Package org.cytoscape.io.read
Class AbstractCyNetworkReader
java.lang.Object
org.cytoscape.work.AbstractTask
org.cytoscape.io.read.AbstractCyNetworkReader
- All Implemented Interfaces:
CyNetworkReader
,Task
Cytoscape Backwards Compatibility (SPI Interface): We expect that this interface will be implemented. Therefore to maintain backwards compatibility this interface will only be modified for major version updates.
Module: io-api
To use this in your app, include the following dependency in your POM:
<dependency> <groupId>org.cytoscape</groupId> <artifactId>io-api</artifactId> </dependency>
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Field Summary
Modifier and TypeFieldDescriptionprotected CyApplicationManager
protected CyNetworkFactory
Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork.protected CyNetworkViewFactory
Will be used for creating network views.protected InputStream
Data stream for the networks to be created.protected CyNetwork[]
Array of networks to be returned.Fields inherited from class org.cytoscape.work.AbstractTask
cancelled
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Constructor Summary
ConstructorDescriptionAbstractCyNetworkReader(InputStream inputStream, CyApplicationManager cyApplicationManager, CyNetworkFactory cyNetworkFactory, CyNetworkManager cyNetworkManager, CyRootNetworkManager cyRootNetworkManager)
AbstractCyNetworkReader(InputStream inputStream, CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory cyNetworkFactory, CyNetworkManager cyNetworkManager, CyRootNetworkManager cyRootNetworkManager)
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Method Summary
Modifier and TypeMethodDescriptionReturns an array of networks read after executing the run() method ofTask
.protected CyNetworkViewFactory
Returns map from key value to existing CyNode.protected CyRootNetwork
Get target network collection, i.e., parent root network for all networks to be loaded.getTitle()
void
setNetworkViewRendererList(ListSingleSelection<NetworkViewRenderer> rendererList)
void
setRootNetworkList(ListSingleSelection<String> roots)
void
setTargetColumnList(ListSingleSelection<String> colList)
Methods inherited from class org.cytoscape.work.AbstractTask
cancel, getTaskIterator, insertTasksAfterCurrentTask, insertTasksAfterCurrentTask, run, setTaskIterator
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.cytoscape.io.read.CyNetworkReader
buildCyNetworkView
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Field Details
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inputStream
Data stream for the networks to be created. -
networks
Array of networks to be returned. -
cyNetworkViewFactory
Will be used for creating network views. -
cyNetworkFactory
Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork. -
cyApplicationManager
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Constructor Details
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AbstractCyNetworkReader
public AbstractCyNetworkReader(InputStream inputStream, CyApplicationManager cyApplicationManager, CyNetworkFactory cyNetworkFactory, CyNetworkManager cyNetworkManager, CyRootNetworkManager cyRootNetworkManager) -
AbstractCyNetworkReader
public AbstractCyNetworkReader(InputStream inputStream, CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory cyNetworkFactory, CyNetworkManager cyNetworkManager, CyRootNetworkManager cyRootNetworkManager)
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Method Details
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getTitle
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getRootNetworkList
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setRootNetworkList
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getTargetColumnList
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setTargetColumnList
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getNetworkViewRendererList
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setNetworkViewRendererList
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getNetworks
Description copied from interface:CyNetworkReader
Returns an array of networks read after executing the run() method ofTask
.- Specified by:
getNetworks
in interfaceCyNetworkReader
- Returns:
- an array of networks read after executing the run() method of
Task
.
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getRootNetwork
Get target network collection, i.e., parent root network for all networks to be loaded.- Returns:
- Root network for this network collection. If there is no such root, returns null.
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getNodeMap
Returns map from key value to existing CyNode.- Returns:
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getNetworkViewFactory
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