cytoscape.data.readers
Class XGMMLReader

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

All Implemented Interfaces:

GraphReader

public class XGMMLReader
extends Object
implements GraphReader

XGMMLReader. This version is Metanode-compatible.

Author:

kono

Field Summary

protected static String	BOOLEAN_TYPE
protected static String	COMPLEX_TYPE
protected static String	DIAMOND
protected static String	EDGE
protected static String	ELLIPSE
protected static String	FLOAT_TYPE
protected static String	GRAPH
protected static String	GRAPHICS
protected static String	HEXAGON
protected static String	INT_TYPE
protected static String	LABEL
protected static String	LINE
protected static String	LIST_TYPE
protected static String	MAP_TYPE
protected static String	NODE
protected static String	OCTAGON
protected static String	PARALELLOGRAM
protected static String	POINT
protected static String	RECTANGLE
protected static String	SOURCE
protected static String	STRING_TYPE
protected static String	TARGET
protected static String	TRIANGLE

Constructor Summary

XGMMLReader(InputStream is)

XGMMLReader(InputStream is, List view)

XGMMLReader(String fileName)

Method Summary

protected void	createGraph(Graph network) Create graph directly from JAXB objects
Color	getBackgroundColor()
Color	getColor(String colorString)
CyAttributes	getEdgeAttributes()
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()
RdfRDF	getNetworkMetadata()
String	getNetworkName()
CyAttributes	getNodeAttributes()
int[]	getNodeIndicesArray() Part of interface contract
giny.model.RootGraph	getRootGraph()
void	layout(giny.view.GraphView myView) Based on the graphic attribute, layout the graph.
protected void	layoutEdge(giny.view.GraphView myView)
protected void	layoutEdgeGraphics(giny.view.GraphView myView, Graphics graphics, giny.view.EdgeView edgeView)
protected void	layoutNode(giny.view.GraphView myView) Layout nodes
protected void	layoutNodeGraphics(giny.view.GraphView myView, Graphics graphics, giny.view.NodeView nodeView)
void	read()
void	read(boolean canonicalizeNodeNames)
protected void	readAttributes()
protected void	readEdge()
void	readIndex()
protected void	readNode()

Methods inherited from class java.lang.Object

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

Field Detail

GRAPH

protected static String GRAPH

NODE

protected static String NODE

EDGE

protected static String EDGE

GRAPHICS

protected static String GRAPHICS

LABEL

protected static String LABEL

SOURCE

protected static String SOURCE

TARGET

protected static String TARGET

RECTANGLE

protected static String RECTANGLE

ELLIPSE

protected static String ELLIPSE

LINE

protected static String LINE

POINT

protected static String POINT

DIAMOND

protected static String DIAMOND

HEXAGON

protected static String HEXAGON

OCTAGON

protected static String OCTAGON

PARALELLOGRAM

protected static String PARALELLOGRAM

TRIANGLE

protected static String TRIANGLE

FLOAT_TYPE

protected static final String FLOAT_TYPE

See Also:

Constant Field Values

INT_TYPE

protected static final String INT_TYPE

See Also:

Constant Field Values

STRING_TYPE

protected static final String STRING_TYPE

See Also:

Constant Field Values

LIST_TYPE

protected static final String LIST_TYPE

See Also:

Constant Field Values

BOOLEAN_TYPE

protected static final String BOOLEAN_TYPE

See Also:

Constant Field Values

MAP_TYPE

protected static final String MAP_TYPE

See Also:

Constant Field Values

COMPLEX_TYPE

protected static final String COMPLEX_TYPE

See Also:

Constant Field Values

Constructor Detail

XGMMLReader

public XGMMLReader(String fileName)

XGMMLReader

public XGMMLReader(InputStream is)

XGMMLReader

public XGMMLReader(InputStream is,
                   List view)

Method Detail

readIndex

public void readIndex()
               throws javax.xml.bind.JAXBException,
                      FileNotFoundException

Throws:

javax.xml.bind.JAXBException

FileNotFoundException

read

public void read()
          throws IOException

Specified by:

read in interface GraphReader

Throws:

IOException

createGraph

protected void createGraph(Graph network)

Create graph directly from JAXB objects

Parameters:

network -

getMetanodeList

public List getMetanodeList()

readAttributes

protected void readAttributes()

readNode

protected void readNode()

readEdge

protected void readEdge()

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(giny.view.GraphView myView)

Based on the graphic attribute, layout the graph.

Specified by:

layout in interface GraphReader

Parameters:

myView -

layoutNode

protected void layoutNode(giny.view.GraphView myView)

Layout nodes

layoutNodeGraphics

protected void layoutNodeGraphics(giny.view.GraphView myView,
                                  Graphics graphics,
                                  giny.view.NodeView nodeView)

layoutEdge

protected void layoutEdge(giny.view.GraphView myView)

layoutEdgeGraphics

protected void layoutEdgeGraphics(giny.view.GraphView myView,
                                  Graphics graphics,
                                  giny.view.EdgeView edgeView)

getNodeIndicesArray

public int[] getNodeIndicesArray()

Part of interface contract

Specified by:

getNodeIndicesArray in interface GraphReader

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Part of interace contract

Specified by:

getEdgeIndicesArray in interface GraphReader

getNetworkID

public String getNetworkID()

getNetworkName

public String getNetworkName()

getNetworkMetadata

public RdfRDF getNetworkMetadata()

getColor

public Color getColor(String colorString)

getBackgroundColor

public Color getBackgroundColor()

read

public void read(boolean canonicalizeNodeNames)
          throws IOException

Specified by:

read in interface GraphReader

Throws:

IOException

getRootGraph

public giny.model.RootGraph getRootGraph()

Specified by:

getRootGraph in interface GraphReader

getNodeAttributes

public CyAttributes getNodeAttributes()

Specified by:

getNodeAttributes in interface GraphReader

getEdgeAttributes

public CyAttributes getEdgeAttributes()

Specified by:

getEdgeAttributes in interface GraphReader