<?xml version="1.0" encoding="UTF-8"?>
<project 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>de.proteinms.omxparser</groupId>
    <artifactId>omssa-parser</artifactId>
    <packaging>jar</packaging>
    <version>${version.number}</version> <!-- version number is set below -->
    <name>omssa-parser</name>
    <description>OMSSA Parser is a Java based parser for OMSSA (Open Mass Spectrometry Search Algorithm) omx files.</description>
    <url>http://omssa-parser.googlecode.com/</url>


    <!-- Set the version number for the whole project -->
    <properties>
        <version.number>1.5.2</version.number>
    </properties>


    <!-- License -->
    <licenses>
        <license>
            <name>The Apache Software License, Version 2.0</name>
            <url>http://www.apache.org/licenses/LICENSE-2.0</url>
        </license>
    </licenses>


    <!-- Developers -->
    <developers>
        <developer>
            <name>Harald Barsnes</name>
            <id>harald</id>
            <email>harald.barsnes@biomed.uib.no</email>
            <organization>Department of Biomedicine, University of Bergen, Norway</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Lennart Martens</name>
            <id>lennart</id>
            <email>lennart.martens@ebi.ac.uk</email>
            <organization>Proteomics Services Team, PANDA Group, EMBL-European Bioinformatics Institute</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Steffen Huber</name>
            <id>steffen</id>
            <email>s.ch.h@gmx.de</email>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
        <developer>
            <name>Marc Vaudel</name>
            <id>marc</id>
            <email>marc.vaudel AT isas.de</email>
            <organization>ISAS</organization>
            <roles>
                <role>Java Developer</role>
            </roles>
        </developer>
    </developers>


    <!-- Build -->
    <build>

        <!-- Resources -->
        <resources>
            <resource>
                <directory>src/main/resources</directory>
            </resource>
            <resource>
                <directory>./</directory>
                <includes>
                    <include>omssa-parser.properties</include>
                </includes>
                <filtering>true</filtering>
            </resource>
        </resources>

        <!-- Plugins -->
        <plugins>

            <!-- Compiler plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>1.5</source>
                    <target>1.5</target>
                    <showDeprecation>true</showDeprecation>
                    <debug>true</debug>
                </configuration>
            </plugin>

            <!-- Jar plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                            <mainClass>de.proteinms.omxparser.tools.OmssaViewerWrapper</mainClass>
                            <addClasspath>true</addClasspath>
                            <classpathPrefix>lib</classpathPrefix>
                        </manifest>
                    </archive>
                    <outputDirectory>${project.build.directory}/${project.name}-${project.version}/</outputDirectory>
                </configuration>
            </plugin>

            <!-- Dependency plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>copy-dependencies</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/${project.name}-${project.version}/lib</outputDirectory>
                            <overWriteReleases>true</overWriteReleases>
                            <overWriteSnapshots>true</overWriteSnapshots>
                            <excludeTransitive>false</excludeTransitive>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Resources plugin -->
            <plugin>
                <artifactId>maven-resources-plugin</artifactId>
                <version>2.3</version>
                <executions>
                    <execution>
                        <id>copy-resources</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/${project.name}-${project.version}</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>src/main/resources/props</directory>
                                </resource>
                                <resource>
                                    <directory>./</directory>
                                    <includes>
                                        <include>README.txt</include>
                                        <include>omssa-viewer.ico</include>
                                        <include>LICENSE-2.0.txt</include>
                                    </includes>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Source plugin -->
            <!--<plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <executions>
                    <execution>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>-->

            <!-- Javadoc plugin -->
            <!--<plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <executions>
                    <execution>
                        <phase>process-resources</phase>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>-->
            
        </plugins>
    </build>


    <!-- Repositores -->
    <repositories>
        <!-- UGent Genesis Maven repository -->
        <repository>
            <id>genesis-maven2-repository</id>
            <name>Genesis maven2 repository</name>
            <url>http://genesis.UGent.be/maven2</url>
            <layout>default</layout>
        </repository>
    </repositories>


    <!-- Distribution Management -->
    <distributionManagement>
        <repository>
            <id>genesis-maven2-repo</id>
            <name>Genesis Maven Repository</name>
            <url>scp://genesis.ugent.be/home/maven/public_html/maven2</url>
        </repository>
    </distributionManagement>


    <!-- Dependencies -->
    <dependencies>

        <dependency>
            <groupId>xpp3</groupId>
            <artifactId>xpp3</artifactId>
            <version>1.1.4c</version>
            <type>jar</type>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.15</version>
            <exclusions>
                <exclusion>
                    <artifactId>jms</artifactId>
                    <groupId>javax.jms</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>jmxri</artifactId>
                    <groupId>com.sun.jmx</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>jmxtools</artifactId>
                    <groupId>com.sun.jdmk</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>mail</artifactId>
                    <groupId>javax.mail</groupId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.swinglabs</groupId>
            <artifactId>swing-layout</artifactId>
            <version>1.0.3</version>
            <scope>compile</scope>
        </dependency>
        <dependency>
            <groupId>com.compomics</groupId>
            <artifactId>utilities</artifactId>
            <version>3.7.6</version>
            <exclusions>
                <exclusion>
                    <artifactId>xz</artifactId>
                    <groupId>org.tukaani</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>xtandem-parser</artifactId>
                    <groupId>de.proteinms.xtandemparser</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>omssa-parser</artifactId>
                    <groupId>de.proteinms.omxparser</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>mail</artifactId>
                    <groupId>javax.mail</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>ols-dialog</artifactId>
                    <groupId>no.uib</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>mascotdatfile</artifactId>
                    <groupId>com.compomics</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>jmzml</artifactId>
                    <groupId>uk.ac.ebi.jmzml</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>braf</artifactId>
                    <groupId>uk.ac.ebi.pride.tools</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>derby</artifactId>
                    <groupId>org.apache.derby</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>pdf-transcoder</artifactId>
                    <groupId>batik</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>batik-all</artifactId>
                    <groupId>batik</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>swingx</artifactId>
                    <groupId>org.swinglabs</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>commons-compress</artifactId>
                    <groupId>org.apache.commons</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>commons-math</artifactId>
                    <groupId>commons-math</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>xercesImpl</artifactId>
                    <groupId>xerces</groupId>
                </exclusion>
            </exclusions>
        </dependency>
        
        <dependency>
            <groupId>no.uib</groupId>
            <artifactId>jsparklines</artifactId>
            <version>0.5.36</version>
        </dependency>
    </dependencies>
</project>
