Author: pwang
Date: 2009-07-24 16:17:27 -0700 (Fri, 24 Jul 2009)
New Revision: 17565
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
Log:
Add support for phyloXML format
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
2009-07-24 23:16:38 UTC (rev 17564)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/actions/PhyloTreeImportAction.java
2009-07-24 23:17:27 UTC (rev 17565)
@@ -12,7 +12,14 @@
import org.cytoscape.phylotree.PhylotreePlugin;
import org.cytoscape.phylotree.ui.PhyloFileDialog;
import org.cytoscape.phylotree.parser.*;
+import org.forester.io.parsers.PhylogenyParserException;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+
import java.io.File;
+import java.io.IOException;
import java.util.List;
import java.util.Iterator;
@@ -37,61 +44,100 @@
return;
}
- if (pFormat.equalsIgnoreCase("Phylip")){
+ if (pFormat.equalsIgnoreCase("phylip")){
+ loadnetwork_phylip(pFile);
+ }
+ else if (pFormat.equalsIgnoreCase("phyloxml")){
+ loadnetwork_phyloXML(pFile);
+ }
+ }
+
+
+ private void loadnetwork_phylip(File pFile) {
+ // Use the parser to read the file
- // Use the parser to read the file
+ // Parse the file
+ PhylipTreeImpl phylipParser = new PhylipTreeImpl(pFile);
+
+ CyNetwork cyNetwork = Cytoscape.createNetwork(pFile.getName(),
true);
+
+ CyAttributes cyAttributes = Cytoscape.getEdgeAttributes();
+
+
+ // 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();
- // Parse the file
- PhylipTreeImpl phylipParser = new PhylipTreeImpl(pFile);
+ // Get edges
+ List<PhylotreeEdge> edgeList =
phylipParser.getEdges(pNode);
- CyNetwork cyNetwork =
Cytoscape.createNetwork(pFile.getName(), true);
-
- CyAttributes cyAttributes =
Cytoscape.getEdgeAttributes();
-
-
- // 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();)
+ // For each edge, create the two nodes connected if
they do not exist
+ for(Iterator<PhylotreeEdge> edgeListIterator =
edgeList.iterator(); edgeListIterator.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();
+ PhylotreeEdge pEdge = edgeListIterator.next();
- CyNode node1 =
Cytoscape.getCyNode(pEdge.getSourceNode().getName(), true);
- CyNode node2 =
Cytoscape.getCyNode(pEdge.getTargetNode().getName(), true);
-
- CyEdge cyEdge =
Cytoscape.getCyEdge(node1, node2, Semantics.INTERACTION, "pp", true, true);
+ CyNode node1 =
Cytoscape.getCyNode(pEdge.getSourceNode().getName(), true);
+ CyNode node2 =
Cytoscape.getCyNode(pEdge.getTargetNode().getName(), true);
- // Get edge attributes and set them
- List<Object> edgeAttributes =
phylipParser.getEdgeAttribute(pEdge);
-
cyAttributes.setAttribute(cyEdge.getIdentifier(), "branchLength",
(Double)edgeAttributes.get(0));
- cyNetwork.addEdge(cyEdge);
- cyNetwork.addNode(node1);
- cyNetwork.addNode(node2);
-
-
- }
-
+ CyEdge cyEdge = Cytoscape.getCyEdge(node1,
node2, Semantics.INTERACTION, "pp", true, true);
+
+ // Get edge attributes and set them
+ List<Object> edgeAttributes =
phylipParser.getEdgeAttribute(pEdge);
+
cyAttributes.setAttribute(cyEdge.getIdentifier(), "branchLength",
(Double)edgeAttributes.get(0));
+ cyNetwork.addEdge(cyEdge);
+ cyNetwork.addNode(node1);
+ cyNetwork.addNode(node2);
+ }
+ }
+
+ cyAttributes.setUserEditable("branchLength", false);
+ cyAttributes.setUserVisible("branchLength", true);
+
+ // Apply default layout
+ CyLayouts.getLayout("slanted_cladogram").doLayout();
+
+ // Apply visual style
+ Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED, null,
"phyloVizMap.props");
+ }
+
+ private void loadnetwork_phyloXML(File pFile) {
+ PhyloXmlParser parser = new PhyloXmlParser();
+
+ parser.setSource(pFile);
+
+ Phylogeny[] trees;
+ try {
+ trees = parser.parse();
+ }
+ catch (PhylogenyParserException ppe){
+ // give some message here
+ return;
+ }
+ catch(IOException ioe){
+ // give some message here
+ return;
+ }
+
+ for (int i=0; i< trees.length; i++){
+ PhylogenyNodeIterator it =
trees[i].iteratorLevelOrder();
+
+ // process each node, get node, edge and attributes
+ while (it.hasNext()){
+ PhylogenyNode node = (PhylogenyNode) it.next();
+ //String nodeName = node.getNodeName();
+ //NodeData nodeData = node.getNodeData(); //
for attributes
+ //Node parent = node.getParent(); // for edge
+
}
-
- cyAttributes.setUserEditable("branchLength", false);
- cyAttributes.setUserVisible("branchLength", true);
-
- // Apply default layout
- CyLayouts.getLayout("slanted_cladogram").doLayout();
-
- // Apply visual style
- Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED,
null, "phyloVizMap.props");
-
}
+
+ //build Cytoscape network here, create Cytoscape attributes here
+
}
+
}
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