Description

<dependency>
    <groupId>org.biojava</groupId>
    <artifactId>biojava-structure</artifactId>
    <version>5.2.1</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">
	<modelVersion>4.0.0</modelVersion>
	<parent>
		<artifactId>biojava</artifactId>
		<groupId>org.biojava</groupId>
		<version>5.2.1</version>
	</parent>
	<artifactId>biojava-structure</artifactId>
	<name>biojava-structure</name>
	<description>The protein structure modules of BioJava.</description>
	<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>

	<dependencies>

		<dependency>
			<groupId>org.rcsb</groupId>
			<artifactId>mmtf-api</artifactId>
            <version>${mmtf.version}</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.rcsb</groupId>
			<artifactId>mmtf-serialization</artifactId>
            <version>${mmtf.version}</version>
			<scope>compile</scope>
		</dependency>
		      <dependency>
            <groupId>org.rcsb</groupId>
            <artifactId>mmtf-codec</artifactId>
            <version>${mmtf.version}</version>
            <scope>compile</scope>
        </dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-alignment</artifactId>
			<version>5.2.1</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>5.2.1</version>
			<scope>compile</scope>
		</dependency>

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

		<dependency>
			<groupId>org.jgrapht</groupId>
  			<artifactId>jgrapht-core</artifactId>
  			<version>1.1.0</version>
		</dependency>

		<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
		  Note versions are set in parent pom in dependency management section -->
		<dependency>
		    <groupId>javax.xml.bind</groupId>
		    <artifactId>jaxb-api</artifactId>
		</dependency>
		<dependency>
			<groupId>com.sun.xml.bind</groupId>
			<artifactId>jaxb-core</artifactId>
		</dependency>
		<dependency>
			<groupId>com.sun.xml.bind</groupId>
			<artifactId>jaxb-impl</artifactId>
		</dependency>
		<dependency>
			<groupId>javax.activation</groupId>
			<artifactId>activation</artifactId>
		</dependency>

		<!-- logging dependencies (managed by parent pom, don't set versions or
			scopes here) -->
		<dependency>
        	<groupId>org.slf4j</groupId>
        	<artifactId>slf4j-api</artifactId>
    	</dependency>
    	<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-slf4j-impl</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-api</artifactId>
  		</dependency>
  		<dependency>
    		<groupId>org.apache.logging.log4j</groupId>
    		<artifactId>log4j-core</artifactId>
  		</dependency>
		<!--  Testing related dependencies -->

		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>xmlunit</groupId>
			<artifactId>xmlunit</artifactId>
			<version>1.6</version>
			<scope>test</scope>
		</dependency>

	</dependencies>

	<properties>
		<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
		<timestamp>${maven.build.timestamp}</timestamp>
	</properties>
	<build>

		<plugins>

			<!-- Excluding demo package is required for avoiding namespace clashes
				(demo package is in all modules) for signing the jar. See issue #387 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <excludes>
                        <exclude>demo/**</exclude>
                    </excludes>
                </configuration>
            </plugin>

			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-resources-plugin</artifactId>
			</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.gz</include>
					<include>**/*.mat</include>
					<include>**/*.xml</include>
				</includes>
			</resource>
		</resources>

	</build>


</project>