Author: chinmoy
Date: 2009-06-30 21:03:40 -0700 (Tue, 30 Jun 2009)
New Revision: 17176
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
Log:
Network creation and attributes added to ImportTreeFromFile
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
2009-07-01 03:07:32 UTC (rev 17175)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
2009-07-01 04:03:40 UTC (rev 17176)
@@ -1,10 +1,20 @@
package org.cytoscape.phylotree.actions;
import java.awt.event.ActionEvent;
+
+import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.data.Semantics;
import cytoscape.util.CytoscapeAction;
import org.cytoscape.phylotree.PhylotreePlugin;
import org.cytoscape.phylotree.ui.PhyloFileDialog;
+import org.cytoscape.phylotree.parser.*;
import java.io.File;
+import java.util.List;
+import java.util.Iterator;
public class PhyloTreeImportAction extends CytoscapeAction{
@@ -27,14 +37,50 @@
if (pFormat.equalsIgnoreCase("Phylip")){
- // use the parser to read the file
+ // Use the parser to read the file
+ // Parse the file
+ PhylipTreeImpl phylipParser = new PhylipTreeImpl(pFile);
- // create a network
+ CyNetwork cyNetwork =
Cytoscape.createNetwork(pFile.getName(), true);
+ CyAttributes cyAttributes =
Cytoscape.getEdgeAttributes();
- // create attribute
+ // Get all nodes in the PHYLIP tree
+ List<PhylotreeNode> nodeList =
phylipParser.getNodeList();
+ // For each node, get all edges
+ for(Iterator<PhylotreeNode> nodeListIterator =
nodeList.iterator(); nodeListIterator.hasNext();)
+ {
+ PhylotreeNode pNode = nodeListIterator.next();
+
+ // Get edges
+ List<PhylotreeEdge> edgeList =
phylipParser.getEdges(pNode);
+
+ // For each edge, create the two nodes
connected if they do not exist
+ for(Iterator<PhylotreeEdge> edgeListIterator =
edgeList.iterator(); edgeListIterator.hasNext();)
+ {
+ PhylotreeEdge pEdge =
edgeListIterator.next();
+
+ CyNode node2 =
Cytoscape.getCyNode(pEdge.getSourceNode().getName(), true);
+ CyNode node1 =
Cytoscape.getCyNode(pEdge.getTargetNode().getName(), true);
+
+ CyEdge cyEdge =
Cytoscape.getCyEdge(node1, node2, Semantics.INTERACTION, "pp", true, false);
+
+ // Get edge attributes and set them
+ List<Object> edgeAttributes =
phylipParser.getEdgeAttribute(pEdge);
+
cyAttributes.setAttribute(cyEdge.getIdentifier(), "branchLength",
(Double)edgeAttributes.get(0));
+ cyNetwork.addEdge(cyEdge);
+ }
+
+
+ }
+
+ cyAttributes.setUserEditable("branchLength", false);
+ cyAttributes.setUserVisible("branchLength", true);
+
+
+
}
}
}
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-07-01 03:07:32 UTC (rev 17175)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/parser/PhylipTreeImpl.java
2009-07-01 04:03:40 UTC (rev 17176)
@@ -35,6 +35,7 @@
public PhylipTreeImpl(File pTreeFile){
treeStr = getTreeTextFromFile(pTreeFile);
+ nodeList = new LinkedList<PhylotreeNode>();
parse();
}
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