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)

Method Summary

void	doPostProcessing(CyNetwork network) Executes post-processing: no-op.
Color	getBackgroundColor()
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	getMetanodeList()
String	getNetworkID()
cytoscape.generated2.RdfRDF	getNetworkMetadata()
String	getNetworkName() Gets the name of the network.
int[]	getNodeIndicesArray() Part of interace contract
void	layout(GraphView myView) Based on the graphic attributes, layout the graph.
void	read() Reads/imports the graph.
void	setNetworkAttributes(CyNetwork cyNetwork) This should be called after other classes actually creates CyNetwork object.

Methods inherited from class cytoscape.data.readers.AbstractGraphReader

getEdgeAttributes, getNodeAttributes, getRootGraph, read

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)

Method Detail

read

public void read()
          throws IOException

Description copied from interface: GraphReader

Reads/imports the graph.

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

Throws:

IOException - IO Errors.

getMetanodeList

public List getMetanodeList()

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

layout

public void layout(GraphView myView)

Based on the graphic attributes, layout the graph.

Specified by:

layout in interface GraphReader

Overrides:

layout in class AbstractGraphReader

Parameters:

myView - GINY's graph view object.

getNodeIndicesArray

public int[] getNodeIndicesArray()

Part of interace contract

Specified by:

getNodeIndicesArray in interface GraphReader

Overrides:

getNodeIndicesArray in class AbstractGraphReader

Returns:

array of node indices from the root graph.

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Part of interace contract

Specified by:

getEdgeIndicesArray in interface GraphReader

Overrides:

getEdgeIndicesArray in class AbstractGraphReader

Returns:

array of edges indices from the root graph.

getNetworkID

public String getNetworkID()

getNetworkName

public String getNetworkName()

Description copied from interface: GraphReader

Gets the name of the network.

Specified by:

getNetworkName in interface GraphReader

Overrides:

getNetworkName in class AbstractGraphReader

Returns:

Returns the networkName.

getNetworkMetadata

public cytoscape.generated2.RdfRDF getNetworkMetadata()

getColor

public Color getColor(String colorString)

Convert a valid string into Color object.

Parameters:

colorString -

Returns:

Color object.

getBackgroundColor

public Color getBackgroundColor()

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)

Description copied from class: AbstractGraphReader

Executes post-processing: no-op.

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader