C G N O R T V W

C

checkedRun(TaskMonitor) - Method in class org.wikipathways.cytoscapeapp.ResultTask

Run the task and return its result.

create() - Method in interface org.wikipathways.cytoscapeapp.WPClientFactory

Create a new WikiPathways client.

createReader(Reader, CyNetwork, GpmlConversionMethod, boolean) - Method in interface org.wikipathways.cytoscapeapp.GpmlReaderFactory

Creates a task iterator that reads the GPML pathway from gpmlContents and builds the converted GPML pathway in the given network.

createReaderAndViewBuilder(Reader, CyNetworkView, GpmlConversionMethod, boolean) - Method in interface org.wikipathways.cytoscapeapp.GpmlReaderFactory

Creates a task iterator that reads the GPML pathway from gpmlContents, builds the converted GPML pathway, and builds the network view.

createReaderAndViewBuilder(Reader, GpmlConversionMethod) - Method in interface org.wikipathways.cytoscapeapp.GpmlReaderFactory

Creates a task iterator that reads the GPML pathway from gpmlContents, builds the converted GPML pathway, and builds the network view.

createViewBuilder(CyNetwork, CyNetworkView) - Method in interface org.wikipathways.cytoscapeapp.GpmlReaderFactory

Creates a task iterator that builds the network view for a network that contains a GPML pathway.

G

get() - Method in class org.wikipathways.cytoscapeapp.ResultTask

Return the result that checkedRun returned.

getId() - Method in class org.wikipathways.cytoscapeapp.WPPathway

getName() - Method in class org.wikipathways.cytoscapeapp.WPPathway

getRevision() - Method in class org.wikipathways.cytoscapeapp.WPPathway

getSpecies() - Method in class org.wikipathways.cytoscapeapp.WPPathway

getUrl() - Method in class org.wikipathways.cytoscapeapp.WPPathway

GpmlConversionMethod - Enum in org.wikipathways.cytoscapeapp

Used in GpmlReaderFactory to specify how GPML pathways are converted to Cytoscape networks.

GpmlReaderFactory - Interface in org.wikipathways.cytoscapeapp

Creates TaskIterators for reading a GPML document and converting it to a Cytoscape network.

N

newFreeTextSearchTask(String, String) - Method in interface org.wikipathways.cytoscapeapp.WPClient

Return a task that searches WikiPathways for pathways that match the given query.

newGPMLContentsTask(WPPathway) - Method in interface org.wikipathways.cytoscapeapp.WPClient

Return a task that provides the Reader containing the GPML contents of pathway.

newPathwayInfoTask(String) - Method in interface org.wikipathways.cytoscapeapp.WPClient

Return a task that retrieves pathway info for a given pathway ID.

newSpeciesTask() - Method in interface org.wikipathways.cytoscapeapp.WPClient

Return a task that retrieves the list of species recognized by WikiPathways.

O

org.wikipathways.cytoscapeapp - package org.wikipathways.cytoscapeapp

R

result - Variable in class org.wikipathways.cytoscapeapp.ResultTask

ResultTask<T> - Class in org.wikipathways.cytoscapeapp

Specifies a task that can return a result.

ResultTask() - Constructor for class org.wikipathways.cytoscapeapp.ResultTask

run(TaskMonitor) - Method in class org.wikipathways.cytoscapeapp.ResultTask

T

toString() - Method in class org.wikipathways.cytoscapeapp.WPPathway

V

valueOf(String) - Static method in enum org.wikipathways.cytoscapeapp.GpmlConversionMethod

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.wikipathways.cytoscapeapp.GpmlConversionMethod

Returns an array containing the constants of this enum type, in the order they are declared.

W

WPClient - Interface in org.wikipathways.cytoscapeapp

Issues requests to WikiPathways.

WPClientFactory - Interface in org.wikipathways.cytoscapeapp

Used as an OSGi service to create new WikiPathways clients.

WPPathway - Class in org.wikipathways.cytoscapeapp

Represents a pathway on WikiPathways.

WPPathway(String, String, String, String, String) - Constructor for class org.wikipathways.cytoscapeapp.WPPathway

C G N O R T V W