pom.xml

<?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">

	<!-- for releasing to Maven Central / OSS Sonatype -->
	<parent>
		<groupId>org.sonatype.oss</groupId>
		<artifactId>oss-parent</artifactId>
		<version>9</version>
	</parent>

	<modelVersion>4.0.0</modelVersion>
	<groupId>org.biojava</groupId>
	<artifactId>biojava</artifactId>
	<packaging>pom</packaging>
	<version>4.0.0-SNAPSHOT</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>
	<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>
	<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>HEAD</tag>
	</scm>
	<repositories>
		<!-- The BioJava repository -->
		<repository>
			<id>biojava-maven-repo</id>
			<name>BioJava repository</name>
			<url>http://www.biojava.org/download/maven/</url>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
		</repository>
	</repositories>
	<!-- This section required for release at Maven Central. For a full list 
		of Developers, please see https://github.com/orgs/biojava/members For a list 
		of contributors, please see https://github.com/biojava/biojava/graphs/contributors -->
	<developers>
		<developer>
			<id>andreas</id>
			<name>Andreas Prlic</name>
			<email>andreas.prlic@gmail.com</email>
			<url>http://www.spice-3d.org</url>
			<organization>University of California, San Diego</organization>
			<organizationUrl>http://www.rcsb.org</organizationUrl>
			<roles>
				<role>project lead</role>
				<role>architect</role>
				<role>developer</role>
			</roles>
			<timezone>-9</timezone>
			<properties>
				<picUrl>http://tinyurl.com/mymsfga</picUrl>
			</properties>
		</developer>
		<developer>
			<name>Amr AL-HOSSARY</name>
		</developer>
		<developer>
			<name>Andreas Dräger</name>
		</developer>
		<developer>
			<name>Andy Yates</name>
		</developer>
		<developer>
			<name>Carmelo Foti</name>
		</developer>
		<developer>
			<name>Chuan Hock Koh</name>
		</developer>
		<developer>
			<name>Douglas Myers-Turnbull</name>
		</developer>
		<developer>
			<name>Gediminas Rimsa</name>
		</developer>
		<developer>
			<name>George Waldon</name>
		</developer>
		<developer>
			<name>Hannes Brandstätter-Müller</name>
		</developer>
		<developer>
			<name>Elinow</name>
		</developer>
		<developer>
			<name>Jianjiong Gao</name>
		</developer>
		<developer>
			<name>Jonathan Warren</name>
		</developer>
		<developer>
			<name>Jose Manuel Duarte</name>
		</developer>
		<developer>
			<name>Jules Jacobsen</name>
		</developer>
		<developer>
			<name>Karl Nicholas</name>
		</developer>
		<developer>
			<name>Mark Chapman</name>
		</developer>
		<developer>
			<name>Michael Heuer</name>
		</developer>
		<developer>
			<name>Peter Rose</name>
		</developer>
		<developer>
			<name>Peter Troshin</name>
		</developer>
		<developer>
			<name>Richard Holland</name>
		</developer>
		<developer>
			<name>Robert Thornton</name>
		</developer>
		<developer>
			<name>Scooter Willis</name>
		</developer>
		<developer>
			<name>Spencer Bliven</name>
		</developer>
		<developer>
			<name>Sylvain Foisy</name>
		</developer>
	</developers>


	<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>
					<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>
						<!-- work around for GPG hanging issue http://jira.codehaus.org/browse/MGPG-9 -->
						<mavenExecutorId>forked-path</mavenExecutorId>
					</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>

				<!-- required for OSSRH release, see http://central.sonatype.org/pages/how-to-generate-pgp-signatures-with-maven.html -->
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-release-plugin</artifactId>
					<version>2.5</version>
					<configuration>
						<autoVersionSumodules>true</autoVersionSumodules>
						<!--<mavenExecutorId>forked-path</mavenExecutorId> -->
						<!--<useReleaseProfile>false</useReleaseProfile> -->
						<!--<arguments>${arguments} -Psonatype-oss-release</arguments> -->
					</configuration>
				</plugin>


			</plugins>
		</pluginManagement>


		<plugins>

			<!-- for deployment on OSS Sonatype -->
			<plugin>
				<groupId>org.sonatype.plugins</groupId>
				<artifactId>nexus-staging-maven-plugin</artifactId>
				<version>1.6.1</version>
				<extensions>true</extensions>
				<configuration>
					<serverId>ossrh</serverId>
					<nexusUrl>https://oss.sonatype.org/</nexusUrl>
					<autoReleaseAfterClose>true</autoReleaseAfterClose>
				</configuration>
			</plugin>

			<!-- for digital signing of code -->
			<!--<plugin> -->
			<!--<groupId>org.apache.maven.plugins</groupId> -->
			<!--<artifactId>maven-gpg-plugin</artifactId> -->
			<!--<version>1.5</version> -->
			<!--<executions> -->
			<!--<execution> -->
			<!--<id>sign-artifacts</id> -->
			<!--<phase>verify</phase> -->
			<!--<goals> -->
			<!--<goal>sign</goal> -->
			<!--</goals> -->
			<!--</execution> -->
			<!--</executions> -->
			<!--</plugin> -->

			<!-- give more memory for junit tests -->
			<plugin>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>2.17</version>
				<configuration>
					<argLine>-Xmx1500M</argLine>
					<reuseForks>false</reuseForks>
					<forkCount>1</forkCount>

					<excludes>
						<!-- we exclude by default the long parsing tests, they will only be 
							executed if explicitly called -->
						<exclude>**/TestLongPdbVsMmCifParsing.java</exclude>

					</excludes>
				</configuration>
			</plugin>


			<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>
				<artifactId>maven-javadoc-plugin</artifactId>
				<version>2.9.1</version>
				<configuration>
					<aggregate>true</aggregate>
					<breakiterator>true</breakiterator>
					<quiet>true</quiet>
					<source>1.5</source>
					<verbose>false</verbose>
					<linksource>true</linksource>
					<detectlinks>true</detectlinks>
				</configuration>
			</plugin>
			<plugin>
				<artifactId>maven-project-info-reports-plugin</artifactId>
				<version>2.7</version>
				<reportSets>
					<reportSet>
						<reports>
							<report>index</report>
							<report>summary</report>
							<report>modules</report>
							<report>scm</report>
							<report>dependency-management</report>
							<report>dependencies</report>
							<report>dependency-convergence</report>
							<report>distribution-management</report>
						</reports>
					</reportSet>
				</reportSets>
			</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>

		<profile>
			<id>release-sign-artifacts</id>
			<activation>
				<property>
					<name>performRelease</name>
					<value>true</value>
				</property>
			</activation>
			<build>
				<plugins>
					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-gpg-plugin</artifactId>
						<version>1.5</version>
						<executions>
							<execution>
								<id>sign-artifacts</id>
								<phase>verify</phase>
								<goals>
									<goal>sign</goal>
								</goals>
							</execution>
						</executions>
					</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>