Author: kono
Date: 2010-02-10 23:35:57 -0800 (Wed, 10 Feb 2010)
New Revision: 19290
Modified:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KGMLReader.java
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
Log:
Node generator partially finished.
Modified:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KGMLReader.java
===================================================================
---
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KGMLReader.java
2010-02-11 02:50:36 UTC (rev 19289)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KGMLReader.java
2010-02-11 07:35:57 UTC (rev 19290)
@@ -12,17 +12,24 @@
import org.cytoscape.data.reader.kgml.generated.Pathway;
import cytoscape.CyNetwork;
-import cytoscape.data.readers.GraphReader;
-import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.data.readers.AbstractGraphReader;
import cytoscape.util.URLUtil;
-public class KGMLReader implements GraphReader {
+public class KGMLReader extends AbstractGraphReader {
private static final String PACKAGE_NAME =
"org.cytoscape.data.reader.kgml.generated";
private URL targetURL;
+
+ private int[] nodeIdx;
+ private int[] edgeIdx;
+
+ private String networkName;
+
+ private PathwayMapper mapper;
public KGMLReader(final String fileName) {
+ super(fileName);
System.out.println("File name = " + fileName);
try {
this.targetURL = (new File(fileName)).toURI().toURL();
@@ -33,33 +40,23 @@
}
@Override
- public void doPostProcessing(CyNetwork arg0) {
- // TODO Auto-generated method stub
-
+ public void doPostProcessing(CyNetwork network) {
+ mapper.updateView(network);
}
@Override
public int[] getEdgeIndicesArray() {
- // TODO Auto-generated method stub
- return null;
+ return edgeIdx;
}
@Override
- public CyLayoutAlgorithm getLayoutAlgorithm() {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
public String getNetworkName() {
- // TODO Auto-generated method stub
- return null;
+ return networkName;
}
@Override
public int[] getNodeIndicesArray() {
- // TODO Auto-generated method stub
- return null;
+ return nodeIdx;
}
@Override
@@ -77,6 +74,8 @@
is = URLUtil.getBasicInputStream(targetURL);
pathway = (Pathway) unmarshaller.unmarshal(is);
+ networkName = pathway.getTitle();
+
} catch (Exception e) {
e.printStackTrace();
@@ -86,12 +85,10 @@
is.close();
}
}
-
- System.out.println("Got Pathway: " + pathway.getName());
-
- final PathwayMapper mapper = new PathwayMapper(pathway);
+
+ mapper = new PathwayMapper(pathway);
mapper.doMapping();
-
+ nodeIdx = mapper.getNodeIdx();
}
Modified:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
===================================================================
---
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
2010-02-11 02:50:36 UTC (rev 19289)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
2010-02-11 07:35:57 UTC (rev 19290)
@@ -1,41 +1,111 @@
package org.cytoscape.data.reader.kgml;
+import giny.view.NodeView;
+
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import org.cytoscape.data.reader.kgml.generated.Entry;
+import org.cytoscape.data.reader.kgml.generated.Graphics;
import org.cytoscape.data.reader.kgml.generated.Pathway;
import cytoscape.CyEdge;
+import cytoscape.CyNetwork;
import cytoscape.CyNode;
import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.view.CyNetworkView;
+import cytoscape.visual.NodeShape;
public class PathwayMapper {
+
+ private enum KEGGShape {
+ CIRCLE("circle", NodeShape.ELLIPSE), RECTANGLE("rectangle",
NodeShape.RECT),
+ ROUND_RECTANGLE("roundrectangle", NodeShape.ROUND_RECT);
+
+ private String tag;
+ private NodeShape shape;
+
+ private KEGGShape(final String tag, final NodeShape shape) {
+ this.shape = shape;
+ this.tag = tag;
+ }
+
+ public static int getShape(final String shape) {
+ for(KEGGShape keggShape: KEGGShape.values()) {
+ if(keggShape.tag.equals(shape)) {
+ return keggShape.shape.getGinyShape();
+ }
+ }
+
+ return NodeShape.RECT.getGinyShape();
+ }
+ }
+
+
private Pathway pathway;
+ private int[] nodeIdx;
+ private int[] edgeIdx;
+
public PathwayMapper(final Pathway pathway) {
this.pathway = pathway;
}
public void doMapping() {
mapNode();
-
-
}
+ private final Map<String, Entry> entryMap = new HashMap<String,
Entry>();
+ final Map<String, CyNode> nodeMap = new HashMap<String, CyNode>();
+
private void mapNode() {
+
+ final String pathwayID = pathway.getName();
final List<Entry> components = pathway.getEntry();
- final List<CyNode> nodeList = new ArrayList<CyNode>();
final List<CyEdge> edgeList = new ArrayList<CyEdge>();
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+
for(final Entry comp:components) {
- final CyNode node = Cytoscape.getCyNode(comp.getId(),
true);
- nodeList.add(node);
+ CyNode node = Cytoscape.getCyNode(pathwayID+ "-" +
comp.getId(), true);
+ nodeAttr.setAttribute(node.getIdentifier(),
"KEGG.name", comp.getName());
+ nodeMap.put(comp.getId(), node);
+ entryMap.put(comp.getId(), comp);
}
- Cytoscape.createNetwork(nodeList, edgeList,
pathway.getTitle());
+
+ nodeIdx = new int[nodeMap.values().size()];
+ int idx = 0;
+ for(CyNode node: nodeMap.values()) {
+ nodeIdx[idx] = node.getRootGraphIndex();
+ idx++;
+ }
}
+ protected void updateView(final CyNetwork network) {
+
+ final CyNetworkView view =
Cytoscape.getNetworkView(network.getIdentifier());
+ final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+
+ for (String key:nodeMap.keySet()) {
+
+ final NodeView nv = view.getNodeView(nodeMap.get(key));
+ Graphics nodeGraphics = entryMap.get(key).getGraphics();
+
nv.setXPosition(Double.parseDouble(nodeGraphics.getX()));
+
nv.setYPosition(Double.parseDouble(nodeGraphics.getY()));
+
nv.setWidth(Double.parseDouble(nodeGraphics.getWidth()));
+
nv.setHeight(Double.parseDouble(nodeGraphics.getHeight()));
+ nv.setShape(KEGGShape.getShape(nodeGraphics.getType()));
+ }
+ }
+
+ public int[] getNodeIdx() {
+ return nodeIdx;
+ }
+
}
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