updated top pom file for the new structure
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Tramy Nguyen
parent
e9c8fa4641
commit
e1bbeedd54
2 changed files with 53 additions and 318 deletions
368
pom.xml
368
pom.xml
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@ -2,337 +2,71 @@
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>MyersResearchGroup</groupId>
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<groupId>edu.utah.ece.async</groupId>
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<artifactId>iBioSim</artifactId>
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<version>0.0.1-SNAPSHOT</version>
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<packaging>pom</packaging>
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<name>iBioSim</name>
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<description>CAD tool aimed for the modeling, analysis, and design of genetic circuits. This tool supports both SBML and SBOL data models.</description>
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<url>https://github.com/MyersResearchGroup/iBioSim</url>
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<licenses>
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<license>
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<name>Apache License, Version 2.0</name>
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<url>http://www.apache.org/licenses/LICENSE-2.0</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<issueManagement>
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<system>GitHub Issues</system>
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<url>https://github.com/MyersResearchGroup/iBioSim/issues</url>
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</issueManagement>
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<properties>
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<!-- We have to make sure we're building on the same charset on all platforms
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or bad things happen. -->
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<modules>
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<module>frontend</module>
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<module>conversion</module>
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<module>dataModels</module>
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<module>backend</module>
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</modules>
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<build>
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<sourceDirectory>src</sourceDirectory>
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<resources>
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<resource>
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<directory>src</directory>
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<excludes>
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<exclude>**/*.java</exclude>
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</excludes>
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</resource>
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</resources>
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<plugins>
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<plugin>
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<!-- settings for javac. -->
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<artifactId>maven-compiler-plugin</artifactId>
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<version>3.5.1</version>
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<configuration>
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<source>1.8</source>
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<target>1.8</target>
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<excludes>
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<exclude>dataModels/biomodel/util/Validation.java</exclude>
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<exclude>test/gcm2sbml/*.java</exclude>
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<exclude>test/scripts/*.java</exclude>
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</excludes>
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<exclude>conversion/src/test/resources/edu/utah/ece/async/gcm2sbml/*.java</exclude>
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<exclude>conversion/src/test/resources/edu/utah/ece/async/scripts/*.java</exclude>
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<!-- Build an executable JAR -->
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<version>2.4</version>
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<configuration>
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<archive>
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<manifest>
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<addClasspath>true</addClasspath>
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<classpathPrefix>lib/</classpathPrefix>
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<mainClass>org.sbolstandard.core2.SBOLValidate</mainClass>
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</manifest>
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</archive>
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</configuration>
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</plugin>
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<!-- todo: add any other plugins needed here -->
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</plugins>
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</build>
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<repositories>
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<repository>
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<id>ebi</id>
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<name>ebi</name>
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<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
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</repository>
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<repository>
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<id>jboss</id>
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<name>jboss</name>
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<url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
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</repository>
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<repository>
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<id>netbeans</id>
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<name>netbeans</name>
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<url>http://bits.netbeans.org/maven2/</url>
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</repository>
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<repository>
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<id>osgeo</id>
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<name>osgeo</name>
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<url>http://download.osgeo.org/webdav/geotools/</url>
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</repository>
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<repository>
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<id>alfresco</id>
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<name>alfresco</name>
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<url>https://artifacts.alfresco.com/nexus/content/repositories/public/</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>commons-httpclient</groupId>
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<artifactId>commons-httpclient</artifactId>
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<version>3.1</version>
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</dependency>
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<dependency>
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<groupId>org.antlr</groupId>
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<artifactId>antlr</artifactId>
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<version>3.4</version>
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</dependency>
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<dependency>
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<groupId>org.antlr</groupId>
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<artifactId>antlr-runtime</artifactId>
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<version>3.4</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-awt-util</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-anim</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-bridge</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-codec</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-css</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-dom</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-ext</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-extension</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-gui-util</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-gvt</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-parser</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-script</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-svg-dom</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-svggen</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-swing</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-transcoder</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-util</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>org.apache.xmlgraphics</groupId>
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<artifactId>batik-xml</artifactId>
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<version>1.8</version>
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</dependency>
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<dependency>
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<groupId>uk.ac.ebi.biomodels</groupId>
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<artifactId>biomodels-wslib</artifactId>
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<version>1.21</version>
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</dependency>
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<dependency>
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<groupId>colt</groupId>
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<artifactId>colt</artifactId>
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<version>1.2.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-math3</artifactId>
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<version>3.6.1</version>
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</dependency>
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<dependency>
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<groupId>com.google.code.gson</groupId>
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<artifactId>gson</artifactId>
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<version>2.8.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient-cache</artifactId>
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<version>4.5.2</version>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpcore</artifactId>
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<version>4.4.4</version>
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</dependency>
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<dependency>
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<groupId>org.jfree</groupId>
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<artifactId>jcommon</artifactId>
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<version>1.0.17</version>
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</dependency>
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<dependency>
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<groupId>org.jdom</groupId>
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<artifactId>jdom-contrib</artifactId>
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<version>1.1.3</version>
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</dependency>
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<dependency>
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<groupId>org.jfree</groupId>
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<artifactId>jfreechart</artifactId>
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<version>1.0.14</version>
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</dependency>
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<dependency>
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<groupId>org.jmathml</groupId>
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<artifactId>jmathml</artifactId>
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<version>2.2.1</version>
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</dependency>
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<dependency>
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<groupId>com.joptimizer</groupId>
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<artifactId>joptimizer</artifactId>
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<version>3.4.0</version>
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</dependency>
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<dependency>
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<groupId>org.sbml.jsbml</groupId>
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<artifactId>jsbml</artifactId>
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<version>1.2</version>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.12</version>
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</dependency>
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<dependency>
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<groupId>javax.mail</groupId>
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<artifactId>mail</artifactId>
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<version>1.4.7</version>
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</dependency>
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<dependency>
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<groupId>org.netbeans.api</groupId>
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<artifactId>org-jdesktop-layout</artifactId>
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<version>RELEASE691</version>
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</dependency>
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<dependency>
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<groupId>org.w3c</groupId>
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<artifactId>dom</artifactId>
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<version>2.3.0-jaxb-1.0.6</version>
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</dependency>
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<dependency>
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<groupId>wsdl4j</groupId>
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<artifactId>wsdl4j</artifactId>
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<version>1.6.2</version>
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</dependency>
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<dependency>
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<groupId>xalan</groupId>
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<artifactId>xalan</artifactId>
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<version>2.6.0</version>
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</dependency>
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<dependency>
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<groupId>xom</groupId>
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<artifactId>xom</artifactId>
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<version>1.2</version>
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</dependency>
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<dependency>
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<groupId>org.eclipse.birt.runtime.3_7_1</groupId>
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<artifactId>org.mozilla.javascript</artifactId>
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<version>1.7.2</version>
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</dependency>
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<dependency>
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<groupId>org.jdesktop</groupId>
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<artifactId>swing-layout</artifactId>
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<version>1.0.2</version>
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</dependency>
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<dependency>
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<groupId>com.lowagie</groupId>
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<artifactId>itext</artifactId>
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<version>2.1.5</version>
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</dependency>
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<dependency>
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<groupId>org.tinyjee.jgraphx</groupId>
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<artifactId>jgraphx</artifactId>
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<version>3.4.1.3</version>
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</dependency>
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<dependency>
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<groupId>net.sf.trove4j</groupId>
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<artifactId>trove4j</artifactId>
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<version>3.0.1</version>
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</dependency>
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<dependency>
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<groupId>org.openrdf.sesame</groupId>
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<artifactId>sesame-model</artifactId>
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<version>4.1.2</version>
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</dependency>
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<dependency>
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<groupId>org.kohsuke</groupId>
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<artifactId>github-api</artifactId>
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<version>1.84</version>
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</dependency>
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</dependencies>
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</project>
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