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pom.xml
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<?xml version="1.0"?>
<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>biojava</artifactId>
<groupId>org.biojava</groupId>
<version>4.0.1-SNAPSHOT</version>
</parent>
<artifactId>biojava-protein-comparison-tool</artifactId>
<packaging>jar</packaging>
<name>biojava-protein-comparison-tool</name>
<url>http://source.rcsb.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
<maven.build.timestamp.format>yyyyMMdd</maven.build.timestamp.format>
<timestamp>${maven.build.timestamp}</timestamp>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment-ffx</artifactId>
<version>4.1.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core-ffx</artifactId>
<version>4.1.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure-ffx</artifactId>
<version>4.1.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure-gui-ffx</artifactId>
<version>4.1.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.sourceforge.jmol</groupId>
<artifactId>jmol</artifactId>
<version>13.0.14</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-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>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<!-- Minimizing removes jmol and log4j -->
<minimizeJar>false</minimizeJar>
<artifactSet>
<excludes>
<exclude>junit:junit</exclude>
</excludes>
</artifactSet>
<filters>
<filter>
<artifact>net.sourceforge.jmol:jmol</artifact>
<excludes>
<exclude>javax/vecmath/**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.biojava:biojava-structure-ffx</artifact>
<excludes>
<exclude>demo/DemoFATCAT*</exclude>
<exclude>demo/DemoCE*</exclude>
</excludes>
</filter>
<filter>
<!-- Exclude signature files -->
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Specification-Vendor>Open Bioinformatics Foundation</Specification-Vendor>
<Implementation-Vendor>Open Bioinformatics Foundation</Implementation-Vendor>
<Specification-Version>${project.version}</Specification-Version>
<Implementation-Version>${project.version}</Implementation-Version>
<Specification-Title>${project.name}</Specification-Title>
<Implementation-Title>${project.name}</Implementation-Title>
<Main-Class>org.biojava.nbio.structure.align.gui.AlignmentGui</Main-Class>
<Implementation-Build>${buildNumber}</Implementation-Build>
</manifestEntries>
</transformer>
<!-- This bit merges the various META-INF/services files -->
<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
</transformers>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<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>
<configuration>
<finalName>${project.artifactId}-${project.version}</finalName>
<appendAssemblyId>false</appendAssemblyId>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>1.3</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>create</goal>
</goals>
</execution>
</executions>
<configuration>
<doCheck>false</doCheck>
<doUpdate>false</doUpdate>
</configuration>
</plugin>
</plugins>
</build>
</project>