cytoscape.data.readers
Class GMLReader2

java.lang.Object
  cytoscape.data.readers.GMLReader2

All Implemented Interfaces:

GraphReader

public class GMLReader2
extends Object
implements GraphReader

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	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 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	GRAPHICS
protected static String	H
protected static String	HEXAGON
protected static String	ID
protected static String	LABEL
protected static String	LINE
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	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

Constructor Summary

GMLReader2(String filename)
Constructor.

GMLReader2(String filename, cytoscape.task.TaskMonitor taskMonitor)
Constructor.

Method Summary

void	applyMaps(String mapSuffix, String VSName)
protected void	createGraph() This will create the graph model objects.
void	extract()
protected void	extractEdge(List list, String edgeName)
protected void	extractEdgeAttributes(List 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
CyAttributes	getEdgeAttributes()
int[]	getEdgeIndicesArray() Part of interace contract
static LineType	getLineType(int width)
List	getList() Returns a list containing the gml object tree
CyAttributes	getNodeAttributes()
int[]	getNodeIndicesArray() Part of interface contract
giny.model.RootGraph	getRootGraph()
protected void	initializeStructures()
void	layout(giny.view.GraphView myView)
protected void	layoutEdge(giny.view.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(giny.view.GraphView myView, List list, giny.view.EdgeView edgeView) Assign edge graphics properties
protected void	layoutEdgeGraphicsLine(giny.view.GraphView myView, List list, giny.view.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(giny.view.GraphView myView, List list) Lays Out the Graph, based on GML.
protected void	layoutNode(giny.view.GraphView myView, List list) Assign node properties based on the values in the list matched to the "node" key.
protected void	layoutNodeGraphics(giny.view.GraphView myView, List list, giny.view.NodeView nodeView) This will assign node graphic properties based on the values in the list matches to the "graphics" key word
void	read()
void	read(boolean canonicalize)
protected void	readEdge(List list) This will extract the model information from the list which is matched to an "edge" key.
protected void	readGML(List list) This function takes the root level list which defines a gml objec tree
protected void	readGraph(List list) This function takes in a list which was given as the value to a "graph" key underneath the main gml list
protected void	readNode(List list) This will extract the model information from the list which is matched a "node" key
protected void	releaseStructures()
void	setEdgeMaps(VisualMappingManager vizmapper)
void	setNodeMaps(VisualMappingManager vizmapper)
void	showMaps()

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

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...)

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

X

protected static String X

Y

protected static String Y

H

protected static String H

W

protected static String W

TYPE

protected static String TYPE

ID

protected static String ID

ROOT_INDEX

protected static String ROOT_INDEX

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

FILL

protected static String FILL

WIDTH

protected static String WIDTH

STRAIGHT_LINES

protected static String STRAIGHT_LINES

CURVED_LINES

protected static String CURVED_LINES

SOURCE_ARROW

protected static String SOURCE_ARROW

TARGET_ARROW

protected static String TARGET_ARROW

ARROW

protected static String ARROW

ARROW_NONE

protected static String ARROW_NONE

ARROW_FIRST

protected static String ARROW_FIRST

ARROW_LAST

protected static String ARROW_LAST

ARROW_BOTH

protected static String ARROW_BOTH

OUTLINE

protected static String OUTLINE

OUTLINE_WIDTH

protected static String OUTLINE_WIDTH

DEFAULT_EDGE_INTERACTION

protected static String DEFAULT_EDGE_INTERACTION

VERSION

protected static String VERSION

CREATOR

protected static String CREATOR

Constructor Detail

GMLReader2

public GMLReader2(String filename)

Constructor.

Parameters:

filename - File name.

GMLReader2

public GMLReader2(String filename,
                  cytoscape.task.TaskMonitor taskMonitor)

Constructor.

Parameters:

filename - File name.

taskMonitor - TaskMonitor Object.

Method Detail

setNodeMaps

public void setNodeMaps(VisualMappingManager vizmapper)

setEdgeMaps

public void setEdgeMaps(VisualMappingManager vizmapper)

applyMaps

public void applyMaps(String mapSuffix,
                      String VSName)

read

public void read(boolean canonicalize)

Specified by:

read in interface GraphReader

read

public void read()

Specified by:

read in interface GraphReader

getList

public List 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 list)

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

readGraph

protected void readGraph(List list)

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

readNode

protected void readNode(List list)

This will extract the model information from the list which is matched a "node" key

readEdge

protected void readEdge(List list)

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

layout

public void layout(giny.view.GraphView myView)

Specified by:

layout in interface GraphReader

extract

public void extract()

extractGraph

protected void extractGraph(List list)

extractNode

protected void extractNode(List list)

extractEdge

protected void extractEdge(List list,
                           String edgeName)

layoutGraph

protected void layoutGraph(giny.view.GraphView myView,
                           List list)

Lays Out the Graph, based on GML.

layoutNode

protected void layoutNode(giny.view.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(giny.view.GraphView myView,
                                  List list,
                                  giny.view.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 list,
                                     String edgeName)

getLineType

public static LineType getLineType(int width)

showMaps

public void showMaps()

layoutEdge

protected void layoutEdge(giny.view.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(giny.view.GraphView myView,
                                  List list,
                                  giny.view.EdgeView edgeView)

Assign edge graphics properties

layoutEdgeGraphicsLine

protected void layoutEdgeGraphicsLine(giny.view.GraphView myView,
                                      List list,
                                      giny.view.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

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Part of interace contract

Specified by:

getEdgeIndicesArray in interface GraphReader

getRootGraph

public giny.model.RootGraph getRootGraph()

Specified by:

getRootGraph in interface GraphReader

Returns:

null, there is no GML reader available outside of Y-Files right now

getNodeAttributes

public CyAttributes getNodeAttributes()

Specified by:

getNodeAttributes in interface GraphReader

Returns:

the node attributes that were read in from the GML file.

getEdgeAttributes

public CyAttributes getEdgeAttributes()

Specified by:

getEdgeAttributes in interface GraphReader

Returns:

the edge attributes that were read in from the GML file.

getColor

public Color getColor(String colorString)

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