Author: scooter
Date: 2008-09-06 21:18:08 -0700 (Sat, 06 Sep 2008)
New Revision: 14847
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/Matrix.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/treeview/model/TreeViewModel.java
Log:
Make sure we can handle integer attributes also.
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/Matrix.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/Matrix.java
2008-09-07 03:51:44 UTC (rev 14846)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/Matrix.java
2008-09-07 04:18:08 UTC (rev 14847)
@@ -366,14 +366,22 @@
// For each edge, get the attribute and update the matrix and
mask values
int index = 0;
int column;
+ byte attributeType = edgeAttributes.getType(weight);
for (CyNode node: nodeList) {
this.rowLabels[index] = node.getIdentifier();
this.rowNodes[index] = node;
this.columnLabels[index] = node.getIdentifier();
// Get the list of adjacent edges
- List<CyEdge> edgeList =
network.getAdjacentEdgesList(node, true, true, true);
+ List<CyEdge> edgeList =
network.getAdjacentEdgesList(node, true, true, true);
for (CyEdge edge: edgeList) {
- Double val =
edgeAttributes.getDoubleAttribute(edge.getIdentifier(), weight);
+ Double val = null;
+ if (attributeType ==
CyAttributes.TYPE_FLOATING) {
+ val =
edgeAttributes.getDoubleAttribute(edge.getIdentifier(), weight);
+ } else {
+ Integer v =
edgeAttributes.getIntegerAttribute(edge.getIdentifier(), weight);
+ if (v != null)
+ val =
Double.valueOf(v.toString());
+ }
if (edge.getSource() == node) {
column =
nodeList.indexOf(edge.getTarget());
matrix[index][column] = val;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/treeview/model/TreeViewModel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/treeview/model/TreeViewModel.java
2008-09-07 03:51:44 UTC (rev 14846)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/treeview/model/TreeViewModel.java
2008-09-07 04:18:08 UTC (rev 14847)
@@ -128,12 +128,20 @@
for (int cell = 0; cell < nGene*nExpr; cell++)
exprData[cell] = DataModel.NODATA;
+ byte attributeType = edgeAttributes.getType(attribute);
Iterator edgeIterator = network.edgesIterator();
while (edgeIterator.hasNext()) {
CyEdge edge = (CyEdge)edgeIterator.next();
CyNode source = (CyNode)edge.getSource();
CyNode target = (CyNode)edge.getTarget();
- Double val =
edgeAttributes.getDoubleAttribute(edge.getIdentifier(), attribute);
+ Double val = null;
+ if (attributeType ==
CyAttributes.TYPE_FLOATING) {
+ val =
edgeAttributes.getDoubleAttribute(edge.getIdentifier(), attribute);
+ } else if (attributeType ==
CyAttributes.TYPE_INTEGER) {
+ Integer v =
edgeAttributes.getIntegerAttribute(edge.getIdentifier(), attribute);
+ if (v != null)
+ val =
Double.valueOf(v.toString());
+ }
int gene =
geneList.indexOf(source.getIdentifier());
int expr =
geneList.indexOf(target.getIdentifier());
// System.out.println("Edge
"+source.getIdentifier()+"("+gene+") "+
@@ -151,7 +159,18 @@
for (String nodeName: geneList) {
int expr = 0;
for (String attribute: arrayList) {
- Double val =
nodeAttributes.getDoubleAttribute(nodeName, attribute);
+ byte attributeType =
nodeAttributes.getType(attribute);
+ Double val = null;
+ if (attributeType ==
CyAttributes.TYPE_FLOATING) {
+ val =
nodeAttributes.getDoubleAttribute(nodeName, attribute);
+ } else if (attributeType ==
CyAttributes.TYPE_INTEGER) {
+ Integer v =
nodeAttributes.getIntegerAttribute(nodeName, attribute);
+ if (v != null)
+ val =
Double.valueOf(v.toString());
+ else
+ val = null;
+ }
+
if (val == null) {
exprData[gene*nExpr + expr] =
DataModel.NODATA;
} else {
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