Author: pwang
Date: 2011-10-28 12:45:18 -0700 (Fri, 28 Oct 2011)
New Revision: 27330
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/networks/hashNetworks/FloatHashNetwork.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/networks/hashNetworks/FloatHashNetwork.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/networks/hashNetworks/FloatHashNetwork.java
2011-10-28 19:39:36 UTC (rev 27329)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/networks/hashNetworks/FloatHashNetwork.java
2011-10-28 19:45:18 UTC (rev 27330)
@@ -1,6 +1,6 @@
package org.idekerlab.PanGIAPlugin.networks.hashNetworks;
-import giny.model.Edge;
+import org.cytoscape.model.CyEdge;
import java.io.BufferedWriter;
import java.io.IOException;
@@ -21,9 +21,8 @@
import org.idekerlab.PanGIAPlugin.utilities.IIterator;
import org.idekerlab.PanGIAPlugin.utilities.files.FileIterator;
import org.idekerlab.PanGIAPlugin.utilities.files.FileUtil;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyTable;
import org.idekerlab.PanGIAPlugin.data.StringVector;
public class FloatHashNetwork extends SFNetwork implements Iterable<SFEdge> {
@@ -51,16 +50,24 @@
super(selfOk, directed);
this.edgeMap = new HashMap<SEdge,
SFEdge>(network.getEdgeCount());
this.nodeMap = new HashMap<String, Set<SEdge>>();
- final CyAttributes edgeAttrs = Cytoscape.getEdgeAttributes();
+ //final CyTable edgeAttrs = network.getDefaultEdgeTable();
- for (Integer edgeIdx: network.getEdgeIndicesArray()) {
- final Edge edge = network.getEdge(edgeIdx);
- final Double attrValue =
edgeAttrs.getDoubleAttribute(edge.getIdentifier(), edgeAttrName);
+// for (Integer edgeIdx: network.getEdgeIndicesArray()) {
+// final CyEdge edge = network.getEdge(edgeIdx);
+// final Double attrValue =
edgeAttrs.getDoubleAttribute(edge.getCyRow().get("name", String.class),
edgeAttrName);
+// if (attrValue != null)
+// add(new
UndirectedSFEdge(edge.getSource().getCyRow().get("name", String.class),
edge.getTarget().getCyRow().get("name", String.class),
+// attrValue.floatValue()));
+// }
+
+ Iterator<CyEdge> edgeIt = network.getEdgeList().iterator();
+ while (edgeIt.hasNext()){
+ final CyEdge edge = edgeIt.next();
+ final Double attrValue =
edge.getCyRow().get(edgeAttrName, Double.class);
if (attrValue != null)
- add(new
UndirectedSFEdge(edge.getSource().getIdentifier(),
edge.getTarget().getIdentifier(),
- attrValue.floatValue()));
- }
-
+ add(new
UndirectedSFEdge(edge.getSource().getCyRow().get("name", String.class),
edge.getTarget().getCyRow().get("name", String.class),
+ attrValue.floatValue()));
+ }
}
@@ -75,7 +82,7 @@
this.add(e.source().value(), e.target().value(),
e.value());
}
- private void convert(final CyNetwork network, final CyAttributes
edgeAttr, final String attrName) {
+ private void convert(final CyNetwork network, final CyTable edgeAttr,
final String attrName) {
}
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