Search Java Classes and Packages
#Cytoscape.data Classes and Interfaces - 121 results found.
| Name | Description | Type | Package | Framework |
| AbstractGraphReader | Class | cytoscape.data.readers | CytoScape | |
| Aliases | Simpler version of Thesaurus. | Class | cytoscape.data.synonyms | CytoScape |
| AliasType | enum AliasTypeextends Enum | Class | cytoscape.data.synonyms | CytoScape |
| Annotation | Store any number of classifications for named entities, each of which is from a specified species, and where the classifications are all terms from an | Class | cytoscape.data.annotation | CytoScape |
| AnnotationDescription | Distinguish among different ontologies, by curator and type. | Class | cytoscape.data.annotation | CytoScape |
| AnnotationFlatFileReader | Class | cytoscape.data.annotation.readers | CytoScape | |
| AnnotationXmlReader | Class | cytoscape.data.annotation.readers | CytoScape | |
| AttribTopoGraphNode | Represents a node in a topological graph. | Class | cytoscape.data | CytoScape |
| AttributeFilter | Interface for defining CyEdge-based filters used for determining which Edges should be used for a particular operation, such as | Interface | cytoscape.data | CytoScape |
| AttributeImportQuery | Class | cytoscape.data.webservice | CytoScape | |
| AttributeSaverDialog | Dialog box to save various attributes. | Class | cytoscape.data | CytoScape |
| AttributeValueVisitor | Interface for defining attribute value visitors--operations to perform on each attribute value using CyAttributesUtils. | Interface | cytoscape.data | CytoScape |
| BioDataServer | Class | cytoscape.data.servers | CytoScape | |
| BioDataServerInterface | Interface | cytoscape.data.servers | CytoScape | |
| BioDataServerRmi | This is the actual class which implements BioDataServer Methods. | Class | cytoscape.data.servers | CytoScape |
| BookmarkReader | Class | cytoscape.data.readers | CytoScape | |
| clear | Class | cytoscape.data.servers | CytoScape | |
| CountedIterator | A java. | Interface | cytoscape.data.attr | CytoScape |
| CyAttributes | CyAttributes provides access to network, node, and edge attributes within Cytoscape. | Interface | cytoscape.data | CytoScape |
| CyAttributesImpl | Class | cytoscape.data | CytoScape | |
| CyAttributesReader | Class | cytoscape.data.readers | CytoScape | |
| CyAttributesUtils | Class | cytoscape.data | CytoScape | |
| CyAttributesUtils .AttributeType | Class | cytoscape.data | CytoScape | |
| CyAttributesWriter | CyAttributeWriter extracted from AttributeSaverDialog. | Class | cytoscape.data.writers | CytoScape |
| CyNetworkUtilities | This class provides static methods that operate on a CyNetwork to perform various useful tasks. | Class | cytoscape.data | CytoScape |
| CytoscapeSessionReader | Reader to load CYtoscape Session file (. | Class | cytoscape.data.readers | CytoScape |
| CytoscapeSessionWriter | Write session states into files. | Class | cytoscape.data.writers | CytoScape |
| CyWebServiceEvent | Event object used by Web Service Clients and the core. | Class | cytoscape.data.webservice | CytoScape |
| CyWebServiceEvent .WSEventType | Class | cytoscape.data.webservice | CytoScape | |
| CyWebServiceEvent .WSResponseType | Will be used to catch the signal from WS. | Class | cytoscape.data.webservice | CytoScape |
| CyWebServiceEventListener | Listener for Web Service Event handling. | Interface | cytoscape.data.webservice | CytoScape |
| CyWebServiceEventSupport | Class | cytoscape.data.webservice | CytoScape | |
| CyWebServiceException | Class | cytoscape.data.webservice | CytoScape | |
| CyWebServiceException .WSErrorCode | Class | cytoscape.data.webservice | CytoScape | |
| DatabaseSearchResult | Class | cytoscape.data.webservice | CytoScape | |
| DBCrossReferenceReader | Reader for database cross reference file. | Class | cytoscape.data.ontology.readers | CytoScape |
| DBCrossReferences | Database cress reference. | Class | cytoscape.data.ontology | CytoScape |
| DBReference | Represents an entry in the database cross reference. | Class | cytoscape.data.ontology | CytoScape |
| DBXrefKeywords | enum DBXrefKeywordsextends Enum | Class | cytoscape.data.ontology.readers | CytoScape |
| EqnAttrTracker | Constructor SummaryEqnAttrTracker()Methods inherited from class java. | Class | cytoscape.data.readers | CytoScape |
| ExpressionData | This class provides a reader for the common file format for expression data and an interface to access the data. | Class | cytoscape.data | CytoScape |
| ExtensibleMultiHashMapModel | Please try to restrain from using this class. | Class | cytoscape.data.attr.util | CytoScape |
| FlattenIntVectors | given a vector which nests other vectors, each resolving eventually to a list of Integers, flatten it out into a simple 1-level-deep | Class | cytoscape.data.annotation | CytoScape |
| GeneOntology | Gene Ontology object based on general Ontology. | Class | cytoscape.data.ontology | CytoScape |
| GeneOntology .GOAspect | Class | cytoscape.data.ontology | CytoScape | |
| getCanonicalName | Class | cytoscape.data.servers | CytoScape | |
| getCommonName | Class | cytoscape.data.servers | CytoScape | |
| GMLException | Exception for GML Reader. | Class | cytoscape.data.readers | CytoScape |
| GMLNode | This class represents a GMLNode. | Class | cytoscape.data.readers | CytoScape |
| GMLParser | The purpose of this class is to translate GML into an object tree, and print out an object tree into GML | Class | cytoscape.data.readers | CytoScape |
| GMLReader | This class is responsible for converting a gml object tree into cytoscape objects New features to the current version: 1. | Class | cytoscape.data.readers | CytoScape |
| GMLTag | enum GMLTagextends Enum | Class | cytoscape.data.readers | CytoScape |
| GMLTree | This class wraps around GMLNode and provides various methods for constructing a tree structure given other data. | Class | cytoscape.data.readers | CytoScape |
| GMLWriter | The 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 a | Class | cytoscape.data.readers | CytoScape |
| GOTerm | A Gene Ontology term. | Class | cytoscape.data.ontology | CytoScape |
| GraphReader | Interface for Reading in Cytoscape Graphs. | Interface | cytoscape.data.readers | CytoScape |
| ImportHandler | Central registry for all Cytoscape import classes. | Class | cytoscape.data | CytoScape |
| Interaction | Interaction. | Class | cytoscape.data | CytoScape |
| InteractionsReader | Reader for graphs in the interactions file format. | Class | cytoscape.data.readers | CytoScape |
| InteractionWriter | A few utility methods to assist in writing SIF files. | Class | cytoscape.data.writers | CytoScape |
| KeyValue | Key and Value pair in GML file. | Class | cytoscape.data.readers | CytoScape |
| loadAnnotation | load an annotation into an rmi biodata server. | Class | cytoscape.data.servers | CytoScape |
| loadAnnotationFromFlatFiles | load an annotation into an rmi biodata server. | Class | cytoscape.data.servers | CytoScape |
| loadThesaurus | load an thesaurus into an rmi biodata server. | Class | cytoscape.data.servers | CytoScape |
| MetadataEntries | enum MetadataEntriesextends Enum | Class | cytoscape.data.readers | CytoScape |
| MetadataParser | Manipulates network metadata for loading and saving. | Class | cytoscape.data.readers | CytoScape |
| mRNAMeasurement | Class | cytoscape.data | CytoScape | |
| MultiHashMap | This interface consists of the API specification to bind attribute values to objects. | Interface | cytoscape.data.attr | CytoScape |
| MultiHashMapDefinition | This interface contains the API specification for creating attribute definitions. | Interface | cytoscape.data.attr | CytoScape |
| MultiHashMapDefinitionListener | Interface | cytoscape.data.attr | CytoScape | |
| MultiHashMapFactory | This class provides access to implementations of MultiHashMap and MultiHashMapDefinition. | Class | cytoscape.data.attr.util | CytoScape |
| MultiHashMapHelpers | This class contains static utilitarian methods that return information pertaining to attributes. | Class | cytoscape.data.attr.util | CytoScape |
| MultiHashMapListener | Interface | cytoscape.data.attr | CytoScape | |
| NestedNetworkReader | Special interface for Graph readers which read nested networks from a file. | Interface | cytoscape.data.readers | CytoScape |
| NetworkData | There is an event fired anytime that a value is modified, you need to be listener to the attribute name though. | Class | cytoscape.data | CytoScape |
| NetworkExpansionMenu | Class | cytoscape.data.webservice.util | CytoScape | |
| NetworkImportWebServiceClient | Interface | cytoscape.data.webservice | CytoScape | |
| NNFParser | Parser for NNF files. | Class | cytoscape.data.readers | CytoScape |
| NNFReader | Graph file reader for NNF files. | Class | cytoscape.data.readers | CytoScape |
| OBOFlatFileReader | This is a general OBO (Open Biomedical Ontologies: http://obo. | Class | cytoscape.data.ontology.readers | CytoScape |
| OBOHeaderTags | enum OBOHeaderTagsextends Enum | Class | cytoscape.data.ontology.readers | CytoScape |
| OBOTags | enum OBOTagsextends Enum | Class | cytoscape.data.ontology.readers | CytoScape |
| Ontology | Contains a collection of OntologyTerms, each of which may have pointers to other terms, creating a hierarchical controlled vocabulary. | Class | cytoscape.data.annotation | CytoScape |
| Ontology | General Ontology class which implements interface from BioJava project. | Class | cytoscape.data.ontology | CytoScape |
| OntologyDescription | Distinguish among different ontologies, by curator and type. | Class | cytoscape.data.annotation | CytoScape |
| OntologyFactory | Class | cytoscape.data.ontology | CytoScape | |
| OntologyFlatFileReader | Class | cytoscape.data.annotation.readers | CytoScape | |
| OntologyReader | Interface for all ontology file readers. | Interface | cytoscape.data.ontology.readers | CytoScape |
| OntologyServer | Ontology Server which manages ontologies, aliases, and bookmarks. | Class | cytoscape.data.servers | CytoScape |
| OntologyServer .OntologyType | Class | cytoscape.data.servers | CytoScape | |
| OntologyTerm | Represents one node in an ontology, which is a hierarchical classification of entities using a controlled vocabulary. | Class | cytoscape.data.annotation | CytoScape |
| OntologyTerm | Simple in-memory implementation of an ontology term based on BioJava's This implementation uses CyNetwork and CyAttributes as its actual data | Class | cytoscape.data.ontology | CytoScape |
| OntologyTerm .SynonymType | Class | cytoscape.data.ontology | CytoScape | |
| OntologyXmlReader | Class | cytoscape.data.annotation.readers | CytoScape | |
| SelectEvent | Events that are fired when the selected state of a Node or Edge, or a group of Nodes or Edges, is changed. | Class | cytoscape.data | CytoScape |
| SelectEventListener | Listener for SelectEvents fired by a SelectFilter object. | Interface | cytoscape.data | CytoScape |
| SelectFilter | This class implements the ability to set the selected state of every node or edge in a GraphPerspective. | Class | cytoscape.data | CytoScape |
| Semantics | This class defines names for certain data attributes that are commonly used within Cytoscape. | Class | cytoscape.data | CytoScape |
| status | Class | cytoscape.data.servers | CytoScape | |
| TextFileReader | Class | cytoscape.data.readers | CytoScape | |
| TextHttpReader | Class | cytoscape.data.readers | CytoScape | |
| TextJarReader | Class | cytoscape.data.readers | CytoScape | |
| Thesaurus | todo (pshannon, 25 oct 2002): there may be multiple canonicalNames for the same common name. | Class | cytoscape.data.synonyms | CytoScape |
| ThesaurusFlatFileReader | Read synonyms from flat file. | Class | cytoscape.data.synonyms.readers | CytoScape |
| Triple | Extract partial graph structure. | Class | cytoscape.data.ontology | CytoScape |
| UnifiedNetworkImportDialog | Default GUI component for network import web service clients. | Class | cytoscape.data.webservice.ui | CytoScape |
| VisualStyleBuilder | Based on the graph/node/edge view information, build new Visual Style. | Class | cytoscape.data.readers | CytoScape |
| WebServiceClient | Web service client wrapper for Cytoscape. | Interface | cytoscape.data.webservice | CytoScape |
| WebServiceClientGUI | Web service client which has custom component should implements this interface. | Interface | cytoscape.data.webservice.ui | CytoScape |
| WebServiceClientGUI .IconSize | Class | cytoscape.data.webservice.ui | CytoScape | |
| WebServiceClientImpl | Abstract class for all web service clients. | Class | cytoscape.data.webservice | CytoScape |
| WebServiceClientImplWithGUI | Class | cytoscape.data.webservice | CytoScape | |
| WebServiceClientManager | Web Service Client Manager manages available web service clients in Cytoscape. | Class | cytoscape.data.webservice | CytoScape |
| WebServiceClientManager .ClientType | ClientType defines types/characteristics of the web service clients. | Class | cytoscape.data.webservice | CytoScape |
| WebServiceContextMenu | Context menu for web service clients. | Class | cytoscape.data.webservice.ui | CytoScape |
| WebServiceContextMenuListener | Class | cytoscape.data.webservice.ui | CytoScape | |
| WebServiceThemeInstall | Class | cytoscape.data.webservice.util | CytoScape | |
| WSImportResultDialog | Class | cytoscape.data.webservice.ui | CytoScape | |
| XGMMLException | Exception for XGMML Reader. | Class | cytoscape.data.readers | CytoScape |
| XGMMLReader | This version is Metanode-compatible. | Class | cytoscape.data.readers | CytoScape |
| XGMMLWriter | Write network and attributes in XGMML format and marshall it in a streme. | Class | cytoscape.data.writers | CytoScape |