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