pom.xml

<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.rcsb</groupId>
	<artifactId>structurecodec</artifactId>
	<version>0.3.0-SNAPSHOT</version>
	<name>Structure Codec</name>
	<url>https://github.com/rcsb/structurecodec</url>
	<organization>
		<name>RCSB</name>
		<url>http://www.rcsb.org</url>
	</organization>
	<description>Provides high-density compression and decompression of biomolecular structures.</description>

	<properties>
		<jdk.version>1.7</jdk.version>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
		<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
		<timestamp>${maven.build.timestamp}</timestamp>

        <biojava.version>4.0.0</biojava.version>
	</properties>

	<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>
		</repository>

		<repository>
			<id>rcsb-pdb-maven-repo</id>
			<name>RCSB PDB Maven Repository</name>
			<url>http://nexus.rcsb.org/nexus/content/groups/public/</url>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
			<releases>
				<enabled>true</enabled>
			</releases>
		</repository>

	</repositories>

	<scm>
		<developerConnection>scm:git:git@github.com:rcsb/structurecodec.git</developerConnection>
		<connection>scm:git:git@github.com:rcsb/structurecodec.git</connection>
		<url>https://github.com/rcsb/structurecodec</url>
		<tag>HEAD</tag>
	</scm>
	<issueManagement>
		<url>https://github.com/rcsb/structurecodec/issues</url>
		<system>Github</system>
	</issueManagement>

	<!-- where Maven deploy will deploy project jars/wars -->
	<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>

	<dependencies>
		<dependency>
			<groupId>java3d</groupId>
			<artifactId>vecmath</artifactId>
			<version>1.3.1</version>
		</dependency>

		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-structure</artifactId>
			<version>${biojava.version}</version>

		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-structure-gui</artifactId>
			<version>${biojava.version}</version>

		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-ws</artifactId>
			<version>${biojava.version}</version>

		</dependency>
		<dependency>
			<groupId>org.rcsb</groupId>
			<artifactId>ava-core</artifactId>
			<version>2013-11-1-SNAPSHOT</version>

		</dependency>
		<dependency>
			<groupId>mysql</groupId>
			<artifactId>mysql-connector-java</artifactId>
			<version>5.1.15</version>

		</dependency>
		<dependency>
			<groupId>jfree</groupId>
			<artifactId>jfreechart</artifactId>
			<version>1.0.12</version>

		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.11</version>
			<scope>test</scope>
		</dependency>

		<dependency>
			<groupId>org.mockito</groupId>
			<artifactId>mockito-all</artifactId>
			<version>1.9.5</version>
		</dependency>


		<dependency>
			<groupId>commons-cli</groupId>
			<artifactId>commons-cli</artifactId>
			<version>1.2</version>
		</dependency>

		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-core</artifactId>
			<version>2.0-beta9</version>
		</dependency>

		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-api</artifactId>
			<version>2.0-beta9</version>
		</dependency>

		<dependency>
			<groupId>xmlunit</groupId>
			<artifactId>xmlunit</artifactId>
			<version>1.4</version>
		</dependency>

		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math3</artifactId>
			<version>3.2</version>
		</dependency>

	</dependencies>
	<build>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.1</version>
				<configuration>
					<fork>true</fork>
					<source>${jdk.version}</source>
					<target>${jdk.version}</target>
					<maxmem>2000m</maxmem>
				</configuration>
			</plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-resources-plugin</artifactId>
				<version>2.6</version>
			</plugin>

			<plugin>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>2.17</version>
				<configuration>
					<argLine>-Xms256m -Xmx2000M</argLine>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jar-plugin</artifactId>
				<version>2.4</version>
				<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.apache.maven.plugins</groupId>
				<artifactId>maven-release-plugin</artifactId>
				<version>2.5</version>
			</plugin>

		</plugins>
		<resources>
			<resource>
				<directory>src/main/resources</directory>
				<filtering>true</filtering>
				<includes>
					<include>**/*.properties</include>
				</includes>
			</resource>
			<resource>
				<directory>src/main/resources</directory>
				<filtering>false</filtering>
				<includes>
					<!-- <include>**/*.cif.gz</include> <include>**/*.pdb</include> <include>**/*.mat</include> -->
				</includes>
			</resource>
		</resources>

		<extensions>
			<extension>
				<groupId>org.apache.maven.wagon</groupId>
				<artifactId>wagon-ssh</artifactId>
				<version>2.3</version>
			</extension>
		</extensions>

	</build>

	<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>1.2</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>

</project>