cytoscape.data.readers
Class GMLReader

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

All Implemented Interfaces:

GraphReader

public class GMLReader
extends AbstractGraphReader

This class is responsible for converting a gml object tree into cytoscape objects New features to the current version: 1. Small bug fixes. 2. Translate all features in the GML file. This includes 3. New Visual Style will be generated when you call this class. The new style saves all visual features (like node shape) and will not be lost even after other style selected.

Field Summary

protected static String	ARROW
protected static String	ARROW_BOTH
protected static String	ARROW_FIRST
protected static String	ARROW_LAST
protected static String	ARROW_NONE
protected static String	COMMENT
protected static String	CREATOR
protected static String	CURVED_LINES
protected static String	DEFAULT_EDGE_INTERACTION
protected static String	DIAMOND
protected static String	EDGE
protected static String	ELLIPSE
protected static String	FILL
protected static String	GRAPH
protected static String	GRAPHICS
protected static String	H
protected static String	HEXAGON
protected static String	ID The following are all taken to be reserved keywords for gml (note that not all of them are actually keywords according to the spec) Currently, only keywords below are supported by the Visual Style generation methods.
protected static String	LABEL
protected static String	LINE
protected static String	NAME
protected static String	NODE
protected static String	OCTAGON
protected static String	OUTLINE
protected static String	OUTLINE_WIDTH
protected static String	PARALELLOGRAM
protected static String	POINT
protected static String	RECTANGLE
protected static String	ROOT_INDEX
protected static String	SOURCE
protected static String	SOURCE_ARROW
protected static String	STRAIGHT_LINES
protected static String	TARGET
protected static String	TARGET_ARROW
protected static String	TITLE
protected static String	TRIANGLE
protected static String	TYPE
protected static String	VERSION
protected static String	W
protected static String	WIDTH
protected static String	X
protected static String	Y
protected static String	YED_DELTA
protected static String	YED_DIAMOND
protected static String	YED_SHORT
protected static String	YED_SOURCE_ARROW
protected static String	YED_STANDARD
protected static String	YED_TARGET_ARROW
protected static String	YED_WHITE_DELTA
protected static String	YED_WHITE_DIAMOND

Fields inherited from class cytoscape.data.readers.AbstractGraphReader

fileName, title

Constructor Summary

GMLReader(InputStream is, String name)
Constructor.
This is usually used for remote file loading.

GMLReader(String filename)
Constructor.

GMLReader(String filename, TaskMonitor taskMonitor)
Constructor.

Method Summary

protected void	createGraph() This will create the graph model objects.
void	doPostProcessing(CyNetwork net) DOCUMENT ME!
void	extract() DOCUMENT ME!
protected void	extractEdge(List<KeyValue> list, String edgeName)
protected void	extractEdgeAttributes(List<KeyValue> list, String edgeName)
protected void	extractGraph(List list)
protected void	extractNode(List list)
protected void	extractNodeAttributes(List list, String nodeName)
Color	getColor(String colorString) Create a color object from the string like it is stored in a gml file
int[]	getEdgeIndicesArray() Part of interace contract
CyLayoutAlgorithm	getLayoutAlgorithm() getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph.
List<KeyValue>	getList() Returns a list containing the gml object tree
int[]	getNodeIndicesArray() Part of interface contract
protected void	initializeStructures()
void	layout(CyNetworkView myView) layout the graph based on the GML values we read
protected void	layoutEdge(GraphView myView, List list, String edgeName) Assign edge visual properties based on pairs in the list matched to the "edge" key world
protected void	layoutEdgeGraphics(GraphView myView, List<KeyValue> list, EdgeView edgeView) Assign edge graphics properties
protected void	layoutEdgeGraphicsLine(GraphView myView, List list, EdgeView edgeView) Assign bend points based on the contents of the list associated with a "Line" key We make sure that there is both an x,y present in the underlying point list before trying to generate a bend point
protected void	layoutGraph(GraphView myView, List list) Lays Out the Graph, based on GML.
protected void	layoutNode(GraphView myView, List list) Assign node properties based on the values in the list matched to the "node" key.
protected void	layoutNodeGraphics(GraphView myView, List list, NodeView nodeView) This will assign node graphic properties based on the values in the list matches to the "graphics" key word
void	read() Read GML file contents
protected void	readEdge(List<KeyValue> list) This will extract the model information from the list which is matched to an "edge" key.
protected void	readGML(List<KeyValue> list) This function takes the root level list which defines a gml objec tree
protected void	readGraph(List<KeyValue> list) This function takes in a list which was given as the value to a "graph" key underneath the main gml list
protected void	releaseStructures()
void	setTaskMonitor(TaskMonitor monitor) Sets the task monitor we want to use
void	showMaps() DOCUMENT ME!

Methods inherited from class cytoscape.data.readers.AbstractGraphReader

getNetworkName

Methods inherited from class java.lang.Object

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

Field Detail

ID

protected static final String ID

The following are all taken to be reserved keywords for gml (note that not all of them are actually keywords according to the spec) Currently, only keywords below are supported by the Visual Style generation methods. (Maybe we need some documents on "cytoscape-style" GML format...)

See Also:

Constant Field Values

NAME

protected static final String NAME

See Also:

Constant Field Values

LABEL

protected static final String LABEL

See Also:

Constant Field Values

COMMENT

protected static final String COMMENT

See Also:

Constant Field Values

VERSION

protected static final String VERSION

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Constant Field Values

CREATOR

protected static final String CREATOR

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Constant Field Values

TITLE

protected static final String TITLE

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Constant Field Values

GRAPH

protected static final String GRAPH

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Constant Field Values

NODE

protected static final String NODE

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Constant Field Values

EDGE

protected static final String EDGE

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Constant Field Values

GRAPHICS

protected static final String GRAPHICS

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Constant Field Values

SOURCE

protected static final String SOURCE

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TARGET

protected static final String TARGET

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Constant Field Values

X

protected static final String X

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Y

protected static final String Y

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Constant Field Values

H

protected static final String H

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W

protected static final String W

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TYPE

protected static final String TYPE

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Constant Field Values

ROOT_INDEX

protected static final String ROOT_INDEX

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Constant Field Values

RECTANGLE

protected static final String RECTANGLE

See Also:

Constant Field Values

ELLIPSE

protected static final String ELLIPSE

See Also:

Constant Field Values

LINE

protected static final String LINE

See Also:

Constant Field Values

POINT

protected static final String POINT

See Also:

Constant Field Values

DIAMOND

protected static final String DIAMOND

See Also:

Constant Field Values

HEXAGON

protected static final String HEXAGON

See Also:

Constant Field Values

OCTAGON

protected static final String OCTAGON

See Also:

Constant Field Values

PARALELLOGRAM

protected static final String PARALELLOGRAM

See Also:

Constant Field Values

TRIANGLE

protected static final String TRIANGLE

See Also:

Constant Field Values

FILL

protected static final String FILL

See Also:

Constant Field Values

WIDTH

protected static final String WIDTH

See Also:

Constant Field Values

STRAIGHT_LINES

protected static final String STRAIGHT_LINES

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Constant Field Values

CURVED_LINES

protected static final String CURVED_LINES

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Constant Field Values

SOURCE_ARROW

protected static final String SOURCE_ARROW

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TARGET_ARROW

protected static final String TARGET_ARROW

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Constant Field Values

YED_SOURCE_ARROW

protected static final String YED_SOURCE_ARROW

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Constant Field Values

YED_TARGET_ARROW

protected static final String YED_TARGET_ARROW

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Constant Field Values

YED_DELTA

protected static final String YED_DELTA

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Constant Field Values

YED_STANDARD

protected static final String YED_STANDARD

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Constant Field Values

YED_DIAMOND

protected static final String YED_DIAMOND

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Constant Field Values

YED_SHORT

protected static final String YED_SHORT

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Constant Field Values

YED_WHITE_DELTA

protected static final String YED_WHITE_DELTA

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Constant Field Values

YED_WHITE_DIAMOND

protected static final String YED_WHITE_DIAMOND

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ARROW

protected static final String ARROW

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Constant Field Values

ARROW_NONE

protected static final String ARROW_NONE

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Constant Field Values

ARROW_FIRST

protected static final String ARROW_FIRST

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ARROW_LAST

protected static final String ARROW_LAST

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Constant Field Values

ARROW_BOTH

protected static final String ARROW_BOTH

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Constant Field Values

OUTLINE

protected static final String OUTLINE

See Also:

Constant Field Values

OUTLINE_WIDTH

protected static final String OUTLINE_WIDTH

See Also:

Constant Field Values

DEFAULT_EDGE_INTERACTION

protected static final String DEFAULT_EDGE_INTERACTION

See Also:

Constant Field Values

Constructor Detail

GMLReader

public GMLReader(String filename)

Constructor.

Parameters:

filename - File name.

GMLReader

public GMLReader(InputStream is,
                 String name)

Constructor.
This is usually used for remote file loading.

Parameters:

is - Input stream of GML file,

GMLReader

public GMLReader(String filename,
                 TaskMonitor taskMonitor)

Constructor.

Parameters:

filename - File name.

taskMonitor - TaskMonitor Object.

Method Detail

setTaskMonitor

public void setTaskMonitor(TaskMonitor monitor)

Sets the task monitor we want to use

Overrides:

setTaskMonitor in class AbstractGraphReader

Parameters:

monitor - the TaskMonitor to use

read

public void read()

Read GML file contents

Specified by:

read in interface GraphReader

Specified by:

read in class AbstractGraphReader

getList

public List<KeyValue> getList()

Returns a list containing the gml object tree

initializeStructures

protected void initializeStructures()

releaseStructures

protected void releaseStructures()

createGraph

protected void createGraph()

This will create the graph model objects. This function expects node labels to be unique and edge labels to be unique between a particular source and target If this condition is not met, an error will be printed to the console, and the object will be skipped. That is, it is as though that particular object never existed in the gml file. If an edge depends on a node that was skipped, then that edge will be skipped as well.

readGML

protected void readGML(List<KeyValue> list)

This function takes the root level list which defines a gml objec tree

readGraph

protected void readGraph(List<KeyValue> list)

This function takes in a list which was given as the value to a "graph" key underneath the main gml list

readEdge

protected void readEdge(List<KeyValue> list)

This will extract the model information from the list which is matched to an "edge" key.

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 GML values we read

Parameters:

myView - the view of the network we want to layout

extract

public void extract()

DOCUMENT ME!

extractGraph

protected void extractGraph(List list)

extractNode

protected void extractNode(List list)

extractEdge

protected void extractEdge(List<KeyValue> list,
                           String edgeName)

layoutGraph

protected void layoutGraph(GraphView myView,
                           List list)

Lays Out the Graph, based on GML.

layoutNode

protected void layoutNode(GraphView myView,
                          List list)

Assign node properties based on the values in the list matched to the "node" key. Mostly just a wrapper around layoutNodeGraphics

layoutNodeGraphics

protected void layoutNodeGraphics(GraphView myView,
                                  List list,
                                  NodeView nodeView)

This will assign node graphic properties based on the values in the list matches to the "graphics" key word

extractNodeAttributes

protected void extractNodeAttributes(List list,
                                     String nodeName)

extractEdgeAttributes

protected void extractEdgeAttributes(List<KeyValue> list,
                                     String edgeName)

showMaps

public void showMaps()

DOCUMENT ME!

layoutEdge

protected void layoutEdge(GraphView myView,
                          List list,
                          String edgeName)

Assign edge visual properties based on pairs in the list matched to the "edge" key world

layoutEdgeGraphics

protected void layoutEdgeGraphics(GraphView myView,
                                  List<KeyValue> list,
                                  EdgeView edgeView)

Assign edge graphics properties

layoutEdgeGraphicsLine

protected void layoutEdgeGraphicsLine(GraphView myView,
                                      List list,
                                      EdgeView edgeView)

Assign bend points based on the contents of the list associated with a "Line" key We make sure that there is both an x,y present in the underlying point list before trying to generate a bend point

getNodeIndicesArray

public int[] getNodeIndicesArray()

Part of interface 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!

getColor

public Color getColor(String colorString)

Create a color object from the string like it is stored in a gml file

doPostProcessing

public void doPostProcessing(CyNetwork net)

DOCUMENT ME!

Specified by:

doPostProcessing in interface GraphReader

Overrides:

doPostProcessing in class AbstractGraphReader

Parameters:

net - DOCUMENT ME!