedOozieProvisionFileJob
-
- getBundle_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getBundleInfo(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
getBundleInfo.
- getCategory() - Method in enum io.seqware.pipeline.SqwKeys
-
For documentation
- getCategoryDescription() - Method in enum io.seqware.pipeline.SqwKeys.Categories
-
For documentation
- getCell() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
-
- getCenterName() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getCenterName() - Method in class io.seqware.webservice.generated.model.Study
-
- getCenterName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field centerName.
- getCenterName() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field centerName.
- getCenterProjectName() - Method in class io.seqware.webservice.generated.model.Study
-
- getCenterProjectName() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field centerProjectName.
- getChildId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getChildId() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getChildren() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field children.
- getChildren() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field children.
- getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getChildSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field childSample.
- getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field childSample.
- getChildSampleId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getChildSampleId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getChildSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getChildSamples.
- getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getChildSamples.
- getChildSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getChildSamples.
- getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getChildSamples.
- getChildSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the child samples of a parent sample.
- getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getClassesDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field classesDir.
- getClassPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getClient() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- getClientNotes() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getClientNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field clientNotes.
- getCliString() - Method in enum io.seqware.Engines.TYPES
-
- getCmd() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getCmd() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getCode() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getCode() - Method in class io.seqware.webservice.generated.model.Organism
-
- getCode() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field code.
- getColorMatrix() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field colorMatrix.
- getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field colorMatrix.
- getColorMatrixCode() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field colorMatrixCode.
- getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field colorMatrixCode.
- getCommand() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field command.
- getCommand() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field command.
- getCommand() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field command.
- getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getCommand() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- getCommonName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getCompleted() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field completed.
- getCompute() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getComputeReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field computeReq.
- getConfigPath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field configPath.
- getConfigs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getConfirmEmailAddress() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Getter for the field confirmEmailAddress.
- getConfirmPassword() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Getter for the field confirmPassword.
- getConstructionProtocol() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getConstructionProtocol() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field constructionProtocol.
- getCountFile() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field countFile.
- getCountFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getCountFiles.
- getCountFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getCountFiles.
- getCountFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getCountFiles.
- getCountFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getCountFiles.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field createTimestamp.
- getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field createTimestamp.
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Ius
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Registration
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Sample
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Study
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getCreateTstmp() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getCriteria() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Getter for the field criteria.
- getCurrentSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentSelectedFiles.
- getCurrentSelectedNodes(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentSelectedNodes.
- getCurrentWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentWorkflow.
- getCurrentWorkflowParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getCurrentWorkflowParam.
- getCurrentWorkingDir() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getCurrentWorkingDir() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getCurrentWorkingDir() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field currentWorkingDir.
- getCwd() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field cwd.
- getCycleCoord() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getCycleCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field cycleCoord.
- getCycleCount() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCycleCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycleCount.
- getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycleCount.
- getCycleDescriptor() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCycleDescriptor() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field cycleDescriptor.
- getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycleDescriptor.
- getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycleDescriptor.
- getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycles.
- getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycles.
- getCycleSequence() - Method in class io.seqware.webservice.generated.model.Lane
-
- getCycleSequence() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field cycleSequence.
- getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field cycleSequence.
- getDate() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getDax() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getDax() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field dax.
- getDaysUntilDue() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getDaysUntilDue() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field daysUntilDue.
- getDb() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getDb() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
Getter for the field db.
- getDB(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- getDbmd() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
Getter for the field dbmd.
- getDecodeMethod() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getDecodeMethod() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field decodeMethod.
- getDecryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Gets cipher by DecryptKey.
- getDecryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
getDecryptCipher.
- getDEFAULT_DB_HOST() - Method in class io.seqware.metadb.util.TestDatabaseCreator
-
- getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getDEFAULT_DB_HOST() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getDefaultValue() - Method in enum io.seqware.pipeline.SqwKeys
-
This is the value used to populate our auto-generated documentation
- getDefaultValue() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field defaultValue.
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.ClientServerConsistencyCheck
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck
-
- getDescription() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check
-
- getDescription() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface
-
Describes the check and indicates what may be wrong
- getDescription() - Method in enum io.seqware.pipeline.SqwKeys
-
For documentation
- getDescription() - Method in class io.seqware.webservice.generated.model.Expense
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getDescription() - Method in class io.seqware.webservice.generated.model.File
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Ius
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Lane
-
- getDescription() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getDescription() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getDescription() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Platform
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Processing
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getDescription() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Sample
-
- getDescription() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Study
-
- getDescription() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getDescription() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getDescription() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getDescription() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field description.
- getDescription() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field description.
- getDeveloperMl() - Method in class io.seqware.webservice.generated.model.Registration
-
- getDirContext() - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
-
getDirContext.
- getDirectories() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getDirectoriesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
-
Getter for the field directoriesNumber.
- getDirectorySize() - Method in class net.sourceforge.solexatools.util.FileFinder
-
getDirectorySize.
- getDisplay() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field display.
- getDisplay() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getDisplayName() - Method in class io.seqware.webservice.generated.model.FileType
-
- getDisplayName() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getDisplayName() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getDisplayName() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field displayName.
- getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field displayName.
- getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field displayName.
- getDisplayName() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field displayName.
- getDisplayValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field displayValue.
- getDomainObject() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Getter for the field domainObject.
- getDomainObject() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Getter for the field domainObject.
- getEmail() - Method in class io.seqware.webservice.generated.model.Registration
-
- getEmailAddress() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field emailAddress.
- getEncryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Gets cipher by EncryptKey.
- getEncryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
getEncryptCipher.
- getEnd() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field end.
- getEndDate() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getEndDate() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field endDate.
- getEndPage() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field endPage.
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.AbstractFacade
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExpenseAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExpenseFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentLibraryDesignFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentLinkFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ExperimentSpotDesignReadSpecFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileReportFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.FileTypeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.InvoiceAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.InvoiceFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.IusWorkflowRunsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneTypeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LaneWorkflowRunsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibrarySelectionFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibrarySourceFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.LibraryStrategyFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.OrganismFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.PlatformFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingExperimentsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingFilesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingIusFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingLanesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingRelationshipFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingSamplesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingSequencerRunsFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ProcessingStudiesFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.RegistrationFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SampleReportFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.SequencerRunFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareStudyFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.StudyTypeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowParamFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowParamValueFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunAttributeFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunFacadeREST
-
- getEntityManager() - Method in class io.seqware.webservice.generated.controller.WorkflowRunParamFacadeREST
-
- getEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getEnvironmentReport() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Retrieves all environmental information from the web-service
- getEnvironmentReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getEnvironmentReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getEnvironmentReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getEnvironmentReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getError() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
Getter for the field error.
- getErrorCnt() - Method in class net.sourceforge.seqware.common.model.Lane
-
getErrorCnt.
- getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getErrorCnt.
- getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
getErrorCnt.
- getErrorCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field errorCount.
- getExecutionEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getExistingType() - Method in class io.seqware.webservice.generated.model.Study
-
- getExistingType() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field existingType.
- getExistingTypeInt() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field existingTypeInt.
- getExitCode() - Method in exception net.sourceforge.seqware.pipeline.runner.PluginRunner.ExitException
-
- getExitStatus() - Method in class io.seqware.webservice.generated.model.Processing
-
- getExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field exitStatus.
- getExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field exitStatus.
- getExpectedBasecall() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getExpectedBaseCall() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field expectedBaseCall.
- getExpectedNumberReads() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExpectedNumberReads() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expectedNumberReads.
- getExpectedNumberRuns() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExpectedNumberRuns() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expectedNumberRuns.
- getExpectedNumberSpots() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExpectedNumberSpots() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExpectedNumberSpots() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expectedNumberSpots.
- getExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field expectedNumReads.
- getExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field expectedNumRuns.
- getExpectedNumSpots() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field expectedNumSpots.
- getExpenseAttributeCollection() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseAttributeId() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getExpenseCollection() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getExpenseFinishedTstmp() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseId() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseId() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getExpenseId() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field expenseId.
- getExpenses() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field expenses.
- getExpenseType() - Method in class io.seqware.webservice.generated.model.Expense
-
- getExpenseType() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field expenseType.
- getExperiment(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getExperiment.
- getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperiment(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field experiment.
- getExperiment() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field experiment.
- getExperimentAttributeCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentAttributeId() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getExperimentAttributeId() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field experimentAttributeId.
- getExperimentAttributes() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentAttributes.
- getExperimentAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of experimentAttributes
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Platform
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getExperimentCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getExperimentDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of experimentDescription
- getExperimentHtml(Experiment, Registration, String, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getExperimentHtml.
- getExperimentId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getExperimentId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getExperimentId() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentId.
- getExperimentLibraryDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentLibraryDesign.
- getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getExperimentLibraryDesignCollection() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getExperimentLibraryDesignId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentLibraryDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getExperimentLibraryDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field experimentLibraryDesignId.
- getExperimentLibraryDesigns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getExperimentLibraryDesigns.
- getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentLibraryDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentLibraryDesignService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getExperimentLibraryDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentLibraryDesignService.
- getExperimentLibraryDesignServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
- getExperimentLinkCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentLinkId() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getExperimentName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of experimentName
- getExperiments() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field experiments.
- getExperiments() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field experiments.
- getExperimentService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field experimentService.
- getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field experimentService.
- getExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getExperimentServiceBean.
- getExperimentsFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get experiments from a study.
- getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field experimentSpotDesign.
- getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field experimentSpotDesign.
- getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getExperimentSpotDesignId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getExperimentSpotDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field experimentSpotDesignId.
- getExperimentSpotDesignReadSpecCollection() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getExperimentSpotDesignReadSpecId() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getExperimentSpotDesignReadSpecId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field experimentSpotDesignReadSpecId.
- getExperimentSpotDesignReadSpecs() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getPlatforms.
- getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentSpotDesignReadSpecs() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentSpotDesignReadSpecService.
- getExperimentSpotDesignReadSpecServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
- getExperimentSpotDesigns() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getExperimentSpotDesigns.
- getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getExperimentSpotDesigns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getExperimentSpotDesignService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getExperimentSpotDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field experimentSpotDesignService.
- getExperimentSpotDesignServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
- getExperimentSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getExpLibDesignDesc() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignDesc.
- getExpLibDesignName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignName.
- getExpLibDesignProtocol() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignProtocol.
- getExpLibDesignSelection() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignSelection.
- getExpLibDesignSource() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignSource.
- getExpLibDesignStrategy() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expLibDesignStrategy.
- getExpSpotDesignAdapterSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expSpotDesignAdapterSpec.
- getExpSpotDesignReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expSpotDesignReadsPerSpot.
- getExpSpotDesignTagSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field expSpotDesignTagSpec.
- getExtension() - Method in class io.seqware.webservice.generated.model.FileType
-
- getExtension() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field extension.
- getExtension(String) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
getExtension.
- getExternalId() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getExternalId() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field externalId.
- getFailed() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field failed.
- getFailedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFailedCount.
- getFailedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFailedCount.
- getFile() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field file.
- getFile(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getFile.
- getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getFile.
- getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getFile.
- getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getFile.
- getFile() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Getter for the field file.
- getFile() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field file.
- getFile() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field file.
- getFileAttributeCollection() - Method in class io.seqware.webservice.generated.model.File
-
- getFileAttributeId() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getFileAttributeId() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Getter for the field fileAttributeId.
- getFileAttributes(Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
-
Returns a complete set of attributes for a give File.
- getFileAttributes(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
-
Returns a complete set of attributes for a give File.
- getFileAttributes() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field fileAttributes.
- getFileAttributeService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field fileAttributeService.
- getFileAttributeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getFileAttributeServiceBean.
- getFileCollection() - Method in class io.seqware.webservice.generated.model.FileType
-
- getFileCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getFileCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getFileHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getFileHtml.
- getFileHtml(Processing, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getFileHtml.
- getFileHtml(Processing, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getFileHtml.
- getFileId() - Method in class io.seqware.webservice.generated.model.File
-
- getFileId() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getFileId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getFileId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- getFileId() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field fileId.
- getFileMetaType() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getFileMetaType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field fileMetaType.
- getFileMetaType() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field fileMetaType.
- getFilename() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getFileName() - Method in class net.sourceforge.seqware.common.model.File
-
getFileName.
- getFilename(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
- getFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Gets the file name.
- getFilename() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getFileName(String) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
-
getFileName.
- getFileOne() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileOne.
- getFilePath() - Method in class io.seqware.webservice.generated.model.File
-
- getFilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getFilePath() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field filePath.
- getFilePath() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getFilePath(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.FileService
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
getFiles.
- getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getFiles.
- getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
-
getFiles.
- getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
-
getFiles.
- getFiles() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field files.
- getFiles() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field files.
- getFiles() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field files.
- getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
This should only be called from the back-end and should not be called by workflow developers.
- getFiles(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
getFiles.
- getFiles() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field files.
- getFilesArray() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Getter for the field filesArray.
- getFileService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field fileService.
- getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field fileService.
- getFileServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getFileServiceBean.
- getFileSize(String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getFileSize.
- getFilesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
-
Getter for the field filesNumber.
- getFileStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getFileSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getFileTwo() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileTwo.
- getFileTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileTwoURL.
- getFileType() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field fileType.
- getFileType() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field fileType.
- getFileType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileType.
- getFileTypeId() - Method in class io.seqware.webservice.generated.model.File
-
- getFileTypeId() - Method in class io.seqware.webservice.generated.model.FileType
-
- getFileTypeId() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field fileTypeId.
- getFileTypeId() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field fileTypeId.
- getFileTypeId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileTypeId.
- getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field fileTypeService.
- getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Getter for the field fileTypeService.
- getFileUploadService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field fileUploadService.
- getFileURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field fileURL.
- getFileURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field fileURL.
- getFileValidationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getFileValidationServiceBean.
- getFinalized() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getFinishedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getFinishedCount.
- getFinishedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getFinishedCount.
- getFinishedTimestamp() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field finishedTimestamp.
- getFirstId(String) - Static method in class net.sourceforge.solexatools.util.Constant
-
getFirstId.
- getFirstName() - Method in class io.seqware.webservice.generated.model.Registration
-
- getFirstName() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field firstName.
- getFlowCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field flowCount.
- getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field flowCount.
- getFlowSequence() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field flowSequence.
- getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field flowSequence.
- getFolderStore() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field folderStore.
- getFolderStore() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field folderStore.
- getForceRunAll() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getFs_default_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getFs_defaultFS() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getFs_hdfs_impl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getFullName.
- getFullyPaid() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getGcrOutputFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getGroupingStrategy() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getHeader() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
Deprecated.
- getHeader() - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
-
getHeader.
- getHost() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getHost() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getHost() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Deprecated.
- getHost() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field host.
- getHost() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field host.
- getHtml() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field html.
- getHtml() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field html.
- getHtml() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field html.
- getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getHtml.
- getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
-
getHtml.
- getHtml(Object, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getHtml.
- getHtml(WorkflowRun, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getHtml.
- getHtml(Sample, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getHtml.
- getHtml(Processing, WorkflowRun, Registration, String, List<String>, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
-
getHtml.
- getHttpInputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getHttpInputStream.
- getId() - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- getId() - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- getId() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getId() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field id.
- getId() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
-
Getter for the field id.
- getId(String) - Static method in class net.sourceforge.solexatools.util.Constant
-
getId.
- getIdentitySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field identitySamples.
- getIdsSelectedLane(HttpServletRequest, WorkflowParam) - Method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getIdsSelectedLane.
- getImmediateInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field immediateInputFiles.
- getIndividualName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getIndividualName() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field individualName.
- getIndividualNumber() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getInfo() - Method in class net.sourceforge.seqware.common.model.FileType
-
getInfo.
- getInfo() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field info.
- getIniFile() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getIniFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field iniFile.
- getInMemory() - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- getInputAlgorithm() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getInputAlgorithm() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field inputAlgorithm.
- getInputFileAccessions() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getInstance() - Static method in class net.sourceforge.seqware.common.ContextImpl
-
getInstance.
- getInstance() - Static method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
-
- getInstitution() - Method in class io.seqware.webservice.generated.model.Registration
-
- getInstitution() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field institution.
- getInstrumentModel() - Method in class io.seqware.webservice.generated.model.Platform
-
- getInstrumentModel() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field instrumentModel.
- getInstrumentName() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field instrumentName.
- getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field instrumentName.
- getInvitationCode() - Method in class io.seqware.webservice.generated.model.Registration
-
- getInvitationCode() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field invitationCode.
- getInvoice() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field invoice.
- getInvoiceAttributeCollection() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getInvoiceAttributeId() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getInvoiceCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getInvoiceId() - Method in class io.seqware.webservice.generated.model.Expense
-
- getInvoiceId() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getInvoiceId() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getInvoiceId() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field invoiceId.
- getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
-
Getter for the field invoiceService.
- getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
-
Getter for the field invoiceService.
- getIsEnd() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field isEnd.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field isHasFile.
- getIsHasFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field isHasFile.
- getIsInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
-
Getter for the field isInvitationCode.
- getIsPublic() - Method in class io.seqware.webservice.generated.model.Sample
-
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field isSelected.
- getIsSelected() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field isSelected.
- getIsStart() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field isStart.
- getIUS(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get ius by sw accession
- getIUS(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getIUS(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getIUS(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getIUS(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getIus() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field ius.
- getIUS() - Method in class net.sourceforge.seqware.common.model.Lane
-
getIUS.
- getIUS() - Method in class net.sourceforge.seqware.common.model.Processing
-
getIUS.
- getIus() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field ius.
- getIUS() - Method in class net.sourceforge.seqware.common.model.Sample
-
getIUS.
- getIus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Getter for the field ius.
- getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field ius.
- getIusAttributeCollection() - Method in class io.seqware.webservice.generated.model.Ius
-
- getIusAttributeId() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getIusAttributeId() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Getter for the field iusAttributeId.
- getIusAttributes() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field iusAttributes.
- getIusAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusAttributes
- getIusCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getIusCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getIusCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getIusDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusDescription
- getIUSFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get IUSes (barcodes) from a lane or sample.
- getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getIUSHtml(IUS, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getIUSHtml.
- getIusId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getIusId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getIusId() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getIusId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- getIusId() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getIusId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getIusId() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field iusId.
- getIusName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusName
- getIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field iusService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
-
Getter for the field iusService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
getIUSService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
getIUSService.
- getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field iusService.
- getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
getIUSService.
- getIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getIUSServiceBean.
- getIusSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of iusSkip
- getIusSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getIusWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.Ius
-
- getIusWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getIusWorkflowRunsId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- getJobList() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getJobs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
get all jobs in current workflow
- getJobScript() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob
-
- getJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field joinDevelopersMailingList.
- getJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field joinUsersMailingList.
- getJson(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildLimitedWorkflowRunsResource
-
- getJsonEscapeAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
-
getJsonEscapeAlgorithm.
- getJsonEscapeDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeDefaultValue.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.File
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.IUS
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Lane
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Processing
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Sample
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Study
-
getJsonEscapeDescription.
- getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getJsonEscapeDescription.
- getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeDescription200.
- getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Study
-
getJsonEscapeDescription200.
- getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeDisplayName.
- getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
getJsonEscapeDisplayName.
- getJsonEscapeFileName() - Method in class net.sourceforge.seqware.common.model.File
-
getJsonEscapeFileName.
- getJsonEscapeFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getJsonEscapeFullName.
- getJsonEscapeKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeKey.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.IUS
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Lane
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Sample
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getJsonEscapeName.
- getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
getJsonEscapeName.
- getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
-
getJsonEscapeTitle.
- getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Sample
-
getJsonEscapeTitle.
- getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Study
-
getJsonEscapeTitle.
- getJsonEscapeType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeType.
- getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
getJsonEscapeValue.
- getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
getJsonEscapeValue.
- getKey() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getKey() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field key.
- getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field key.
- getKey() - Method in enum net.sourceforge.seqware.common.util.maptools.ReservedIniKeys
-
- getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Getter for the field key.
- getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Getter for the field key.
- getKeyValueFromFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
getKeyValueFromFile.
- getLabel() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getLabel() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field label.
- getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field label.
- getLane(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLane.
- getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLane(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLane() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field lane.
- getLane() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getLane() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Getter for the field lane.
- getLane1() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane1.
- getLane2() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane2.
- getLane3() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane3.
- getLane4() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane4.
- getLane5() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane5.
- getLane6() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane6.
- getLane7() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane7.
- getLane8() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lane8.
- getLaneAttributeCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneAttributeId() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getLaneAttributeId() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field laneAttributeId.
- getLaneAttributes() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field laneAttributes.
- getLaneAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.Organism
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getLaneCollection() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Getter for the field laneCount.
- getLaneCycleDescriptor() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneCycleDescriptor
- getLaneDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneDescription
- getLaneHtml(Lane, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getLaneHtml.
- getLaneHtml(Lane, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getLaneHtml.
- getLaneId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getLaneId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getLaneId() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field laneId.
- getLaneIndex() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneIndex() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field laneIndex.
- getLaneName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneName
- getLaneNumber() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneNumber
- getLanes() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field lanes.
- getLanes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of lanes
- getLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.validation.LaneValidator
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field laneService.
- getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field laneService.
- getLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLaneServiceBean.
- getLanesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get Lanes from a sequencer run.
- getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLaneSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of laneSkip
- getLaneSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getLaneTypeId() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getLaneWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLaneWorkflowRunsCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getLaneWorkflowRunsId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- getLastName() - Method in class io.seqware.webservice.generated.model.Registration
-
- getLastName() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field lastName.
- getLastUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Registration
-
- getLayout() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getLayout() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field layout.
- getLength() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getLength() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field length.
- getLibraries() - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
-
Returns a complete list of libraries.
- getLibraries(Map<String, String>) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
-
Returns a list of libraries that match all attributes provided in the give attributes Map.
- getLibraries() - Method in interface net.sourceforge.seqware.common.business.LibraryService
-
Returns a complete list of libraries.
- getLibraries(Map<String, String>) - Method in interface net.sourceforge.seqware.common.business.LibraryService
-
Returns a list of libraries that match all attributes provided in the give attributes Map.
- getLibraries(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
-
Returns list of libraries that contain the attribute attributeName=attributeValue.
- getLibraries() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
-
Returns a complete list of libraries.
- getLibraries(String, String) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
-
Returns list of libraries that contain the attribute attributeName=attributeValue.
- getLibraries() - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
-
Returns a complete list of libraries.
- getLibrarySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field librarySamples.
- getLibrarySelection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLibrarySelection() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getLibrarySelectionAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of librarySelectionAcc
- getLibrarySelectionId() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getLibrarySelectionId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Getter for the field librarySelectionId.
- getLibrarySelections() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLibrarySelections.
- getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLibrarySelectionService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field librarySelectionService.
- getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field librarySelectionService.
- getLibrarySelectionServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibrarySelectionServiceBean.
- getLibraryService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field libraryService.
- getLibraryServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibraryServiceBean.
- getLibrarySizeCode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getLibrarySource() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLibrarySource() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLibrarySource.
- getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLibrarySource() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getLibrarySourceAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of librarySourceAcc
- getLibrarySourceId() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getLibrarySourceId() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Getter for the field librarySourceId.
- getLibrarySourceService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field librarySourceService.
- getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field librarySourceService.
- getLibrarySourceServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibrarySourceServiceBean.
- getLibrarySourceTemplateType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of librarySourceTemplateType
- getLibraryStrategies() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getLibraryStrategies.
- getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getLibraryStrategy() - Method in class io.seqware.webservice.generated.model.Lane
-
- getLibraryStrategy() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getLibraryStrategyAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of libraryStrategyAcc
- getLibraryStrategyId() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getLibraryStrategyId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Getter for the field libraryStrategyId.
- getLibraryStrategyService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field libraryStrategyService.
- getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field libraryStrategyService.
- getLibraryStrategyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getLibraryStrategyServiceBean.
- getLibraryType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getLibraryType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field libraryType.
- getLimsAdmin() - Method in class io.seqware.webservice.generated.model.Registration
-
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.FileList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.IntegerList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.IUSList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LaneList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.OrganismList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.PlatformList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.SampleList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
-
getList.
- getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
-
getList.
- getLocalhost(OptionSet) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
-
Get the localhost and a return value describing the failure condition if we are unable to get the localhost
- getLocalhost() - Static method in class net.sourceforge.seqware.pipeline.plugins.ITUtility
-
- getLongName() - Method in class net.sourceforge.seqware.common.model.Platform
-
getLongName.
- getLongName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getLookupToken() - Method in interface io.seqware.pipeline.api.WorkflowEngine
-
An engine-specific token for this workflow run that can be used to lookup relevant runtime data.
- getLookupToken() - Method in class io.seqware.pipeline.engines.whitestar.WhiteStarWorkflowEngine
-
- getLookupToken() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
-
- getMainClass() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
return the main class for a Java job, or the script.pl for a perl Job
- getMapred_job_tracker() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getMaxMemory() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getMd5sum() - Method in class io.seqware.webservice.generated.model.File
-
- getMd5sum() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field md5sum.
- getMd5sum() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getMd5sum() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getMeaning() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
-
- getMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getMemReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field memReq.
- getMetadata() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Getter for the field metadata.
- getMetadata() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field metadata.
- getMetadata() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
-
- getMetadata_output_dir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getMetadata_output_file_prefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- getMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getMetaType() - Method in class io.seqware.webservice.generated.model.File
-
- getMetaType() - Method in class io.seqware.webservice.generated.model.FileType
-
- getMetaType() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field metaType.
- getMetaType() - Method in class net.sourceforge.seqware.common.model.FileType
-
Getter for the field metaType.
- getMetaType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getMetaType() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getMimeType() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getModelAndView(String, ModelAndView) - Static method in class net.sourceforge.solexatools.util.StudyBuildTree
-
getModelAndView.
- getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.Organism
-
- getModelId() - Method in class net.sourceforge.seqware.common.model.Platform
-
- getModelId() - Method in interface net.sourceforge.seqware.common.model.SecondTierModel
-
Get the id for this model
- getModelId() - Method in class net.sourceforge.seqware.common.model.StudyType
-
- getModuleType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
-
Getter for the field moduleType.
- getName() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getName() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getName() - Method in class io.seqware.webservice.generated.model.Ius
-
- getName() - Method in class io.seqware.webservice.generated.model.Lane
-
- getName() - Method in class io.seqware.webservice.generated.model.LaneType
-
- getName() - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- getName() - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- getName() - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- getName() - Method in class io.seqware.webservice.generated.model.Organism
-
- getName() - Method in class io.seqware.webservice.generated.model.Platform
-
- getName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getName() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getName() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getName() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getName() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getName() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field name.
- getName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of name
- getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
-
getName.
- getName() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
-
getName.
- getName() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getNameNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field nameNode.
- getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
getNamespace.
- getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- getNcbiTaxid() - Method in class io.seqware.webservice.generated.model.Organism
-
- getNcbiTaxId() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field ncbiTaxId.
- getNetwork() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getNetworkReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field networkReq.
- getNewType() - Method in class io.seqware.webservice.generated.model.Study
-
- getNewType() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field newType.
- getNodeHtml(Processing, Registration, String, boolean, boolean, boolean, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getNodeHtml.
- getNodeHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getNodeHtml.
- getNodeIds(Object) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
-
getNodeIds.
- getNominalLength() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getNominalLength() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field nominalLength.
- getNominalSdev() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getNominalSdev() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field nominalSdev.
- getNoOp() - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- getNotes() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field notes.
- getNotRunned() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field notRunned.
- getOffspringProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field offspringProcessings.
- getOkTo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getOOZIE_APP_ROOT() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_JOBTRACKER() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_NAMENODE() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_QUEUENAME() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_URL() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOOZIE_WORK_DIR() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getOozieWorkingDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
-
getOptionParser is an internal method to parse command line args.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
-
Deprecated.
getOptionParser is an internal method to parse command line args.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
getOptionParser.
- getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
-
- getOrderedJobs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp
-
- getOrganism() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field organism.
- getOrganism() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field organism.
- getOrganismId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getOrganismId() - Method in class io.seqware.webservice.generated.model.Organism
-
- getOrganismId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getOrganismId() - Method in class net.sourceforge.seqware.common.model.Organism
-
Getter for the field organismId.
- getOrganismId() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field organismId.
- getOrganismId() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getOrganisms() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getOrganisms.
- getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getOrganismService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field organismService.
- getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field organismService.
- getOrganismServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getOrganismServiceBean.
- getOriginalFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Getter for the field originalFileName.
- getOutput() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
- getOutputDir() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Getter for the field outputDir.
- getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- getOutputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field outputFiles.
- getOutputLineCapacity() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- getOutputPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getOwner() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field owner.
- getOwner() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field owner.
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.File
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Study
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getOwnerId() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getOwnerUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getPage() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Getter for the field page.
- getPageInfo(HttpServletRequest, String, List, List, String, String, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
getPageInfo.
- getPageInfoSD(HttpServletRequest, String, List, List, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
getPageInfoSD.
- getPageNumber(HttpServletRequest, Study, List<Study>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
getPageNumber.
- getPaidAmount() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getPaidAmount() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field paidAmount.
- getPairedEnd() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field pairedEnd.
- getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field pairedEnd.
- getPairedEnd() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getPairedFilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field pairedFilePath.
- getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field pairedFilePath.
- getPairedOrientation() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getPairedOrientation() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field pairedOrientation.
- getParameters() - Method in class io.seqware.webservice.generated.model.Processing
-
- getParameters() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field parameters.
- getParameters() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field parameters.
- getParameters() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field parameters.
- getParams() - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Getter for the field params.
- getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getParentId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getParentId() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getParentId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- getParentLane(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getParentLane.
- getParentProcessing(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
getParentProcessing.
- getParentProcessingAccession() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getParentProcessingAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field parentProcessingAccession.
- getParentProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field parentProcessings.
- getParents() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field parents.
- getParents() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field parents.
- getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
add all parent jobs
- getParents() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getParentSample() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of parentSample
- getParentSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the parent samples of a sample.
- getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getParentWorkflowAccessions() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getPassword() - Method in class io.seqware.webservice.generated.model.Registration
-
- getPassword() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field password.
- getPasswordHint() - Method in class io.seqware.webservice.generated.model.Registration
-
- getPasswordHint() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field passwordHint.
- getPathToFirstFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field pathToFirstFile.
- getPathToSecondFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field pathToSecondFile.
- getPayee() - Method in class io.seqware.webservice.generated.model.Registration
-
- getPeakMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getPeakThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- getPending() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field pending.
- getPermanentBundleLocation() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getPermanentBundleLocation() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field permanentBundleLocation.
- getPermBundleLocation() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field permBundleLocation.
- getPlatform() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field platform.
- getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field platform.
- getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field platform.
- getPlatformId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getPlatformId() - Method in class io.seqware.webservice.generated.model.Platform
-
- getPlatformId() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getPlatformId() - Method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field platformId.
- getPlatformId() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- getPlatformInt() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field platformInt.
- getPlatformInt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field platformInt.
- getPlatforms() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getPlatforms.
- getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getPlatformService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field platformService.
- getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Getter for the field platformService.
- getPlatformServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getPlatformServiceBean.
- getPossibleValues() - Method in enum io.seqware.pipeline.SqwKeys
-
For documentation
- getPOSTGRE_DB() - Static method in class io.seqware.metadb.util.TestDatabaseCreator
-
- getPOSTGRE_PASSWORD() - Method in class io.seqware.metadb.util.TestDatabaseCreator
-
- getPOSTGRE_USER() - Method in class io.seqware.metadb.util.TestDatabaseCreator
-
- getPricePerUnit() - Method in class io.seqware.webservice.generated.model.Expense
-
- getPricePerUnit() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field pricePerUnit.
- getPricePerUnitString() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field pricePerUnit.
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.BundleDir_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.CLICheck
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.ClientServerConsistencyCheck
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.DB_WS_ConsistencyCheck
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.HDFS_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.Oozie_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.Script_Check
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.TutorialCheck
-
- getPriority() - Method in class io.seqware.pipeline.plugins.sanity.checks.WS_Check
-
- getPriority() - Method in interface io.seqware.pipeline.plugins.sanity.SanityCheckPluginInterface
-
Indicate the priority of the check, higher is later
- getPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getPrivate.
- getProcess() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field process.
- getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.Lane
-
getProcessedCnt.
- getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getProcessedCnt.
- getProcessedCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field processedCount.
- getProcessExitStatus() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field processExitStatus.
- getProcessExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field processExitStatus.
- getProcessing(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getProcessing.
- getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getProcessing(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getProcessing() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field processing.
- getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field processing.
- getProcessingAccession() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the field processingAccession.
- getProcessingAttributeCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingAttributeId() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getProcessingAttributeId() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Getter for the field processingAttributeId.
- getProcessingAttributes() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field processingAttributes.
- getProcessingByChildId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field processingByChildId.
- getProcessingByParentId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field processingByParentId.
- getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.Lane
-
getProcessingCnt.
- getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
getProcessingCnt.
- getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
getProcessingCnt.
- getProcessingCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getProcessingCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getProcessingCollection1() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getProcessingCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field processingCount.
- getProcessingExperimentsCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getProcessingExperimentsCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingExperimentServiceBean.
- getProcessingExperimentsId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getProcessingExperimentsId() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field processingExperimentsId.
- getProcessingExperimentsService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingExperimentsService.
- getProcessingFilesCollection() - Method in class io.seqware.webservice.generated.model.File
-
- getProcessingFilesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingFilesId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- getProcessingHtml(Processing, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getProcessingHtml.
- getProcessingId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getProcessingId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getProcessingId() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field processingId.
- getProcessingIusCollection() - Method in class io.seqware.webservice.generated.model.Ius
-
- getProcessingIusCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingIusId() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getProcessingIusId() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field processingIusId.
- getProcessingIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingIusService.
- getProcessingIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingIUSServiceBean.
- getProcessingLanesCollection() - Method in class io.seqware.webservice.generated.model.Lane
-
- getProcessingLanesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingLaneService.
- getProcessingLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingLaneServiceBean.
- getProcessingLanesId() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getProcessingLanesId() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field processingLanesId.
- getProcessingRelations(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getProcessingRelations.
- getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getProcessingRelationshipCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingRelationshipCollection1() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingRelationshipId() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getProcessingRelationshipId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field processingRelationshipId.
- getProcessingRelationshipService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingRelationshipService.
- getProcessingRelationshipServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingRelationshipServiceBean.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field processings.
- getProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field processings.
- getProcessingSamplesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingSamplesCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getProcessingSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingSampleServiceBean.
- getProcessingSamplesId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getProcessingSamplesId() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field processingSamplesId.
- getProcessingSamplesService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingSamplesService.
- getProcessingsByWorkflow(WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
getProcessingsByWorkflow.
- getProcessingSequencerRunsCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingSequencerRunsCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getProcessingSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingSequencerRunService.
- getProcessingSequencerRunsId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getProcessingSequencerRunsId() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field processingSequencerRunsId.
- getProcessingSequencerRunsServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingSequencerRunsServiceBean.
- getProcessingService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field processingService.
- getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field processingService.
- getProcessingServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingServiceBean.
- getProcessingStudiesCollection() - Method in class io.seqware.webservice.generated.model.Processing
-
- getProcessingStudiesCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getProcessingStudiesId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getProcessingStudiesId() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field processingStudiesId.
- getProcessingStudiesService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field processingStudiesService.
- getProcessingStudiesServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getProcessingStudiesServiceBean.
- getProjectCode() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- getProjectId() - Method in class io.seqware.webservice.generated.model.Study
-
- getProjectId() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field projectId.
- getProperty(String) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
getProperty.
- getProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
get the user defined INI files properties
- getProvisionedPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getPublic() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getPublic.
- getQsubOptions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getQualityMultiplier() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityMultiplier() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityMultiplier.
- getQualityNumberOfLevels() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityNumberOfLevels() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityNumberOfLevels.
- getQualityScorer() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityScorer() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getQualityScorer() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityScorer.
- getQualityType() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getQualityType() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field qualityType.
- getQueryValue(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
-
- getQueue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getQueue() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getRandom() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getReadClass() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadClass() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readClass.
- getReader() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
Getter for the field reader.
- getReadIndex() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadIndex() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readIndex.
- getReadLabel() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readLabel.
- getReadSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getReadSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field readSpec.
- getReadSpecs() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field readSpecs.
- getReadsPerSpot() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field readsPerSpot.
- getReadType() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- getReadType() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Getter for the field readType.
- getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field readyToProcess.
- getRefLane() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field refLane.
- getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field refLane.
- getRegions() - Method in class io.seqware.webservice.generated.model.Lane
-
- getRegions() - Method in class io.seqware.webservice.generated.model.Sample
-
- getRegions() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field regions.
- getRegions() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field regions.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field registration.
- getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field registration.
- getRegistration(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security
-
getRegistration.
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.Registration
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getRegistrationId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getRegistrationId() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field registrationId.
- getRegistrationService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field registrationService.
- getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
-
Getter for the field registrationService.
- getRegistrationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getRegistrationServiceBean.
- getRelationship() - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- getRelationship() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getRelationship() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Getter for the field relationship.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForSequencerRun.
- getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForSequencerRun.
- getReportForSequencerRuns(String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForSequencerRuns.
- getReportForSequencerRuns(String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForSequencerRuns.
- getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
-
getReportForStudy.
- getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
getReportForStudy.
- getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
-
getReportForStudy.
- getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForStudy.
- getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
-
getReportForStudy.
- getRepresentation(Document) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
-
getRepresentation.
- getRequestedTypeList(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
-
getRequestedTypeList.
- getRequestedTypeList(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
getRequestedTypeList.
- getRequirements() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
get job requirements
- getReturnValue() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field returnValue.
- getRootProcessing(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
getRootProcessing.
- getRootProcessing(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
-
getRootProcessing.
- getRootProcessing(WorkflowRun) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
-
getRootProcessing.
- getRootProcessingName() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getRootProcessingSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getRootSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getRootSample.
- getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getRootSample.
- getRootSample(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getRootSample.
- getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getRootSample.
- getRootSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field rootSample.
- getRootSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
getRootSamples.
- getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
getRootSamples.
- getRootSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
getRootSamples.
- getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
-
getRootSamples.
- getRowId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getRowId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getRowId() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field rowId.
- getRowId() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field rowId.
- getRows() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Getter for the field rows.
- getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getRowsForSequencerRun.
- getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getRowsForSequencerRun.
- getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getRowsForSequencerRun.
- getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getRowsForSequencerRun.
- getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getRowsWithSequencerRuns.
- getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getRowsWithSequencerRuns.
- getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getRowsWithSequencerRuns.
- getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getRowsWithSequencerRuns.
- getRunAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runAttributes
- getRunCenter() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field runCenter.
- getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field runCenter.
- getRunDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runDescription
- getRunFilePath() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runFilePath
- getRunInfo() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.CreateFromScratch
-
- getRunName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runName
- getRunningCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
getRunningCount.
- getRunningCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
getRunningCount.
- getRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
- getRunsFromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Using a workflow SWID, find all of the workflow runs, and report on each of the workflow runs the files, samples and processing
events associated with each.
- getRunSkip() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of runSkip
- getRunStartTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field runStartTimestamp.
- getRunStartTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getRunStartTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field runStartTstmp.
- getRunStopTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field runStopTimestamp.
- getRunStopTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getRunStopTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field runStopTstmp.
- getS3InputStream(String, int, long, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3InputStream.
- getS3InputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3InputStream.
- getS3Url(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3Url.
- getS3Url(String, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
getS3Url.
- getSample(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get sample by swa
- getSample(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSample(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getSample(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSample(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field sample.
- getSample() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field sample.
- getSampleAttributeCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleAttributeId() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getSampleAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Getter for the field sampleAttributeId.
- getSampleAttributes() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field sampleAttributes.
- getSampleAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of sampleAttributes
- getSampleByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
- getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSampleByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSampleCode() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sampleCode.
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Organism
-
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getSampleCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleCollection1() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of sampleDescription
- getSampleHierarchies() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
-
- getSampleHtml(Sample, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getSampleHtml.
- getSampleHtml(Sample, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getSampleHtml.
- getSampleId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.Ius
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getSampleId() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getSampleId() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field sampleId.
- getSampleId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field sampleId.
- getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- getSampleRelationshipCollection() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleRelationshipCollection1() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSampleRelationshipId() - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- getSampleReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sampleReportService.
- getSampleReportServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSampleReportServiceBean.
- getSamples() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field samples.
- getSamples() - Method in class net.sourceforge.seqware.common.model.Lane
-
getSamples.
- getSamples() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field samples.
- getSamples() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field samples.
- getSamples() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of samples
- getSampleService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.validation.SampleValidator
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field sampleService.
- getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Getter for the field sampleService.
- getSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSampleServiceBean.
- getSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the samples from an experiment.
- getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSampleSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getSampleType() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sampleType.
- getScientificName() - Method in class io.seqware.webservice.generated.model.Sample
-
- getScriptsDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getSelectedIds(HttpServletRequest, String, String[], String[]) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
getSelectedIds.
- getSelectedWorkflowParamValue(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getSelectedWorkflowParamValue.
- getSelection() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getSelection() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field selection.
- getSender() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Getter for the field sender.
- getSequencerRun(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getSequencerRun.
- getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSequencerRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field sequencerRun.
- getSequencerRun() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSequencerRun(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getSequencerRun.
- getSequencerRun(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getSequencerRun.
- getSequencerRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Getter for the field sequencerRun.
- getSequencerRunAttributeCollection() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSequencerRunAttributeId() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getSequencerRunAttributeId() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field sequencerRunAttributeId.
- getSequencerRunAttributes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field sequencerRunAttributes.
- getSequencerRunByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
- getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getSequencerRunByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getSequencerRunCollection() - Method in class io.seqware.webservice.generated.model.Platform
-
- getSequencerRunCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getSequencerRunHtml(SequencerRun, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getSequencerRunHtml.
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getSequencerRunId() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field sequencerRunId.
- getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field sequencerRunId.
- getSequencerRunReport() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getSequencerRunReport.
- getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getSequencerRunReport.
- getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getSequencerRunReport.
- getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getSequencerRunReport.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getSequencerRunReportIds.
- getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getSequencerRunReportIds.
- getSequencerRuns() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field sequencerRuns.
- getSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field sequencerRunService.
- getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Getter for the field sequencerRunService.
- getSequencerRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSequencerRunServiceBean.
- getSequencerRunSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getSequencerRunValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field sequencerRunValidator.
- getSequencerRunWizardDTO() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
getSequencerRunWizardDTO.
- getSequencerRunWizardValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Getter for the field sequencerRunWizardValidator.
- getSequenceSpace() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getSequenceSpace() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field sequenceSpace.
- getSEQWARE_DB() - Method in class io.seqware.metadb.util.TestDatabaseCreator
-
- getSEQWARE_DB() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getSEQWARE_DB() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getSEQWARE_PASSWORD() - Method in class io.seqware.metadb.util.TestDatabaseCreator
-
- getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getSEQWARE_PASSWORD() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getSEQWARE_USER() - Method in class io.seqware.metadb.util.TestDatabaseCreator
-
- getSEQWARE_USER() - Method in class net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator
-
- getSEQWARE_USER() - Method in class net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator
-
- getSeqware_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getSeqwareAccession() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSeqwareRevision() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getSeqwareRevision() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field seqwareRevision.
- getSeqwareVersion() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getSeqwareVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field seqwareVersion.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Platform
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field serialVersionUID.
- getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field serialVersionUID.
- getServerBuilt() - Method in enum net.sourceforge.seqware.webservice.resources.TomcatVersion
-
- getServerNumber() - Method in enum net.sourceforge.seqware.webservice.resources.TomcatVersion
-
- getSessionFactory() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field sessionFactory.
- getSessionFactoryBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getSessionFactoryBean.
- getSettingKey() - Method in enum io.seqware.pipeline.SqwKeys
-
Returns the name of the key to be used in the seqware settings file
- getSettings() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
The output keys are always uppercase!
- getSettingsFilePath() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
- getSettingsValue(SqwKeys) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
Get the value of a key if defined or the default value if not defined.
- getSharedStudies() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field sharedStudies.
- getSharedWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field sharedWorkflowRuns.
- getShareStudyCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareStudyCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getShareStudyId() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getShareStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field shareStudyId.
- getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field shareStudyService.
- getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Getter for the field shareStudyService.
- getShareWorkflowRun(String, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
-
getShareWorkflowRun.
- getShareWorkflowRun(String, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
-
getShareWorkflowRun.
- getShareWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getShareWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getShareWorkflowRunId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getShareWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field shareWorkflowRunId.
- getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Getter for the field shareWorkflowRunService.
- getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field shareWorkflowRunService.
- getShortName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getSingleWorkflowRun(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Using a workflow run SWID, report on the files, samples and processing events associated with the run.
- getSize() - Method in class io.seqware.webservice.generated.model.File
-
- getSize() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field size.
- getSize() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getSize() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- getSkip() - Method in class io.seqware.webservice.generated.model.File
-
- getSkip() - Method in class io.seqware.webservice.generated.model.Ius
-
- getSkip() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSkip() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSkip() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSkip() - Method in class net.sourceforge.seqware.common.model.File
-
- getSkip() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field skip.
- getSkip() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field skip.
- getSkip() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field skip.
- getSkip() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field skip.
- getSlide1FilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlide1LaneCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlide2FilePath() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlide2LaneCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlideCount() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideOneFilePath.
- getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideOneFilePath.
- getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideOneLaneCount.
- getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideOneLaneCount.
- getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideTwoFilePath.
- getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideTwoFilePath.
- getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field slideTwoLaneCount.
- getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field slideTwoLaneCount.
- getSortKeySample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field sortKeySample.
- getSource() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getSource() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field source.
- getSourcePath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getSourceReader(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
This attempts to resume if passed in startPosition > 0.
- getSpotDesignReadSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field spotDesignReadSpec.
- getSql() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
Getter for the field sql.
- getStartDate() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getStartDate() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field startDate.
- getStartPage() - Method in class net.sourceforge.solexatools.util.PageInfo
-
Getter for the field startPage.
- getState() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getState() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field state.
- getStatus() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getStatus() - Method in class io.seqware.webservice.generated.model.Processing
-
- getStatus() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getStatus() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getStatus() - Method in class io.seqware.webservice.generated.model.Study
-
- getStatus() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatus.
- getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatus.
- getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatus.
- getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatus.
- getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatus.
- getStatus() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.Processing
-
- getStatus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field status.
- getStatus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field status.
- getStatus() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
-
- getStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of the sequencer run status
- getStatusCmd() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStatusCmd() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field statusCmd.
- getStatusCount(Study, WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
Count the number of workflow runs with the given status, under the given study
- getStatusCount(Study, WorkflowRunStatus) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
-
Count the number of workflow runs with the given status, under the given study
- getStatuses() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field statuses.
- getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForSequencerRun.
- getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForSequencerRun.
- getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForSequencerRun.
- getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForSequencerRun.
- getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForStudy.
- getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForStudy.
- getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForStudy.
- getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForStudy.
- getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getStatusesForWorkflow.
- getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getStatusesForWorkflow.
- getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getStatusesForWorkflow.
- getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForWorkflow.
- getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getStatusesForWorkflow.
- getStderr() - Method in class io.seqware.webservice.generated.model.Processing
-
- getStderr() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStderr() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field stderr.
- getStdErr() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field stdErr.
- getStderr() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field stderr.
- getStderrFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the file where the stderr will be redirected.
- getStdout() - Method in class io.seqware.webservice.generated.model.Processing
-
- getStdout() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getStdout() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field stdout.
- getStdOut() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field stdOut.
- getStdout() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field stdout.
- getStdoutFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Getter for the file where the stdout will be redirected.
- getStrategy() - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- getStrategy() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Getter for the field strategy.
- getStrExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field strExpectedNumberReads.
- getStrExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field strExpectedNumberRuns.
- getStrExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field strExpectedNumReads.
- getStrExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field strExpectedNumRuns.
- getStrLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Getter for the field strLaneCount.
- getStrRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field strRefLane.
- getStrStartURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field strStartURL.
- getStrStartURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field strStartURL.
- getStudies() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field studies.
- getStudy(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get study by swa
- getStudy(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getStudy(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getStudy(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getStudy(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getStudy() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Getter for the field study.
- getStudy() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Getter for the field study.
- getStudy(Experiment) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudy(Sample) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudy(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudy(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
-
getStudy.
- getStudyAttributeCollection() - Method in class io.seqware.webservice.generated.model.Study
-
- getStudyAttributeId() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getStudyAttributeId() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Getter for the field studyAttributeId.
- getStudyAttributes() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field studyAttributes.
- getStudyAttributes() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyAttributes
- getStudyByName(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
- getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getStudyByName(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getStudyCenterName() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyCenterName
- getStudyCenterProject() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyCenterProject
- getStudyCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getStudyCollection() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getStudyDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Getter for the field studyDAO.
- getStudyDescription() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyDescription
- getStudyId() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.FileReport
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.Study
-
- getStudyId() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field studyId.
- getStudyId() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field studyId.
- getStudyService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.validation.StudyValidator
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableController
-
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field studyService.
- getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Getter for the field studyService.
- getStudyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getStudyServiceBean.
- getStudySwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- getStudyTitle() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of studyTitle
- getStudyType() - Method in class io.seqware.webservice.generated.model.Lane
-
- getStudyType() - Method in class net.sourceforge.seqware.common.model.Lane
-
- getStudyType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- getStudyTypeAcc() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Get the value of studyTypeAcc
- getStudyTypeDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Getter for the field studyTypeDAO.
- getStudyTypeId() - Method in class io.seqware.webservice.generated.model.StudyType
-
- getStudyTypeId() - Method in class net.sourceforge.seqware.common.model.StudyType
-
Getter for the field studyTypeId.
- getStudyTypes() - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getStudyTypes.
- getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getStudyTypeService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
- getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Getter for the field studyTypeService.
- getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Getter for the field studyTypeService.
- getStudyTypeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getStudyTypeServiceBean.
- getStydyHtml(Study, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getStydyHtml.
- getStydyHtml(Study, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
-
getStydyHtml.
- getSubject(String, String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
-
getSubject.
- getSubjectEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
-
Getter for the field subjectEmail.
- getSummaryData(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getSummaryData.
- getSummaryLines() - Method in class net.sourceforge.solexatools.util.SummaryData
-
Getter for the field summaryLines.
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Expense
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.File
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Invoice
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Ius
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Lane
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Processing
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Sample
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Study
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getSwAccession() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field swAccession.
- getSwAccession() - Method in interface net.sourceforge.seqware.common.model.FirstTierModel
-
A unique identifier for entities that are unique within the SeqWare database.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Invoice
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field swAccession.
- getSwAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field swAccession.
- getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
-
getSyntax.
- getTag() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.Ius
-
- getTag() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getTag() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getTag() - Method in class net.sourceforge.seqware.common.model.Attribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field tag.
- getTag() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
getTag.
- getTag() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- getTags() - Method in class io.seqware.webservice.generated.model.Lane
-
- getTags() - Method in class io.seqware.webservice.generated.model.Sample
-
- getTags() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field tags.
- getTags() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field tags.
- getTags() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
the key-value from metadata.xml
- getTagSpec() - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- getTagSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Getter for the field tagSpec.
- getTargetedResequencing() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of targetedResequencing
- getTaskGroup() - Method in class io.seqware.webservice.generated.model.Processing
-
- getTaxonId() - Method in class io.seqware.webservice.generated.model.Sample
-
- getTemplate() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field template.
- getTemplate() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field template.
- getTemplateEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
-
Getter for the field templateEmail.
- getTemplatePath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field templatePath.
- getTemplateType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field templateType.
- getTest() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getTestCmd() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field testCmd.
- getTests() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
- getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- getThreads() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
- getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- getTimeTaken() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field timeTaken.
- getTissSource() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Getter for the field tissSource.
- getTissueOrigin() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of tissueOrigin
- getTissuePreparation() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of tissuePreparation
- getTissueType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Get the value of tissueType
- getTitle() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getTitle() - Method in class io.seqware.webservice.generated.model.Sample
-
- getTitle() - Method in class io.seqware.webservice.generated.model.Study
-
- getTitle() - Method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
-
- getTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field title.
- getTitle() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field title.
- getTitle() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field title.
- getTotal() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Getter for the field total.
- getTotalPrice() - Method in class io.seqware.webservice.generated.model.Expense
-
- getTotalPrice() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field totalPrice.
- getTotalPriceString() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field totalPrice.
- getTotalUnits() - Method in class io.seqware.webservice.generated.model.Expense
-
- getTotalUnits() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field totalUnits.
- getType() - Method in class io.seqware.webservice.generated.model.File
-
- getType() - Method in class io.seqware.webservice.generated.model.Lane
-
- getType() - Method in class io.seqware.webservice.generated.model.Sample
-
- getType() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getType() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getType() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field type.
- getType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- getType() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Getter for the field type.
- getTypeNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field typeNode.
- getUids(NamingEnumeration<SearchResult>) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
-
getUids.
- getUniqueDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
return the unique dir associate with the file if the file type is input, the provisioned file will be output to
provisionfiles/uniquedir + filename
- getUnit() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getUnit() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getUnit() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getUnit() - Method in class net.sourceforge.seqware.common.model.Attribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
- getUnit() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
- getUnit() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
getUnit.
- getUnit() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- getUnits() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getUnits() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getUnits() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field units.
- getUnits() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Getter for the field units.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field updateTimestamp.
- getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field updateTimestamp.
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Experiment
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Ius
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Lane
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Processing
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Sample
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Study
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getUpdateTstmp() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field updateValidator.
- getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
getUpdateValidator.
- getUrl() - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- getUrl() - Method in class io.seqware.webservice.generated.model.File
-
- getUrl() - Method in class io.seqware.webservice.generated.model.Processing
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- getUrl() - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- getUrl() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Getter for the field url.
- getUrl() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getUrl() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field url.
- getUrlLabel() - Method in class io.seqware.webservice.generated.model.File
-
- getUrlLabel() - Method in class io.seqware.webservice.generated.model.Processing
-
- getUrlLabel() - Method in class net.sourceforge.seqware.common.model.File
-
Getter for the field urlLabel.
- getUrlLabel() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field urlLabel.
- getUrlLabel() - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- getUrlLabel() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field urlLabel.
- getUseIparIntensities() - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Getter for the field useIparIntensities.
- getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Getter for the field useIparIntensities.
- getUseOneURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field useOneURL.
- getUserMl() - Method in class io.seqware.webservice.generated.model.Registration
-
- getUsername() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getUsername() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getUsername() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field username.
- getUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field userName.
- getUseTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Getter for the field useTwoURL.
- getUseURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Getter for the field useURL.
- getValidationReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field validationReportService.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
getValidator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Getter for the field validator.
- getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Getter for the field validator.
- getValue() - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getValue() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getValue() - Method in class net.sourceforge.seqware.common.model.Attribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
getValue.
- getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Getter for the field value.
- getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- getValues() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field values.
- getVersion() - Method in class io.seqware.webservice.generated.model.Processing
-
- getVersion() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getVersion() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field version.
- getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getViaAccessions(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the models corresponding to potential accessions
- getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getViaAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getViaParentAccessions(int[]) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get the models corresponding to potential parent accessions
- getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getViaParentAccessions(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getViewName(String) - Static method in class net.sourceforge.solexatools.util.Constant
-
getViewName.
- getVisibleParams() - Method in class net.sourceforge.solexatools.util.SummaryData
-
Getter for the field visibleParams.
- getVisibleWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getVisibleWorkflowParams.
- getVisibleWorkflowParamsWithDifferentValue() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getVisibleWorkflowParamsWithDifferentValue.
- getWebResource() - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- getWfRuns() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Getter for the field wfRuns.
- getWidth() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- getWorkflow(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get a workflow
- getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
Get a workflow
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflow.
- getWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_directory_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_engine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflow_run_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflowAccession(String, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowAccession.
- getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowAccession.
- getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowAccession.
- getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowAccession.
- getWorkflowAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getWorkflowAccession() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field workflowAccession.
- getWorkflowAccession() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getWorkflowAccessionsToCheck() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- getWorkflowAttributeCollection() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowAttributeId() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getWorkflowAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
Getter for the field workflowAttributeId.
- getWorkflowAttributes() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowAttributes.
- getWorkflowBaseDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
- getWorkflowClass() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowClass() - Method in class net.sourceforge.seqware.common.model.Workflow
-
- getWorkflowClass() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- getWorkflowCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getWorkflowDataModel(String, int, int, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory
-
load metadata.xml and load the class.
- getWorkflowDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Getter for the field workflowDir.
- getWorkflowEngine(AbstractWorkflowDataModel, Map<String, String>, boolean) - Static method in class io.seqware.pipeline.api.WorkflowTools
-
- getWorkflowEngine() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowEngine() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.Workflow
-
- getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- getWorkflowEngine() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.SampleReport
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getWorkflowId() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowId() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowId.
- getWorkflowInfo() - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
-
getWorkflowInfo.
- getWorkflowParam() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field workflowParam.
- getWorkflowParamCollection() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowParamId() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getWorkflowParamId() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Getter for the field workflowParamId.
- getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field workflowParamId.
- getWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowParams.
- getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowParams.
- getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowParams.
- getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowParams.
- getWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowParams.
- getWorkflowParamService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowParamService.
- getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Getter for the field workflowParamService.
- getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
-
Getter for the field workflowParamService.
- getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Getter for the field workflowParamService.
- getWorkflowParamServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowParamServiceBean.
- getWorkflowParamsWithDifferentFileMetaType() - Method in class net.sourceforge.seqware.common.model.Workflow
-
getWorkflowParamsWithDifferentFileMetaType.
- getWorkflowParamValueCollection() - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- getWorkflowParamValueId() - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- getWorkflowParamValueId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Getter for the field workflowParamValueId.
- getWorkflowParamValueService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowParamValueService.
- getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Getter for the field workflowParamValueService.
- getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Getter for the field workflowParamValueService.
- getWorkflowParamValueServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowParamValueServiceBean.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field workflowRun.
- getWorkflowRun(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRun.
- getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRun.
- getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRun.
- getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Expense
-
Getter for the field workflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field workflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
Getter for the field workflowRun.
- getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Getter for the field workflowRun.
- getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- getWorkflowRunAttributeCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowRunAttributeId() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getWorkflowRunAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
Getter for the field workflowRunAttributeId.
- getWorkflowRunAttributes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflowRunAttributes.
- getWorkflowRunByAncestorWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field workflowRunByAncestorWorkflowRunId.
- getWorkflowRunByStatusCmd(String) - Static method in class io.seqware.WorkflowRuns
-
Convert from status command to workflow run
- getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.File
-
- getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Registration
-
- getWorkflowRunCollection() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowRunHtml(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getWorkflowRunHtml.
- getWorkflowRunHtmlWithIUSs(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
-
getWorkflowRunHtmlWithIUSs.
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Expense
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.Processing
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- getWorkflowRunId() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
-
Getter for the field workflowRunId.
- getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Getter for the field workflowRunId.
- getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflowRunId.
- getWorkflowRunParam(SortedSet<WorkflowParam>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
getWorkflowRunParam.
- getWorkflowRunParamCollection() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowRunParamId() - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- getWorkflowRunParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
getWorkflowRunParamId.
- getWorkflowRunParams() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Getter for the field workflowRunParams.
- getWorkflowRunProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Getter for the field workflowRunProcessings.
- getWorkflowRunReport(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReport.
- getWorkflowRunReport(WorkflowRunStatus, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReport.
- getWorkflowRunReport(Integer, WorkflowRunStatus, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
- getWorkflowRunReport(Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReport.
- getWorkflowRunReport(WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunReport(Integer, WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunReport.
- getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunReport.
- getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunReport(WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunReport(Integer, WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunReport.
- getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunReport.
- getWorkflowRunReport(WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunReport(Integer, WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReport.
- getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReport.
- getWorkflowRunReport(WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReport.
- getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReport.
- getWorkflowRunReport(Integer, WorkflowRunStatus, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunReportStdErr(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReportStdErr.
- getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReportStdErr.
- getWorkflowRunReportStdOut(int) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunReportStdOut.
- getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunReportStdOut.
- getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.IUS
-
Getter for the field workflowRuns.
- getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Lane
-
Getter for the field workflowRuns.
- getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Workflow
-
Getter for the field workflowRuns.
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Returns the workflow_runs associated with a group of files.
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Returns the workflow_runs associated with a group of input files.
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Returns the workflow_runs associated with a group of input files.
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunsAssociatedWithInputFiles(List<Integer>, List<Integer>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunsByStatus.
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunsByStatus.
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunsByStatus.
- getWorkflowRunsByStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunsByStatus.
- getWorkflowRunsByStatusCmd(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
Get workflow run by status cmd (oozie job id in oozie).
- getWorkflowRunsByStatusCmd(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
- getWorkflowRunsByStatusCmd(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunsByStatusCmd(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
- getWorkflowRunsByStatusCmd(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
- getWorkflowRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Getter for the field workflowRunService.
- getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
-
Getter for the field workflowRunService.
- getWorkflowRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowRunServiceBean.
- getWorkflowRunWithWorkflow(String) - Method in interface net.sourceforge.seqware.common.metadata.Metadata
-
getWorkflowRunWithWorkflow.
- getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
-
getWorkflowRunWithWorkflow.
- getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataInMemory
-
- getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
-
getWorkflowRunWithWorkflow.
- getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
-
getWorkflowRunWithWorkflow.
- getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getWorkflows.
- getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getWorkflows.
- getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getWorkflows.
- getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getWorkflows.
- getWorkflowService() - Method in class net.sourceforge.seqware.common.ContextImpl
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
-
Getter for the field workflowService.
- getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
-
Getter for the field workflowService.
- getWorkflowServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
-
getWorkflowServiceBean.
- getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
getWorkflowsForStudy.
- getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
-
getWorkflowsForStudy.
- getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
getWorkflowsForStudy.
- getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
-
getWorkflowsForStudy.
- getWorkflowSqwVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
getWorkflowSqwVersion.
- getWorkflowsRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
getWorkflowsRun.
- getWorkflowTemplate() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowTemplate() - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- getWorkflowType() - Method in class io.seqware.webservice.generated.model.Workflow
-
- getWorkflowType() - Method in class net.sourceforge.seqware.common.model.Workflow
-
- getWorkflowType() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- getWorkflowType() - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Get the value of workflowType
- getWorkingDirectory() - Method in interface io.seqware.pipeline.api.WorkflowEngine
-
The working directory for the prepared workflow run, or null if not yet prepared or if not applicable for the concrete engine.
- getWorkingDirectory() - Method in class io.seqware.pipeline.engines.whitestar.WhiteStarWorkflowEngine
-
- getWorkingDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
-
- getWS(Map<String, String>) - Static method in class net.sourceforge.seqware.common.metadata.MetadataFactory
-
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.IUSIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.LaneIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.queries.EnvironmentResource
-
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentLibraryDesignResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignReadSpecResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentSpotDesignResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
-
getXml.
- getXML() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
-
getXML.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
-
getXml.
- getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
-
getXml.
- givesPermission(Registration) - Method in class net.sourceforge.seqware.common.security.PermissionsAware
-
- givesPermission(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.security.PermissionsAware
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Expense
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.File
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Invoice
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.IUS
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Lane
-
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Registration
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Study
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Short-circuit permission checking by providing a set of entities that have already been checked
- givesPermissionInternal(Registration, Set<Integer>) - Method in class net.sourceforge.seqware.common.security.PermissionsAware
-
Short-circuit permission checking by providing a set of entities that have already been checked
- s3ConnectionTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- S3CreateFileURLs - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module simply lists files at the S3 URL you provide and creates temporary URLs that can be shared with others.
- S3CreateFileURLs() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
-
- S3DeleteFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module simply lists files at the S3 URL you provide.
- S3DeleteFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
- S3ListFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module simply lists files at the S3 URL you provide.
- S3ListFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
- s3MaxConnections - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- s3MaxErrorRetry - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- s3SocketTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
-
- S3UploadDirectory - Class in net.sourceforge.seqware.pipeline.modules.utilities
-
Purpose:
This module uses the Amazon API to recursively upload a directory to an S3 bucket.
- S3UploadDirectory() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
-
- safe(String) - Static method in class net.sourceforge.seqware.common.util.Str
-
Returns a String suitable to be used in multiple contexts, e.g., as part of a filename.
- Sample - Class in io.seqware.webservice.generated.model
-
- Sample() - Constructor for class io.seqware.webservice.generated.model.Sample
-
- Sample(Integer) - Constructor for class io.seqware.webservice.generated.model.Sample
-
- Sample(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.Sample
-
- Sample - Class in net.sourceforge.seqware.common.model
-
- Sample() - Constructor for class net.sourceforge.seqware.common.model.Sample
-
Constructor for Sample.
- SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"
- SAMPLE_CHILD - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SAMPLE_CHILD="s_child"
- SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"
- SAMPLE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant SAMPLE_PREFIX="sam_"
- SAMPLE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SAMPLE_SAMPLE="s_sample"
- SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"
- SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
Constant SAMPLE_SWID="sw"
- SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"
- SampleAttribute - Class in io.seqware.webservice.generated.model
-
- SampleAttribute() - Constructor for class io.seqware.webservice.generated.model.SampleAttribute
-
- SampleAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleAttribute
-
- SampleAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SampleAttribute
-
- SampleAttribute - Class in net.sourceforge.seqware.common.model
-
SampleAttribute generated by hbm2java
- SampleAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
-
Constructor for SampleAttribute.
- SampleAttribute(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
-
Constructor for SampleAttribute.
- SampleAttribute(int, Sample, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
-
Constructor for SampleAttribute.
- SampleAttributeDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleAttributeDAO interface.
- SampleAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SampleAttributeDAOHibernate class.
- SampleAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
-
- SampleAttributeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleAttributeFacadeREST
-
- SampleController - Class in net.sourceforge.solexatools.webapp.controller
-
SampleController
- SampleController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
-
Constructor for SampleController.
- SampleController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
-
Constructor for SampleController.
- SampleDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleDAO interface.
- SampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SampleDAOHibernate class.
- SampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
-
Constructor for SampleDAOHibernate.
- SampleDetailsLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
-
SampleDetailsLineItem class.
- SampleDetailsLineItem(SequencerRun, Lane, IUS) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
-
Constructor for SampleDetailsLineItem.
- SampleDetailsWorkflowLineItems - Class in net.sourceforge.solexatools.webapp.metamodel
-
SampleDetailsWorkflowLineItems class.
- SampleDetailsWorkflowLineItems(Sample) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
Constructor for SampleDetailsWorkflowLineItems.
- SampleDetailsWorkflowLineItems(Processing) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
-
Constructor for SampleDetailsWorkflowLineItems.
- SampleFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleFacadeREST
-
- SampleHierarchies - Class in net.sourceforge.seqware.queryengine.webservice.model
-
- SampleHierarchies() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
-
- SampleHierarchy - Class in net.sourceforge.seqware.queryengine.webservice.model
-
- SampleHierarchy() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- SampleHierarchyPlugin - Class in net.sourceforge.seqware.pipeline.plugins.checkdb.plugins
-
Checks the metadb for issues specifically with the sample hierarchy.
- SampleHierarchyPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.plugins.SampleHierarchyPlugin
-
- SampleHierarchyResource - Class in net.sourceforge.seqware.webservice.resources.queries
-
- SampleHierarchyResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleHierarchyResource
-
- SampleIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
-
SampleIDFilter class.
- SampleIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
-
- SampleIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SampleIDResource class.
- SampleIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
-
Constructor for SampleIDResource.
- SampleInfo - Class in net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection
-
- SampleInfo() - Constructor for class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- SampleList - Class in net.sourceforge.seqware.common.model.lists
-
SampleList class.
- SampleList() - Constructor for class net.sourceforge.seqware.common.model.lists.SampleList
-
Constructor for SampleList.
- SampleRelationship - Class in io.seqware.webservice.generated.model
-
- SampleRelationship() - Constructor for class io.seqware.webservice.generated.model.SampleRelationship
-
- SampleRelationship(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleRelationship
-
- SampleRelationshipFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleRelationshipFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleRelationshipFacadeREST
-
- SampleReport - Class in io.seqware.webservice.generated.model
-
- SampleReport() - Constructor for class io.seqware.webservice.generated.model.SampleReport
-
- SampleReport(Integer) - Constructor for class io.seqware.webservice.generated.model.SampleReport
-
- SampleReportDAO - Interface in net.sourceforge.seqware.common.dao
-
SampleReportDAO interface.
- SampleReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SampleReportDAOHibernate class.
- SampleReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
-
- SampleReportFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SampleReportFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SampleReportFacadeREST
-
- SampleReportRow - Class in net.sourceforge.seqware.common.model
-
SampleReportRow class.
- SampleReportRow() - Constructor for class net.sourceforge.seqware.common.model.SampleReportRow
-
- SampleReportService - Interface in net.sourceforge.seqware.common.business
-
SampleReportService interface.
- SampleReportService.Status - Enum in net.sourceforge.seqware.common.business
-
- SampleReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
SampleReportServiceImpl class.
- SampleReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
- SampleResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SampleResource class.
- SampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleResource
-
Constructor for SampleResource.
- SampleService - Interface in net.sourceforge.seqware.common.business
-
SampleService interface.
- SampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
SampleServiceImpl class.
- SampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
Constructor for SampleServiceImpl.
- SampleSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- SampleSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Constructor for SampleSetupController.
- SampleValidator - Class in net.sourceforge.solexatools.validation
-
SampleValidator class.
- SampleValidator() - Constructor for class net.sourceforge.solexatools.validation.SampleValidator
-
Constructor for SampleValidator.
- SampleWorkflowRunsController - Class in net.sourceforge.solexatools.webapp.controller
-
SampleWorkflowRunsController class.
- SampleWorkflowRunsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
- SanityCheck - Class in io.seqware.pipeline.plugins.sanity
-
A database validation tool for your SeqWare metadb
- SanityCheck() - Constructor for class io.seqware.pipeline.plugins.sanity.SanityCheck
-
Constructor for HelloWorld.
- SanityCheckPluginInterface - Interface in io.seqware.pipeline.plugins.sanity
-
Specifies an interface for checks that can be done for a SeqWare install
- saveAscInSession(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
-
saveAscInSession.
- saveAscInSession(HttpServletRequest, String) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
saveAscInSession.
- saveFile(MultipartFile, String, Registration) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
-
saveFile.
- saveFile(MultipartFile, String, Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
-
saveFile.
- SaveOpenNodeController - Class in net.sourceforge.solexatools.webapp.controller
-
SaveOpenNodeController class.
- SaveOpenNodeController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Constructor for SaveOpenNodeController.
- saveSelectedWorkflowParamValue(HttpServletRequest, Integer, String) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
saveSelectedWorkflowParamValue.
- scheduleInstalledBundle(String, List<String>, boolean, List<String>, List<String>, List<String>, String, String, Set<Integer>) - Method in class io.seqware.pipeline.api.Scheduler
-
This method just needs a sw_accession value from the workflow table and an ini file(s) in order to schedule a workflow.
- scheduleInstalledBundle(String, List<String>, boolean, List<String>, List<String>, List<String>, String, String, Set<Integer>, boolean) - Method in class io.seqware.pipeline.api.Scheduler
-
This method just needs a sw_accession value from the workflow table and an ini file(s) in order to schedule a workflow.All needed
info is pulled from the workflow table which was populated when the workflow was installed.
- Scheduler - Class in io.seqware.pipeline.api
-
This class performs the actual work of scheduling a workflow.
- Scheduler(Metadata, Map<String, String>) - Constructor for class io.seqware.pipeline.api.Scheduler
-
Constructor for BasicWorkflow.
- Script_Check - Class in io.seqware.pipeline.plugins.sanity.checks
-
Runs through our CLI tutorial
- Script_Check() - Constructor for class io.seqware.pipeline.plugins.sanity.checks.Script_Check
-
- scriptFileName(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieBashJob
-
- SCRIPTS_SUBDIR - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
The sub-directory (of the working directory) in which generated script files will be placed.
- scriptsDir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- scriptsDir(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- SEARCH_CASE_SENSITIVE - Static variable in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Constant SEARCH_CASE_SENSITIVE="search.checked"
- SearchController - Class in net.sourceforge.solexatools.webapp.controller
-
SearchController class.
- SearchController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchController
-
Constructor for SearchController.
- SearchResultsController - Class in net.sourceforge.solexatools.webapp.controller
-
SearchResultsController class.
- SearchResultsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsController
-
- SearchResultsListController - Class in net.sourceforge.solexatools.webapp.controller
-
SearchResultsListController class.
- SearchResultsListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Constructor for SearchResultsListController.
- SecondTierModel - Interface in net.sourceforge.seqware.common.model
-
This links together all models that do not have sw_accession
- secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
-
- secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
-
- secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
-
- Security - Class in net.sourceforge.solexatools
-
Security class.
- Security() - Constructor for class net.sourceforge.solexatools.Security
-
- SELECTED_FILES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Constant SELECTED_FILES="selectedLaunchFiles"
- SELECTED_NODES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Constant SELECTED_NODES="launchSelectedNodes"
- SELECTED_VALUES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
Constant SELECTED_VALUES="selectedWorkflowParamValueId"
- selectExperimentNode(List<String>, Study) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectExperimentNode.
- SelectInputController - Class in net.sourceforge.solexatools.webapp.controller
-
SelectInputController class.
- SelectInputController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Constructor for SelectInputController.
- SelectInputController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Constructor for SelectInputController.
- SelectInputListController - Class in net.sourceforge.solexatools.webapp.controller
-
SelectInputListController class.
- SelectInputListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Constructor for SelectInputListController.
- selectIUSNode(List<String>, Sample) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectIUSNode.
- selectNullParentCountQuery(EntityManager, int) - Static method in class io.seqware.webservice.generated.model.Sample
-
- selectProcessingNode(List<String>, WorkflowRun) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- selectProcessingNode(List<String>, Processing) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- selectProcessingNode(List<String>, Lane) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- selectProcessingNode(List<String>, IUS) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectProcessingNode.
- SelectQueryRunner - Class in net.sourceforge.seqware.pipeline.plugins.checkdb
-
A class that allows plugin writers to only do select queries without any risk of leaving open connections or other unfriendliness
- SelectQueryRunner(MetadataDB) - Constructor for class net.sourceforge.seqware.pipeline.plugins.checkdb.SelectQueryRunner
-
- selectSampleNode(List<String>, Experiment) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectSampleNode.
- selectStudyNode(List<String>, List<Study>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectStudyNode.
- selectWorkflowRunNode(List<String>, List<WorkflowRun>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
-
selectWorkflowRunNode.
- separateFiles(List<ReturnValue>, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
-
Constant SEPARATOR="java.io.File.separator"
- SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
-
Constant SEPARATOR="java.io.File.separator"
- SEQ_RUN_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SEQ_RUN_ID="seq_run_id"
- SEQUENCER_RUN_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}
- SEQUENCER_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"
- SEQUENCER_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"
- SEQUENCER_RUN_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}
- SEQUENCER_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant SEQUENCER_VIEW="redirect:/sequencerRunList.htm"
- SequencerRun - Class in io.seqware.webservice.generated.model
-
- SequencerRun() - Constructor for class io.seqware.webservice.generated.model.SequencerRun
-
- SequencerRun(Integer) - Constructor for class io.seqware.webservice.generated.model.SequencerRun
-
- SequencerRun(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.SequencerRun
-
- SequencerRun - Class in net.sourceforge.seqware.common.model
-
- SequencerRun() - Constructor for class net.sourceforge.seqware.common.model.SequencerRun
-
Constructor for SequencerRun.
- SequencerRunAttribute - Class in io.seqware.webservice.generated.model
-
- SequencerRunAttribute() - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- SequencerRunAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- SequencerRunAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- SequencerRunAttribute - Class in net.sourceforge.seqware.common.model
-
SequencerRunAttribute generated by Morgan Taschuk
- SequencerRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Constructor for SequencerRunAttribute.
- SequencerRunAttribute(int, SequencerRunWizardDTO) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Constructor for SequencerRunAttribute.
- SequencerRunAttribute(int, SequencerRunWizardDTO, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Constructor for SequencerRunAttribute.
- SequencerRunAttributeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SequencerRunAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SequencerRunAttributeFacadeREST
-
- SequencerRunController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunController
- SequencerRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Constructor for SequencerRunController.
- SequencerRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Constructor for SequencerRunController.
- SequencerRunControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunController
- SequencerRunControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Constructor for SequencerRunControllerDTO.
- SequencerRunControllerDTO(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Constructor for SequencerRunControllerDTO.
- SequencerRunDAO - Interface in net.sourceforge.seqware.common.dao
-
SequencerRunDAO interface.
- SequencerRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
SequencerRunDAOHibernate class.
- SequencerRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
-
Constructor for SequencerRunDAOHibernate.
- SequencerRunDTO - Class in net.sourceforge.seqware.common.model
-
- SequencerRunDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Constructor for SequencerRunDTO.
- SequencerRunFacadeREST - Class in io.seqware.webservice.generated.controller
-
- SequencerRunFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.SequencerRunFacadeREST
-
- SequencerRunHtmlUtil - Class in net.sourceforge.solexatools.util
-
SequencerRunHtmlUtil class.
- SequencerRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
-
- SequencerRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SequencerRunIDResource class.
- SequencerRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
-
Constructor for SequencerRunIDResource.
- SequencerRunList - Class in net.sourceforge.seqware.common.model.lists
-
SequencerRunList class.
- SequencerRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.SequencerRunList
-
Constructor for SequencerRunList.
- SequencerRunListController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- SequencerRunListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
-
Constructor for SequencerRunListController.
- SequencerRunListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunListDetailsController class.
- SequencerRunListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Constructor for SequencerRunListDetailsController.
- SequencerRunReportId - Class in net.sourceforge.seqware.common.model
-
SequencerRunReportId class.
- SequencerRunReportId() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunReportId
-
- SequencerRunReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
- SequencerRunReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
-
- SequencerRunReportTableController - Class in net.sourceforge.solexatools.webapp.controller
-
- SequencerRunReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
- SequencerRunResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
SequencerRunResource class.
- SequencerRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
-
Constructor for SequencerRunResource.
- SequencerRunService - Interface in net.sourceforge.seqware.common.business
-
SequencerRunService interface.
- SequencerRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
SequencerRunServiceImpl class.
- SequencerRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
Constructor for SequencerRunServiceImpl.
- SequencerRunSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencingRunSetupController
- SequencerRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
-
Constructor for SequencerRunSetupController.
- SequencerRunSetupControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
-
SequencingRunSetupController
- SequencerRunSetupControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
-
Constructor for SequencerRunSetupControllerDTO.
- SequencerRunStatus - Enum in io.seqware.common.model
-
- SequencerRunValidator - Class in net.sourceforge.solexatools.validation
-
SequencerRunValidator class.
- SequencerRunValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunValidator
-
Constructor for SequencerRunValidator.
- SequencerRunWizardController - Class in net.sourceforge.solexatools.webapp.controller
-
SequencerRunWizardController class.
- SequencerRunWizardController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Constructor for SequencerRunWizardController.
- SequencerRunWizardController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Constructor for SequencerRunWizardController.
- SequencerRunWizardDTO - Class in net.sourceforge.seqware.common.model
-
SequencerRunWizardDTO class.
- SequencerRunWizardDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Constructor for SequencerRunWizardDTO.
- SequencerRunWizardSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
- SequencerRunWizardSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Constructor for SequencerRunWizardSetupController.
- SequencerRunWizardValidator - Class in net.sourceforge.solexatools.validation
-
SequencerRunWizardValidator class.
- SequencerRunWizardValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
-
Constructor for SequencerRunWizardValidator.
- SEQWARE_SETTINGS_PROPERTY - Static variable in class net.sourceforge.seqware.common.util.configtools.ConfigTools
-
Constant SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"
- SeqwareAccessionIDResource - Class in net.sourceforge.seqware.webservice.resources
-
SeqwareAccessionIDResource class.
- SeqwareAccessionIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
-
- SeqwareAccessionResource - Class in net.sourceforge.seqware.webservice.resources
-
SeqwareAccessionResource class.
- SeqwareAccessionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
-
- seqwareJar - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- seqwareJarPath - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- SeqWareVerifier - Class in net.sourceforge.seqware.queryengine.webservice.security
-
SeqWareVerifier class.
- SeqWareVerifier() - Constructor for class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
-
- SeqWareWebServiceApplication - Class in net.sourceforge.seqware.queryengine.webservice.controller
-
SeqWareWebServiceApplication class.
- SeqWareWebServiceApplication() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
-
- SeqWareWebServiceApplication.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller
-
http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
- SeqWareWebServiceApplication.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
-
- SeqWareWebServiceApplication.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
-
- SeqWareWebServiceClient - Class in io.seqware.webservice.client
-
Separate custom code from base client that would be destroyed during a regeneration
- SeqWareWebServiceClient(String) - Constructor for class io.seqware.webservice.client.SeqWareWebServiceClient
-
Constructor that uses default baseURI
- SeqWareWebServiceClient(String, String) - Constructor for class io.seqware.webservice.client.SeqWareWebServiceClient
-
Constructs a SeqWare web service client for the given resource and url.
- SeqWareWebserviceClient - Class in io.seqware.webservice.generated.client
-
Jersey REST client generated for REST resource:OrganismFacadeREST [io.seqware.webservice.model.organism]
USAGE:
- SeqWareWebserviceClient() - Constructor for class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- SeqWareWebserviceClient(String) - Constructor for class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
Constructs a SeqWare web service client for the given resource and url.
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp
-
- set_processing_update_tstmp_if_null(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
- setAbstract1(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setAbstractStr(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field abstractStr.
- setAccession(int) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- setAccession(int) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- setAccession(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setAccession(String) - Method in class io.seqware.webservice.generated.model.Organism
-
- setAccession(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setAccession(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field accession.
- setAccession(String) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field accession.
- setAccession(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field accession.
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setActive(Boolean) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field active.
- setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field active.
- setAdapters(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setAdapters(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field adapters.
- setAdapterSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field adapterSpec.
- setAddedSurcharge(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setAddedSurcharge(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field addedSurcharge.
- setAdminModelClass(String) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- setAdminModelClass(String) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- setAgent(String) - Method in class io.seqware.webservice.generated.model.Expense
-
- setAgent(String) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field agent.
- setAlgo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
set the job algorithm
- setAlgorithm(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field algorithm.
- setAlgorithm(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field algorithm.
- setAlgorithm(String) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field algorithm.
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setAlias(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field alias.
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field alias.
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field alias.
- setAlias(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field alias.
- setAlign(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setAllInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field allInputFiles.
- setAllItems(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field allItems.
- setAncestorWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.Processing
-
- setAnonymizedName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setAnonymizedName(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field anonymizedName.
- setArguments(List<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setAssayType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of assayType
- setAsText(String) - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
- setAttached(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setAttribute(String, String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
setAttribute.
- setAttributeParent(T) - Method in class net.sourceforge.seqware.common.model.Attribute
-
Associate this attribute with its parent
- setAttributeParent(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
- setAttributeParent(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
- setAttributeParent(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
- setAttributeParent(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
- setAttributeParent(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
- setAttributeParent(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
- setAttributeParent(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
- setAttributeParent(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
- setAttributeParent(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
- setAttributeParent(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
- setAttributes(Map<String, String>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field attributes.
- setBarcode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of barcode
- setBaseCaller(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setBaseCaller(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setBaseCaller(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field baseCaller.
- setBaseCoord(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setBaseCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field baseCoord.
- setBaseDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field baseDir.
- setBaseIniFile(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setBaseIniFile(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field baseIniFile.
- setCell(List<String>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
-
- setCenterName(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setCenterName(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field centerName.
- setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field centerName.
- setCenterProjectName(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setCenterProjectName(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field centerProjectName.
- setChildId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setChildId(Sample) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setChildren(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field children.
- setChildren(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field children.
- setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field childSample.
- setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field childSample.
- setChildSampleId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setChildSampleId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setClassesDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field classesDir.
- setClient(Client) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- setClientNotes(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setClientNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field clientNotes.
- setCmd(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setCmd(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setCode(String) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setCode(String) - Method in class io.seqware.webservice.generated.model.Organism
-
- setCode(String) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field code.
- setColorMatrix(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field colorMatrix.
- setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field colorMatrix.
- setColorMatrixCode(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field colorMatrixCode.
- setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field colorMatrixCode.
- setCommand(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field command.
- setCommand(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field command.
- setCommand(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field command.
- setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setCommand(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set the job command
- setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setCommonName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setCompleted(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field completed.
- setCompute(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setComputeReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field computeReq.
- setConfig(Map<String, String>) - Method in class io.seqware.pipeline.plugins.UserSettingsPlugin
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Let's you set the config this object should use.
- setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Let's you set the config this object should use.
- setConfigPath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field configPath.
- setConfigs(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the key-value properties for workflow
- setConfirmEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Setter for the field confirmEmailAddress.
- setConfirmPassword(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Setter for the field confirmPassword.
- setConstructionProtocol(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setConstructionProtocol(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field constructionProtocol.
- setCountFile(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field countFile.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field createTimestamp.
- setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field createTimestamp.
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Ius
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Registration
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Sample
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Study
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setCreateTstmp(Date) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setCriteria(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Setter for the field criteria.
- setCurrentSelectedFiles(HttpServletRequest, List<File>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
setCurrentSelectedFiles.
- setCurrentSelectedNodes(HttpServletRequest, List<String>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
-
setCurrentSelectedNodes.
- setCurrentWorkingDir(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setCurrentWorkingDir(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setCurrentWorkingDir(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field currentWorkingDir.
- setCwd(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field cwd.
- setCycleCoord(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setCycleCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field cycleCoord.
- setCycleCount(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCycleCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycleCount.
- setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycleCount.
- setCycleDescriptor(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCycleDescriptor(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field cycleDescriptor.
- setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycleDescriptor.
- setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycleDescriptor.
- setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycles.
- setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycles.
- setCycleSequence(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setCycleSequence(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field cycleSequence.
- setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field cycleSequence.
- setDataDecryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Sets data decryption key.
- setDataEncryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Sets data encryption key.
- setDate(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the pre-defined date variable
- setDax(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setDax(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field dax.
- setDaysUntilDue(Integer) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setDaysUntilDue(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field daysUntilDue.
- setDb(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setDecodeMethod(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setDecodeMethod(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field decodeMethod.
- setDefaultValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setDefaultValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field defaultValue.
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Expense
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.File
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Platform
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setDescription(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.StudyType
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setDescription(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field description.
- setDescription(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field description.
- setDeveloperMl(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setDisplay(Boolean) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setDisplay(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field display.
- setDisplay(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setDisplayName(String) - Method in class io.seqware.webservice.generated.model.FileType
-
- setDisplayName(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setDisplayName(String) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field displayName.
- setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field displayName.
- setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field displayName.
- setDisplayName(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field displayName.
- setDisplayValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field displayValue.
- setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
-
Setter for the field domainObject.
- setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Setter for the field domainObject.
- setEarliestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Set the value of earliestDate.
- setEmail(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field emailAddress.
- setEnd(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field end.
- setEndDate(Date) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setEndDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field endDate.
- setEndPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field endPage.
- setErrorCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field errorCount.
- setExecutionEnv(Environment.ExecutionEnvironment) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
set the execution environment
- setExistingType(StudyType) - Method in class io.seqware.webservice.generated.model.Study
-
- setExistingType(StudyType) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field existingType.
- setExistingTypeInt(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field existingTypeInt.
- setExitStatus(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field exitStatus.
- setExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field exitStatus.
- setExpectedBasecall(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setExpectedBaseCall(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field expectedBaseCall.
- setExpectedNumberReads(BigInteger) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExpectedNumberReads(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExpectedNumberReads(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expectedNumberReads.
- setExpectedNumberRuns(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExpectedNumberRuns(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExpectedNumberRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expectedNumberRuns.
- setExpectedNumberSpots(BigInteger) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExpectedNumberSpots(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExpectedNumberSpots(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expectedNumberSpots.
- setExpectedNumReads(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field expectedNumReads.
- setExpectedNumRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field expectedNumRuns.
- setExpectedNumSpots(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field expectedNumSpots.
- setExpenseAttributeCollection(Collection<ExpenseAttribute>) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setExpenseCollection(Collection<Expense>) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setExpenseFinishedTstmp(Date) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseId(Integer) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseId(Expense) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setExpenseId(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field expenseId.
- setExpenses(Set<Expense>) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field expenses.
- setExpenseType(String) - Method in class io.seqware.webservice.generated.model.Expense
-
- setExpenseType(String) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field expenseType.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field experiment.
- setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field experiment.
- setExperiment(Experiment, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setExperiment.
- setExperimentAttributeCollection(Collection<ExperimentAttribute>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setExperimentAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field experimentAttributeId.
- setExperimentAttributes(Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentAttributes.
- setExperimentAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of experimentAttributes
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Platform
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setExperimentCollection(Collection<Experiment>) - Method in class io.seqware.webservice.generated.model.Study
-
- setExperimentDAO(ExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
setExperimentDAO.
- setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
setExperimentDAO.
- setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field experimentDAO.
- setExperimentDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of experimentDescription
- setExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setExperimentId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setExperimentId(Experiment) - Method in class io.seqware.webservice.generated.model.Sample
-
- setExperimentId(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentId.
- setExperimentLibraryDesign(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentLibraryDesign.
- setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setExperimentLibraryDesignCollection(Collection<ExperimentLibraryDesign>) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
-
setExperimentLibraryDesignDAO.
- setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
-
setExperimentLibraryDesignDAO.
- setExperimentLibraryDesignId(ExperimentLibraryDesign) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentLibraryDesignId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setExperimentLibraryDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field experimentLibraryDesignId.
- setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentLibraryDesignService.
- setExperimentLinkCollection(Collection<ExperimentLink>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentLinkId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setExperimentName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of experimentName
- setExperiments(Set<Experiment>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field experiments.
- setExperiments(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field experiments.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field experimentService.
- setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field experimentService.
- setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field experimentSpotDesign.
- setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field experimentSpotDesign.
- setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
-
setExperimentSpotDesignDAO.
- setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
-
setExperimentSpotDesignDAO.
- setExperimentSpotDesignId(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setExperimentSpotDesignId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setExperimentSpotDesignId(ExperimentSpotDesign) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setExperimentSpotDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field experimentSpotDesignId.
- setExperimentSpotDesignReadSpecCollection(Collection<ExperimentSpotDesignReadSpec>) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
-
setExperimentSpotDesignReadSpecDAO.
- setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
-
setExperimentSpotDesignReadSpecDAO.
- setExperimentSpotDesignReadSpecId(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setExperimentSpotDesignReadSpecId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field experimentSpotDesignReadSpecId.
- setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentSpotDesignReadSpecService.
- setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field experimentSpotDesignService.
- setExperimentSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setExpLibDesignDesc(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignDesc.
- setExpLibDesignName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignName.
- setExpLibDesignProtocol(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignProtocol.
- setExpLibDesignSelection(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignSelection.
- setExpLibDesignSource(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignSource.
- setExpLibDesignStrategy(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expLibDesignStrategy.
- setExpSpotDesignAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expSpotDesignAdapterSpec.
- setExpSpotDesignReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expSpotDesignReadsPerSpot.
- setExpSpotDesignTagSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field expSpotDesignTagSpec.
- setExtension(String) - Method in class io.seqware.webservice.generated.model.FileType
-
- setExtension(String) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field extension.
- setExternalId(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setExternalId(String) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field externalId.
- setFailed(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field failed.
- setFile(MultipartFile) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field file.
- setFile(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Setter for the field file.
- setFile(File) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field file.
- setFile(File) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field file.
- setFileAttributeCollection(Collection<FileAttribute>) - Method in class io.seqware.webservice.generated.model.File
-
- setFileAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setFileAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
Setter for the field fileAttributeId.
- setFileAttributes(Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field fileAttributes.
- setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.FileType
-
- setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setFileCollection(Collection<File>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setFileDAO(FileDAO) - Method in interface net.sourceforge.seqware.common.business.FileService
-
setFileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
setFileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
Setter for the field fileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
Sets a private member variable with an instance of an implementation of FileDAO.
- setFileForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForSequrncerRun.
- setFileForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForStudy.
- setFileForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForWorkflowRun.
- setFileForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setFileForWorkflowRunRunning.
- setFileId(Integer) - Method in class io.seqware.webservice.generated.model.File
-
- setFileId(File) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setFileId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setFileId(File) - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- setFileId(Integer) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field fileId.
- setFileMetaType(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setFileMetaType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field fileMetaType.
- setFileMetaType(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field fileMetaType.
- setFilename(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setFilename(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setFileOne(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileOne.
- setFilePath(String) - Method in class io.seqware.webservice.generated.model.File
-
- setFilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field filePath.
- setFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setFilePath(File) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setFileReportDAO(FileReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
-
Setter for the field fileReportDAO.
- setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Setter for the field fileReportService.
- setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field fileReportService.
- setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field fileReportService.
- setFiles(Set<File>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field files.
- setFiles(List<File>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field files.
- setFiles(ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field files.
- setFiles(List<File>) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field files.
- setFilesArray(ArrayList<File>) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Setter for the field filesArray.
- setFileService(FileService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field fileService.
- setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field fileService.
- setFileStatus(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setFileSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setFileTwo(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileTwo.
- setFileTwoURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileTwoURL.
- setFileType(FileType) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field fileType.
- setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field fileType.
- setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileType.
- setFileTypeDAO(FileTypeDAO) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
-
setFileTypeDAO.
- setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
-
setFileTypeDAO.
- setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field fileTypeDAO.
- setFileTypeId(FileType) - Method in class io.seqware.webservice.generated.model.File
-
- setFileTypeId(Integer) - Method in class io.seqware.webservice.generated.model.FileType
-
- setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field fileTypeId.
- setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field fileTypeId.
- setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileTypeId.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field fileTypeService.
- setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Setter for the field fileTypeService.
- setFileUploadService(FileUploadService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field fileUploadService.
- setFileURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field fileURL.
- setFileURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field fileURL.
- setFinalized(Boolean) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setFinalized(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field finalized.
- setFinishedTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field finishedTimestamp.
- setFirstName(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setFirstName(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field firstName.
- setFlowCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field flowCount.
- setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field flowCount.
- setFlowSequence(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field flowSequence.
- setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field flowSequence.
- setFolderStore(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field folderStore.
- setFolderStore(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field folderStore.
- setForceCopy(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
when forceCopy is true, it will pass "--forcecopy" argument to provisionFileJob
- setForceRunAll(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setFs_default_name(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setFs_defaultFS(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setFs_hdfs_impl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setFullyPaid(Boolean) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setFullyPaid(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field fullyPaid.
- setGcrOutputFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setGcrSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setGcrSkipIfOutputExists(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setGroupingStrategy(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setHasMetadataWriteback(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
job specific metadata is not supported yet
- setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setHeader(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
Deprecated.
- setHost(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setHost(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setHost(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Deprecated.
- setHost(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field host.
- setHost(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field host.
- setHtml(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field html.
- setHtml(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field html.
- setHtml(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field html.
- setId(int) - Method in class io.seqware.webservice.controller.ModelAccessionIDTuple
-
- setId(int) - Method in class io.seqware.webservice.generated.controller.ModelAccessionIDTuple
-
- setId(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field id.
- setIdentitySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field identitySamples.
- setImmediateInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field immediateInputFiles.
- setIndividualName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setIndividualName(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field individualName.
- setIndividualNumber(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- setInfo(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field info.
- setIniFile(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setIniFile(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field iniFile.
- setInputAlgorithm(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setInputAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field inputAlgorithm.
- setInputFileAccessions(Set<Integer>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setInstitution(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setInstitution(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field institution.
- setInstrumentModel(String) - Method in class io.seqware.webservice.generated.model.Platform
-
- setInstrumentModel(String) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field instrumentModel.
- setInstrumentName(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field instrumentName.
- setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field instrumentName.
- setInvitationCode(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setInvitationCode(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field invitationCode.
- setInvoice(Invoice) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field invoice.
- setInvoiceAttributeCollection(Collection<InvoiceAttribute>) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setInvoiceAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setInvoiceCollection(Collection<Invoice>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setInvoiceDAO(InvoiceDAO) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
-
setInvoiceDAO.
- setInvoiceDAO(InvoiceDAO) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
-
setInvoiceDAO.
- setInvoiceId(Invoice) - Method in class io.seqware.webservice.generated.model.Expense
-
- setInvoiceId(Integer) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setInvoiceId(Invoice) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setInvoiceId(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field invoiceId.
- setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
-
Setter for the field invoiceService.
- setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
-
Setter for the field invoiceService.
- setIsEnd(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field isEnd.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field isHasFile.
- setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field isHasFile.
- setIsInput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
isInput = @param isInput isOutput = !@param isInput
- setIsOutput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
isInput = !@param isOutput isOutput = @param isOutput
- setIsPublic(Boolean) - Method in class io.seqware.webservice.generated.model.Sample
-
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field isSelected.
- setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field isSelected.
- setIsStart(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field isStart.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field ius.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Setter for the field ius.
- setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Lane
-
setIUS.
- setIUS(Set<IUS>) - Method in class net.sourceforge.seqware.common.model.Processing
-
setIUS.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field ius.
- setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Sample
-
setIUS.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field ius.
- setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field ius.
- setIus(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field ius.
- setIus(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field ius.
- setIusAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Adds a new ius attribute if the tag does not exist for this ius, or changes the value of an existing ius attribute.
- setIusAttributeCollection(Collection<IusAttribute>) - Method in class io.seqware.webservice.generated.model.Ius
-
- setIusAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setIusAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Setter for the field iusAttributeId.
- setIusAttributes(Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field iusAttributes.
- setIusAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusAttributes
- setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setIusCollection(Collection<Ius>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
setIUSDAO.
- setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
setIUSDAO.
- setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
Sets a private member variable with an instance of an implementation of IUSDAO.
- setIUSDAO(IUSDAO) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
setIUSDAO.
- setIusDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusDescription
- setIusId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setIusId(Integer) - Method in class io.seqware.webservice.generated.model.Ius
-
- setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setIusId(Ius) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- setIusId(Ius) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setIusId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setIusId(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field iusId.
- setIusName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusName
- setIusService(IUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field iusService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
setIUSService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
-
Setter for the field iusService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
setIUSService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
setIUSService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
setIUSService.
- setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field iusService.
- setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
setIUSService.
- setIusSkip(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of iusSkip
- setIusSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setIusWorkflowRunsCollection(Collection<IusWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.Ius
-
- setIusWorkflowRunsCollection(Collection<IusWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setIusWorkflowRunsId(Integer) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- setJoinDevelopersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field joinDevelopersMailingList.
- setJoinUsersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field joinUsersMailingList.
- setKey(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setKey(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field key.
- setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field key.
- setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Setter for the field key.
- setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Setter for the field key.
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setLabel(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field label.
- setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field label.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field lane.
- setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field lane.
- setLane(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setLane1(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane1.
- setLane2(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane2.
- setLane3(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane3.
- setLane4(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane4.
- setLane5(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane5.
- setLane6(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane6.
- setLane7(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane7.
- setLane8(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lane8.
- setLaneAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Adds a new lane attribute if the tag does not exist for this lane, or changes the value of an existing lane attribute.
- setLaneAttributeCollection(Collection<LaneAttribute>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setLaneAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field laneAttributeId.
- setLaneAttributes(Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field laneAttributes.
- setLaneAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Organism
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setLaneCollection(Collection<Lane>) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setLaneCount(int) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Setter for the field laneCount.
- setLaneCycleDescriptor(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneCycleDescriptor
- setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field laneDAO.
- setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
setLaneDAO.
- setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
Sets a private member variable with an instance of an implementation of LaneDAO.
- setLaneDAO(LaneDAO) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
setLaneDAO.
- setLaneDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneDescription
- setLaneForSequrncerRun(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setLaneForSequrncerRun.
- setLaneForStudy(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setLaneForStudy.
- setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.Ius
-
- setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- setLaneId(Lane) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setLaneId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setLaneId(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field laneId.
- setLaneIndex(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneIndex(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field laneIndex.
- setLaneName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneName
- setLaneNumber(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneNumber, and sets the 'geo_lane' attribute.
- setLanes(Set<Lane>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field lanes.
- setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field lanes.
- setLanes(Set<LaneInfo>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of lanes
- setLaneService(LaneService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.validation.LaneValidator
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field laneService.
- setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field laneService.
- setLanesForView(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
-
setLanesForView.
- setLaneSkip(Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of laneSkip
- setLaneString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setLaneSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setLaneTypeId(Integer) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setLaneWorkflowRunsCollection(Collection<LaneWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLaneWorkflowRunsCollection(Collection<LaneWorkflowRuns>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setLaneWorkflowRunsId(Integer) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- setLastName(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLastName(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field lastName.
- setLastUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLatestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
Set the value of latestDate.
- setLayout(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setLayout(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field layout.
- setLength(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field length.
- setLibrarySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field librarySamples.
- setLibrarySelection(LibrarySelection) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLibrarySelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setLibrarySelectionAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of librarySelectionAcc
- setLibrarySelectionDAO(LibrarySelectionDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
-
setLibrarySelectionDAO.
- setLibrarySelectionDAO(LibrarySelectionDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
-
setLibrarySelectionDAO.
- setLibrarySelectionId(Integer) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setLibrarySelectionId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Setter for the field librarySelectionId.
- setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field librarySelectionService.
- setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field librarySelectionService.
- setLibraryService(LibraryService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field libraryService.
- setLibrarySizeCode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Sets the library size code and sets the 'geo_library_size_code' attribute.
- setLibrarySource(LibrarySource) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLibrarySource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setLibrarySourceAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of librarySourceAcc
- setLibrarySourceDAO(LibrarySourceDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
-
setLibrarySourceDAO.
- setLibrarySourceDAO(LibrarySourceDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
-
setLibrarySourceDAO.
- setLibrarySourceId(Integer) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setLibrarySourceId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Setter for the field librarySourceId.
- setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field librarySourceService.
- setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field librarySourceService.
- setLibrarySourceTemplateType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of librarySourceTemplateType sets the 'geo_library_source_template_type' attribute.
- setLibraryStrategy(LibraryStrategy) - Method in class io.seqware.webservice.generated.model.Lane
-
- setLibraryStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setLibraryStrategyAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of libraryStrategyAcc
- setLibraryStrategyDAO(LibraryStrategyDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
-
setLibraryStrategyDAO.
- setLibraryStrategyDAO(LibraryStrategyDAO) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
-
setLibraryStrategyDAO.
- setLibraryStrategyId(Integer) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setLibraryStrategyId(Integer) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Setter for the field libraryStrategyId.
- setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field libraryStrategyService.
- setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field libraryStrategyService.
- setLibraryType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Sets the library type and sets the 'geo_library_type' attribute .
- setLibraryType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field libraryType.
- setLimsAdmin(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setLIMSAdmin(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
setLIMSAdmin.
- setList(List<ExperimentLibraryDesign>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentLibraryDesignList
-
setList.
- setList(List<Experiment>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
-
setList.
- setList(List<ExperimentSpotDesign>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignList
-
setList.
- setList(List<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentSpotDesignReadSpecList
-
setList.
- setList(List<File>) - Method in class net.sourceforge.seqware.common.model.lists.FileList
-
setList.
- setList(List<Integer>) - Method in class net.sourceforge.seqware.common.model.lists.IntegerList
-
setList.
- setList(List<IUS>) - Method in class net.sourceforge.seqware.common.model.lists.IUSList
-
setList.
- setList(List<Lane>) - Method in class net.sourceforge.seqware.common.model.lists.LaneList
-
setList.
- setList(List<LibrarySelection>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
-
setList.
- setList(List<LibrarySource>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
-
setList.
- setList(List<LibraryStrategy>) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
-
setList.
- setList(List<Organism>) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList
-
setList.
- setList(List<Platform>) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList
-
setList.
- setList(List<Processing>) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
-
setList.
- setList(List<ReturnValue>) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
-
setList.
- setList(List<Sample>) - Method in class net.sourceforge.seqware.common.model.lists.SampleList
-
setList.
- setList(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
-
setList.
- setList(List<Study>) - Method in class net.sourceforge.seqware.common.model.lists.StudyList
-
setList.
- setList(List<StudyType>) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList
-
setList.
- setList(List<Workflow>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
-
setList.
- setList(List<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
-
setList.
- setList(List<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
-
setList.
- setList(Collection<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
-
setList.
- setList(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
-
setList.
- setLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setLocal(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setLocal() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
Sets this job to run locally.
- setLocal(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
Sets whether this job should run locally.
- setLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setLocal(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setLongName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setMapred_job_tracker(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
- setMaxMemory(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set max memory
- setMd5sum(String) - Method in class io.seqware.webservice.generated.model.File
-
- setMd5sum(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field md5sum.
- setMd5sum(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setMd5sum(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setMemReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field memReq.
- setMetadata(Metadata) - Method in class io.seqware.pipeline.plugins.UserSettingsPlugin
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Setter for the field metadata.
- setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field metadata.
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Lets you set the metadata object
- setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Lets you set the metadata object
- setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- setMetadataWriteback(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setMetadataWriteBack(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line
- setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setMetaType(String) - Method in class io.seqware.webservice.generated.model.File
-
- setMetaType(String) - Method in class io.seqware.webservice.generated.model.FileType
-
- setMetaType(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field metaType.
- setMetaType(String) - Method in class net.sourceforge.seqware.common.model.FileType
-
Setter for the field metaType.
- setMetaType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setMetaType(List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setMetaws(Metadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setMimeType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setName(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LaneType
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LibrarySelection
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LibrarySource
-
- setName(String) - Method in class io.seqware.webservice.generated.model.LibraryStrategy
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Organism
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Platform
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setName(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setName(String) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setName(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setName(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.StudyType
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field name.
- setName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of name
- setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the workflow name
- setName(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setNameNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field nameNode.
- setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
setNamespace.
- setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- setNcbiTaxid(Integer) - Method in class io.seqware.webservice.generated.model.Organism
-
- setNcbiTaxId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field ncbiTaxId.
- setNetwork(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setNetworkReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field networkReq.
- setNewType(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setNewType(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field newType.
- SetNodeIdInSession - Class in net.sourceforge.solexatools.util
-
SetNodeIdInSession class.
- SetNodeIdInSession() - Constructor for class net.sourceforge.solexatools.util.SetNodeIdInSession
-
- setNominalLength(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setNominalLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field nominalLength.
- setNominalSdev(Double) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setNominalSdev(Long) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field nominalSdev.
- setNotes(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field notes.
- setNotRunned(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field notRunned.
- setOffspringProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field offspringProcessings.
- setOkTo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setOOZIE_APP_ROOT(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_JOBTRACKER(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_NAMENODE(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_QUEUENAME(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_URL(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- setOOZIE_WORK_DIR(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
- SetOperations - Class in net.sourceforge.seqware.pipeline.tools
-
Taken from http://www.java2s.com/Code/Java/Collections-Data-Structure/
Setoperationsunionintersectiondifferencesymmetricdifferenceissubsetissuperset.htm
- SetOperations() - Constructor for class net.sourceforge.seqware.pipeline.tools.SetOperations
-
- setOrganism(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field organism.
- setOrganism(Organism) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field organism.
- setOrganismDAO(OrganismDAO) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
-
setOrganismDAO.
- setOrganismDAO(OrganismDAO) - Method in interface net.sourceforge.seqware.common.business.OrganismService
-
setOrganismDAO.
- setOrganismId(Organism) - Method in class io.seqware.webservice.generated.model.Lane
-
- setOrganismId(Integer) - Method in class io.seqware.webservice.generated.model.Organism
-
- setOrganismId(Organism) - Method in class io.seqware.webservice.generated.model.Sample
-
- setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
-
Setter for the field organismId.
- setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field organismId.
- setOrganismId(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Sets the organismId, as long as the organism id is over 0.
- setOrganismService(OrganismService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field organismService.
- setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field organismService.
- setOriginalFileName(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Setter for the field originalFileName.
- setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
-
Setter for the field outputDir.
- setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
-
- setOutputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field outputFiles.
- setOutputLineCapacity(Integer) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
-
Set the number of lines of stdout and stderr to output
- setOutputPath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field owner.
- setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field owner.
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.File
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Ius
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Lane
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Processing
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Sample
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Study
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setOwnerId(Registration) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setOwnerUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setPage(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Setter for the field page.
- setPaidAmount(BigInteger) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setPaidAmount(Double) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field paidAmount.
- setPairedEnd(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field pairedEnd.
- setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field pairedEnd.
- setPairedEnd(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of pairedEnd
- setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- setPairedFilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field pairedFilePath.
- setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field pairedFilePath.
- setPairedOrientation(String) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setPairedOrientation(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field pairedOrientation.
- setParameters(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setParameters(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field parameters.
- setParameters(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field parameters.
- setParameters(List<String>) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
setParameters.
- setParameters(List<String>) - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
-
setParameters.
- setParams(List<String>) - Method in class io.seqware.pipeline.plugins.UserSettingsPlugin
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunFilesInitialPopulationPlugin
-
Lets you set a List of params so the plugin can deal with parameters
- setParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryLine
-
Setter for the field params.
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setParentAccessions(Collection<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set parent accessiosns for the job
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
set the parent accessions for provision file job
- setParentId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setParentId(Sample) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setParentId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- setParentProcessingAccession(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setParentProcessingAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field parentProcessingAccession.
- setParentProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field parentProcessings.
- setParents(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field parents.
- setParents(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field parents.
- setParents(Collection<Job>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
set parent jobs
- setParentWorkflowAccessions(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setPassword(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setPassword(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field password.
- setPasswordHint(String) - Method in class io.seqware.webservice.generated.model.Registration
-
- setPasswordHint(String) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field passwordHint.
- setPathToFirstFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field pathToFirstFile.
- setPathToSecondFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field pathToSecondFile.
- setPayee(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setPayee(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field payee.
- setPeakMemory(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
set the max memory for the workflow
- setPeakThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
-
set the max threads for the workflow
- setPending(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field pending.
- setPermanentBundleLocation(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setPermanentBundleLocation(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field permanentBundleLocation.
- setPermBundleLocation(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field permBundleLocation.
- setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field platform.
- setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field platform.
- setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field platform.
- setPlatformDAO(PlatformDAO) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
-
setPlatformDAO.
- setPlatformDAO(PlatformDAO) - Method in interface net.sourceforge.seqware.common.business.PlatformService
-
setPlatformDAO.
- setPlatformId(Platform) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setPlatformId(Integer) - Method in class io.seqware.webservice.generated.model.Platform
-
- setPlatformId(Platform) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setPlatformId(Integer) - Method in class net.sourceforge.seqware.common.model.Platform
-
Setter for the field platformId.
- setPlatformId(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- setPlatformInt(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field platformInt.
- setPlatformInt(int) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field platformInt.
- setPlatformService(PlatformService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field platformService.
- setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Setter for the field platformService.
- setPricePerUnit(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setPricePerUnit(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field pricePerUnit.
- setPrivate(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
-
setPrivate.
- setProcCountInfo(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
setProcCountInfo.
- setProcCountInfo(List<SequencerRun>) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
-
setProcCountInfo.
- setProcess(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setProcess(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field process.
- setProcessedCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field processedCount.
- setProcessExitStatus(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field processExitStatus.
- setProcessExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field processExitStatus.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field processing.
- setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field processing.
- setProcessingAccession(int) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field processingAccession.
- setProcessingAttributeCollection(Collection<ProcessingAttribute>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setProcessingAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Setter for the field processingAttributeId.
- setProcessingAttributes(Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field processingAttributes.
- setProcessingByChildId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field processingByChildId.
- setProcessingByParentId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field processingByParentId.
- setProcessingCollection(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setProcessingCollection(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setProcessingCollection1(Collection<Processing>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setProcessingCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field processingCount.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field processingDAO.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
Sets a private member variable with an instance of an implementation of ProcessingDAO.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
setProcessingDAO.
- setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
Setter for the field processingDAO.
- setProcessingDAO(ProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
setProcessingDAO.
- setProcessingExperimentsCollection(Collection<ProcessingExperiments>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setProcessingExperimentsCollection(Collection<ProcessingExperiments>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
-
setProcessingExperimentsDAO.
- setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
-
setProcessingExperimentsDAO.
- setProcessingExperimentsId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setProcessingExperimentsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field processingExperimentsId.
- setProcessingExperimentsService(ProcessingExperimentsService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingExperimentsService.
- setProcessingFilesCollection(Collection<ProcessingFiles>) - Method in class io.seqware.webservice.generated.model.File
-
- setProcessingFilesCollection(Collection<ProcessingFiles>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingFilesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- setProcessingForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForSequrncerRun.
- setProcessingForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForStudy.
- setProcessingForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForWorkflowRun.
- setProcessingForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setProcessingForWorkflowRunRunning.
- setProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setProcessingId(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingFiles
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setProcessingId(Processing) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setProcessingId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field processingId.
- setProcessingIusCollection(Collection<ProcessingIus>) - Method in class io.seqware.webservice.generated.model.Ius
-
- setProcessingIusCollection(Collection<ProcessingIus>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingIUSDAO(ProcessingIUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
-
setProcessingIUSDAO.
- setProcessingIUSDAO(ProcessingIUSDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
-
setProcessingIUSDAO.
- setProcessingIusId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setProcessingIusId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field processingIusId.
- setProcessingIusService(ProcessingIUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingIusService.
- setProcessingLanesCollection(Collection<ProcessingLanes>) - Method in class io.seqware.webservice.generated.model.Lane
-
- setProcessingLanesCollection(Collection<ProcessingLanes>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingLanesDAO(ProcessingLanesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
-
setProcessingLanesDAO.
- setProcessingLanesDAO(ProcessingLanesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
-
setProcessingLanesDAO.
- setProcessingLaneService(ProcessingLanesService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingLaneService.
- setProcessingLanesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setProcessingLanesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field processingLanesId.
- setProcessingRelationshipCollection(Collection<ProcessingRelationship>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingRelationshipCollection1(Collection<ProcessingRelationship>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
-
setProcessingRelationshipDAO.
- setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
-
setProcessingRelationshipDAO.
- setProcessingRelationshipId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setProcessingRelationshipId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field processingRelationshipId.
- setProcessingRelationshipService(ProcessingRelationshipService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingRelationshipService.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field processings.
- setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field processings.
- setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field processings.
- setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field processings.
- setProcessingSamplesCollection(Collection<ProcessingSamples>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingSamplesCollection(Collection<ProcessingSamples>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
-
setProcessingSamplesDAO.
- setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
-
setProcessingSamplesDAO.
- setProcessingSamplesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setProcessingSamplesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field processingSamplesId.
- setProcessingSamplesService(ProcessingSamplesService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingSamplesService.
- setProcessingSequencerRunsCollection(Collection<ProcessingSequencerRuns>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingSequencerRunsCollection(Collection<ProcessingSequencerRuns>) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
-
setProcessingSequencerRunsDAO.
- setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
-
setProcessingSequencerRunsDAO.
- setProcessingSequencerRunService(ProcessingSequencerRunsService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingSequencerRunService.
- setProcessingSequencerRunsId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setProcessingSequencerRunsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field processingSequencerRunsId.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field processingService.
- setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field processingService.
- setProcessingsForView(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
-
setProcessingsForView.
- setProcessingStudiesCollection(Collection<ProcessingStudies>) - Method in class io.seqware.webservice.generated.model.Processing
-
- setProcessingStudiesCollection(Collection<ProcessingStudies>) - Method in class io.seqware.webservice.generated.model.Study
-
- setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
-
setProcessingStudiesDAO.
- setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
-
setProcessingStudiesDAO.
- setProcessingStudiesId(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setProcessingStudiesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field processingStudiesId.
- setProcessingStudiesService(ProcessingStudiesService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field processingStudiesService.
- setProjectCode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
- setProjectId(int) - Method in class io.seqware.webservice.generated.model.Study
-
- setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field projectId.
- setPublic(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
-
setPublic.
- setQsubOptions(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
Allows specifying options to qsub.
- setQualityMultiplier(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityMultiplier(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityMultiplier.
- setQualityNumberOfLevels(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityNumberOfLevels(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityNumberOfLevels.
- setQualityScorer(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityScorer(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setQualityScorer(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityScorer.
- setQualityType(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setQualityType(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field qualityType.
- setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setQueue(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set the queue
- setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setRandom(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the pre-defined random variable
- setReadClass(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadClass(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readClass.
- setReader(BufferedReader) - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
-
Setter for the field reader.
- setReadIndex(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadIndex(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readIndex.
- setReadLabel(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readLabel.
- setReadSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setReadSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field readSpec.
- setReadSpecs(SortedSet<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field readSpecs.
- setReadsPerSpot(Integer) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field readsPerSpot.
- setReadType(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesignReadSpec
-
- setReadType(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
-
Setter for the field readType.
- setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field readyToProcess.
- setRefLane(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field refLane.
- setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field refLane.
- setRegions(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setRegions(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setRegions(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field regions.
- setRegions(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field regions.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field registration.
- setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field registration.
- setRegistrationDAO(RegistrationDAO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
-
setRegistrationDAO.
- setRegistrationDAO(RegistrationDAO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
-
setRegistrationDAO.
- setRegistrationId(Integer) - Method in class io.seqware.webservice.generated.model.Registration
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setRegistrationId(Registration) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setRegistrationId(Integer) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field registrationId.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
-
Setter for the field registrationService.
- setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field registrationService.
- setRelationship(String) - Method in class io.seqware.webservice.generated.model.ProcessingRelationship
-
- setRelationship(String) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setRelationship(String) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
-
Setter for the field relationship.
- setRequirements(Collection<Requirement>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setReturnValue(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field returnValue.
- setRootProcessingName(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setRootProcessingSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setRootSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field rootSample.
- setRowId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setRowId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field rowId.
- setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field rowId.
- setRows(List<Flexigrid.Cells>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Setter for the field rows.
- setRunAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Adds a new run attribute if the tag does not exist for this run, or changes the value of an existing run attribute.
- setRunAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runAttributes
- setRunCenter(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field runCenter.
- setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field runCenter.
- setRunDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runDescription
- setRunFilePath(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runFilePath
- setRunName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runName
- setRunSkip(boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of runSkip
- setRunStartTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field runStartTimestamp.
- setRunStartTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing
-
- setRunStartTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field runStartTstmp.
- setRunStopTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field runStopTimestamp.
- setRunStopTstmp(Date) - Method in class io.seqware.webservice.generated.model.Processing
-
- setRunStopTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field runStopTstmp.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field sample.
- setSample(Sample) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field sample.
- setSample(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field sample.
- setSampleAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Adds a new sample attribute if the tag does not exist for this sample, or changes the value of an existing sample attribute.
- setSampleAttributeCollection(Collection<SampleAttribute>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setSampleAttributeId(int) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Setter for the field sampleAttributeId.
- setSampleAttributes(Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field sampleAttributes.
- setSampleAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of sampleAttributes
- setSampleCode(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sampleCode.
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Organism
-
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setSampleCollection(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleCollection1(Collection<Sample>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field sampleDAO.
- setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
setSampleDAO.
- setSampleDAO(SampleDAO) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
setSampleDAO.
- setSampleDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of sampleDescription
- setSampleForStudy(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSampleForStudy.
- setSampleForWorkflowRun(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSampleForWorkflowRun.
- setSampleForWorkflowRunRunning(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSampleForWorkflowRunRunning.
- setSampleHierarchies(List<SampleHierarchy>) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
-
- setSampleId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.Ius
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setSampleId(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleId(Sample) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setSampleId(SequencerRun) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field sampleId.
- setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field sampleId.
- setSampleId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
-
- setSampleRelationshipCollection(Collection<SampleRelationship>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleRelationshipCollection1(Collection<SampleRelationship>) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSampleRelationshipId(Integer) - Method in class io.seqware.webservice.generated.model.SampleRelationship
-
- setSampleReportDAO(SampleReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
-
Setter for the field sampleReportDAO.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sampleReportService.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Setter for the field sampleReportService.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field sampleReportService.
- setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field sampleReportService.
- setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field samples.
- setSamples(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field samples.
- setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field samples.
- setSamples(Set<SampleInfo>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of samples
- setSampleService(SampleService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.validation.SampleValidator
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field sampleService.
- setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
-
Setter for the field sampleService.
- setSampleSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setSampleType(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sampleType.
- setScientificName(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSelection(LibrarySelection) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setSelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field selection.
- setSender(MailSender) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
-
Setter for the field sender.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field sequencerRun.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field sequencerRun.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field sequencerRun.
- setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field sequencerRun.
- setSequencerRun(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSequencerRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setSequencerRun.
- setSequencerRunAttributeCollection(Collection<SequencerRunAttribute>) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSequencerRunAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setSequencerRunAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Setter for the field sequencerRunAttributeId.
- setSequencerRunAttributes(Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field sequencerRunAttributes.
- setSequencerRunCollection(Collection<SequencerRun>) - Method in class io.seqware.webservice.generated.model.Platform
-
- setSequencerRunCollection(Collection<SequencerRun>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field sequencerRunDAO.
- setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
-
setSequencerRunDAO.
- setSequencerRunDAO(SequencerRunDAO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
-
setSequencerRunDAO.
- setSequencerRunId(SequencerRun) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSequencerRunId(SequencerRun) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setSequencerRunId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setSequencerRunId(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field sequencerRunId.
- setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field sequencerRunId.
- setSequencerRuns(Set<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field sequencerRuns.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field sequencerRunService.
- setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Setter for the field sequencerRunService.
- setSequencerRunSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setSequencerRunValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field sequencerRunValidator.
- setSequencerRunWizardDTO(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setSequencerRunWizardDTO.
- setSequencerRunWizardValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
-
Setter for the field sequencerRunWizardValidator.
- setSequenceSpace(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setSequenceSpace(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field sequenceSpace.
- setSeqwareAccession(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSeqwareAccessionString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSeqwareRevision(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setSeqwareRevision(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field seqwareRevision.
- setSeqwareVersion(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setSeqwareVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field seqwareVersion.
- setSessionFactory(SessionFactory) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field sessionFactory.
- setSharedStudies(SortedSet<ShareStudy>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field sharedStudies.
- setSharedWorkflowRuns(SortedSet<ShareWorkflowRun>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field sharedWorkflowRuns.
- setShareStudyCollection(Collection<ShareStudy>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareStudyCollection(Collection<ShareStudy>) - Method in class io.seqware.webservice.generated.model.Study
-
- setShareStudyDAO(ShareStudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
-
setShareStudyDAO.
- setShareStudyDAO(ShareStudyDAO) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
-
setShareStudyDAO.
- setShareStudyId(Integer) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setShareStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field shareStudyId.
- setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field shareStudyService.
- setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field shareStudyService.
- setShareWorkflowRunCollection(Collection<ShareWorkflowRun>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setShareWorkflowRunCollection(Collection<ShareWorkflowRun>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
-
setShareWorkflowRunDAO.
- setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
-
setShareWorkflowRunDAO.
- setShareWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setShareWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field shareWorkflowRunId.
- setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Setter for the field shareWorkflowRunService.
- setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field shareWorkflowRunService.
- setSize(BigInteger) - Method in class io.seqware.webservice.generated.model.File
-
- setSize(Long) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field size.
- setSize(Long) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setSize(Long) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSizeString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.File
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Ius
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSkip(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.File
-
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field skip.
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field skip.
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field skip.
- setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field skip.
- setSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setSlide1FilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlide1LaneCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlide2FilePath(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlide2LaneCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlideCount(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideOneFilePath.
- setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideOneFilePath.
- setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideOneLaneCount.
- setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideOneLaneCount.
- setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideTwoFilePath.
- setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideTwoFilePath.
- setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field slideTwoLaneCount.
- setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field slideTwoLaneCount.
- setSortable(boolean) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setSortKeySample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field sortKeySample.
- setSource(LibrarySource) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setSource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field source.
- setSourcePath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setSpotDesignReadSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field spotDesignReadSpec.
- setStartDate(Date) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setStartDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field startDate.
- setStartPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
-
Setter for the field startPage.
- setState(String) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setState(InvoiceState) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field state.
- setStatus(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setStatus(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
-
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field status.
- setStatus(ProcessingStatus) - Method in class net.sourceforge.seqware.common.model.Processing
-
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field status.
- setStatus(SequencerRunStatus) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field status.
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field status.
- setStatus(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field status.
- setStatus(WorkflowRunStatus) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field status.
- setStatus(SequencerRunStatus) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of the sequencer run status
- setStatusCmd(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStatusCmd(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field statusCmd.
- setStatuses(String[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field statuses.
- setStderr(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setStderr(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStderr(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field stderr.
- setStdErr(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field stdErr.
- setStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field stderr.
- setStderr(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
-
setStderr.
- setStderrFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Added by Xiaoshu Wang: Setter for the file that will be used to redirect stderr
- setStdout(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setStdout(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setStdout(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field stdout.
- setStdOut(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field stdOut.
- setStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field stdout.
- setStdout(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
-
setStdout.
- setStdoutFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
-
Setter for the field stdoutFile.
- setStrategy(LibraryStrategy) - Method in class io.seqware.webservice.generated.model.ExperimentLibraryDesign
-
- setStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
-
Setter for the field strategy.
- setStrExpectedNumberReads(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field strExpectedNumberReads.
- setStrExpectedNumberRuns(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field strExpectedNumberRuns.
- setStrExpectedNumReads(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field strExpectedNumReads.
- setStrExpectedNumRuns(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field strExpectedNumRuns.
- setStrLaneCount(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
-
Setter for the field strLaneCount.
- setStrRefLane(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field strRefLane.
- setStrStartURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field strStartURL.
- setStrStartURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field strStartURL.
- setStudies(Set<Study>) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field studies.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.FileReportRow
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
-
Setter for the field study.
- setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Setter for the field study.
- setStudy(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setStudy.
- setStudyAttribute(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Adds a new study attribute if the tag does not exist for this study, or changes the value of an existing study attribute.
- setStudyAttributeCollection(Collection<StudyAttribute>) - Method in class io.seqware.webservice.generated.model.Study
-
- setStudyAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setStudyAttributeId(int) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Setter for the field studyAttributeId.
- setStudyAttributes(Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field studyAttributes.
- setStudyAttributes(Set<TagValueUnit>) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyAttributes
- setStudyCenterName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyCenterName
- setStudyCenterProject(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyCenterProject
- setStudyCollection(Collection<Study>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setStudyCollection(Collection<Study>) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
-
Setter for the field studyDAO.
- setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
setStudyDAO.
- setStudyDAO(StudyDAO) - Method in interface net.sourceforge.seqware.common.business.StudyService
-
setStudyDAO.
- setStudyDescription(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyDescription
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.FileReport
-
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setStudyId(Integer) - Method in class io.seqware.webservice.generated.model.Study
-
- setStudyId(Study) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field studyId.
- setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field studyId.
- setStudyService(StudyService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.validation.StudyValidator
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableController
-
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field studyService.
- setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
-
Setter for the field studyService.
- setStudySwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
-
- setStudyTitle(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of studyTitle
- setStudyType(StudyType) - Method in class io.seqware.webservice.generated.model.Lane
-
- setStudyType(StudyType) - Method in class net.sourceforge.seqware.common.model.Lane
-
- setStudyType(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
- setStudyTypeAcc(int) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.LaneInfo
-
Set the value of studyTypeAcc
- setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Setter for the field studyTypeDAO.
- setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
-
setStudyTypeDAO.
- setStudyTypeDAO(StudyTypeDAO) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
-
setStudyTypeDAO.
- setStudyTypeId(Integer) - Method in class io.seqware.webservice.generated.model.StudyType
-
- setStudyTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.StudyType
-
Setter for the field studyTypeId.
- setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
- setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
Setter for the field studyTypeService.
- setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Setter for the field studyTypeService.
- setSummaryLines(List<SummaryLine>) - Method in class net.sourceforge.solexatools.util.SummaryData
-
Setter for the field summaryLines.
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Expense
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.File
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Invoice
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Ius
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Lane
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Processing
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Study
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setSwAccession(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field swAccession.
- setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field swAccession.
- setTag(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.Ius
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setTag(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setTag(String) - Method in class net.sourceforge.seqware.common.model.Attribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field tag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field tag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field tag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
setTag.
- setTag(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- setTags(String) - Method in class io.seqware.webservice.generated.model.Lane
-
- setTags(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setTags(String) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field tags.
- setTags(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field tags.
- setTags(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set the key-value properties from metadata.xml
- setTagSpec(String) - Method in class io.seqware.webservice.generated.model.ExperimentSpotDesign
-
- setTagSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
-
Setter for the field tagSpec.
- setTargetedResequencing(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of targetedResequencing and sets the 'geo_targeted_resequencing' attribute.
- setTaskGroup(Boolean) - Method in class io.seqware.webservice.generated.model.Processing
-
- setTaskGroup(boolean) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field taskGroup.
- setTaxonId(Integer) - Method in class io.seqware.webservice.generated.model.Sample
-
- setTemplate(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field template.
- setTemplate(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field template.
- setTemplatePath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field templatePath.
- setTemplateType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field templateType.
- setTest(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setTestCmd(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field testCmd.
- setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
-
- setThreads(int) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
-
set the max thread number
- setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobBatch
-
- setTimeTaken(String) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field timeTaken.
- SETTINGSFILENOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant SETTINGSFILENOTFOUND=13
- setTissSource(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Setter for the field tissSource.
- setTissueOrigin(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of tissueOrigin and sets the 'geo_tissue_origin' attribute.
- setTissuePreparation(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of tissuePreparation, and sets the 'geo_tissue_preparation' attribute.
- setTissueType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.SampleInfo
-
Set the value of tissueType and sets the 'geo_tissue_type' attribute.
- setTitle(String) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setTitle(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setTitle(String) - Method in class io.seqware.webservice.generated.model.Study
-
- setTitle(String) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field title.
- setTitle(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field title.
- setTitle(String) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field title.
- setTotal(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
-
Setter for the field total.
- setTotalPrice(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setTotalPrice(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field totalPrice.
- setTotalUnits(BigInteger) - Method in class io.seqware.webservice.generated.model.Expense
-
- setTotalUnits(Double) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field totalUnits.
- setType(String) - Method in class io.seqware.webservice.generated.model.File
-
- setType(LaneType) - Method in class io.seqware.webservice.generated.model.Lane
-
- setType(String) - Method in class io.seqware.webservice.generated.model.Sample
-
- setType(String) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setType(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setType(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field type.
- setType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setType(Requirement.Type) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- setType(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- setType(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
-
Setter for the field type.
- setTypeNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field typeNode.
- setUnit(String) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setUnit(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setUnit(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.Attribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
setUnit.
- setUnit(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setUnits(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
Setter for the field units.
- setUnits(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
Setter for the field units.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field updateTimestamp.
- setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field updateTimestamp.
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Experiment
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Ius
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Lane
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Processing
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Sample
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareStudy
-
- setUpdateTstmp(Date) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Study
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setUpdateTstmp(Timestamp) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field updateValidator.
- setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
setUpdateValidator.
- setupDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author.
- setupEnvironment() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author generally people don't override this.
- setupFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author the place to specify inputs and outputs to the program also, a user can specify inputs and
outputs on jobs directly in which case they are still provisioned properly with respect to the job (inputs before, outputs after)
when you define inputs/outputs here they are provisioned before all jobs and after all jobs respectively
- setupWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
to be Overridden by the workflow author you generally don't call this as the workflow author since it promotes hardcoding this will
typically be filled in by maven Called via reflection in WorkflowDataModelFactory
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ExperimentLink
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.File
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingExperiments
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingIus
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingLanes
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingSamples
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingSequencerRuns
-
- setUrl(String) - Method in class io.seqware.webservice.generated.model.ProcessingStudies
-
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
-
Setter for the field url.
- setUrl(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setUrl(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field url.
- setUrlLabel(String) - Method in class io.seqware.webservice.generated.model.File
-
- setUrlLabel(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.File
-
Setter for the field urlLabel.
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field urlLabel.
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
-
- setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field urlLabel.
- setUseCheckFile(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setUseIparIntensities(Boolean) - Method in class io.seqware.webservice.generated.model.SequencerRun
-
- setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
-
Setter for the field useIparIntensities.
- setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
-
Setter for the field useIparIntensities.
- setUseOneURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field useOneURL.
- setUserMl(boolean) - Method in class io.seqware.webservice.generated.model.Registration
-
- setUsername(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setUsername(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setUsername(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field username.
- setUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field userName.
- setUseTwoURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
-
Setter for the field useTwoURL.
- setUseURL(Boolean) - Method in class net.sourceforge.seqware.common.business.UploadFile
-
Setter for the field useURL.
- setValidationReportService(ValidationReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field validationReportService.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
-
setValidator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Setter for the field validator.
- setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
-
Setter for the field validator.
- setValue(String) - Method in class io.seqware.webservice.generated.model.ExpenseAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.ExperimentAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.FileAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.InvoiceAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.IusAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.LaneAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.ProcessingAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.SampleAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.SequencerRunAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.StudyAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setValue(String) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setValue(String) - Method in class net.sourceforge.seqware.common.model.Attribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
setValue.
- setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.TagValueUnit
-
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
-
Setter for the field value.
- setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
-
- setValues(SortedSet<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field values.
- setVerbose(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
-
Enable class verbose mode.
- setVerbose(boolean) - Static method in class net.sourceforge.seqware.common.util.Log
-
override the log4j.properties
- setVersion(String) - Method in class io.seqware.webservice.generated.model.Processing
-
- setVersion(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setVersion(String) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field version.
- setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
set workflow version
- setVisibleParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryData
-
Setter for the field visibleParams.
- setWebResource(WebResource) - Method in class io.seqware.webservice.generated.client.SeqWareWebserviceClient
-
- setWfRuns(WorkflowRun[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Setter for the field wfRuns.
- setWidth(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
-
- setWithHasFile(SortedSet<Experiment>) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
-
setWithHasFile.
- setWithHasFile(Set<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService
-
setWithHasFile.
- setWithHasFile(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
-
setWithHasFile.
- setWithHasFile(Set<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
-
setWithHasFile.
- setWithHasFile(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
-
setWithHasFile.
- setWithHasFile(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
-
setWithHasFile.
- setWithHasFile(Set<Processing>) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
setWithHasFile.
- setWithHasFile(Set<Processing>, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
-
setWithHasFile.
- setWithHasFile(Integer, SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
-
setWithHasFile.
- setWithHasFile(SortedSet<IUS>) - Method in interface net.sourceforge.seqware.common.business.IUSService
-
setWithHasFile.
- setWithHasFile(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.business.LaneService
-
setWithHasFile.
- setWithHasFile(Set<Processing>) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
setWithHasFile.
- setWithHasFile(Set<Processing>, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
-
setWithHasFile.
- setWithHasFile(Integer, SortedSet<Sample>) - Method in interface net.sourceforge.seqware.common.business.SampleService
-
setWithHasFile.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
-
Setter for the field workflow.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
-
Setter for the field workflow.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field workflow.
- setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflow.
- setWorkflow_engine(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
default is pegasus
- setWorkflowAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setWorkflowAccession(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field workflowAccession.
- setWorkflowAccession(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setWorkflowAccessionsToCheck(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- setWorkflowAttributeCollection(Collection<WorkflowAttribute>) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setWorkflowAttributes(Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowAttributes.
- setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
-
- setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
-
set the workflowBundle directory
- setWorkflowClass(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
- setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- setWorkflowCollection(Collection<Workflow>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setWorkflowDAO(WorkflowDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
-
setWorkflowDAO.
- setWorkflowDAO(WorkflowDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
-
setWorkflowDAO.
- setWorkflowDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
Setter for the field workflowDir.
- setWorkflowEngine(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowEngine(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
- setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
- setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- setWorkflowId(Integer) - Method in class io.seqware.webservice.generated.model.SampleReport
-
- setWorkflowId(Integer) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowAttribute
-
- setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setWorkflowId(Workflow) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowId(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowId.
- setWorkflowParam(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field workflowParam.
- setWorkflowParamCollection(Collection<WorkflowParam>) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowParamDAO(WorkflowParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
-
setWorkflowParamDAO.
- setWorkflowParamDAO(WorkflowParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
-
setWorkflowParamDAO.
- setWorkflowParamId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setWorkflowParamId(WorkflowParam) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
-
Setter for the field workflowParamId.
- setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field workflowParamId.
- setWorkflowParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowParams.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowParamService.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
-
Setter for the field workflowParamService.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
-
Setter for the field workflowParamService.
- setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Setter for the field workflowParamService.
- setWorkflowParamValueCollection(Collection<WorkflowParamValue>) - Method in class io.seqware.webservice.generated.model.WorkflowParam
-
- setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
-
setWorkflowParamValueDAO.
- setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
-
setWorkflowParamValueDAO.
- setWorkflowParamValueId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowParamValue
-
- setWorkflowParamValueId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
-
Setter for the field workflowParamValueId.
- setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowParamValueService.
- setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
-
Setter for the field workflowParamValueService.
- setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
-
Setter for the field workflowParamValueService.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Expense
-
Setter for the field workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
-
Setter for the field workflowRun.
- setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
Setter for the field workflowRun.
- setWorkflowRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRun.
- setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
- setWorkflowRunAttributeCollection(Collection<WorkflowRunAttribute>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowRunAttributeId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setWorkflowRunAttributes(Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflowRunAttributes.
- setWorkflowRunByAncestorWorkflowRunId(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field workflowRunByAncestorWorkflowRunId.
- setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.File
-
- setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.Registration
-
- setWorkflowRunCollection(Collection<WorkflowRun>) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowRunDAO(WorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
setWorkflowRunDAO.
- setWorkflowRunDAO(WorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
-
setWorkflowRunDAO.
- setWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.Expense
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.IusWorkflowRuns
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.LaneWorkflowRuns
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.Processing
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- setWorkflowRunId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.WorkflowRunAttribute
-
- setWorkflowRunId(WorkflowRun) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
-
Setter for the field workflowRunId.
- setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Setter for the field workflowRunId.
- setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflowRunId.
- setWorkflowRunParamCollection(Collection<WorkflowRunParam>) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
-
setWorkflowRunParamDAO.
- setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
-
Setter for the field workflowRunParamDAO.
- setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
-
setWorkflowRunParamDAO.
- setWorkflowRunParamId(Integer) - Method in class io.seqware.webservice.generated.model.WorkflowRunParam
-
- setWorkflowRunParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
-
setWorkflowRunParamId.
- setWorkflowRunParams(SortedSet<WorkflowRunParam>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
-
Setter for the field workflowRunParams.
- setWorkflowRunProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
-
Setter for the field workflowRunProcessings.
- setWorkflowRunRunning(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRunRunning.
- setWorkflowRunRunningWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRunRunningWithSample.
- setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.IUS
-
Setter for the field workflowRuns.
- setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Lane
-
Setter for the field workflowRuns.
- setWorkflowRuns(SortedSet<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Workflow
-
Setter for the field workflowRuns.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.RetryAnalysisWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Setter for the field workflowRunService.
- setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
-
Setter for the field workflowRunService.
- setWorkflowRunWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
-
setWorkflowRunWithSample.
- setWorkflows(ArrayList<WorkflowInfo>) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
-
Setter for the field workflows.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.seqware.common.ContextImpl
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
-
Setter for the field workflowService.
- setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
-
Setter for the field workflowService.
- setWorkflowSqwVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
setWorkflowSqwVersion.
- setWorkflowTemplate(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowTemplate(String) - Method in class io.seqware.webservice.generated.model.WorkflowRun
-
- setWorkflowType(String) - Method in class io.seqware.webservice.generated.model.Workflow
-
- setWorkflowType(String) - Method in class net.sourceforge.seqware.common.model.Workflow
-
- setWorkflowType(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
-
- setWorkflowType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.RunInfo
-
Set the value of workflowType
- SGE_MAX_MEMORY_PARAM_VARIABLE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
Variable identifier to be used within the qsub max-memory parameter to specify the value.
- SGE_THREADS_PARAM_VARIABLE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
Variable identifier to be used within the qsub threads parameter to specify the value.
- SGE_XMLNS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
-
Namespace of the Oozie SGE action xml node.
- ShareStudy - Class in io.seqware.webservice.generated.model
-
- ShareStudy() - Constructor for class io.seqware.webservice.generated.model.ShareStudy
-
- ShareStudy(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareStudy
-
- ShareStudy(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareStudy
-
- ShareStudy - Class in net.sourceforge.seqware.common.model
-
ShareStudy class.
- ShareStudy() - Constructor for class net.sourceforge.seqware.common.model.ShareStudy
-
Constructor for ShareStudy.
- ShareStudyDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareStudyDAO interface.
- ShareStudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareStudyDAOHibernate class.
- ShareStudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
-
Constructor for ShareStudyDAOHibernate.
- ShareStudyFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareStudyFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareStudyFacadeREST
-
- ShareStudyService - Interface in net.sourceforge.seqware.common.business
-
ShareStudyService interface.
- ShareStudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareStudyServiceImpl class.
- ShareStudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
-
Constructor for ShareStudyServiceImpl.
- ShareValidatorController - Class in net.sourceforge.solexatools.webapp.controller
-
ShareValidatorController class.
- ShareValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
-
Constructor for ShareValidatorController.
- ShareWorkflowRun - Class in io.seqware.webservice.generated.model
-
- ShareWorkflowRun() - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- ShareWorkflowRun(Integer) - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- ShareWorkflowRun(Integer, Date) - Constructor for class io.seqware.webservice.generated.model.ShareWorkflowRun
-
- ShareWorkflowRun - Class in net.sourceforge.seqware.common.model
-
ShareWorkflowRun class.
- ShareWorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.ShareWorkflowRun
-
Constructor for ShareWorkflowRun.
- ShareWorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao
-
ShareWorkflowRunDAO interface.
- ShareWorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
ShareWorkflowRunDAOHibernate class.
- ShareWorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
-
Constructor for ShareWorkflowRunDAOHibernate.
- ShareWorkflowRunFacadeREST - Class in io.seqware.webservice.generated.controller
-
- ShareWorkflowRunFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.ShareWorkflowRunFacadeREST
-
- ShareWorkflowRunService - Interface in net.sourceforge.seqware.common.business
-
ShareWorkflowRunService interface.
- ShareWorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
ShareWorkflowRunServiceImpl class.
- ShareWorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
-
Constructor for ShareWorkflowRunServiceImpl.
- SignUpController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
- SignUpController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SignUpController
-
Constructor for SignUpController.
- SIZE_COUNT_FILE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
-
Constant SIZE_COUNT_FILE=5
- SIZE_COUNT_TREE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
-
Constant SIZE_COUNT_TREE=20
- sleep(int) - Static method in class net.sourceforge.seqware.common.util.processtools.ProcessTools
-
sleep.
- SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_NAME="sortname"
- SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Constant SORT_NAME="sortname"
- SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_NAME="sortname"
- SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_ORDER="sortorder"
- SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Constant SORT_ORDER="sortorder"
- SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_ORDER="sortorder"
- SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_ORDER_ASC="asc"
- SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_ORDER_ASC="asc"
- SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
-
Constant SORT_ORDER_DESC="desc"
- SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant SORT_ORDER_DESC="desc"
- spaceSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
-
- SQLQUERYFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant SQLQUERYFAILED=82
- SqwFile - Class in net.sourceforge.seqware.pipeline.workflowV2.model
-
a file object which has all information for provision
- SqwFile() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
-
- SqwKeys - Enum in io.seqware.pipeline
-
This binds together all of the keys in the .seqware/settings file as a precursor to auto-generating documentation for them.
- SqwKeys.Categories - Enum in io.seqware.pipeline
-
- stackTraceToString(Throwable) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
-
stackTraceToString.
- standard - Variable in enum net.sourceforge.seqware.pipeline.plugins.fileprovenance.ProvenanceUtility.HumanProvenanceFilters
-
- startCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
-
An alternate runner that launches a process and returns it so that the caller can process it's output directly.
- STATE_FILENAME - Static variable in class io.seqware.pipeline.engines.whitestar.Persistence
-
- status - Variable in exception net.sourceforge.seqware.common.util.ExitException
-
- stderr - Variable in class net.sourceforge.seqware.common.module.ReturnValue
-
- stderr(String) - Static method in class net.sourceforge.seqware.common.util.Log
-
stderr.
- StderrRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
-
Annotation type to tag where to start Stderr redirect
Created by IntelliJ IDEA.
- stderrWithTime(String) - Static method in class net.sourceforge.seqware.common.util.Log
-
- stdout - Variable in class net.sourceforge.seqware.common.module.ReturnValue
-
- stdout(String) - Static method in class net.sourceforge.seqware.common.util.Log
-
stdout.
- STDOUTERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant STDOUTERR=90
- StdoutRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
-
Interface for declaring when to do the Created by IntelliJ IDEA.
- stdoutWithTime(String) - Static method in class net.sourceforge.seqware.common.util.Log
-
Output to stdout with the time pre-pended
- Str - Class in net.sourceforge.seqware.common.util
-
- Str() - Constructor for class net.sourceforge.seqware.common.util.Str
-
- Str.UnsafeName - Exception in net.sourceforge.seqware.common.util
-
- Str.UnsafeName(String) - Constructor for exception net.sourceforge.seqware.common.util.Str.UnsafeName
-
- StringTruncator - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object
-
This class enforces names for the Oozie workflow engine that are less than or equal to 50 characters but are still unique.
- StringTruncator() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.StringTruncator
-
- stripInvalidXmlCharacters(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
-
Stolen from https://stackoverflow.com/questions/93655/stripping-invalid-xml-characters-in-java/9635310#9635310
- Studies - Class in io.seqware
-
- Studies() - Constructor for class io.seqware.Studies
-
- studiesTsv() - Static method in class io.seqware.Studies
-
- Study - Class in io.seqware.webservice.generated.model
-
- Study() - Constructor for class io.seqware.webservice.generated.model.Study
-
- Study(Integer) - Constructor for class io.seqware.webservice.generated.model.Study
-
- Study(Integer, String, String, String, int, Date) - Constructor for class io.seqware.webservice.generated.model.Study
-
- Study - Class in net.sourceforge.seqware.common.model
-
- Study() - Constructor for class net.sourceforge.seqware.common.model.Study
-
Constructor for Study.
- STUDY_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"
- STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
Constant STUDY_ID="study_id"
- STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constant STUDY_ID="study_id"
- STUDY_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant STUDY_PREFIX="study_"
- STUDY_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_SWA="Header.STUDY_SWA.getTitle()"
- STUDY_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"
- STUDY_TITLE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
-
Constant STUDY_TITLE="Header.STUDY_TITLE.getTitle()"
- STUDY_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
-
Constant STUDY_VIEW="redirect:/myStudyList.htm"
- StudyAttribute - Class in io.seqware.webservice.generated.model
-
- StudyAttribute() - Constructor for class io.seqware.webservice.generated.model.StudyAttribute
-
- StudyAttribute(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyAttribute
-
- StudyAttribute(Integer, String, String) - Constructor for class io.seqware.webservice.generated.model.StudyAttribute
-
- StudyAttribute - Class in net.sourceforge.seqware.common.model
-
StudyAttribute generated by hbm2java
- StudyAttribute() - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
-
Constructor for StudyAttribute.
- StudyAttribute(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
-
Constructor for StudyAttribute.
- StudyAttribute(int, Study, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
-
Constructor for StudyAttribute.
- StudyAttributeDAO - Interface in net.sourceforge.seqware.common.dao
-
StudyAttributeDAO interface.
- StudyAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
StudyAttributeDAOHibernate class.
- StudyAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
-
- StudyAttributeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- StudyAttributeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyAttributeFacadeREST
-
- StudyBuildTree - Class in net.sourceforge.solexatools.util
-
StudyBuildTree class.
- StudyBuildTree() - Constructor for class net.sourceforge.solexatools.util.StudyBuildTree
-
- StudyController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyController
- StudyController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
-
Constructor for StudyController.
- StudyController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
-
Constructor for StudyController.
- StudyDAO - Interface in net.sourceforge.seqware.common.dao
-
StudyDAO interface.
- StudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
StudyDAOHibernate class.
- StudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
-
Constructor for StudyDAOHibernate.
- StudyFacadeREST - Class in io.seqware.webservice.generated.controller
-
- StudyFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyFacadeREST
-
- StudyHtmlUtil - Class in net.sourceforge.solexatools.util
-
StudyHtmlUtil class.
- StudyHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.StudyHtmlUtil
-
- StudyIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
StudyIDResource class.
- StudyIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
-
Constructor for StudyIDResource.
- StudyList - Class in net.sourceforge.seqware.common.model.lists
-
StudyList class.
- StudyList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyList
-
Constructor for StudyList.
- StudyListController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudyListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListController
-
Constructor for StudyListController.
- StudyListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyListDetailsController class.
- StudyListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
-
Constructor for StudyListDetailsController.
- StudyListDetailsFlatController - Class in net.sourceforge.solexatools.webapp.controller
-
- StudyListDetailsFlatController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
-
- StudyReportBoxController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyReportBoxController class.
- StudyReportBoxController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
-
- StudyReportController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudyReportController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportController
-
Constructor for StudyReportController.
- StudyReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyReportSetupController class.
- StudyReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
-
- StudyReportTableController - Class in net.sourceforge.solexatools.webapp.controller
-
StudyReportTableController class.
- StudyReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
-
Constructor for StudyReportTableController.
- StudyResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
StudyResource class.
- StudyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyResource
-
Constructor for StudyResource.
- StudySampleReportFileLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
-
StudySampleReportFileLineItem class.
- StudySampleReportFileLineItem(Sample, Sample, IUS, File) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
-
Constructor for StudySampleReportFileLineItem.
- StudySampleReportLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
-
StudySampleReportLineItem class.
- StudySampleReportLineItem(Sample, Sample, String[]) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
-
Constructor for StudySampleReportLineItem.
- StudyService - Interface in net.sourceforge.seqware.common.business
-
StudyService interface.
- StudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
StudyServiceImpl class.
- StudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
-
Constructor for StudyServiceImpl.
- StudySetupController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudySetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudySetupController
-
Constructor for StudySetupController.
- StudyTableController - Class in net.sourceforge.solexatools.webapp.controller
-
RegistrationSetupController
- StudyTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyTableController
-
Constructor for AnalisysListController.
- StudyTableControllerDetails - Class in net.sourceforge.solexatools.webapp.controller
-
TODO:
* it would be best if this controller would actually render the workflow_runs too.
- StudyTableControllerDetails() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyTableControllerDetails
-
Constructor for AnalisysListController.
- StudyType - Class in io.seqware.webservice.generated.model
-
- StudyType() - Constructor for class io.seqware.webservice.generated.model.StudyType
-
- StudyType(Integer) - Constructor for class io.seqware.webservice.generated.model.StudyType
-
- StudyType(Integer, String) - Constructor for class io.seqware.webservice.generated.model.StudyType
-
- StudyType - Class in net.sourceforge.seqware.common.model
-
StudyType class.
- StudyType() - Constructor for class net.sourceforge.seqware.common.model.StudyType
-
- StudyTypeDAO - Interface in net.sourceforge.seqware.common.dao
-
StudyTypeDAO interface.
- StudyTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
-
StudyTypeDAOHibernate class.
- StudyTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
-
Constructor for StudyTypeDAOHibernate.
- StudyTypeFacadeREST - Class in io.seqware.webservice.generated.controller
-
- StudyTypeFacadeREST() - Constructor for class io.seqware.webservice.generated.controller.StudyTypeFacadeREST
-
- StudyTypeList - Class in net.sourceforge.seqware.common.model.lists
-
StudyTypeList class.
- StudyTypeList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyTypeList
-
Constructor for StudyTypeList.
- StudyTypeResource - Class in net.sourceforge.seqware.webservice.resources.tables
-
ExperimentResource class.
- StudyTypeResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
-
Constructor for ExperimentResource.
- StudyTypeService - Interface in net.sourceforge.seqware.common.business
-
StudyTypeService interface.
- StudyTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
-
StudyTypeServiceImpl class.
- StudyTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
-
Constructor for StudyTypeServiceImpl.
- StudyUpdateValidator - Class in net.sourceforge.solexatools.validation
-
- StudyUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyUpdateValidator
-
- StudyValidator - Class in net.sourceforge.solexatools.validation
-
StudyValidator class.
- StudyValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyValidator
-
Constructor for StudyValidator.
- subList(int, int, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subList.
- subList(HttpServletRequest, String, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subList.
- subList(HttpServletRequest, String, int, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subList.
- subListSD(HttpServletRequest, String, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
-
subListSD.
- submitCancel(int...) - Static method in class io.seqware.WorkflowRuns
-
- submitRetry(int...) - Static method in class io.seqware.WorkflowRuns
-
- SUCCESS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
-
Constant SUCCESS=0
- SummaryData - Class in net.sourceforge.solexatools.util
-
SummaryData class.
- SummaryData() - Constructor for class net.sourceforge.solexatools.util.SummaryData
-
Constructor for SummaryData.
- SummaryLaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
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SummaryLaunchWorkflowController class.
- SummaryLaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
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Constructor for SummaryLaunchWorkflowController.
- SummaryLaunchWorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
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Constructor for SummaryLaunchWorkflowController.
- SummaryLine - Class in net.sourceforge.solexatools.util
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SummaryLine class.
- SummaryLine() - Constructor for class net.sourceforge.solexatools.util.SummaryLine
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Constructor for SummaryLine.
- supports(Class) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.LaneValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.LoginValidator
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Returns true if this Validator supports the specified Class, and false otherwise.
- supports(Class) - Method in class net.sourceforge.solexatools.validation.SampleValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.StudyValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator
- supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator
- supportsCancel(String) - Static method in class io.seqware.Engines
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Check whether the workflow engine supports cancel.
- supportsRetry(String) - Static method in class io.seqware.Engines
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Check whether the workflow engine supports retry.
- symDifference(Set<T>, Set<T>) - Static method in class net.sourceforge.seqware.pipeline.tools.SetOperations
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