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@AimeeD90
AimeeD90 committed Aug 6, 2018
1 parent 66f1db9 commit eba7ab6
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Showing 9 changed files with 961 additions and 395 deletions.
168 changes: 85 additions & 83 deletions .idea/artifacts/pClean_jar.xml
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13 changes: 13 additions & 0 deletions .idea/libraries/Maven__de_proteinms_xtandemparser_xtandem_parser_1_13_0.xml
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1 change: 1 addition & 0 deletions pClean.iml
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Expand Up @@ -77,6 +77,7 @@
<orderEntry type="library" name="Maven: avalon-framework:avalon-framework:4.1.3" level="project" />
<orderEntry type="library" name="Maven: psidev.psi.tools:xxindex:0.11" level="project" />
<orderEntry type="library" name="Maven: cpdetector:cpdetector:1.0.7" level="project" />
<orderEntry type="library" name="Maven: de.proteinms.xtandemparser:xtandem-parser:1.13.0" level="project" />
<orderEntry type="library" name="Maven: org.apache.maven.plugins:maven-resources-plugin:2.4.3" level="project" />
<orderEntry type="library" name="Maven: org.apache.maven:maven-plugin-api:2.0.6" level="project" />
<orderEntry type="library" name="Maven: org.apache.maven:maven-project:2.0.6" level="project" />
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95 changes: 57 additions & 38 deletions pom.xml
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Expand Up @@ -45,6 +45,12 @@
<version>3.6.0</version>
</dependency>

<!-- https://mvnrepository.com/artifact/de.proteinms.xtandemparser/xtandem-parser -->
<dependency>
<groupId>de.proteinms.xtandemparser</groupId>
<artifactId>xtandem-parser</artifactId>
<version>1.13.0</version>
</dependency>

<dependency>
<groupId>org.apache.maven.plugins</groupId>
Expand All @@ -62,11 +68,22 @@
</license>
</licenses>

<!--build-->
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<resources>
<resource>
<targetPath>.</targetPath>
<directory>src/main/resources</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>

<plugins>
<!--compiler plugin-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.5</version>
<configuration>
Expand All @@ -75,22 +92,27 @@
</configuration>
</plugin>

<!-- Assembly plugin-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.5.3</version>
<configuration>
<archive>
<manifest>
<mainClass>Preprocessing.pCleanMainClass</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>
jar-with-dependencies
</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
<manifest>
<mainClass>Preprocessing.pCleanMainClass</mainClass>
</manifest>
</archive>
</configuration>

<executions>
<execution>
<id>make-assembly</id>
Expand All @@ -102,50 +124,47 @@
</executions>
</plugin>


<!-- Jar plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
<mainClass>Preprocessing.pCleanMainClass</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>lib</classpathPrefix>
</manifest>
</archive>
<outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}
</outputDirectory>
</configuration>
</plugin>

<!-- Dependency plugin -->
<!--maven shade plugin-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
<goal>shade</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}/lib
</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<excludeTransitive>false</excludeTransitive>
<!-- <finalName>${project.artifactId}-${project.version}-jar-w-reduced-deps</finalName> -->
<finalName>${project.artifactId}</finalName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>Preprocessing.pCleanMainClass</mainClass>
</transformer>
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>

<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>**/.svn/**</exclude>
<!-- <exclude>**/*.java</exclude> -->
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>


</plugins>
</build>

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2 changes: 1 addition & 1 deletion src/main/java/Preprocessing/JPeakPair.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
package Preprocessing;

/**
* Format output information in _edge.txt files.
* FDRutility.PsmsConverter output information in _edge.txt files.
*
* Created by dengyamei on 03/07/2018.
*/
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