| 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.adapters |
Looks like converters from collections to XML.
|
| 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.webapp.controller |
Portal stuff, to be assessed.
|
| net.sourceforge.solexatools.webapp.metamodel |
Portal stuff, to be assessed.
|
| Modifier and Type | Method and Description |
|---|---|
IUS |
IUSService.findByID(Integer id)
findByID.
|
IUS |
IUSService.findBySWAccession(Integer swAccession)
findBySWAccession.
|
IUS |
IUSService.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSService.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<IUS> |
IUSService.find(String sequencerRunName,
Integer lane,
String sampleName)
find.
|
List<IUS> |
IUSService.findBelongsToStudy(Study study)
findBelongsToStudy.
|
List<IUS> |
IUSService.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<IUS> |
IUSService.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<IUS> |
IUSService.list()
list.
|
SortedSet<IUS> |
IUSService.listWithHasFile(SortedSet<IUS> list,
String metaType)
listWithHasFile.
|
SortedSet<IUS> |
IUSService.setWithHasFile(SortedSet<IUS> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IUSService.delete(IUS ius,
boolean deleteRealFiles)
delete.
|
ProcessingIus |
ProcessingIUSService.findByProcessingIUS(Processing processing,
IUS ius)
findByProcessingIUS.
|
Set<WorkflowRun> |
WorkflowRunService.findRunsForIUS(IUS ius)
findRunsForIUS.
|
SampleReportService.Status |
SampleReportService.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
Integer |
IUSService.insert(IUS ius)
insert.
|
Integer |
IUSService.insert(Registration registration,
IUS ius)
insert.
|
void |
IUSService.update(IUS ius)
update.
|
void |
IUSService.update(Registration registration,
IUS ius)
update.
|
IUS |
IUSService.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSService.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
void |
FileUploadService.uploadFile(IUS ius,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<IUS> |
IUSService.listWithHasFile(SortedSet<IUS> list,
String metaType)
listWithHasFile.
|
SortedSet<IUS> |
IUSService.setWithHasFile(SortedSet<IUS> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
IUS |
IUSServiceImpl.findByID(Integer id)
findByID.
|
IUS |
IUSServiceImpl.findBySWAccession(Integer swAccession)
findBySWAccession.
|
IUS |
IUSServiceImpl.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSServiceImpl.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<IUS> |
IUSServiceImpl.find(String sequencerRunName,
Integer lane,
String sampleName)
find.
|
List<IUS> |
IUSServiceImpl.findBelongsToStudy(Study study)
findBelongsToStudy.
|
List<IUS> |
IUSServiceImpl.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<IUS> |
IUSServiceImpl.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<IUS> |
IUSServiceImpl.list()
list.
|
SortedSet<IUS> |
IUSServiceImpl.listWithHasFile(SortedSet<IUS> list,
String metaType)
listWithHasFile.
|
SortedSet<IUS> |
IUSServiceImpl.setWithHasFile(SortedSet<IUS> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IUSServiceImpl.delete(IUS ius,
boolean deleteRealFiles)
delete.
|
ProcessingIus |
ProcessingIUSServiceImpl.findByProcessingIUS(Processing processing,
IUS ius)
findByProcessingIUS.
|
Set<WorkflowRun> |
WorkflowRunServiceImpl.findRunsForIUS(IUS ius)
findRunsForIUS.
|
SampleReportService.Status |
SampleReportServiceImpl.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
Integer |
IUSServiceImpl.insert(IUS obj)
insert.
|
Integer |
IUSServiceImpl.insert(Registration registration,
IUS ius)
insert.
|
void |
IUSServiceImpl.update(IUS obj)
update.
|
void |
IUSServiceImpl.update(Registration registration,
IUS ius)
update.
|
IUS |
IUSServiceImpl.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSServiceImpl.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
void |
FileUploadServiceImpl.uploadFile(IUS ius,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<IUS> |
IUSServiceImpl.listWithHasFile(SortedSet<IUS> list,
String metaType)
listWithHasFile.
|
SortedSet<IUS> |
IUSServiceImpl.setWithHasFile(SortedSet<IUS> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
IUS |
IUSDAO.findByID(Integer id)
findByID.
|
IUS |
IUSDAO.findBySWAccession(Integer swAccession)
findBySWAccession.
|
IUS |
IUSDAO.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSDAO.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<IUS> |
IUSDAO.find(String sequencerRunName,
Integer lane,
String sampleName)
find.
|
List<IUS> |
IUSDAO.findBelongsToStudy(Study study)
findBelongsToStudy.
|
List<IUS> |
IUSDAO.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<IUS> |
IUSDAO.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<IUS> |
IUSDAO.list()
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IUSDAO.delete(IUS obj)
delete.
|
List<IUSAttribute> |
IUSAttributeDAO.findAll(IUS ius)
findAll.
|
ProcessingIus |
ProcessingIUSDAO.findByProcessingIUS(Processing processing,
IUS ius)
findByProcessingIUS.
|
Set<WorkflowRun> |
WorkflowRunDAO.findRunsForIUS(IUS ius)
findRunsForIUS.
|
SampleReportService.Status |
SampleReportDAO.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
Integer |
IUSDAO.insert(IUS obj)
insert.
|
Integer |
IUSDAO.insert(Registration registration,
IUS obj)
insert.
|
void |
IUSDAO.update(IUS obj)
update.
|
void |
IUSDAO.update(Registration registration,
IUS ius)
update.
|
IUS |
IUSDAO.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSDAO.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
IUS |
IUSDAOHibernate.findByID(Integer id)
findByID.
|
IUS |
IUSDAOHibernate.findBySWAccession(Integer swAccession)
findBySWAccession.
|
IUS |
IUSDAOHibernate.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSDAOHibernate.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<IUS> |
IUSDAOHibernate.find(String sequencerRunName,
Integer lane,
String sampleName)
find.
|
List<IUS> |
IUSDAOHibernate.findBelongsToStudy(Study study)
findBelongsToStudy.
|
List<IUS> |
IUSDAOHibernate.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<IUS> |
IUSDAOHibernate.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<IUS> |
IUSDAOHibernate.list()
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IUSDAOHibernate.delete(IUS obj)
delete.
|
List<IUSAttribute> |
IUSAttributeDAOHibernate.findAll(IUS ius)
findAll.
|
ProcessingIus |
ProcessingIUSDAOHibernate.findByProcessingIUS(Processing processing,
IUS ius)
findByProcessingIUS.
|
Set<WorkflowRun> |
WorkflowRunDAOHibernate.findRunsForIUS(IUS ius)
findRunsForIUS.
|
SampleReportService.Status |
SampleReportDAOHibernate.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
Integer |
IUSDAOHibernate.insert(IUS obj)
insert.
|
Integer |
IUSDAOHibernate.insert(Registration registration,
IUS obj)
insert.
|
void |
IUSDAOHibernate.update(IUS obj)
update.
|
void |
IUSDAOHibernate.update(Registration registration,
IUS ius)
update.
|
IUS |
IUSDAOHibernate.updateDetached(IUS ius)
updateDetached.
|
IUS |
IUSDAOHibernate.updateDetached(Registration registration,
IUS ius)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
IUS |
MetadataWS.LowLevel.existsIUS(String searchString) |
IUS |
MetadataWS.getIUS(int swAccession) |
IUS |
Metadata.getIUS(int swAccession)
Get ius by sw accession
|
IUS |
MetadataNoConnection.getIUS(int swAccession) |
IUS |
MetadataDB.getIUS(int swAccession) |
IUS |
MetadataInMemory.getIUS(int swAccession) |
| Modifier and Type | Method and Description |
|---|---|
List<IUS> |
MetadataWS.getIUSFrom(int laneOrSampleAccession) |
List<IUS> |
Metadata.getIUSFrom(int laneOrSampleAccession)
Get IUSes (barcodes) from a lane or sample.
|
List<IUS> |
MetadataNoConnection.getIUSFrom(int laneOrSampleAccession) |
List<IUS> |
MetadataDB.getIUSFrom(int laneOrSampleAccession) |
List<IUS> |
MetadataInMemory.getIUSFrom(int laneOrSampleAccession) |
| Modifier and Type | Method and Description |
|---|---|
IUS |
ProcessingIus.getIus()
Getter for the field
ius. |
IUS |
SampleReportRow.getIus()
Getter for the field
ius. |
IUS |
IUSAttribute.getIus()
Getter for the field
ius. |
IUS |
FileReportRow.getIus()
Getter for the field
ius. |
IUS |
SequencerRunReportId.getIus()
Getter for the field
ius. |
| Modifier and Type | Method and Description |
|---|---|
SortedSet<IUS> |
WorkflowRun.getIus()
Getter for the field
ius. |
SortedSet<IUS> |
Lane.getIus()
Getter for the field
ius. |
SortedSet<IUS> |
Sample.getIUS()
getIUS.
|
SortedSet<IUS> |
Lane.getIUS()
getIUS.
|
Set<IUS> |
Processing.getIUS()
getIUS.
|
| Modifier and Type | Method and Description |
|---|---|
int |
IUS.compareTo(IUS that) |
void |
IUSAttribute.setAttributeParent(IUS parent) |
void |
ProcessingIus.setIus(IUS ius)
Setter for the field
ius. |
void |
SampleReportRow.setIus(IUS ius)
Setter for the field
ius. |
void |
IUSAttribute.setIus(IUS ius)
Setter for the field
ius. |
void |
FileReportRow.setIus(IUS ius)
Setter for the field
ius. |
void |
SequencerRunReportId.setIus(IUS ius)
Setter for the field
ius. |
| Modifier and Type | Method and Description |
|---|---|
void |
Processing.setIUS(Set<IUS> ius)
setIUS.
|
void |
WorkflowRun.setIus(SortedSet<IUS> ius)
Setter for the field
ius. |
void |
Sample.setIUS(SortedSet<IUS> ius)
setIUS.
|
void |
Lane.setIUS(SortedSet<IUS> ius)
setIUS.
|
| Constructor and Description |
|---|
IUSAttribute(int iusAttributeId,
IUS ius)
Constructor for IUSAttribute.
|
IUSAttribute(int iusAttributeId,
IUS ius,
String tag,
String value,
String units)
Constructor for IUSAttribute.
|
ProcessingIus(int processingIusId,
IUS ius,
Processing processing)
Constructor for ProcessingIus.
|
ProcessingIus(int processingIusId,
IUS ius,
Processing processing,
String description,
String label,
String url,
Integer swAccession)
Constructor for ProcessingIus.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<IUS> |
XmlizeIUSSortedSet.unmarshal(IUSList vt) |
| Modifier and Type | Method and Description |
|---|---|
IUSList |
XmlizeIUSSortedSet.marshal(SortedSet<IUS> bt) |
| Modifier and Type | Field and Description |
|---|---|
protected List<IUS> |
IUSList.tList |
| Modifier and Type | Method and Description |
|---|---|
List<IUS> |
IUSList.getList()
getList.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IUSList.add(IUS ex)
add.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IUSList.setList(List<IUS> list)
setList.
|
| Modifier and Type | Method and Description |
|---|---|
static SortedSet<IUS> |
BulkUtil.selectIUSNode(List<String> selectedIds,
Sample sample)
selectIUSNode.
|
| Modifier and Type | Method and Description |
|---|---|
static String |
SequencerRunHtmlUtil.getAllHtml(IUS ius,
Registration registration,
String openingNodeId,
boolean isOpenProc,
boolean isVisibleProc,
String treeType)
getAllHtml.
|
static String |
StudyHtmlUtil.getAllHtml(IUS ius,
Registration registration,
String openingNodeId,
Integer currPosId,
List<String> listNodeId,
boolean isOpenProc,
boolean isVisibleProc,
String treeType)
getAllHtml.
|
static String |
NodeHtmlUtil.getIUSHtml(IUS ius,
Registration registration,
String typeTree,
String openingNodeId,
boolean isOpenProc,
boolean isVisibleProc,
String treeType)
getIUSHtml.
|
static Set<Processing> |
BulkUtil.selectProcessingNode(List<String> selectedIds,
IUS ius)
selectProcessingNode.
|
| Modifier and Type | Method and Description |
|---|---|
org.springframework.web.servlet.ModelAndView |
IUSController.handleCancel(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
IUS command)
Handles the user's request to cancel.
|
org.springframework.web.servlet.ModelAndView |
IUSController.handleDelete(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
IUS command)
Handles the user's request to delete their ius.
|
org.springframework.web.servlet.ModelAndView |
IUSController.handleUpdate(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
IUS command)
Handles the user's request to delete their ius.
|
| Modifier and Type | Method and Description |
|---|---|
IUS |
StudySampleReportFileLineItem.getIus()
Getter for the field
ius. |
IUS |
SampleDetailsLineItem.getIus()
Getter for the field
ius. |
| Modifier and Type | Method and Description |
|---|---|
void |
SampleDetailsWorkflowLineItems.addProcessings(IUS ius)
addProcessings.
|
void |
StudySampleReportFileLineItem.setIus(IUS ius)
Setter for the field
ius. |
| Constructor and Description |
|---|
SampleDetailsLineItem(SequencerRun sr,
Lane lane,
IUS ius)
Constructor for SampleDetailsLineItem.
|
StudySampleReportFileLineItem(Sample root,
Sample child,
IUS ius,
File file)
Constructor for StudySampleReportFileLineItem.
|
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