Author: pwang
Date: 2010-08-17 17:15:10 -0700 (Tue, 17 Aug 2010)
New Revision: 21431
Removed:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLReader.java
Log:
Not needed
Deleted:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLReader.java
2010-08-18 00:12:19 UTC (rev 21430)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/gml/GMLReader.java
2010-08-18 00:15:10 UTC (rev 21431)
@@ -1,1058 +0,0 @@
-/*
- File: GMLReader.java
-
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-package org.cytoscape.io.internal.read.gml;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.Vector;
-
-import org.cytoscape.io.internal.read.AbstractNetworkReader;
-import org.cytoscape.io.internal.read.VisualStyleBuilder;
-import org.cytoscape.view.layout.CyLayoutAlgorithm;
-import org.cytoscape.view.layout.LayoutAdapter;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.View;
-import org.cytoscape.view.model.CyNetworkView;
-//import org.cytoscape.vizmap.ArrowShape;
-//import org.cytoscape.vizmap.NodeShape;
-//import org.cytoscape.vizmap.VisualPropertyType;
-import org.cytoscape.work.TaskMonitor;
-
-
-/**
- * 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.
- */
-public class GMLReader extends AbstractNetworkReader {
- /**
- * 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...)
- */
-
- // Graph Tags
- public static String GRAPH = "graph";
- public static String NODE = "node";
- public static String EDGE = "edge";
- public static String GRAPHICS = "graphics";
- public static String LABEL = "label";
- public static String SOURCE = "source";
- public static String TARGET = "target";
- public static String IS_DIRECTED = "directed";
-
- // The following elements are in "graphics" section of GML
- public static String X = "x";
- public static String Y = "y";
- public static String H = "h";
- public static String W = "w";
- public static String TYPE = "type";
- public static String ID = "id";
- public static String ROOT_INDEX = "root_index";
-
- // Shapes used in Cytoscape (not GML standard)
- // In GML, they are called "type"
- public static String RECTANGLE = "rectangle";
- public static String ELLIPSE = "ellipse";
- public static String LINE = "Line"; // This is the Polyline object.
- // no support for now...
- public static String POINT = "point";
- public static String DIAMOND = "diamond";
- public static String HEXAGON = "hexagon";
- public static String OCTAGON = "octagon";
- public static String PARALELLOGRAM = "parallelogram";
- public static String TRIANGLE = "triangle";
-
- // Other GML "graphics" attributes
- public static String FILL = "fill";
- public static String WIDTH = "width";
- public static String STRAIGHT_LINES = "line";
- public static String CURVED_LINES = "curved";
- public static String SOURCE_ARROW = "source_arrow";
- public static String TARGET_ARROW = "target_arrow";
-
- // States of the ends of arrows
- public static String ARROW = "arrow";
- public static String ARROW_NONE = "none";
- public static String ARROW_FIRST = "first";
- public static String ARROW_LAST = "last";
- public static String ARROW_BOTH = "both";
- public static String OUTLINE = "outline";
- public static String OUTLINE_WIDTH = "outline_width";
- public static String DEFAULT_EDGE_INTERACTION = "pp";
- public static String VERSION = "Version";
- public static String CREATOR = "Creator";
-
- private Color DEF_COLOR = new Color(153, 153, 255);
-
- private VisualStyleBuilder graphStyle = null;
-
- // Entries in the file
- List keyVals;
-
- // Node ID's
- Map<String,CyNode> nodeIDMap;
- List<Integer> nodes;
- List<Integer> sources;
- List<Integer> targets;
- List<Boolean> directionality_flags;
- Vector<String> node_labels;
- Vector<String> edge_labels;
- Vector<KeyValue> edge_root_index_pairs;
- Vector<KeyValue> node_root_index_pairs;
- Vector<CyEdge> edge_names;
- Vector<String> node_names;
-
- private TaskMonitor taskMonitor;
-
- // Name for the new visual style
- String styleName;
-
- // New Visual Style comverted from GML file.
- //VisualStyle gmlstyle;
-
- // Hashes for node & edge attributes
- Map<String,Double> nodeW;
-
- // Hashes for node & edge attributes
- Map<String,Double> nodeH;
-
- // Hashes for node & edge attributes
-// Map<String,NodeShape> nodeShape;
-
- // Hashes for node & edge attributes
- Map<String,String> nodeCol;
-
- // Hashes for node & edge attributes
- Map<String,Double> nodeBWidth;
-
- // Hashes for node & edge attributes
- Map<String,String> nodeBCol;
- Map<String,String> edgeCol;
- Map<String,Float> edgeWidth;
- Map<String,String> edgeArrow;
- Map<String,String> edgeShape;
-
- // The InputStream
- InputStream inputStream = null;
-
- CyNetwork network;
-
- /**
- * Constructor.<br>
- * This is usually used for remote file loading.
- *
- * @param is
- * Input stream of GML file,
- *
- */
- public GMLReader(CyNetwork net) {
-
- network = net;
-
- // Set new style name
- edge_names = new Vector<CyEdge>();
- node_names = new Vector<String>();
- // TODO fix name
- graphStyle = new VisualStyleBuilder("fixme", false);
- graphStyle.setNodeSizeLocked(false);
-
- }
-
- public void setInput(InputStream is) {
- if ( is == null )
- throw new NullPointerException("input stream is null");
- inputStream = is;
- }
-
- /**
- * Sets the task monitor we want to use
- *
- * @param monitor the TaskMonitor to use
- */
- public void setTaskMonitor(TaskMonitor monitor) {
- this.taskMonitor = monitor;
- }
-
- public CyNetwork getReadNetwork() {
- return network;
- }
-
- public List<CyNetworkView> getReadNetworkViews() {
- return null;
- }
-
- public String[] getExtensions() {
- return new String[]{"gml"};
- }
-
- public String[] getContentTypes() {
- return new String[]{"text/plain"};
- }
-
- public String getExtensionDescription() {
- return "GML files";
- }
-
- /**
- * DOCUMENT ME!
- */
- public Map<Class<?>, Object> read() throws IOException {
- try {
- keyVals = (new GMLParser(inputStream)).parseList();
- } catch (Exception io) {
- io.printStackTrace();
- throw new RuntimeException(io.getMessage());
- }
-
- initializeStructures();
-
- readGML(keyVals); // read the GML file
- createGraph(); // create the graph AND new visual style
-
- //
- // New features are called here:
- // 1 Extract (virtually) all attributes from the GML file
- // 2 Generate new VS
- // 3 Apply the new VS to the current window of Cytoscape
- //
- // Extract node & edge attributes
- extract();
-
- releaseStructures();
-
- return readObjects;
- }
-
- /**
- * Returns a list containing the gml object tree
- */
- public List getList() {
- return keyVals;
- }
-
- protected void initializeStructures() {
- nodes = new ArrayList<Integer>();
- sources = new ArrayList<Integer>();
- targets = new ArrayList<Integer>();
- directionality_flags = new ArrayList<Boolean>();
- node_labels = new Vector<String>();
- edge_labels = new Vector<String>();
- edge_root_index_pairs = new Vector<KeyValue>();
- node_root_index_pairs = new Vector<KeyValue>();
- }
-
- protected void releaseStructures() {
- nodes = null;
- sources = null;
- targets = null;
- directionality_flags = null;
- node_labels = null;
- edge_labels = null;
- edge_root_index_pairs = null;
- node_root_index_pairs = null;
- }
-
- /**
- * 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.
- */
- protected void createGraph() {
-
- nodeIDMap = new HashMap<String,CyNode>(nodes.size());
-
- Map<Integer,Integer> gml_id2order = new
HashMap<Integer,Integer>(nodes.size());
- Set<String> nodeNameSet = new HashSet<String>(nodes.size());
-
- // Add All Nodes to Network
- for (int idx = 0; idx < nodes.size(); idx++) {
- // Report Status Value
- if (taskMonitor != null) {
- // TODO: set proper number
-
//taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(2, idx,
nodes.size()));
- }
-
- String label = node_labels.get(idx);
-
- if (nodeNameSet.add(label)) {
- CyNode node = network.addNode();
- node.attrs().set("name",label);
-
- nodeIDMap.put(label, node);
- gml_id2order.put(nodes.get(idx), idx);
- node_root_index_pairs.get(idx).value =
Integer.valueOf(node.getIndex());
- } else {
- throw new RuntimeException("GML id " +
nodes.get(idx) + " has a duplicated label: " + label);
- }
- }
-
- nodeNameSet = null;
-
- Set<String> edgeNameSet = new HashSet<String>(sources.size());
-
- // Add All Edges to Network
- for (int idx = 0; idx < sources.size(); idx++) {
- // Report Status Value
- if (taskMonitor != null) {
- // TODO: set proper number
-
//taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(3, idx,
sources.size()));
- }
-
- if (gml_id2order.containsKey(sources.get(idx)) &&
gml_id2order.containsKey(targets.get(idx))) {
- String label = edge_labels.get(idx);
- String sourceName =
node_labels.get(gml_id2order.get(sources.get(idx)));
- String targetName =
node_labels.get(gml_id2order.get(targets.get(idx)));
- String edgeName = sourceName + " (" + label +
") " + targetName;
- Boolean isDirected =
directionality_flags.get(idx);
-
- int duplicate_count = 1;
-
- while (!edgeNameSet.add(edgeName)) {
- edgeName = sourceName + " (" + label +
") " + targetName + "_" + duplicate_count;
- duplicate_count += 1;
- }
-
-
- CyNode node_1 = nodeIDMap.get( sourceName );
- CyNode node_2 = nodeIDMap.get( targetName );
- CyEdge edge = network.addEdge(node_1, node_2,
isDirected.booleanValue());
- edge.attrs().set("name", edgeName);
- edge.attrs().set("interaction", label);
- edge_names.add(idx, edge);
-
- edge_root_index_pairs.get(idx).value =
Integer.valueOf(edge.getIndex());
- } else {
- throw new RuntimeException("Non-existant
source/target node for edge with gml (source,target): "
- + sources.get(idx) + ","
+ targets.get(idx));
- }
- }
-
- edgeNameSet = null;
- }
-
- /**
- * This function takes the root level list which defines a gml objec
tree
- */
- protected void readGML(List list) {
- // Report Progress Message
- int counter = 0;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- // Report Progress Value
- if (taskMonitor != null) {
- //TODO: set proper number
-
//taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(1, counter,
list.size()));
- counter++;
- }
-
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GRAPH)) {
- readGraph((List) keyVal.value);
- }
- }
- }
-
- /**
- * This function takes in a list which was given as the value to a
"graph"
- * key underneath the main gml list
- */
- @SuppressWarnings("unchecked") // KeyValue.value cast
- protected void readGraph(List list) {
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(NODE)) {
- readNode((List) keyVal.value);
- }
-
- if (keyVal.key.equals(EDGE)) {
- readEdge((List) keyVal.value);
- }
- }
- }
-
- /**
- * This will extract the model information from the list which is
matched a
- * "node" key
- */
- protected void readNode(List<KeyValue> list) {
- String label = "";
- boolean contains_id = false;
- int id = 0;
- KeyValue root_index_pair = null;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(ID)) {
- contains_id = true;
- id = ((Integer) keyVal.value).intValue();
- } else if (keyVal.key.equals(LABEL)) {
- label = (String) keyVal.value;
- } else if (keyVal.key.equals(ROOT_INDEX)) {
- root_index_pair = keyVal;
- }
- }
-
- if (label.equals("") || label.matches("\\s+")) {
- label = String.valueOf(id);
- }
-
- if (root_index_pair == null) {
- root_index_pair = new KeyValue(ROOT_INDEX, null);
- list.add(root_index_pair);
- }
-
- if (!contains_id) {
- StringWriter stringWriter = new StringWriter();
-
- try {
- GMLParser.printList(list, stringWriter);
- } catch (Exception e) {
- throw new RuntimeException(e.getMessage());
- }
-
- throw new RuntimeException("The node-associated list\n"
+ stringWriter
- + "is missing an id field");
- } else {
- node_root_index_pairs.add(root_index_pair);
- nodes.add(id);
- node_labels.add(label);
- node_names.add(label);
- }
- }
-
- /**
- * This will extract the model information from the list which is
matched to
- * an "edge" key.
- */
- protected void readEdge(List<KeyValue> list) {
- String label = DEFAULT_EDGE_INTERACTION;
- boolean contains_source = false;
- boolean contains_target = false;
- Boolean isDirected = Boolean.TRUE; // use pre-3.0 cytoscape's
as default
- int source = 0;
- int target = 0;
- KeyValue root_index_pair = null;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(SOURCE)) {
- contains_source = true;
- source = ((Integer) keyVal.value).intValue();
- } else if (keyVal.key.equals(TARGET)) {
- contains_target = true;
- target = ((Integer) keyVal.value).intValue();
- } else if (keyVal.key.equals(LABEL)) {
- label = (String) keyVal.value;
- } else if (keyVal.key.equals(ROOT_INDEX)) {
- root_index_pair = keyVal;
- } else if (keyVal.key.equals(IS_DIRECTED)) {
- if (((Integer)keyVal.value) == 1){
- isDirected = Boolean.FALSE;
- } else {
- isDirected = Boolean.TRUE;
- }
- }
- }
-
- if (root_index_pair == null) {
- root_index_pair = new KeyValue(ROOT_INDEX, null);
- list.add(root_index_pair);
- }
-
- if (!contains_source || !contains_target) {
- StringWriter stringWriter = new StringWriter();
-
- try {
- GMLParser.printList(list, stringWriter);
- } catch (Exception e) {
- throw new RuntimeException(e.getMessage());
- }
-
- throw new RuntimeException("The edge-associated list\n"
+ stringWriter
- + " is missing a source or
target key");
- } else {
- sources.add(source);
- targets.add(target);
- directionality_flags.add(isDirected);
-
- edge_labels.add(label);
- edge_root_index_pairs.add(root_index_pair);
- }
- }
-
- /**
- * 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
- *
- * @return the CyLayoutAlgorithm to use
- */
- public CyLayoutAlgorithm getLayoutAlgorithm() {
- return new LayoutAdapter() {
- public void doLayout(CyNetworkView networkView,
TaskMonitor monitor) {
- layout(networkView);
- }
- };
- }
-
- /**
- * layout the graph based on the GML values we read
- *
- * @param myView the view of the network we want to layout
- */
- public void layout(CyNetworkView myView) {
- if ((myView == null) || (myView.getModel().getNodeCount() ==
0)) {
- return;
- }
-
- if (keyVals == null) {
- throw new RuntimeException("Failed to read gml file on
initialization");
- }
-
- for (Iterator it = keyVals.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GRAPH)) {
- layoutGraph(myView, (List) keyVal.value);
- }
- }
- }
-
- //
- /**
- * DOCUMENT ME!
- */
- public void extract() {
- if (keyVals == null) {
- throw new RuntimeException("Failed to read gml file on
initialization");
- }
-
- for (Iterator it = keyVals.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GRAPH)) {
- extractGraph((List) keyVal.value);
- }
- }
- }
-
- protected void extractGraph(List list) {
- CyEdge edge = null;
-
- // Count the current edge
- int ePtr = 0;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- final KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(NODE)) {
- extractNode((List) keyVal.value);
- } else if (keyVal.key.equals(EDGE)) {
- edge = edge_names.get(ePtr);
- ePtr++;
- extractEdge((List) keyVal.value, edge);
- }
- }
- }
-
- @SuppressWarnings("unchecked") // KeyValue.value cast
- protected void extractNode(List list) {
- List graphics_list = null;
- String label = null;
- CyNode node = null;
-
- int tempid = 0;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(ROOT_INDEX)) {
- if (keyVal.value == null) {
- return;
- }
- } else if (keyVal.key.equals(GRAPHICS)) {
- graphics_list = (List) keyVal.value;
- } else if (keyVal.key.equals(LABEL)) {
- label = (String) keyVal.value;
- node = nodeIDMap.get(label);
- } else if (keyVal.key.equals(ID)) {
- tempid = ((Integer) keyVal.value).intValue();
- }
- }
-
- if (graphics_list != null) {
- if (node == null) {
- System.out.println("ERROR: node is missing for
node ID: " + tempid);
- return;
- }
-
- extractNodeAttributes(graphics_list, node);
- }
- }
-
- @SuppressWarnings("unchecked") // KeyValue.value cast
- protected void extractEdge(List list, CyEdge edge) {
- List graphics_list = null;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(ROOT_INDEX)) {
- if (keyVal.value == null) {
- return;
- }
- } else if (keyVal.key.equals(GRAPHICS)) {
- graphics_list = (List) keyVal.value;
- }
- }
-
- if (graphics_list != null) {
- extractEdgeAttributes(graphics_list, edge);
- }
- }
-
- /**
- * Lays Out the Graph, based on GML.
- */
- @SuppressWarnings("unchecked") // KeyValue.value cast
- protected void layoutGraph(final CyNetworkView myView, List list) {
- CyEdge edge = null;
-
- // Count the current edge
- int ePtr = 0;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- final KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(NODE)) {
- layoutNode(myView, (List) keyVal.value);
- } else if (keyVal.key.equals(EDGE)) {
- edge = edge_names.get(ePtr);
- ePtr++;
- layoutEdge(myView, (List) keyVal.value, edge);
- }
- }
- }
-
- /**
- * Assign node properties based on the values in the list matched to the
- * "node" key. Mostly just a wrapper around layoutNodeGraphics
- */
- protected void layoutNode(CyNetworkView myView, List list) {
- Integer root_index = null;
- List graphics_list = null;
- String label = null;
- int tempid = 0;
-
- View<CyNode> view = null;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(ROOT_INDEX)) {
- /*
- * For some reason we didn't make an object for
this node give
- * up now
- */
- if (keyVal.value == null) {
- return;
- }
-
- root_index = (Integer) keyVal.value;
- } else if (keyVal.key.equals(GRAPHICS)) {
- graphics_list = (List) keyVal.value;
- } else if (keyVal.key.equals(LABEL)) {
- label = (String) keyVal.value;
- } else if (keyVal.key.equals(ID)) {
- tempid = ((Integer) keyVal.value).intValue();
- }
- }
-
- // System.out.print( "In layout, Root index is: " + root_index
);
- // System.out.print( " Checking label: " + label );
- view =
myView.getNodeView(network.getNode(root_index.intValue()));
-
-// TODO update for new view
-// if (label != null) {
-// view.getLabel().setText(label);
-// } else {
-// view.getLabel().setText("node(" + tempid + ")");
-// }
-
- if (graphics_list != null) {
- layoutNodeGraphics(myView, graphics_list, view);
-
- }
- }
-
- /**
- * This will assign node graphic properties based on the values in the
list
- * matches to the "graphics" key word
- */
- protected void layoutNodeGraphics(CyNetworkView myView, List list,
View<CyNode> nodeView) {
- /*
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(X)) {
- nodeView.setXPosition(((Number)
keyVal.value).doubleValue());
- } else if (keyVal.key.equals(Y)) {
- nodeView.setYPosition(((Number)
keyVal.value).doubleValue());
- } else if (keyVal.key.equals(H)) {
- nodeView.setHeight(((Number)
keyVal.value).doubleValue());
- } else if (keyVal.key.equals(W)) {
- nodeView.setWidth(((Number)
keyVal.value).doubleValue());
- } else if (keyVal.key.equals(FILL)) {
- nodeView.setUnselectedPaint(getColor((String)
keyVal.value));
- } else if (keyVal.key.equals(OUTLINE)) {
- nodeView.setBorderPaint(getColor((String)
keyVal.value));
- } else if (keyVal.key.equals(OUTLINE_WIDTH)) {
- nodeView.setBorderWidth(((Number)
keyVal.value).floatValue());
- } else if (keyVal.key.equals(TYPE)) {
- String type = (String) keyVal.value;
-
- if (type.equals(ELLIPSE)) {
- nodeView.setShape(NodeView.ELLIPSE);
- } else if (type.equals(RECTANGLE)) {
- nodeView.setShape(NodeView.RECTANGLE);
- } else if (type.equals(DIAMOND)) {
- nodeView.setShape(NodeView.DIAMOND);
- } else if (type.equals(HEXAGON)) {
- nodeView.setShape(NodeView.HEXAGON);
- } else if (type.equals(OCTAGON)) {
- nodeView.setShape(NodeView.OCTAGON);
- } else if (type.equals(PARALELLOGRAM)) {
-
nodeView.setShape(NodeView.PARALELLOGRAM);
- } else if (type.equals(TRIANGLE)) {
- nodeView.setShape(NodeView.TRIANGLE);
- }
- }
- }
- */
- }
-
- //
- // Extract node attributes from GML file
- @SuppressWarnings("unchecked") // KeyValue.value cast
- protected void extractNodeAttributes(List<KeyValue> list, CyNode node) {
- // Put all attributes into hashes.
- // Key is the node name
- // (Assume we do not have duplicate node name.)
- /*
- CyRow attrs = node.attrs();
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(X) || keyVal.key.equals(Y)) {
- // Do nothing.
- } else if (keyVal.key.equals(H)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.NODE_HEIGHT, ""+keyVal.value);
- } else if (keyVal.key.equals(W)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.NODE_WIDTH, ""+keyVal.value);
- } else if (keyVal.key.equals(FILL)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.NODE_FILL_COLOR, ""+keyVal.value);
- } else if (keyVal.key.equals(OUTLINE)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.NODE_BORDER_COLOR, ""+keyVal.value);
- } else if (keyVal.key.equals(WIDTH)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.NODE_LINE_WIDTH, ""+keyVal.value);
- } else if (keyVal.key.equals(TYPE)) {
- String type = (String) keyVal.value;
- graphStyle.addProperty(attrs,
VisualPropertyType.NODE_SHAPE,type);
- }
- }
- */
- }
-
-
- //
- // Extract edge attributes from GML input
- //
- protected void extractEdgeAttributes(List<KeyValue> list, CyEdge edge) {
-/*
- String value = null;
- boolean isArrow = false;
- String edgeFill = DEF_COLOR.toString();
- String arrowShape = ARROW_NONE;
- CyRow attrs = edge.attrs();
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(LINE)) {
- // This represents "Polyline," which is a line
(usually an edge)
- // with arbitrary number of anchors.
- // Current version of CS does not support this,
so ignore this
- // at this point of time...
- } else if (keyVal.key.equals(WIDTH)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_LINE_WIDTH, new String(keyVal.value.toString()));
- } else if (keyVal.key.equals(FILL)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_COLOR, new String(keyVal.value.toString()));
- edgeFill = keyVal.value.toString();
- } else if (keyVal.key.equals(ARROW)) {
- isArrow = true;
- ArrowShape shape = ArrowShape.ARROW;
- String arrowName = shape.getName();
-
- if
(keyVal.value.toString().equalsIgnoreCase(ARROW_FIRST)) {
- arrowShape = ARROW_FIRST;
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
- }
- else if
(keyVal.value.toString().equalsIgnoreCase(ARROW_LAST)) {
- arrowShape = ARROW_LAST;
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
- }
- else if
(keyVal.value.toString().equalsIgnoreCase(ARROW_BOTH)) {
- arrowShape = ARROW_BOTH;
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
- }
- else {// none
- }
-
- } else if (keyVal.key.equals(TYPE)) {
- value = (String) keyVal.value;
-
- if (value.equals(STRAIGHT_LINES)) {
- // edgeShape.put(edgeName, (String)
keyVal.value);
- } else if (value.equals(CURVED_LINES)) {
- //
edgeView.setLineType(EdgeView.CURVED_LINES);
- }
- } else if (keyVal.value.equals(SOURCE_ARROW)) {
- //
edgeView.setSourceEdgeEnd(((Number)keyVal.value).intValue());
- } else if (keyVal.value.equals(TARGET_ARROW)) {
- //
edgeView.setTargetEdgeEnd(((Number)keyVal.value).intValue());
- }
- }
-
- // make the arrow color the same as edge
- if (isArrow) {
- if (arrowShape.equals(ARROW_FIRST)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
- }
- else if (arrowShape.equals(ARROW_LAST)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
- }
- else if (arrowShape.equals(ARROW_BOTH)) {
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
- graphStyle.addProperty(attrs,
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
- }
- }
- */
- }
-
- /**
- * Assign edge visual properties based on pairs in the list matched to
the
- * "edge" key world
- */
- @SuppressWarnings("unchecked") // KeyValue.value cast
- protected void layoutEdge(CyNetworkView myView, List<KeyValue> list,
CyEdge edge) {
- View<CyEdge> edgeView = null;
- List graphics_list = null;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(ROOT_INDEX)) {
- /*
- * Previously, we didn't make an object for
this edge for some
- * reason. Don't try to go any further.
- */
- if (keyVal.value == null) {
- return;
- }
-
- edgeView =
myView.getEdgeView(network.getEdge(((Integer) keyVal.value).intValue()));
- } else if (keyVal.key.equals(GRAPHICS)) {
- graphics_list = (List) keyVal.value;
- }
- }
-
- if ((edgeView != null) && (graphics_list != null)) {
- layoutEdgeGraphics(myView, graphics_list, edgeView);
-
- }
- }
-
- /**
- * Assign edge graphics properties
- */
-
- // Bug fix by Kei
- // Some of the conditions used "value."
- // They should be key.
- // Now this method correctly translate the GML input file
- // into graphics.
- //
- @SuppressWarnings("unchecked") // KeyValue.value cast
- protected void layoutEdgeGraphics(CyNetworkView myView, List<KeyValue>
list, View<CyEdge> edgeView) {
- /*
- // Local vars.
- String value = null;
- KeyValue keyVal = null;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
- keyVal = (KeyValue) it.next();
-
- // This is a polyline obj. However, it will be
translated into
- // straight line.
- if (keyVal.key.equals(LINE)) {
- layoutEdgeGraphicsLine(myView, (List)
keyVal.value, edgeView);
- } else if (keyVal.key.equals(WIDTH)) {
- edgeView.setStrokeWidth(((Number)
keyVal.value).floatValue());
- } else if (keyVal.key.equals(FILL)) {
- edgeView.setUnselectedPaint(getColor((String)
keyVal.value));
- } else if (keyVal.key.equals(TYPE)) {
- value = (String) keyVal.value;
-
- if (value.equals(STRAIGHT_LINES)) {
-
edgeView.setLineType(EdgeView.STRAIGHT_LINES);
- } else if (value.equals(CURVED_LINES)) {
-
edgeView.setLineType(EdgeView.CURVED_LINES);
- }
- } else if (keyVal.key.equals(ARROW)) {
- // The position of the arrow.
- // There are 4 states: no arrows, both ends
have arrows, source,
- // or target.
- //
- // The arrow type below is hard-coded since GML
does not
- // support shape of the arrow.
- if (keyVal.value.equals(ARROW_FIRST)) {
- edgeView.setSourceEdgeEnd(2);
- } else if (keyVal.value.equals(ARROW_LAST)) {
- edgeView.setTargetEdgeEnd(2);
- } else if (keyVal.value.equals(ARROW_BOTH)) {
- edgeView.setSourceEdgeEnd(2);
- edgeView.setTargetEdgeEnd(2);
- } else if (keyVal.value.equals(ARROW_NONE)) {
- // Do nothing. No arrows.
- }
-
- if (keyVal.key.equals(SOURCE_ARROW)) {
- edgeView.setSourceEdgeEnd(((Number)
keyVal.value).intValue());
- } else if (keyVal.value.equals(TARGET_ARROW)) {
- edgeView.setTargetEdgeEnd(((Number)
keyVal.value).intValue());
- }
- }
- }
- */
- }
-
- /**
- * 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 layoutEdgeGraphicsLine(CyNetworkView myView,
List<KeyValue> list, View<CyEdge> edgeView) {
- /*
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(POINT)) {
- Number x = null;
- Number y = null;
-
- for (Iterator pointIt = ((List)
keyVal.value).iterator(); pointIt.hasNext();) {
- KeyValue pointVal = (KeyValue)
pointIt.next();
-
- if (pointVal.key.equals(X)) {
- x = (Number) pointVal.value;
- } else if (pointVal.key.equals(Y)) {
- y = (Number) pointVal.value;
- }
- }
-
- if (!((x == null) || (y == null))) {
- Point2D.Double pt = new
Point2D.Double(x.doubleValue(), y.doubleValue());
- edgeView.getBend().addHandle(pt);
- }
- }
- }
- */
- }
-
- /**
- * Create a color object from the string like it is stored in a gml file
- */
- private Color getColor(String colorString) {
- return new Color(Integer.parseInt(colorString.substring(1),
16));
- }
-
- public <T> T getReadData(Class<T> type) throws IllegalStateException,
- IllegalArgumentException {
- // TODO Auto-generated method stub
- return null;
- }
-
- public Set<Class<?>> getSupportedDataTypes() {
- // TODO Auto-generated method stub
- return null;
- }
-
- public void setInputStream(InputStream is) {
- // TODO Auto-generated method stub
-
- }
-
-}
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