Author: rodche
Date: 2010-01-30 20:19:47 -0800 (Sat, 30 Jan 2010)
New Revision: 19085
Removed:
coreplugins/trunk/cPath2/lib/biopax.jar
Modified:
coreplugins/trunk/cPath2/build.xml
coreplugins/trunk/cPath2/plugin.props
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java
Log:
PathwayCommons (cpath2) plugin: cleaned some deprecated code; ant script
polished; biopax.jar removed from /lib (because it's available in the
cytoscape's /lib);
Modified: coreplugins/trunk/cPath2/build.xml
===================================================================
--- coreplugins/trunk/cPath2/build.xml 2010-01-31 04:16:37 UTC (rev 19084)
+++ coreplugins/trunk/cPath2/build.xml 2010-01-31 04:19:47 UTC (rev 19085)
@@ -2,190 +2,190 @@
<!-- build.xml - Build file for Cytoscape cPath2 Plug In -->
<project default="all" name="Cytoscape cPath 2 PlugIn">
- <!-- Project Name -->
- <property name="project_name" value="cpath2"/>
- <!-- Version Numbers -->
- <property name="version" value="1_0"/>
- <!-- Define Check Style Task -->
- <!-- The directory containing source code -->
- <property name="src.dir" value="src"/>
+ <!-- Project Name -->
+ <property name="project_name" value="cpath2"/>
+ <!-- Version Numbers -->
+ <property name="version" value="1_0"/>
+ <!-- Define Check Style Task -->
+ <!-- The directory containing source code -->
+ <property name="src.dir" value="src"/>
<!-- The Cytoscape lib directory -->
<property name="cytoscape_lib_dir" value="../../cytoscape/lib"/>
<!-- The Cytoscape jar directory -->
<property name="cytoscape_jar_dir" value="../../cytoscape"/>
<!-- The Cytoscape plugin directory (core) -->
<property name="cytoscape_plugin_dir" value="../../cytoscape/plugins"/>
- <!-- The directory containing the configuration files -->
- <property name="config.dir" value="config"/>
- <!-- Temporary build directories -->
- <property name="build.dir" value="build"/>
- <property name="build.classes" value="${build.dir}/classes"/>
- <!-- Jars directory -->
- <property name="jars.dir" value="${build.dir}/jars"/>
+ <!-- The directory containing the configuration files -->
+ <property name="config.dir" value="config"/>
+ <!-- Temporary build directories -->
+ <property name="build.dir" value="build"/>
+ <property name="build.classes" value="${build.dir}/classes"/>
+ <!-- Jars directory -->
+ <property name="jars.dir" value="${build.dir}/jars"/>
<!-- Jar file -->
- <property name="project_jar" value="${project_name}.jar"/>
- <!-- PlugIns directory -->
- <property name="plugins.dir" value="plugins"/>
- <!-- Styles Directory -->
- <property name="style.dir" value="style"/>
- <!-- Release directories -->
- <property name="release.dir" value="${build.dir}/release"/>
- <!-- Versioned Release Directory -->
- <property name="version_release.dir"
+ <property name="project_jar" value="${project_name}.jar"/>
+ <!-- PlugIns directory -->
+ <property name="plugins.dir" value="plugins"/>
+ <!-- Styles Directory -->
+ <property name="style.dir" value="style"/>
+ <!-- Release directories -->
+ <property name="release.dir" value="${build.dir}/release"/>
+ <!-- Versioned Release Directory -->
+ <property name="version_release.dir"
value="${release.dir}/${project_name}_${version}"/>
- <!-- Zip Release directories -->
- <property name="zip.dir" value="${build.dir}/zip_release"/>
- <!-- Global "magic" property for <javac> -->
- <property name="build.compiler" value="modern"/>
- <!-- Junit Directory -->
- <property name="junit.dir" value="${build.dir}/junit"/>
- <!-- Temp Directory -->
- <property name="temp.dir" value="temp"/>
+ <!-- Zip Release directories -->
+ <property name="zip.dir" value="${build.dir}/zip_release"/>
+ <!-- Global "magic" property for <javac> -->
+ <property name="build.compiler" value="modern"/>
+ <!-- Junit Directory -->
+ <property name="junit.dir" value="${build.dir}/junit"/>
+ <!-- Temp Directory -->
+ <property name="temp.dir" value="temp"/>
- <!-- Classpath with all lib JAR Files -->
- <path id="classpath">
- <pathelement path="${build.classes}"/>
- <fileset dir="${cytoscape_lib_dir}/build-libs">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape_lib_dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="${cytoscape_jar_dir}">
- <include name="cytoscape.jar"/>
- </fileset>
- <fileset dir="${cytoscape_plugin_dir}">
- <include name="biopax.jar"/>
- </fileset>
- <fileset dir="lib">
- <include name="*.jar"/>
- </fileset>
- </path>
+ <!-- Classpath with all lib JAR Files -->
+ <path id="classpath">
+ <pathelement path="${build.classes}"/>
+ <fileset dir="${cytoscape_lib_dir}/build-libs">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="${cytoscape_lib_dir}">
+ <include name="*.jar" />
+ </fileset>
+ <fileset dir="${cytoscape_jar_dir}">
+ <include name="cytoscape.jar" />
+ </fileset>
+ <fileset dir="${cytoscape_plugin_dir}">
+ <include name="biopax.jar" />
+ </fileset>
+ <fileset dir="lib">
+ <include name="*.jar" />
+ </fileset>
+ </path>
- <!-- For XJC compiler task -->
- <taskdef name="xjc" classname="com.sun.tools.xjc.XJCTask">
- <classpath refid="classpath" />
- </taskdef>
+ <!-- For XJC compiler task -->
+ <taskdef name="xjc" classname="com.sun.tools.xjc.XJCTask">
+ <classpath refid="classpath" />
+ </taskdef>
- <!-- Target to create the build directories prior to compilation -->
- <target name="prepare">
- <mkdir dir="${build.dir}"/>
- <mkdir dir="${build.dir}/docs"/>
- <mkdir dir="${build.classes}"/>
- <mkdir dir="${jars.dir}"/>
- <echo>"basedir ${basedir}"</echo>
- </target>
+ <!-- Target to create the build directories prior to compilation -->
+ <target name="prepare">
+ <mkdir dir="${build.dir}" />
+ <mkdir dir="${build.dir}/docs" />
+ <mkdir dir="${build.classes}" />
+ <mkdir dir="${jars.dir}"/>
+ <echo>"basedir ${basedir}"</echo>
+ </target>
- <!-- Generate package using XJC compiler -->
- <target name="bind" depends="prepare" description="Run XJC to generate new
packages.">
- <mkdir
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/search_response"/>
- <xjc schema="xml/SearchResponse.xsd"
+ <!-- Generate package using XJC compiler -->
+ <target name="bind" depends="prepare" description="Run XJC to generate
new packages.">
+ <mkdir
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/search_response"/>
+ <xjc schema="xml/SearchResponse.xsd"
destdir="${src.dir}"
package="org.cytoscape.coreplugin.cpath2.schemas.search_response">
- <produces
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/search_response"/>
- <arg value="-nv"/>
- </xjc>
- <mkdir
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/summary_response"/>
- <xjc schema="xml/SummaryResponse.xsd"
+ <produces
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/search_response"/>
+ <arg value="-nv"/>
+ </xjc>
+ <mkdir
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/summary_response"/>
+ <xjc schema="xml/SummaryResponse.xsd"
destdir="${src.dir}"
package="org.cytoscape.coreplugin.cpath2.schemas.summary_response">
- <produces
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/summary_response"/>
- <arg value="-nv"/>
- </xjc>
- </target>
+ <produces
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas/summary_response"/>
+ <arg value="-nv"/>
+ </xjc>
+ </target>
- <!-- Target to clean out all directories -->
- <target description="Removes all generated files." name="clean">
- <delete dir="${build.dir}"/>
- <delete dir="${jars.dir}"/>
- <delete dir="${plugins.dir}"/>
- <delete dir="${junit.dir}"/>
- <delete dir="${temp.dir}"/>
- <delete>
- <fileset dir="." includes="*.log"/>
- <fileset dir="." includes="*.gz"/>
- </delete>
- <delete dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas"/>
- </target>
+ <!-- Target to clean out all directories -->
+ <target description="Removes all generated files." name="clean">
+ <delete dir="${build.dir}"/>
+ <delete dir="${jars.dir}"/>
+ <delete dir="${plugins.dir}"/>
+ <delete dir="${junit.dir}"/>
+ <delete dir="${temp.dir}"/>
+ <delete>
+ <fileset dir="." includes="*.log"/>
+ <fileset dir="." includes="*.gz"/>
+ </delete>
+ <delete
dir="${src.dir}/org/cytoscape/coreplugin/cpath2/schemas"/>
+ </target>
- <!-- Target to compile all code -->
- <target depends="bind" description="Compiles all source code."
+ <!-- Target to compile all code -->
+ <target depends="bind" description="Compiles all source code."
name="compile">
- <javac debug="true" debuglevel="source,lines,var"
+ <javac debug="true" debuglevel="source,lines,var"
source="1.5"
target="1.5"
destdir="${build.classes}" nowarn="on" srcdir="${src.dir}"
deprecation="true">
- <classpath refid="classpath"/>
- </javac>
+ <classpath refid="classpath"/>
+ </javac>
- <!-- Copy all resources -->
- <copy todir="${build.classes}">
- <fileset dir="${src.dir}">
- <exclude name="**/*.java"/>
- </fileset>
- </copy>
+ <!-- Copy all resources -->
+ <copy todir="${build.classes}">
+ <fileset dir="${src.dir}">
+ <exclude name="**/*.java"/>
+ </fileset>
+ </copy>
- <!-- Copy plugin.props -->
- <copy todir="${build.classes}/org/cytoscape/coreplugin/cpath2/plugin"
+ <!-- Copy plugin.props -->
+ <copy
todir="${build.classes}/org/cytoscape/coreplugin/cpath2/plugin"
file="plugin.props"/>
- </target>
+ </target>
- <!-- Target to Run Cytoscape with CPath2 Plugin -->
- <target depends="jar" description="Runs Cytoscape with cPath2 Plugin."
+ <!-- Target to Run Cytoscape with CPath2 Plugin -->
+ <target depends="jar" description="Runs Cytoscape with cPath2 Plugin."
name="run">
- <copy todir="${plugins.dir}">
- <fileset dir="${jars.dir}">
- <include name="${project_jar}"/>
+ <copy todir="${plugins.dir}">
+ <fileset dir="${jars.dir}">
+ <include name="${project_jar}"/>
</fileset>
- </copy>
- <java classname="cytoscape.CyMain" classpathref="classpath"
+ </copy>
+ <java classname="cytoscape.CyMain" classpathref="classpath"
fork="true" maxmemory="1000M">
- <arg line="-p plugins/cpath2.jar"/>
- <arg line="-p ${cytoscape_plugin_dir}/biopax.jar"/>
- <arg line="-p ${cytoscape_plugin_dir}/yLayouts.jar"/>
- <arg line="-p ${cytoscape_plugin_dir}/quick_find.jar"/>
- <arg line="-p ${cytoscape_plugin_dir}/browser.jar"/>
- <arg line="-p ${cytoscape_plugin_dir}/linkout.jar"/>
- </java>
- </target>
+ <arg line="-p plugins/cpath2.jar"/>
+ <arg line="-p ${cytoscape_plugin_dir}/biopax.jar"/>
+ <arg line="-p ${cytoscape_plugin_dir}/yLayouts.jar"/>
+ <arg line="-p ${cytoscape_plugin_dir}/quick_find.jar"/>
+ <arg line="-p ${cytoscape_plugin_dir}/browser.jar"/>
+ <arg line="-p ${cytoscape_plugin_dir}/linkout.jar"/>
+ </java>
+ </target>
- <!-- Target to Create PlugIn JAR -->
- <target depends="compile" description="Creates PlugIn JAR" name="jar">
+ <!-- Target to Create PlugIn JAR -->
+ <target depends="compile" description="Creates PlugIn JAR" name="jar">
- <!-- Start clean -->
- <delete dir="${jars.dir}"/>
- <mkdir dir="${jars.dir}"/>
+ <!-- Start clean -->
+ <delete dir="${jars.dir}"/>
+ <mkdir dir="${jars.dir}"/>
- <!-- Unjar Third Party Libs -->
- <mkdir dir="temp"/>
- <unjar dest="${temp.dir}">
- <fileset dir="lib">
- <include name="*.jar"/>
- </fileset>
- </unjar>
+ <!-- Unjar Third Party Libs -->
+ <mkdir dir="temp"/>
+ <unjar dest="${temp.dir}">
+ <fileset dir="lib">
+ <include name="*.jar"/>
+ </fileset>
+ </unjar>
- <!-- Create cPath2 Jar -->
- <jar destfile="${jars.dir}/${project_jar}">
- <fileset dir="${build.classes}"/>
- <fileset dir="${temp.dir}"/>
- <manifest>
- <attribute name="Cytoscape-Plugin"
value="org.cytoscape.coreplugin.cpath2.plugin.CPathPlugIn2"/>
- </manifest>
- </jar>
- <delete dir="${temp.dir}"/>
- </target>
+ <!-- Create cPath2 Jar -->
+ <jar destfile="${jars.dir}/${project_jar}">
+ <fileset dir="${build.classes}"/>
+ <fileset dir="${temp.dir}"/>
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
value="org.cytoscape.coreplugin.cpath2.plugin.CPathPlugIn2"/>
+ </manifest>
+ </jar>
+ <delete dir="${temp.dir}"/>
+ </target>
- <!-- Target to Run CheckStyle on all Source Code -->
- <!-- Uses the Sun Coding Conventions Configuration -->
- <target description="Checks Sun Coding Conventions" name="check">
- <checkstyle config="${config.dir}/sun_checks.xml">
- <fileset dir="${src.dir}/org">
- <include name="**/*.java"/>
- </fileset>
- </checkstyle>
- </target>
+ <!-- Target to Run CheckStyle on all Source Code -->
+ <!-- Uses the Sun Coding Conventions Configuration -->
+ <target description="Checks Sun Coding Conventions" name="check">
+ <checkstyle config="${config.dir}/sun_checks.xml">
+ <fileset dir="${src.dir}/org">
+ <include name="**/*.java"/>
+ </fileset>
+ </checkstyle>
+ </target>
- <!-- Builds and tests everything -->
- <target depends="jar" description="Builds and tests everything"
name="all"/>
+ <!-- Builds and tests everything -->
+ <target depends="jar" description="Builds and tests everything"
name="all"/>
</project>
Deleted: coreplugins/trunk/cPath2/lib/biopax.jar
===================================================================
(Binary files differ)
Modified: coreplugins/trunk/cPath2/plugin.props
===================================================================
--- coreplugins/trunk/cPath2/plugin.props 2010-01-31 04:16:37 UTC (rev
19084)
+++ coreplugins/trunk/cPath2/plugin.props 2010-01-31 04:19:47 UTC (rev
19085)
@@ -15,14 +15,14 @@
cytoscapeVersion=2.7
# Category, use one of the categories listed on the
http://cytoscape.org/plugins2.php site
-pluginCategory=Network and Attribute I/O
+pluginCategory=Core
# URL to a website that gives more information about your plugin, Ex.
http://my-lab-site.org
projectURL=http://www.pathwaycommons.org
# List of authors. Note each author and institution pair are separated by a :
(colon)
# each additional author institution pair must be separated from other pairs
by a ; (semicolon)
-pluginAuthorsIntsitutions=Ethan Cerami, Benjamin Gross, Chris Sander:Memorial
Sloan-Kettering Cancer Center;Igor Rodchenkov, Gary Bader:Uniersity of Toronto
+pluginAuthorsIntsitutions=Ethan Cerami, Benjamin Gross and Chris
Sander:Memorial Sloan-Kettering Cancer Center;Igor Rodchenkov and Gary
Bader:University of Toronto
# Date this plugin/plugin version was released
releaseDate=January 29, 2010
Modified:
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java
===================================================================
---
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java
2010-01-31 04:16:37 UTC (rev 19084)
+++
coreplugins/trunk/cPath2/src/org/cytoscape/coreplugin/cpath2/cytoscape/BinarySifVisualStyleUtil.java
2010-01-31 04:19:47 UTC (rev 19085)
@@ -49,20 +49,19 @@
if (visualStyle == null) {
visualStyle = new VisualStyle(BINARY_SIF_VISUAL_STYLE);
- NodeAppearanceCalculator nac = new NodeAppearanceCalculator();
+ NodeAppearanceCalculator nac =
visualStyle.getNodeAppearanceCalculator();
// set node opacity
nac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.NODE_OPACITY,
125);
// unlock node size
- nac.setNodeSizeLocked(false);
+
visualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
createNodeShapes(nac);
createNodeColors(nac);
createNodeLabel(nac);
- EdgeAppearanceCalculator eac = new EdgeAppearanceCalculator();
-
eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_LINE_WIDTH,
- 4.0);
+ EdgeAppearanceCalculator eac =
visualStyle.getEdgeAppearanceCalculator();
+
eac.getDefaultAppearance().set(cytoscape.visual.VisualPropertyType.EDGE_LINE_WIDTH,4.0);
createEdgeColor (eac);
createDirectedEdges (eac);
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