| 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 |
|---|---|
Lane |
LaneService.findByID(Integer laneID)
findByID.
|
Lane |
LaneService.findByName(String name)
findByName.
|
Lane |
LaneService.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Lane |
LaneService.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneService.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Lane> |
LaneService.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Lane> |
LaneService.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<Lane> |
LaneService.list()
list.
|
List<Lane> |
LaneService.list(List<Integer> laneIds)
list.
|
SortedSet<Lane> |
LaneService.listWithHasFile(SortedSet<Lane> list,
String metaType)
listWithHasFile.
|
SortedSet<Lane> |
LaneService.setWithHasFile(SortedSet<Lane> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneService.delete(Lane lane,
boolean deleteRealFiles)
delete.
|
ProcessingLanes |
ProcessingLanesService.findByProcessingLane(Processing processing,
Lane lane)
findByProcessingLane.
|
SampleReportService.Status |
SampleReportService.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
void |
LaneService.insert(Lane lane)
insert.
|
Integer |
LaneService.insert(Registration registration,
Lane lane)
insert.
|
void |
LaneService.update(Lane lane)
update.
|
void |
LaneService.update(Registration registration,
Lane lane)
update.
|
Lane |
LaneService.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneService.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
void |
FileUploadService.uploadFile(Lane lane,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<Lane> |
LaneService.listWithHasFile(SortedSet<Lane> list,
String metaType)
listWithHasFile.
|
SortedSet<Lane> |
LaneService.setWithHasFile(SortedSet<Lane> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
Lane |
LaneServiceImpl.findByID(Integer laneID)
findByID.
|
Lane |
LaneServiceImpl.findByName(String name)
findByName.
|
Lane |
LaneServiceImpl.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Lane |
LaneServiceImpl.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneServiceImpl.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Lane> |
LaneServiceImpl.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Lane> |
LaneServiceImpl.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<Lane> |
LaneServiceImpl.list()
list.
|
List<Lane> |
LaneServiceImpl.list(List<Integer> laneIds)
list.
|
SortedSet<Lane> |
LaneServiceImpl.listWithHasFile(SortedSet<Lane> list,
String metaType)
listWithHasFile.
|
SortedSet<Lane> |
LaneServiceImpl.setWithHasFile(SortedSet<Lane> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneServiceImpl.delete(Lane lane,
boolean deleteRealFiles)
delete.
|
ProcessingLanes |
ProcessingLanesServiceImpl.findByProcessingLane(Processing processing,
Lane lane)
findByProcessingLane.
|
SampleReportService.Status |
SampleReportServiceImpl.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
void |
LaneServiceImpl.insert(Lane lane)
insert.
|
Integer |
LaneServiceImpl.insert(Registration registration,
Lane lane)
insert.
|
void |
LaneServiceImpl.update(Lane lane)
update.
|
void |
LaneServiceImpl.update(Registration registration,
Lane lane)
update.
|
Lane |
LaneServiceImpl.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneServiceImpl.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
void |
FileUploadServiceImpl.uploadFile(Lane lane,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<Lane> |
LaneServiceImpl.listWithHasFile(SortedSet<Lane> list,
String metaType)
listWithHasFile.
|
SortedSet<Lane> |
LaneServiceImpl.setWithHasFile(SortedSet<Lane> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
Lane |
LaneDAO.findByID(Integer laneId)
findByID.
|
Lane |
LaneDAO.findByName(String name)
findByName.
|
Lane |
LaneDAO.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Lane |
LaneDAO.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneDAO.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Lane> |
LaneDAO.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Lane> |
LaneDAO.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<Lane> |
LaneDAO.list()
list.
|
List<Lane> |
LaneDAO.list(List<Integer> laneIds)
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneDAO.delete(Lane lane)
delete.
|
ProcessingLanes |
ProcessingLanesDAO.findByProcessingLane(Processing processing,
Lane lane)
findByProcessingLane.
|
SampleReportService.Status |
SampleReportDAO.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
Integer |
LaneDAO.insert(Lane lane)
insert.
|
Integer |
LaneDAO.insert(Registration registration,
Lane lane)
insert.
|
void |
LaneDAO.update(Lane lane)
update.
|
void |
LaneDAO.update(Registration registration,
Lane lane)
update.
|
Lane |
LaneDAO.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneDAO.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneDAO.delete(SortedSet<Lane> lanes)
delete.
|
| Modifier and Type | Method and Description |
|---|---|
Lane |
LaneDAOHibernate.findByID(Integer expID)
findByID.
|
Lane |
LaneDAOHibernate.findByName(String name)
findByName.
|
Lane |
LaneDAOHibernate.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Lane |
LaneDAOHibernate.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneDAOHibernate.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Lane> |
LaneDAOHibernate.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Lane> |
LaneDAOHibernate.findByOwnerID(Integer registrationId)
findByOwnerID.
|
List<Lane> |
LaneDAOHibernate.list()
list.
|
List<Lane> |
LaneDAOHibernate.list(List<Integer> laneIds)
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneDAOHibernate.delete(Lane lane)
delete.
|
List<LaneAttribute> |
LaneLinkDAO.findAll(Lane lane)
findAll.
|
List<LaneAttribute> |
LaneLinkDAOHibernate.findAll(Lane lane)
findAll.
|
List<LaneAttribute> |
LaneAttributeDAO.findAll(Lane lane)
findAll.
|
List<LaneAttribute> |
LaneAttributeDAOHibernate.findAll(Lane lane)
findAll.
|
ProcessingLanes |
ProcessingLanesDAOHibernate.findByProcessingLane(Processing processing,
Lane lane)
findByProcessingLane.
|
SampleReportService.Status |
SampleReportDAOHibernate.getStatus(Study study,
Sample sample,
IUS ius,
Lane lane,
SequencerRun seqRun,
Workflow workflow)
getStatus.
|
Integer |
LaneDAOHibernate.insert(Lane lane)
insert.
|
Integer |
LaneDAOHibernate.insert(Registration registration,
Lane lane)
insert.
|
void |
LaneDAOHibernate.update(Lane lane)
update.
|
void |
LaneDAOHibernate.update(Registration registration,
Lane lane)
update.
|
Lane |
LaneDAOHibernate.updateDetached(Lane lane)
updateDetached.
|
Lane |
LaneDAOHibernate.updateDetached(Registration registration,
Lane lane)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneDAOHibernate.delete(SortedSet<Lane> lanes)
delete.
|
| Modifier and Type | Method and Description |
|---|---|
Lane |
MetadataWS.LowLevel.existsLane(String searchString) |
Lane |
MetadataWS.getLane(int laneAccession) |
Lane |
Metadata.getLane(int laneAccession)
getLane.
|
Lane |
MetadataNoConnection.getLane(int laneAccession) |
Lane |
MetadataDB.getLane(int laneAccession) |
Lane |
MetadataInMemory.getLane(int laneAccession) |
| Modifier and Type | Method and Description |
|---|---|
List<Lane> |
MetadataWS.getLanesFrom(int sequencerRunAccession) |
List<Lane> |
Metadata.getLanesFrom(int sequencerRunAccession)
Get Lanes from a sequencer run.
|
List<Lane> |
MetadataNoConnection.getLanesFrom(int sequencerRunAccession) |
List<Lane> |
MetadataDB.getLanesFrom(int sequencerRunAccession) |
List<Lane> |
MetadataInMemory.getLanesFrom(int sequencerRunAccession) |
| Modifier and Type | Method and Description |
|---|---|
Lane |
SampleReportRow.getLane()
Getter for the field
lane. |
Lane |
IUS.getLane()
Getter for the field
lane. |
Lane |
FileReportRow.getLane()
Getter for the field
lane. |
Lane |
ProcessingLanes.getLane()
Getter for the field
lane. |
Lane |
LaneAttribute.getLane()
Getter for the field
lane. |
Lane |
SequencerRunReportId.getLane()
Getter for the field
lane. |
Lane |
SequencerRunDTO.getLane1()
Getter for the field
lane1. |
Lane |
SequencerRunDTO.getLane2()
Getter for the field
lane2. |
Lane |
SequencerRunDTO.getLane3()
Getter for the field
lane3. |
Lane |
SequencerRunDTO.getLane4()
Getter for the field
lane4. |
Lane |
SequencerRunDTO.getLane5()
Getter for the field
lane5. |
Lane |
SequencerRunDTO.getLane6()
Getter for the field
lane6. |
Lane |
SequencerRunDTO.getLane7()
Getter for the field
lane7. |
Lane |
SequencerRunDTO.getLane8()
Getter for the field
lane8. |
| Modifier and Type | Method and Description |
|---|---|
SortedSet<Lane> |
Sample.getLanes()
Getter for the field
lanes. |
SortedSet<Lane> |
WorkflowRun.getLanes()
Getter for the field
lanes. |
SortedSet<Lane> |
SequencerRun.getLanes()
Getter for the field
lanes. |
SortedSet<Lane> |
SequencerRunDTO.getLanes()
Getter for the field
lanes. |
Set<Lane> |
Processing.getLanes()
Getter for the field
lanes. |
| Modifier and Type | Method and Description |
|---|---|
int |
Lane.compareTo(Lane that) |
void |
LaneAttribute.setAttributeParent(Lane parent) |
void |
SampleReportRow.setLane(Lane lane)
Setter for the field
lane. |
void |
IUS.setLane(Lane lane)
Setter for the field
lane. |
void |
FileReportRow.setLane(Lane lane)
Setter for the field
lane. |
void |
ProcessingLanes.setLane(Lane lane)
Setter for the field
lane. |
void |
LaneAttribute.setLane(Lane lane)
Setter for the field
lane. |
void |
SequencerRunReportId.setLane(Lane lane)
Setter for the field
lane. |
void |
SequencerRunDTO.setLane1(Lane lane1)
Setter for the field
lane1. |
void |
SequencerRunDTO.setLane2(Lane lane2)
Setter for the field
lane2. |
void |
SequencerRunDTO.setLane3(Lane lane3)
Setter for the field
lane3. |
void |
SequencerRunDTO.setLane4(Lane lane4)
Setter for the field
lane4. |
void |
SequencerRunDTO.setLane5(Lane lane5)
Setter for the field
lane5. |
void |
SequencerRunDTO.setLane6(Lane lane6)
Setter for the field
lane6. |
void |
SequencerRunDTO.setLane7(Lane lane7)
Setter for the field
lane7. |
void |
SequencerRunDTO.setLane8(Lane lane8)
Setter for the field
lane8. |
| Modifier and Type | Method and Description |
|---|---|
void |
Processing.setLanes(Set<Lane> lanes)
Setter for the field
lanes. |
void |
Sample.setLanes(SortedSet<Lane> lanes)
Setter for the field
lanes. |
void |
WorkflowRun.setLanes(SortedSet<Lane> lanes)
Setter for the field
lanes. |
void |
SequencerRun.setLanes(SortedSet<Lane> lanes)
Setter for the field
lanes. |
void |
SequencerRunDTO.setLanes(SortedSet<Lane> lanes)
Setter for the field
lanes. |
void |
Sample.setLanesForView(SortedSet<Lane> lanes)
setLanesForView.
|
| Constructor and Description |
|---|
LaneAttribute(int laneAttributeId,
Lane lane)
Constructor for LaneAttribute.
|
LaneAttribute(int laneAttributeId,
Lane lane,
String tag,
String value,
String units)
Constructor for LaneAttribute.
|
ProcessingLanes(int processingLanesId,
Processing processing,
Lane lane)
Constructor for ProcessingLanes.
|
ProcessingLanes(int processingLanesId,
Processing processing,
Lane lane,
String description,
String label,
String url,
Integer swAccession)
Constructor for ProcessingLanes.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<Lane> |
XmlizeLaneSortedSet.unmarshal(LaneList vt) |
| Modifier and Type | Method and Description |
|---|---|
LaneList |
XmlizeLaneSortedSet.marshal(SortedSet<Lane> bt) |
| Modifier and Type | Field and Description |
|---|---|
protected List<Lane> |
LaneList.tList |
| Modifier and Type | Method and Description |
|---|---|
List<Lane> |
LaneList.getList()
getList.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneList.add(Lane ex)
add.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LaneList.setList(List<Lane> list)
setList.
|
| Modifier and Type | Method and Description |
|---|---|
static Lane |
SequencerRunHtmlUtil.getParentLane(Processing processing,
Integer parentId)
getParentLane.
|
| Modifier and Type | Method and Description |
|---|---|
static String |
TreeNodeHtmlUtil.getAllHtml(Lane lane,
Registration registration,
Integer openingNodeId,
String treeType)
getAllHtml.
|
static String |
SequencerRunHtmlUtil.getAllHtml(Lane lane,
Registration registration,
String openingNodeId,
String treeType)
getAllHtml.
|
static String |
TreeNodeHtmlUtil.getLaneHtml(Lane lane,
Registration registration,
Integer openingNodeId)
getLaneHtml.
|
static String |
NodeHtmlUtil.getLaneHtml(Lane lane,
Registration registration,
String typeTree,
String openingNodeId,
String treeType)
getLaneHtml.
|
static SequencerRun |
FindRootUtil.getSequencerRun(Lane lane)
getSequencerRun.
|
static Study |
FindRootUtil.getStudy(Lane lane)
getStudy.
|
static Set<Processing> |
BulkUtil.selectProcessingNode(List<String> selectedIds,
Lane lane)
selectProcessingNode.
|
static void |
SetNodeIdInSession.setLaneForSequrncerRun(Lane lane,
javax.servlet.http.HttpServletRequest request)
setLaneForSequrncerRun.
|
static void |
SetNodeIdInSession.setLaneForStudy(Lane lane,
javax.servlet.http.HttpServletRequest request)
setLaneForStudy.
|
| Modifier and Type | Method and Description |
|---|---|
org.springframework.web.servlet.ModelAndView |
FileController.handleCancel(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to cancel the lane or the lane update page.
|
org.springframework.web.servlet.ModelAndView |
LaneController.handleCancel(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to cancel the lane or the lane update page.
|
org.springframework.web.servlet.ModelAndView |
LaneController.handleDelete(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to delete their lane.
|
org.springframework.web.servlet.ModelAndView |
FileController.handleReset(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to reset the lane page during a new or update lane.
|
org.springframework.web.servlet.ModelAndView |
LaneController.handleReset(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to reset the lane page during a new or update lane.
|
org.springframework.web.servlet.ModelAndView |
FileController.handleSubmit(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to submit a new lane.
|
org.springframework.web.servlet.ModelAndView |
LaneController.handleSubmit(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to submit a new lane.
|
org.springframework.web.servlet.ModelAndView |
FileController.handleUpdate(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to update their lane.
|
org.springframework.web.servlet.ModelAndView |
LaneController.handleUpdate(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Lane command)
Handles the user's request to update their lane.
|
| Modifier and Type | Method and Description |
|---|---|
Lane |
SampleDetailsLineItem.getLane()
Getter for the field
lane. |
| Constructor and Description |
|---|
SampleDetailsLineItem(SequencerRun sr,
Lane lane,
IUS ius)
Constructor for SampleDetailsLineItem.
|
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