Author: kono
Date: 2010-01-29 12:17:28 -0800 (Fri, 29 Jan 2010)
New Revision: 19072
Modified:
cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java
cytoscape/trunk/src/cytoscape/data/readers/GraphReader.java
Log:
Deprecated layout() method removed.
Modified: cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
2010-01-29 19:53:58 UTC (rev 19071)
+++ cytoscape/trunk/src/cytoscape/data/readers/AbstractGraphReader.java
2010-01-29 20:17:28 UTC (rev 19072)
@@ -143,10 +143,4 @@
public void setTaskMonitor(TaskMonitor monitor) {
}
- /**
- * @deprecated Use getLayoutAlgorithm().doLayout(view) instead. Will be
removed 5/2008.
- */
- public void layout(GraphView view) {
- getLayoutAlgorithm().doLayout((CyNetworkView)view);
- }
}
Modified: cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java 2010-01-29
19:53:58 UTC (rev 19071)
+++ cytoscape/trunk/src/cytoscape/data/readers/GMLReader.java 2010-01-29
20:17:28 UTC (rev 19072)
@@ -168,6 +168,7 @@
IntArrayList nodes;
IntArrayList sources;
IntArrayList targets;
+
Vector node_labels;
Vector edge_labels;
Vector edge_root_index_pairs;
@@ -180,11 +181,8 @@
private PercentUtil percentUtil;
// Name for the new visual style
- String styleName;
+ private String styleName;
- // New Visual Style comverted from GML file.
- //VisualStyle gmlstyle;
-
// Hashes for node & edge attributes
HashMap nodeW;
@@ -268,7 +266,7 @@
}
private String createVSName() {
- return getNetworkName() + " Style";
+ return getNetworkName();
}
private void initializeHash() {
@@ -324,7 +322,7 @@
/**
* Returns a list containing the gml object tree
*/
- public List getList() {
+ public List<KeyValue> getList() {
return keyVals;
}
@@ -452,22 +450,21 @@
/**
* This function takes the root level list which defines a gml objec
tree
*/
- protected void readGML(List list) {
+ @SuppressWarnings("unchecked")
+ protected void readGML(final List<KeyValue> list) {
// Report Progress Message
int counter = 0;
-
- for (Iterator it = list.iterator(); it.hasNext();) {
+ final int size = list.size();
+
+ for (KeyValue keyVal: list) {
// Report Progress Value
if (taskMonitor != null) {
-
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(1, counter,
list.size()));
+
taskMonitor.setPercentCompleted(percentUtil.getGlobalPercent(1, counter, size));
counter++;
}
- KeyValue keyVal = (KeyValue) it.next();
-
- if (keyVal.key.equals(GRAPH)) {
- readGraph((List) keyVal.value);
- }
+ if (keyVal.key.equals(GRAPH))
+ readGraph((List<KeyValue>) keyVal.value);
}
}
@@ -475,15 +472,14 @@
* This function takes in a list which was given as the value to a
"graph"
* key underneath the main gml list
*/
+ @SuppressWarnings("unchecked")
protected void readGraph(final List<KeyValue> list) {
for (KeyValue keyVal: list) {
- if (keyVal.key.equals(NODE)) {
- readNode((List) keyVal.value);
- }
+ if (keyVal.key.equals(NODE))
+ readNode((List<KeyValue>) keyVal.value);
- if (keyVal.key.equals(EDGE)) {
- readEdge((List) keyVal.value);
- }
+ if (keyVal.key.equals(EDGE))
+ readEdge((List<KeyValue>) keyVal.value);
}
}
Modified: cytoscape/trunk/src/cytoscape/data/readers/GraphReader.java
===================================================================
--- cytoscape/trunk/src/cytoscape/data/readers/GraphReader.java 2010-01-29
19:53:58 UTC (rev 19071)
+++ cytoscape/trunk/src/cytoscape/data/readers/GraphReader.java 2010-01-29
20:17:28 UTC (rev 19072)
@@ -58,14 +58,6 @@
public void read() throws IOException;
/**
- * Lays out the graph.
- *
- * @param myView
- * @deprecated Use getLayoutAlgorithm().doLayout(view) instead. Will be
removed 5/2008.
- */
- public void layout(GraphView myView);
-
- /**
* Returns the CyLayoutAlgorithm used to layout the graph
*
* @param myView
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