<?xml version="1.0" encoding="UTF-8"?>
-<project default="proteocache" name="Build ProteoCache - Results repository for the Dundee Resource" basedir=".">
-
- <property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
-
- <!-- Distributive file names-->
- <property name="distdir" value="distro"/>
- <mkdir dir="${distdir}" />
+<project default="proteocache" name="Build ProteoCache - Caching framework for the Dundee Resource" basedir=".">
<!-- projects details -->
+ <property name="proteocache_version" value="0.1.0"/>
<property name="project.url" value="http://www.compbio.dundee.ac.uk/proteocache"/>
<property name="product" value="ProteoCache"/>
<property name="author" value="Alexander Sherstnev"/>
-
- <!-- dependencies on other compbio projects -->
- <property name="compbio-annotation" value="compbio-annotations-1.0.jar"/>
- <property name="compbio-util" value="compbio-util-1.4.jar"/>
- <property name="compbio-ga" value="compbio-ga-1.0.jar"/>
-
+ <!-- Distributive file names-->
+ <property name="distdir" value="distribution"/>
+ <mkdir dir="${distdir}" />
<!-- products -->
- <property name="proteocache_version" value="2.1.0"/>
- <property name="datamodel" value="${distdir}/datamodel-${proteocache_version}.jar"/>
- <property name="datamodel-src" value="${distdir}/datamodel-src-${proteocache_version}.jar"/>
- <property name="min-proteocache-client" value="${distdir}/min-proteocache-client-${proteocache_version}.jar"/>
- <property name="min-proteocache-client-nolog" value="${distdir}/min-proteocache-client-nolog-${proteocache_version}.jar"/>
- <property name="proteocache-client-src" value="${distdir}/proteocache-client-src-${proteocache_version}.jar"/>
- <property name="aacon-ws-client" value="${distdir}/aacon-ws-client.jar"/>
- <property name="full-proteocache-client" value="${distdir}/full-proteocache-client-${proteocache_version}.jar"/>
+ <property name="proteocache-war" value="${distdir}/proteocache-${proteocache_version}.war"/>
+ <property name="proteocache-jar" value="${distdir}/proteocache-${proteocache_version}.jar"/>
<property name="proteocache-source-jar" value="${distdir}/proteocache-src-${proteocache_version}.jar"/>
- <property name="full-proteocache-client-pack" value="${distdir}/full-proteocache-client-${proteocache_version}-pack.zip"/>
- <property name="proteocache" value="${distdir}/proteocache.war"/>
- <!-- TODO
- <property name="proteocache-dundee" value="${distdir}/proteocache-dundee.war"/>
- -->
- <property name="proteocache-no-binaries" value="${distdir}/proteocache-no-binaries.war"/>
- <property name="binaries" value="${distdir}/binaries.zip"/>
- <property name="proteocache-devel-web" value="${distdir}/proteocache-devel-website.zip"/>
-
- <!--Whole project archive -->
<property name="proteocache-project" value="${distdir}/proteocache-project.zip"/>
-
<!-- java -->
- <property name="test.src" location="${basedir}/testsrc" />
<property name="classes" location="${basedir}/WEB-INF/classes" />
- <property name="lib.path" location="${basedir}/lib" />
+ <property name="ext.lib.path" location="${basedir}/lib" />
<property name="web.lib.path" location="${basedir}/WEB-INF/lib" />
- <property name="test.lib.path" location="${basedir}/testsrc/lib" />
- <property name="activity.log" location="${basedir}/activity.log" />
- <!-- add libraries -->
+ <!-- add external and internal libraries -->
<path id="project.classpath">
- <fileset dir="${lib.path}">
- <include name="*.jar" />
- </fileset>
<fileset dir="${web.lib.path}">
<include name="*.jar" />
</fileset>
- </path>
-
- <!-- add test classes -->
- <path id="test.classpath">
- <fileset dir="${test.lib.path}">
+ <fileset dir="${ext.lib.path}">
<include name="*.jar" />
</fileset>
- <pathelement location="${classes}" />
</path>
- <fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
- <!-- Datamodel -->
- <include name="compbio/data/**"/>
- <include name="compbio/metadata/**"/>
- <!-- Engine -->
+ <fileset dir="${basedir}/WEB-INF/classes/" id="allcodes">
+ <include name="compbio/datadb/**"/>
<include name="compbio/engine/**"/>
- <!-- Casscode -->
- <include name="compbio/casscode/**"/>
- <!-- Logging configuration -->
+ <include name="compbio/server/**"/>
</fileset>
+<!-- ###################################################################################################################################### -->
+<!-- Main targets -->
+
<!-- Clean temp directories -->
<target name="clean">
<delete dir="${classes}" />
- <delete dir="${basedir}/logs" />
- <delete file="${distdir}/binaries.zip" />
- <delete file="${basedir}/activity.log" />
- <delete file="${basedir}/derby.log" />
<mkdir dir="${classes}" />
<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
</target>
- <!-- Clean up temp directories and dist directory (all jar, zip, and war files deleted) -->
+ <!-- Clean up temporary directories and dist directory (all jar, zip, and war files deleted) -->
<target name="full-clean" depends="clean">
<delete>
<fileset dir="${distdir}">
</delete>
</target>
- <target name="clearStatDB" description="Remove all records from statistics database">
- <echo>Cleaning Statistics database</echo>
- <java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">
- <jvmarg value="-Dlog4j.configuration=file:log/log4j.properties.statdb" />
- <classpath refid="project.classpath" />
- </java>
- </target>
-
<!--
- The compilation order is
- 1. datamodel
- 2. engine
- 3. casscode
- 4. testscr
- 5. webservices
- Packages of the lower order could not have dependencies on the packages on the next layer.
- So, casscode (layer 3) depends on the enginesand the datamodel but engine does not depend on
- anything in casscode or any other layers above. Testsrc is not allowed to test webservices.
+ Compile with optimisation. testsrc is not compiled
+ Packages of the lower order should not have dependencies on the packages
+ on the next layer. So datadb (layer 3) depends on the engine classes but
+ engine does not depend on anything in datadb
-->
- <target name="compile_with_debug" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug enabled.">
+ <target name="compile" depends="clean" description="Multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled.">
<!-- copy files to class path-->
<copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
- <!-- Complile the datamodel first -->
- <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6"
- source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
- <compilerarg value="-Xlint:unchecked"/>
- <classpath refid="project.classpath" />
- </javac>
- <!-- Complile the engines -->
- <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6"
- source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
- <compilerarg value="-Xlint:unchecked"/>
- <classpath refid="project.classpath" />
- </javac>
- <!-- Complile the casscode -->
- <javac srcdir="${basedir}/casscode" destdir="${classes}" target="1.6"
- source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
- <compilerarg value="-Xlint:unchecked"/>
- <classpath refid="project.classpath" />
- </javac>
- <!-- Complile the webservices -->
- <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6"
- source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
- <compilerarg value="-Xlint:unchecked"/>
- <classpath refid="project.classpath" />
- </javac>
- <!-- Complile the tests -->
- <javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6"
- source="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
- <compilerarg value="-Xlint:unchecked"/>
- <classpath refid="project.classpath" />
- <classpath refid="test.classpath" />
- </javac>
- </target>
-
- <!--
- Compile with optimisation. Do not compile testsrc
- The compilation order is
- 1. datamodel
- 2. engine
- 3. casscode
- 4. webservices
- Packages of the lower order could not have dependencies on the packages on the next layer.
- So casscode (layer 3) depends on the engine and the datamodel but engine does not depend
- on anything in casscode or any other layers above.
- -->
- <target name="compile" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled. Tests are not compiled.">
- <!-- copy files to class path-->
- <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
- <!-- Complile the datamodel -->
- <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+ <!-- Complile engine -->
+ <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.7" source="1.7" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
<compilerarg value="-Xlint:-unchecked" />
<classpath refid="project.classpath" />
</javac>
- <!-- Complile the engine -->
- <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
- <compilerarg value="-Xlint:-all" />
+ <!-- Complile database code -->
+ <javac srcdir="${basedir}/datadb" destdir="${classes}" target="1.7" source="1.7" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+ <compilerarg value="-Xlint:all" />
<compilerarg value="-Xlint:-unchecked" />
<classpath refid="project.classpath" />
</javac>
- <!-- Complile the casscode -->
- <javac srcdir="${basedir}/casscode" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
+ <!-- Complile the server -->
+ <javac srcdir="${basedir}/server" destdir="${classes}" target="1.7" source="1.7" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
<compilerarg value="-Xlint:-unchecked" />
<classpath refid="project.classpath" />
</javac>
- <!-- Complile the webservices -->
- <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6" source="1.6" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
- <compilerarg value="-Xlint:-unchecked" />
- <classpath refid="project.classpath" />
- </javac>
- </target>
-
- <target name="datamodel-jar" depends="compile" description="Pack data model classes">
- <echo>Jar file: Minimal WS client jar</echo>
- <delete file="${basedir}/${datamodel}">
- </delete>
- <jar jarfile="${basedir}/${datamodel}">
- <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
- <include name="${compbio-util}"/>
- <include name="${compbio-annotation}"/>
- </zipgroupfileset>
- <fileset dir="${basedir}/WEB-INF/classes/">
- <include name="compbio/data/sequence/*.class"/>
- <include name="compbio/metadata/*.class"/>
- </fileset>
- <manifest>
- <attribute name="Built-By" value="${author}" />
- <attribute name="Class-Path" value="." />
- <attribute name="Implementation-Title" value="Datamodel for ${product} " />
- <attribute name="Implementation-Vendor" value="${author}" />
- <attribute name="Implementation-URL" value="${project.url}" />
- </manifest>
- </jar>
- </target>
-
- <target name="minimal-proteocache-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
- <echo>Jar file: Minimal WS client jar</echo>
- <delete file="${basedir}/${min-proteocache-client}"></delete>
- <jar jarfile="${basedir}/${min-proteocache-client}">
- <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
- <fileset dir="${basedir}/WEB-INF/classes/">
- <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
- <include name="compbio/data/msa/**"/>
- <include name="compbio/ws/client/**"/>
- </fileset>
- <zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
- <manifest>
- <attribute name="Built-By" value="${author}" />
- <attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
- <attribute name="Class-Path" value="." />
- <attribute name="Implementation-Title" value="Minimal ${product} Client" />
- <attribute name="Implementation-Vendor" value="${author}" />
- <attribute name="Implementation-URL" value="${project.url}" />
- </manifest>
- </jar>
- <delete file="${basedir}/${min-proteocache-client-nolog}"></delete>
- <jar jarfile="${basedir}/${min-proteocache-client-nolog}">
- <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
- <fileset dir="${basedir}/WEB-INF/classes/">
- <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
- <include name="compbio/data/msa/**"/>
- <include name="compbio/ws/client/**"/>
- </fileset>
- <manifest>
- <attribute name="Built-By" value="${author}" />
- <attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
- <attribute name="Class-Path" value="." />
- <attribute name="Implementation-Title" value="Minimal ${product} Client" />
- <attribute name="Implementation-Vendor" value="${author}" />
- <attribute name="Implementation-URL" value="${project.url}" />
- </manifest>
- </jar>
</target>
- <target name="full-proteocache-client-jar" depends="compile" description="Pack datamodel, engine and casscode">
- <echo>Jar file: Full ProteoCache client jar</echo>
- <delete file="${full-proteocache-client}">
+ <target name="source-jar" description="Pack java sources">
+ <delete file="${proteocache-source-jar}">
</delete>
- <jar jarfile="${full-proteocache-client}">
- <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
- <include name="${compbio-util}"/>
- <include name="${compbio-annotation}"/>
- <include name="drmaa.jar"/>
- </zipgroupfileset>
- <fileset refid="fullclient"/>
- <manifest>
- <attribute name="Built-By" value="${author}" />
- <attribute name="Class-Path" value="." />
- <attribute name="Implementation-Title" value="Full ${product} Client" />
- <attribute name="Implementation-Vendor" value="${author}" />
- <attribute name="Implementation-URL" value="${project.url}" />
- </manifest>
- </jar>
- </target>
-
- <target name="full-proteocache-client" depends="full-proteocache-client-jar" description="Pack sources and configuration files">
- <echo>Packing binaries, and configuration files</echo>
- <zip destfile="${full-proteocache-client-pack}" >
- <zipgroupfileset file="${binaries}" />
- <zipfileset dir="conf" prefix="conf" >
- <exclude name="**/temp/**"/>
- </zipfileset>
- <fileset file="${full-proteocache-client}" />
- </zip>
- </target>
-
-
- <target name="source-jar" depends="datamodel-source-jar" description="Pack java sources">
- <delete file="${basedir}/${proteocache-source-jar}">
- </delete>
- <jar jarfile="${basedir}/${proteocache-source-jar}">
- <zipgroupfileset excludes="META-INF/*.MF" file="${datamodel-src}"/>
- <fileset dir="${basedir}/casscode">
+ <jar jarfile="${proteocache-source-jar}">
+ <fileset dir="${basedir}/datadb">
<include name="**"/>
</fileset>
<fileset dir="${basedir}/engine">
<include name="**"/>
</fileset>
- <fileset dir="${basedir}/webservices/">
+ <fileset dir="${basedir}/server/">
<include name="**"/>
</fileset>
<manifest>
</jar>
</target>
- <target name="datamodel-source-jar" depends="compile" description="Pack java sources">
- <delete file="${datamodel-src}">
- </delete>
- <jar jarfile="${datamodel-src}">
- <fileset dir="${basedir}/datamodel">
- <include name="**"/>
- </fileset>
- <zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
- <include name="**"/>
- </zipgroupfileset>
- <manifest>
- <attribute name="Built-By" value="${author}" />
- <attribute name="Implementation-Title" value="${product} Datamodel Source Code Archive" />
- <attribute name="Implementation-Vendor" value="${author}" />
- <attribute name="Implementation-URL" value="${project.url}" />
- </manifest>
- </jar>
- </target>
-
- <target name="full-proteocache-jar" depends="compile" description="Pack datamodel, engine, casscode, configuration, binaries and webservices">
- <echo>Jar file: Full WS client jar</echo>
- <delete file="${full-proteocache-client}">
- </delete>
- <jar jarfile="${full-proteocache-client}">
- <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
- <include name="log4j-1.2.15.jar"/>
- <include name="${compbio-util}"/>
- <include name="${compbio-annotation}"/>
- <include name="drmaa.jar"/>
- </zipgroupfileset>
- <fileset refid="fullclient">
- </fileset>
- <fileset dir="${basedir}/WEB-INF/classes/">
- <!-- Statistics web application -->
- <include name="compbio/stat/**"/>
- <!-- Web services-->
- <include name="compbio/ws/**"/>
- </fileset>
- <!-- Set WSTester as main to help user to test their deployments -->
+ <target name="build-proteocache-jar" depends="compile" description="Pack all compiled codes, configuration, ...">
+ <echo>Build full jar</echo>
+ <delete file="${proteocache-jar}"></delete>
+ <jar jarfile="${proteocache-jar}">
+<!-- <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" ></zipgroupfileset>-->
+ <fileset refid="allcodes"></fileset>
+ <fileset dir="${basedir}/WEB-INF/classes/"></fileset>
+ <!-- Set compbio.server.MainTester as main to help user to test their deployments -->
<manifest>
<attribute name="Built-By" value="${author}" />
<attribute name="Class-Path" value="." />
- <attribute name="Main-Class" value="compbio.ws.client.WSTester" />
+ <attribute name="Main-Class" value="compbio.server.MainTester" />
<attribute name="Implementation-Title" value="${product}" />
<attribute name="Implementation-Vendor" value="${author}" />
<attribute name="Implementation-URL" value="${project.url}" />
</jar>
</target>
- <target name="proteocache-no-binaries" depends="full-proteocache-jar, clearStatDB" description="Prepare proteocache war file without native binaries">
- <echo>Preparing a war file without binaries</echo>
- <delete file="${proteocache-no-binaries}">
- </delete>
- <zip destfile="${proteocache-no-binaries}" whenempty="create">
+ <target name="proteocache-server" depends="build-proteocache-jar" description="Prepare ProteoCache war file">
+ <echo>Prepare ProteoCache war file</echo>
+ <delete file="${proteocache-war}"></delete>
+ <zip destfile="${proteocache-war}" whenempty="create">
<zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
<exclude name="classes"/>
- <!-- These are included into JABA client so exclude the jars -->
- <exclude name="lib/drmaa.jar"/>
- <exclude name="lib/log4j-1.2.15.jar"/>
- <exclude name="lib/${compbio-annotation}"/>
- <exclude name="lib/${compbio-util}"/>
-
<include name="web.xml"/>
- <include name="sun-jaxws.xml"/>
<include name="lib/*"/>
</zipfileset>
- <zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
- <zipfileset dir="${basedir}/statpages" prefix="statpages" />
- <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
- <zipfileset dir="conf" prefix="conf" >
- <exclude name="**/temp/**"/>
- </zipfileset>
- <!-- Add proteocache web site apart from the binary archive -->
- <zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>
- <zipfileset dir="." includes="${full-proteocache-client}" fullpath="WEB-INF/lib/proteocache-client.jar"/>
+ <zipfileset dir="." includes="${proteocache-jar}" fullpath="WEB-INF/lib/proteocache.jar"/>
+ <zipfileset dir="conf" prefix="conf" />
+ <!-- Add ProteoCache static web site pages apart from the binary archive -->
+ <zipfileset dir="${basedir}/website" excludes="tests/**, template.html"/>
<!-- Put a copy of log4j configuration file where it can be used -->
<zipfileset dir="log" includes="log4j.properties" prefix="WEB-INF/classes"/>
</zip>
</target>
- <target name="build-devel-website" description="Pack developement related pages, tests, javadoc" >
- <echo>Packing data for internal web site</echo>
- <delete file="${proteocache-devel-web}">
- </delete>
- <zip destfile="${proteocache-devel-web}" whenempty="create">
- <!-- Add proteocache web site apart from the binary archive -->
- <zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>
- </zip>
- </target>
-
- <target name="proteocache-complete" depends="proteocache-no-binaries" description="Prepare proteocache war file without runtime dependency - JAXWS jars">
- <echo>Preparing a complete war file</echo>
- <delete file="${proteocache}">
- </delete>
- <copy tofile="${proteocache}" file="${proteocache-no-binaries}"/>
- <zip destfile="${proteocache}" update="true" >
- <zipgroupfileset file="${binaries}" />
- </zip>
- </target>
-
- <target name="build-all" depends="full-proteocache-client, minimal-proteocache-client-jar, proteocache-no-binaries, proteocache-complete, datamodel-jar, datamodel-source-jar, source-jar" description="Build-all the distributives"/>
+ <target name="all" depends="proteocache-server, source-jar" description="Build all files"/>
<!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->
- <target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">
+ <target name="archive" description="Pack everything in the project for those who do not have access to SVN" depends="full-clean">
<delete file="${proteocache-project}">
</delete>
<zip destfile="${proteocache-project}" whenempty="create" >
- <fileset dir="." excludes="${distdir}/**, jobsout/**, test-output/**, **.svn, dundee-conf/**, TODO.txt, IDEAS.txt, ${activity.log}, **/*.zip, **/*.war"/>
- <!-- Add jobsout directory but no content -->
- <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="*/**"/>
+ <fileset dir="." excludes="${distdir}/**, **.git, **/*.zip, **/*.war"/>
</zip>
</target>
+<!-- ###################################################################################################################################### -->
<!-- Test targets -->
+
+ <property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
+
+ <!-- add test library -->
+ <path id="test.classpath">
+ <fileset dir="${basedir}/testsrc/lib">
+ <include name="*.jar" />
+ </fileset>
+ <pathelement location="${classes}" />
+ </path>
+ <!--
+ Packages of the lower order should not have dependencies on the packages
+ on the next layer. So datadb (layer 3) depends on the engine classes but
+ engine does not depend on anything in datadb
+ -->
+ <target name="compile_with_debug" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug enabled.">
+ <!-- copy files to class path-->
+ <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
+ <!-- Complile the engine classes -->
+ <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the database classes -->
+ <javac srcdir="${basedir}/datadb" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the server classes -->
+ <javac srcdir="${basedir}/server" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ </javac>
+ <!-- Complile the tests -->
+ <javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.7" source="1.7" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
+ <compilerarg value="-Xlint:unchecked"/>
+ <classpath refid="project.classpath" />
+ <classpath refid="test.classpath" />
+ </javac>
+ </target>
+
+
<taskdef name="testNG" classname="org.testng.TestNGAntTask">
<classpath refid="test.classpath">
</classpath>
</testNG>
</target>
- <target name="Test_engines" depends="compile_with_debug">
- <delete file="${activity.log}"/>
- <testNG groups="engine" haltonfailure="true" verbose="3" enableassert="true" >
- <jvmarg value="-server" />
- <jvmarg value="-enableassertions" />
- <jvmarg value="-Xms1024m" />
- <jvmarg value="-Xmx1024m" />
- <classfileset dir="${classes}" includes="**/*.class" />
- <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
- <classpath refid="test.classpath" />
- <classpath refid="project.classpath" />
- <sysproperty key="TestingDataPath" value="${data.src}"/>
- </testNG>
- </target>
-
<target name="All_cluster_independent_windows_only_tests" depends="compile_with_debug">
<delete file="${activity.log}" failonerror="false"/>
<testNG excludedgroups="cluster, non_windows" haltonfailure="true" verbose="3" enableassert="true" >
+++ /dev/null
-package compbio.cassandra;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.InputStream;
-import java.util.Iterator;
-import java.util.Scanner;
-
-//import compbio.util.Util;
-
-/**
- * Reads files with FASTA formatted sequences. All the information in the FASTA
- * header is preserved including trailing white spaces. All the white spaces are
- * removed from the sequence.
- *
- * Examples of the correct input:
- *
- * <pre>
- *
- * >zedpshvyzg
- * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
- *
- * >xovkactesa
- * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
- * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
- * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
- * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
- *
- * >ntazzewyvv
- * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
- * EASINM AQQWRSLPPSRIMKLNG HGCDCMHSHMEAD DTKQSGIKGTFWNG HDAQWLCRWG
- * EFITEA WWGRWGAITFFHAH ENKNEIQECSDQNLKE SRTTCEIID TCHLFTRHLDGW
- * RCEKCQANATHMTW ACTKSCAEQW FCAKELMMN
- * W KQMGWRCKIFRKLFRDNCWID FELPWWPICFCCKGLSTKSHSAHDGDQCRRW WPDCARDWLGPGIRGEF
- * FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
- *
- * > 12 d t y wi k jbke
- * KLSHHDCD
- * N
- * H
- * HSKCTEPHCGNSHQMLHRDP
- * CCDQCQSWEAENWCASMRKAILF
- *
- * </pre>
- *
- * @author Peter Troshin
- * @version 1.0 April 2011
- *
- */
-public class FastaReader implements Iterator<FastaSequence> {
-
- private final Scanner input;
- /**
- * Delimiter for the scanner
- */
- private final String DELIM = ">";
-
- /**
- * Header data can contain non-ASCII symbols and read in UTF8
- *
- * @param inputFile
- * the file containing the list of FASTA formatted sequences to
- * read from
- * @throws FileNotFoundException
- * if the input file is not found
- * @throws IllegalStateException
- * if the close method was called on this instance
- *
- */
- public FastaReader(final String inputFile) throws FileNotFoundException {
- input = new Scanner(new File(inputFile), "UTF8");
- input.useDelimiter(DELIM);
- Runtime.getRuntime().addShutdownHook(new Thread() {
-
- @Override
- public void run() {
- if (input != null) {
- input.close();
- }
- }
- });
- }
-
- /**
- * This class will not close the incoming stream! So the client should do
- * so.
- *
- * @param inputStream
- * @throws FileNotFoundException
- */
- public FastaReader(final InputStream inputStream)
- throws FileNotFoundException {
- input = new Scanner(inputStream);
- input.useDelimiter(DELIM);
- }
-
- /**
- * {@inheritDoc}
- *
- * @throws IllegalStateException
- * if the close method was called on this instance
- */
- @Override
- public boolean hasNext() {
- return input.hasNext();
- }
-
- /**
- * Reads the next FastaSequence from the input
- *
- * @throws AssertionError
- * if the header or the sequence is missing
- * @throws IllegalStateException
- * if the close method was called on this instance
- * @throws MismatchException
- * - if there were no more FastaSequence's.
- */
- @Override
- public FastaSequence next() {
- String fastaHeader = input.next();
- while (fastaHeader.indexOf("\n") < 0 && input.hasNext()) {
- fastaHeader = fastaHeader.concat(">");
- fastaHeader = fastaHeader.concat(input.next());
- }
- return FastaReader.toFastaSequence(fastaHeader);
- }
-
- /**
- * Not implemented
- */
- @Override
- public void remove() {
- throw new UnsupportedOperationException();
- }
-
- /**
- * Call this method to close the connection to the input file if you want to
- * free up the resources. The connection will be closed on the JVM shutdown
- * if this method was not called explicitly. No further reading on this
- * instance of the FastaReader will be possible after calling this method.
- */
- public void close() {
- input.close();
- }
-
- private static FastaSequence toFastaSequence(final String singleFastaEntry) {
-
- // assert !Util.isEmpty(singleFastaEntry) :
- // "Empty String where FASTA sequence is expected!";
-
- int nlineidx = singleFastaEntry.indexOf("\n");
- if (nlineidx < 0) {
- throw new AssertionError(
- "The FASTA sequence must contain the header information"
- + " separated by the new line from the sequence. Given sequence does not appear to "
- + "contain the header! Given data:\n "
- + singleFastaEntry);
- }
- String header = singleFastaEntry.substring(0, nlineidx);
-
- // Get rid of the new line chars (should cover common cases)
- header = header.replaceAll("\r", "");
-
- String sequence = singleFastaEntry.substring(nlineidx);
-
- /*
- * if (Util.isEmpty(sequence)) { throw new AssertionError(
- * "Empty sequences are not allowed! Please make sure the " +
- * " data is in the FASTA format! Given data:\n " + singleFastaEntry); }
- */
- return new FastaSequence(header, sequence);
- }
-}
git://source.jalview.org / proteocache.git / commitdiff