<?xml version="1.0" encoding="UTF-8"?>

<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>org.biojava</groupId>

<artifactId>biojava</artifactId>

<packaging>pom</packaging>

<version>3.0.8</version>

<name>biojava</name>

<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.</description>

<url>http://www.biojava.org</url>

<organization>

<name>BioJava</name>

<url>http://www.biojava.org</url>

</organization>

<licenses>

<license>

<name>GNU LGPL v2</name>

<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>

<distribution>repo</distribution>

</license>

</licenses>

<scm>

<connection>scm:git:git://github.com/biojava/biojava.git</connection>

<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>

<url>https://github.com/biojava/biojava</url>

<tag>biojava-3.0.8</tag>

</scm>

<repositories>

<repository>

<id>maven2-repository.dev.java.net</id>

<name>Java.net Maven 2 Repository</name>

<url>http://download.java.net/maven/2</url>

</repository>

<repository>

<id>maven-repository.dev.java.net</id>

<name>Java.net Maven 1 Repository (legacy)</name>

<url>http://download.java.net/maven/1</url>

<layout>default</layout>

</repository>

<repository>

<id>biojava-maven-repo</id>

<name>BioJava repository</name>

<url>http://www.biojava.org/download/maven/</url>

<snapshots>

<enabled>true</enabled>

</snapshots>

<releases>

<enabled>true</enabled>

</releases>

</repository>

</repositories>

<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>default</layout>

</pluginRepository>

</pluginRepositories>

<distributionManagement>

<downloadUrl>http://www.biojava.org/download/maven/</downloadUrl>

<repository>

<uniqueVersion>false</uniqueVersion>

<id>biojava-maven-repo</id>

<name>BioJava Maven Repository</name>

<url>scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/</url>

<layout>default</layout>

</repository>

<snapshotRepository>

<uniqueVersion>false</uniqueVersion>

<id>biojava-maven-repo</id>

<name>BioJava Maven Repository</name>

<url>scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/</url>

<layout>default</layout>

</snapshotRepository>

</distributionManagement>

<properties>

<jdk.version>1.6</jdk.version>

<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

<project.build.targetEncoding>UTF-8</project.build.targetEncoding>

<maxmem>512M</maxmem>

</properties>

<build>

<pluginManagement>

<plugins>

<plugin>

<artifactId>maven-clean-plugin</artifactId>

<version>2.5</version>

</plugin>

<plugin>

<artifactId>maven-compiler-plugin</artifactId>

<version>3.1</version>

<configuration>

<source>${jdk.version}</source>

<target>${jdk.version}</target>

</configuration>

</plugin>

<plugin>

<artifactId>maven-dependency-plugin</artifactId>

<version>2.7</version>

</plugin>

<plugin>

<artifactId>maven-jar-plugin</artifactId>

<version>2.4</version>

</plugin>

<plugin>

<artifactId>maven-scm-plugin</artifactId>

<version>1.9</version>

</plugin>

<plugin>

<artifactId>maven-source-plugin</artifactId>

<version>2.2.1</version>

</plugin>

<plugin>

<artifactId>maven-surefire-plugin</artifactId>

<version>2.17</version>

<configuration>

<argLine>-Xms256m -Xmx2000M</argLine>

<reuseForks>false</reuseForks>

<forkCount>1</forkCount>

</configuration>

</plugin>

<plugin>

<groupId>net.sf</groupId>

<artifactId>stat-scm</artifactId>

<version>1.2.0</version>

</plugin>

<plugin>

<groupId>org.jvnet.jaxb2.maven2</groupId>

<artifactId>maven-jaxb2-plugin</artifactId>

<version>0.8.3</version>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-release-plugin</artifactId>

<version>2.5</version>

<configuration>

<tagBase>svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/tags</tagBase>

<remoteTagging>true</remoteTagging>

<preparationGoals>clean install</preparationGoals>

<autoVersionSubmodules>true</autoVersionSubmodules>

</configuration>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-javadoc-plugin</artifactId>

<version>2.9.1</version>

<configuration>

<maxmemory>256m</maxmemory>

<footer>&lt;script src="http://www.google-analytics.com/urchin.js"

type="text/javascript"&gt;&lt;/script&gt;&lt;script

type="text/javascript"&gt;_uacct =

"UA-1326640-1";urchinTracker();&lt;/script&gt;</footer>

</configuration>

</plugin>

<plugin>

<artifactId>maven-assembly-plugin</artifactId>

<version>2.4</version>

<configuration>

<descriptors>

<descriptor>src/main/assembly/assembly.xml</descriptor>

</descriptors>

</configuration>

<!-- Attach the creation of the assembly to the package phase. -->

<executions>

<execution>

<id>assemble</id>

<phase>package</phase>

<goals>

<goal>single</goal>

</goals>

</execution>

</executions>

</plugin>

<plugin>

<groupId>org.codehaus.mojo</groupId>

<artifactId>findbugs-maven-plugin</artifactId>

<version>2.5.3</version>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-checkstyle-plugin</artifactId>

<version>2.12</version>

</plugin>

</plugins>

</pluginManagement>

<plugins>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-jar-plugin</artifactId>

<configuration>

<archive>

<addMavenDescriptor>false</addMavenDescriptor>

<manifest>

<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>

<addDefaultImplementationEntries>true</addDefaultImplementationEntries>

</manifest>

<manifestEntries>

<Trusted-Library>true</Trusted-Library>

<Permissions>all-permissions</Permissions>

<Codebase>*</Codebase>

<Application-Name>BioJava</Application-Name>

</manifestEntries>

</archive>

</configuration>

</plugin>

<plugin>

<groupId>org.codehaus.mojo</groupId>

<artifactId>findbugs-maven-plugin</artifactId>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-checkstyle-plugin</artifactId>

<configuration>

<!-- <enableFilesSummary>true</enableFilesSummary> <enableSeveritySummary>true</enableSeveritySummary> -->

<enableRulesSummary>false</enableRulesSummary>

<!-- <consoleOutput>true</consoleOutput> -->

</configuration>

</plugin>

</plugins>

<extensions>

<extension>

<groupId>org.apache.maven.wagon</groupId>

<artifactId>wagon-ssh</artifactId>

<version>2.6</version>

</extension>

</extensions>

</build>

<dependencyManagement>

<dependencies>

<dependency>

<groupId>junit</groupId>

<artifactId>junit</artifactId>

<version>4.11</version>

<scope>test</scope>

</dependency>

<dependency>

<groupId>javax.xml.bind</groupId>

<artifactId>jaxb-api</artifactId>

<version>2.2</version>

</dependency>

<dependency>

<groupId>xerces</groupId>

<artifactId>xercesImpl</artifactId>

<version>2.4.0</version>

</dependency>

</dependencies>

</dependencyManagement>

<reporting>

<plugins>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-project-info-reports-plugin</artifactId>

<version>2.7</version>

</plugin>

<plugin>

<artifactId>maven-javadoc-plugin</artifactId>

<version>2.9.1</version>

<configuration>

<aggregate>true</aggregate>

<minmemory>140m</minmemory>

<maxmemory>140m</maxmemory>

<breakiterator>true</breakiterator>

<quiet>true</quiet>

<source>1.6</source>

<verbose>false</verbose>

<linksource>true</linksource>

<!-- <detectLinks>true</detectLinks> -->

<links>

<!-- JSE -->

<link>http://docs.oracle.com/javase/6/docs/api/</link>

<!-- Libraries -->

<!-- <link>http://jakarta.apache.org/commons/collections/apidocs</link>

<link>http://logging.apache.org/log4j/docs/api/</link>

<link>http://jakarta.apache.org/regexp/apidocs/</link>

<link>http://jakarta.apache.org/velocity/api/</link>

</links>

</configuration>

</plugin>

<plugin>

<groupId>net.sf</groupId>

<artifactId>stat-scm</artifactId>

<version>1.2.0</version>

<configuration>

<includes>

<include>**/*.java</include>

</includes>

<excludes>

<exclude>**/test/**/*.java</exclude>

</excludes>

<tags>3.0</tags>

<tagsDir>/releases/</tagsDir>

<cacheDir>/statsvn/</cacheDir>

<title>BioJava SVN statistics</title>

</configuration>

</plugin>

<plugin>

<groupId>org.codehaus.mojo</groupId>

<artifactId>findbugs-maven-plugin</artifactId>

<version>2.5.3</version>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-checkstyle-plugin</artifactId>

<version>2.12</version>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-jxr-plugin</artifactId>

<version>2.4</version>

</plugin>

</plugins>

</reporting>

<profiles>

<!-- Note: before you can use this build profile you need to set up an

environment that contains correctly signed keys. Configure the keystore properties

and the profile in ~/.m2/settings.xml -->

<profile>

<id>codesigning</id>

<activation>

<activeByDefault>false</activeByDefault>

</activation>

<build>

<plugins>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-jarsigner-plugin</artifactId>

<version>1.3.1</version>

<executions>

<execution>

<id>sign</id>

<goals>

<goal>sign</goal>

</goals>

</execution>

</executions>

<configuration>

<verbose>true</verbose>

<certs>true</certs>

<storetype>${keystore.type}</storetype>

<keystore>${keystore.path}</keystore>

<alias>${keystore.alias}</alias>

<storepass>${keystore.store.password}</storepass>

<keypass>${keystore.key.password}</keypass>

<signedjar>${project.build.directory}/${project.build.finalName}.jar</signedjar>

<verify>true</verify>

<verbose>true</verbose>

<goal>sign</goal>

<arguments>

<argument>-tsa</argument>

<argument>https://timestamp.geotrust.com/tsa</argument>

</arguments>

</configuration>

</plugin>

</plugins>

</build>

</profile>

</profiles>

<modules>

<module>biojava3-core</module>

<module>biojava3-phylo</module>

<module>biojava3-alignment</module>

<module>biojava3-structure</module>

<module>integrationtest</module>

<module>biojava3-structure-gui</module>

<module>biojava3-sequencing</module>

<module>biojava3-genome</module>

<module>biojava3-modfinder</module>

<module>biojava3-ws</module>

<module>biojava3-protein-disorder</module>

<module>biojava3-aa-prop</module>

<module>protein-comparison-tool</module>

<module>biojava3-survival</module>

<module>biojava3-ontology</module>

</modules>

<inceptionYear>2000</inceptionYear>

<issueManagement>

<system>Github</system>

<url>https://github.com/biojava/biojava/issues</url>

</issueManagement>

<ciManagement>

<system>CruiseControl</system>

<url>http://ccpublic.rcsb.org/</url>

</ciManagement>

</project>