All Classes
AboutBox
AbstractBioPAXImportTaskFactory
AbstractClusterNetworksTaskFactory
AbstractExcludeIntermediateNodesTaskFactory
AbstractModularViewTaskFactory
AbstractTask
AccessionNumberTable
ACSNProcedures
AgilentCGHMapping
analyseInstallSpyLog
analyzeSBMLFile
Attribute
BindingFeature
BindingFeatureImpl
BindingFeatureListener
BiNoMPlugin
BiNoMPlugin
BiNoMPluginAction
BiNoMPluginDialog
BiochemicalPathwayStep
BiochemicalPathwayStepImpl
BiochemicalPathwayStepListener
BiochemicalReaction
BiochemicalReactionImpl
BiochemicalReactionListener
BiographUtils
BioPAX
BioPAX2CellDesigner
BioPAX2Cytoscape
BioPAX2SBML
biopax_DASH_level3_DOT_owlFactory
BioPAXAssociateSource
BioPAXAssociateSourceTask
BioPAXAttrDesc
BioPAXAttrDescProto
BioPAXAttrDescProto.SubType
BioPAXAttrDescProto.Type
BioPAXAttrDescProtoFactory
BioPAXClassDesc
BioPAXClassDesc.HierarchyScanner
BioPAXClassDescFactory
BioPAXClassTree
BioPAXClassTree
BioPAXClassTreeFrame
BioPAXConnectedComponents
BioPAXConnectedComponents
BioPAXDBRepository
BioPAXDisplayIndexInfo
BioPAXDisplayIndexInfoDialog
BioPAXDoubleAttrDesc
BioPAXDoubleListAttrDesc
BioPAXExportTask
BioPAXExportToFile
BioPAXGenerateIndex
BioPAXGenerateIndexDialog
BioPAXGenerateIndexTask
BioPAXGraphMapper
BioPAXGraphMappingService
BioPAXGraphQuery
BioPAXGraphQueryEngine
BioPAXImportBaseTask
BioPAXImportDialog
BioPAXImportFromFile
BioPAXImportFromFile
BioPAXImportFromURL
BioPAXImportTask
BioPAXImportTask
BioPAXImportTaskFactory
BioPAXImportTaskFactory
BioPAXIndex2Tables
BioPAXIndexPathAnalysis
BioPAXIndexRepository
BioPAXIntegerAttrDesc
BioPAXIntegerListAttrDesc
BioPAXLoadIndex
BioPAXLoadIndexDialog
BioPAXLoadIndexTask
BioPAXMerge
BioPAXNamingService
BioPAXNamingServiceManager
BioPAXObject
BioPAXObjectAttrDesc
BioPAXObjectFactory
BioPAXObjectListAttrDesc
BioPAXPathAnalysis
BioPAXPropertyBrowser
BioPAXPropertyBrowser
BioPAXPropertyBrowserFrame
BioPAXPropertyBrowserPanel
BioPAXPropertyEditFrame
BioPAXPropertyManager
BioPAXPropertyManager
BioPAXPropertyUtils
BioPAXPropertyUtils.ObjectLabel
BioPAXRepository
BioPAXSaveAssociated
BioPAXSelectEntities
BioPAXSelectEntitiesDialog
BioPAXSelectEntitiesTask
BioPAXSourceDB
BioPAXStandardQuery
BioPAXStandardQuery
BioPAXStandardQueryDialog
BioPAXStandardQueryTask
BioPAXStringAttrDesc
BioPAXStringListAttrDesc
BioPAXSyncNetworks
BioPAXSyncNetworksDialog
BioPAXToCellDesignerConverter
BioPAXToCytoscapeConverter
BioPAXToCytoscapeConverter.Graph
BioPAXToCytoscapeConverter.Option
BioPAXToggleNamingService
BioPAXToSBMLConverter
BioPAXUtilities
BioPAXViewQueryLog
BioPAXViewQueryLogDialog
BioPAXVisualStyleDefinition
BioSource
BioSourceImpl
BioSourceListener
BipartiteGraph
BlogCreator
CalcCentrality
CalcCentralityTask
Catalysis
CatalysisImpl
CatalysisListener
CDesigner2BioPAX
CellDesigner
CellDesigner2BioPAX
CellDesigner2Cytoscape
CellDesignerAssociateSource
CellDesignerAssociateSourceTask
CellDesignerColorProteins
CellDesignerColorSpecies
CellDesignerExportTask
CellDesignerExportToFile
CellDesignerExportToFileDialog
CellDesignerGenerator
CellDesignerImportFromFile
CellDesignerImportTask
CellDesignerPathwayStaining
CellDesignerSourceDB
CellDesignerToBioPAXConverter
CellDesignerToCytoscapeConverter
CellDesignerToCytoscapeConverter.Graph
CellDesignerVisualStyleDefinition
CellularLocationVocabulary
CellularLocationVocabularyImpl
CellularLocationVocabularyListener
CellVocabulary
CellVocabularyImpl
CellVocabularyListener
checkCellDesignerFile
CheckCellDesignerFile
checkCellDesignerFileDialog
checkCellDesignerFileTask
ChemicalStructure
ChemicalStructureImpl
ChemicalStructureListener
ClusterByShortPath
ClusterByShortPathTask
ClusterNetworks
ClusterNetworks
ClusterNetworksDialog
ClusterNetworksTask
ClusterNetworksTask
ClusterNetworksTaskFactory
ClusterNetworksTaskFactory
colorCellDesignerProteins
colorCellDesignerProteinsDialog
colorCellDesignerProteinsTask
CombinationGenerator
ComboBoxes
Complex
ComplexAssembly
ComplexAssemblyImpl
ComplexAssemblyListener
ComplexImpl
ComplexListener
ComputeNaviCellMaps
ComputingByBFS
ConnectedComponents
ConnectedComponents
ConnectedComponentsTask
ConnectedComponentsTask
ConnectionToDatabases
Control
ControlImpl
ControlledVocabulary
ControlledVocabularyImpl
ControlledVocabularyListener
ControlListener
Conversion
ConversionImpl
ConversionListener
ConvertReactionNetworkToEntityNetwork
ConvertReactionNetworkToEntityNetworkTask
ConvertToUndirectedGraph
ConvertToUndirectedGraphTask
CopySelectedNodesAndEdges
CovalentBindingFeature
CovalentBindingFeatureImpl
CovalentBindingFeatureListener
CreateConnectionsBetweenNests
createNeighborhoodSets
createNeighborhoodSetsDialog
CreateNestNetwork
CreateSetIntersectionGraph
CSML
CSMLImportFromFile
CSMLImportTask
CSMLToCytoscapeConverter
CycleDecomposition
CycleDecomposition
CycleDecompositionTask
CycleDecompositionTask
Cytoscape2BioPAX
Cytoscape2CellDesigner
Cytoscape2SBML
CytoscapeToBioPAXConverter
CytoscapeToCellDesignerConverter
DatabaseComparison
DataPathConsistencyAnalyzer
Degradation
DegradationImpl
DegradationListener
DeltaG
DeltaGImpl
DeltaGListener
DestroyUnusedNetworksAsNest
DestroyUnusedNetworksAsNestTask
Dna
DnaImpl
DnaListener
DnaReference
DnaReferenceImpl
DnaReferenceListener
DnaRegion
DnaRegionImpl
DnaRegionListener
DnaRegionReference
DnaRegionReferenceImpl
DnaRegionReferenceListener
DoubleNetworkDifference
DoubleNetworkDifferenceDialog
Edge
EdgesFromOtherNetwork
EdgesFromOtherNetworkDialog
EdgesFromOtherNetworkTask
Element
Entity
EntityFeature
EntityFeatureImpl
EntityFeatureListener
EntityImpl
EntityListener
EntityReference
EntityReferenceImpl
EntityReferenceListener
EntityReferenceTypeVocabulary
EntityReferenceTypeVocabularyImpl
EntityReferenceTypeVocabularyListener
Evidence
EvidenceCodeVocabulary
EvidenceCodeVocabularyImpl
EvidenceCodeVocabularyListener
EvidenceImpl
EvidenceListener
ExcludeIntermediateNodes
ExcludeIntermediateNodes
ExcludeIntermediateNodesDialog
ExcludeIntermediateNodesTask
ExcludeIntermediateNodesTask
ExcludeIntermediateNodesTaskFactory
ExcludeIntermediateNodesTaskFactory
ExperimentalForm
ExperimentalFormImpl
ExperimentalFormListener
ExperimentalFormVocabulary
ExperimentalFormVocabularyImpl
ExperimentalFormVocabularyListener
extractCellDesignerNotes
extractCellDesignerNotesDialog
extractCellDesignerNotesTask
ExtractGMTFromCellDesigner
ExtractReactionNetwork
ExtractReactionNetwork
ExtractReactionNetworkTask
ExtractReactionNetworkTask
ExtractSubnetwork
ExtractSubnetworkDialog
ExtractSubnetworkTask
FindCommonNodes
FormatProteinNotes
FragmentFeature
FragmentFeatureImpl
FragmentFeatureListener
FromToNodes
Gene
GeneImpl
GeneListener
GeneticInteraction
GeneticInteractionImpl
GeneticInteractionListener
GeneticInteractionNetworks
GMTFile
Graph
GraphAlgorithms
GraphDocumentFactory
GraphDocumentFactory
GraphicUtils
GraphUtils
GraphXGMMLParser
GridBagDialog
ImportFromAINDialogConstitutiveReactions
ImportFromAINDialogFamily
ImportFromAINTask
ImportFromSimpleTextInfluenceFile
IndexPathAnalysisDialog
IndexPathAnalysisTask
InfluenceAreaInArray
InfluenceAreaInAttribute
InfluenceArrayAsGraphic
InfluenceArrayAsText
InfluenceByAttribute
InfluenceFeatures
InputReachParameter
InsertCellDesignerParameters
insertMassActionLaws
Interaction
InteractionGraph
InteractionImpl
InteractionListener
InteractionVocabulary
InteractionVocabularyImpl
InteractionVocabularyListener
InterOf2SelectedNests
KEGGAccess
KPrime
KPrimeImpl
KPrimeListener
LaplaceMatToSif
LinearizeNetwork
LinearizeNetwork
LinearizeNetworkTask
LinearizeNetworkTask
ListAllNodes
ListAllNodesDialog
ListAllReactions
ListAllReactionsDialog
ListComponents
ListDialog
ListNodesByNest
MakeCanonicalView
MaterialComponents
MaterialComponents
MaterialComponentsTask
MaterialComponentsTask
Matrix2Color
MergeNetworksAndFilter
MergeNetworksAndFilterTask
MergeNetworksAndFilterTaskFactory
MergeSelectedNests
MergingMaps
mergingMaps
MergingMapsDialog
MergingMapsProcessor
MergingMapsTask
MLLabel
ModificationFeature
ModificationFeatureImpl
ModificationFeatureListener
modifyCellDesignerNotes
ModifyCellDesignerNotes
modifyCellDesignerNotesDialog
modifyCellDesignerNotesTask
ModularView
ModularView
ModularViewDialog
ModularViewTask
ModularViewTask
ModularViewTaskFactory
ModularViewTaskFactory
Modulation
ModulationImpl
ModulationListener
ModuleVisualStyle
MolecularInteraction
MolecularInteractionImpl
MolecularInteractionListener
MonoMolecularReactionsAsEdges
MonoMolecularReactionsAsEdges
MonoMolecularReactionsAsEdgesTask
MonoMolecularReactionsAsEdgesTask
NestInNodeAttribute
NestMerging
NestUtils
NetworkDifference
NetworkFactory
NetworkFactory
NetworkIntersection
NetworkOperation
NetworkOperation.Estimator
NetworksUpdate
NetworksUpdateConfirmDialog
NetworksUpdateDialog
NetworksUpdateTask
NetworkUnion
NetworkUtils
NetworkUtils
Node
NodesAndEdgesClipboard
OFTENAnalysis
OmegaScoreData
OptimalCombinationAnalyzer
OptimalCutSetAnalyzer
OptimalCutSetAnalyzerDialog
OptimalCutSetAnalyzerTask
OptimalCutSetGenesDialog
OptimalCutSetReportDialog
OptimalCutSetVisuDialog
OptionParser
OWLExtensionFilter
PackInNestNode
Pair
parseBioPAX
parseCellDesigner
PasteNodesAndEdges
PasteNodesAndEdgesDialog
Path
PathAnalysis
PathAnalysisDialog
PathAnalysisTask
PathConsistencyAnalyzer
PathConsistencyAnalyzerBootstrapDialog
PathConsistencyAnalyzerBootstrapTask
PathConsistencyAnalyzerDialog
PathConsistencyAnalyzerPathDialog
PathConsistencyAnalyzerReportDialog
PathConsistencyAnalyzerTask
Pathway
PathwayImpl
PathwayListener
pathwayStainingCellDesigner
pathwayStainingCellDesignerDialog
pathwayStainingCellDesignerTask
PathwayStep
PathwayStepImpl
PathwayStepListener
PavingData
PavingDialog
PhenotypeVocabulary
PhenotypeVocabularyImpl
PhenotypeVocabularyListener
PhysicalEntity
PhysicalEntityImpl
PhysicalEntityListener
Plugin
PowerfulTokenizer
prepareCellDesignerFile
ProduceClickableMap
ProduceClickableMap.NaviCellException
ProduceNaviCellMapFiles
ProduceNaviCellMapFilesDialog
ProduceNaviCellMapFilesTask
Protein
ProteinImpl
ProteinListener
ProteinReference
ProteinReferenceImpl
ProteinReferenceListener
Provenance
ProvenanceImpl
ProvenanceListener
PruneGraph
PruneGraph
PruneGraphTask
PruneGraphTask
PublicationXref
PublicationXrefImpl
PublicationXrefListener
RecreateLostConnectionsInsideNests
RecreateLostConnectionsInsideNestsTask
RelationshipTypeVocabulary
RelationshipTypeVocabularyImpl
RelationshipTypeVocabularyListener
RelationshipXref
RelationshipXrefImpl
RelationshipXrefListener
RemoveNonExpressedProteins
Rna
RnaImpl
RnaListener
RnaReference
RnaReferenceImpl
RnaReferenceListener
RnaRegion
RnaRegionImpl
RnaRegionListener
RnaRegionReference
RnaRegionReferenceImpl
RnaRegionReferenceListener
SampleAction
SamplePlugin
SamplePluginDialog
SBML
SBMLExportTask
SBMLExportToFile
Score
ScoreImpl
ScoreListener
SelectDownstreamNeighbours
SelectEdgesBetweenSelectedNodes
SelectNodesByAttributeSubstring
SelectNodesByAttributeSubstringDialog
SelectUpstreamNeighbours
SequenceInterval
SequenceIntervalImpl
SequenceIntervalListener
SequenceLocation
SequenceLocationImpl
SequenceLocationListener
SequenceModificationVocabulary
SequenceModificationVocabularyImpl
SequenceModificationVocabularyListener
SequenceRegionVocabulary
SequenceRegionVocabularyImpl
SequenceRegionVocabularyListener
SequenceSite
SequenceSiteImpl
SequenceSiteListener
SetOverlapAnalysis
ShortPathClustering
ShowClipboardContents
ShowClipboardContentsDialog
ShowTextDialog
SignsOfPaths
SimpleTable
SimpleTextInfluence2BioPAX
SimpleTextInfluenceToBioPAX
Skeleton
SmallMolecule
SmallMoleculeImpl
SmallMoleculeListener
SmallMoleculeReference
SmallMoleculeReferenceImpl
SmallMoleculeReferenceListener
SpeciesStructure
Stoichiometry
StoichiometryImpl
StoichiometryListener
StronglyConnectedComponents
StronglyConnectedComponents
StronglyConnectedComponentsTask
StronglyConnectedComponentsTask
StructureAnalysisUtils
StructureAnalysisUtils.Option
SubnetworkProperties
TaskManager
TemplateReaction
TemplateReactionImpl
TemplateReactionListener
TemplateReactionRegulation
TemplateReactionRegulationImpl
TemplateReactionRegulationListener
test
test1
test2
TestAIN
TestAutomaticStructureAnalysis
testBioBasePathway
TestBioPAX
testBioPAX1
testBioPAXExtract
testBioPAXExtractAPO
TestBioPAXGraphMapper
testBioPAXManipulation
testBioPAXMerge
testBioPAXQueryEngine
TestBioPAXQueryEngineEB
testCellDesigner
testCellDesignerFile
testChangeProteinSize
testCSML
TestDialog
testDialogs
TestEB
testEwingNetwork
testExtractBioPAX
TestFindAllPaths
testFindingPath
TestGraphAlgo
TestGraphAlgo.ElemScore
testGraphMappingService
testGraphPruning
testJastor
TestJastorEB
testJavolution
TestMaterialComponents
TestMergeMapsACSN
testMergeNetworksAndFilter
TestMergingMapsCD
TestMergingMapsDialog
TestMinCutSet
TestModuleDecomposition
testNamingService
testNetworkFactory
TestNetworkOP
TestNIPath
TestOPtCutSet
testPath
TestPiquantDialog
testRBpathway
testRemoveEditPoints
testSAX
TestSetSet
testStructureAnalysis
testTranspath
TestWordPress
TestXGMML
TextBox
TextBoxDialog
TissueVocabulary
TissueVocabularyImpl
TissueVocabularyListener
Transpath
Transpath2BioPAX
Transport
TransportImpl
TransportListener
TransportWithBiochemicalReaction
TransportWithBiochemicalReactionImpl
TransportWithBiochemicalReactionListener
TwoListDialog
UnificationXref
UnificationXrefImpl
UnificationXrefListener
UpdateInfluenceAttrib
UtilityClass
UtilityClassImpl
UtilityClassListener
Utils
Utils
Utils.Transparency
VisualStyleDefinition
VisualStyleDefinition.ImageDefinition
VisualStyleDefinition.ObjectMapping
VisualStyleFactory
WordPressBlogCreator
WordPressTest
workMatlabOvidiu
XGMML
XGMMLExport
XGMMLExtensionFilter
Xref
XrefImpl
XrefListener