| 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.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. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
SequencerRun | 
SequencerRunService.findByID(Integer expID)
 findByID. 
 | 
SequencerRun | 
SequencerRunService.findByName(String name)
 findByName. 
 | 
SequencerRun | 
SequencerRunService.findBySWAccession(Integer swAccession)
 findBySWAccession. 
 | 
SequencerRun | 
SequencerRunService.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunService.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
SequencerRunService.findByCriteria(String criteria,
              boolean isCaseSens)
 findByCriteria. 
 | 
List<SequencerRun> | 
SequencerRunService.findByOwnerID(Integer registrationId)
 findByOwnerID. 
 | 
List<SequencerRun> | 
SequencerRunService.list()
 list. 
 | 
List<SequencerRun> | 
SequencerRunService.list(Registration registration)
 list. 
 | 
List<SequencerRun> | 
SequencerRunService.list(Registration registration,
    Boolean isAsc)
 list. 
 | 
List<SequencerRun> | 
SequencerRunService.setProcCountInfo(List<SequencerRun> list)
 setProcCountInfo. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
int | 
SampleReportService.countOfRows(SequencerRun seqRun)
 countOfRows. 
 | 
int | 
FileReportService.countOfRows(SequencerRun sr)
 countOfRows. 
 | 
int | 
SampleReportService.countOfStatus(SequencerRun seqRun,
             SampleReportService.Status status)
 countOfStatus. 
 | 
int | 
SampleReportService.countOfStatus(SequencerRun seqRun,
             Workflow workflow,
             SampleReportService.Status status)
 countOfStatus. 
 | 
void | 
SequencerRunService.delete(SequencerRun sequencerRun)
 delete. 
 | 
ProcessingSequencerRuns | 
ProcessingSequencerRunsService.findByProcessingSequencerRun(Processing processing,
                            SequencerRun sequencerRun)
 findByProcessingSequencerRun. 
 | 
List<FileReportRow> | 
FileReportService.getReportForSequencerRun(SequencerRun seqRun)
 getReportForSequencerRun. 
 | 
List<FileReportRow> | 
FileReportService.getReportForSequencerRun(SequencerRun seqRun,
                        String sortField,
                        String orderTypeSeqRun)
 getReportForSequencerRun. 
 | 
List<FileReportRow> | 
FileReportService.getReportForSequencerRun(SequencerRun seqRun,
                        String sortField,
                        String sortOrder,
                        int i,
                        int rowsPages)
 getReportForSequencerRun. 
 | 
List<SampleReportRow> | 
SampleReportService.getRowsForSequencerRun(SequencerRun sr)
 getRowsForSequencerRun. 
 | 
List<SequencerRunReportId> | 
SampleReportService.getSequencerRunReportIds(SequencerRun seqRun)
 getSequencerRunReportIds. 
 | 
List<SequencerRunReportId> | 
SampleReportService.getSequencerRunReportIds(SequencerRun seqRun,
                        String sortField,
                        String orderType)
 getSequencerRunReportIds. 
 | 
List<SequencerRunReportId> | 
SampleReportService.getSequencerRunReportIds(SequencerRun seqRun,
                        String sortField,
                        String sortOrder,
                        int offset,
                        int limit)
 getSequencerRunReportIds. 
 | 
SampleReportService.Status | 
SampleReportService.getStatus(Study study,
         Sample sample,
         IUS ius,
         Lane lane,
         SequencerRun seqRun,
         Workflow workflow)
 getStatus. 
 | 
List<SampleReportService.Status> | 
SampleReportService.getStatusesForSequencerRun(SequencerRun seqRun)
 getStatusesForSequencerRun. 
 | 
List<SampleReportService.Status> | 
SampleReportService.getStatusesForWorkflow(SequencerRun seqRun,
                      Workflow workflow)
 getStatusesForWorkflow. 
 | 
List<Workflow> | 
SampleReportService.getWorkflows(SequencerRun seqRun)
 getWorkflows. 
 | 
Integer | 
SequencerRunService.insert(Registration registration,
      SequencerRun sequencerRun)
 insert. 
 | 
void | 
ProcessingService.insert(Registration registration,
      SequencerRun sequencerRun,
      Processing processing)
 insert. 
 | 
Integer | 
SequencerRunService.insert(SequencerRun sequencerRun)
 insert. 
 | 
void | 
ProcessingService.insert(SequencerRun sequencerRun,
      Processing processing)
 insert. 
 | 
List<Workflow> | 
WorkflowService.listSequencerRunsWorkflows(SequencerRun sr)
 listSequencerRunsWorkflows. 
 | 
void | 
SequencerRunService.update(Registration registration,
      SequencerRun sequencerRun)
 update. 
 | 
void | 
SequencerRunService.update(SequencerRun sequencerRun)
 update. 
 | 
SequencerRun | 
SequencerRunService.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunService.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
void | 
FileUploadService.uploadFile(SequencerRun sequencerRun,
          UploadFile uploadFile,
          FileType fileType,
          Registration registration)
 uploadFile. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
SequencerRunService.setProcCountInfo(List<SequencerRun> list)
 setProcCountInfo. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
SequencerRun | 
SequencerRunServiceImpl.findByID(Integer expID)
 findByID. 
 | 
SequencerRun | 
SequencerRunServiceImpl.findByName(String name)
 findByName. 
 | 
SequencerRun | 
SequencerRunServiceImpl.findBySWAccession(Integer swAccession)
 findBySWAccession. 
 | 
SequencerRun | 
SequencerRunServiceImpl.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunServiceImpl.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
SequencerRunServiceImpl.findByCriteria(String criteria,
              boolean isCaseSens)
 findByCriteria. 
 | 
List<SequencerRun> | 
SequencerRunServiceImpl.findByOwnerID(Integer registrationId)
 findByOwnerID. 
 | 
List<SequencerRun> | 
SequencerRunServiceImpl.list()
 list. 
 | 
List<SequencerRun> | 
SequencerRunServiceImpl.list(Registration registration)
 list. 
 | 
List<SequencerRun> | 
SequencerRunServiceImpl.list(Registration registration,
    Boolean isAsc)
 list. 
 | 
List<SequencerRun> | 
SequencerRunServiceImpl.setProcCountInfo(List<SequencerRun> list)
 setProcCountInfo. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
int | 
FileReportServiceImpl.countOfRows(SequencerRun sr)
 countOfRows. 
 | 
int | 
SampleReportServiceImpl.countOfRows(SequencerRun seqRun)
 countOfRows. 
 | 
int | 
SampleReportServiceImpl.countOfStatus(SequencerRun seqRun,
             SampleReportService.Status status)
 countOfStatus. 
 | 
int | 
SampleReportServiceImpl.countOfStatus(SequencerRun seqRun,
             Workflow workflow,
             SampleReportService.Status status)
 countOfStatus. 
 | 
void | 
SequencerRunServiceImpl.delete(SequencerRun sequencerRun)
 delete. 
 | 
ProcessingSequencerRuns | 
ProcessingSequencerRunsServiceImpl.findByProcessingSequencerRun(Processing processing,
                            SequencerRun sequencerRun)
 findByProcessingSequencerRun. 
 | 
List<FileReportRow> | 
FileReportServiceImpl.getReportForSequencerRun(SequencerRun seqRun)
 getReportForSequencerRun. 
 | 
List<FileReportRow> | 
FileReportServiceImpl.getReportForSequencerRun(SequencerRun seqRun,
                        String sortField,
                        String orderTypeSeqRun)
 getReportForSequencerRun. 
 | 
List<FileReportRow> | 
FileReportServiceImpl.getReportForSequencerRun(SequencerRun seqRun,
                        String sortField,
                        String sortOrder,
                        int offset,
                        int limit)
 getReportForSequencerRun. 
 | 
List<SampleReportRow> | 
SampleReportServiceImpl.getRowsForSequencerRun(SequencerRun sr)
 getRowsForSequencerRun. 
 | 
List<SequencerRunReportId> | 
SampleReportServiceImpl.getSequencerRunReportIds(SequencerRun seqRun)
 getSequencerRunReportIds. 
 | 
List<SequencerRunReportId> | 
SampleReportServiceImpl.getSequencerRunReportIds(SequencerRun seqRun,
                        String sortField,
                        String orderType)
 getSequencerRunReportIds. 
 | 
List<SequencerRunReportId> | 
SampleReportServiceImpl.getSequencerRunReportIds(SequencerRun seqRun,
                        String sortField,
                        String sortOrder,
                        int offset,
                        int limit)
 getSequencerRunReportIds. 
 | 
SampleReportService.Status | 
SampleReportServiceImpl.getStatus(Study study,
         Sample sample,
         IUS ius,
         Lane lane,
         SequencerRun seqRun,
         Workflow workflow)
 getStatus. 
 | 
List<SampleReportService.Status> | 
SampleReportServiceImpl.getStatusesForSequencerRun(SequencerRun seqRun)
 getStatusesForSequencerRun. 
 | 
List<SampleReportService.Status> | 
SampleReportServiceImpl.getStatusesForWorkflow(SequencerRun seqRun,
                      Workflow workflow)
 getStatusesForWorkflow. 
 | 
List<Workflow> | 
SampleReportServiceImpl.getWorkflows(SequencerRun seqRun)
 getWorkflows. 
 | 
Integer | 
SequencerRunServiceImpl.insert(Registration registration,
      SequencerRun sequencerRun)
 insert. 
 | 
void | 
ProcessingServiceImpl.insert(Registration registration,
      SequencerRun sequencerRun,
      Processing processing)
 insert. 
 | 
Integer | 
SequencerRunServiceImpl.insert(SequencerRun sequencerRun)
 insert. 
 | 
void | 
ProcessingServiceImpl.insert(SequencerRun sequencerRun,
      Processing processing)
 insert. 
 | 
List<Workflow> | 
WorkflowServiceImpl.listSequencerRunsWorkflows(SequencerRun sr)
 listSequencerRunsWorkflows. 
 | 
void | 
SequencerRunServiceImpl.update(Registration registration,
      SequencerRun sequencerRun)
 update. 
 | 
void | 
SequencerRunServiceImpl.update(SequencerRun sequencerRun)
 update. 
 | 
SequencerRun | 
SequencerRunServiceImpl.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunServiceImpl.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
void | 
FileUploadServiceImpl.uploadFile(SequencerRun sequencerRun,
          UploadFile uploadFile,
          FileType fileType,
          Registration registration)
 uploadFile. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
SequencerRunServiceImpl.setProcCountInfo(List<SequencerRun> list)
 setProcCountInfo. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
SequencerRun | 
SequencerRunDAO.findByID(Integer expID)
 findByID. 
 | 
SequencerRun | 
SequencerRunDAO.findByName(String name)
 findByName. 
 | 
SequencerRun | 
SequencerRunDAO.findBySWAccession(Integer swAccession)
 findBySWAccession. 
 | 
SequencerRun | 
SequencerRunDAO.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunDAO.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
SequencerRunDAO.findByCriteria(String criteria,
              boolean isCaseSens)
 findByCriteria. 
 | 
List<SequencerRun> | 
SequencerRunDAO.findByOwnerID(Integer registrationId)
 findByOwnerID. 
 | 
List<SequencerRun> | 
SequencerRunDAO.list()
 list. 
 | 
List<SequencerRun> | 
SequencerRunDAO.list(Registration registration,
    Boolean isAsc)
 list. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
int | 
FileReportDAO.countOfRows(SequencerRun sr)
 countOfRows. 
 | 
int | 
SampleReportDAO.countOfRows(SequencerRun seqRun)
 countOfRows. 
 | 
int | 
SampleReportDAO.countOfStatus(SequencerRun seqRun,
             SampleReportService.Status status)
 countOfStatus. 
 | 
int | 
SampleReportDAO.countOfStatus(SequencerRun seqRun,
             Workflow workflow,
             SampleReportService.Status status)
 countOfStatus. 
 | 
void | 
SequencerRunDAO.delete(SequencerRun sequencerRun)
 delete. 
 | 
ProcessingSequencerRuns | 
ProcessingSequencerRunsDAO.findByProcessingSequencerRun(Processing processing,
                            SequencerRun sequencerRun)
 findByProcessingSequencerRun. 
 | 
List<FileReportRow> | 
FileReportDAO.getReportForSequencerRun(SequencerRun seqRun)
 getReportForSequencerRun. 
 | 
List<FileReportRow> | 
FileReportDAO.getReportForSequencerRun(SequencerRun seqRun,
                        String orderField,
                        String sortOrder,
                        int offset,
                        int limit)
 getReportForSequencerRun. 
 | 
List<SampleReportRow> | 
SampleReportDAO.getRowsForSequencerRun(SequencerRun sr)
 getRowsForSequencerRun. 
 | 
List<SequencerRunReportId> | 
SampleReportDAO.getSequencerRunReportIds(SequencerRun seqRun)
 getSequencerRunReportIds. 
 | 
List<SequencerRunReportId> | 
SampleReportDAO.getSequencerRunReportIds(SequencerRun seqRun,
                        String sortField,
                        String sortOrder,
                        int offset,
                        int limit)
 getSequencerRunReportIds. 
 | 
SampleReportService.Status | 
SampleReportDAO.getStatus(Study study,
         Sample sample,
         IUS ius,
         Lane lane,
         SequencerRun seqRun,
         Workflow workflow)
 getStatus. 
 | 
List<SampleReportService.Status> | 
SampleReportDAO.getStatusesForSequencerRun(SequencerRun seqRun)
 getStatusesForSequencerRun. 
 | 
List<SampleReportService.Status> | 
SampleReportDAO.getStatusesForWorkflow(SequencerRun seqRun,
                      Workflow workflow)
 getStatusesForWorkflow. 
 | 
List<Workflow> | 
SampleReportDAO.getWorkflows(SequencerRun seqRun)
 getWorkflows. 
 | 
Integer | 
SequencerRunDAO.insert(Registration registration,
      SequencerRun sequencerRun)
 insert. 
 | 
Integer | 
SequencerRunDAO.insert(SequencerRun sequencerRun)
 insert. 
 | 
List<Workflow> | 
WorkflowDAO.listWorkflows(SequencerRun sr)
 listWorkflows. 
 | 
void | 
SequencerRunDAO.update(Registration registration,
      SequencerRun sequencerRun)
 update. 
 | 
void | 
SequencerRunDAO.update(SequencerRun sequencerRun)
 update. 
 | 
SequencerRun | 
SequencerRunDAO.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunDAO.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
SequencerRun | 
SequencerRunDAOHibernate.findByID(Integer expID)
 findByID. 
 | 
SequencerRun | 
SequencerRunDAOHibernate.findByName(String name)
 findByName. 
 | 
SequencerRun | 
SequencerRunDAOHibernate.findBySWAccession(Integer swAccession)
 findBySWAccession. 
 | 
SequencerRun | 
SequencerRunDAOHibernate.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunDAOHibernate.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
SequencerRunDAOHibernate.findByCriteria(String criteria,
              boolean isCaseSens)
 findByCriteria. 
 | 
List<SequencerRun> | 
SequencerRunDAOHibernate.findByOwnerID(Integer registrationId)
 findByOwnerID. 
 | 
List<SequencerRun> | 
SequencerRunDAOHibernate.list()
 list. 
 | 
List<SequencerRun> | 
SequencerRunDAOHibernate.list(Registration registration,
    Boolean isAsc)
 list. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
int | 
SampleReportDAOHibernate.countOfRows(SequencerRun seqRun)
 countOfRows. 
 | 
int | 
FileReportDAOHibernate.countOfRows(SequencerRun sr)
 countOfRows. 
 | 
int | 
SampleReportDAOHibernate.countOfStatus(SequencerRun seqRun,
             SampleReportService.Status status)
 countOfStatus. 
 | 
int | 
SampleReportDAOHibernate.countOfStatus(SequencerRun seqRun,
             Workflow workflow,
             SampleReportService.Status status)
 countOfStatus. 
 | 
void | 
SequencerRunDAOHibernate.delete(SequencerRun sequencerRun)
 delete. 
 | 
ProcessingSequencerRuns | 
ProcessingSequencerRunsDAOHibernate.findByProcessingSequencerRun(Processing processing,
                            SequencerRun sequencerRun)
 findByProcessingSequencerRun. 
 | 
List<FileReportRow> | 
FileReportDAOHibernate.getReportForSequencerRun(SequencerRun seqRun)
 getReportForSequencerRun. 
 | 
List<FileReportRow> | 
FileReportDAOHibernate.getReportForSequencerRun(SequencerRun seqRun,
                        String orderField,
                        String sortOrder,
                        int offset,
                        int limit)
 getReportForSequencerRun. 
 | 
List<SampleReportRow> | 
SampleReportDAOHibernate.getRowsForSequencerRun(SequencerRun sr)
 getRowsForSequencerRun. 
 | 
List<SequencerRunReportId> | 
SampleReportDAOHibernate.getSequencerRunReportIds(SequencerRun seqRun)
 getSequencerRunReportIds. 
 | 
List<SequencerRunReportId> | 
SampleReportDAOHibernate.getSequencerRunReportIds(SequencerRun seqRun,
                        String sortField,
                        String sortOrder,
                        int offset,
                        int limit)
 getSequencerRunReportIds. 
 | 
SampleReportService.Status | 
SampleReportDAOHibernate.getStatus(Study study,
         Sample sample,
         IUS ius,
         Lane lane,
         SequencerRun seqRun,
         Workflow workflow)
 getStatus. 
 | 
List<SampleReportService.Status> | 
SampleReportDAOHibernate.getStatusesForSequencerRun(SequencerRun seqRun)
 getStatusesForSequencerRun. 
 | 
List<SampleReportService.Status> | 
SampleReportDAOHibernate.getStatusesForWorkflow(SequencerRun seqRun,
                      Workflow workflow)
 getStatusesForWorkflow. 
 | 
List<Workflow> | 
SampleReportDAOHibernate.getWorkflows(SequencerRun seqRun)
 getWorkflows. 
 | 
Integer | 
SequencerRunDAOHibernate.insert(Registration registration,
      SequencerRun sequencerRun)
 insert. 
 | 
Integer | 
SequencerRunDAOHibernate.insert(SequencerRun sequencerRun)
 insert. 
 | 
List<Workflow> | 
WorkflowDAOHibernate.listWorkflows(SequencerRun sr)
 listWorkflows. 
 | 
void | 
SequencerRunDAOHibernate.update(Registration registration,
      SequencerRun sequencerRun)
 update. 
 | 
void | 
SequencerRunDAOHibernate.update(SequencerRun sequencerRun)
 update. 
 | 
SequencerRun | 
SequencerRunDAOHibernate.updateDetached(Registration registration,
              SequencerRun sequencerRun)
 updateDetached. 
 | 
SequencerRun | 
SequencerRunDAOHibernate.updateDetached(SequencerRun sequencerRun)
 updateDetached. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
SequencerRun | 
MetadataWS.LowLevel.existsSequencerRun(String searchString)  | 
SequencerRun | 
MetadataWS.getSequencerRun(int sequencerRunAccession)  | 
SequencerRun | 
Metadata.getSequencerRun(int sequencerRunAccession)
 getSequencerRun. 
 | 
SequencerRun | 
MetadataNoConnection.getSequencerRun(int sequencerRunAccession)  | 
SequencerRun | 
MetadataDB.getSequencerRun(int sequencerRunAccession)  | 
SequencerRun | 
MetadataInMemory.getSequencerRun(int sequencerRunAccession)  | 
SequencerRun | 
MetadataWS.getSequencerRunByName(String name)  | 
SequencerRun | 
Metadata.getSequencerRunByName(String name)  | 
SequencerRun | 
MetadataNoConnection.getSequencerRunByName(String name)  | 
SequencerRun | 
MetadataDB.getSequencerRunByName(String name)  | 
SequencerRun | 
MetadataInMemory.getSequencerRunByName(String name)  | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
MetadataWS.getAllSequencerRuns()
 getAllSequencerRuns. 
 | 
List<SequencerRun> | 
Metadata.getAllSequencerRuns()
Get all of the sequencer runs in the DB. 
 | 
List<SequencerRun> | 
MetadataNoConnection.getAllSequencerRuns()  | 
List<SequencerRun> | 
MetadataDB.getAllSequencerRuns()  | 
List<SequencerRun> | 
MetadataInMemory.getAllSequencerRuns()  | 
| Modifier and Type | Class and Description | 
|---|---|
class  | 
SequencerRunWizardDTO
 SequencerRunWizardDTO class. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
SequencerRun | 
ProcessingSequencerRuns.getSequencerRun()
 Getter for the field  
sequencerRun. | 
SequencerRun | 
SampleReportRow.getSequencerRun()
 Getter for the field  
sequencerRun. | 
SequencerRun | 
Lane.getSequencerRun()
 Getter for the field  
sequencerRun. | 
SequencerRun | 
SequencerRunReportId.getSequencerRun()
 Getter for the field  
sequencerRun. | 
| Modifier and Type | Method and Description | 
|---|---|
Set<SequencerRun> | 
Processing.getSequencerRuns()
 Getter for the field  
sequencerRuns. | 
| Modifier and Type | Method and Description | 
|---|---|
int | 
SequencerRun.compareTo(SequencerRun that) | 
void | 
ProcessingSequencerRuns.setSequencerRun(SequencerRun sequencerRun)
 Setter for the field  
sequencerRun. | 
void | 
SampleReportRow.setSequencerRun(SequencerRun sequencerRun)
 Setter for the field  
sequencerRun. | 
void | 
Lane.setSequencerRun(SequencerRun sequencerRun)
 Setter for the field  
sequencerRun. | 
void | 
SequencerRunReportId.setSequencerRun(SequencerRun sequencerRun)
 Setter for the field  
sequencerRun. | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
Processing.setSequencerRuns(Set<SequencerRun> sequencerRuns)
 Setter for the field  
sequencerRuns. | 
| Constructor and Description | 
|---|
ProcessingSequencerRuns(int processingSequencerRunsId,
                       Processing processing,
                       SequencerRun sequencerRun)
 Constructor for ProcessingSequencerRuns. 
 | 
ProcessingSequencerRuns(int processingSequencerRunsId,
                       Processing processing,
                       SequencerRun sequencerRun,
                       String description,
                       String label,
                       String url,
                       Integer swAccession)
 Constructor for ProcessingSequencerRuns. 
 | 
| Modifier and Type | Field and Description | 
|---|---|
protected List<SequencerRun> | 
SequencerRunList.tList  | 
| Modifier and Type | Method and Description | 
|---|---|
List<SequencerRun> | 
SequencerRunList.getList()
 getList. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
SequencerRunList.add(SequencerRun ex)
 add. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
SequencerRunList.setList(List<SequencerRun> list)
 setList. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
static SequencerRun | 
FindRootUtil.getSequencerRun(Lane lane)
 getSequencerRun. 
 | 
static SequencerRun | 
FindRootUtil.getSequencerRun(Processing processing)
 getSequencerRun. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
static String | 
NodeHtmlUtil.getSequencerRunHtml(SequencerRun sequencerRun,
                   Registration registration,
                   String openingNodeId,
                   String treeType)
 getSequencerRunHtml. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
void | 
SequencerRunValidator.validateRefLane(SequencerRun sequencerRun,
               org.springframework.validation.Errors errors)
 validateRefLane. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
org.springframework.web.servlet.ModelAndView | 
SequencerRunControllerDTO.handleCancel(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to cancel the experiment or the experiment update page. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunController.handleCancel(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to cancel the experiment or the experiment update page. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunWizardController.handleDelete(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to delete their study. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunControllerDTO.handleReset(javax.servlet.http.HttpServletRequest request,
           javax.servlet.http.HttpServletResponse response,
           SequencerRun command)
Handles the user's request to reset the experiment page during a new or update experiment. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunController.handleReset(javax.servlet.http.HttpServletRequest request,
           javax.servlet.http.HttpServletResponse response,
           SequencerRun command)
Handles the user's request to reset the experiment page during a new or update experiment. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunControllerDTO.handleSubmit(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to submit a new experiment. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunController.handleSubmit(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to submit a new experiment. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunWizardController.handleUpdate(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to update their registration. 
 | 
org.springframework.web.servlet.ModelAndView | 
WorkflowRunController.handleUpdate(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to update their registration. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunControllerDTO.handleUpdate(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to update their experiment. 
 | 
org.springframework.web.servlet.ModelAndView | 
SequencerRunController.handleUpdate(javax.servlet.http.HttpServletRequest request,
            javax.servlet.http.HttpServletResponse response,
            SequencerRun command)
Handles the user's request to update their experiment. 
 | 
| Modifier and Type | Method and Description | 
|---|---|
SequencerRun | 
SampleDetailsLineItem.getSequencerRun()
 Getter for the field  
sequencerRun. | 
| Constructor and Description | 
|---|
SampleDetailsLineItem(SequencerRun sr,
                     Lane lane,
                     IUS ius)
 Constructor for SampleDetailsLineItem. 
 | 
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