| Package | Description |
|---|---|
| io.seqware |
Provides new utility classes.
|
| io.seqware.pipeline.engines.whitestar |
This is a simple reference implementation of a seqware engine used for development and debugging.
|
| net.sourceforge.seqware.common.business |
Looks like auto-generated classes for Hibernate.
|
| net.sourceforge.seqware.common.business.impl |
Looks like auto-generated implementation for Hibernate classes.
|
| net.sourceforge.seqware.common.dao |
More hibernate auto-generated.
|
| net.sourceforge.seqware.common.dao.hibernate |
More hibernate auto-generated.
|
| net.sourceforge.seqware.common.hibernate |
Looks like utility classes for navigating the metadb.
|
| net.sourceforge.seqware.common.hibernate.reports |
A row of the workflow run report.
|
| net.sourceforge.seqware.common.metadata |
Critical classes that effectively convert API calls into actions against the DB and web service.
|
| net.sourceforge.seqware.common.model |
Hibernate model classes for the metadb.
|
| net.sourceforge.seqware.common.model.adapters |
Looks like converters from collections to XML.
|
| net.sourceforge.seqware.common.model.comparator |
Comparator, used in Hibernate.
|
| net.sourceforge.seqware.common.model.lists |
Looks like various container classes for XML serialization.
|
| net.sourceforge.seqware.common.module |
Utility classes really.
|
| net.sourceforge.seqware.common.security |
Interface that unifies model objects that have the concept of permissions.
|
| net.sourceforge.seqware.common.util.maptools |
Tools for converting ini files to maps.
|
| net.sourceforge.seqware.pipeline.plugins |
Create and manipulate databases for extended testing.
|
| net.sourceforge.seqware.pipeline.plugins.fileprovenance |
Dump out the file provenance report to the user.
|
| net.sourceforge.seqware.pipeline.workflowV2 |
Back-end for the Java workflow language and Oozie engine.
|
| net.sourceforge.seqware.webservice.resources |
Base classes for web resources.
|
| net.sourceforge.seqware.webservice.resources.queries |
Report various things about the metadb.
|
| net.sourceforge.seqware.webservice.resources.tables |
More basic web resources.
|
| net.sourceforge.solexatools |
Portal stuff, to be assessed.
|
| net.sourceforge.solexatools.util |
Portal stuff, to be assessed.
|
| net.sourceforge.solexatools.validation |
Portal stuff, to be assessed.
|
| net.sourceforge.solexatools.webapp.controller |
Portal stuff, to be assessed.
|
| net.sourceforge.solexatools.webapp.metamodel |
Portal stuff, to be assessed.
|
| Class and Description |
|---|
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| Experiment |
| ExperimentLibraryDesign
ExperimentLibraryDesign class.
|
| ExperimentSpotDesign
ExperimentSpotDesign class.
|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| File
File class.
|
| FileAttribute |
| FileReportRow
FileReportRow class.
|
| FileType
FileType class.
|
| Invoice
Invoice class.
|
| InvoiceState |
| IUS |
| Lane |
| LibrarySelection
LibrarySelection class.
|
| LibrarySource
LibrarySource class.
|
| LibraryStrategy
LibraryStrategy class.
|
| Organism
Organism class.
|
| Platform
Platform class.
|
| Processing |
| ProcessingExperiments
ProcessingExperiments generated by hbm2java
|
| ProcessingIus
ProcessingIus generated by hbm2java
|
| ProcessingLanes
ProcessingLanes generated by hbm2java
|
| ProcessingRelationship
ProcessingRelationship generated by hbm2java
|
| ProcessingSamples
ProcessingSamples generated by hbm2java
|
| ProcessingSequencerRuns
ProcessingSequencerRuns generated by hbm2java
|
| ProcessingStudies
ProcessingStudies generated by hbm2java
|
| Registration
Registration
|
| RegistrationDTO |
| Sample |
| SampleReportRow
SampleReportRow class.
|
| SequencerRun |
| SequencerRunReportId
SequencerRunReportId class.
|
| SequencerRunWizardDTO
SequencerRunWizardDTO class.
|
| ShareStudy
ShareStudy class.
|
| ShareWorkflowRun
ShareWorkflowRun class.
|
| Study |
| StudyType
StudyType class.
|
| UploadSequence |
| Workflow
Workflow class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowParamValue
WorkflowParamValue class.
|
| WorkflowRun
WorkflowRun class.
|
| WorkflowRunParam
WorkflowRunParam class.
|
| Class and Description |
|---|
| Experiment |
| ExperimentLibraryDesign
ExperimentLibraryDesign class.
|
| ExperimentSpotDesign
ExperimentSpotDesign class.
|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| File
File class.
|
| FileAttribute |
| FileReportRow
FileReportRow class.
|
| FileType
FileType class.
|
| Invoice
Invoice class.
|
| InvoiceState |
| IUS |
| Lane |
| LibrarySelection
LibrarySelection class.
|
| LibrarySource
LibrarySource class.
|
| LibraryStrategy
LibraryStrategy class.
|
| Organism
Organism class.
|
| Platform
Platform class.
|
| Processing |
| ProcessingExperiments
ProcessingExperiments generated by hbm2java
|
| ProcessingIus
ProcessingIus generated by hbm2java
|
| ProcessingLanes
ProcessingLanes generated by hbm2java
|
| ProcessingRelationship
ProcessingRelationship generated by hbm2java
|
| ProcessingSamples
ProcessingSamples generated by hbm2java
|
| ProcessingSequencerRuns
ProcessingSequencerRuns generated by hbm2java
|
| ProcessingStudies
ProcessingStudies generated by hbm2java
|
| Registration
Registration
|
| RegistrationDTO |
| Sample |
| SampleReportRow
SampleReportRow class.
|
| SequencerRun |
| SequencerRunReportId
SequencerRunReportId class.
|
| SequencerRunWizardDTO
SequencerRunWizardDTO class.
|
| ShareStudy
ShareStudy class.
|
| ShareWorkflowRun
ShareWorkflowRun class.
|
| Study |
| StudyType
StudyType class.
|
| UploadSequence |
| Workflow
Workflow class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowParamValue
WorkflowParamValue class.
|
| WorkflowRun
WorkflowRun class.
|
| WorkflowRunParam
WorkflowRunParam class.
|
| Class and Description |
|---|
| Experiment |
| ExperimentAttribute
ExperimentAttribute generated by hbm2java
|
| ExperimentLibraryDesign
ExperimentLibraryDesign class.
|
| ExperimentSpotDesign
ExperimentSpotDesign class.
|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| File
File class.
|
| FileAttribute |
| FileReportRow
FileReportRow class.
|
| FileType
FileType class.
|
| Invoice
Invoice class.
|
| InvoiceState |
| IUS |
| IUSAttribute
IusAttribute generated by hbm2java
|
| Lane |
| LibrarySelection
LibrarySelection class.
|
| LibrarySource
LibrarySource class.
|
| LibraryStrategy
LibraryStrategy class.
|
| Organism
Organism class.
|
| Platform
Platform class.
|
| Processing |
| ProcessingAttribute
ProcessingAttribute generated by hbm2java
|
| ProcessingExperiments
ProcessingExperiments generated by hbm2java
|
| ProcessingIus
ProcessingIus generated by hbm2java
|
| ProcessingLanes
ProcessingLanes generated by hbm2java
|
| ProcessingRelationship
ProcessingRelationship generated by hbm2java
|
| ProcessingSamples
ProcessingSamples generated by hbm2java
|
| ProcessingSequencerRuns
ProcessingSequencerRuns generated by hbm2java
|
| ProcessingStudies
ProcessingStudies generated by hbm2java
|
| Registration
Registration
|
| Sample |
| SampleAttribute
SampleAttribute generated by hbm2java
|
| SampleReportRow
SampleReportRow class.
|
| SequencerRun |
| SequencerRunReportId
SequencerRunReportId class.
|
| SequencerRunWizardDTO
SequencerRunWizardDTO class.
|
| ShareStudy
ShareStudy class.
|
| ShareWorkflowRun
ShareWorkflowRun class.
|
| Study |
| StudyAttribute
StudyAttribute generated by hbm2java
|
| StudyType
StudyType class.
|
| Workflow
Workflow class.
|
| WorkflowAttribute
WorkflowAttribute class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowParamValue
WorkflowParamValue class.
|
| WorkflowRun
WorkflowRun class.
|
| WorkflowRunAttribute
WorkflowRunAttribute class.
|
| WorkflowRunParam
WorkflowRunParam class.
|
| Class and Description |
|---|
| Experiment |
| ExperimentAttribute
ExperimentAttribute generated by hbm2java
|
| ExperimentLibraryDesign
ExperimentLibraryDesign class.
|
| ExperimentSpotDesign
ExperimentSpotDesign class.
|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| File
File class.
|
| FileAttribute |
| FileReportRow
FileReportRow class.
|
| FileType
FileType class.
|
| Invoice
Invoice class.
|
| InvoiceState |
| IUS |
| IUSAttribute
IusAttribute generated by hbm2java
|
| Lane |
| LaneAttribute
LaneAttribute generated by hbm2java
|
| LibrarySelection
LibrarySelection class.
|
| LibrarySource
LibrarySource class.
|
| LibraryStrategy
LibraryStrategy class.
|
| Organism
Organism class.
|
| Platform
Platform class.
|
| Processing |
| ProcessingAttribute
ProcessingAttribute generated by hbm2java
|
| ProcessingExperiments
ProcessingExperiments generated by hbm2java
|
| ProcessingIus
ProcessingIus generated by hbm2java
|
| ProcessingLanes
ProcessingLanes generated by hbm2java
|
| ProcessingRelationship
ProcessingRelationship generated by hbm2java
|
| ProcessingSamples
ProcessingSamples generated by hbm2java
|
| ProcessingSequencerRuns
ProcessingSequencerRuns generated by hbm2java
|
| ProcessingStudies
ProcessingStudies generated by hbm2java
|
| Registration
Registration
|
| Sample |
| SampleAttribute
SampleAttribute generated by hbm2java
|
| SampleReportRow
SampleReportRow class.
|
| SequencerRun |
| SequencerRunReportId
SequencerRunReportId class.
|
| SequencerRunWizardDTO
SequencerRunWizardDTO class.
|
| ShareStudy
ShareStudy class.
|
| ShareWorkflowRun
ShareWorkflowRun class.
|
| Study |
| StudyAttribute
StudyAttribute generated by hbm2java
|
| StudyType
StudyType class.
|
| Workflow
Workflow class.
|
| WorkflowAttribute
WorkflowAttribute class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowParamValue
WorkflowParamValue class.
|
| WorkflowRun
WorkflowRun class.
|
| WorkflowRunAttribute
WorkflowRunAttribute class.
|
| WorkflowRunParam
WorkflowRunParam class.
|
| Class and Description |
|---|
| File
File class.
|
| Processing |
| Sample |
| Study |
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| File
File class.
|
| Processing |
| Sample |
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| Experiment |
| ExperimentAttribute
ExperimentAttribute generated by hbm2java
|
| ExperimentLibraryDesign
ExperimentLibraryDesign class.
|
| ExperimentSpotDesign
ExperimentSpotDesign class.
|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| File
File class.
|
| FileAttribute |
| FileProvenanceParam |
| FirstTierModel
This links together all models that have a FirstTierModel.
|
| IUS |
| IUSAttribute
IusAttribute generated by hbm2java
|
| Lane |
| LaneAttribute
LaneAttribute generated by hbm2java
|
| LibrarySelection
LibrarySelection class.
|
| LibrarySource
LibrarySource class.
|
| LibraryStrategy
LibraryStrategy class.
|
| Organism
Organism class.
|
| ParentAccessionModel
This links together all models that can be used to resolve a parent accession
|
| Platform
Platform class.
|
| Processing |
| ProcessingAttribute
ProcessingAttribute generated by hbm2java
|
| Sample |
| SampleAttribute
SampleAttribute generated by hbm2java
|
| SequencerRun |
| SequencerRunAttribute
SequencerRunAttribute generated by Morgan Taschuk
|
| Study |
| StudyAttribute
StudyAttribute generated by hbm2java
|
| StudyType
StudyType class.
|
| Workflow
Workflow class.
|
| WorkflowAttribute
WorkflowAttribute class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowRun
WorkflowRun class.
|
| WorkflowRunAttribute
WorkflowRunAttribute class.
|
| Class and Description |
|---|
| Annotatable
This links together all models that can be annotated
|
| Attribute
Attribute interface.
|
| Expense
Expense class.
|
| Experiment |
| ExperimentAttribute
ExperimentAttribute generated by hbm2java
|
| ExperimentLibraryDesign
ExperimentLibraryDesign class.
|
| ExperimentSpotDesign
ExperimentSpotDesign class.
|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| File
File class.
|
| FileAttribute |
| FileProvenanceParam |
| FileType
FileType class.
|
| FirstTierModel
This links together all models that have a FirstTierModel.
|
| Invoice
Invoice class.
|
| InvoiceState |
| IUS |
| IUSAttribute
IusAttribute generated by hbm2java
|
| Lane |
| LaneAttribute
LaneAttribute generated by hbm2java
|
| LibrarySelection
LibrarySelection class.
|
| LibrarySource
LibrarySource class.
|
| LibraryStrategy
LibraryStrategy class.
|
| Organism
Organism class.
|
| ParentAccessionModel
This links together all models that can be used to resolve a parent accession
|
| Platform
Platform class.
|
| Processing |
| ProcessingAttribute
ProcessingAttribute generated by hbm2java
|
| Registration
Registration
|
| Sample |
| SampleAttribute
SampleAttribute generated by hbm2java
|
| SecondTierModel
This links together all models that do not have sw_accession
|
| SequencerRun |
| SequencerRunAttribute
SequencerRunAttribute generated by Morgan Taschuk
|
| SequencerRunWizardDTO
SequencerRunWizardDTO class.
|
| ShareStudy
ShareStudy class.
|
| ShareWorkflowRun
ShareWorkflowRun class.
|
| Study |
| StudyAttribute
StudyAttribute generated by hbm2java
|
| StudyType
StudyType class.
|
| Workflow
Workflow class.
|
| WorkflowAttribute
WorkflowAttribute class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowParamValue
WorkflowParamValue class.
|
| WorkflowRun
WorkflowRun class.
|
| WorkflowRunAttribute
WorkflowRunAttribute class.
|
| WorkflowRunParam
WorkflowRunParam class.
|
| Class and Description |
|---|
| File
File class.
|
| IUS |
| Lane |
| Class and Description |
|---|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| Class and Description |
|---|
| Experiment |
| ExperimentLibraryDesign
ExperimentLibraryDesign class.
|
| ExperimentSpotDesign
ExperimentSpotDesign class.
|
| ExperimentSpotDesignReadSpec
ExperimentSpotDesignReadSpec class.
|
| File
File class.
|
| IUS |
| Lane |
| LibrarySelection
LibrarySelection class.
|
| LibrarySource
LibrarySource class.
|
| LibraryStrategy
LibraryStrategy class.
|
| Organism
Organism class.
|
| Platform
Platform class.
|
| Processing |
| Sample |
| SequencerRun |
| Study |
| StudyType
StudyType class.
|
| Workflow
Workflow class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowParamValue
WorkflowParamValue class.
|
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| FileAttribute |
| Class and Description |
|---|
| Registration
Registration
|
| Class and Description |
|---|
| WorkflowRunParam
WorkflowRunParam class.
|
| Class and Description |
|---|
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| FileProvenanceParam |
| Class and Description |
|---|
| Workflow
Workflow class.
|
| Class and Description |
|---|
| Registration
Registration
|
| Class and Description |
|---|
| File
File class.
|
| Processing |
| Class and Description |
|---|
| Attribute
Attribute interface.
|
| File
File class.
|
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| Registration
Registration
|
| Class and Description |
|---|
| Experiment |
| File
File class.
|
| IUS |
| Lane |
| Processing |
| Registration
Registration
|
| Sample |
| SequencerRun |
| Study |
| Workflow
Workflow class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowRun
WorkflowRun class.
|
| WorkflowRunParam
WorkflowRunParam class.
|
| Class and Description |
|---|
| Experiment |
| Sample |
| SequencerRun |
| SequencerRunWizardDTO
SequencerRunWizardDTO class.
|
| Study |
| Class and Description |
|---|
| Experiment |
| File
File class.
|
| IUS |
| Lane |
| Processing |
| Registration
Registration
|
| RegistrationDTO |
| Sample |
| SequencerRun |
| SequencerRunWizardDTO
SequencerRunWizardDTO class.
|
| Study |
| UploadSequence |
| Workflow
Workflow class.
|
| WorkflowParam
WorkflowParam class.
|
| WorkflowParamValue
WorkflowParamValue class.
|
| WorkflowRun
WorkflowRun class.
|
| Class and Description |
|---|
| File
File class.
|
| IUS |
| Lane |
| Processing |
| Sample |
| SequencerRun |
| WorkflowRun
WorkflowRun class.
|
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