Package org.cytoscape.io.read

Class AbstractCyNetworkReader

java.lang.Object

org.cytoscape.work.AbstractTask

org.cytoscape.io.read.AbstractCyNetworkReader

All Implemented Interfaces:

CyNetworkReader, Task

public abstract class AbstractCyNetworkReader
extends AbstractTask
implements CyNetworkReader

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>

Field Summary

Fields

Modifier and Type	Field	Description
protected CyApplicationManager	cyApplicationManager
protected final CyNetworkFactory	cyNetworkFactory	Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork.
protected final CyNetworkViewFactory	cyNetworkViewFactory	Will be used for creating network views.
protected InputStream	inputStream	Data stream for the networks to be created.
protected CyNetwork[]	networks	Array of networks to be returned.

Fields inherited from class org.cytoscape.work.AbstractTask

cancelled

Constructor Summary

Constructors

Constructor	Description
AbstractCyNetworkReader(InputStream inputStream, CyApplicationManager cyApplicationManager, CyNetworkFactory cyNetworkFactory, CyNetworkManager cyNetworkManager, CyRootNetworkManager cyRootNetworkManager)
AbstractCyNetworkReader(InputStream inputStream, CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory cyNetworkFactory, CyNetworkManager cyNetworkManager, CyRootNetworkManager cyRootNetworkManager)

Method Summary

Modifier and Type	Method	Description
CyNetwork[]	getNetworks()	Returns an array of networks read after executing the run() method of Task.
protected CyNetworkViewFactory	getNetworkViewFactory()
ListSingleSelection<NetworkViewRenderer>	getNetworkViewRendererList()
protected Map<Object,CyNode>	getNodeMap()	Returns map from key value to existing CyNode.
protected final CyRootNetwork	getRootNetwork()	Get target network collection, i.e., parent root network for all networks to be loaded.
ListSingleSelection<String>	getRootNetworkList()
ListSingleSelection<String>	getTargetColumnList()
String	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

Methods inherited from interface org.cytoscape.work.Task

cancel, run

Field Details

inputStream

protected InputStream inputStream

Data stream for the networks to be created.

networks

protected CyNetwork[] networks

Array of networks to be returned.

cyNetworkViewFactory

protected final CyNetworkViewFactory cyNetworkViewFactory

Will be used for creating network views.

cyNetworkFactory

protected final CyNetworkFactory cyNetworkFactory

Will be used to create new CySubNetwork if this reader needs to create new CyRootNetwork.

cyApplicationManager

protected CyApplicationManager cyApplicationManager

Constructor Details

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)

Method Details

getTitle

public String getTitle()

getRootNetworkList

public ListSingleSelection<String> getRootNetworkList()

setRootNetworkList

public void setRootNetworkList(ListSingleSelection<String> roots)

getTargetColumnList

public ListSingleSelection<String> getTargetColumnList()

setTargetColumnList

public void setTargetColumnList(ListSingleSelection<String> colList)

getNetworkViewRendererList

public ListSingleSelection<NetworkViewRenderer> getNetworkViewRendererList()

setNetworkViewRendererList

public void setNetworkViewRendererList(ListSingleSelection<NetworkViewRenderer> rendererList)

getNetworks

public CyNetwork[] getNetworks()

Description copied from interface: CyNetworkReader

Returns an array of networks read after executing the run() method of Task.

Specified by:

getNetworks in interface CyNetworkReader

Returns:

an array of networks read after executing the run() method of Task.

getRootNetwork

protected final CyRootNetwork 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.

getNodeMap

protected Map<Object,CyNode> getNodeMap()

Returns map from key value to existing CyNode.

Returns:

getNetworkViewFactory

protected CyNetworkViewFactory getNetworkViewFactory()