biojava
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- DependenciesDependencies
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>5.0.0-alpha3</version>
</dependency><?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>5.0.0-alpha3</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>1.8</jdk.version>
<maven.enforcer.jdk-version>1.8</maven.enforcer.jdk-version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
<maxmem>512M</maxmem>
<slf4j.version>1.7.14</slf4j.version>
<log4j.version>2.5</log4j.version>
</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>biojava-5.0.0-alpha3</tag>
</scm>
<!-- 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>3.0.0</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.6</version>
</plugin>
<plugin>
<artifactId>maven-scm-plugin</artifactId>
<version>1.9.4</version>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>2.4</version>
</plugin>
<plugin>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.19.1</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>0.13.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.3</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>2.10.3</version>
<configuration>
<additionalparam>-Xdoclint:none</additionalparam>
<maxmemory>256m</maxmemory>
<footer><script src="http://www.google-analytics.com/urchin.js"
type="text/javascript"></script><script
type="text/javascript">_uacct =
"UA-1326640-1";urchinTracker();</script></footer>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.2</version>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</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>3.0.3</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>1.4</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.17</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.7</version>
</plugin>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.4.1</version>
<executions>
<execution>
<id>enforce-java</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireJavaVersion>
<version>${maven.enforcer.jdk-version}</version>
</requireJavaVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- for deployment on OSS Sonatype -->
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.6</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>2.19.1</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>
<exclude>**/TestAtomCachePerformance.java</exclude>
<exclude>**/EcodInstallationTest.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>
<plugin>
<groupId>com.versioneye</groupId>
<artifactId>versioneye-maven-plugin</artifactId>
<version>3.5.1</version>
</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>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<!-- binding for log4j 2 -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<version>${log4j.version}</version>
<!-- runtime scope includes the test scope as well -->
<scope>runtime</scope>
</dependency>
<!-- Log4j API and Core implementation required for binding -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j.version}</version>
<!-- runtime scope includes the test scope as well -->
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j.version}</version>
<!-- runtime scope includes the test scope as well -->
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.biojava.thirdparty</groupId>
<artifactId>forester</artifactId>
<version>1.038</version>
</dependency>
</dependencies>
</dependencyManagement>
<reporting>
<plugins>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.1</version>
<configuration>
<aggregate>true</aggregate>
<breakiterator>true</breakiterator>
<quiet>true</quiet>
<source>1.7</source>
<verbose>false</verbose>
<linksource>true</linksource>
</configuration>
</plugin>
<plugin>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.8.1</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>3.0.3</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.17</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jxr-plugin</artifactId>
<version>2.5</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>1.4</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>1.6</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<modules>
<module>biojava-core</module>
<module>biojava-phylo</module>
<module>biojava-alignment</module>
<module>biojava-structure</module>
<module>biojava-integrationtest</module>
<module>biojava-structure-gui</module>
<module>biojava-sequencing</module>
<module>biojava-genome</module>
<module>biojava-modfinder</module>
<module>biojava-ws</module>
<module>biojava-protein-disorder</module>
<module>biojava-aa-prop</module>
<module>biojava-survival</module>
<module>biojava-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>