| 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.
|
| Modifier and Type | Method and Description |
|---|---|
Experiment |
ExperimentService.findByID(Integer expID)
findByID.
|
Experiment |
ExperimentService.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Experiment |
ExperimentService.findByTitle(String name)
findByTitle.
|
Experiment |
ExperimentService.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentService.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Experiment> |
ExperimentService.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Experiment> |
ExperimentService.findByOwnerID(Integer registrationID)
findByOwnerID.
|
List<Experiment> |
ExperimentService.list()
list.
|
List<Experiment> |
ExperimentService.list(Registration registration)
list.
|
List<Experiment> |
ExperimentService.list(Study study)
list.
|
SortedSet<Experiment> |
ExperimentService.listWithHasFile(SortedSet<Experiment> list,
String metaType)
listWithHasFile.
|
SortedSet<Experiment> |
ExperimentService.setWithHasFile(SortedSet<Experiment> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExperimentService.delete(Experiment experiment,
boolean deleteRealFiles)
delete.
|
ProcessingExperiments |
ProcessingExperimentsService.findByProcessingExperiment(Processing processing,
Experiment experiment)
findByProcessingExperiment.
|
Integer |
ExperimentService.insert(Experiment experiment)
insert.
|
Integer |
ExperimentService.insert(Registration registration,
Experiment experiment)
insert.
|
void |
ExperimentService.merge(Experiment experiment)
merge.
|
void |
ExperimentService.update(Experiment experiment)
update.
|
void |
ExperimentService.update(Registration registration,
Experiment experiment)
update.
|
Experiment |
ExperimentService.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentService.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
void |
FileUploadService.uploadFile(Experiment experiment,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<Experiment> |
ExperimentService.listWithHasFile(SortedSet<Experiment> list,
String metaType)
listWithHasFile.
|
SortedSet<Experiment> |
ExperimentService.setWithHasFile(SortedSet<Experiment> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
Experiment |
ExperimentServiceImpl.findByID(Integer expID)
findByID.
|
Experiment |
ExperimentServiceImpl.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Experiment |
ExperimentServiceImpl.findByTitle(String title)
findByTitle.
|
Experiment |
ExperimentServiceImpl.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentServiceImpl.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Experiment> |
ExperimentServiceImpl.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Experiment> |
ExperimentServiceImpl.findByOwnerID(Integer registrationID)
findByOwnerID.
|
List<Experiment> |
ExperimentServiceImpl.list()
list.
|
List<Experiment> |
ExperimentServiceImpl.list(Registration registration)
list.
|
List<Experiment> |
ExperimentServiceImpl.list(Study study)
list.
|
SortedSet<Experiment> |
ExperimentServiceImpl.listWithHasFile(SortedSet<Experiment> list,
String metaType)
listWithHasFile.
|
SortedSet<Experiment> |
ExperimentServiceImpl.setWithHasFile(SortedSet<Experiment> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExperimentServiceImpl.delete(Experiment experiment,
boolean deleteRealFiles)
delete.
|
ProcessingExperiments |
ProcessingExperimentsServiceImpl.findByProcessingExperiment(Processing processing,
Experiment experiment)
findByProcessingExperiment.
|
Integer |
ExperimentServiceImpl.insert(Experiment experiment)
insert.
|
Integer |
ExperimentServiceImpl.insert(Registration registration,
Experiment experiment)
insert.
|
void |
ExperimentServiceImpl.merge(Experiment experiment)
merge.
|
void |
ExperimentServiceImpl.update(Experiment experiment)
update.
|
void |
ExperimentServiceImpl.update(Registration registration,
Experiment experiment)
update.
|
Experiment |
ExperimentServiceImpl.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentServiceImpl.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
void |
FileUploadServiceImpl.uploadFile(Experiment experiment,
UploadFile uploadFile,
FileType fileType,
Registration registration)
uploadFile.
|
| Modifier and Type | Method and Description |
|---|---|
SortedSet<Experiment> |
ExperimentServiceImpl.listWithHasFile(SortedSet<Experiment> list,
String metaType)
listWithHasFile.
|
SortedSet<Experiment> |
ExperimentServiceImpl.setWithHasFile(SortedSet<Experiment> list)
setWithHasFile.
|
| Modifier and Type | Method and Description |
|---|---|
Experiment |
ExperimentDAO.findByID(Integer studyID)
findByID.
|
Experiment |
ExperimentDAO.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Experiment |
ExperimentDAO.findByTitle(String title)
findByTitle.
|
Experiment |
ExperimentDAO.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentDAO.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Experiment> |
ExperimentDAO.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Experiment> |
ExperimentDAO.findByOwnerID(Integer registrationID)
findByOwnerID.
|
List<Experiment> |
ExperimentDAO.list()
list.
|
List<Experiment> |
ExperimentDAO.list(Registration registration)
list.
|
List<Experiment> |
ExperimentDAO.list(Study study)
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExperimentDAO.delete(Experiment sequencerRun)
delete.
|
List<ExperimentAttribute> |
ExperimentAttributeDAO.findAll(Experiment experiment)
findAll.
|
ProcessingExperiments |
ProcessingExperimentsDAO.findByProcessingExperiment(Processing processing,
Experiment experiment)
findByProcessingExperiment.
|
Integer |
ExperimentDAO.insert(Experiment sequencerRun)
insert.
|
Integer |
ExperimentDAO.insert(Registration registration,
Experiment sequencerRun)
insert.
|
void |
ExperimentDAO.merge(Experiment experiment)
merge.
|
void |
ExperimentDAO.update(Experiment sequencerRun)
update.
|
void |
ExperimentDAO.update(Registration registration,
Experiment experiment)
update.
|
Experiment |
ExperimentDAO.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentDAO.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
Experiment |
ExperimentDAOHibernate.findByID(Integer expID)
findByID.
|
Experiment |
ExperimentDAOHibernate.findBySWAccession(Integer swAccession)
findBySWAccession.
|
Experiment |
ExperimentDAOHibernate.findByTitle(String title)
findByTitle.
|
Experiment |
ExperimentDAOHibernate.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentDAOHibernate.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
List<Experiment> |
ExperimentDAOHibernate.findByCriteria(String criteria,
boolean isCaseSens)
findByCriteria.
|
List<Experiment> |
ExperimentDAOHibernate.findByOwnerID(Integer registrationID)
findByOwnerID.
|
List<Experiment> |
ExperimentDAOHibernate.list()
list.
|
List<Experiment> |
ExperimentDAOHibernate.list(Registration registration)
list.
|
List<Experiment> |
ExperimentDAOHibernate.list(Study study)
list.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExperimentDAOHibernate.delete(Experiment experiment)
delete.
|
List<ExperimentAttribute> |
ExperimentAttributeDAOHibernate.findAll(Experiment experiment)
findAll.
|
ProcessingExperiments |
ProcessingExperimentsDAOHibernate.findByProcessingExperiment(Processing processing,
Experiment experiment)
findByProcessingExperiment.
|
Integer |
ExperimentDAOHibernate.insert(Experiment experiment)
insert.
|
Integer |
ExperimentDAOHibernate.insert(Registration registration,
Experiment experiment)
insert.
|
void |
ExperimentDAOHibernate.merge(Experiment experiment)
merge.
|
void |
ExperimentDAOHibernate.update(Experiment experiment)
update.
|
void |
ExperimentDAOHibernate.update(Registration registration,
Experiment experiment)
update.
|
Experiment |
ExperimentDAOHibernate.updateDetached(Experiment experiment)
updateDetached.
|
Experiment |
ExperimentDAOHibernate.updateDetached(Registration registration,
Experiment experiment)
updateDetached.
|
| Modifier and Type | Method and Description |
|---|---|
Experiment |
MetadataWS.LowLevel.existsExperiment(String searchString) |
Experiment |
MetadataWS.getExperiment(int swAccession) |
Experiment |
Metadata.getExperiment(int swAccession)
getExperiment.
|
Experiment |
MetadataNoConnection.getExperiment(int swAccession) |
Experiment |
MetadataDB.getExperiment(int swAccession) |
Experiment |
MetadataInMemory.getExperiment(int swAccession) |
| Modifier and Type | Method and Description |
|---|---|
List<Experiment> |
MetadataWS.getExperimentsFrom(int studyAccession) |
List<Experiment> |
Metadata.getExperimentsFrom(int studyAccession)
Get experiments from a study.
|
List<Experiment> |
MetadataNoConnection.getExperimentsFrom(int studyAccession) |
List<Experiment> |
MetadataDB.getExperimentsFrom(int studyAccession) |
List<Experiment> |
MetadataInMemory.getExperimentsFrom(int studyAccession) |
| Modifier and Type | Method and Description |
|---|---|
Experiment |
ExperimentAttribute.getExperiment()
Getter for the field
experiment. |
Experiment |
Sample.getExperiment()
Getter for the field
experiment. |
Experiment |
ProcessingExperiments.getExperiment()
Getter for the field
experiment. |
Experiment |
FileReportRow.getExperiment()
Getter for the field
experiment. |
| Modifier and Type | Method and Description |
|---|---|
SortedSet<Experiment> |
Study.getExperiments()
Getter for the field
experiments. |
Set<Experiment> |
Processing.getExperiments()
Getter for the field
experiments. |
| Modifier and Type | Method and Description |
|---|---|
int |
Experiment.compareTo(Experiment that) |
void |
ExperimentAttribute.setAttributeParent(Experiment parent) |
void |
ExperimentAttribute.setExperiment(Experiment experiment)
Setter for the field
experiment. |
void |
Sample.setExperiment(Experiment experiment)
Setter for the field
experiment. |
void |
ProcessingExperiments.setExperiment(Experiment experiment)
Setter for the field
experiment. |
void |
FileReportRow.setExperiment(Experiment experiment)
Setter for the field
experiment. |
| Modifier and Type | Method and Description |
|---|---|
void |
Processing.setExperiments(Set<Experiment> experiments)
Setter for the field
experiments. |
void |
Study.setExperiments(SortedSet<Experiment> experiments)
Setter for the field
experiments. |
| Constructor and Description |
|---|
ExperimentAttribute(int experimentAttributeId,
Experiment experiment)
Constructor for ExperimentAttribute.
|
ExperimentAttribute(int experimentAttributeId,
Experiment experiment,
String tag,
String value,
String units)
Constructor for ExperimentAttribute.
|
ProcessingExperiments(int processingExperimentsId,
Processing processing,
Experiment experiment)
Constructor for ProcessingExperiments.
|
ProcessingExperiments(int processingExperimentsId,
Processing processing,
Experiment experiment,
String description,
String label,
String url,
Integer swAccession)
Constructor for ProcessingExperiments.
|
| Modifier and Type | Field and Description |
|---|---|
protected List<Experiment> |
ExperimentList.tList |
| Modifier and Type | Method and Description |
|---|---|
List<Experiment> |
ExperimentList.getList()
getList.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExperimentList.add(Experiment ex)
add.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExperimentList.setList(List<Experiment> list)
setList.
|
| Modifier and Type | Method and Description |
|---|---|
static SortedSet<Experiment> |
BulkUtil.selectExperimentNode(List<String> selectedIds,
Study study)
selectExperimentNode.
|
| Modifier and Type | Method and Description |
|---|---|
static String |
TreeNodeHtmlUtil.getAllHtml(Experiment experiment,
Registration registration,
Integer openingNodeId,
String treeType)
getAllHtml.
|
static String |
NodeHtmlUtil.getExperimentHtml(Experiment experiment,
Registration registration,
String typeTree,
String openingNodeId,
boolean isOpenProc,
String treeType)
getExperimentHtml.
|
static Study |
FindRootUtil.getStudy(Experiment experiment)
getStudy.
|
static SortedSet<Sample> |
BulkUtil.selectSampleNode(List<String> selectedIds,
Experiment experiment)
selectSampleNode.
|
static void |
SetNodeIdInSession.setExperiment(Experiment experiment,
javax.servlet.http.HttpServletRequest request)
setExperiment.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ExperimentValidator.validateExpectedNumberReads(Experiment experiment,
org.springframework.validation.Errors errors)
validateExpectedNumberReads.
|
void |
ExperimentValidator.validateExpectedNumberRuns(Experiment experiment,
org.springframework.validation.Errors errors)
validateExpectedNumberRuns.
|
void |
ExperimentValidator.validateTitle(Experiment experiment,
org.springframework.validation.Errors errors)
Determines if the experiment's email address and confirm email address match.
|
void |
ExperimentUpdateValidator.validateTitle(Experiment experiment,
org.springframework.validation.Errors errors) |
| Modifier and Type | Method and Description |
|---|---|
org.springframework.web.servlet.ModelAndView |
ExperimentController.handleReset(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Experiment command)
Handles the user's request to reset the experiment page during a new or update experiment.
|
org.springframework.web.servlet.ModelAndView |
ExperimentController.handleSubmit(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Experiment command)
Handles the user's request to submit a new study.
|
org.springframework.web.servlet.ModelAndView |
ExperimentController.handleUpdate(javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response,
Experiment command)
Handles the user's request to update their study.
|
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