Author: rodche
Date: 2010-01-27 18:16:22 -0800 (Wed, 27 Jan 2010)
New Revision: 19057
Added:
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/ParentFinder.java
Modified:
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
Log:
Improved/optimized "parent finder" code
Modified:
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
===================================================================
---
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
2010-01-28 01:27:03 UTC (rev 19056)
+++
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
2010-01-28 02:16:22 UTC (rev 19057)
@@ -39,14 +39,11 @@
import cytoscape.logger.CyLogger;
import org.biopax.paxtools.controller.EditorMap;
-import org.biopax.paxtools.controller.Fetcher;
import org.biopax.paxtools.io.simpleIO.SimpleEditorMap;
import org.biopax.paxtools.io.simpleIO.SimpleReader;
import org.biopax.paxtools.model.BioPAXElement;
-import org.biopax.paxtools.model.BioPAXFactory;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
-import org.biopax.paxtools.controller.PropertyEditor;
import org.biopax.paxtools.model.level3.*;
import org.biopax.paxtools.model.level2.*;
import org.biopax.paxtools.util.ClassFilterSet;
@@ -779,7 +776,7 @@
/**
* For a BioPAX element,
- * find parent pathway or interaction name.
+ * find parent pathways names.
*
* @param bpe
* @param model
@@ -791,13 +788,12 @@
Set<? extends BioPAXElement> procs =
BioPaxUtil.getObjects(model, pathway.class, Pathway.class);
Set<BioPAXElement> pathways = fetchParentNodeNames(bpe, procs);
- /*
- if(pathways.isEmpty()) {
- procs = BioPaxUtil.getObjects(model, interaction.class,
Interaction.class);
- pathways = fetchParentNodeNames(bpe, procs);
- }
- */
-
+ //if(pathways.isEmpty()) {
+ // // then find interactions
+ // procs = BioPaxUtil.getObjects(model, interaction.class,
Interaction.class);
+ // pathways = fetchParentNodeNames(bpe, procs);
+ //}
+
if(!pathways.isEmpty()) {
for(BioPAXElement pw : pathways) {
pathwayNames.add(getNodeName(pw));
@@ -820,42 +816,12 @@
*/
public static Set<BioPAXElement> fetchParentNodeNames(BioPAXElement
bpe, Set<? extends BioPAXElement> procs) {
Set<BioPAXElement> parents = new HashSet<BioPAXElement>();
- Fetcher fetcher;
- BioPAXFactory factory;
- /*
- * Customized Fetcher is to fix the issue with Level2 - when
NEXT-STEP
- * leads out of the pathway... (do not worry - those pathway
steps that
- * are part of the pathway must be in the PATHWAY-COMPONENTS
set)
- * Also, skipping sub-pathways
- */
- if((bpe instanceof Level2Element)) {
- fetcher = new Fetcher(editorMapLevel2)
- {
- public void visit(BioPAXElement bpe, Model
model,
- PropertyEditor editor) {
- if
(!editor.getProperty().equals("NEXT-STEP"))
- {
- super.visit(bpe, model, editor);
- }
- }
- };
- factory = BioPAXLevel.L2.getDefaultFactory();
- } else if(bpe instanceof Level3Element) {
- fetcher = new Fetcher(editorMapLevel3);
- factory = BioPAXLevel.L3.getDefaultFactory();
- } else {
- return parents;
- }
-
+ EditorMap editorMap = (bpe instanceof Level2Element) ?
editorMapLevel2 : editorMapLevel3;
+ ParentFinder parentFinder = new ParentFinder(editorMap);
for (BioPAXElement proc : procs) {
- Model m = factory.createModel();
- fetcher.fetch(proc, m);
- //System.out.println(bpe + " " + bpe.getRDFId() + ";
proc: " + proc + " " + proc.getModelInterface().getSimpleName() );
- if (m.containsID(bpe.getRDFId())) {
+ if(!parents.contains(proc) &&
parentFinder.isParentChild(proc, bpe))
parents.add(proc);
- }
}
-
return parents;
}
@@ -974,4 +940,5 @@
return (b1 != null && b1) || (b2 != null && b2);
}
+
}
\ No newline at end of file
Added:
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/ParentFinder.java
===================================================================
---
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/ParentFinder.java
(rev 0)
+++
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/ParentFinder.java
2010-01-28 02:16:22 UTC (rev 19057)
@@ -0,0 +1,53 @@
+package cytoscape.coreplugins.biopax.util;
+
+import org.biopax.paxtools.controller.AbstractTraverser;
+import org.biopax.paxtools.controller.EditorMap;
+import org.biopax.paxtools.controller.PropertyEditor;
+import org.biopax.paxtools.model.BioPAXElement;
+import org.biopax.paxtools.model.Model;
+
+/**
+ *
+ *
+ * @author rodch
+ *
+ */
+public final class ParentFinder extends AbstractTraverser {
+ private BioPAXElement query;
+ private boolean found;
+
+ public ParentFinder(EditorMap editorMap) {
+ super(editorMap);
+ }
+
+ @Override
+ protected void visitValue(Object value, BioPAXElement parent, Model
model,
+ PropertyEditor editor) {
+ // skip if already found or it's not a object property
+ if(!found && value instanceof BioPAXElement
+ // explicit fix for the Level2: do not follow
next steps...
+ && !editor.getProperty().equals("NEXT-STEP")) {
+ if(query.equals(value)) {
+ found = true;
+ } else {
+ // continue into the value's values:
+ traverse((BioPAXElement)value, model);
+ }
+ }
+ }
+
+ /**
+ * True if the 'parent' element is in fact contains 'child'
+ * (recursively)
+ *
+ * @param parent
+ * @return
+ */
+ public boolean isParentChild(BioPAXElement parent, BioPAXElement child)
{
+ query = child;
+ found = false;
+ run(parent, null);
+ return found;
+ }
+
+}
\ No newline at end of file
Property changes on:
csplugins/trunk/toronto/rodche/BioPAX/src/cytoscape/coreplugins/biopax/util/ParentFinder.java
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Name: svn:mime-type
+ text/plain
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