Author: kono
Date: 2010-07-15 13:55:12 -0700 (Thu, 15 Jul 2010)
New Revision: 20940
Modified:
coreplugins/trunk/TableImport/src/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkLineParser.java
Log:
Bug ID 0001960: "Network Input Delimiter Issue" is fixed. Trailing spaces are
treated as valid values (if delimiter is not space).
Modified:
coreplugins/trunk/TableImport/src/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkLineParser.java
===================================================================
---
coreplugins/trunk/TableImport/src/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkLineParser.java
2010-07-15 19:57:51 UTC (rev 20939)
+++
coreplugins/trunk/TableImport/src/edu/ucsd/bioeng/coreplugin/tableImport/reader/NetworkLineParser.java
2010-07-15 20:55:12 UTC (rev 20940)
@@ -81,44 +81,27 @@
public void parseEntry(String[] parts) {
final Edge edge = addNodeAndEdge(parts);
- if (edge != null) {
+ if (edge != null)
addEdgeAttributes(edge, parts);
- }
}
+
private Edge addNodeAndEdge(final String[] parts) {
- final Node source;
- if (nmp.getSourceIndex().equals(-1) == false &&
(nmp.getSourceIndex() <= (parts.length - 1)) && (parts[nmp.getSourceIndex()] !=
null)) {
- source =
Cytoscape.getCyNode(parts[nmp.getSourceIndex()].trim(), true);
- nodeList.add(source.getRootGraphIndex());
- } else {
- source = null;
- }
+ final Node source = createNode(parts, nmp.getSourceIndex());
+ final Node target = createNode(parts, nmp.getTargetIndex());
- final Node target;
-
- if (nmp.getTargetIndex().equals(-1) == false &&
(nmp.getTargetIndex() <= (parts.length - 1)) && (parts[nmp.getTargetIndex()] !=
null)) {
- target =
Cytoscape.getCyNode(parts[nmp.getTargetIndex()].trim(), true);
- nodeList.add(target.getRootGraphIndex());
- } else {
- target = null;
- }
-
// Single column nodes list. Just add nodes.
- if(source == null || target == null) {
- // do not create edge.
+ if(source == null || target == null)
return null;
- }
final String interaction;
if ((nmp.getInteractionIndex() == -1) ||
(nmp.getInteractionIndex() > (parts.length - 1))
|| (parts[nmp.getInteractionIndex()] == null)) {
interaction = nmp.getDefaultInteraction();
- } else {
- interaction = parts[nmp.getInteractionIndex()].trim();
- }
+ } else
+ interaction = parts[nmp.getInteractionIndex()];
final Edge edge;
edge = Cytoscape.getCyEdge(source, target,
Semantics.INTERACTION, interaction, true, true);
@@ -126,6 +109,18 @@
return edge;
}
+
+
+ private Node createNode(final String[] parts, final Integer nodeIndex) {
+ final Node node;
+ if (nodeIndex.equals(-1) == false && (nodeIndex <=
(parts.length - 1)) && (parts[nodeIndex] != null)) {
+ node = Cytoscape.getCyNode(parts[nodeIndex], true);
+ nodeList.add(node.getRootGraphIndex());
+ } else
+ node = null;
+
+ return node;
+ }
private void addEdgeAttributes(final Edge edge, final String[] parts) {
for (int i = 0; i < parts.length; i++) {
--
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