Author: scooter
Date: 2010-09-25 16:45:04 -0700 (Sat, 25 Sep 2010)
New Revision: 22061
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/build.xml
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
Log:
Add clustermaker showDialog command and switch to maven-ized ant
Modified: csplugins/trunk/ucsf/scooter/clusterMaker/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/build.xml 2010-09-25 13:24:26 UTC
(rev 22060)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/build.xml 2010-09-25 23:45:04 UTC
(rev 22061)
@@ -1,69 +1,258 @@
-<?xml version = "1.0"?>
-<project name = "clusterMaker" default = "jar" basedir = ".">
+
+<project name="MyPlugin"
+ default="all"
+ basedir="."
+ xmlns:artifact="antlib:org.apache.maven.artifact.ant">
+
+ <!-- =================================================================== -->
+ <!-- Project Settings -->
+ <!-- -->
+ <!-- Adjust each property listed in this target with the appropriate -->
+ <!-- information for this project. -->
+ <!-- =================================================================== -->
+ <target name="settings">
+
+ <!-- The name of your plugin and resulting jar file -->
+ <property name="name" value="clusterMaker"/>
+
+ <!-- The package that contains your plugin class. -->
+ <property name="plugin.class.package" value="clusterMaker"/>
+
+ <!-- The name of your plugin class, i.e. the one that extends Cytoscape
plugin. -->
+ <property name="plugin.class.name"
value="${plugin.class.package}.ClusterMaker"/>
+
+ <!-- The version of your plugin. To support plugin.props, make sure the
+ version is expressed in decimal notation, e.g. 3.0, 3.1, 3.14, etc.
-->
+ <property name="version" value="1.7"/>
+
+ <!-- The version of Cytoscape that you depend on. -->
+ <property name="cytoscape.version" value="2.8.0-beta2-SNAPSHOT"/>
+
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Project initialization settings -->
+ <!-- Most developers shouldn't *need* to adjust any settings here. -->
+ <!-- =================================================================== -->
+ <target name="init"
+ depends="settings" >
+ <tstamp/>
+ <echo message="Building ${name} version ${version} ..."/>
+
+ <!-- Inheritable properties -->
+ <property name="debug" value="on"/>
+ <property name="optimize" value="off"/>
+ <property name="deprecation" value="on"/>
+ <property name="fork" value="false"/>
+
+ <!-- Define the directories -->
+ <property name="root.dir" value="."/>
+ <property name="resources.dir" value="${root.dir}/resources"/>
+ <property name="src.dir" value="${root.dir}/src"/>
+ <property name="tests.dir" value="${root.dir}/tests"/>
+ <property name="build.dir" value="${root.dir}/build"/>
+ <property name="lib.dir" value="${root.dir}/lib"/>
+ <property name="javadoc.dir" value="${build.dir}/API"/>
+ <property name="log.dir" value="${build.dir}/logs" />
+ <property name="junit.report.dir" value="${log.dir}/junit-reports" />
+
+ <!-- Define the relevant files -->
+ <property name="project.jar" value="${name}-${version}.jar"/>
+ <property name="test.jar" value="${name}-${version}-tests.jar"/>
+
+ <!-- Define external dependencies -->
+ <artifact:remoteRepository
+ id="cytoscape_releases"
+
url="http://cytoscape.wodaklab.org/nexus/content/repositories/releases/"; />
+ <artifact:remoteRepository
+ id="cytoscape_snapshots"
+
url="http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/"; />
+ <artifact:dependencies pathId="dependency.classpath">
+ <dependency groupId="cytoscape"
+ artifactId="application"
+ version="${cytoscape.version}"/>
+ <dependency groupId="junit"
+ artifactId="junit"
+ version="3.8.1"/>
+ </artifact:dependencies>
+
+ <!-- Define the class path -->
+ <path id="project.class.path">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <path refid="dependency.classpath"/>
+ </path>
- <property name = "src" location = "src"/>
- <property name = "build" location = "build"/>
- <property name = "build.compiler" value = "modern"/>
- <!-- path to Cytoscape under development (CVS) -->
- <property name = "lib" location = "../../../../cytoscape"/>
- <property name = "jar" location = "jar"/>
- <property name = "doc" location = "doc"/>
+ <!-- Define the junit class path - It needs to find what we just built -->
+ <path id="junit.class.path" >
+ <fileset dir="${root.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="${lib.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <path refid="dependency.classpath"/>
+ </path>
- <property name="cytoscape.plugin" value="${lib}/plugins"/>
+ <!-- Make sure tests is in the right place -->
+ <condition property="tests.ok">
+ <and>
+ <available file="${tests.dir}" />
+ </and>
+ </condition>
- <path id = "classpath">
- <fileset dir = "${lib}">
- <include name = "**/*.jar"/>
- </fileset>
- </path>
+ </target>
- <target name="prepare">
- <mkdir dir="${build}"/>
- </target>
+ <!-- =================================================================== -->
+ <!-- Compiles the project -->
+ <!-- =================================================================== -->
+ <target name="compile"
+ depends="init" >
+ <mkdir dir="${build.dir}"/>
+ <mkdir dir="${log.dir}"/>
+ <javac srcdir="${src.dir}"
+ classpathref="project.class.path"
+ destdir="${build.dir}"
+ debug="${debug}"
+ deprecation="${deprecation}"
+ optimize="${optimize}"
+ fork="${fork}">
+ <compilerarg line="-Xlint:all -Xlint:-path"/>
+ </javac>
+ <echo message="Successfully ran compile task!"/>
+ </target>
- <target name="compile" depends = "prepare" description="Compile with
Cytoscape under development">
- <!-- Compile the java code from ${src} into ${build} -->
- <javac source = "1.5" debug="true" deprecation="true" srcdir = "${src}"
destdir="${build}" encoding="ISO-8859-1">
- <classpath refid = "classpath"/>
- </javac>
- </target>
- <target name="clean" description="clean up" >
- <!-- Delete the ${build} and ${src} directory trees -->
- <delete dir="${build}"/>
- <delete dir="${jar}"/>
- </target>
+ <!-- =================================================================== -->
+ <!-- Creates the project jar file -->
+ <!-- =================================================================== -->
+ <target name="jar"
+ depends="compile" >
+ <filter token="version" value="${version}"/>
+ <copy file="${resources.dir}/plugin.props"
+ todir="${build.dir}/${plugin.class.package}"
+ filtering="true"
+ overwrite="true"/>
+ <unjar dest="${build.dir}">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar" />
+ </fileset>
+ </unjar>
- <target name="jar" depends="compile" description="makes a jar for Cytoscape
under development">
- <mkdir dir = "${jar}"/>
- <copy todir="build/clusterMaker" file="resources/plugin.props"/>
- <jar jarfile="${jar}/clusterMaker.jar">
+ <jar destfile="${project.jar}" >
+ <fileset dir="${build.dir}" includes="**"/>
<manifest>
- <attribute name="Cytoscape-Plugin" value="clusterMaker.ClusterMaker"
/>
+ <attribute name="Cytoscape-Plugin" value="${plugin.class.name}"/>
</manifest>
- <fileset dir="${build}"/>
- </jar>
- </target>
+ </jar>
+ <echo message="Successfully ran jar task!"/>
+ </target>
- <target name = "run" depends="jar" description = "Run under development">
- <java classname = "cytoscape.CyMain" classpathref = "classpath"
- fork = "true" maxmemory = "1g">
- <arg line = "--JLD"/>
- <arg line = "${jar}/clusterMaker.jar"/>
- <arg line = "-vt"/>
- <arg line = "5000"/>
- </java>
- </target>
+ <!-- =================================================================== -->
+ <!-- Compiles the tests -->
+ <!-- Note that this compilation occurs AFTER the distribution jar has -->
+ <!-- been created, so that the tests aren't distributed. -->
+ <!-- =================================================================== -->
+ <target name="compile-tests"
+ depends="jar"
+ if="tests.ok">
+ <javac srcdir="${tests.dir}"
+ classpathref="project.class.path"
+ destdir="${build.dir}"
+ debug="${debug}"
+ deprecation="${deprecation}"
+ optimize="${optimize}"
+ source="1.5"
+ target="1.5"
+ fork="${fork}">
+ <compilerarg line="-Xlint:all -Xlint:-path"/>
+ </javac>
+ <echo message="Successfully ran compile-tests task!"/>
+ </target>
+ <!-- =================================================================== -->
+ <!-- Creates the project-tests.jar file -->
+ <!-- =================================================================== -->
+ <target name="jar-tests"
+ depends="compile-tests"
+ if="tests.ok">
+ <jar jarfile="${test.jar}"
+ basedir="${build.dir}" >
+ </jar>
+ <echo message="Successfully ran jar-tests task!"/>
+ </target>
- <!-- Target to Run JavaDoc -->
- <target name="doc" description="Runs JavaDoc.">
- <javadoc packagenames="clusterMaker.*" sourcepath="src" source="1.5"
destdir="doc"
- classpathref="classpath_release" >
- <link href = "http://java.sun.com/j2se/1.5.0/docs/api/"/>
- <link href = "http://csbi.sourceforge.net/API/"/>
- <link href = "http://chianti.ucsd.edu/Cyto-2_6_0/javadoc/"; />
- </javadoc>
- </target>
+ <!-- =================================================================== -->
+ <!-- Runs the unit tests. -->
+ <!-- =================================================================== -->
+ <target name="test"
+ depends="jar-tests"
+ if="tests.ok">
+ <junit printsummary="yes"
+ haltonfailure="no"
+ maxmemory="256m" >
+ <classpath refid="junit.class.path"/>
+ <formatter type="plain"
+ usefile="true" />
+ <formatter type="xml"
+ usefile="true" />
+ <batchtest fork="yes"
+ todir="${log.dir}"
+ failureProperty="junit.test.failure"
+ errorProperty="junit.test.failure">
+ <fileset dir="${tests.dir}"
+ includes="**/*Test.java"
+ excludes="**/AllTests.java" />
+ </batchtest>
+ </junit>
+ <mkdir dir="${junit.report.dir}"/>
+ <junitreport todir="${junit.report.dir}">
+ <fileset dir="${log.dir}">
+ <include name="TEST-*.xml"/>
+ </fileset>
+ <report format="frames" todir="${junit.report.dir}"/>
+ </junitreport>
+ <fail message="TEST FAILURE!!! Details: ${junit.report.dir}/index.html"
+ if="junit.test.failure"/>
+ <echo message="Successfully ran test task!"/>
+ </target>
+ <!-- =================================================================== -->
+ <!-- Creates the API documentation -->
+ <!-- =================================================================== -->
+ <target name="docs"
+ depends="init" >
+ <mkdir dir="${javadoc.dir}"/>
+ <javadoc sourcepath="${src.dir}"
+ destdir="${javadoc.dir}"
+ packagenames="*"
+ classpathref="project.class.path"
+ author="true"
+ version="true"
+ use="true"
+ splitindex="true"
+ noindex="false"
+ windowtitle="${name} API"
+ doctitle="${name}" />
+ <echo message="Successfully ran docs task!"/>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Do everything -->
+ <!-- =================================================================== -->
+ <target name="all" depends="jar,test,docs" />
+
+ <!-- =================================================================== -->
+ <!-- Clean up, get back to original state -->
+ <!-- =================================================================== -->
+ <target name="clean"
+ depends="init">
+ <delete dir="${build.dir}"/>
+ <delete file="${project.jar}"/>
+ <delete file="${test.jar}"/>
+ <echo message="Successfully ran clean task!"/>
+ </target>
+
</project>
+
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2010-09-25 13:24:26 UTC (rev 22060)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2010-09-25 23:45:04 UTC (rev 22061)
@@ -229,7 +229,7 @@
// Create the dialog
ClusterSettingsDialog settingsDialog = new
ClusterSettingsDialog(alg);
// Pop it up
- settingsDialog.actionPerformed(e);
+ settingsDialog.showDialog();
} else if (viz != null) {
viz.startViz();
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
2010-09-25 13:24:26 UTC (rev 22060)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
2010-09-25 23:45:04 UTC (rev 22061)
@@ -54,6 +54,7 @@
// clusterMaker imports
import clusterMaker.ClusterMaker;
+import clusterMaker.ui.ClusterSettingsDialog;
import clusterMaker.ui.ClusterTask;
import clusterMaker.algorithms.AbstractNetworkClusterer;
import clusterMaker.algorithms.ClusterAlgorithm;
@@ -63,7 +64,8 @@
HASCLUSTER("hasCluster", "Test to see if this network has a cluster of
the requested type", "type"),
GETNETCLUSTER("getNetworkCluster", "Get a cluster of the requested type
and the requested clustertype (node or attribute)",
"type"),
- GETEISENCLUSTER("getCluster", "Get a cluster of the requested
clustertype (node or attribute)", "type=hierarchical|clustertype=node");
+ GETEISENCLUSTER("getCluster", "Get a cluster of the requested
clustertype (node or attribute)", "type=hierarchical|clustertype=node"),
+ SHOWDIALOG("showDialog", "Show the clusterMaker dialog","type");
private String command = null;
private String argList = null;
@@ -142,6 +144,13 @@
throw new RuntimeException("clustertype must be
'node' or 'attribute'");
}
+ } else if (BuiltIn.SHOWDIALOG.equals(command)) {
+ // Get the algorithm
+ ClusterAlgorithm alg = getAlgorithm(args, command);
+ // Show it
+ ClusterSettingsDialog settingsDialog = new
ClusterSettingsDialog(alg);
+ settingsDialog.showDialog();
+ result.addMessage("done");
} else if (algMap.containsKey(command)) {
// Get the algorithm
ClusterAlgorithm alg = algMap.get(command);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
2010-09-25 13:24:26 UTC (rev 22060)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
2010-09-25 23:45:04 UTC (rev 22061)
@@ -107,6 +107,13 @@
setResizable(false);
}
+ public void showDialog() {
+ initialize();
+ pack();
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ setVisible(true);
+ }
+
/**
* DOCUMENT ME!
*
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