<?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>3.0.7</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-3.0.7</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>1.8.1</version>
				</plugin>
				<plugin>
					<artifactId>maven-source-plugin</artifactId>
					<version>2.2.1</version>
				</plugin>
				<plugin>
					<artifactId>maven-surefire-plugin</artifactId>
					<version>2.14.1</version>
					<configuration>
						<argLine>-Xms256m -Xmx2000M</argLine>
					</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>2.3.2</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</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>2.5.2</version>
				</plugin>


				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-checkstyle-plugin</artifactId>
					<version>2.10</version>
				</plugin>
				
			</plugins>
		</pluginManagement>


		<plugins>
			<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>2.4</version>
			</extension>
		</extensions>

	</build>

	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>junit</groupId>
				<artifactId>junit</artifactId>
				<version>4.10</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>2.6</version>
			</plugin>
			<plugin>
				<artifactId>maven-javadoc-plugin</artifactId>
				<version>2.9</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://jakarta.apache.org/commons/logging/apidocs/</link> <link>http://www.junit.org/junit/javadoc/</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>2.5.2</version>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-checkstyle-plugin</artifactId>
				<version>2.10</version>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jxr-plugin</artifactId>
				<version> 2.1 </version>
			</plugin>
		</plugins>

	</reporting>

	<modules>

		<module>biojava3-core</module>
		<module>biojava3-phylo</module>
		<module>biojava3-sequencing</module>
		<module>biojava3-structure</module>
		<module>biojava3-structure-gui</module>
		<module>biojava3-genome</module>
		<module>biojava3-modfinder</module>
		<module>biojava3-alignment</module>
		<module>biojava3-ws</module>
		<module>biojava3-protein-disorder</module>
		<module>biojava3-aa-prop</module>
		<module>integrationtest</module>
		<module>protein-comparison-tool</module>

	</modules>
	<inceptionYear>2000</inceptionYear>
</project>
