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#Cytoscape.data Classes and Interfaces - 121 results found.
NameDescriptionTypePackageFramework
AbstractGraphReaderClasscytoscape.data.readersCytoScape
AliasesSimpler version of Thesaurus.Classcytoscape.data.synonymsCytoScape
AliasTypeenum AliasTypeextends Enum Aliases are always belongs to one of these types.Classcytoscape.data.synonymsCytoScape
AnnotationStore any number of classifications for named entities, each of which is from a specified species, and where the classifications are all terms from anClasscytoscape.data.annotationCytoScape
AnnotationDescriptionDistinguish among different ontologies, by curator and type.Classcytoscape.data.annotationCytoScape
AnnotationFlatFileReaderClasscytoscape.data.annotation.readersCytoScape
AnnotationXmlReaderClasscytoscape.data.annotation.readersCytoScape
AttribTopoGraphNodeRepresents a node in a topological graph.Classcytoscape.dataCytoScape
AttributeFilterInterface for defining CyEdge-based filters used for determining which Edges should be used for a particular operation, such asInterfacecytoscape.dataCytoScape
AttributeImportQueryClasscytoscape.data.webserviceCytoScape
AttributeSaverDialogDialog box to save various attributes.Classcytoscape.dataCytoScape
AttributeValueVisitorInterface for defining attribute value visitors--operations to perform on each attribute value using CyAttributesUtils.Interfacecytoscape.dataCytoScape
BioDataServerClasscytoscape.data.serversCytoScape
BioDataServerInterfaceInterfacecytoscape.data.serversCytoScape
BioDataServerRmiThis is the actual class which implements BioDataServer Methods.Classcytoscape.data.serversCytoScape
BookmarkReaderClasscytoscape.data.readersCytoScape
clearClasscytoscape.data.serversCytoScape
CountedIteratorA java.Interfacecytoscape.data.attrCytoScape
CyAttributesCyAttributes provides access to network, node, and edge attributes within Cytoscape.Interfacecytoscape.dataCytoScape
CyAttributesImplClasscytoscape.dataCytoScape
CyAttributesReaderClasscytoscape.data.readersCytoScape
CyAttributesUtilsClasscytoscape.dataCytoScape
CyAttributesUtils .AttributeTypeClasscytoscape.dataCytoScape
CyAttributesWriterCyAttributeWriter extracted from AttributeSaverDialog.Classcytoscape.data.writersCytoScape
CyNetworkUtilitiesThis class provides static methods that operate on a CyNetwork to perform various useful tasks.Classcytoscape.dataCytoScape
CytoscapeSessionReaderReader to load CYtoscape Session file (.Classcytoscape.data.readersCytoScape
CytoscapeSessionWriterWrite session states into files.Classcytoscape.data.writersCytoScape
CyWebServiceEventEvent object used by Web Service Clients and the core.Classcytoscape.data.webserviceCytoScape
CyWebServiceEvent .WSEventTypeClasscytoscape.data.webserviceCytoScape
CyWebServiceEvent .WSResponseTypeWill be used to catch the signal from WS.Classcytoscape.data.webserviceCytoScape
CyWebServiceEventListenerListener for Web Service Event handling.Interfacecytoscape.data.webserviceCytoScape
CyWebServiceEventSupportClasscytoscape.data.webserviceCytoScape
CyWebServiceExceptionClasscytoscape.data.webserviceCytoScape
CyWebServiceException .WSErrorCodeClasscytoscape.data.webserviceCytoScape
DatabaseSearchResultClasscytoscape.data.webserviceCytoScape
DBCrossReferenceReaderReader for database cross reference file.Classcytoscape.data.ontology.readersCytoScape
DBCrossReferencesDatabase cress reference.Classcytoscape.data.ontologyCytoScape
DBReferenceRepresents an entry in the database cross reference.Classcytoscape.data.ontologyCytoScape
DBXrefKeywordsenum DBXrefKeywordsextends EnumEnum Constant SummaryABBREVIATIONClasscytoscape.data.ontology.readersCytoScape
EqnAttrTrackerConstructor SummaryEqnAttrTracker()Methods inherited from class java.Classcytoscape.data.readersCytoScape
ExpressionDataThis class provides a reader for the common file format for expression data and an interface to access the data.Classcytoscape.dataCytoScape
ExtensibleMultiHashMapModelPlease try to restrain from using this class.Classcytoscape.data.attr.utilCytoScape
FlattenIntVectorsgiven a vector which nests other vectors, each resolving eventually to a list of Integers, flatten it out into a simple 1-level-deepClasscytoscape.data.annotationCytoScape
GeneOntologyGene Ontology object based on general Ontology.Classcytoscape.data.ontologyCytoScape
GeneOntology .GOAspectClasscytoscape.data.ontologyCytoScape
getCanonicalNameClasscytoscape.data.serversCytoScape
getCommonNameClasscytoscape.data.serversCytoScape
GMLExceptionException for GML Reader.Classcytoscape.data.readersCytoScape
GMLNodeThis class represents a GMLNode.Classcytoscape.data.readersCytoScape
GMLParserThe purpose of this class is to translate GML into an object tree, and print out an object tree into GMLClasscytoscape.data.readersCytoScape
GMLReaderThis class is responsible for converting a gml object tree into cytoscape objects New features to the current version: 1.Classcytoscape.data.readersCytoScape
GMLTagenum GMLTagextends EnumEnum Constant SummaryARROWClasscytoscape.data.readersCytoScape
GMLTreeThis class wraps around GMLNode and provides various methods for constructing a tree structure given other data.Classcytoscape.data.readersCytoScape
GMLWriterThe purpse of this class is to translate cytoscape data structures into a gml object tree, we can then use the gml parser to write this tree out into aClasscytoscape.data.readersCytoScape
GOTermA Gene Ontology term.Classcytoscape.data.ontologyCytoScape
GraphReaderInterface for Reading in Cytoscape Graphs.Interfacecytoscape.data.readersCytoScape
ImportHandlerCentral registry for all Cytoscape import classes.Classcytoscape.dataCytoScape
InteractionInteraction.Classcytoscape.dataCytoScape
InteractionsReaderReader for graphs in the interactions file format.Classcytoscape.data.readersCytoScape
InteractionWriterA few utility methods to assist in writing SIF files.Classcytoscape.data.writersCytoScape
KeyValueKey and Value pair in GML file.Classcytoscape.data.readersCytoScape
loadAnnotationload an annotation into an rmi biodata server.Classcytoscape.data.serversCytoScape
loadAnnotationFromFlatFilesload an annotation into an rmi biodata server.Classcytoscape.data.serversCytoScape
loadThesaurusload an thesaurus into an rmi biodata server.Classcytoscape.data.serversCytoScape
MetadataEntriesenum MetadataEntriesextends EnumEntries in the network metadata.Classcytoscape.data.readersCytoScape
MetadataParserManipulates network metadata for loading and saving.Classcytoscape.data.readersCytoScape
mRNAMeasurementClasscytoscape.dataCytoScape
MultiHashMapThis interface consists of the API specification to bind attribute values to objects.Interfacecytoscape.data.attrCytoScape
MultiHashMapDefinitionThis interface contains the API specification for creating attribute definitions.Interfacecytoscape.data.attrCytoScape
MultiHashMapDefinitionListenerInterfacecytoscape.data.attrCytoScape
MultiHashMapFactoryThis class provides access to implementations of MultiHashMap and MultiHashMapDefinition.Classcytoscape.data.attr.utilCytoScape
MultiHashMapHelpersThis class contains static utilitarian methods that return information pertaining to attributes.Classcytoscape.data.attr.utilCytoScape
MultiHashMapListenerInterfacecytoscape.data.attrCytoScape
NestedNetworkReaderSpecial interface for Graph readers which read nested networks from a file.Interfacecytoscape.data.readersCytoScape
NetworkDataThere is an event fired anytime that a value is modified, you need to be listener to the attribute name though.Classcytoscape.dataCytoScape
NetworkExpansionMenuClasscytoscape.data.webservice.utilCytoScape
NetworkImportWebServiceClientInterfacecytoscape.data.webserviceCytoScape
NNFParserParser for NNF files.Classcytoscape.data.readersCytoScape
NNFReaderGraph file reader for NNF files.Classcytoscape.data.readersCytoScape
OBOFlatFileReader This is a general OBO (Open Biomedical Ontologies: http://obo.Classcytoscape.data.ontology.readersCytoScape
OBOHeaderTagsenum OBOHeaderTagsextends EnumEnum Constant SummaryAUTO_GENERATED_BYClasscytoscape.data.ontology.readersCytoScape
OBOTagsenum OBOTagsextends EnumTags used in OBO file:Classcytoscape.data.ontology.readersCytoScape
OntologyContains a collection of OntologyTerms, each of which may have pointers to other terms, creating a hierarchical controlled vocabulary.Classcytoscape.data.annotationCytoScape
OntologyGeneral Ontology class which implements interface from BioJava project.Classcytoscape.data.ontologyCytoScape
OntologyDescriptionDistinguish among different ontologies, by curator and type.Classcytoscape.data.annotationCytoScape
OntologyFactoryClasscytoscape.data.ontologyCytoScape
OntologyFlatFileReaderClasscytoscape.data.annotation.readersCytoScape
OntologyReaderInterface for all ontology file readers.Interfacecytoscape.data.ontology.readersCytoScape
OntologyServerOntology Server which manages ontologies, aliases, and bookmarks.Classcytoscape.data.serversCytoScape
OntologyServer .OntologyTypeClasscytoscape.data.serversCytoScape
OntologyTermRepresents one node in an ontology, which is a hierarchical classification of entities using a controlled vocabulary.Classcytoscape.data.annotationCytoScape
OntologyTermSimple in-memory implementation of an ontology term based on BioJava's This implementation uses CyNetwork and CyAttributes as its actual dataClasscytoscape.data.ontologyCytoScape
OntologyTerm .SynonymTypeClasscytoscape.data.ontologyCytoScape
OntologyXmlReaderClasscytoscape.data.annotation.readersCytoScape
SelectEventEvents that are fired when the selected state of a Node or Edge, or a group of Nodes or Edges, is changed.Classcytoscape.dataCytoScape
SelectEventListenerListener for SelectEvents fired by a SelectFilter object.Interfacecytoscape.dataCytoScape
SelectFilterThis class implements the ability to set the selected state of every node or edge in a GraphPerspective.Classcytoscape.dataCytoScape
SemanticsThis class defines names for certain data attributes that are commonly used within Cytoscape.Classcytoscape.dataCytoScape
statusClasscytoscape.data.serversCytoScape
TextFileReaderClasscytoscape.data.readersCytoScape
TextHttpReaderClasscytoscape.data.readersCytoScape
TextJarReaderClasscytoscape.data.readersCytoScape
Thesaurustodo (pshannon, 25 oct 2002): there may be multiple canonicalNames for the same common name.Classcytoscape.data.synonymsCytoScape
ThesaurusFlatFileReaderRead synonyms from flat file.Classcytoscape.data.synonyms.readersCytoScape
TripleExtract partial graph structure.Classcytoscape.data.ontologyCytoScape
UnifiedNetworkImportDialogDefault GUI component for network import web service clients.Classcytoscape.data.webservice.uiCytoScape
VisualStyleBuilderBased on the graph/node/edge view information, build new Visual Style.Classcytoscape.data.readersCytoScape
WebServiceClientWeb service client wrapper for Cytoscape.Interfacecytoscape.data.webserviceCytoScape
WebServiceClientGUIWeb service client which has custom component should implements this interface.Interfacecytoscape.data.webservice.uiCytoScape
WebServiceClientGUI .IconSizeClasscytoscape.data.webservice.uiCytoScape
WebServiceClientImplAbstract class for all web service clients.Classcytoscape.data.webserviceCytoScape
WebServiceClientImplWithGUIClasscytoscape.data.webserviceCytoScape
WebServiceClientManagerWeb Service Client Manager manages available web service clients in Cytoscape.Classcytoscape.data.webserviceCytoScape
WebServiceClientManager .ClientTypeClientType defines types/characteristics of the web service clients.Classcytoscape.data.webserviceCytoScape
WebServiceContextMenuContext menu for web service clients.Classcytoscape.data.webservice.uiCytoScape
WebServiceContextMenuListenerClasscytoscape.data.webservice.uiCytoScape
WebServiceThemeInstallClasscytoscape.data.webservice.utilCytoScape
WSImportResultDialogClasscytoscape.data.webservice.uiCytoScape
XGMMLExceptionException for XGMML Reader.Classcytoscape.data.readersCytoScape
XGMMLReader This version is Metanode-compatible.Classcytoscape.data.readersCytoScape
XGMMLWriterWrite network and attributes in XGMML format and marshall it in a streme.Classcytoscape.data.writersCytoScape