Author: mes
Date: 2010-09-15 10:31:22 -0700 (Wed, 15 Sep 2010)
New Revision: 21870
Modified:
csplugins/trunk/ucsd/mes/VennDiagram/build.xml
csplugins/trunk/ucsd/mes/VennDiagram/resources/plugin.props
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
Log:
bug fix for non-intersecting sets
Modified: csplugins/trunk/ucsd/mes/VennDiagram/build.xml
===================================================================
--- csplugins/trunk/ucsd/mes/VennDiagram/build.xml 2010-09-15 17:26:05 UTC
(rev 21869)
+++ csplugins/trunk/ucsd/mes/VennDiagram/build.xml 2010-09-15 17:31:22 UTC
(rev 21870)
@@ -1,5 +1,5 @@
-<project name="VennDiagram" default="all" basedir=".">
+<project name="VennDiagram" default="all" basedir="."
xmlns:artifact="antlib:org.apache.maven.artifact.ant">
<!-- =================================================================== -->
<!-- Initialization target -->
@@ -7,7 +7,7 @@
<target name="init">
<tstamp/>
<property name="name" value="VennDiagram"/>
- <property name="version" value="1.0.1"/>
+ <property name="version" value="1.0"/>
<echo message="Building ${name} version ${version} ..."/>
@@ -19,8 +19,6 @@
<!-- Define the directories -->
<property name="root.dir" value="."/>
- <property name="cytoscape.dir" value="${root.dir}/../../../../cytoscape"/>
- <property name="cytoscape.lib.dir" value="${cytoscape.dir}/lib"/>
<property name="resources.dir" value="${root.dir}/resources"/>
<property name="src.dir" value="${root.dir}/src"/>
<property name="tests.dir" value="${root.dir}/tests"/>
@@ -33,27 +31,29 @@
<property name="project.jar" value="${name}.jar"/>
<property name="test.jar" value="${name}-tests.jar"/>
+ <artifact:remoteRepository
+ id="cytoscape_releases"
+
url="http://cytoscape.wodaklab.org/nexus/content/repositories/releases/"; />
+ <artifact:remoteRepository
+ id="cytoscape_snapshots"
+
url="http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/"; />
+ <artifact:dependencies pathId="dependency.classpath">
+ <dependency groupId="cytoscape"
+ artifactId="application"
+ version="2.8.0-beta1"/>
+ </artifact:dependencies>
+
<!-- Define the class path -->
<path id="project.class.path">
- <fileset dir="${cytoscape.dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape.lib.dir}">
- <include name="*.jar"/>
- </fileset>
+ <path refid="dependency.classpath"/>
</path>
<!-- Define the junit class path - It needs to find what we just built -->
<path id="junit.class.path" >
+ <path refid="dependency.classpath"/>
<fileset dir="${root.dir}">
<include name="*.jar"/>
</fileset>
- <fileset dir="${cytoscape.dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape.lib.dir}">
- <include name="*.jar"/>
- </fileset>
</path>
<!-- Make sure tests is in the right place -->
@@ -92,12 +92,11 @@
<!-- =================================================================== -->
<target name="jar"
depends="compile" >
-<!--
- <copy toDir="${build.dir}">
- <fileset dir="${resources.dir}/testData" includes="*" />
- </copy>
--->
- <copy file="${resources.dir}/plugin.props"
todir="${build.dir}/edu/uic/ncdm/venn"/>
+ <filter token="version" value="${version}"/>
+ <copy file="${resources.dir}/plugin.props"
+ todir="${build.dir}/edu/uic/ncdm/venn"
+ filtering="true"
+ overwrite="true"/>
<jar destfile="${project.jar}" >
<fileset dir="${build.dir}"
includes="**"/>
Modified: csplugins/trunk/ucsd/mes/VennDiagram/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsd/mes/VennDiagram/resources/plugin.props 2010-09-15
17:26:05 UTC (rev 21869)
+++ csplugins/trunk/ucsd/mes/VennDiagram/resources/plugin.props 2010-09-15
17:31:22 UTC (rev 21870)
@@ -11,10 +11,10 @@
pluginDescription=This plugin generates a Venn/Euler Diagram of shared nodes
for a selection of networks.
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.1
+pluginversi...@version@
# Compatible Cytoscape version
-cytoscapeVersion=2.5,2.6,2.7
+cytoscapeVersion=2.5,2.6,2.7,2.8
# Category, use one of the categories listed on the website or create your own
pluginCategory=Analysis
@@ -24,7 +24,3 @@
# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
pluginAuthorsIntsitutions=Leland Wilkinson:University of Illinois,
Chicago;Mike Smoot:UC San Diego
-# -- The following properties should be set ONLY BY CORE PLUGINS -- #
-downloadURL=http://cytoscape.org/plugins/plugins.xml
-uniqueID=1123456641
-
Modified:
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
===================================================================
---
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
2010-09-15 17:26:05 UTC (rev 21869)
+++
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
2010-09-15 17:31:22 UTC (rev 21870)
@@ -303,12 +303,12 @@
}
public void computeInitialConfiguration() {
- if (nCircles < 3) {
+ double[][] s = computeDistanceMatrix();
+ if (s == null) {
fixedStart();
return;
}
- double[][] s = computeDistanceMatrix();
double[] q = new double[nCircles];
double[][] x = new double[nCircles][2];
@@ -353,6 +353,7 @@
}
private double[][] computeDistanceMatrix() {
+ int nIntersections = 0;
double[][] s = new double[nCircles][nCircles];
for (int i = 0; i < nPolygons; i++) {
char[] c = encode(i);
@@ -367,12 +368,16 @@
}
}
}
- for (int i = 1; i < s.length; i++) {
- for (int j = 0; j < i; j++) {
- s[i][j] = -s[i][j];
- s[j][i] = s[i][j];
+ for (int j = 1; j < s.length; j++) {
+ for (int k = 0; k < j; k++) {
+ if (s[j][k] != 0)
+ nIntersections++;
+ s[j][k] = -s[j][k];
+ s[k][j] = s[j][k];
}
}
+ if (nIntersections < nCircles)
+ s = null;
return s;
}
--
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