Author: kono
Date: 2010-02-11 02:45:18 -0800 (Thu, 11 Feb 2010)
New Revision: 19292
Added:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGShape.java
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:
Edge generator added. Relations only.
Added:
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGShape.java
===================================================================
---
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGShape.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KEGGShape.java
2010-02-11 10:45:18 UTC (rev 19292)
@@ -0,0 +1,34 @@
+package org.cytoscape.data.reader.kgml;
+
+import cytoscape.visual.NodeShape;
+
+public enum KEGGShape {
+ CIRCLE("circle", NodeShape.ELLIPSE), RECTANGLE("rectangle",
+ NodeShape.RECT), ROUND_RECTANGLE("roundrectangle",
+ NodeShape.ROUND_RECT), LINE("line", null);
+
+ 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)) {
+ if (keggShape.shape == null)
+ return -1;
+ else
+ return keggShape.shape.getGinyShape();
+ }
+ }
+
+ return NodeShape.RECT.getGinyShape();
+ }
+
+ public String getTag() {
+ return this.tag;
+ }
+}
\ No newline at end of file
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 09:28:41 UTC (rev 19291)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/KGMLReader.java
2010-02-11 10:45:18 UTC (rev 19292)
@@ -89,6 +89,7 @@
mapper = new PathwayMapper(pathway);
mapper.doMapping();
nodeIdx = mapper.getNodeIdx();
+ edgeIdx = mapper.getEdgeIdx();
}
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 09:28:41 UTC (rev 19291)
+++
csplugins/trunk/ucsd/kono/KGMLReader/src/org/cytoscape/data/reader/kgml/PathwayMapper.java
2010-02-11 10:45:18 UTC (rev 19292)
@@ -12,6 +12,8 @@
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 org.cytoscape.data.reader.kgml.generated.Relation;
+import org.cytoscape.data.reader.kgml.generated.Subtype;
import cytoscape.CyEdge;
import cytoscape.CyNetwork;
@@ -32,34 +34,7 @@
import cytoscape.visual.mappings.PassThroughMapping;
public class PathwayMapper {
-
- private enum KEGGShape {
- CIRCLE("circle", NodeShape.ELLIPSE), RECTANGLE("rectangle",
- NodeShape.RECT),
ROUND_RECTANGLE("roundrectangle",
- NodeShape.ROUND_RECT), LINE("line", null);
-
- 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)) {
- if (keggShape.shape == null)
- return -1;
- else
- return
keggShape.shape.getGinyShape();
- }
- }
-
- return NodeShape.RECT.getGinyShape();
- }
- }
-
+
private final Pathway pathway;
private final String pathwayName;
@@ -73,6 +48,7 @@
public void doMapping() {
mapNode();
+ mapEdge();
}
private final Map<String, Entry> entryMap = new HashMap<String,
Entry>();
@@ -87,7 +63,7 @@
final CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
for (final Entry comp : components) {
- if
(!comp.getGraphics().getType().equals(KEGGShape.LINE.tag)) {
+ if
(!comp.getGraphics().getType().equals(KEGGShape.LINE.getTag())) {
CyNode node = Cytoscape.getCyNode(pathwayID +
"-"
+ comp.getId(), true);
nodeAttr.setAttribute(node.getIdentifier(),
"KEGG.name", comp
@@ -104,6 +80,37 @@
idx++;
}
}
+
+ private void mapEdge() {
+ final List<Relation> relations = pathway.getRelation();
+ final List<CyEdge> edges = new ArrayList<CyEdge>();
+
+ for(Relation rel: relations) {
+ final String ent1 = rel.getEntry1();
+ final String ent2 = rel.getEntry2();
+
+ final List<Subtype> subs = rel.getSubtype();
+ final String type = rel.getType();
+ CyNode source = nodeMap.get(ent1);
+ CyNode target = nodeMap.get(ent2);
+ CyNode compound = nodeMap.get(subs.get(0).getValue());
+ System.out.println(source.getIdentifier());
+ System.out.println(target.getIdentifier());
+ System.out.println(compound.getIdentifier() + "\n\n");
+ CyEdge edge1 = Cytoscape.getCyEdge(source, compound,
"interaction", type, true);
+ CyEdge edge2 = Cytoscape.getCyEdge(compound, target,
"interaction", type, true);
+ edges.add(edge1);
+ edges.add(edge2);
+ }
+
+ edgeIdx = new int[edges.size()];
+ int idx = 0;
+ for (CyEdge edge : edges) {
+ edgeIdx[idx] = edge.getRootGraphIndex();
+ idx++;
+ }
+
+ }
protected void updateView(final CyNetwork network) {
@@ -204,4 +211,8 @@
return nodeIdx;
}
+ public int[] getEdgeIdx() {
+ return edgeIdx;
+ }
+
}
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