cytoscape.data.readers
Class XGMMLReader

java.lang.Object
  cytoscape.data.readers.AbstractGraphReader
      cytoscape.data.readers.XGMMLReader

All Implemented Interfaces:

GraphReader

public class XGMMLReader
extends AbstractGraphReader

XGMML file reader.
This version is Metanode-compatible.

Since:

Cytoscape 2.3

Version:

1.0

Author:

kono

See Also:

XGMMLWriter

Constructor Summary

XGMMLReader(InputStream is)
Constructor.

XGMMLReader(String fileName)
Constructor.

XGMMLReader(String fileName, cytoscape.task.TaskMonitor monitor)
Creates a new XGMMLReader object.

Method Summary

void	doPostProcessing(CyNetwork network) DOCUMENT ME!
Color	getBackgroundColor() DOCUMENT ME!
Color	getColor(String colorString) Convert a valid string into Color object.
int[]	getEdgeIndicesArray() Part of interace contract
Point2D	getGraphViewCenter() Returns the graph view center.
Double	getGraphViewZoomLevel() Returns the zoom level read from the the xgmml file.
List	getGroupList() DOCUMENT ME!
CyLayoutAlgorithm	getLayoutAlgorithm() getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph.
String	getNetworkID() DOCUMENT ME!
cytoscape.generated2.RdfRDF	getNetworkMetadata() DOCUMENT ME!
String	getNetworkName() DOCUMENT ME!
int[]	getNodeIndicesArray() Part of interace contract
void	layout(CyNetworkView myView) layout the graph based on the graphic attributes
void	read() DOCUMENT ME!
void	setNetworkAttributes(CyNetwork cyNetwork) This should be called after other classes actually creates CyNetwork object.

Methods inherited from class cytoscape.data.readers.AbstractGraphReader

layout

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

XGMMLReader

public XGMMLReader(String fileName)

Constructor.
This is for local XGMML file.

Parameters:

fileName - File name of local XGMML file.

Throws:

FileNotFoundException

XGMMLReader

public XGMMLReader(InputStream is)

Constructor.
This is usually used for remote file loading.

Parameters:

is - Input stream of XGMML file,

XGMMLReader

public XGMMLReader(String fileName,
                   cytoscape.task.TaskMonitor monitor)

Creates a new XGMMLReader object.

Parameters:

fileName - DOCUMENT ME!

monitor - DOCUMENT ME!

Method Detail

read

public void read()
          throws IOException

DOCUMENT ME!

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

Throws:

IOException - DOCUMENT ME!

getGroupList

public List getGroupList()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getGraphViewZoomLevel

public Double getGraphViewZoomLevel()

Returns the zoom level read from the the xgmml file.

Returns:

Double

getGraphViewCenter

public Point2D getGraphViewCenter()

Returns the graph view center.

Returns:

Double

getLayoutAlgorithm

public CyLayoutAlgorithm getLayoutAlgorithm()

getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph. In our case, we just return a stub that will call our internal layout routine, which will just use the default layout, but with our task monitor

Specified by:

getLayoutAlgorithm in interface GraphReader

Overrides:

getLayoutAlgorithm in class AbstractGraphReader

Returns:

the CyLayoutAlgorithm to use

layout

public void layout(CyNetworkView myView)

layout the graph based on the graphic attributes

Parameters:

myView - the view of the network we want to layout

getNodeIndicesArray

public int[] getNodeIndicesArray()

Part of interace contract

Specified by:

getNodeIndicesArray in interface GraphReader

Overrides:

getNodeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Part of interace contract

Specified by:

getEdgeIndicesArray in interface GraphReader

Overrides:

getEdgeIndicesArray in class AbstractGraphReader

Returns:

DOCUMENT ME!

getNetworkID

public String getNetworkID()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getNetworkName

public String getNetworkName()

Description copied from class: AbstractGraphReader

DOCUMENT ME!

Specified by:

getNetworkName in interface GraphReader

Overrides:

getNetworkName in class AbstractGraphReader

Returns:

Returns the networkName.

getNetworkMetadata

public cytoscape.generated2.RdfRDF getNetworkMetadata()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getColor

public Color getColor(String colorString)

Convert a valid string into Color object.

Parameters:

colorString -

Returns:

Color object.

getBackgroundColor

public Color getBackgroundColor()

DOCUMENT ME!

Returns:

DOCUMENT ME!

setNetworkAttributes

public void setNetworkAttributes(CyNetwork cyNetwork)

This should be called after other classes actually creates CyNetwork object. Otherwise, Network ID mismatch problem occures between CyNetwork object and Network CyAttributes!

Parameters:

cyNetwork - CyNetwork object for the loaded network.

doPostProcessing

public void doPostProcessing(CyNetwork network)

DOCUMENT ME!

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader

Parameters:

network - DOCUMENT ME!