Author: kono
Date: 2011-03-30 19:07:00 -0700 (Wed, 30 Mar 2011)
New Revision: 24636
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
Log:
Fixed tab reader to remove prefix of name attribute.
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2011-03-31 02:03:42 UTC (rev 24635)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2011-03-31 02:07:00 UTC (rev 24636)
@@ -126,21 +126,22 @@
sourceID = entry[0].split(SEPARATOR);
targetID = entry[1].split(SEPARATOR);
-
+ final String sourceRawID =
sourceID[0].split(":")[1];
+ final String targetRawID =
targetID[0].split(":")[1];
- CyNode source = nodeMap.get(sourceID[0]);
+ CyNode source = nodeMap.get(sourceRawID);
if(source == null) {
source = network.addNode();
- nodeMap.put(sourceID[0], source);
+ nodeMap.put(sourceRawID, source);
}
- CyNode target = nodeMap.get(targetID[0]);
+ CyNode target = nodeMap.get(targetRawID);
if(target == null) {
target = network.addNode();
- nodeMap.put(targetID[0], target);
+ nodeMap.put(targetRawID, target);
}
- source.getCyRow().set(CyTableEntry.NAME,
sourceID[0]);
- target.getCyRow().set(CyTableEntry.NAME,
targetID[0]);
+ source.getCyRow().set(CyTableEntry.NAME,
sourceRawID);
+ target.getCyRow().set(CyTableEntry.NAME,
targetRawID);
// Set type if not protein
if (sourceID[0].contains(CHEBI)) {
@@ -203,9 +204,11 @@
if (buf != null && buf.length == 2) {
attrName = ATTR_PREFIX + buf[0];
- if(row.getTable().getColumn(attrName) == null)
+ if(row.getTable().getColumn(attrName) == null) {
row.getTable().createColumn(attrName,
String.class, false);
-
+ row.getTable().createColumn(attrName + ".name",
String.class, false);
+ }
+
matcher = miNamePttr.matcher(buf[1]);
if (matcher.find()) {
taxonName = matcher.group();
@@ -289,9 +292,9 @@
final Double score =
Double.parseDouble(scoreString);
row.set(key + "." + scoreType, score);
} catch (Exception e) {
- if (scoreString != null
- &&
scoreString.trim().equals("") == false)
- row.set(key + "." + scoreType,
scoreString);
+// if (scoreString != null
+// &&
scoreString.trim().equals("") == false)
+// row.set(key + "." + scoreType,
scoreString);
continue;
}
--
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