<?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>3.1.0</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-3.1.0</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://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>2.5.3</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>