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GeneDB-master
Jogra
src
org
genedb
jogra
controller
ImageFormBean.java
ImageUtils.java
domain
BasicGene.java
ExpressionZoneEditor.java
FeatureCvTerm.java
Gene.java
GeneDBMessage.java
Term.java
drawing
ApplicationClosingEvent.java
ApplicationMode.java
BaseForm.java
ExtensionFileFilter.java
ImagePanel.java
Jogra.java
JograBusiness.java
JograBusinessImpl.java
JograLogin.java
JograLoginService.java
JograPlugin.java
JograProgressBar.java
OpenWindowEvent.java
Pair.java
SplashWindow.java
plugins
ButtonChangeDocumentListener.java
CCFrame.java
CCPanel.java
ConflictComponentFactory.java
CvEditor.java
GeneEditor.java
GeneList.java
GeneView.java
GeneViewModel.java
GeneViewTest.java
GoFrame.java
GoPanel.java
NameNotePanel.java
Notes.java
OrganismEditor.java
OrganismPanel.java
OrganismTree.java
TermRationaliser.java
services
BasicGeneService.java
DatabaseLogin.java
ExtendedOrganism.java
ExtendedOrganismManager.java
FilteringJList.java
GeneService.java
LockAndNotificationService.java
LockStatus.java
Message.java
MessageService.java
MethodResult.java
NamedVector.java
RationaliserJList.java
RationaliserResult.java
SqlGeneService.java
SqlTermService.java
TermService.java
ng
src
org
genedb
anttasks
Password.java
aop
HazelcastAspect.java
db
adhoc
PanGenomeManager.java
PhylonodeManager.java
Query.java
analyzers
AllNamesAnalyzer.java
AlphaNumericAnalyzer.java
AlphaNumericTokenizer.java
audit
ChangeSet.java
ChangeTracker.java
HibernateChangeSet.java
HibernateChangeTracker.java
dao
AuditDao.java
BaseDao.java
CvDao.java
GeneralDao.java
OrganismDao.java
PhylogenyDao.java
PubDao.java
SequenceDao.java
domain
hibernateImpls
BasicGeneServiceImpl.java
GeneServiceImpl.java
LockAndNotificationServiceImpl.java
MessageServiceImpl.java
ProductServiceImpl.java
luceneImpls
BasicGeneServiceImpl.java
misc
GeneDBMessage.java
GeneListReservations.java
Message.java
MethodResult.java
SemanticLog.java
objects
BasicGene.java
Chromosome.java
CompoundLocatedFeature.java
DatabasePolypeptideRegion.java
Exon.java
ExtendedOrganism.java
ExtendedOrganismManager.java
Gap.java
Gene.java
InterProHit.java
LocatedFeature.java
PolypeptideRegion.java
PolypeptideRegionGroup.java
Product.java
SimplePolypeptideRegion.java
SimpleRegionGroup.java
Transcript.java
TranscriptComponent.java
UTR.java
services
BasicGeneService.java
GeneService.java
LockAndNotificationService.java
LockStatus.java
MessageService.java
ProductService.java
fixup
FixResidues.java
TypeCodes.java
helpers
LocationBridge.java
NameLookup.java
loading
AGPLoader.java
EmblFile.java
EmblLoader.java
EmblLocation.java
FastaFile.java
FastaLoader.java
FeatureTable.java
FeatureUtils.java
FileProcessor.java
GoEvidenceCode.java
GoInstance.java
LoadAGP.java
LoadEmbl.java
LoadFasta.java
LoadOrthologues.java
LoadPileups.java
LoadSNPs.java
LoadVulgar.java
LoggingDataSource.java
ParsingException.java
RfamLoader.java
Similarity.java
SkipRetryAbort.java
SynonymManager.java
VulgarLoader.java
auxiliary
AddFeatureProperty.java
Clear.java
ClearDGPI.java
ClearDomains.java
ClearHTH.java
ClearOPIReferences.java
ClearPlasmoAP.java
ClearRfam.java
ClearSignalP.java
ClearTMHMM.java
ClonedGenomicInsertLoader.java
DGPILoader.java
DeleteRedundantGOTerms.java
DomainFile.java
DomainLoader.java
GOALoader.java
HTHLoader.java
Load.java
Loader.java
LocationLoader.java
OPIReferenceLoader.java
PhosphopeptideLoader.java
PlasmoAPLoader.java
RenameFeature.java
RfamLoader.java
SignalPLoader.java
SystemPropertyOverridingDataSource.java
TMHMMLoader.java
taxon
TaxonNameType.java
TaxonNode.java
TaxonNodeArrayPropertyEditor.java
TaxonNodeList.java
TaxonNodeListFormatter.java
TaxonNodeManager.java
TaxonUtils.java
io
xstream
MultiMapConvertor.java
query
AbstractQuery.java
BasicQueryI.java
Detailer.java
NumberedQueryI.java
Param.java
QueryConstants.java
QueryI.java
QueryPlaceHolder.java
QueryStringParser.java
Result.java
ResultCompatibility.java
SimpleListResult.java
StorageMethod.java
bool
BooleanOp.java
BooleanQuery.java
BooleanQueryNode.java
compatability
AlwaysTrueResultDataSetCompatibility.java
IdentityResultCompatibility.java
NullResultCompatibility.java
ResultCompatibilityChain.java
custom
GenesByURI.java
generation
QueryAnnotationProcessor.java
history
History.java
SimpleHistory.java
hql
HqlQueryTemplate.java
jdbc
JdbcQuery.java
JdbcQueryTemplate.java
params
AbstractParam.java
BooleanParam.java
FloatParam.java
IntParam.java
ListConstraint.java
SimpleListConstraintDelegate.java
StringParam.java
StringParamFromList.java
parsing
BasicQueryStringParser.java
sql
DataSourceAware.java
SimpleJdbcTemplateAware.java
SqlListConstraintDelegate.java
SqlQuery.java
querying
core
BooleanQuery.java
BooleanQueryMode.java
CachedParamDetails.java
CopyOfLuceneQueryModsNotCompleted.java
HqlQuery.java
HtmlFormDetails.java
LuceneIndex.java
LuceneIndexFactory.java
LuceneQuery.java
NumericQueryVisibility.java
PagedQuery.java
Parameter.java
Query.java
QueryBeanGenerator.java
QueryClass.java
QueryDetails.java
QueryException.java
QueryFactory.java
QueryParam.java
QueryTemplate.java
QueryUtils.java
QueryVisibility.java
history
HistoryItem.java
HistoryManager.java
HistoryType.java
QueryHistoryItem.java
parsing
ExprLexer.java
ExprParser.java
QueryLineParser.java
tmpquery
AdvancedQuery.java
AdvancedSearchCategory.java
AnnotationStatusQuery.java
BrowseCategory.java
ChangedGeneFeaturesQuery.java
ControlledCurationQuery.java
CurationQuery.java
DateAndTypeQuery.java
DateCountQuery.java
DateQuery.java
DbxrefQuery.java
EcQuery.java
GeneDetail.java
GeneLocationQuery.java
GeneSummary.java
GeneSummaryMotif.java
GeneTypeQuery.java
GenesByDbQuery.java
GoQuery.java
IdsToGeneDetailQuery.java
IdsToGeneSummaryQuery.java
MotifQuery.java
NameProductQuery.java
OrganismHqlQuery.java
OrganismLuceneQuery.java
PfamQuery.java
ProductQuery.java
ProteinLengthQuery.java
ProteinMassQuery.java
ProteinMatchClusterOrthologueQuery.java
ProteinNumTMQuery.java
ProteinTargetingSeqQuery.java
QuickSearchQuery.java
SimpleNameQuery.java
SuggestQuery.java
TaxonQuery.java
TopLevelFeaturesQuery.java
smallapps
WebImageGenerator.java
util
ColorUtils.java
Counters.java
DumpObject.java
FontFactoryBean.java
FontSize.java
GeneDBFormattingConversionServiceFactoryBean.java
IterableArray.java
MD5Util.java
MutableInteger.java
Pair.java
SequenceUtils.java
SynchronizedTwoKeyMap.java
TranslationException.java
Translator.java
Triplet.java
TwoKeyMap.java
web
applications
motifsearch
FastaEntry.java
FastaLoader.java
filters
UriSessionIdFilter.java
gui
AllocatedCompoundFeature.java
ArtemisColours.java
BdbDiagramCache.java
ContextMapDiagram.java
ContextMapWindowController.java
ContextMapWindowServlet.java
DiagramCache.java
DiagramLayout.java
ImageCreationException.java
ImageMapSummary.java
InitHeadlessToolkitServlet.java
MakeTransparentPixel.java
ProteinMapDiagram.java
RenderedContextMap.java
RenderedDiagram.java
RenderedDiagramFactory.java
RenderedProteinMap.java
TrackedDiagram.java
UnmodifiableBitSet.java
filters
ComboFeatureFilter.java
NamedStrandedFeatureFilter.java
RNAFilter.java
menu
CompositeMenu.java
Menu.java
SimpleMenu.java
mvc
controller
AnnotationChangesRssController.java
AnnotationChangesRssViewer.java
ArtemisLaunchController.java
BaseController.java
BasketController.java
BrowseBean.java
BrowseBeanName.java
BrowseCategoryController.java
BrowseTermController.java
ClassicCompatabilityController.java
CommonUrlController.java
ComplexQueryController.java
ContextMapController.java
DbController.java
DbLinkRedirectController.java
DbXRefListener.java
FastaFile.java
FeatureSequenceController.java
FeedbackController.java
GeneDBSessionListener.java
GeneDBWebUtils.java
GeneSection.java
GeneUtils.java
GmodRestControllerV1.java
GoAssociationUtils.java
GoLookup.java
HazelCastServletContextListener.java
HistoryController.java
HistoryManagerFactory.java
HomepageController.java
HtmlUtils.java
HttpSessionHistoryManager.java
HttpSessionHistoryManagerFactory.java
IdListController.java
ImageController.java
Message.java
MiscPageController.java
ModelBuilder.java
NameLookup.java
NamedFeatureController.java
NewsItem.java
NumberNameConverter.java
OrganismChooserController.java
OrganismTypeEditor.java
OrthologsController.java
PfamLookup.java
QueryForm.java
RegionCommand.java
RestController.java
ResultBean.java
ResultCacheSessionListener.java
ResultHit.java
Results.java
ResultsHolder.java
RootController.java
SearchHit.java
SequenceDestination.java
SequenceDistributorController.java
SequenceType.java
Strand.java
TaxonManagerListener.java
TracerController.java
TranscriptFeatureController.java
WebConstants.java
WsQueryController.java
analysis
MotifSearchController.java
MotifSearcher.java
cgview
CachedFile.java
CachedFileFactory.java
download
AbstractGeneDBFormController.java
BaseCachingController.java
DownloadBean.java
DownloadController.java
DownloadProcess.java
DownloadProcessUtil.java
FeatureDTOAdaptor.java
FormatBase.java
FormatCSV.java
FormatExcel.java
FormatFASTA.java
FormatHTML.java
GeneDetailFieldValueExctractor.java
OutputContent.java
OutputDestination.java
OutputFormat.java
OutputManager.java
OutputOption.java
QueryController.java
QueryListController.java
QuickSearchQueryController.java
ResultEntry.java
ResultsController.java
ResultsNavigatorController.java
SequenceType.java
WebUtils.java
model
AnnotationChangesRssContent.java
BerkeleyMapFactory.java
BmfComparison.java
CacheDBHelper.java
CacheSynchroniser.java
ConfigurableGeneDBSessionFactoryBean.java
DTOFactory.java
DbXRefDTO.java
DtoDb.java
FeatureCvTermDTO.java
FeatureDTO.java
GeneDTO.java
IndexSynchroniser.java
IndexUpdater.java
LuceneIndexBuilder.java
LuceneIndicesComparison.java
MembraneStructureComponentDTO.java
MergeBerkeleyIndices.java
MergeLuceneIndices.java
PeriodicUpdater.java
PolypeptideDTO.java
PopulateCaches.java
PopulateLuceneDictionary.java
PopulateLuceneIndices.java
ResultsCacheFactory.java
SmallPopulateLuceneIndices.java
TranscriptDTO.java
TranscriptDTOAnalyzer.java
TranscriptDTOAnalyzer2.java
TranscriptDTOFactory.java
load
AbstractTranscriptLoader.java
ClusterIdAndOrthologueNamesMapper.java
DbxRefMapper.java
FeatureCVTermPropMapper.java
FeatureCvtermMapper.java
FeatureMapper.java
FeaturePropMapper.java
FeatureRelationshipMapper.java
FeatureTypeMapper.java
GeneMapper.java
OrganismMapper.java
PolypeptideMapper.java
PolypeptidePropertiesHelper.java
PubNameMapper.java
SynonymTypeMapper.java
TimerHelper.java
TopLevelFeatureMapper.java
TranscriptFeatureCVTermLoader.java
TranscriptFeaturePropLoader.java
TranscriptLoader.java
TranscriptMapper.java
TranscriptRegionMapper.java
TranscriptUpdater.java
simple
SimpleFeature.java
SimpleFeatureMapper.java
SimpleGene.java
SimpleGeneMapper.java
SimplePolypeptide.java
SimplePolypeptideMapper.java
SimpleTopLevelFeatureMapper.java
SimpleTranscript.java
SimpleTranscriptLoader.java
SimpleTranscriptMapper.java
types
DBXRefType.java
DtoObjectArrayField.java
DtoStringArrayField.java
FeatureCVTPropType.java
FeatureCvtermType.java
FeaturePropType.java
PepRegionGroupType.java
PeptidePropertiesType.java
SynonymType.java
TranscriptRegionType.java
view
FileCheckingFreemarkerViewResolver.java
FileCheckingInternalResourceViewResolver.java
PrefixViewResolver.java
ServiceView.java
UriSuffixServiceViewResolver.java
tags
bool
QueryTreeWalker.java
db
AbstractHomepageTag.java
BreadcrumbTag.java
DbNameTag.java
DbXRefLinkTag.java
DisplayPhylogeny.java
DisplaySimilarity.java
FilteredPropertyLoopTag.java
HomepageSelectTag.java
HomepageTreeTag.java
HyperlinkDbsInText.java
ListStringTag.java
OrganismNameTag.java
PhylonodeHomePageListTag.java
PropertyFilterTag.java
QuickSearchMessageTag.java
QuickSearchTaxonomicGraphTag.java
SimpleSelectTag.java
TableWrapper.java
TaxonNameTag.java
misc
DebugTag.java
DisplayDateTag.java
FormatSequenceTag.java
HistoryTag.java
ListItemsTag.java
SystematicNameFormatTag.java
UrlTag.java
utils
DownloadUtils.java
Gff3Utils.java
Grep.java
gmod
schema
bulk
AbstractIterator.java
BulkProcessor.java
DataIntegrityViolation.java
DatabaseException.java
ProcessingException.java
TranscriptHandler.java
TranscriptInfo.java
cfg
ChadoAnnotationConfiguration.java
ChadoAnnotationException.java
ChadoAnnotationSettingsFactory.java
ChadoSessionFactoryBean.java
FeatureType.java
FeatureTypeUtils.java
FilteringSessionFactory.java
OrganismHeirachy.java
feature
AbstractExon.java
AbstractGene.java
AminoAcid.java
ApicoplastChromosome.java
BACEnd.java
Centromere.java
Chromosome.java
CloneInsert.java
ClonedGenomicInsert.java
ConjugativeTransposon.java
Contig.java
CytoplasmicRegion.java
DNATransposon.java
Deletion.java
DinucleotideRepeatMicrosatelliteFeature.java
DirectRepeatRegion.java
EST.java
ESTMatch.java
Exon.java
ExtramembraneRegion.java
FivePrimeUTR.java
GPIAnchorCleavageSite.java
Gap.java
Gene.java
GenomicIsland.java
HelixTurnHelix.java
Insertion.java
IntegratedMobileGeneticElement.java
IntegratedPlasmid.java
IntramembraneRegion.java
Intron.java
InvertedRepeatRegion.java
Junction.java
LinearDoubleStrandedDNAChromosome.java
LongTerminalRepeat.java
MRNA.java
Match.java
MatchPart.java
MembraneStructure.java
MembraneStructureComponent.java
Microsatellite.java
MitochondrialChromosome.java
MobileGeneticElement.java
ModifiedAminoAcidFeature.java
NcRNA.java
NonCytoplasmicRegion.java
NucleotideMatch.java
PCRProduct.java
Plasmid.java
PolycistronicTranscript.java
Polypeptide.java
PolypeptideDomain.java
PolypeptideMotif.java
PolypeptideRegion.java
PolypeptideStructuralMotif.java
PrimaryTranscript.java
ProductiveTranscript.java
Promoter.java
Prophage.java
ProteinMatch.java
Pseudogene.java
PseudogenicExon.java
PseudogenicTranscript.java
RNApol_I_Promoter.java
RRNA.java
Read.java
Reagent.java
Region.java
Remark.java
RepeatRegion.java
RepeatUnit.java
SECISElement.java
SNP.java
ScRNA.java
SequenceAlteration.java
SequenceDifference.java
SequenceVariant.java
SignalPeptide.java
SnRNA.java
SnoRNA.java
SpliceSite.java
SplicedLeaderRNA.java
Supercontig.java
TRNA.java
TandemRepeat.java
TetraNucleotideRepeatMicrosatelliteFeature.java
ThreePrimeUTR.java
TopLevelFeature.java
Transcript.java
TranscriptRegion.java
TransmembraneRegion.java
TransposableElement.java
TrinucleotideRepeatMicrosatelliteFeature.java
UORF.java
UTR.java
mapped
Analysis.java
AnalysisFeature.java
AnalysisProp.java
Cv.java
CvTerm.java
CvTermDbXRef.java
CvTermPath.java
CvTermProp.java
CvTermRelationship.java
CvTermSynonym.java
Db.java
DbXRef.java
DbXRefProp.java
Feature.java
FeatureCvTerm.java
FeatureCvTermDbXRef.java
FeatureCvTermProp.java
FeatureCvTermPub.java
FeatureDbXRef.java
FeatureLoc.java
FeatureLocPub.java
FeatureProp.java
FeaturePropPub.java
FeaturePub.java
FeatureRelationship.java
FeatureRelationshipProp.java
FeatureRelationshipPropPub.java
FeatureRelationshipPub.java
FeatureSynonym.java
HasPubsAndDbXRefs.java
Organism.java
OrganismDbXRef.java
OrganismProp.java
Phylonode.java
PhylonodeDbXRef.java
PhylonodeOrganism.java
PhylonodeProp.java
PhylonodePub.java
PhylonodeRelationship.java
Phylotree.java
PhylotreePub.java
Project.java
Pub.java
PubAuthor.java
PubDbXRef.java
PubProp.java
PubRelationship.java
Synonym.java
utils
CollectionUtils.java
CompoundLocation.java
CountedName.java
CvTermUtils.java
GeneNameOrganism.java
LocationUtils.java
ObjectManager.java
PeptideProperties.java
Rankable.java
RankableUtils.java
SimilarityI.java
SingleLocation.java
Strand.java
StrandedLocation.java
propinterface
PropertyI.java
test
org
genedb
db
audit
HibernateChangeTrackerTest.java
MockChangeSetImpl.java
MockChangeTrackerImpl.java
dao
PhylogenyDaoTest.java
domain
test
BasicGeneHelper.java
MockBasicGeneService.java
loading
EmblFileTest.java
EmblLoaderBergheiTest.java
EmblLoaderMansoniTest.java
EmblLoaderReloadTest.java
EmblLoaderSyntheticTest.java
EmblLoaderTestHelper.java
EmblLocationTest.java
FastaFileTest.java
FastaLoaderTest.java
FeatureTester.java
OrthologueLoaderClusteredTest.java
OrthologueLoaderImplicitClusterTest.java
OrthologueLoaderUnclusteredTest.java
OrthologueTester.java
TestLogger.java
auxiliary
DomainLoaderTest.java
HTHLoaderTest.java
RfamLoaderTest.java
test
tools
BuildTestDatabase.java
querying
tmpquery
HibernateTest.java
MockProteinLengthQuery.java
ProteinLengthQueryTest.java
QuickSearchQueryTest.java
SimpleNameQueryTest.java
util
CountersTest.java
IterableArrayTest.java
web
gui
ContextMapDiagramTest.java
DiagramLayoutTest.java
mvc
controller
download
DownloadTest.java
model
CacheSynchTestDelegate.java
TestAbstractUpdater.java
gmod
schema
mapped
MockChromosome.java
MockTranscript.java
test
HibernateTest.java
package org.genedb.querying.history; public enum HistoryType { QUERY, MANUAL, BASKET, AUTO_BASKET; }