Author: kono
Date: 2010-01-29 15:28:21 -0800 (Fri, 29 Jan 2010)
New Revision: 19076
Modified:
cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java
cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java
Log:
Fixed GML reader bug (ID 2139). Also, attributes in GML file will be imported.
Tested with GML files generated by igraph.
Modified: cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java 2010-01-29
22:33:00 UTC (rev 19075)
+++ cytoscape/trunk/src/cytoscape/data/readers/GMLParser.java 2010-01-29
23:28:21 UTC (rev 19076)
@@ -92,7 +92,7 @@
/**
* Constructor has to initialize the relevenat regular expression
patterns
*/
- public GMLParser(StreamTokenizer tokenizer) {
+ public GMLParser(final StreamTokenizer tokenizer) {
this.tokenizer = tokenizer;
}
@@ -175,16 +175,17 @@
public List<KeyValue> parseList() throws IOException, ParseException {
final List<KeyValue> result = new ArrayList<KeyValue>();
+ String key;
+ Object value;
while (isKey()) {
- String key = parseKey();
+ key = parseKey();
- if (key == null) {
+ if (key == null)
throw new ParseException("Bad key",
tokenizer.lineno());
- }
tokenizer.nextToken();
- Object value = parseValue();
+ value = parseValue();
if (value == null) {
throw new ParseException(
@@ -204,7 +205,7 @@
*/
private boolean isKey() {
/*
- * A key must be some kind of wrod
+ * A key must be some kind of word
*/
if (tokenizer.ttype != StreamTokenizer.TT_WORD) {
return false;
@@ -237,7 +238,7 @@
* not supposed ot have a couple things in it, but I don't really have a
* check for that.
*/
- private boolean isString() {
+ private boolean isQuatedString() {
return tokenizer.ttype == QUOTE_CHAR;
}
@@ -267,38 +268,33 @@
* has already been found to not be the end of file
*/
private Object parseValue() throws IOException, ParseException {
- Object result = null;
- if (tokenizer.ttype == StreamTokenizer.TT_EOL) {
- return result;
- }
+ if (tokenizer.ttype == StreamTokenizer.TT_EOL)
+ return null;
- if (isString()) {
+ if (isQuatedString())
return tokenizer.sval;
- }
- if (isInteger()) {
- return new Integer(tokenizer.sval);
- }
+ if (isInteger())
+ return Integer.parseInt(tokenizer.sval);
- if (isReal()) {
- return new Double(tokenizer.sval);
- }
+ if (isReal())
+ return Double.parseDouble(tokenizer.sval);
if (isList()) {
tokenizer.nextToken();
- List list = parseList();
+ final List<KeyValue> list = parseList();
if (!tokenizer.sval.equals(LIST_CLOSE)) {
throw new ParseException("Unterminated list",
tokenizer
.lineno());
}
-
return list;
}
-
- return result;
+
+ // Treat as a regular string value.
+ return tokenizer.sval;
}
/**
Modified: cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java 2010-01-29
22:33:00 UTC (rev 19075)
+++ cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java 2010-01-29
23:28:21 UTC (rev 19076)
@@ -37,6 +37,7 @@
package cytoscape.data.readers;
import giny.model.Edge;
+import giny.model.GraphObject;
import giny.model.Node;
import giny.view.EdgeView;
import giny.view.GraphView;
@@ -46,10 +47,12 @@
import java.awt.geom.Point2D;
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;
@@ -73,7 +76,6 @@
import cytoscape.visual.NodeShape;
import cytoscape.visual.VisualPropertyType;
-
/**
* 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
@@ -85,19 +87,26 @@
/**
* 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...)
*/
+ // Global tags
+ protected static final String ID = "id";
+ protected static final String NAME = "name";
+ protected static final String LABEL = "label";
+ protected static final String COMMENT = "comment";
+ protected static final String VERSION = "Version";
+ protected static final String CREATOR = "Creator";
+
// Graph Tags
protected static final String GRAPH = "graph";
protected static final String NODE = "node";
protected static final String EDGE = "edge";
protected static final String GRAPHICS = "graphics";
- protected static final String LABEL = "label";
protected static final String SOURCE = "source";
protected static final String TARGET = "target";
@@ -107,7 +116,7 @@
protected static final String H = "h";
protected static final String W = "w";
protected static final String TYPE = "type";
- protected static final String ID = "id";
+
protected static final String ROOT_INDEX = "root_index";
// Shapes used in Cytoscape (not GML standard)
@@ -115,7 +124,7 @@
protected static final String RECTANGLE = "rectangle";
protected static final String ELLIPSE = "ellipse";
protected static final String LINE = "Line"; // This is the Polyline
object.
- // no support for now...
+ // no support for now...
protected static final String POINT = "point";
protected static final String DIAMOND = "diamond";
protected static final String HEXAGON = "hexagon";
@@ -150,12 +159,13 @@
protected static final String OUTLINE = "outline";
protected static final String OUTLINE_WIDTH = "outline_width";
protected static final String DEFAULT_EDGE_INTERACTION = "pp";
- protected static final String VERSION = "Version";
- protected static final String CREATOR = "Creator";
+ private static final String VIZMAP_PREFIX = "vizmap:";
+
private static final Color DEF_COLOR = new Color(153, 153, 255);
-
- private String vsbSwitch =
CytoscapeInit.getProperties().getProperty("visualStyleBuilder");
+
+ private String vsbSwitch = CytoscapeInit.getProperties().getProperty(
+ "visualStyleBuilder");
private VisualStyleBuilder graphStyle = null;
private static CyLogger logger = CyLogger.getLogger(GMLReader.class);
@@ -168,13 +178,20 @@
IntArrayList nodes;
IntArrayList sources;
IntArrayList targets;
-
- Vector node_labels;
- Vector edge_labels;
+
+ private List<String> nodeLabels;
+ private List<String> edgeLabels;
+
+ // Storage for CyAttributes
+ private List<Map<String, Object>> nodeAttributes;
+ private List<Map<String, Object>> edgeAttributes;
+
Vector edge_root_index_pairs;
Vector node_root_index_pairs;
- Vector edge_names;
- Vector node_names;
+
+ private List<String> edgeNames;
+ private List<String> nodeNames;
+
IntArrayList giny_nodes;
IntArrayList giny_edges;
private TaskMonitor taskMonitor;
@@ -208,8 +225,9 @@
/**
* Constructor.
- *
- * @param filename File name.
+ *
+ * @param filename
+ * File name.
*/
public GMLReader(final String filename) {
this(filename, null);
@@ -218,10 +236,10 @@
/**
* Constructor.<br>
* This is usually used for remote file loading.
- *
+ *
* @param is
* Input stream of GML file,
- *
+ *
*/
public GMLReader(final InputStream is, final String name) {
super(name);
@@ -236,9 +254,11 @@
/**
* Constructor.
- *
- * @param filename File name.
- * @param taskMonitor TaskMonitor Object.
+ *
+ * @param filename
+ * File name.
+ * @param taskMonitor
+ * TaskMonitor Object.
*/
public GMLReader(final String filename, final TaskMonitor taskMonitor) {
super(filename);
@@ -256,10 +276,11 @@
}
/**
- * Sets the task monitor we want to use
- *
- * @param monitor the TaskMonitor to use
- */
+ * Sets the task monitor we want to use
+ *
+ * @param monitor
+ * the TaskMonitor to use
+ */
public void setTaskMonitor(TaskMonitor monitor) {
this.taskMonitor = monitor;
percentUtil = new PercentUtil(3);
@@ -270,32 +291,32 @@
}
private void initializeHash() {
- edge_names = new Vector();
- node_names = new Vector();
+ edgeNames = new ArrayList<String>();
+ nodeNames = new ArrayList<String>();
+ nodeAttributes = new ArrayList<Map<String, Object>>();
+ edgeAttributes = new ArrayList<Map<String, Object>>();
}
-
// Initialize variables for the new style created from GML
private void initStyle() {
graphStyle = new VisualStyleBuilder(styleName, false);
graphStyle.setNodeSizeLocked(false);
}
-
/**
- * Read GML file contents
+ * Read GML file contents
*/
public void read() {
try {
- try {
- keyVals = (new GMLParser(inputStream)).parseList();
- } finally {
- if (inputStream != null) {
- inputStream.close();
- }
- }
+ try {
+ keyVals = (new
GMLParser(inputStream)).parseList();
+ } finally {
+ if (inputStream != null) {
+ inputStream.close();
+ }
+ }
} catch (Exception io) {
- logger.warn("Error reading GML file: "+io.getMessage(),
io);
+ logger.warn("Error reading GML file: " +
io.getMessage(), io);
if (taskMonitor != null)
taskMonitor.setException(io, io.getMessage());
@@ -330,8 +351,8 @@
nodes = new IntArrayList();
sources = new IntArrayList();
targets = new IntArrayList();
- node_labels = new Vector();
- edge_labels = new Vector();
+ nodeLabels = new ArrayList<String>();
+ edgeLabels = new ArrayList<String>();
edge_root_index_pairs = new Vector();
node_root_index_pairs = new Vector();
}
@@ -340,12 +361,38 @@
nodes = null;
sources = null;
targets = null;
- node_labels = null;
- edge_labels = null;
+ nodeLabels = null;
+ edgeLabels = null;
edge_root_index_pairs = null;
node_root_index_pairs = null;
}
+ private void mapAttributes(final GraphObject obj,
+ final CyAttributes attrs, final Map<String, Object>
attrMap) {
+
+ for (String attrName : attrMap.keySet()) {
+ final Object attrVal = attrMap.get(attrName);
+ if (attrVal == null)
+ continue;
+
+ try {
+ if (attrVal instanceof Double) {
+ attrs.setAttribute(obj.getIdentifier(),
attrName,
+ (Double) attrVal);
+ } else if (attrVal instanceof Integer) {
+ attrs.setAttribute(obj.getIdentifier(),
attrName,
+ (Integer) attrVal);
+ } else {
+ attrs.setAttribute(obj.getIdentifier(),
attrName,
+ attrVal.toString());
+ }
+ } catch (IllegalArgumentException e) {
+ continue;
+ }
+
+ }
+ }
+
/**
* This will create the graph model objects. This function expects node
* labels to be unique and edge labels to be unique between a particular
@@ -360,29 +407,41 @@
giny_nodes = new IntArrayList(nodes.size());
OpenIntIntHashMap gml_id2order = new
OpenIntIntHashMap(nodes.size());
- Set nodeNameSet = new HashSet(nodes.size());
+ Set<String> nodeNameSet = new HashSet<String>(nodes.size());
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+
// Add All Nodes to Network
for (int idx = 0; idx < nodes.size(); idx++) {
// Report Status Value
- if (taskMonitor != null) {
-
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(2, idx,
nodes.size()));
- }
+ if (taskMonitor != null)
+
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(2,
+ idx, nodes.size()));
- String label = (String) node_labels.get(idx);
+ final String label = nodeLabels.get(idx);
+ Node node;
+
if (nodeNameSet.add(label)) {
- Node node = (Node) Cytoscape.getCyNode(label,
true);
+ node = Cytoscape.getCyNode(label, true);
+ if (nodeLabels.get(idx) != null)
+
nodeAttr.setAttribute(node.getIdentifier(), LABEL,
+ nodeLabels.get(idx));
+ if (nodeNames.get(idx) != null)
+
nodeAttr.setAttribute(node.getIdentifier(), NAME, nodeNames
+ .get(idx));
+
+ // Map attributes
+ mapAttributes(node, nodeAttr,
nodeAttributes.get(idx));
+
giny_nodes.add(node.getRootGraphIndex());
nodeIDMap.put(nodes.get(idx),
node.getRootGraphIndex());
gml_id2order.put(nodes.get(idx), idx);
- ((KeyValue)
node_root_index_pairs.get(idx)).value = (new Integer(node
-
.getRootGraphIndex()));
+ ((KeyValue)
node_root_index_pairs.get(idx)).value = (new Integer(
+ node.getRootGraphIndex()));
} else {
- throw new GMLException("GML id " +
nodes.get(idx) + " has a duplicated label: "
- + label);
-
- //
((KeyValue)node_root_index_pairs.get(idx)).value = null;
+ throw new GMLException("GML id " +
nodes.get(idx)
+ + " has a duplicated ID: " +
label);
}
}
@@ -392,33 +451,38 @@
Set edgeNameSet = new HashSet(sources.size());
- CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ final CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
// Add All Edges to Network
for (int idx = 0; idx < sources.size(); idx++) {
// Report Status Value
if (taskMonitor != null) {
-
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(3, idx,
sources.size()));
+
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(3,
+ idx, sources.size()));
}
if (gml_id2order.containsKey(sources.get(idx))
- && gml_id2order.containsKey(targets.get(idx))) {
- String label = (String) edge_labels.get(idx);
- String sourceName = (String)
node_labels.get(gml_id2order.get(sources.get(idx)));
- String targetName = (String)
node_labels.get(gml_id2order.get(targets.get(idx)));
- String edgeName =
CyEdge.createIdentifier(sourceName, label, targetName);
+ &&
gml_id2order.containsKey(targets.get(idx))) {
+ String label = (String) edgeLabels.get(idx);
+ String sourceName = (String)
nodeLabels.get(gml_id2order
+ .get(sources.get(idx)));
+ String targetName = (String)
nodeLabels.get(gml_id2order
+ .get(targets.get(idx)));
+ String edgeName =
CyEdge.createIdentifier(sourceName, label,
+ targetName);
int duplicate_count = 1;
while (!edgeNameSet.add(edgeName)) {
- edgeName =
CyEdge.createIdentifier(sourceName, label, targetName) + "_"
- + duplicate_count;
+ edgeName =
CyEdge.createIdentifier(sourceName, label,
+ targetName)
+ + "_" + duplicate_count;
duplicate_count += 1;
}
// String tempstr = "E name is :" + idx + "=="
+ edgeName;
- edge_names.add(idx, edgeName);
+ edgeNames.add(idx, edgeName);
Edge edge =
Cytoscape.getRootGraph().getEdge(edgeName);
@@ -427,20 +491,22 @@
Node node_2 =
Cytoscape.getCyNode(targetName);
// edge = (Edge) rootGraph.getEdge
// (rootGraph.createEdge(node_1,
node_2));
- edge = Cytoscape.getCyEdge(node_1,
node_2, Semantics.INTERACTION, label, true,
- true);
+ edge = Cytoscape.getCyEdge(node_1,
node_2,
+ Semantics.INTERACTION,
label, true, true);
}
// Set correct ID, canonical name and
interaction name
edge.setIdentifier(edgeName);
- edgeAttributes.setAttribute(edgeName,
Semantics.INTERACTION, label);
+ edgeAttr.setAttribute(edgeName,
Semantics.INTERACTION, label);
+ mapAttributes(edge, edgeAttr,
edgeAttributes.get(idx));
giny_edges.add(edge.getRootGraphIndex());
- ((KeyValue)
edge_root_index_pairs.get(idx)).value = (new Integer(edge
-
.getRootGraphIndex()));
+ ((KeyValue)
edge_root_index_pairs.get(idx)).value = (new Integer(
+ edge.getRootGraphIndex()));
} else {
- throw new GMLException("Non-existant
source/target node for edge with gml (source,target): "
- + sources.get(idx) + ","
+ targets.get(idx));
+ throw new GMLException(
+ "Non-existant source/target
node for edge with gml (source,target): "
+ +
sources.get(idx) + "," + targets.get(idx));
}
}
@@ -455,11 +521,12 @@
// Report Progress Message
int counter = 0;
final int size = list.size();
-
- for (KeyValue keyVal: list) {
+
+ for (KeyValue keyVal : list) {
// Report Progress Value
if (taskMonitor != null) {
-
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(1, counter, size));
+
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(1,
+ counter, size));
counter++;
}
@@ -474,7 +541,7 @@
*/
@SuppressWarnings("unchecked")
protected void readGraph(final List<KeyValue> list) {
- for (KeyValue keyVal: list) {
+ for (KeyValue keyVal : list) {
if (keyVal.key.equals(NODE))
readNode((List<KeyValue>) keyVal.value);
@@ -487,22 +554,28 @@
* This will extract the model information from the list which is
matched a
* "node" key
*/
- protected void readNode(List list) {
+ private void readNode(final List<KeyValue> list) {
String label = "";
+ String name = null;
+ final Map<String, Object> attr = new HashMap<String, Object>();
+
boolean contains_id = false;
int id = 0;
KeyValue root_index_pair = null;
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
+ for (final KeyValue keyVal : list) {
if (keyVal.key.equals(ID)) {
contains_id = true;
- id = ((Integer) keyVal.value).intValue();
+ id = (Integer) keyVal.value;
} else if (keyVal.key.equals(LABEL)) {
- label = (String) keyVal.value;
+ label = keyVal.value.toString();
+ } else if (keyVal.key.equals(NAME)) {
+ name = keyVal.value.toString();
} else if (keyVal.key.equals(ROOT_INDEX)) {
root_index_pair = keyVal;
+ } else if (!keyVal.key.equals(GRAPHICS) &&
!keyVal.key.startsWith(VIZMAP_PREFIX)) {
+ // This is a regular attribute value
+ attr.put(keyVal.key, keyVal.value);
}
}
@@ -516,7 +589,7 @@
}
if (!contains_id) {
- StringWriter stringWriter = new StringWriter();
+ final StringWriter stringWriter = new StringWriter();
try {
GMLParser.printList(list, stringWriter);
@@ -525,12 +598,14 @@
}
throw new GMLException("The node-associated list\n" +
stringWriter
- + "is missing an id field");
+ + "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);
+ nodeLabels.add(label);
+ nodeNames.add(name);
+
+ nodeAttributes.add(attr);
}
}
@@ -538,17 +613,16 @@
* This will extract the model information from the list which is
matched to
* an "edge" key.
*/
- protected void readEdge(List list) {
+ protected void readEdge(final List<KeyValue> list) {
String label = DEFAULT_EDGE_INTERACTION;
boolean contains_source = false;
boolean contains_target = false;
int source = 0;
int target = 0;
KeyValue root_index_pair = null;
+ final Map<String, Object> attr = new HashMap<String, Object>();
- for (Iterator it = list.iterator(); it.hasNext();) {
- KeyValue keyVal = (KeyValue) it.next();
-
+ for (final KeyValue keyVal: list) {
if (keyVal.key.equals(SOURCE)) {
contains_source = true;
source = ((Integer) keyVal.value).intValue();
@@ -559,6 +633,8 @@
label = (String) keyVal.value;
} else if (keyVal.key.equals(ROOT_INDEX)) {
root_index_pair = keyVal;
+ } else if (!keyVal.key.equals(GRAPHICS) &&
!keyVal.key.startsWith(VIZMAP_PREFIX)) {
+ attr.put(keyVal.key, keyVal.value);
}
}
@@ -577,36 +653,39 @@
}
throw new GMLException("The edge-associated list\n" +
stringWriter
- + " is missing a source or
target key");
+ + " is missing a source or target key");
} else {
sources.add(source);
targets.add(target);
- edge_labels.add(label);
+ edgeLabels.add(label);
edge_root_index_pairs.add(root_index_pair);
+
+ edgeAttributes.add(attr);
}
}
/**
- * 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
- *
+ * 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);
- }
- };
+ 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
+ *
+ * @param myView
+ * the view of the network we want to layout
*/
public void layout(CyNetworkView myView) {
if ((myView == null) || (myView.nodeCount() == 0)) {
@@ -614,7 +693,8 @@
}
if (keyVals == null) {
- throw new RuntimeException("Failed to read gml file on
initialization");
+ throw new RuntimeException(
+ "Failed to read gml file on
initialization");
}
for (Iterator it = keyVals.iterator(); it.hasNext();) {
@@ -628,11 +708,12 @@
//
/**
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void extract() {
if (keyVals == null) {
- throw new RuntimeException("Failed to read gml file on
initialization");
+ throw new RuntimeException(
+ "Failed to read gml file on
initialization");
}
for (Iterator it = keyVals.iterator(); it.hasNext();) {
@@ -656,7 +737,7 @@
if (keyVal.key.equals(NODE)) {
extractNode((List) keyVal.value);
} else if (keyVal.key.equals(EDGE)) {
- edgeName = (String) edge_names.get(ePtr);
+ edgeName = (String) edgeNames.get(ePtr);
ePtr++;
extractEdge((List) keyVal.value, edgeName);
}
@@ -688,7 +769,8 @@
if (graphics_list != null) {
if (label == null) {
label = "node" + tempid;
- logger.info("Warning: node label is missing for
node ID: " + tempid);
+ logger.info("Warning: node label is missing for
node ID: "
+ + tempid);
}
extractNodeAttributes(graphics_list, label);
@@ -726,12 +808,6 @@
if (keyVal.key.equals(NODE))
layoutNode(myView, (List) keyVal.value);
-
- // } else if
(keyVal.key.equals(EDGE)) {
- // edgeName = (String)
edge_names.get(ePtr);
- // ePtr++;
- // layoutEdge(myView,
(List) keyVal.value, edgeName);
- // }
}
}
@@ -787,7 +863,8 @@
* This will assign node graphic properties based on the values in the
list
* matches to the "graphics" key word
*/
- protected void layoutNodeGraphics(GraphView myView, List list, NodeView
nodeView) {
+ protected void layoutNodeGraphics(GraphView myView, List list,
+ NodeView nodeView) {
for (Iterator it = list.iterator(); it.hasNext();) {
KeyValue keyVal = (KeyValue) it.next();
@@ -839,21 +916,26 @@
if (keyVal.key.equals(X) || keyVal.key.equals(Y)) {
// Do nothing.
} else if (keyVal.key.equals(H)) {
- graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_HEIGHT, "" + keyVal.value);
+ graphStyle.addProperty(nodeName,
+ VisualPropertyType.NODE_HEIGHT,
"" + keyVal.value);
} else if (keyVal.key.equals(W)) {
- graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_WIDTH, "" + keyVal.value);
+ graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_WIDTH,
+ "" + keyVal.value);
} else if (keyVal.key.equals(FILL)) {
- graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_FILL_COLOR,
- "" + keyVal.value);
+ graphStyle.addProperty(nodeName,
+
VisualPropertyType.NODE_FILL_COLOR, "" + keyVal.value);
} else if (keyVal.key.equals(OUTLINE)) {
- graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_BORDER_COLOR,
- "" + keyVal.value);
+ graphStyle
+ .addProperty(nodeName,
+
VisualPropertyType.NODE_BORDER_COLOR, ""
+
+ keyVal.value);
} else if (keyVal.key.equals(WIDTH)) {
- graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_LINE_WIDTH,
- "" + keyVal.value);
+ graphStyle.addProperty(nodeName,
+
VisualPropertyType.NODE_LINE_WIDTH, "" + keyVal.value);
} else if (keyVal.key.equals(TYPE)) {
String type = (String) keyVal.value;
- graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_SHAPE, type);
+ graphStyle.addProperty(nodeName,
VisualPropertyType.NODE_SHAPE,
+ type);
}
}
}
@@ -875,11 +957,12 @@
// Current version of CS does not support this,
so ignore this
// at this point of time...
} else if (keyVal.key.equals(WIDTH)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_LINE_WIDTH,
- new
String(keyVal.value.toString()));
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_LINE_WIDTH, new String(
+
keyVal.value.toString()));
} else if (keyVal.key.equals(FILL)) {
graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_COLOR,
- new
String(keyVal.value.toString()));
+ new
String(keyVal.value.toString()));
edgeFill = keyVal.value.toString();
} else if (keyVal.key.equals(ARROW)) {
isArrow = true;
@@ -889,57 +972,71 @@
if
(keyVal.value.toString().equalsIgnoreCase(ARROW_FIRST)) {
arrowShape = ARROW_FIRST;
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_SHAPE,
- arrowName);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
} else if
(keyVal.value.toString().equalsIgnoreCase(ARROW_LAST)) {
arrowShape = ARROW_LAST;
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_SHAPE,
- arrowName);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
} else if
(keyVal.value.toString().equalsIgnoreCase(ARROW_BOTH)) {
arrowShape = ARROW_BOTH;
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_SHAPE,
- arrowName);
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_SHAPE,
- arrowName);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
}
} else if (keyVal.key.equals(TYPE)) {
value = (String) keyVal.value;
if (value.equals(STRAIGHT_LINES)) {
- //edgeShape.put(edgeName, (String)
keyVal.value);
+ // edgeShape.put(edgeName, (String)
keyVal.value);
} else if (value.equals(CURVED_LINES)) {
//
edgeView.setLineType(EdgeView.CURVED_LINES);
}
} else if (keyVal.key.equals(SOURCE_ARROW)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_SHAPE,
-
ArrowShape.getArrowShape(((Number) keyVal.value).intValue())
- .getName());
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_SHAPE, ArrowShape
+ .getArrowShape(
+
((Number) keyVal.value).intValue())
+ .getName());
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
} else if (keyVal.key.equals(TARGET_ARROW)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_SHAPE,
-
ArrowShape.getArrowShape(((Number) keyVal.value).intValue())
- .getName());
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_SHAPE, ArrowShape
+ .getArrowShape(
+
((Number) keyVal.value).intValue())
+ .getName());
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
} else if (keyVal.key.equals(YED_SOURCE_ARROW)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_SHAPE,
-
convertYEDArrowShape(keyVal.value.toString()));
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_SHAPE,
+
convertYEDArrowShape(keyVal.value.toString()));
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
} else if (keyVal.key.equals(YED_TARGET_ARROW)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_SHAPE,
-
convertYEDArrowShape(keyVal.value.toString()));
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_SHAPE,
+
convertYEDArrowShape(keyVal.value.toString()));
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
}
}
// make the arrow color the same as edge
if (isArrow) {
if (arrowShape.equals(ARROW_FIRST)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
} else if (arrowShape.equals(ARROW_LAST)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
} else if (arrowShape.equals(ARROW_BOTH)) {
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
- graphStyle.addProperty(edgeName,
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_SRCARROW_COLOR, edgeFill);
+ graphStyle.addProperty(edgeName,
+
VisualPropertyType.EDGE_TGTARROW_COLOR, edgeFill);
}
}
}
@@ -949,7 +1046,8 @@
if (yedArrow.equals(YED_DELTA) ||
yedArrow.equals(YED_WHITE_DELTA))
shape = ArrowShape.DELTA.getName();
- else if (yedArrow.equals(YED_DIAMOND) ||
yedArrow.equals(YED_WHITE_DIAMOND))
+ else if (yedArrow.equals(YED_DIAMOND)
+ || yedArrow.equals(YED_WHITE_DIAMOND))
shape = ArrowShape.DIAMOND.getName();
else if (yedArrow.equals(YED_STANDARD) ||
yedArrow.equals(YED_SHORT))
shape = ArrowShape.ARROW.getName();
@@ -958,15 +1056,15 @@
}
/**
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showMaps() {
String e = null;
String n = null;
String temp = null;
- for (int i = 0; i < edge_names.size(); i++) {
- e = (String) edge_names.get(i);
+ for (int i = 0; i < edgeNames.size(); i++) {
+ e = (String) edgeNames.get(i);
temp = e + ": ";
temp = temp + edgeCol.get(e) + ", ";
temp = temp + edgeWidth.get(e) + ", ";
@@ -997,7 +1095,8 @@
return;
}
- edgeView = myView.getEdgeView(((Integer)
keyVal.value).intValue());
+ edgeView = myView.getEdgeView(((Integer)
keyVal.value)
+ .intValue());
} else if (keyVal.key.equals(GRAPHICS)) {
graphics_list = (List) keyVal.value;
}
@@ -1010,11 +1109,12 @@
/**
* Assign edge graphics properties
*/
- protected void layoutEdgeGraphics(GraphView myView, List<KeyValue>
list, EdgeView edgeView) {
+ protected void layoutEdgeGraphics(GraphView myView, List<KeyValue> list,
+ EdgeView edgeView) {
// Local vars.
String value = null;
- // KeyValue keyVal = null;
+ // KeyValue keyVal = null;
for (KeyValue keyVal : list) {
// This is a polyline obj. However, it will be
translated into
// straight line.
@@ -1062,7 +1162,8 @@
* "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(GraphView myView, List list,
EdgeView edgeView) {
+ protected void layoutEdgeGraphicsLine(GraphView myView, List list,
+ EdgeView edgeView) {
for (Iterator it = list.iterator(); it.hasNext();) {
KeyValue keyVal = (KeyValue) it.next();
@@ -1070,7 +1171,8 @@
Number x = null;
Number y = null;
- for (Iterator pointIt = ((List)
keyVal.value).iterator(); pointIt.hasNext();) {
+ for (Iterator pointIt = ((List)
keyVal.value).iterator(); pointIt
+ .hasNext();) {
KeyValue pointVal = (KeyValue)
pointIt.next();
if (pointVal.key.equals(X)) {
@@ -1081,7 +1183,8 @@
}
if (!((x == null) || (y == null))) {
- Point2D.Double pt = new
Point2D.Double(x.doubleValue(), y.doubleValue());
+ Point2D.Double pt = new
Point2D.Double(x.doubleValue(), y
+ .doubleValue());
edgeView.getBend().addHandle(pt);
}
}
@@ -1114,9 +1217,10 @@
}
/**
- * DOCUMENT ME!
- *
- * @param net DOCUMENT ME!
+ * DOCUMENT ME!
+ *
+ * @param net
+ * DOCUMENT ME!
*/
public void doPostProcessing(final CyNetwork net) {
@@ -1126,7 +1230,7 @@
return;
if ((init.getMode() == CyInitParams.GUI)
- || (init.getMode() == CyInitParams.EMBEDDED_WINDOW)) {
+ || (init.getMode() ==
CyInitParams.EMBEDDED_WINDOW)) {
if (!((vsbSwitch != null) && vsbSwitch.equals("off"))) {
graphStyle.buildStyle();
}
--
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