Description

<dependency>
    <groupId>org.biojava</groupId>
    <artifactId>biojava-structure</artifactId>
    <version>7.2.4</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>7.2.4</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>${ciftools.artifact}</artifactId>
			<version>${ciftools.version}</version>
		</dependency>
		<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>
			<exclusions>
				<!-- This is needed because mmtf uses slf4j 1.7 and the log4j2 slf4j1 binding, somehow clashing with slf4j2 in this repo -->
				<exclusion>
					<groupId>org.apache.logging.log4j</groupId>
					<artifactId>log4j-slf4j-impl</artifactId>
				</exclusion>
			</exclusions>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-alignment</artifactId>
			<version>7.2.4</version>
			<scope>compile</scope>
		</dependency>
		<dependency>
			<groupId>org.biojava</groupId>
			<artifactId>biojava-core</artifactId>
			<version>7.2.4</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>
			<!-- Pin! Java 8 requires 1.4.0 -->
			<version>1.4.0</version>
		</dependency>

		<dependency>
			<groupId>jakarta.xml.bind</groupId>
			<artifactId>jakarta.xml.bind-api</artifactId>
		</dependency>
		<dependency>
			<groupId>org.glassfish.jaxb</groupId>
			<artifactId>jaxb-runtime</artifactId>
		</dependency>

		<!-- Used for json deserialization in PDBStatus -->
		<dependency>
			<groupId>com.fasterxml.jackson.core</groupId>
			<artifactId>jackson-databind</artifactId>
			<version>2.13.4.2</version>
		</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-slf4j2-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>
		<!-- Junit5 dependencies, defined in parent pom. -->
		<dependency>
			<groupId>org.junit.jupiter</groupId>
			<artifactId>junit-jupiter-engine</artifactId>
		</dependency>
		<dependency>
			<groupId>org.junit.jupiter</groupId>
			<artifactId>junit-jupiter-params</artifactId>
		</dependency>
		<dependency>
			<groupId>org.junit.vintage</groupId>
			<artifactId>junit-vintage-engine</artifactId>
		</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>