Author: ruschein
Date: 2010-02-02 08:18:45 -0800 (Tue, 02 Feb 2010)
New Revision: 19117
Added:
csplugins/trunk/util.compression/
csplugins/trunk/util.compression/build.xml
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
Log:
This is where experimental code should go.
Copied: csplugins/trunk/util.compression (from rev 19105,
corelibs/trunk/util.compression)
Copied: csplugins/trunk/util.compression/build.xml (from rev 19116,
corelibs/trunk/util.compression/build.xml)
===================================================================
--- csplugins/trunk/util.compression/build.xml (rev 0)
+++ csplugins/trunk/util.compression/build.xml 2010-02-02 16:18:45 UTC (rev
19117)
@@ -0,0 +1,204 @@
+
+<project name="cytoscape-util-compression" default="all" basedir=".">
+
+ <!-- =================================================================== -->
+ <!-- Initialization target -->
+ <!-- =================================================================== -->
+ <target name="init">
+ <tstamp/>
+ <property name="name" value="cytoscape-util-compression"/>
+ <property name="version" value="1.0.1"/>
+
+ <echo message="Building ${name} version ${version} ..."/>
+
+ <!-- Inheritable properties -->
+ <property name="debug" value="on"/>
+ <property name="optimize" value="off"/>
+ <property name="deprecation" value="on"/>
+ <property name="fork" value="false"/>
+
+ <!-- Define the directories -->
+ <property name="root.dir" value="."/>
+ <property name="lib.dir" value="${root.dir}/lib"/>
+ <property name="src.dir" value="${root.dir}/src"/>
+ <property name="tests.dir" value="${root.dir}/tests"/>
+ <property name="build.dir" value="${root.dir}/build"/>
+ <property name="javadoc.dir" value="${root.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="${name}.jar"/>
+ <property name="test.jar" value="${name}-tests.jar"/>
+
+ <!-- Define the class path - Defaults to everything in the lib.dir -->
+ <path id="project.class.path">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ </path>
+
+ <!-- Define the junit class path - It needs to find what we just built -->
+ <path id="junit.class.path" >
+ <fileset dir="${root.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="${lib.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ </path>
+
+ <!-- Make sure tests is in the right place -->
+ <condition property="tests.ok">
+ <and>
+ <available file="${tests.dir}" />
+ </and>
+ </condition>
+
+ </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="${optimize}"
+ source="1.5"
+ target="1.5"
+ fork="${fork}">
+<!--
+ <compilerarg line="-Xlint:all -Xlint:-path"/>
+-->
+ </javac>
+ <echo message="Successfully ran compile task!"/>
+ </target>
+
+
+ <!-- =================================================================== -->
+ <!-- Creates the project jar file -->
+ <!-- =================================================================== -->
+ <target name="jar"
+ depends="compile" >
+ <mkdir dir="${lib.dir}"/>
+ <jar destfile="${project.jar}" >
+ <fileset dir="${build.dir}"
+ includes="**"/>
+ </jar>
+ <echo message="Successfully ran jar task!"/>
+ </target>
+
+ <!-- =================================================================== -->
+ <!-- Compiles the tests -->
+ <!-- Note that this compilation occurs AFTER the distribution jar has -->
+ <!-- been created, so that the tests aren't distributed. -->
+ <!-- =================================================================== -->
+ <target name="compile-tests"
+ depends="jar"
+ if="tests.ok">
+ <javac srcdir="${tests.dir}"
+ classpathref="project.class.path"
+ destdir="${build.dir}"
+ debug="${debug}"
+ deprecation="${deprecation}"
+ optimize="${optimize}"
+ 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="${build.dir}" >
+ </jar>
+ <echo message="Successfully ran jar-tests task!"/>
+ </target>
+
+
+
+ <!-- =================================================================== -->
+ <!-- Runs the unit tests. -->
+ <!-- =================================================================== -->
+ <target name="test"
+ depends="jar-tests"
+ if="tests.ok">
+ <junit printsummary="yes"
+ haltonfailure="no"
+ maxmemory="256m" >
+ <classpath refid="junit.class.path"/>
+ <formatter type="plain"
+ usefile="true" />
+ <formatter type="xml"
+ usefile="true" />
+ <batchtest fork="yes"
+ todir="${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,docs,test" />
+
+ <!-- =================================================================== -->
+ <!-- Clean up, get back to original state -->
+ <!-- =================================================================== -->
+ <target name="clean"
+ depends="init">
+ <delete dir="${build.dir}"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete file="${project.jar}"/>
+ <delete file="${test.jar}"/>
+ <echo message="Successfully ran clean task!"/>
+ </target>
+
+</project>
+
Copied:
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
(from rev 19106,
corelibs/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java)
===================================================================
---
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
(rev 0)
+++
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
2010-02-02 16:18:45 UTC (rev 19117)
@@ -0,0 +1,7 @@
+package org.cytoscape.util.compression;
+
+
+interface IntCompressor {
+ int[] compress(final int[] uncompressedData);
+ int[] expand(final int[] compressedData);
+}
Copied:
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
(from rev 19106,
corelibs/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java)
===================================================================
---
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
(rev 0)
+++
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
2010-02-02 16:18:45 UTC (rev 19117)
@@ -0,0 +1,37 @@
+package org.cytoscape.util.compression;
+
+
+class DynamicIntArray {
+ private static final int DEFAULT_INITIAL_CAPACITY = 1000;
+ private int[] array;
+ private int nextIndex = 0;
+
+ DynamicIntArray(final int initialCapacity) {
+ if (initialCapacity > 0)
+ array = new int[initialCapacity];
+ else
+ array = new int[DEFAULT_INITIAL_CAPACITY];
+ }
+
+ void append(final int newValue) {
+ if (nextIndex >= array.length)
+ resize();
+
+ array[nextIndex++] = newValue;
+ }
+
+ private void resize() {
+ final int[] newArray = new int[array.length << 1];
+ System.arraycopy(array, 0, newArray, 0, array.length);
+ array = newArray;
+ }
+}
+
+
+public class RLEIntCompressor {
+ public int[] compress(final int[] uncompressedData) {
+ }
+
+ public int[] expand(final int[] compressedData) {
+ }
+}
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