Uses of Class net.sourceforge.seqware.common.model.Workflow (SeqWare 1.1.2 API)

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Packages that use Workflow
Package	Description
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.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.lists	Looks like various container classes for XML serialization.
net.sourceforge.seqware.pipeline.workflowV2	Back-end for the Java workflow language and Oozie engine.
net.sourceforge.solexatools.util	Portal stuff, to be assessed.
net.sourceforge.solexatools.webapp.controller	Portal stuff, to be assessed.

Uses of Workflow in net.sourceforge.seqware.common.business

Methods in net.sourceforge.seqware.common.business that return Workflow
Modifier and Type	Method and Description
`Workflow`	WorkflowService.`findByID(Integer wfID)` findByID.
`Workflow`	WorkflowService.`findByIDWithParams(Integer wfID)` findByIDWithParams.
`Workflow`	WorkflowService.`findBySWAccession(Integer swAccession)` findBySWAccession.
`Workflow`	WorkflowService.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowService.`updateDetached(Workflow workflow)` updateDetached.

Methods in net.sourceforge.seqware.common.business that return types with arguments of type Workflow
Modifier and Type	Method and Description
`List<Workflow>`	WorkflowService.`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`List<Workflow>`	WorkflowService.`findByName(String name)` findByName.
`List<Workflow>`	SampleReportService.`getWorkflows(SequencerRun seqRun)` getWorkflows.
`List<Workflow>`	SampleReportService.`getWorkflowsForStudy(Study study)` getWorkflowsForStudy.
`List<Workflow>`	WorkflowService.`list()` list.
`List<Workflow>`	WorkflowService.`list(Registration registration)` list.
`List<Workflow>`	WorkflowService.`listMyShared(Registration registration)` listMyShared.
`List<Workflow>`	WorkflowRunService.`listRelatedWorkflows(Registration registration)` listRelatedWorkflows.
`List<Workflow>`	WorkflowService.`listSequencerRunsWorkflows(SequencerRun sr)` listSequencerRunsWorkflows.
`List<Workflow>`	WorkflowService.`listSharedWithMe(Registration registration)` listSharedWithMe.

Methods in net.sourceforge.seqware.common.business with parameters of type Workflow
Modifier and Type	Method and Description
`int`	SampleReportService.`countOfStatus(SequencerRun seqRun, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`int`	SampleReportService.`countOfStatus(Study study, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`void`	WorkflowService.`delete(Workflow workflow)` delete.
`SampleReportService.Status`	SampleReportService.`getStatus(Study study, Sample sample, IUS ius, Lane lane, SequencerRun seqRun, Workflow workflow)` getStatus.
`SampleReportService.Status`	SampleReportService.`getStatus(Study study, Sample childSample, Workflow workflow)` getStatus.
`List<SampleReportService.Status>`	SampleReportService.`getStatusesForWorkflow(SequencerRun seqRun, Workflow workflow)` getStatusesForWorkflow.
`List<SampleReportService.Status>`	SampleReportService.`getStatusesForWorkflow(Study study, Workflow workflow)` getStatusesForWorkflow.
`Integer`	WorkflowService.`insert(Registration registration, Workflow workflow)` insert.
`Integer`	WorkflowService.`insert(Workflow workflow)` Inserts a new Workflow and returns its sw_accession number.
`void`	WorkflowService.`update(Registration registration, Workflow workflow)` update.
`void`	WorkflowService.`update(Workflow workflow)` update.
`Workflow`	WorkflowService.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowService.`updateDetached(Workflow workflow)` updateDetached.

Uses of Workflow in net.sourceforge.seqware.common.business.impl

Methods in net.sourceforge.seqware.common.business.impl that return Workflow
Modifier and Type	Method and Description
`Workflow`	WorkflowServiceImpl.`findByID(Integer wfID)` findByID.
`Workflow`	WorkflowServiceImpl.`findByIDWithParams(Integer wfID)` findByIDWithParams.
`Workflow`	WorkflowServiceImpl.`findBySWAccession(Integer swAccession)` findBySWAccession.
`Workflow`	WorkflowServiceImpl.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowServiceImpl.`updateDetached(Workflow workflow)` updateDetached.

Methods in net.sourceforge.seqware.common.business.impl that return types with arguments of type Workflow
Modifier and Type	Method and Description
`List<Workflow>`	WorkflowServiceImpl.`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`List<Workflow>`	WorkflowServiceImpl.`findByName(String name)` findByName.
`List<Workflow>`	SampleReportServiceImpl.`getWorkflows(SequencerRun seqRun)` getWorkflows.
`List<Workflow>`	SampleReportServiceImpl.`getWorkflowsForStudy(Study study)` getWorkflowsForStudy.
`List<Workflow>`	WorkflowServiceImpl.`list()` list.
`List<Workflow>`	WorkflowServiceImpl.`list(Registration registration)` list.
`List<Workflow>`	WorkflowServiceImpl.`listMyShared(Registration registration)` listMyShared.
`List<Workflow>`	WorkflowRunServiceImpl.`listRelatedWorkflows(Registration registration)` listRelatedWorkflows.
`List<Workflow>`	WorkflowServiceImpl.`listSequencerRunsWorkflows(SequencerRun sr)` listSequencerRunsWorkflows.
`List<Workflow>`	WorkflowServiceImpl.`listSharedWithMe(Registration registration)` listSharedWithMe.

Methods in net.sourceforge.seqware.common.business.impl with parameters of type Workflow
Modifier and Type	Method and Description
`int`	SampleReportServiceImpl.`countOfStatus(SequencerRun seqRun, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`int`	SampleReportServiceImpl.`countOfStatus(Study study, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`void`	WorkflowServiceImpl.`delete(Workflow workflow)` delete.
`SampleReportService.Status`	SampleReportServiceImpl.`getStatus(Study study, Sample sample, IUS ius, Lane lane, SequencerRun seqRun, Workflow workflow)` getStatus.
`SampleReportService.Status`	SampleReportServiceImpl.`getStatus(Study study, Sample childSample, Workflow workflow)` getStatus.
`List<SampleReportService.Status>`	SampleReportServiceImpl.`getStatusesForWorkflow(SequencerRun seqRun, Workflow workflow)` getStatusesForWorkflow.
`List<SampleReportService.Status>`	SampleReportServiceImpl.`getStatusesForWorkflow(Study study, Workflow workflow)` getStatusesForWorkflow.
`Integer`	WorkflowServiceImpl.`insert(Registration registration, Workflow workflow)` insert.
`Integer`	WorkflowServiceImpl.`insert(Workflow workflow)` Inserts a new Workflow and returns its sw_accession number.
`void`	WorkflowServiceImpl.`update(Registration registration, Workflow workflow)` update.
`void`	WorkflowServiceImpl.`update(Workflow workflow)` update.
`Workflow`	WorkflowServiceImpl.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowServiceImpl.`updateDetached(Workflow workflow)` updateDetached.

Uses of Workflow in net.sourceforge.seqware.common.dao

Methods in net.sourceforge.seqware.common.dao that return Workflow
Modifier and Type	Method and Description
`Workflow`	WorkflowDAO.`findByID(Integer wfID)` findByID.
`Workflow`	WorkflowDAO.`findBySWAccession(Integer swAccession)` findBySWAccession.
`Workflow`	WorkflowDAO.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowDAO.`updateDetached(Workflow workflow)` updateDetached.

Methods in net.sourceforge.seqware.common.dao that return types with arguments of type Workflow
Modifier and Type	Method and Description
`List<Workflow>`	WorkflowDAO.`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`List<Workflow>`	WorkflowDAO.`findByName(String name)` findByName.
`List<Workflow>`	SampleReportDAO.`getWorkflows(SequencerRun seqRun)` getWorkflows.
`List<Workflow>`	SampleReportDAO.`getWorkflowsForStudy(Study study)` getWorkflowsForStudy.
`List<Workflow>`	WorkflowDAO.`list()` list.
`List<Workflow>`	WorkflowDAO.`list(Registration registration)` list.
`List<Workflow>`	WorkflowDAO.`listMyShared(Registration registration)` listMyShared.
`List<Workflow>`	WorkflowRunDAO.`listRelatedWorkflows(Registration registration)` listRelatedWorkflows.
`List<Workflow>`	WorkflowDAO.`listSharedWithMe(Registration registration)` listSharedWithMe.
`List<Workflow>`	WorkflowDAO.`listWorkflows(SequencerRun sr)` listWorkflows.

Methods in net.sourceforge.seqware.common.dao with parameters of type Workflow
Modifier and Type	Method and Description
`int`	SampleReportDAO.`countOfStatus(SequencerRun seqRun, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`int`	SampleReportDAO.`countOfStatus(Study study, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`void`	WorkflowDAO.`delete(Workflow workflow)` delete.
`List<WorkflowAttribute>`	WorkflowAttributeDAO.`get(Workflow workflow)` get.
`SampleReportService.Status`	SampleReportDAO.`getStatus(Study study, Sample sample, IUS ius, Lane lane, SequencerRun seqRun, Workflow workflow)` getStatus.
`SampleReportService.Status`	SampleReportDAO.`getStatus(Study study, Sample childSample, Workflow workflow)` getStatus.
`List<SampleReportService.Status>`	SampleReportDAO.`getStatusesForWorkflow(SequencerRun seqRun, Workflow workflow)` getStatusesForWorkflow.
`List<SampleReportService.Status>`	SampleReportDAO.`getStatusesForWorkflow(Study study, Workflow workflow)` getStatusesForWorkflow.
`Integer`	WorkflowDAO.`insert(Registration registration, Workflow workflow)` insert.
`Integer`	WorkflowDAO.`insert(Workflow workflow)` Inserts a new Workflow and returns its sw_accession number.
`void`	WorkflowDAO.`update(Registration registration, Workflow workflow)` update.
`void`	WorkflowDAO.`update(Workflow workflow)` update.
`Workflow`	WorkflowDAO.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowDAO.`updateDetached(Workflow workflow)` updateDetached.

Uses of Workflow in net.sourceforge.seqware.common.dao.hibernate

Methods in net.sourceforge.seqware.common.dao.hibernate that return Workflow
Modifier and Type	Method and Description
`Workflow`	WorkflowDAOHibernate.`findByID(Integer wfID)` findByID.
`Workflow`	WorkflowDAOHibernate.`findBySWAccession(Integer swAccession)` findBySWAccession.
`Workflow`	WorkflowDAOHibernate.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowDAOHibernate.`updateDetached(Workflow workflow)` updateDetached.

Methods in net.sourceforge.seqware.common.dao.hibernate that return types with arguments of type Workflow
Modifier and Type	Method and Description
`List<Workflow>`	WorkflowDAOHibernate.`findByCriteria(String criteria, boolean isCaseSens)` findByCriteria.
`List<Workflow>`	WorkflowDAOHibernate.`findByName(String name)` findByName.
`List<Workflow>`	SampleReportDAOHibernate.`getWorkflows(SequencerRun seqRun)` getWorkflows.
`List<Workflow>`	SampleReportDAOHibernate.`getWorkflowsForStudy(Study study)` getWorkflowsForStudy.
`List<Workflow>`	WorkflowDAOHibernate.`list()` list.
`List<Workflow>`	WorkflowDAOHibernate.`list(Registration registration)` list.
`List<Workflow>`	WorkflowDAOHibernate.`listMyShared(Registration registration)` listMyShared.
`List<Workflow>`	WorkflowRunDAOHibernate.`listRelatedWorkflows(Registration registration)` listRelatedWorkflows.
`List<Workflow>`	WorkflowDAOHibernate.`listSharedWithMe(Registration registration)` listSharedWithMe.
`List<Workflow>`	WorkflowDAOHibernate.`listWorkflows(SequencerRun sr)` listWorkflows.

Methods in net.sourceforge.seqware.common.dao.hibernate with parameters of type Workflow
Modifier and Type	Method and Description
`int`	SampleReportDAOHibernate.`countOfStatus(SequencerRun seqRun, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`int`	SampleReportDAOHibernate.`countOfStatus(Study study, Workflow workflow, SampleReportService.Status status)` countOfStatus.
`void`	WorkflowDAOHibernate.`delete(Workflow workflow)` delete.
`List<WorkflowAttribute>`	WorkflowAttributeDAOHibernate.`get(Workflow workflow)` get.
`SampleReportService.Status`	SampleReportDAOHibernate.`getStatus(Study study, Sample sample, IUS ius, Lane lane, SequencerRun seqRun, Workflow workflow)` getStatus.
`SampleReportService.Status`	SampleReportDAOHibernate.`getStatus(Study study, Sample childSample, Workflow workflow)` getStatus.
`List<SampleReportService.Status>`	SampleReportDAOHibernate.`getStatusesForWorkflow(SequencerRun seqRun, Workflow workflow)` getStatusesForWorkflow.
`List<SampleReportService.Status>`	SampleReportDAOHibernate.`getStatusesForWorkflow(Study study, Workflow workflow)` getStatusesForWorkflow.
`Integer`	WorkflowDAOHibernate.`insert(Registration registration, Workflow workflow)` insert.
`Integer`	WorkflowDAOHibernate.`insert(Workflow workflow)` Inserts a new Workflow and returns its sw_accession number.
`void`	WorkflowDAOHibernate.`update(Registration registration, Workflow workflow)` update.
`void`	WorkflowDAOHibernate.`update(Workflow workflow)` update.
`Workflow`	WorkflowDAOHibernate.`updateDetached(Registration registration, Workflow workflow)` updateDetached.
`Workflow`	WorkflowDAOHibernate.`updateDetached(Workflow workflow)` updateDetached.

Uses of Workflow in net.sourceforge.seqware.common.metadata

Methods in net.sourceforge.seqware.common.metadata that return Workflow
Modifier and Type	Method and Description
`static Workflow`	MetadataWS.`convertParamsToWorkflow(String baseCommand, String name, String description, String version1, String configFile, boolean storeProvisionDir, String provisionDir, String templateFile, boolean storeArchiveZip, String archiveZip, String workflow_class, String workflow_type, String workflow_engine, String seqware_version)`
`Workflow`	MetadataWS.LowLevel.`existsWorkflow(String searchString)`
`Workflow`	MetadataWS.`getWorkflow(int workflowAccession)` Get a workflow
`Workflow`	Metadata.`getWorkflow(int workflowAccession)` Get a workflow
`Workflow`	MetadataNoConnection.`getWorkflow(int workflowAccession)`
`Workflow`	MetadataDB.`getWorkflow(int workflowAccession)`
`Workflow`	MetadataInMemory.`getWorkflow(int workflowAccession)`

Methods in net.sourceforge.seqware.common.metadata with parameters of type Workflow
Modifier and Type	Method and Description
`protected ReturnValue`	MetadataWS.`addWorkflowParam(HashMap<String,Map<String,String>> hm, String key, Workflow workflow)`
`protected static WorkflowParam`	MetadataWS.`convertMapToWorkflowParam(Map<String,String> details, Workflow workflow)`
`static Map<String,String>`	MetadataWS.`convertWorkflowToMap(Workflow workflow)`

Uses of Workflow in net.sourceforge.seqware.common.model

Methods in net.sourceforge.seqware.common.model that return Workflow
Modifier and Type	Method and Description
`Workflow`	WorkflowParam.`getWorkflow()` Getter for the field `workflow`.
`Workflow`	WorkflowRun.`getWorkflow()` Getter for the field `workflow`.
`Workflow`	SampleReportRow.`getWorkflow()` Getter for the field `workflow`.
`Workflow`	WorkflowAttribute.`getWorkflow()` Getter for the field `workflow`.

Methods in net.sourceforge.seqware.common.model with parameters of type Workflow
Modifier and Type	Method and Description
`int`	WorkflowRun.`compareTo(Workflow that)` compareTo.
`int`	Workflow.`compareTo(Workflow that)`
`void`	WorkflowAttribute.`setAttributeParent(Workflow parent)`
`void`	WorkflowParam.`setWorkflow(Workflow workflow)` Setter for the field `workflow`.
`void`	WorkflowRun.`setWorkflow(Workflow workflow)` Setter for the field `workflow`.
`void`	SampleReportRow.`setWorkflow(Workflow workflow)` Setter for the field `workflow`.
`void`	WorkflowAttribute.`setWorkflow(Workflow workflow)` Setter for the field `workflow`.

Uses of Workflow in net.sourceforge.seqware.common.model.lists

Fields in net.sourceforge.seqware.common.model.lists with type parameters of type Workflow
Modifier and Type	Field and Description
`protected List<Workflow>`	WorkflowList.`tList`

Methods in net.sourceforge.seqware.common.model.lists that return types with arguments of type Workflow
Modifier and Type	Method and Description
`List<Workflow>`	WorkflowList.`getList()` getList.

Methods in net.sourceforge.seqware.common.model.lists with parameters of type Workflow
Modifier and Type	Method and Description
`void`	WorkflowList.`add(Workflow ex)` add.

Method parameters in net.sourceforge.seqware.common.model.lists with type arguments of type Workflow
Modifier and Type	Method and Description
`void`	WorkflowList.`setList(List<Workflow> list)` setList.

Uses of Workflow in net.sourceforge.seqware.pipeline.workflowV2

Methods in net.sourceforge.seqware.pipeline.workflowV2 with parameters of type Workflow
Modifier and Type	Method and Description
`static boolean`	WorkflowV2Utility.`requiresNewLauncher(Workflow workflow)`

Uses of Workflow in net.sourceforge.solexatools.util

Methods in net.sourceforge.solexatools.util that return Workflow
Modifier and Type	Method and Description
`static Workflow`	LaunchWorkflowUtil.`getCurrentWorkflow(javax.servlet.http.HttpServletRequest request)` getCurrentWorkflow.

Uses of Workflow in net.sourceforge.solexatools.webapp.controller

Methods in net.sourceforge.solexatools.webapp.controller with parameters of type Workflow
Modifier and Type	Method and Description
`org.springframework.web.servlet.ModelAndView`	WorkflowParamController.`handleCancel(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to cancel the study or the study update page.
`org.springframework.web.servlet.ModelAndView`	SummaryLaunchWorkflowController.`handleCancel(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to cancel the study or the study update page.
`org.springframework.web.servlet.ModelAndView`	WorkflowController.`handleCancel(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to cancel the study or the study update page.
`org.springframework.web.servlet.ModelAndView`	WorkflowParamValueController.`handleCancel(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to cancel the study or the study update page.
`org.springframework.web.servlet.ModelAndView`	WorkflowController.`handleDelete(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to delete their study.
`org.springframework.web.servlet.ModelAndView`	SummaryLaunchWorkflowController.`handleNext(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to submit a new study.
`org.springframework.web.servlet.ModelAndView`	SelectInputController.`handleNext(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to submit a new study.
`org.springframework.web.servlet.ModelAndView`	SummaryLaunchWorkflowController.`handlePrevious(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to cancel the study or the study update page.
`org.springframework.web.servlet.ModelAndView`	SelectInputController.`handlePrevious(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to cancel the study or the study update page.
`org.springframework.web.servlet.ModelAndView`	WorkflowParamController.`handleReset(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to reset the study page during a new or update study.
`org.springframework.web.servlet.ModelAndView`	WorkflowController.`handleReset(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to reset the study page during a new or update study.
`org.springframework.web.servlet.ModelAndView`	WorkflowParamValueController.`handleReset(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to reset the study page during a new or update study.
`org.springframework.web.servlet.ModelAndView`	WorkflowController.`handleSubmit(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to submit a new study.
`org.springframework.web.servlet.ModelAndView`	WorkflowController.`handleUpdate(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response, Workflow command)` Handles the user's request to update their study.

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