Author: mes Date: 2010-08-03 12:05:25 -0700 (Tue, 03 Aug 2010) New Revision: 21139
Added: cytoscape/trunk/pom.xml cytoscape/trunk/src/ Removed: cytoscape/trunk/application/pom.xml cytoscape/trunk/application/src/ Log: moved application project back to top level Deleted: cytoscape/trunk/application/pom.xml =================================================================== --- cytoscape/trunk/application/pom.xml 2010-08-03 18:58:42 UTC (rev 21138) +++ cytoscape/trunk/application/pom.xml 2010-08-03 19:05:25 UTC (rev 21139) @@ -1,584 +0,0 @@ -<project xmlns="http://maven.apache.org/POM/4.0.0"; - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 - http://maven.apache.org/maven-v4_0_0.xsd";> - <modelVersion>4.0.0</modelVersion> - - <groupId>cytoscape</groupId> - <artifactId>application</artifactId> - <version>2.8.0-SNAPSHOT</version> - <packaging>jar</packaging> - <name>Cytoscape Application</name> - - <properties> - <corelibs.version>2.8.0-SNAPSHOT</corelibs.version> - <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> - </properties> - - <build> - - <!-- This block allows fields to be substituted into resource files, - such as the version number in cytoscape.props. --> - <resources> - <resource> - <directory>src/main/resources</directory> - <filtering>true</filtering> - </resource> - </resources> - - <plugins> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-compiler-plugin</artifactId> - <configuration> - <source>1.5</source> - <target>1.5</target> - </configuration> - </plugin> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-surefire-plugin</artifactId> - <configuration> - <argLine>-Xmx256m</argLine> - <redirectTestOutputToFile>true</redirectTestOutputToFile> - </configuration> - </plugin> - <!-- - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-javadoc-plugin</artifactId> - <configuration> - <encoding>UTF-8</encoding> - <locale>en</locale> - <javadocVersion>1.5</javadocVersion> - <links> - <link>http://download.oracle.com/javase/1.5.0/docs/api/</link> - </links> - <footer>Cytoscape API</footer> - <header>Cytoscape API</header> - <bottom>Copyright 2010 Cytoscape Consortium. All rights reserved.</bottom> - </configuration> - <executions> - <execution> - <id>attach-javadocs</id> - <goals> - <goal>jar</goal> - </goals> - </execution> - </executions> - </plugin> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-source-plugin</artifactId> - <executions> - <execution> - <id>attach-sources</id> - <goals> - <goal>jar</goal> - </goals> - </execution> - </executions> - </plugin> - --> - <plugin> - <groupId>org.jvnet.jaxb2.maven2</groupId> - <artifactId>maven-jaxb2-plugin</artifactId> - <executions> - <execution> - <id>session</id> - <goals> - <goal>generate</goal> - </goals> - <configuration> - <schemaDirectory>src/main/resources/xsd</schemaDirectory> - <schemaIncludes> - <include>cysession.xsd</include> - </schemaIncludes> - <generatePackage>cytoscape.generated</generatePackage> - <verbose>true</verbose> - <removeOldOutput>false</removeOldOutput> - <forceRegenerate>true</forceRegenerate> - </configuration> - </execution> - <execution> - <id>bookmarks</id> - <goals> - <goal>generate</goal> - </goals> - <configuration> - <schemaDirectory>src/main/resources/xsd</schemaDirectory> - <schemaIncludes> - <include>bookmarks.xsd</include> - </schemaIncludes> - <generatePackage>cytoscape.bookmarks</generatePackage> - <verbose>true</verbose> - <removeOldOutput>false</removeOldOutput> - <forceRegenerate>true</forceRegenerate> - </configuration> - </execution> - </executions> - </plugin> - <plugin> - <artifactId>maven-assembly-plugin</artifactId> - <version>2.2-beta-5</version> - <configuration> - <descriptors> - <descriptor>src/main/assembly/application.xml</descriptor> - <descriptor>src/main/assembly/distribution.xml</descriptor> - </descriptors> - <archive> - <manifest> - <mainClass>cytoscape.CyMain</mainClass> - </manifest> - </archive> - </configuration> - <executions> - <execution> - <id>make-assembly</id> - <phase>package</phase> - <goals> - <goal>single</goal> - </goals> - </execution> - </executions> - </plugin> - - <!-- Used to create the splash and credit screens. - The rasterizing needs to happen after the svg files - have been copied and filtered so that the version - number is correct. --> - <plugin> - <groupId>org.codehaus.mojo</groupId> - <artifactId>batik-maven-plugin</artifactId> - <version>1.0-beta-1</version> - <configuration> - <srcDir>${project.build.directory}/classes/cytoscape/images</srcDir> - <destDir>${project.build.directory}/classes/cytoscape/images</destDir> - </configuration> - <executions> - <execution> - <!-- just needs to happen after resources are copied --> - <phase>compile</phase> - <goals> - <goal>rasterize</goal> - </goals> - </execution> - </executions> - </plugin> - </plugins> - </build> - - <pluginRepositories> - <pluginRepository> - <id>maven2-repository.dev.java.net</id> - <name>Java.net Maven 2 Repository</name> - <url>http://download.java.net/maven/2 - </url> - </pluginRepository> - <pluginRepository> - <id>maven-repository.dev.java.net</id> - <name>Java.net Maven 1 Repository (legacy)</name> - <url>http://download.java.net/maven/1 - </url> - <layout>legacy</layout> - </pluginRepository> - </pluginRepositories> - - <!-- - Don't add additional repositories! - We want everything coming from either Maven Central or our repository. - Remember, it's easy to add third party jars to our repository. - --> - <repositories> - <repository> - <id>cytoscape_snapshots</id> - <snapshots> - <enabled>true</enabled> - </snapshots> - <releases> - <enabled>false</enabled> - </releases> - <name>Cytoscape Snapshots</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url> - </repository> - <repository> - <id>cytoscape_releases</id> - <snapshots> - <enabled>false</enabled> - </snapshots> - <releases> - <enabled>true</enabled> - </releases> - <name>Cytoscape Releases</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url> - </repository> - <repository> - <id>cytoscape_thirdparty</id> - <snapshots> - <enabled>false</enabled> - </snapshots> - <releases> - <enabled>true</enabled> - </releases> - <name>Cytoscape Third Party</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url> - </repository> - </repositories> - - <dependencies> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>3.8.1</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>util-intr</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>graph-dynamic</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>graph-fixed</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>giny</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>render-immed</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>render-stateful</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>render-export</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>fing</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>phoebe-dnd</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>geom-spacial</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>geom-rtree</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>undo-support</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>equations</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>task</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>ding</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>obo</artifactId> - <version>${corelibs.version}</version> - </dependency> - <dependency> - <groupId>cytoscape.corelibs</groupId> - <artifactId>commons-cli-1-x-cytocape-custom</artifactId> - <version>${corelibs.version}</version> - </dependency> - - <!-- swingx --> - <dependency> - <groupId>org.cytoscape.wrappers</groupId> - <artifactId>com.l2fprod.common.sheet</artifactId> - <version>7.3</version> - </dependency> - <dependency> - <groupId>org.cytoscape.wrappers</groupId> - <artifactId>org.swinglabs.swingx</artifactId> - <version>0.9.7</version> - </dependency> - <dependency> - <groupId>org.cytoscape.wrappers</groupId> - <artifactId>com.l2fprod.common.shared</artifactId> - <version>7.3</version> - </dependency> - <dependency> - <groupId>org.cytoscape.wrappers</groupId> - <artifactId>com.l2fprod.common.fontchooser</artifactId> - <version>7.3</version> - </dependency> - - <dependency> - <groupId>cytoscape-sun</groupId> - <artifactId>jhall</artifactId> - <version>1.0</version> - </dependency> - - <dependency> - <groupId>com.lowagie</groupId> - <artifactId>itext</artifactId> - <version>2.0.8</version> - </dependency> - - <dependency> - <groupId>colt</groupId> - <artifactId>colt</artifactId> - <version>1.2.0</version> - </dependency> - - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>biojava</artifactId> - <version>1.4</version> - </dependency> - - <dependency> - <groupId>org.jdom</groupId> - <artifactId>jdom</artifactId> - <version>1.1</version> - </dependency> - - <dependency> - <groupId>org.swinglabs</groupId> - <artifactId>swing-layout</artifactId> - <version>1.0.3</version> - </dependency> - - <dependency> - <groupId>com.jgoodies</groupId> - <artifactId>looks</artifactId> - <version>2.1.4</version> - </dependency> - - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-export</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphics2d</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphicsio</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphicsio-ps</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphicsio-svg</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-graphicsio-java</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-io</artifactId> - <version>2.0.2</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-swing</artifactId> - <version>2.0.3</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-util</artifactId> - <version>2.0.2</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-xml</artifactId> - <version>2.1.1</version> - </dependency> - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>freehep-jas-plotter</artifactId> - <version>2.2</version> - </dependency> - - <dependency> - <groupId>org.apache.lucene</groupId> - <artifactId>lucene-core</artifactId> - <version>3.0.1</version> - </dependency> - - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>tclib</artifactId> - <version>1.0</version> - </dependency> - - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>violinstrings</artifactId> - <version>1.0.2</version> - </dependency> - - <dependency> - <groupId>cytoscape-temp</groupId> - <artifactId>install4j</artifactId> - <version>4.0</version> - </dependency> - - <dependency> - <groupId>cytoscape-sun</groupId> - <artifactId>jaxb-api</artifactId> - <version>1.0</version> - </dependency> - <dependency> - <groupId>cytoscape-sun</groupId> - <artifactId>jaxb-impl</artifactId> - <version>1.0</version> - </dependency> - - - <!-- coreplugins --> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>advanced-network-merge</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>automatic-layout</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>biomart-client</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>biopax</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>editor</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>equation-functions</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>manual-layout</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>ncbi-client</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>psi-mi</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>psi-mi</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>rfilters</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>sbml-reader</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>table-import</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>attribute-browser</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>cpath</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>cpath2</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - <dependency> - <groupId>cytoscape.coreplugins</groupId> - <artifactId>linkout</artifactId> - <version>2.8.0-SNAPSHOT</version> - <classifier>jar-with-dependencies</classifier> - </dependency> - - </dependencies> - -</project> - Copied: cytoscape/trunk/pom.xml (from rev 21138, cytoscape/trunk/application/pom.xml) =================================================================== --- cytoscape/trunk/pom.xml (rev 0) +++ cytoscape/trunk/pom.xml 2010-08-03 19:05:25 UTC (rev 21139) @@ -0,0 +1,584 @@ +<project xmlns="http://maven.apache.org/POM/4.0.0"; + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 + http://maven.apache.org/maven-v4_0_0.xsd";> + <modelVersion>4.0.0</modelVersion> + + <groupId>cytoscape</groupId> + <artifactId>application</artifactId> + <version>2.8.0-SNAPSHOT</version> + <packaging>jar</packaging> + <name>Cytoscape Application</name> + + <properties> + <corelibs.version>2.8.0-SNAPSHOT</corelibs.version> + <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> + </properties> + + <build> + + <!-- This block allows fields to be substituted into resource files, + such as the version number in cytoscape.props. --> + <resources> + <resource> + <directory>src/main/resources</directory> + <filtering>true</filtering> + </resource> + </resources> + + <plugins> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-compiler-plugin</artifactId> + <configuration> + <source>1.5</source> + <target>1.5</target> + </configuration> + </plugin> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-surefire-plugin</artifactId> + <configuration> + <argLine>-Xmx256m</argLine> + <redirectTestOutputToFile>true</redirectTestOutputToFile> + </configuration> + </plugin> + <!-- + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-javadoc-plugin</artifactId> + <configuration> + <encoding>UTF-8</encoding> + <locale>en</locale> + <javadocVersion>1.5</javadocVersion> + <links> + <link>http://download.oracle.com/javase/1.5.0/docs/api/</link> + </links> + <footer>Cytoscape API</footer> + <header>Cytoscape API</header> + <bottom>Copyright 2010 Cytoscape Consortium. All rights reserved.</bottom> + </configuration> + <executions> + <execution> + <id>attach-javadocs</id> + <goals> + <goal>jar</goal> + </goals> + </execution> + </executions> + </plugin> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-source-plugin</artifactId> + <executions> + <execution> + <id>attach-sources</id> + <goals> + <goal>jar</goal> + </goals> + </execution> + </executions> + </plugin> + --> + <plugin> + <groupId>org.jvnet.jaxb2.maven2</groupId> + <artifactId>maven-jaxb2-plugin</artifactId> + <executions> + <execution> + <id>session</id> + <goals> + <goal>generate</goal> + </goals> + <configuration> + <schemaDirectory>src/main/resources/xsd</schemaDirectory> + <schemaIncludes> + <include>cysession.xsd</include> + </schemaIncludes> + <generatePackage>cytoscape.generated</generatePackage> + <verbose>true</verbose> + <removeOldOutput>false</removeOldOutput> + <forceRegenerate>true</forceRegenerate> + </configuration> + </execution> + <execution> + <id>bookmarks</id> + <goals> + <goal>generate</goal> + </goals> + <configuration> + <schemaDirectory>src/main/resources/xsd</schemaDirectory> + <schemaIncludes> + <include>bookmarks.xsd</include> + </schemaIncludes> + <generatePackage>cytoscape.bookmarks</generatePackage> + <verbose>true</verbose> + <removeOldOutput>false</removeOldOutput> + <forceRegenerate>true</forceRegenerate> + </configuration> + </execution> + </executions> + </plugin> + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <version>2.2-beta-5</version> + <configuration> + <descriptors> + <descriptor>src/main/assembly/application.xml</descriptor> + <descriptor>src/main/assembly/distribution.xml</descriptor> + </descriptors> + <archive> + <manifest> + <mainClass>cytoscape.CyMain</mainClass> + </manifest> + </archive> + </configuration> + <executions> + <execution> + <id>make-assembly</id> + <phase>package</phase> + <goals> + <goal>single</goal> + </goals> + </execution> + </executions> + </plugin> + + <!-- Used to create the splash and credit screens. + The rasterizing needs to happen after the svg files + have been copied and filtered so that the version + number is correct. --> + <plugin> + <groupId>org.codehaus.mojo</groupId> + <artifactId>batik-maven-plugin</artifactId> + <version>1.0-beta-1</version> + <configuration> + <srcDir>${project.build.directory}/classes/cytoscape/images</srcDir> + <destDir>${project.build.directory}/classes/cytoscape/images</destDir> + </configuration> + <executions> + <execution> + <!-- just needs to happen after resources are copied --> + <phase>compile</phase> + <goals> + <goal>rasterize</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </build> + + <pluginRepositories> + <pluginRepository> + <id>maven2-repository.dev.java.net</id> + <name>Java.net Maven 2 Repository</name> + <url>http://download.java.net/maven/2 + </url> + </pluginRepository> + <pluginRepository> + <id>maven-repository.dev.java.net</id> + <name>Java.net Maven 1 Repository (legacy)</name> + <url>http://download.java.net/maven/1 + </url> + <layout>legacy</layout> + </pluginRepository> + </pluginRepositories> + + <!-- + Don't add additional repositories! + We want everything coming from either Maven Central or our repository. + Remember, it's easy to add third party jars to our repository. + --> + <repositories> + <repository> + <id>cytoscape_snapshots</id> + <snapshots> + <enabled>true</enabled> + </snapshots> + <releases> + <enabled>false</enabled> + </releases> + <name>Cytoscape Snapshots</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url> + </repository> + <repository> + <id>cytoscape_releases</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Releases</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url> + </repository> + <repository> + <id>cytoscape_thirdparty</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Third Party</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url> + </repository> + </repositories> + + <dependencies> + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <version>3.8.1</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>util-intr</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>graph-dynamic</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>graph-fixed</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>giny</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>render-immed</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>render-stateful</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>render-export</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>fing</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>phoebe-dnd</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>geom-spacial</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>geom-rtree</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>undo-support</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>equations</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>task</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>ding</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>obo</artifactId> + <version>${corelibs.version}</version> + </dependency> + <dependency> + <groupId>cytoscape.corelibs</groupId> + <artifactId>commons-cli-1-x-cytocape-custom</artifactId> + <version>${corelibs.version}</version> + </dependency> + + <!-- swingx --> + <dependency> + <groupId>org.cytoscape.wrappers</groupId> + <artifactId>com.l2fprod.common.sheet</artifactId> + <version>7.3</version> + </dependency> + <dependency> + <groupId>org.cytoscape.wrappers</groupId> + <artifactId>org.swinglabs.swingx</artifactId> + <version>0.9.7</version> + </dependency> + <dependency> + <groupId>org.cytoscape.wrappers</groupId> + <artifactId>com.l2fprod.common.shared</artifactId> + <version>7.3</version> + </dependency> + <dependency> + <groupId>org.cytoscape.wrappers</groupId> + <artifactId>com.l2fprod.common.fontchooser</artifactId> + <version>7.3</version> + </dependency> + + <dependency> + <groupId>cytoscape-sun</groupId> + <artifactId>jhall</artifactId> + <version>1.0</version> + </dependency> + + <dependency> + <groupId>com.lowagie</groupId> + <artifactId>itext</artifactId> + <version>2.0.8</version> + </dependency> + + <dependency> + <groupId>colt</groupId> + <artifactId>colt</artifactId> + <version>1.2.0</version> + </dependency> + + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>biojava</artifactId> + <version>1.4</version> + </dependency> + + <dependency> + <groupId>org.jdom</groupId> + <artifactId>jdom</artifactId> + <version>1.1</version> + </dependency> + + <dependency> + <groupId>org.swinglabs</groupId> + <artifactId>swing-layout</artifactId> + <version>1.0.3</version> + </dependency> + + <dependency> + <groupId>com.jgoodies</groupId> + <artifactId>looks</artifactId> + <version>2.1.4</version> + </dependency> + + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-export</artifactId> + <version>2.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-graphics2d</artifactId> + <version>2.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-graphicsio</artifactId> + <version>2.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-graphicsio-ps</artifactId> + <version>2.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-graphicsio-svg</artifactId> + <version>2.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-graphicsio-java</artifactId> + <version>2.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-io</artifactId> + <version>2.0.2</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-swing</artifactId> + <version>2.0.3</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-util</artifactId> + <version>2.0.2</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-xml</artifactId> + <version>2.1.1</version> + </dependency> + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>freehep-jas-plotter</artifactId> + <version>2.2</version> + </dependency> + + <dependency> + <groupId>org.apache.lucene</groupId> + <artifactId>lucene-core</artifactId> + <version>3.0.1</version> + </dependency> + + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>tclib</artifactId> + <version>1.0</version> + </dependency> + + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>violinstrings</artifactId> + <version>1.0.2</version> + </dependency> + + <dependency> + <groupId>cytoscape-temp</groupId> + <artifactId>install4j</artifactId> + <version>4.0</version> + </dependency> + + <dependency> + <groupId>cytoscape-sun</groupId> + <artifactId>jaxb-api</artifactId> + <version>1.0</version> + </dependency> + <dependency> + <groupId>cytoscape-sun</groupId> + <artifactId>jaxb-impl</artifactId> + <version>1.0</version> + </dependency> + + + <!-- coreplugins --> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>advanced-network-merge</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>automatic-layout</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>biomart-client</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>biopax</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>editor</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>equation-functions</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>manual-layout</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>ncbi-client</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>psi-mi</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>psi-mi</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>rfilters</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>sbml-reader</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>table-import</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>attribute-browser</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>cpath</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>cpath2</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + <dependency> + <groupId>cytoscape.coreplugins</groupId> + <artifactId>linkout</artifactId> + <version>2.8.0-SNAPSHOT</version> + <classifier>jar-with-dependencies</classifier> + </dependency> + + </dependencies> + +</project> + -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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