<?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>7.2.0</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>7.2.0</version>

<scope>compile</scope>

</dependency>

<dependency>

<groupId>org.biojava</groupId>

<artifactId>biojava-core</artifactId>

<version>7.2.0</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

<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

<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>