Author: jm
Date: 2011-06-23 12:37:26 -0700 (Thu, 23 Jun 2011)
New Revision: 25901
Modified:
csplugins/trunk/mskcc/gbader/mcode/build.xml
csplugins/trunk/mskcc/gbader/mcode/resources/plugin.props
csplugins/trunk/mskcc/gbader/mcode/src/csplugins/mcode/MCODEResultsPanel.java
Log:
Fixed MCODE so it compiles/runs against Cytoscape 2.6-2.8. Workaround involves
reflection because an API method was renamed :(
Updated build script to accommodate Mavenized 2.7/2.8 layout.
Modified: csplugins/trunk/mskcc/gbader/mcode/build.xml
===================================================================
--- csplugins/trunk/mskcc/gbader/mcode/build.xml 2011-06-23 17:46:25 UTC
(rev 25900)
+++ csplugins/trunk/mskcc/gbader/mcode/build.xml 2011-06-23 19:37:26 UTC
(rev 25901)
@@ -6,16 +6,15 @@
<!-- Change this to the name of your Plug In -->
<!-- The name is used to create the plugin JAR file -->
<property name="plugin.name" value="MCODE" />
- <property name="version" value="1_31" />
+ <property name="version" value="1_32" />
<!-- The directory containing source code -->
<property name="src.dir" value="src" />
<property name="resources.dir" value="resources" />
<property name="cytoscape.dir" value="../../../../cytoscape" />
- <!-- The directory containing library jar files -->
- <property name="lib.dir" value="${cytoscape.dir}/lib" />
-
+ <property name="junit.jar" value="" />
+
<!-- Temporary build directories -->
<property name="build.dir" value="build" />
<property name="build.classes" value="${build.dir}/classes" />
@@ -28,10 +27,11 @@
<!-- Classpath with all lib JAR Files and all Cytoscape Core classes -->
<path id="classpath">
+ <pathelement path="${junit.jar}" />
<pathelement path="${build.classes}" />
<pathelement path="${cytoscape.dir}/cytoscape.jar" />
- <fileset dir="${lib.dir}">
- <include name="**/*.jar" />
+ <fileset dir="${cytoscape.dir}">
+ <include name="lib/*.jar" />
</fileset>
</path>
Modified: csplugins/trunk/mskcc/gbader/mcode/resources/plugin.props
===================================================================
--- csplugins/trunk/mskcc/gbader/mcode/resources/plugin.props 2011-06-23
17:46:25 UTC (rev 25900)
+++ csplugins/trunk/mskcc/gbader/mcode/resources/plugin.props 2011-06-23
19:37:26 UTC (rev 25901)
@@ -11,10 +11,10 @@
pluginDescription=MCODE finds clusters (highly interconnected regions) in a
network. Clusters mean different things in different types of networks. For
instance, clusters in a protein-protein interaction network are often protein
complexes and parts of pathways, while clusters in a protein similarity network
represent protein families.
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=1.31
+pluginVersion=1.32
# Compatible Cytoscape version
-cytoscapeVersion=2.6
+cytoscapeVersion=2.6,2.7,2.8
# Category, use one of the categories listed on the website or create your own
pluginCategory=Analysis
Modified:
csplugins/trunk/mskcc/gbader/mcode/src/csplugins/mcode/MCODEResultsPanel.java
===================================================================
---
csplugins/trunk/mskcc/gbader/mcode/src/csplugins/mcode/MCODEResultsPanel.java
2011-06-23 17:46:25 UTC (rev 25900)
+++
csplugins/trunk/mskcc/gbader/mcode/src/csplugins/mcode/MCODEResultsPanel.java
2011-06-23 19:37:26 UTC (rev 25901)
@@ -12,6 +12,8 @@
import java.awt.Image;
import java.awt.event.ActionEvent;
import java.io.File;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Arrays;
@@ -390,9 +392,7 @@
} else {
clusterArrayList.add(cluster.getClusterName());
}
-
Cytoscape.getNodeAttributes().setAttributeList(
- n.getIdentifier(),
"MCODE_Cluster",
- clusterArrayList);
+
setAttributeList(Cytoscape.getNodeAttributes(), n.getIdentifier(),
"MCODE_Cluster", clusterArrayList);
if (cluster.getSeedNode().intValue() ==
rgi) {
Cytoscape.getNodeAttributes().setAttribute(
@@ -412,6 +412,26 @@
}
/**
+ * This method only exists due to an unfortunately renamed API method.
+ */
+ private void setAttributeList(CyAttributes attributes, String
identifier, String name, List list) {
+ // Try all variants of the renamed API
+ for (String methodName : new String[] {"getAttributeList",
"getListAttribute"}) {
+ try {
+ Method method =
attributes.getClass().getMethod(methodName, String.class, String.class,
List.class);
+ method.invoke(identifier, name, list);
+ return;
+ } catch (SecurityException e) {
+ } catch (NoSuchMethodException e) {
+ } catch (IllegalArgumentException e) {
+ } catch (IllegalAccessException e) {
+ } catch (InvocationTargetException e) {
+ }
+ }
+ return;
+ }
+
+ /**
* Handles the create child network press in the cluster exploration
panel
*/
private class CreateChildAction extends AbstractAction {
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