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mrifflemriffle
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Add ant build. Handle I/L substitutions.
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‎.gitignore

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# Compiled class file
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*.class
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# Log file
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*.log
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# BlueJ files
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*.ctxt
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# Mobile Tools for Java (J2ME)
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.mtj.tmp/
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# Package Files #
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*.ear
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*.tar.gz
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*.rar
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
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hs_err_pid*
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/bin/
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.classpath
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.project
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/deploy/
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/resources/
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/classes/
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/.idea/

‎ant__create_runnable_jar.xml

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<project default="create_run_jar" name="fastaTrimmer.jar Create Runnable Jar for Jar-in-Jar Loader">
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<property name="java_target" value="1.8"/>
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<property name="java_source" value="1.8"/>
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<property name="java.source.character.set" value="iso-8859-1"/>
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<property name="jar.main.class" value="org.uwpr.fasta_trimmer.program.MainProgram" />
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<property name="output_runnable_jar" value="fastaTrimmer.jar"/>
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<property name="deploy" value="deploy" />
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<property name="src" value="src" />
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<property name="classes" value="classes" />
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<available file=".git" type="dir" property="git.present"/>
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<target name="create_run_jar" depends="compile,prepare,git.revision">
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<path id="build.classpath">
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<fileset dir="lib">
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<include name="**/*.jar" />
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</fileset>
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</path>
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<!-- convert classpath to a flat list/string for use in manifest task -->
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<pathconvert property="jars.classpath" pathsep=" ">
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<path refid="build.classpath" />
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<flattenmapper />
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</pathconvert>
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<property name="final.classpath" value="./ ${jars.classpath}"/>
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<echo >Classpath for runnable jar ${final.classpath}</echo>
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<jar destfile="deploy/${output_runnable_jar}">
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<manifest>
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<attribute name="Main-Class" value="org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader"/>
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<attribute name="Rsrc-Main-Class"
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value="${jar.main.class}"/>
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<attribute name="Class-Path" value="."/>
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<attribute name="Rsrc-Class-Path" value="${final.classpath}"/>
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<attribute name="GIT-last-tag-commit-hash" value="${git.last.tag.and.commit.hash}"/>
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<attribute name="GIT-commit-hash" value="${git.last.commit.hash}"/>
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<attribute name="Date" value="${build-info.current-date}" />
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<attribute name="Time" value="${build-info.current-time}" />
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</manifest>
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<zipfileset src="jar-in-jar-loader.zip"/>
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<fileset dir="${classes}"/>
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<zipfileset dir="lib" />
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</jar>
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</target>
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<target name="create_jar_this_project" depends="compile,prepare,git.revision">
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<jar destfile="${jar_this_project_dir}/${output_jar_this_project}">
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<manifest>
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<attribute name="Main-Class" value="${jar.main.class}"/>
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<attribute name="GIT-last-tag-commit-hash" value="${git.last.tag.and.commit.hash}"/>
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<attribute name="GIT-commit-hash" value="${git.last.commit.hash}"/>
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<attribute name="Date" value="${build-info.current-date}" />
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<attribute name="Time" value="${build-info.current-time}" />
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</manifest>
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<fileset dir="${classes}"/>
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<fileset dir="${config}"/>
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</jar>
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</target>
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<target name="prepare">
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<tstamp prefix="build-info">
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<format property="current-date" pattern="d-MMMM-yyyy" locale="en" />
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<format property="current-time" pattern="hh:mm:ss a z" locale="en" />
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<format property="year-month-day" pattern="yyyy-MM-dd" locale="en" />
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</tstamp>
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</target>
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<target name="git.revision"
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description="Store git revision in ${git.last.tag.and.commit.hash} and ${git.last.commit.hash}"
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if="git.present">
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<exec executable="git" outputproperty="git.last.tag.and.commit.hash.from.cmd" failifexecutionfails="false" errorproperty="">
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<arg value="describe"/>
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<arg value="--tags"/>
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<arg value="--always"/>
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<arg value="HEAD"/>
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</exec>
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<echo message="git.last.tag.and.commit.hash.from.cmd: ${git.last.tag.and.commit.hash.from.cmd}"/>
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<condition property="git.last.tag.and.commit.hash" value="${git.last.tag.and.commit.hash.from.cmd}" else="unknown">
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<and>
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<isset property="git.last.tag.and.commit.hash.from.cmd"/>
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<length string="${git.last.tag.and.commit.hash.from.cmd}" trim="yes" length="0" when="greater"/>
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</and>
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</condition>
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<echo message="git.last.tag.and.commit.hash: ${git.last.tag.and.commit.hash}"/>
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<exec executable="git" outputproperty="git.last.commit.hash.from.cmd" failifexecutionfails="false" errorproperty="">
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<arg value="describe"/>
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<arg value="--always"/>
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<arg value="HEAD"/>
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</exec>
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<echo message="git.last.commit.hash.from.cmd: ${git.last.commit.hash.from.cmd}"/>
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<condition property="git.last.commit.hash" value="${git.last.commit.hash.from.cmd}" else="unknown">
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<and>
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<isset property="git.last.commit.hash.from.cmd"/>
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<length string="${git.last.commit.hash.from.cmd}" trim="yes" length="0" when="greater"/>
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</and>
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</condition>
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<echo message="git.last.commit.hash: ${git.last.commit.hash}"/>
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</target>
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<!-- ================================================================================== -->
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<!-- Clean the build directory -->
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<!-- ================================================================================== -->
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<target name="clean" description="Prepare for clean build">
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<delete dir="${classes}"/>
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<mkdir dir="${classes}"/>
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<delete dir="${deploy}" />
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<mkdir dir="${deploy}"/>
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</target>
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<!-- ================================================================================== -->
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<!-- Normal build of application -->
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<!-- ================================================================================== -->
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<target name="compile" depends="clean">
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<!-- <echo message="${toString:compile.classpath}"/> -->
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<javac includeantruntime="false" debug="on" srcdir="src" destdir="${classes}" source="${java_source}" target="${java_target}" encoding="${java.source.character.set}" >
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<classpath refid="compile.classpath"/>
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</javac>
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<!--
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<copy todir="${classes}">
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</copy>
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-->
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<copy todir="${classes}">
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<fileset dir="${src}">
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<exclude name="**/*.java" />
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</fileset>
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</copy>
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</target>
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<!-- classpath -->
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<path id="compile.classpath">
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<fileset dir="lib">
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<include name="**/*.jar"/>
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</fileset>
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</path>
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</project>

‎jar-in-jar-loader.zip

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‎src/org/uwpr/fasta_trimmer/program/FASTATrimmer.java

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/**
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* Return true if the protein sequence contains the given peptide sequence--assuming trypsin was used
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* to digest the proteins.
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* to digest the proteins. Handle I/L substitution
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*
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* @param proteinSequence
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* @param peptideSequence
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private boolean proteinContainsPeptide( String proteinSequence, String peptideSequence ) {
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//System.err.println( "Testing if " + proteinSequence + " contains " + peptideSequence );
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proteinSequence = proteinSequence.replaceAll( "L", "I" );
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peptideSequence = peptideSequence.replaceAll( "L", "I" );
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if( proteinSequence.startsWith( peptideSequence ) )
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return true;
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