Author: ghuck
Date: 2011-07-31 13:46:09 -0700 (Sun, 31 Jul 2011)
New Revision: 26344
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/MinimumSpanningTree.java
Log:
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
2011-07-30 14:49:43 UTC (rev 26343)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/IgraphAPI.java
2011-07-31 20:46:09 UTC (rev 26344)
@@ -98,6 +98,108 @@
return nodeIdMapping;
} // loadGraph()
+ public static double[] computeWeights(String attrName,
+ HashMap<Integer,Integer> mapping,
+ boolean selectedOnly) {
+
+ CyNetwork network = Cytoscape.getCurrentNetwork();
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ double[] weights = new double[network.getEdgeCount() * 2];
+ boolean defaultSet = false;
+ double defaultValue = 0.0;
+ int i = 0;
+ byte type = edgeAttributes.getType(attrName);
+ Iterator<Edge> it = network.edgesIterator();
+
+ if (type == CyAttributes.TYPE_INTEGER) {
+
+ while (it.hasNext()) {
+ Edge e = (CyEdge) it.next();
+
+ Node source = e.getSource();
+ Node target = e.getTarget();
+
+
+ if (!selectedOnly ||
+ (network.isSelected(source) && network.isSelected(target))
){
+ // int s =
nodeIdMapping.get(source.getRootGraphIndex());
+ // int t =
nodeIdMapping.get(target.getRootGraphIndex());
+
+ Integer a =
edgeAttributes.getIntegerAttribute(e.getIdentifier(), attrName);
+ if (null == a) {
+ if (defaultSet) {
+ weights[i] = defaultValue;
+ } else {
+ while (true) {
+ String inputValue =
JOptionPane.showInputDialog("Found an edge without attribute. Please enter a
default value to be used for all edges without attribute " + attrName);
+ try {
+ Double d = Double.parseDouble(inputValue);
+ defaultValue = d.doubleValue();
+ defaultSet = true;
+ break;
+ } catch (Exception ex) {
+
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Please enter a valid
number");
+ }
+ }
+
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "default: " +
defaultValue);
+ }
+
+ } else {
+ weights[i] = a.doubleValue();
+ }
+ i++;
+
+ }
+ } // while
+
+ } else { // (type == CyAttributes.TYPE_FLOATING)
+ while (it.hasNext()) {
+ Edge e = (CyEdge) it.next();
+
+ Node source = e.getSource();
+ Node target = e.getTarget();
+
+ if (!selectedOnly ||
+ (network.isSelected(source) && network.isSelected(target))
){
+
+ Double a =
edgeAttributes.getDoubleAttribute(e.getIdentifier(), attrName);
+ if (null == a) {
+ if (defaultSet) {
+ weights[i] = defaultValue;
+ } else {
+ while (true) {
+ String inputValue =
JOptionPane.showInputDialog("Found an edge without attribute. Please enter a
default value to be used for all edges without attribute " + attrName);
+ try {
+ Double d = Double.parseDouble(inputValue);
+ defaultValue = d.doubleValue();
+ defaultSet = true;
+ break;
+
+ } catch (Exception ex) {
+
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Please enter a valid
number");
+ }
+ }
+
+
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "default: " +
defaultValue);
+ }
+ } else {
+ weights[i] = a.doubleValue();
+ }
+ i++;
+ }
+ } // while
+
+ }
+
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "i = " + i);
+ // if (i != mapping.size())
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "ERROR!
\nNumber of edge attributes do not match number of edges!!");
+// else
+// JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Weights
OK!");
+
+ return weights;
+ }
+
}
\ No newline at end of file
Modified:
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/MinimumSpanningTree.java
===================================================================
---
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/MinimumSpanningTree.java
2011-07-30 14:49:43 UTC (rev 26343)
+++
csplugins/trunk/soc/ghuck/IgraphPlugin/src/cytoscape/plugins/igraph/MinimumSpanningTree.java
2011-07-31 20:46:09 UTC (rev 26344)
@@ -79,25 +79,18 @@
int numEdges;
/* Compute MST */
- if (isWeighted) {
- // Compute weights
- double[] weights;
- weights = new double[mapping.size()];
+ if (isWeighted) {
+ String attribute = chooseEdgeAttribute();
+ double[] weights = IgraphAPI.computeWeights(attribute,
+ mapping,
+ selectedOnly);
- // TODO: Compute weights!!!
-
numEdges = IgraphInterface.minimum_spanning_tree_weighted(mst,
weights);
} else {
numEdges =
IgraphInterface.minimum_spanning_tree_unweighted(mst);
}
-// logger.info("Nodes in MST: " + numNodes);
-// logger.info("Edges in MST: " + numEdges);
-// String nodesString = new String();
-// for (int i = 0; i < 2 * numEdges; i++)
-// nodesString = nodesString + mst[i] + ", ";
-// logger.info("Nodes: "+ nodesString);
/* Create new network & networkView */
CyNetworkView oldView = Cytoscape.getCurrentNetworkView();
@@ -208,4 +201,37 @@
}
+
+ protected static String chooseEdgeAttribute() {
+
+ String attribute;
+
+ // Create a list with all Integer or Double edge attributes
+ CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
+ String[] attrArr = edgeAttributes.getAttributeNames();
+ Vector attrVector = new Vector();
+
+ for (int i = 0; i < attrArr.length; i++) {
+ byte type = edgeAttributes.getType(attrArr[i]);
+ if (type == CyAttributes.TYPE_INTEGER || type ==
CyAttributes.TYPE_FLOATING)
+ attrVector.add(attrArr[i]);
+ }
+
+ if (attrVector.size() == 0) {
+ JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "No suitable
(numeric) edge attribute found.\nWill perform unweighted Minimum Spanning Tree
computation instead.");
+ attribute = "";
+ } else {
+ Object[] possibleValues = attrVector.toArray();
+ attribute = (String)
JOptionPane.showInputDialog(Cytoscape.getDesktop(),
+ "Choose which edge
attribute will be used as weight",
+ "Minimum Spanning
Tree (Weighted)",
+
JOptionPane.INFORMATION_MESSAGE, null,
+ possibleValues,
possibleValues[0]);
+ }
+
+ // JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Edge
attributes:\n" + attribute);
+
+ return attribute;
+ }
+
}
\ No newline at end of file
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
