[med-svn] [prottest] 03/08: Imported Upstream version 3.4.2+dfsg
Andreas Tille
tille at debian.org
Tue May 10 09:52:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository prottest.
commit d45fe9161f627e7193b7d32e92c3baa325bdb2cd
Author: Andreas Tille <tille at debian.org>
Date: Mon May 9 21:05:26 2016 +0200
Imported Upstream version 3.4.2+dfsg
---
COPYING | 0
INSTALL | 0
README.md | 10 +-
build.xml | 109 +++-
buildconf/build-impl.xml | 707 ---------------------
buildconf/project.properties | 80 ---
manifest.mf | 2 +-
.../services/org.jdesktop.application.Application | 0
.../java/es/uvigo/darwin/prottest/ProtTest.java | 40 +-
.../uvigo/darwin/prottest/consensus/Consensus.java | 0
.../uvigo/darwin/prottest/consensus/package.html | 0
.../darwin/prottest/exe/AminoAcidRunEstimator.java | 0
.../prottest/exe/ExternalExecutionManager.java | 0
.../darwin/prottest/exe/ExternalExecutor.java | 0
.../prottest/exe/ParallelModelEstimator.java | 0
.../prottest/exe/PhyMLv3AminoAcidRunEstimator.java | 108 +++-
.../darwin/prottest/exe/PhymlStreamGobbler.java | 0
.../prottest/exe/RaxMLAminoAcidRunEstimator.java | 16 +-
.../darwin/prottest/exe/RaxMLStreamGobbler.java | 0
.../es/uvigo/darwin/prottest/exe/RunEstimator.java | 0
.../darwin/prottest/exe/RunEstimatorImpl.java | 0
.../uvigo/darwin/prottest/exe/StreamGobbler.java | 0
.../java/es/uvigo/darwin/prottest/exe/package.html | 0
.../prottest/exe/util/TemporaryFileManager.java | 0
.../es/uvigo/darwin/prottest/exe/util/package.html | 0
.../darwin/prottest/facade/ProtTestFacade.java | 0
.../darwin/prottest/facade/ProtTestFacadeImpl.java | 0
.../darwin/prottest/facade/ProtTestFacadeMPJ.java | 0
.../prottest/facade/ProtTestFacadeSequential.java | 0
.../prottest/facade/ProtTestFacadeThread.java | 0
.../uvigo/darwin/prottest/facade/TreeFacade.java | 0
.../darwin/prottest/facade/TreeFacadeImpl.java | 0
.../es/uvigo/darwin/prottest/facade/package.html | 0
.../facade/strategy/DistributionStrategy.java | 0
.../prottest/facade/strategy/Distributor.java | 0
.../strategy/DynamicDistributionStrategy.java | 0
.../strategy/HybridDistributionStrategy.java | 0
.../ImprovedDynamicDistributionStrategy.java | 0
.../facade/strategy/MultipleDistributor.java | 0
.../strategy/StaticDistributionStrategy.java | 0
.../darwin/prottest/facade/strategy/package.html | 0
.../facade/thread/ThreadPoolSynchronizer.java | 0
.../darwin/prottest/facade/thread/package.html | 0
.../prottest/facade/util/ProtTestParameterVO.java | 0
.../prottest/facade/util/SelectionChunk.java | 0
.../uvigo/darwin/prottest/facade/util/package.html | 0
.../global/AminoAcidApplicationGlobals.java | 0
.../darwin/prottest/global/ApplicationGlobals.java | 0
.../prottest/global/ProtTestConsoleParameters.java | 2 +
.../darwin/prottest/global/ProtTestConstants.java | 0
.../global/RaxmlAminoAcidApplicationGlobals.java | 0
.../global/options/ApplicationOptions.java | 39 +-
.../options/SerializableApplicationOptions.java | 0
.../darwin/prottest/global/options/package.html | 0
.../es/uvigo/darwin/prottest/global/package.html | 0
.../darwin/prottest/model/AminoAcidModel.java | 0
.../java/es/uvigo/darwin/prottest/model/Model.java | 0
.../es/uvigo/darwin/prottest/model/package.html | 0
.../prottest/model/state/ModelEmptyLkState.java | 0
.../prottest/model/state/ModelFilledLkState.java | 0
.../darwin/prottest/model/state/ModelLkState.java | 0
.../uvigo/darwin/prottest/model/state/package.html | 0
.../prottest/observer/ModelUpdaterObserver.java | 0
.../prottest/observer/ObservableModelUpdater.java | 0
.../es/uvigo/darwin/prottest/observer/package.html | 0
.../java/es/uvigo/darwin/prottest/package.html | 0
.../es/uvigo/darwin/prottest/selection/AIC.java | 0
.../es/uvigo/darwin/prottest/selection/AICc.java | 0
.../es/uvigo/darwin/prottest/selection/BIC.java | 0
.../es/uvigo/darwin/prottest/selection/DT.java | 0
.../prottest/selection/InformationCriterion.java | 0
.../es/uvigo/darwin/prottest/selection/LNL.java | 0
.../selection/model/AICSelectionModel.java | 0
.../selection/model/AICcSelectionModel.java | 0
.../selection/model/BICSelectionModel.java | 0
.../prottest/selection/model/DTSelectionModel.java | 0
.../selection/model/LNLSelectionModel.java | 0
.../prottest/selection/model/SelectionModel.java | 0
.../darwin/prottest/selection/model/package.html | 0
.../uvigo/darwin/prottest/selection/package.html | 0
.../selection/printer/AminoAcidPrintFramework.java | 0
.../prottest/selection/printer/PrintFramework.java | 0
.../darwin/prottest/selection/printer/package.html | 0
.../java/es/uvigo/darwin/prottest/taxa/Taxon.java | 0
.../uvigo/darwin/prottest/taxa/TaxonomicLevel.java | 0
.../es/uvigo/darwin/prottest/taxa/package.html | 0
.../darwin/prottest/tree/TreeDistancesCache.java | 0
.../prottest/tree/TreeEuclideanDistancesCache.java | 0
.../es/uvigo/darwin/prottest/tree/TreeUtils.java | 0
.../uvigo/darwin/prottest/tree/WeightedTree.java | 0
.../es/uvigo/darwin/prottest/tree/package.html | 0
.../es/uvigo/darwin/prottest/util/FixedBitSet.java | 0
.../darwin/prottest/util/ProtTestAlignment.java | 0
.../uvigo/darwin/prottest/util/StatFramework.java | 0
.../es/uvigo/darwin/prottest/util/Utilities.java | 0
.../argumentparser/AminoAcidArgumentParser.java | 0
.../argumentparser/ProtTestArgumentParser.java | 18 +-
.../prottest/util/argumentparser/package.html | 0
.../prottest/util/attributable/Attributable.java | 0
.../util/attributable/AttributableHelper.java | 0
.../darwin/prottest/util/attributable/package.html | 0
.../util/checkpoint/CheckPointManager.java | 0
.../darwin/prottest/util/checkpoint/package.html | 0
.../util/checkpoint/status/ApplicationStatus.java | 0
.../util/checkpoint/status/ProtTestStatus.java | 0
.../prottest/util/checkpoint/status/package.html | 0
.../prottest/util/collection/ModelCollection.java | 0
.../util/collection/ParallelModelCollection.java | 0
.../util/collection/ParallelModelQueue.java | 0
.../util/collection/SingleModelCollection.java | 0
.../darwin/prottest/util/collection/package.html | 0
.../AminoAcidModelNaturalComparator.java | 0
.../prottest/util/comparator/LKComparator.java | 0
.../comparator/ModelDistributionHeuristic.java | 0
.../util/comparator/ModelWeightComparator.java | 0
.../darwin/prottest/util/comparator/package.html | 0
.../util/exception/AlignmentParseException.java | 0
.../prottest/util/exception/ImportException.java | 0
.../util/exception/ModelOptimizationException.java | 0
.../util/exception/ProtTestCheckedException.java | 0
.../util/exception/ProtTestInternalException.java | 0
.../util/exception/TreeFormatException.java | 0
.../prottest/util/factory/ProtTestFactory.java | 0
.../darwin/prottest/util/factory/package.html | 0
.../prottest/util/fileio/AlignmentReader.java | 2 +-
.../darwin/prottest/util/fileio/ImportHelper.java | 0
.../darwin/prottest/util/fileio/NexusExporter.java | 0
.../darwin/prottest/util/fileio/NexusImporter.java | 0
.../prottest/util/fileio/NexusTreeReader.java | 0
.../util/fileio/SimpleNewickTreeReader.java | 0
.../darwin/prottest/util/fileio/TreeReader.java | 0
.../util/logging/ProtTestLogFormatter.java | 0
.../prottest/util/logging/ProtTestLogger.java | 0
.../es/uvigo/darwin/prottest/util/package.html | 0
.../util/printer/ProtTestFormattedOutput.java | 0
.../prottest/util/printer/ProtTestPrinter.java | 35 +-
.../java/es/uvigo/darwin/xprottest/CreditsBox.java | 0
.../es/uvigo/darwin/xprottest/PreferencesView.java | 0
.../uvigo/darwin/xprottest/XProtTestAboutBox.java | 0
.../es/uvigo/darwin/xprottest/XProtTestApp.java | 0
.../es/uvigo/darwin/xprottest/XProtTestView.java | 77 ++-
.../darwin/xprottest/analysis/FrequenciesView.java | 0
.../uvigo/darwin/xprottest/analysis/TreeView.java | 0
.../darwin/xprottest/analysis/TreeWrapper.java | 0
.../xprottest/analysis/consensus/Consensus.java | 0
.../consensus/resources/Consensus.properties | 0
.../analysis/resources/FrequenciesView.properties | 0
.../analysis/resources/TreeView.properties | 0
.../darwin/xprottest/compute/OptionsView.java | 0
.../darwin/xprottest/compute/RunningFrame.java | 0
.../compute/resources/OptionsView.properties | 0
.../compute/resources/RunningFrame.properties | 0
.../xprottest/resources/CreditsBox.properties | 0
.../xprottest/resources/PreferencesView.properties | 0
.../resources/XProtTestAboutBox.properties | 0
.../xprottest/resources/XProtTestApp.properties | 4 +-
.../xprottest/resources/XProtTestView.properties | 0
.../es/uvigo/darwin/xprottest/resources/about.png | Bin 8187 -> 32741 bytes
.../xprottest/resources/busyicons/busy-icon0.png | Bin
.../xprottest/resources/busyicons/busy-icon1.png | Bin
.../xprottest/resources/busyicons/busy-icon10.png | Bin
.../xprottest/resources/busyicons/busy-icon11.png | Bin
.../xprottest/resources/busyicons/busy-icon12.png | Bin
.../xprottest/resources/busyicons/busy-icon13.png | Bin
.../xprottest/resources/busyicons/busy-icon14.png | Bin
.../xprottest/resources/busyicons/busy-icon2.png | Bin
.../xprottest/resources/busyicons/busy-icon3.png | Bin
.../xprottest/resources/busyicons/busy-icon4.png | Bin
.../xprottest/resources/busyicons/busy-icon5.png | Bin
.../xprottest/resources/busyicons/busy-icon6.png | Bin
.../xprottest/resources/busyicons/busy-icon7.png | Bin
.../xprottest/resources/busyicons/busy-icon8.png | Bin
.../xprottest/resources/busyicons/busy-icon9.png | Bin
.../xprottest/resources/busyicons/idle-icon.png | Bin
.../darwin/xprottest/resources/prottestlogo.gif | Bin 11850 -> 29447 bytes
.../es/uvigo/darwin/xprottest/resources/splash.png | Bin 21747 -> 0 bytes
.../darwin/xprottest/results/Bundle.properties | 0
.../darwin/xprottest/results/ErrorLogView.java | 0
.../darwin/xprottest/results/ResultsView.java | 0
.../results/resources/ErrorLogView.properties | 0
.../results/resources/ResultsView.properties | 0
.../darwin/xprottest/util/BrowserLauncher.java | 583 -----------------
.../util/OptimizationStrategyWrapper.java | 0
.../darwin/xprottest/util/TextAreaAppender.java | 0
.../darwin/xprottest/util/TextAreaWriter.java | 0
src/main/resources/CHANGELOG | 11 +-
src/main/resources/COPYING | 0
src/main/resources/README | 35 +-
src/main/resources/THIRDPARTYLICENSES | 0
src/main/resources/bin/README | 10 +
src/main/resources/examples/COX2_PF0016/alignment | 0
src/main/resources/examples/COX2_PF0016/tree | 0
src/main/resources/examples/HIV1.2008.pol.nex | 0
.../examples/Ribosomal_L5_PF00673/alignment | 0
.../resources/examples/Ribosomal_L5_PF00673/tree | 0
src/main/resources/filecluster8.conf.template | 0
src/main/resources/icon.png | Bin 0 -> 44845 bytes
src/main/resources/machines | 0
src/main/resources/models/FLU | 0
src/main/resources/prottest.properties | 0
src/main/resources/prottest3 | 9 +
src/main/resources/runProtTestHPC.sh | 3 +-
src/main/resources/runXProtTestHPC.bat | 2 +-
src/main/resources/runXProtTestHPC.sh | 3 +-
204 files changed, 405 insertions(+), 1500 deletions(-)
diff --git a/COPYING b/COPYING
old mode 100755
new mode 100644
diff --git a/INSTALL b/INSTALL
old mode 100755
new mode 100644
diff --git a/README.md b/README.md
index 399ffcc..98cad56 100644
--- a/README.md
+++ b/README.md
@@ -14,9 +14,11 @@ In addition, given that ProtTest uses Phyml intensively, we encourage users to c
Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704. Phyml
+--------
Discussion group
+--------
-For technical doubts, bug reports or comments, please use the ProtTest forum.
+For technical doubts, bug reports or comments, please use the ProtTest forum: http://groups.google.com/group/prottest
--------
Download
@@ -29,6 +31,12 @@ https://drive.google.com/folderview?id=0ByrkKOPtF_n_dVBBbDVBOEM5b1U
News!
--------
+08/05/2016 - ProtTest 3.4.2 is out. It includes the following updates:
+
+ Removed dependency on Netbeans libraries
+ Check for global binaries on PATH env variable
+ Added prottest3 script for running both GUI and console interfaces
+
25/10/2015 - ProtTest 3.4.1 is out. It includes the following updates:
Fixed bug with number of categories which might induce an error with certain PhyML versions.
diff --git a/build.xml b/build.xml
index 3c418a9..2e6be2a 100755
--- a/build.xml
+++ b/build.xml
@@ -1,36 +1,77 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!-- You may freely edit this file. See commented blocks below for -->
-<!-- some examples of how to customize the build. -->
-<!-- (If you delete it and reopen the project it will be recreated.) -->
-<project name="ProtTest" default="default" basedir=".">
- <description>Builds, tests, and runs the project ProtTest.</description>
- <import file="buildconf/build-impl.xml"/>
-
- <property name="src.resources.dir" value="src/main/resources"/>
- <property name="prottest.lib" value="lib"/>
-
- <target name="-post-jar">
- <mkdir dir="${dist.dir}/bin"/>
- <copy todir="${dist.dir}/bin">
- <fileset dir="${dist.dir}/bin">
- <include name="**/*"/>
- </fileset>
- </copy>
- <copy todir="${dist.dir}">
- <fileset dir="${src.resources.dir}">
- <include name="**/*"/>
- </fileset>
- </copy>
- <mkdir dir="${dist.dir}/lib"/>
- <copy todir="${dist.dir}/lib">
- <fileset dir="${prottest.lib}">
- <include name="**/*"/>
- </fileset>
- </copy>
- <chmod perm="755" dir="${dist.dir}/bin" includes="*"/>
- <chmod perm="755" dir="${dist.dir}" includes="runProtTestHPC.sh"/>
- <chmod perm="755" dir="${dist.dir}" includes="runXProtTestHPC.sh"/>
-
- <delete file="${dist.dir}/README.TXT"/>
- </target>
+<project name="prottest-3.4.2" default="jar" basedir=".">
+
+ <property name="src.dir" location="src/main/java" />
+ <property name="build.base.dir" location="build" />
+ <property name="build.dir" location="${build.base.dir}/classes" />
+ <property name="lib.dir" location="lib" />
+ <property name="dist.dir" location="dist" />
+ <property name="exe.dir" location="${dist.dir}/bin" />
+ <property name="log.dir" location="${dist.dir}/log" />
+ <property name="src.resources.dir" location="src/main/resources" />
+ <property name="html.template.dir" location="${src.resources.dir}/resources" />
+
+ <property name="jarfile" location="${dist.dir}/${ant.project.name}.jar" />
+ <property name="compile.debug" value="false" />
+
+ <fileset id="lib.jars" dir="${lib.dir}">
+ <include name="**/*.jar" />
+ </fileset>
+
+ <path id="lib.path">
+ <fileset refid="lib.jars" />
+ </path>
+
+ <!-- Stub install target. Install should depend on the 'jar' target,
+ and copy the built objects to the 'dist' directory. -->
+ <target name="install" description="Install jar" depends="jar">
+ </target>
+
+ <target name="compile" description="Compile code">
+ <mkdir dir="${build.dir}" />
+ <mkdir dir="${lib.dir}" />
+ <property environment="env" />
+ <property name="java6.boot.classpath" value="${env.JAVA6_BOOTCLASSES}" />
+ <javac srcdir="${src.dir}" destdir="${build.dir}" includeAntRuntime="no"
+ target="1.6" source="1.6" bootclasspath="${java5.boot.classpath}"
+ classpathref="lib.path" debug="${compile.debug}">
+ </javac>
+ </target>
+
+ <target name="jar" depends="compile" description="Build jar">
+ <mkdir dir="${dist.dir}" />
+ <jar jarfile="${jarfile}" basedir="${build.dir}" manifest="manifest.mf">
+ <fileset id="jar.additional" dir="${src.dir}">
+ <include name="**/*.properties" />
+ <include name="**/*.png" />
+ <include name="**/*.gif" />
+ <include name="**/*.html" />
+ </fileset>
+ <!-- Merge library jars into final jar file-->
+ <!--<zipgroupfileset refid="lib.jars"/>-->
+ </jar>
+ <mkdir dir="${dist.dir}/lib" />
+ <copy todir="${dist.dir}/lib">
+ <fileset id="lib.jars" dir="${lib.dir}">
+ <include name="**/*.jar" />
+ </fileset>
+ </copy>
+ <copy todir="${dist.dir}">
+ <fileset dir="${src.resources.dir}">
+ <include name="**/*" />
+ </fileset>
+ </copy>
+ <mkdir dir="${log.dir}" />
+ <chmod perm="755" dir="${dist.dir}" includes="*.sh *.bat prottest3" />
+ <chmod perm="644" dir="${exe.dir}" includes="*" />
+ </target>
+
+ <target name="run" depends="jar" description="Run jar file">
+ <java jar="${jarfile}" fork="yes" failonerror="true" />
+ </target>
+
+ <target name="clean" description="Remove build and dist directories">
+ <delete dir="${build.base.dir}" />
+ <delete dir="${dist.dir}" />
+ </target>
</project>
diff --git a/buildconf/build-impl.xml b/buildconf/build-impl.xml
deleted file mode 100755
index 87cdf6d..0000000
--- a/buildconf/build-impl.xml
+++ /dev/null
@@ -1,707 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-*** GENERATED FROM project.xml - DO NOT EDIT ***
-*** EDIT ../build.xml INSTEAD ***
-
-For the purpose of easier reading the script
-is divided into following sections:
-
- - initialization
- - compilation
- - jar
- - execution
- - debugging
- - javadoc
- - junit compilation
- - junit execution
- - junit debugging
- - applet
- - cleanup
-
- -->
-<project xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3" xmlns:jaxrpc="http://www.netbeans.org/ns/j2se-project/jax-rpc" basedir=".." default="default" name="ProtTest-HPC-impl">
- <fail message="Please build using Ant 1.7.1 or higher.">
- <condition>
- <not>
- <antversion atleast="1.7.1"/>
- </not>
- </condition>
- </fail>
- <target depends="jar,javadoc" description="Build and test whole project." name="default"/>
- <!--
- ======================
- INITIALIZATION SECTION
- ======================
- -->
- <target name="-pre-init">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="-pre-init" name="-init-user">
- <property file="${user.properties.file}"/>
- <!-- The two properties below are usually overridden -->
- <!-- by the active platform. Just a fallback. -->
- <property name="default.javac.source" value="1.4"/>
- <property name="default.javac.target" value="1.4"/>
- </target>
- <target depends="-pre-init,-init-user" name="-init-project">
- <property file="buildconf/configs/${config}.properties"/>
- <property file="buildconf/project.properties"/>
- </target>
- <target depends="-pre-init,-init-user,-init-project,-init-macrodef-property" name="-do-init">
- <available file="${manifest.file}" property="manifest.available"/>
- <available file="${application.splash}" property="splashscreen.available"/>
- <condition property="main.class.available">
- <and>
- <isset property="main.class"/>
- <not>
- <equals arg1="${main.class}" arg2="" trim="true"/>
- </not>
- </and>
- </condition>
- <condition property="manifest.available+main.class">
- <and>
- <isset property="manifest.available"/>
- <isset property="main.class.available"/>
- </and>
- </condition>
- <condition property="do.mkdist">
- <and>
- <isset property="libs.CopyLibs.classpath"/>
- <not>
- <istrue value="${mkdist.disabled}"/>
- </not>
- </and>
- </condition>
- <condition property="manifest.available+main.class+mkdist.available">
- <and>
- <istrue value="${manifest.available+main.class}"/>
- <isset property="do.mkdist"/>
- </and>
- </condition>
- <condition property="manifest.available+main.class+mkdist.available+splashscreen.available">
- <and>
- <istrue value="${manifest.available+main.class+mkdist.available}"/>
- <istrue value="${splashscreen.available}"/>
- </and>
- </condition>
- <condition property="do.archive">
- <not>
- <istrue value="${jar.archive.disabled}"/>
- </not>
- </condition>
- <condition property="do.archive+manifest.available">
- <and>
- <isset property="manifest.available"/>
- <istrue value="${do.archive}"/>
- </and>
- </condition>
- <condition property="do.archive+manifest.available+main.class">
- <and>
- <istrue value="${manifest.available+main.class}"/>
- <istrue value="${do.archive}"/>
- </and>
- </condition>
- <condition property="do.archive+manifest.available+main.class+mkdist.available">
- <and>
- <istrue value="${manifest.available+main.class+mkdist.available}"/>
- <istrue value="${do.archive}"/>
- </and>
- </condition>
- <condition property="do.archive+manifest.available+main.class+mkdist.available+splashscreen.available">
- <and>
- <istrue value="${manifest.available+main.class+mkdist.available+splashscreen.available}"/>
- <istrue value="${do.archive}"/>
- </and>
- </condition>
- <condition property="have.tests">
- <or/>
- </condition>
- <condition property="have.sources">
- <or>
- <available file="${src.java.dir}"/>
- </or>
- </condition>
- <condition property="netbeans.home+have.tests">
- <and>
- <isset property="netbeans.home"/>
- <isset property="have.tests"/>
- </and>
- </condition>
- <condition property="no.javadoc.preview">
- <and>
- <isset property="javadoc.preview"/>
- <isfalse value="${javadoc.preview}"/>
- </and>
- </condition>
- <property name="run.jvmargs" value=""/>
- <property name="javac.compilerargs" value=""/>
- <property name="work.dir" value="${basedir}"/>
- <condition property="no.deps">
- <and>
- <istrue value="${no.dependencies}"/>
- </and>
- </condition>
- <property name="javac.debug" value="true"/>
- <property name="javadoc.preview" value="true"/>
- <property name="application.args" value=""/>
- <property name="source.encoding" value="${file.encoding}"/>
- <property name="runtime.encoding" value="${source.encoding}"/>
- <condition property="javadoc.encoding.used" value="${javadoc.encoding}">
- <and>
- <isset property="javadoc.encoding"/>
- <not>
- <equals arg1="${javadoc.encoding}" arg2=""/>
- </not>
- </and>
- </condition>
- <property name="javadoc.encoding.used" value="${source.encoding}"/>
- <property name="includes" value="**"/>
- <property name="excludes" value=""/>
- <property name="do.depend" value="false"/>
- <condition property="do.depend.true">
- <istrue value="${do.depend}"/>
- </condition>
- <path id="endorsed.classpath.path" path="${endorsed.classpath}"/>
- <condition else="" property="endorsed.classpath.cmd.line.arg" value="-Xbootclasspath/p:'${toString:endorsed.classpath.path}'">
- <length length="0" string="${endorsed.classpath}" when="greater"/>
- </condition>
- <property name="javac.fork" value="false"/>
- <property name="jar.index" value="false"/>
- <available file="${meta.inf.dir}/persistence.xml" property="has.persistence.xml"/>
- </target>
- <target name="-post-init">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="-pre-init,-init-user,-init-project,-do-init" name="-init-check">
- <fail unless="src.java.dir">Must set src.java.dir</fail>
- <fail unless="build.dir">Must set build.dir</fail>
- <fail unless="dist.dir">Must set dist.dir</fail>
- <fail unless="build.classes.dir">Must set build.classes.dir</fail>
- <fail unless="dist.javadoc.dir">Must set dist.javadoc.dir</fail>
- <fail unless="build.test.classes.dir">Must set build.test.classes.dir</fail>
- <fail unless="build.test.results.dir">Must set build.test.results.dir</fail>
- <fail unless="build.classes.excludes">Must set build.classes.excludes</fail>
- <fail unless="dist.jar">Must set dist.jar</fail>
- </target>
- <target name="-init-macrodef-property">
- <macrodef name="property" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute name="name"/>
- <attribute name="value"/>
- <sequential>
- <property name="@{name}" value="${@{value}}"/>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-ap-cmdline-properties" if="ap.supported.internal" name="-init-macrodef-javac-with-processors">
- <macrodef name="javac" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${src.java.dir}" name="srcdir"/>
- <attribute default="${build.classes.dir}" name="destdir"/>
- <attribute default="${javac.classpath}" name="classpath"/>
- <attribute default="${javac.processorpath}" name="processorpath"/>
- <attribute default="${build.generated.sources.dir}/ap-source-output" name="apgeneratedsrcdir"/>
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="${javac.debug}" name="debug"/>
- <attribute default="${empty.dir}" name="sourcepath"/>
- <attribute default="${empty.dir}" name="gensrcdir"/>
- <element name="customize" optional="true"/>
- <sequential>
- <property location="${build.dir}/empty" name="empty.dir"/>
- <mkdir dir="${empty.dir}"/>
- <mkdir dir="@{apgeneratedsrcdir}"/>
- <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
- <src>
- <dirset dir="@{gensrcdir}" erroronmissingdir="false">
- <include name="*"/>
- </dirset>
- </src>
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <compilerarg line="${endorsed.classpath.cmd.line.arg}"/>
- <compilerarg line="${javac.compilerargs}"/>
- <compilerarg value="-processorpath"/>
- <compilerarg path="@{processorpath}:${empty.dir}"/>
- <compilerarg line="${ap.processors.internal}"/>
- <compilerarg line="${annotation.processing.processor.options}"/>
- <compilerarg value="-s"/>
- <compilerarg path="@{apgeneratedsrcdir}"/>
- <compilerarg line="${ap.proc.none.internal}"/>
- <customize/>
- </javac>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-ap-cmdline-properties" name="-init-macrodef-javac-without-processors" unless="ap.supported.internal">
- <macrodef name="javac" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${src.java.dir}" name="srcdir"/>
- <attribute default="${build.classes.dir}" name="destdir"/>
- <attribute default="${javac.classpath}" name="classpath"/>
- <attribute default="${javac.processorpath}" name="processorpath"/>
- <attribute default="${build.generated.sources.dir}/ap-source-output" name="apgeneratedsrcdir"/>
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="${javac.debug}" name="debug"/>
- <attribute default="${empty.dir}" name="sourcepath"/>
- <attribute default="${empty.dir}" name="gensrcdir"/>
- <element name="customize" optional="true"/>
- <sequential>
- <property location="${build.dir}/empty" name="empty.dir"/>
- <mkdir dir="${empty.dir}"/>
- <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
- <src>
- <dirset dir="@{gensrcdir}" erroronmissingdir="false">
- <include name="*"/>
- </dirset>
- </src>
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <compilerarg line="${endorsed.classpath.cmd.line.arg}"/>
- <compilerarg line="${javac.compilerargs}"/>
- <customize/>
- </javac>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-macrodef-javac-with-processors,-init-macrodef-javac-without-processors" name="-init-macrodef-javac">
- <macrodef name="depend" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${src.java.dir}" name="srcdir"/>
- <attribute default="${build.classes.dir}" name="destdir"/>
- <attribute default="${javac.classpath}" name="classpath"/>
- <sequential>
- <depend cache="${build.dir}/depcache" destdir="@{destdir}" excludes="${excludes}" includes="${includes}" srcdir="@{srcdir}">
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- </depend>
- </sequential>
- </macrodef>
- <macrodef name="force-recompile" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${build.classes.dir}" name="destdir"/>
- <sequential>
- <fail unless="javac.includes">Must set javac.includes</fail>
- <pathconvert pathsep="," property="javac.includes.binary">
- <path>
- <filelist dir="@{destdir}" files="${javac.includes}"/>
- </path>
- <globmapper from="*.java" to="*.class"/>
- </pathconvert>
- <delete>
- <files includes="${javac.includes.binary}"/>
- </delete>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-macrodef-junit">
- <macrodef name="junit" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${includes}" name="includes"/>
- <attribute default="${excludes}" name="excludes"/>
- <attribute default="**" name="testincludes"/>
- <sequential>
- <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" showoutput="true" tempdir="${build.dir}">
- <batchtest todir="${build.test.results.dir}"/>
- <classpath>
- <path path="${run.test.classpath}"/>
- </classpath>
- <syspropertyset>
- <propertyref prefix="test-sys-prop."/>
- <mapper from="test-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <formatter type="brief" usefile="false"/>
- <formatter type="xml"/>
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <jvmarg line="${run.jvmargs}"/>
- </junit>
- </sequential>
- </macrodef>
- </target>
- <target depends="-init-debug-args" name="-init-macrodef-nbjpda">
- <macrodef name="nbjpdastart" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="${main.class}" name="name"/>
- <attribute default="${debug.classpath}" name="classpath"/>
- <attribute default="" name="stopclassname"/>
- <sequential>
- <nbjpdastart addressproperty="jpda.address" name="@{name}" stopclassname="@{stopclassname}" transport="${debug-transport}">
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- </nbjpdastart>
- </sequential>
- </macrodef>
- <macrodef name="nbjpdareload" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="${build.classes.dir}" name="dir"/>
- <sequential>
- <nbjpdareload>
- <fileset dir="@{dir}" includes="${fix.classes}">
- <include name="${fix.includes}*.class"/>
- </fileset>
- </nbjpdareload>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-debug-args">
- <property name="version-output" value="java version "${ant.java.version}"/>
- <condition property="have-jdk-older-than-1.4">
- <or>
- <contains string="${version-output}" substring="java version "1.0"/>
- <contains string="${version-output}" substring="java version "1.1"/>
- <contains string="${version-output}" substring="java version "1.2"/>
- <contains string="${version-output}" substring="java version "1.3"/>
- </or>
- </condition>
- <condition else="-Xdebug" property="debug-args-line" value="-Xdebug -Xnoagent -Djava.compiler=none">
- <istrue value="${have-jdk-older-than-1.4}"/>
- </condition>
- <condition else="dt_socket" property="debug-transport-by-os" value="dt_shmem">
- <os family="windows"/>
- </condition>
- <condition else="${debug-transport-by-os}" property="debug-transport" value="${debug.transport}">
- <isset property="debug.transport"/>
- </condition>
- </target>
- <target depends="-init-debug-args" name="-init-macrodef-debug">
- <macrodef name="debug" uri="http://www.netbeans.org/ns/j2se-project/3">
- <attribute default="${main.class}" name="classname"/>
- <attribute default="${debug.classpath}" name="classpath"/>
- <element name="customize" optional="true"/>
- <sequential>
- <java classname="@{classname}" dir="${work.dir}" fork="true">
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <jvmarg line="${debug-args-line}"/>
- <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
- <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
- <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
- <jvmarg line="${run.jvmargs}"/>
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <syspropertyset>
- <propertyref prefix="run-sys-prop."/>
- <mapper from="run-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <customize/>
- </java>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-macrodef-java">
- <macrodef name="java" uri="http://www.netbeans.org/ns/j2se-project/1">
- <attribute default="${main.class}" name="classname"/>
- <attribute default="${run.classpath}" name="classpath"/>
- <element name="customize" optional="true"/>
- <sequential>
- <java classname="@{classname}" dir="${work.dir}" fork="true">
- <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
- <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
- <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
- <jvmarg line="${run.jvmargs}"/>
- <classpath>
- <path path="@{classpath}"/>
- </classpath>
- <syspropertyset>
- <propertyref prefix="run-sys-prop."/>
- <mapper from="run-sys-prop.*" to="*" type="glob"/>
- </syspropertyset>
- <customize/>
- </java>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-macrodef-copylibs">
- <macrodef name="copylibs" uri="http://www.netbeans.org/ns/j2se-project/3">
- <element name="customize" optional="true"/>
- <sequential>
- <property location="${build.classes.dir}" name="build.classes.dir.resolved"/>
- <pathconvert property="run.classpath.without.build.classes.dir">
- <path path="${run.classpath}"/>
- <map from="${build.classes.dir.resolved}" to=""/>
- </pathconvert>
- <pathconvert pathsep=" " property="jar.classpath">
- <path path="${run.classpath.without.build.classes.dir}"/>
- <chainedmapper>
- <flattenmapper/>
- <globmapper from="*" to="lib/*"/>
- </chainedmapper>
- </pathconvert>
- <taskdef classname="org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs" classpath="${libs.CopyLibs.classpath}" name="copylibs"/>
- <copylibs compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}" manifest="${manifest.file}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
- <fileset dir="${build.classes.dir}"/>
- <manifest>
- <attribute name="Class-Path" value="${jar.classpath}"/>
- <customize/>
- </manifest>
- </copylibs>
- </sequential>
- </macrodef>
- </target>
- <target name="-init-presetdef-jar">
- <presetdef name="jar" uri="http://www.netbeans.org/ns/j2se-project/1">
- <jar compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}">
- <j2seproject1:fileset dir="${build.classes.dir}"/>
- </jar>
- </presetdef>
- </target>
- <target name="-init-ap-cmdline-properties">
- <property name="annotation.processing.enabled" value="true"/>
- <property name="annotation.processing.processors.list" value=""/>
- <property name="annotation.processing.processor.options" value=""/>
- <property name="annotation.processing.run.all.processors" value="true"/>
- <property name="javac.processorpath" value="${javac.classpath}"/>
- <property name="javac.test.processorpath" value="${javac.test.classpath}"/>
- <condition property="ap.supported.internal" value="true">
- <not>
- <matches pattern="1\.[0-5](\..*)?" string="${javac.source}"/>
- </not>
- </condition>
- </target>
- <target depends="-init-ap-cmdline-properties" if="ap.supported.internal" name="-init-ap-cmdline-supported">
- <condition else="" property="ap.processors.internal" value="-processor ${annotation.processing.processors.list}">
- <isfalse value="${annotation.processing.run.all.processors}"/>
- </condition>
- <condition else="" property="ap.proc.none.internal" value="-proc:none">
- <isfalse value="${annotation.processing.enabled}"/>
- </condition>
- </target>
- <target depends="-init-ap-cmdline-properties,-init-ap-cmdline-supported" name="-init-ap-cmdline">
- <property name="ap.cmd.line.internal" value=""/>
- </target>
- <target depends="-pre-init,-init-user,-init-project,-do-init,-post-init,-init-check,-init-macrodef-property,-init-macrodef-javac,-init-macrodef-junit,-init-macrodef-nbjpda,-init-macrodef-debug,-init-macrodef-java,-init-presetdef-jar,-init-ap-cmdline" name="init"/>
- <!--
- ===================
- COMPILATION SECTION
- ===================
- -->
- <target name="-deps-jar-init" unless="built-jar.properties">
- <property location="${build.dir}/built-jar.properties" name="built-jar.properties"/>
- <delete file="${built-jar.properties}" quiet="true"/>
- </target>
- <target if="already.built.jar.${basedir}" name="-warn-already-built-jar">
- <echo level="warn" message="Cycle detected: ProtTest-HPC was already built"/>
- </target>
- <target depends="init,-deps-jar-init" name="deps-jar" unless="no.deps">
- <mkdir dir="${build.dir}"/>
- <touch file="${built-jar.properties}" verbose="false"/>
- <property file="${built-jar.properties}" prefix="already.built.jar."/>
- <antcall target="-warn-already-built-jar"/>
- <propertyfile file="${built-jar.properties}">
- <entry key="${basedir}" value=""/>
- </propertyfile>
- </target>
- <target depends="init,-check-automatic-build,-clean-after-automatic-build" name="-verify-automatic-build"/>
- <target depends="init" name="-check-automatic-build">
- <available file="${build.classes.dir}/.netbeans_automatic_build" property="netbeans.automatic.build"/>
- </target>
- <target depends="init" if="netbeans.automatic.build" name="-clean-after-automatic-build">
- <antcall target="clean"/>
- </target>
- <target depends="init,deps-jar" name="-pre-pre-compile">
- <mkdir dir="${build.classes.dir}"/>
- </target>
- <target name="-pre-compile">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target if="do.depend.true" name="-compile-depend">
- <pathconvert property="build.generated.subdirs">
- <dirset dir="${build.generated.sources.dir}" erroronmissingdir="false">
- <include name="*"/>
- </dirset>
- </pathconvert>
- <j2seproject3:depend srcdir="${src.java.dir}:${build.generated.subdirs}"/>
- </target>
- <target depends="init,deps-jar,-pre-pre-compile,-pre-compile, -copy-persistence-xml,-compile-depend" if="have.sources" name="-do-compile">
- <j2seproject3:javac gensrcdir="${build.generated.sources.dir}"/>
- <copy todir="${build.classes.dir}">
- <fileset dir="${src.java.dir}" excludes="${build.classes.excludes},${excludes}" includes="${includes}"/>
- </copy>
- </target>
- <target if="has.persistence.xml" name="-copy-persistence-xml">
- <mkdir dir="${build.classes.dir}/META-INF"/>
- <copy todir="${build.classes.dir}/META-INF">
- <fileset dir="${meta.inf.dir}" includes="persistence.xml"/>
- </copy>
- </target>
- <target name="-post-compile">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-jar,-verify-automatic-build,-pre-pre-compile,-pre-compile,-do-compile,-post-compile" description="Compile project." name="compile"/>
- <target name="-pre-compile-single">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-jar,-pre-pre-compile" name="-do-compile-single">
- <fail unless="javac.includes">Must select some files in the IDE or set javac.includes</fail>
- <j2seproject3:force-recompile/>
- <j2seproject3:javac excludes="" gensrcdir="${build.generated.sources.dir}" includes="${javac.includes}" sourcepath="${src.java.dir}"/>
- </target>
- <target name="-post-compile-single">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-jar,-verify-automatic-build,-pre-pre-compile,-pre-compile-single,-do-compile-single,-post-compile-single" name="compile-single"/>
- <!--
- ====================
- JAR BUILDING SECTION
- ====================
- -->
- <target depends="init" name="-pre-pre-jar">
- <dirname file="${dist.jar}" property="dist.jar.dir"/>
- <mkdir dir="${dist.jar.dir}"/>
- </target>
- <target name="-pre-jar">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,compile,-pre-pre-jar,-pre-jar" if="do.archive" name="-do-jar-without-manifest" unless="manifest.available">
- <j2seproject1:jar/>
- </target>
- <target depends="init,compile,-pre-pre-jar,-pre-jar" if="do.archive+manifest.available" name="-do-jar-with-manifest" unless="manifest.available+main.class">
- <j2seproject1:jar manifest="${manifest.file}"/>
- </target>
- <target depends="init,compile,-pre-pre-jar,-pre-jar" if="do.archive+manifest.available+main.class" name="-do-jar-with-mainclass" unless="manifest.available+main.class+mkdist.available">
- <j2seproject1:jar manifest="${manifest.file}">
- <j2seproject1:manifest>
- <j2seproject1:attribute name="Main-Class" value="${main.class}"/>
- </j2seproject1:manifest>
- </j2seproject1:jar>
- <echo>To run this application from the command line without Ant, try:</echo>
- <property location="${build.classes.dir}" name="build.classes.dir.resolved"/>
- <property location="${dist.jar}" name="dist.jar.resolved"/>
- <pathconvert property="run.classpath.with.dist.jar">
- <path path="${run.classpath}"/>
- <map from="${build.classes.dir.resolved}" to="${dist.jar.resolved}"/>
- </pathconvert>
- <echo>java -cp "${run.classpath.with.dist.jar}" ${main.class}</echo>
- </target>
- <target depends="init,compile,-pre-pre-jar,-pre-jar,-init-macrodef-copylibs" if="do.archive+manifest.available+main.class+mkdist.available+splashscreen.available" name="-do-jar-with-libraries-and-splashscreen">
- <basename file="${application.splash}" property="splashscreen.basename"/>
- <mkdir dir="${build.classes.dir}/META-INF"/>
- <copy failonerror="false" file="${application.splash}" todir="${build.classes.dir}/META-INF"/>
- <j2seproject3:copylibs>
- <customize>
- <attribute name="Main-Class" value="${main.class}"/>
- <attribute name="SplashScreen-Image" value="META-INF/${splashscreen.basename}"/>
- </customize>
- </j2seproject3:copylibs>
- <echo>To run this application from the command line without Ant, try:</echo>
- <property location="${dist.jar}" name="dist.jar.resolved"/>
- <echo>java -jar "${dist.jar.resolved}"</echo>
- </target>
- <target depends="init,compile,-pre-pre-jar,-pre-jar,-init-macrodef-copylibs" if="do.archive+manifest.available+main.class+mkdist.available" name="-do-jar-with-libraries" unless="splashscreen.available">
- <j2seproject3:copylibs>
- <customize>
- <attribute name="Main-Class" value="${main.class}"/>
- </customize>
- </j2seproject3:copylibs>
- <echo>To run this application from the command line without Ant, try:</echo>
- <property location="${dist.jar}" name="dist.jar.resolved"/>
- <echo>java -jar "${dist.jar.resolved}"</echo>
- </target>
- <target name="-post-jar">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,compile,-pre-jar,-do-jar-with-manifest,-do-jar-without-manifest,-do-jar-with-mainclass,-do-jar-with-libraries-and-splashscreen,-do-jar-with-libraries,-post-jar" description="Build JAR." name="jar"/>
- <!--
- =================
- EXECUTION SECTION
- =================
- -->
- <target depends="init,compile" description="Run a main class." name="run">
- <j2seproject1:java>
- <customize>
- <arg line="${application.args}"/>
- </customize>
- </j2seproject1:java>
- </target>
- <target name="-do-not-recompile">
- <property name="javac.includes.binary" value=""/>
- </target>
- <target depends="init,compile-single" name="run-single">
- <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
- <j2seproject1:java classname="${run.class}"/>
- </target>
-
- <!--
- ===============
- JAVADOC SECTION
- ===============
- -->
- <target depends="init" if="have.sources" name="-javadoc-build">
- <mkdir dir="${dist.javadoc.dir}"/>
- <javadoc additionalparam="${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
- <classpath>
- <path path="${javac.classpath}"/>
- </classpath>
- <fileset dir="${src.java.dir}" excludes="${excludes}" includes="${includes}">
- <filename name="**/*.java"/>
- </fileset>
- <fileset dir="${build.generated.sources.dir}" erroronmissingdir="false">
- <include name="**/*.java"/>
- </fileset>
- </javadoc>
- <copy todir="${dist.javadoc.dir}">
- <fileset dir="${src.java.dir}" excludes="${excludes}" includes="${includes}">
- <filename name="**/doc-files/**"/>
- </fileset>
- <fileset dir="${build.generated.sources.dir}" erroronmissingdir="false">
- <include name="**/doc-files/**"/>
- </fileset>
- </copy>
- </target>
- <target depends="init,-javadoc-build" if="netbeans.home" name="-javadoc-browse" unless="no.javadoc.preview">
- <nbbrowse file="${dist.javadoc.dir}/index.html"/>
- </target>
- <target depends="init,-javadoc-build,-javadoc-browse" description="Build Javadoc." name="javadoc"/>
-
- <!--
- ===============
- CLEANUP SECTION
- ===============
- -->
- <target name="-deps-clean-init" unless="built-clean.properties">
- <property location="${build.dir}/built-clean.properties" name="built-clean.properties"/>
- <delete file="${built-clean.properties}" quiet="true"/>
- </target>
- <target if="already.built.clean.${basedir}" name="-warn-already-built-clean">
- <echo level="warn" message="Cycle detected: ProtTest-HPC was already built"/>
- </target>
- <target depends="init,-deps-clean-init" name="deps-clean" unless="no.deps">
- <mkdir dir="${build.dir}"/>
- <touch file="${built-clean.properties}" verbose="false"/>
- <property file="${built-clean.properties}" prefix="already.built.clean."/>
- <antcall target="-warn-already-built-clean"/>
- <propertyfile file="${built-clean.properties}">
- <entry key="${basedir}" value=""/>
- </propertyfile>
- </target>
- <target depends="init" name="-do-clean">
- <delete dir="${build.dir}"/>
- <delete dir="${dist.dir}" followsymlinks="false" includeemptydirs="true"/>
- </target>
- <target name="-post-clean">
- <!-- Empty placeholder for easier customization. -->
- <!-- You can override this target in the ../build.xml file. -->
- </target>
- <target depends="init,deps-clean,-do-clean,-post-clean" description="Clean build products." name="clean"/>
- <target name="-check-call-dep">
- <property file="${call.built.properties}" prefix="already.built."/>
- <condition property="should.call.dep">
- <not>
- <isset property="already.built.${call.subproject}"/>
- </not>
- </condition>
- </target>
- <target depends="-check-call-dep" if="should.call.dep" name="-maybe-call-dep">
- <ant antfile="${call.script}" inheritall="false" target="${call.target}">
- <propertyset>
- <propertyref prefix="transfer."/>
- <mapper from="transfer.*" to="*" type="glob"/>
- </propertyset>
- </ant>
- </target>
-</project>
diff --git a/buildconf/project.properties b/buildconf/project.properties
deleted file mode 100755
index 1785c89..0000000
--- a/buildconf/project.properties
+++ /dev/null
@@ -1,80 +0,0 @@
-application.version=3.4.1
-application.homepage=http://darwin.uvigo.es
-application.title=ProtTest
-application.vendor=Diego Darriba
-build.classes.dir=${build.dir}/classes
-build.classes.excludes=**/*.java,**/*.form
-# This directory is removed when the project is cleaned:
-build.dir=build
-build.generated.dir=${build.dir}/generated
-# Only compile against the classpath explicitly listed here:
-build.sysclasspath=ignore
-build.test.classes.dir=${build.dir}/test/classes
-build.test.results.dir=${build.dir}/test/results
-debug.classpath=\
- ${run.classpath}
-debug.test.classpath=\
- ${run.test.classpath}
-# This directory is removed when the project is cleaned:
-dist.dir=dist
-dist.jar=${dist.dir}/prottest-${application.version}.jar
-dist.javadoc.dir=${dist.dir}/javadoc
-excludes=
-file.reference.AbsoluteLayout.jar=lib/AbsoluteLayout.jar
-file.reference.appframework-1.0.3.jar=lib/appframework-1.0.3.jar
-file.reference.alter.jar=lib/alter.jar
-file.reference.mpj.jar=lib/mpj.jar
-file.reference.pal.jar=lib/pal.jar
-file.reference.ProtTest-HPC-src=src
-file.reference.swing-worker-1.1.jar=lib/swing-worker-1.1.jar
-includes=**
-jar.compress=false
-javac.classpath=\
- ${file.reference.AbsoluteLayout.jar}:\
- ${file.reference.appframework-1.0.3.jar}:\
- ${file.reference.mpj.jar}:\
- ${file.reference.pal.jar}:\
- ${file.reference.alter.jar}:\
- ${file.reference.swing-worker-1.1.jar}
-# Space-separated list of extra javac options
-javac.compilerargs=
-javac.deprecation=true
-javac.source=1.5
-javac.target=1.6
-javac.test.classpath=\
- ${javac.classpath}:\
- ${build.classes.dir}:\
- ${libs.junit_4.classpath}
-javadoc.additionalparam=
-javadoc.author=false
-javadoc.encoding=${source.encoding}
-javadoc.noindex=false
-javadoc.nonavbar=false
-javadoc.notree=false
-javadoc.private=false
-javadoc.splitindex=true
-javadoc.use=true
-javadoc.version=false
-javadoc.windowtitle=
-# Property libs.absolutelayout.classpath is set here just to make sharing of project simpler.
-# The library definition has always preference over this property.
-libs.absolutelayout.classpath=lib/AbsoluteLayout.jar
-#libs.CopyLibs.classpath=lib/org-netbeans-modules-java-j2seproject-copylibstask.jar
-libs.CopyLibs.classpath=lib/copylibs.jar
-main.class=es.uvigo.darwin.prottest.ProtTest
-manifest.file=manifest.mf
-meta.inf.dir=${src.dir}/META-INF
-platform.active=default_platform
-run.classpath=\
- ${javac.classpath}:\
- ${build.classes.dir}
-# Space-separated list of JVM arguments used when running the project
-# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
-# or test-sys-prop.name=value to set system properties for unit tests):
-run.jvmargs=
-run.test.classpath=\
- ${javac.test.classpath}:\
- ${build.test.classes.dir}
-source.encoding=UTF-8
-src.java.dir=src/main/java
-test.java.dir=src/test/java
diff --git a/manifest.mf b/manifest.mf
index cd51d93..be3ae49 100755
--- a/manifest.mf
+++ b/manifest.mf
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
Ant-Version: Apache Ant 1.7.1
Created-By: 19.0-b09 (Sun Microsystems Inc.)
Main-Class: es.uvigo.darwin.prottest.ProtTest
-Class-Path: lib/AbsoluteLayout.jar lib/appframework-1.0.3.jar lib/mpj.
+Class-Path: lib/appframework-1.0.3.jar lib/mpj.
jar lib/pal.jar lib/alter.jar lib/swing-worker-1.1.jar
X-COMMENT: Main-Class will be added automatically by build
diff --git a/src/main/java/META-INF/services/org.jdesktop.application.Application b/src/main/java/META-INF/services/org.jdesktop.application.Application
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/ProtTest.java b/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
old mode 100755
new mode 100644
index 52a3d72..a3b42d7
--- a/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
+++ b/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
@@ -17,10 +17,18 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package es.uvigo.darwin.prottest;
-import static es.uvigo.darwin.prottest.global.ApplicationGlobals.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.logging.Handler;
+import java.util.logging.Level;
-import es.uvigo.darwin.prottest.consensus.Consensus;
import mpi.MPI;
+import pal.misc.Identifier;
+import pal.tree.Tree;
+import es.uvigo.darwin.prottest.consensus.Consensus;
+import es.uvigo.darwin.prottest.exe.PhyMLv3AminoAcidRunEstimator;
import es.uvigo.darwin.prottest.facade.ProtTestFacade;
import es.uvigo.darwin.prottest.facade.ProtTestFacadeMPJ;
import es.uvigo.darwin.prottest.facade.ProtTestFacadeSequential;
@@ -46,14 +54,6 @@ import es.uvigo.darwin.prottest.util.exception.ProtTestInternalException;
import es.uvigo.darwin.prottest.util.factory.ProtTestFactory;
import es.uvigo.darwin.prottest.util.logging.ProtTestLogger;
import es.uvigo.darwin.prottest.util.printer.ProtTestPrinter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-import java.util.logging.Handler;
-import java.util.logging.Level;
-import pal.misc.Identifier;
-import pal.tree.Tree;
/**
* This is the main class of ProtTest. It calls the methods in the
@@ -64,9 +64,9 @@ import pal.tree.Tree;
public class ProtTest {
/** The Constant versionNumber. */
- public static final String versionNumber = "3.4.1";
+ public static final String versionNumber = "3.4.2";
/** The Constant versionDate. */
- public static final String versionDate = "23th January 2014";
+ public static final String versionDate = "8th May 2016";
/** The MPJ rank of the process. It is only useful if MPJ is running.*/
public static int MPJ_ME;
/** The MPJ size of the communicator. It is only useful if MPJ is running.*/
@@ -75,6 +75,10 @@ public class ProtTest {
public static boolean MPJ_RUN;
/** The ProtTest factory. */
private static ProtTestFactory factory;
+
+ public static final String URL_MANUAL = "http://darwin.uvigo.es/download/prottest_manual.pdf";
+ public static final String URL_HOMEPAGE = "http://github.com/ddarriba/prottest3";
+ public static final String URL_DISCUSSION_GROUP = "https://groups.google.com/group/prottest";
/**
* The main method. It initializes the MPJ runtime environment, parses
@@ -85,7 +89,7 @@ public class ProtTest {
*/
public static void main(String[] args) {
- try {
+ try {
args = ProtTestFactory.initialize(args);
} catch (IllegalArgumentException e) {
System.out.println("Illegal argument: " + e.getMessage());
@@ -93,6 +97,12 @@ public class ProtTest {
}
factory = ProtTestFactory.getInstance();
+ // Checking PhyML binary
+ if (!PhyMLv3AminoAcidRunEstimator.checkBinary())
+ {
+ finalize(1);
+ }
+
// initializing MPJ environment (if available)
try {
String[] argsApp = MPI.Init(args);
@@ -120,8 +130,8 @@ public class ProtTest {
getValue(ProtTestArgumentParser.PARAM_NUM_THREADS));
} catch (IllegalArgumentException e) {
if (MPJ_ME == 0) {
- System.err.println("\n" + e.getMessage() + "\n");
- ApplicationOptions.usage();
+ System.err.println("\n" + e.getMessage());
+ System.err.println("Run with -h for help.\n");
}
finalize(1);
} catch (ProtTestInternalException e) {
diff --git a/src/main/java/es/uvigo/darwin/prottest/consensus/Consensus.java b/src/main/java/es/uvigo/darwin/prottest/consensus/Consensus.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/consensus/package.html b/src/main/java/es/uvigo/darwin/prottest/consensus/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/AminoAcidRunEstimator.java b/src/main/java/es/uvigo/darwin/prottest/exe/AminoAcidRunEstimator.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutionManager.java b/src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutionManager.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutor.java b/src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutor.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/ParallelModelEstimator.java b/src/main/java/es/uvigo/darwin/prottest/exe/ParallelModelEstimator.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
old mode 100755
new mode 100644
index 7967ace..870e99e
--- a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
+++ b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
@@ -55,7 +55,7 @@ import es.uvigo.darwin.prottest.util.exception.TreeFormatException;
* @since 3.0
*/
public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
-
+
/** The PhyML implemented matrices. */
public static String[] IMPLEMENTED_MATRICES = {
"JTT",
@@ -74,14 +74,65 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
"HIVw"
};
/** Suffix for temporary statistic files. */
- private static final String STATS_FILE_SUFFIX = "_phyml_stats.txt";
+ private static final String STATS_FILE_SUFFIX = "_phyml_stats";
/** Suffix for temporary tree files. */
- private static final String TREE_FILE_SUFFIX = "_phyml_tree.txt";
+ private static final String TREE_FILE_SUFFIX = "_phyml_tree";
/** Alignment filename. */
private String workAlignment;
/** Custom model substitution matrix file**/
private File modelFile;
+ public static File phymlBinary;
+ public static String phymlBinaryStr;
+
+ private File statsFile;
+ private File treeFile;
+
+ public static boolean checkBinary() {
+ boolean canExecute = false;
+ if (!PhyMLv3AminoAcidRunEstimator.phymlBinary.exists()) {
+ System.err.println("ERROR: PhyML binary not found: " +
+ PhyMLv3AminoAcidRunEstimator.phymlBinary.getAbsolutePath() + "\n");
+ } else if (!PhyMLv3AminoAcidRunEstimator.phymlBinary.canExecute()) {
+ System.err.println("ERROR: PhyML binary exists, but it cannot be executed: " +
+ PhyMLv3AminoAcidRunEstimator.phymlBinary.getAbsolutePath() + "\n");
+ } else {
+ canExecute = true;
+ }
+
+ return canExecute;
+ }
+
+ static {
+ boolean phymlGlobal = APPLICATION_PROPERTIES.getProperty("global-phyml-exe", "false").equalsIgnoreCase("true");
+
+ File exeFilesDir = new File(APPLICATION_PROPERTIES.getProperty("exe-dir", ApplicationGlobals.PATH));
+ if (!exeFilesDir.isAbsolute()) {
+ exeFilesDir = new File(ApplicationGlobals.PATH + File.separator + APPLICATION_PROPERTIES.getProperty("exe-dir", "bin"));
+ }
+
+ phymlBinary = new File(exeFilesDir.getAbsolutePath() + File.separator + "phyml");
+
+ if (phymlGlobal) {
+ String[] pathList = System.getenv("PATH").split(":");
+ for (String path : pathList)
+ {
+ phymlBinary = new File(path + "/phyml");
+ if (phymlBinary.exists() && phymlBinary.canExecute()) {
+ phymlBinaryStr = phymlBinary.getAbsolutePath();
+ break;
+ }
+ }
+ } else {
+ if (phymlBinary.exists() && phymlBinary.canExecute()) {
+ phymlBinaryStr = phymlBinary.getAbsolutePath();
+ } else {
+ phymlBinaryStr = exeFilesDir.getAbsolutePath() + File.separator + getPhymlVersion();
+ }
+ phymlBinary = new File(phymlBinaryStr);
+ }
+ }
+
/**
* Instantiates a new optimizer for amino-acid models
* using PhyML.
@@ -164,6 +215,7 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
tr = TemporaryFileManager.getInstance().getTreeFilename(Thread.currentThread());
topo = "lr";
}
+
try {
Runtime runtime = Runtime.getRuntime();
@@ -322,6 +374,27 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
throw new PhyMLExecutionException("I/O error: " + e.getMessage());
}
+ statsFile = new File(workAlignment + STATS_FILE_SUFFIX);
+ if (!(statsFile.exists() && statsFile.canRead()))
+ {
+ /* try with txt suffix */
+ statsFile = new File(workAlignment + STATS_FILE_SUFFIX + "txt");
+ if (!(statsFile.exists() && statsFile.canRead()))
+ throw new StatsFileFormatException("PhyML",
+ "Stats file does not exist. Please check if PhyML is working.");
+ }
+ statsFile.deleteOnExit();
+
+ treeFile = new File(workAlignment + TREE_FILE_SUFFIX);
+ if (!(treeFile.exists() && treeFile.canRead()))
+ {
+ /* try with txt suffix */
+ treeFile = new File(workAlignment + TREE_FILE_SUFFIX + "txt");
+ if (!(treeFile.exists() && treeFile.canRead()))
+ throw new TreeFormatException(
+ "Tree file does not exist. Please check if PhyML is working correctly.");
+ }
+ treeFile.deleteOnExit();
if (!(readStatsFile() && readTreeFile())) {
return false;
@@ -341,7 +414,7 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
String line;
try {
- FileReader input = new FileReader(workAlignment + STATS_FILE_SUFFIX);
+ FileReader input = new FileReader(statsFile.getAbsolutePath());
BufferedReader br = new BufferedReader(input);
while ((line = br.readLine()) != null) {
pfinerln("[DEBUG] PHYML: " + line);
@@ -405,9 +478,9 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
*/
private boolean readTreeFile()
throws TreeFormatException {
-
+
try {
- model.setTree(new ReadTree(workAlignment + TREE_FILE_SUFFIX));
+ model.setTree(new ReadTree(treeFile.getAbsolutePath()));
} catch (TreeParseException e) {
String errorMsg = "ProtTest: wrong tree format, exiting...";
throw new TreeFormatException(errorMsg);
@@ -415,6 +488,7 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
String errorMsg = "Error: File not found (IO error), exiting...";
throw new TreeFormatException(errorMsg);
}
+
return true;
}
@@ -425,14 +499,8 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
*/
@Override
protected boolean deleteTemporaryFiles() {
- File f;
- f = new File(workAlignment + STATS_FILE_SUFFIX);
- f.delete();
- f = new File(workAlignment + TREE_FILE_SUFFIX);
- f.delete();
- f = new File(TemporaryFileManager.getInstance().getLogFilename(Thread.currentThread()));
- f.delete();
- return true;
+ File f = new File(TemporaryFileManager.getInstance().getLogFilename(Thread.currentThread()));
+ return f.delete();
}
/**
@@ -440,23 +508,23 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
*
* @return the PhyML executable name
*/
- private String getPhymlVersion() {
+ private static String getPhymlVersion() {
String os = System.getProperty("os.name");
String oa = System.getProperty("os.arch");
if (os.startsWith("Mac")) {
if (oa.startsWith("ppc")) {
- return "phyml-prottest-macppc";
+ return null;
} else {
- return "phyml-prottest-macintel";
+ return "PhyML_3.0_macOS_i386";
}
} else if (os.startsWith("Linux")) {
if (oa.contains("md64")) {
- return "phyml-prottest-linux64";
+ return "PhyML_3.0_linux64";
} else {
- return "phyml-prottest-linux";
+ return "PhyML_3.0_linux32";
}
} else if (os.startsWith("Window")) {
- return "phyml-prottest-windows.exe";
+ return "PhyML_3.0_win32.exe";
} else {
return null;
}
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/PhymlStreamGobbler.java b/src/main/java/es/uvigo/darwin/prottest/exe/PhymlStreamGobbler.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/RaxMLAminoAcidRunEstimator.java b/src/main/java/es/uvigo/darwin/prottest/exe/RaxMLAminoAcidRunEstimator.java
old mode 100755
new mode 100644
index bc6f6cb..580501d
--- a/src/main/java/es/uvigo/darwin/prottest/exe/RaxMLAminoAcidRunEstimator.java
+++ b/src/main/java/es/uvigo/darwin/prottest/exe/RaxMLAminoAcidRunEstimator.java
@@ -30,11 +30,13 @@ import es.uvigo.darwin.prottest.util.exception.ModelOptimizationException.PhyMLE
import es.uvigo.darwin.prottest.util.exception.ModelOptimizationException.StatsFileFormatException;
import es.uvigo.darwin.prottest.util.exception.ProtTestInternalException;
import es.uvigo.darwin.prottest.util.exception.TreeFormatException;
+
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
+
import pal.tree.ReadTree;
import pal.tree.TreeParseException;
@@ -100,7 +102,8 @@ public class RaxMLAminoAcidRunEstimator extends AminoAcidRunEstimator {
/* (non-Javadoc)
* @see es.uvigo.darwin.prottest.exe.RunEstimator#optimizeModel(es.uvigo.darwin.prottest.global.options.ApplicationOptions)
*/
- @Override
+ @SuppressWarnings("unused")
+ @Override
public boolean runEstimator() throws ModelOptimizationException {
//let's call Phyml with the proper command line
@@ -163,16 +166,7 @@ public class RaxMLAminoAcidRunEstimator extends AminoAcidRunEstimator {
// the model
str[3] = "-m";
-// if (!Arrays.asList(RAXML_MATRICES).contains(model.getMatrix())) {
-// // check matrix file
-// if (!modelFile.exists()) {
-// throw new ModelNotFoundException(model.getMatrix());
-// }
-// str[9] = "custom";
-// } else {
- str[4] = modelName.toString();
-// }
-
+ str[4] = modelName.toString();
// if (APPLICATION_PROPERTIES.getProperty("phyml_thread_scheduling", "false").equalsIgnoreCase("true")) {
// str[24] = "-t";
// str[25] = String.valueOf(numberOfThreads);
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/RaxMLStreamGobbler.java b/src/main/java/es/uvigo/darwin/prottest/exe/RaxMLStreamGobbler.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/RunEstimator.java b/src/main/java/es/uvigo/darwin/prottest/exe/RunEstimator.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/RunEstimatorImpl.java b/src/main/java/es/uvigo/darwin/prottest/exe/RunEstimatorImpl.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/StreamGobbler.java b/src/main/java/es/uvigo/darwin/prottest/exe/StreamGobbler.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/package.html b/src/main/java/es/uvigo/darwin/prottest/exe/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/util/TemporaryFileManager.java b/src/main/java/es/uvigo/darwin/prottest/exe/util/TemporaryFileManager.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/util/package.html b/src/main/java/es/uvigo/darwin/prottest/exe/util/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacade.java b/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacade.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeImpl.java b/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeImpl.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeMPJ.java b/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeMPJ.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeSequential.java b/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeSequential.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeThread.java b/src/main/java/es/uvigo/darwin/prottest/facade/ProtTestFacadeThread.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/TreeFacade.java b/src/main/java/es/uvigo/darwin/prottest/facade/TreeFacade.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/TreeFacadeImpl.java b/src/main/java/es/uvigo/darwin/prottest/facade/TreeFacadeImpl.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/package.html b/src/main/java/es/uvigo/darwin/prottest/facade/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/DistributionStrategy.java b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/DistributionStrategy.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/Distributor.java b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/Distributor.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/DynamicDistributionStrategy.java b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/DynamicDistributionStrategy.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/HybridDistributionStrategy.java b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/HybridDistributionStrategy.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/ImprovedDynamicDistributionStrategy.java b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/ImprovedDynamicDistributionStrategy.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/MultipleDistributor.java b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/MultipleDistributor.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/StaticDistributionStrategy.java b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/StaticDistributionStrategy.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/strategy/package.html b/src/main/java/es/uvigo/darwin/prottest/facade/strategy/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/thread/ThreadPoolSynchronizer.java b/src/main/java/es/uvigo/darwin/prottest/facade/thread/ThreadPoolSynchronizer.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/thread/package.html b/src/main/java/es/uvigo/darwin/prottest/facade/thread/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/util/ProtTestParameterVO.java b/src/main/java/es/uvigo/darwin/prottest/facade/util/ProtTestParameterVO.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/util/SelectionChunk.java b/src/main/java/es/uvigo/darwin/prottest/facade/util/SelectionChunk.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/facade/util/package.html b/src/main/java/es/uvigo/darwin/prottest/facade/util/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/AminoAcidApplicationGlobals.java b/src/main/java/es/uvigo/darwin/prottest/global/AminoAcidApplicationGlobals.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/ApplicationGlobals.java b/src/main/java/es/uvigo/darwin/prottest/global/ApplicationGlobals.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/ProtTestConsoleParameters.java b/src/main/java/es/uvigo/darwin/prottest/global/ProtTestConsoleParameters.java
old mode 100755
new mode 100644
index 16c2024..c54a511
--- a/src/main/java/es/uvigo/darwin/prottest/global/ProtTestConsoleParameters.java
+++ b/src/main/java/es/uvigo/darwin/prottest/global/ProtTestConsoleParameters.java
@@ -71,4 +71,6 @@ public interface ProtTestConsoleParameters {
public static final String PARAM_LOGGING = "log";
/** Verbose mode parameter token. */
public static final String PARAM_VERBOSE = "verbose";
+ /** Show usage help */
+ public static final String PARAM_HELP = "h";
}
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/ProtTestConstants.java b/src/main/java/es/uvigo/darwin/prottest/global/ProtTestConstants.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/RaxmlAminoAcidApplicationGlobals.java b/src/main/java/es/uvigo/darwin/prottest/global/RaxmlAminoAcidApplicationGlobals.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/options/ApplicationOptions.java b/src/main/java/es/uvigo/darwin/prottest/global/options/ApplicationOptions.java
old mode 100755
new mode 100644
index f4483e9..3770285
--- a/src/main/java/es/uvigo/darwin/prottest/global/options/ApplicationOptions.java
+++ b/src/main/java/es/uvigo/darwin/prottest/global/options/ApplicationOptions.java
@@ -107,6 +107,28 @@ public class ApplicationOptions {
/** Tree search operation */
private String treeSearchOperation = TREE_SEARCH_NNI;
+ @Override
+ public boolean equals(Object obj) {
+System.out.println("Check equals");
+ if (this == obj) return true;
+ if (obj == null) return false;
+ if (getClass() != obj.getClass()) return false;
+ ApplicationOptions other = (ApplicationOptions) obj;
+ if (align_file == null || other.align_file == null) {
+ return false;
+ } else if (!align_file.equals(other.align_file)) {
+ return false;
+ }
+ if (strategyMode != other.strategyMode) return false;
+ if (ncat != other.ncat) return false;
+ if (tree_file != other.tree_file &&
+ (tree_file == null || !tree_file.equals(other.tree_file)))
+ return false;
+ if (!alignment.equals(other.alignment)) return false;
+ if (!tree.equals(other.tree)) return false;
+ return true;
+ }
+
/**
* Sets the number of categories.
*
@@ -556,6 +578,12 @@ public class ApplicationOptions {
*/
public void fillIn(ProtTestArgumentParser arguments) {
+ if(arguments.exists(ProtTestArgumentParser.PARAM_HELP))
+ {
+ usage();
+ System.exit(0);
+ }
+
if (arguments.exists(ProtTestArgumentParser.PARAM_ALIGNMENT_FILE)) {
try {
setAlignment(arguments.getValue(ProtTestArgumentParser.PARAM_ALIGNMENT_FILE));
@@ -696,9 +724,10 @@ public class ApplicationOptions {
println("-------------------------------------------------------------------------------------------------");
println("Basic usage: ");
println(" - Sequential version: ");
- println(" java -jar prottest-2.1.jar -i alignm_file [OPTIONS]");
+ println(" java -jar prottest-"+ProtTest.versionNumber+".jar -i align_file [OPTIONS]");
+ println(" ./prottest3 -i align_file [OPTIONS]");
println(" - Parallel version: ");
- println(" mpjrun.sh -wdir $PWD/ -np [NUM_PROCS] -jar prottest-"+ProtTest.versionNumber+".jar -i alignm_file [OPTIONS]");
+ println(" mpjrun.sh -wdir $PWD/ -np [NUM_PROCS] -jar prottest-"+ProtTest.versionNumber+".jar -i align_file [OPTIONS]");
println("OPTIONS:");
println(" -i alignment_filename");
println(" Alignment input file (required)");
@@ -768,9 +797,9 @@ public class ApplicationOptions {
println("-------------------------------------------------------------------------------------------------");
println("Example: ");
println("- Sequential version:");
- println(" java -jar prottest-"+ProtTest.versionNumber+".jar -i alignm_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5 > output");
+ println(" java -jar prottest-"+ProtTest.versionNumber+".jar -i align_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5 > output");
println("- Parallel version:");
- println(" mpjrun.sh -wdir $PWD/ -np 2 -jar prottest-"+ProtTest.versionNumber+".jar -i alignm_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5");
+ println(" mpjrun.sh -wdir $PWD/ -np 2 -jar prottest-"+ProtTest.versionNumber+".jar -i align_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5");
}
public void reportModelOptimization() {
@@ -828,7 +857,7 @@ public class ApplicationOptions {
if (!(doAIC|doBIC|doAICc|doDT))
sb.append(" lnL");
println(" " + sb.toString());
- println(" Sample size.................: " + sampleSize + " (not calculated yet)");
+ println(" Sample size.................: " + sampleSize);
println(" Other options:");
println(" Display best tree in ASCII..: " + displayASCIITree);
println(" Display best tree in Newick.: " + displayNewickTree);
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/options/SerializableApplicationOptions.java b/src/main/java/es/uvigo/darwin/prottest/global/options/SerializableApplicationOptions.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/options/package.html b/src/main/java/es/uvigo/darwin/prottest/global/options/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/global/package.html b/src/main/java/es/uvigo/darwin/prottest/global/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/model/AminoAcidModel.java b/src/main/java/es/uvigo/darwin/prottest/model/AminoAcidModel.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/model/Model.java b/src/main/java/es/uvigo/darwin/prottest/model/Model.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/model/package.html b/src/main/java/es/uvigo/darwin/prottest/model/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/model/state/ModelEmptyLkState.java b/src/main/java/es/uvigo/darwin/prottest/model/state/ModelEmptyLkState.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/model/state/ModelFilledLkState.java b/src/main/java/es/uvigo/darwin/prottest/model/state/ModelFilledLkState.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/model/state/ModelLkState.java b/src/main/java/es/uvigo/darwin/prottest/model/state/ModelLkState.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/model/state/package.html b/src/main/java/es/uvigo/darwin/prottest/model/state/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/observer/ModelUpdaterObserver.java b/src/main/java/es/uvigo/darwin/prottest/observer/ModelUpdaterObserver.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/observer/ObservableModelUpdater.java b/src/main/java/es/uvigo/darwin/prottest/observer/ObservableModelUpdater.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/observer/package.html b/src/main/java/es/uvigo/darwin/prottest/observer/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/package.html b/src/main/java/es/uvigo/darwin/prottest/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/AIC.java b/src/main/java/es/uvigo/darwin/prottest/selection/AIC.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/AICc.java b/src/main/java/es/uvigo/darwin/prottest/selection/AICc.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/BIC.java b/src/main/java/es/uvigo/darwin/prottest/selection/BIC.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/DT.java b/src/main/java/es/uvigo/darwin/prottest/selection/DT.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/InformationCriterion.java b/src/main/java/es/uvigo/darwin/prottest/selection/InformationCriterion.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/LNL.java b/src/main/java/es/uvigo/darwin/prottest/selection/LNL.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/model/AICSelectionModel.java b/src/main/java/es/uvigo/darwin/prottest/selection/model/AICSelectionModel.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/model/AICcSelectionModel.java b/src/main/java/es/uvigo/darwin/prottest/selection/model/AICcSelectionModel.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/model/BICSelectionModel.java b/src/main/java/es/uvigo/darwin/prottest/selection/model/BICSelectionModel.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/model/DTSelectionModel.java b/src/main/java/es/uvigo/darwin/prottest/selection/model/DTSelectionModel.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/model/LNLSelectionModel.java b/src/main/java/es/uvigo/darwin/prottest/selection/model/LNLSelectionModel.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/model/SelectionModel.java b/src/main/java/es/uvigo/darwin/prottest/selection/model/SelectionModel.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/model/package.html b/src/main/java/es/uvigo/darwin/prottest/selection/model/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/package.html b/src/main/java/es/uvigo/darwin/prottest/selection/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/printer/AminoAcidPrintFramework.java b/src/main/java/es/uvigo/darwin/prottest/selection/printer/AminoAcidPrintFramework.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/printer/PrintFramework.java b/src/main/java/es/uvigo/darwin/prottest/selection/printer/PrintFramework.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/selection/printer/package.html b/src/main/java/es/uvigo/darwin/prottest/selection/printer/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/taxa/Taxon.java b/src/main/java/es/uvigo/darwin/prottest/taxa/Taxon.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/taxa/TaxonomicLevel.java b/src/main/java/es/uvigo/darwin/prottest/taxa/TaxonomicLevel.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/taxa/package.html b/src/main/java/es/uvigo/darwin/prottest/taxa/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/tree/TreeDistancesCache.java b/src/main/java/es/uvigo/darwin/prottest/tree/TreeDistancesCache.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/tree/TreeEuclideanDistancesCache.java b/src/main/java/es/uvigo/darwin/prottest/tree/TreeEuclideanDistancesCache.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/tree/TreeUtils.java b/src/main/java/es/uvigo/darwin/prottest/tree/TreeUtils.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/tree/WeightedTree.java b/src/main/java/es/uvigo/darwin/prottest/tree/WeightedTree.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/tree/package.html b/src/main/java/es/uvigo/darwin/prottest/tree/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/FixedBitSet.java b/src/main/java/es/uvigo/darwin/prottest/util/FixedBitSet.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/ProtTestAlignment.java b/src/main/java/es/uvigo/darwin/prottest/util/ProtTestAlignment.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/StatFramework.java b/src/main/java/es/uvigo/darwin/prottest/util/StatFramework.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/Utilities.java b/src/main/java/es/uvigo/darwin/prottest/util/Utilities.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/AminoAcidArgumentParser.java b/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/AminoAcidArgumentParser.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/ProtTestArgumentParser.java b/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/ProtTestArgumentParser.java
old mode 100755
new mode 100644
index 36f736d..c837602
--- a/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/ProtTestArgumentParser.java
+++ b/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/ProtTestArgumentParser.java
@@ -17,15 +17,21 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package es.uvigo.darwin.prottest.util.argumentparser;
-import static es.uvigo.darwin.prottest.global.ApplicationGlobals.*;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_NCAT;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_STRATEGY_MODE;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_THREADS;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.OPTIMIZE_VALUES;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.TREE_SEARCH_BEST;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.TREE_SEARCH_NNI;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.TREE_SEARCH_SPR;
-import es.uvigo.darwin.prottest.global.ProtTestConsoleParameters;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;
+import es.uvigo.darwin.prottest.global.ProtTestConsoleParameters;
import es.uvigo.darwin.prottest.global.options.ApplicationOptions;
/**
@@ -53,6 +59,8 @@ public abstract class ProtTestArgumentParser
valuesRequired = new HashMap<String, Boolean>();
argumentValues = new HashMap<String, String[]>();
specialArguments = new HashMap<String, Map<String, String>>();
+
+ valuesRequired.put(PARAM_HELP, false);
valuesRequired.put(PARAM_ALIGNMENT_FILE, true);
valuesRequired.put(PARAM_OUTPUT_FILE, true);
valuesRequired.put(PARAM_TREE_FILE, true);
@@ -75,7 +83,7 @@ public abstract class ProtTestArgumentParser
valuesRequired.put(PARAM_TREE_SEARCH_OP, true);
argumentValues.put(PARAM_TREE_SEARCH_OP, treeSearchOps);
-
+
valuesRequired.put(PARAM_NUM_THREADS, true);
valuesRequired.put(PARAM_ALL_FRAMEWORK_COMPARISON, false);
valuesRequired.put(PARAM_DISPLAY_NEWICK_TREE, false);
@@ -125,7 +133,7 @@ public abstract class ProtTestArgumentParser
|| exists(PARAM_DO_AICC) || exists(PARAM_DO_DT))) {
putArgument(PARAM_DO_BIC, "T", arguments);
}
-
+
options.fillIn(this);
}
@@ -159,7 +167,7 @@ public abstract class ProtTestArgumentParser
arg = arg.substring(ARG_TOKEN.length());
if (valuesRequired.containsKey(arg)) {
if (valuesRequired.get(arg)) {
- if (i + 1 < args.length) {
+ if (i + 1 < args.length && !args[i+1].startsWith("-")) {
i++;
String value = args[i];
if (argumentValues.containsKey(arg)) {
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/package.html b/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/attributable/Attributable.java b/src/main/java/es/uvigo/darwin/prottest/util/attributable/Attributable.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/attributable/AttributableHelper.java b/src/main/java/es/uvigo/darwin/prottest/util/attributable/AttributableHelper.java
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/attributable/package.html b/src/main/java/es/uvigo/darwin/prottest/util/attributable/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/CheckPointManager.java b/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/CheckPointManager.java
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/package.html b/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/ApplicationStatus.java b/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/ApplicationStatus.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/ProtTestStatus.java b/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/ProtTestStatus.java
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/package.html b/src/main/java/es/uvigo/darwin/prottest/util/checkpoint/status/package.html
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/collection/ModelCollection.java b/src/main/java/es/uvigo/darwin/prottest/util/collection/ModelCollection.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/collection/ParallelModelCollection.java b/src/main/java/es/uvigo/darwin/prottest/util/collection/ParallelModelCollection.java
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/collection/ParallelModelQueue.java b/src/main/java/es/uvigo/darwin/prottest/util/collection/ParallelModelQueue.java
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/collection/SingleModelCollection.java b/src/main/java/es/uvigo/darwin/prottest/util/collection/SingleModelCollection.java
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/collection/package.html b/src/main/java/es/uvigo/darwin/prottest/util/collection/package.html
old mode 100755
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diff --git a/src/main/java/es/uvigo/darwin/prottest/util/comparator/AminoAcidModelNaturalComparator.java b/src/main/java/es/uvigo/darwin/prottest/util/comparator/AminoAcidModelNaturalComparator.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/comparator/LKComparator.java b/src/main/java/es/uvigo/darwin/prottest/util/comparator/LKComparator.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/comparator/ModelDistributionHeuristic.java b/src/main/java/es/uvigo/darwin/prottest/util/comparator/ModelDistributionHeuristic.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/comparator/ModelWeightComparator.java b/src/main/java/es/uvigo/darwin/prottest/util/comparator/ModelWeightComparator.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/comparator/package.html b/src/main/java/es/uvigo/darwin/prottest/util/comparator/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/exception/AlignmentParseException.java b/src/main/java/es/uvigo/darwin/prottest/util/exception/AlignmentParseException.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/exception/ImportException.java b/src/main/java/es/uvigo/darwin/prottest/util/exception/ImportException.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/exception/ModelOptimizationException.java b/src/main/java/es/uvigo/darwin/prottest/util/exception/ModelOptimizationException.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/exception/ProtTestCheckedException.java b/src/main/java/es/uvigo/darwin/prottest/util/exception/ProtTestCheckedException.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/exception/ProtTestInternalException.java b/src/main/java/es/uvigo/darwin/prottest/util/exception/ProtTestInternalException.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/exception/TreeFormatException.java b/src/main/java/es/uvigo/darwin/prottest/util/exception/TreeFormatException.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/factory/ProtTestFactory.java b/src/main/java/es/uvigo/darwin/prottest/util/factory/ProtTestFactory.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/factory/package.html b/src/main/java/es/uvigo/darwin/prottest/util/factory/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
old mode 100755
new mode 100644
index b39a4c1..8d08537
--- a/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
+++ b/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
@@ -195,7 +195,7 @@ public class AlignmentReader {
String currString;
int size = alignment.getSequenceCount();
for (int i = 0; i < size; i++) {
- currString = (String) seqNames.get(i);
+ currString = seqNames.get(i);
for (int j = i + 1; j < size; j++) {
if (seqNames.get(j).equals(currString)) {
throw new AlignmentParseException("ERROR: There are duplicated taxa names in the alignment: " + currString);
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/ImportHelper.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/ImportHelper.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusExporter.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusExporter.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusImporter.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusImporter.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusTreeReader.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/NexusTreeReader.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/SimpleNewickTreeReader.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/SimpleNewickTreeReader.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/TreeReader.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/TreeReader.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogFormatter.java b/src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogFormatter.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogger.java b/src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogger.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/package.html b/src/main/java/es/uvigo/darwin/prottest/util/package.html
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestFormattedOutput.java b/src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestFormattedOutput.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestPrinter.java b/src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestPrinter.java
old mode 100755
new mode 100644
index 1a7cb51..a1f0f36
--- a/src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestPrinter.java
+++ b/src/main/java/es/uvigo/darwin/prottest/util/printer/ProtTestPrinter.java
@@ -21,8 +21,10 @@ import java.io.PrintWriter;
import java.util.Date;
import es.uvigo.darwin.prottest.ProtTest;
+import es.uvigo.darwin.prottest.exe.PhyMLv3AminoAcidRunEstimator;
import es.uvigo.darwin.prottest.global.options.ApplicationOptions;
import es.uvigo.darwin.prottest.util.logging.ProtTestLogger;
+
import java.io.File;
/**
@@ -55,19 +57,38 @@ public class ProtTestPrinter {
*/
public static void printHeader() {
println("");
- println("");
+ println(ProtTestFormattedOutput.space(94, '-'));
println("ProtTest " + ProtTest.versionNumber
+ ProtTestFormattedOutput.space(27 - ProtTest.versionNumber.length(), ' ') +
"Fast selection of the best-fit models of protein evolution");
- println("(c) 2009-2010 Diego Darriba (1,2), Guillermo Taboada (2), Ramón Doallo (2), David Posada (1)");
+ println("(c) 2009-2016 Diego Darriba (1,2), Guillermo Taboada (2), Ramón Doallo (2), David Posada (1)");
println("(1) Facultad de Biologia, Universidad de Vigo, 36200 Vigo, Spain");
println("(2) Facultade de Informática, Universidade da Coruña, 15071 A Coruña, Spain");
- println("Contact: ddarriba at udc.es, dposada at uvigo.es");
- println("----------------------------------------------------------------------------------------------");
- println("");
- println((new Date()).toString());
- println("OS = " + System.getProperty("os.name") +
+ println(ProtTestFormattedOutput.space(94, '-'));
+ println("Manual:" +
+ ProtTestFormattedOutput.space(87 - ProtTest.URL_MANUAL.length(), ' ') +
+ ProtTest.URL_MANUAL);
+ println("Homepage:" +
+ ProtTestFormattedOutput.space(85 - ProtTest.URL_HOMEPAGE.length(), ' ') +
+ ProtTest.URL_HOMEPAGE);
+ println("Discussion group:" +
+ ProtTestFormattedOutput.space(77 - ProtTest.URL_DISCUSSION_GROUP.length(), ' ') +
+ ProtTest.URL_DISCUSSION_GROUP);
+ println("Contact: ddarriba at h-its.org, dposada at uvigo.es");
+ println(ProtTestFormattedOutput.space(94, '-'));
+ println("");
+ println("Version: " + ProtTest.versionNumber + " : " + ProtTest.versionDate);
+ println("Date: " + (new Date()).toString());
+ println("OS: " + System.getProperty("os.name") +
" (" + System.getProperty("os.version") + ")");
+ println("Arch: " + System.getProperty("os.arch"));
+ println("Java: " + System.getProperty("java.version") +
+ " (" + System.getProperty("java.vendor") + ")");
+// println("VM Mem.(MB)= " +
+// Runtime.getRuntime().totalMemory()/(1024*1024) + " (total) " +
+// Runtime.getRuntime().maxMemory()/(1024*1024) + " (max) " +
+// Runtime.getRuntime().freeMemory()/(1024*1024) + " (free)");
+ println("PhyML: " + PhyMLv3AminoAcidRunEstimator.phymlBinaryStr);
println("");
println("Citation: Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit ");
println(" models of protein evolution. Bioinformatics, 27:1164-1165, 2011");
diff --git a/src/main/java/es/uvigo/darwin/xprottest/CreditsBox.java b/src/main/java/es/uvigo/darwin/xprottest/CreditsBox.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/PreferencesView.java b/src/main/java/es/uvigo/darwin/xprottest/PreferencesView.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/XProtTestAboutBox.java b/src/main/java/es/uvigo/darwin/xprottest/XProtTestAboutBox.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/XProtTestApp.java b/src/main/java/es/uvigo/darwin/xprottest/XProtTestApp.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/XProtTestView.java b/src/main/java/es/uvigo/darwin/xprottest/XProtTestView.java
old mode 100755
new mode 100644
index a72094a..8bca91f
--- a/src/main/java/es/uvigo/darwin/xprottest/XProtTestView.java
+++ b/src/main/java/es/uvigo/darwin/xprottest/XProtTestView.java
@@ -19,7 +19,9 @@ package es.uvigo.darwin.xprottest;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Desktop;
import java.awt.FileDialog;
+import java.awt.Image;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@@ -29,12 +31,14 @@ import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
+import java.net.URI;
import java.util.logging.Handler;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.ActionMap;
import javax.swing.Icon;
+import javax.swing.ImageIcon;
import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JLabel;
@@ -81,7 +85,6 @@ import es.uvigo.darwin.xprottest.compute.OptionsView;
import es.uvigo.darwin.xprottest.compute.RunningFrame;
import es.uvigo.darwin.xprottest.results.ErrorLogView;
import es.uvigo.darwin.xprottest.results.ResultsView;
-import es.uvigo.darwin.xprottest.util.BrowserLauncher;
import es.uvigo.darwin.xprottest.util.TextAreaAppender;
/**
@@ -197,6 +200,9 @@ public final class XProtTestView extends FrameView {
initComponents();
+ Image image = new ImageIcon("icon.png").getImage();
+ getFrame().setIconImage(image);
+
displayWriter = new PrintWriter(new TextAreaAppender(mainTextArea));
lowLevelDisplayWriter = new PrintWriter(new TextAreaAppender(
phymlTextArea));
@@ -341,13 +347,15 @@ public final class XProtTestView extends FrameView {
errorMenuItem = new JMenuItem();
helpMenu = new JMenu();
manualMenuItem = new JMenuItem();
+ homepageMenuItem = new JMenuItem();
+ discgroupMenuItem = new JMenuItem();
aboutMenuItem = new JMenuItem();
org.jdesktop.application.ResourceMap appResourceMap = org.jdesktop.application.Application
.getInstance(es.uvigo.darwin.xprottest.XProtTestApp.class)
.getContext().getResourceMap(XProtTestView.class);
- mainPanel.setSize(new java.awt.Dimension(500, 860));
+ mainPanel.setSize(new java.awt.Dimension(600, 860));
mainPanel.setBorder(new BorderUIResource.EmptyBorderUIResource(
new java.awt.Insets(20, 20, 20, 20)));
mainPanel.setLocation(new java.awt.Point(10, -10));
@@ -355,10 +363,7 @@ public final class XProtTestView extends FrameView {
mainPanel.setAutoscrolls(true);
mainPanel.setLayout(new BorderLayout());
mainPanel.setBackground(null);
-
- // mainPanel.setBackground(resourceMap.getColor("mainPanel.background"));
mainPanel.setName("mainPanel");
- // mainPanel.setPreferredSize(new java.awt.Dimension(500, 600));
mainScrollPane.setSize(590, 800);// new java.awt.Dimension(590, 600));
mainScrollPane.setLocation(new java.awt.Point(20, 20));
@@ -654,12 +659,24 @@ public final class XProtTestView extends FrameView {
helpMenu.setText(bundle.getString("item-help"));
helpMenu.setName("helpMenu");
+ homepageMenuItem.setAction(actionMap.get("openHomepage"));
+ homepageMenuItem.setMnemonic('p');
+ homepageMenuItem.setText(appResourceMap.getString("menu-homepage"));
+ homepageMenuItem.setName("homepageMenuItem");
+ helpMenu.add(homepageMenuItem);
+
manualMenuItem.setAction(actionMap.get("showManual"));
manualMenuItem.setMnemonic('m');
manualMenuItem.setText(appResourceMap.getString("menu-manual"));
manualMenuItem.setName("manualMenuItem");
helpMenu.add(manualMenuItem);
-
+
+ discgroupMenuItem.setAction(actionMap.get("openDiscussionGroup"));
+ discgroupMenuItem.setMnemonic('D');
+ discgroupMenuItem.setText(appResourceMap.getString("menu-discussiongroup"));
+ discgroupMenuItem.setName("discgroupMenuItem");
+ helpMenu.add(discgroupMenuItem);
+
aboutMenuItem.setAction(actionMap.get("showAboutBox"));
aboutMenuItem.setText(bundle.getString("item-about-window"));
aboutMenuItem.setName("aboutMenuItem");
@@ -1082,14 +1099,50 @@ public final class XProtTestView extends FrameView {
}
@Action
+ public void openDiscussionGroup() {
+ try {
+ if (Desktop.isDesktopSupported()) {
+ Desktop desktop = Desktop.getDesktop();
+ URI prottestURI = new URI(ProtTest.URL_DISCUSSION_GROUP);
+ desktop.browse(prottestURI);
+ } else {
+ displayWriter.println("Cannot browse URL. Please open " +
+ ProtTest.URL_DISCUSSION_GROUP + " manually.");
+ }
+ } catch (Exception e) {
+ displayWriter.println("Cannot open URL : " + e.getMessage());
+ }
+ }
+
+ @Action
+ public void openHomepage() {
+ try {
+ if (Desktop.isDesktopSupported()) {
+ Desktop desktop = Desktop.getDesktop();
+ URI prottestURI = new URI(ProtTest.URL_HOMEPAGE);
+ desktop.browse(prottestURI);
+ } else {
+ displayWriter.println("Cannot browse URL. Please open " +
+ ProtTest.URL_HOMEPAGE + " manually.");
+ }
+ } catch (Exception e) {
+ displayWriter.println("Cannot open URL : " + e.getMessage());
+ }
+ }
+
+ @Action
public void showManual() {
try {
- BrowserLauncher
- .openURL("http://darwin.uvigo.es/download/prottest_manual.pdf");
-
- } catch (IOException e) {
+ if (Desktop.isDesktopSupported()) {
+ Desktop desktop = Desktop.getDesktop();
+ URI prottestURI = new URI(ProtTest.URL_MANUAL);
+ desktop.browse(prottestURI);
+ } else {
+ displayWriter.println("Cannot browse URL. Please open " +
+ ProtTest.URL_MANUAL + " manually.");
+ }
+ } catch (Exception e) {
displayWriter.println("Cannot open URL : " + e.getMessage());
-
}
}
@@ -1113,7 +1166,9 @@ public final class XProtTestView extends FrameView {
private JTextArea phymlTextArea;
private JScrollPane mainScrollPane;
private JTextArea mainTextArea;
+ private JMenuItem homepageMenuItem;
private JMenuItem manualMenuItem;
+ private JMenuItem discgroupMenuItem;
private JMenuBar menuBar;
private JMenuItem preferencesMenuItem;
private JMenu resultsMenu;
diff --git a/src/main/java/es/uvigo/darwin/xprottest/analysis/FrequenciesView.java b/src/main/java/es/uvigo/darwin/xprottest/analysis/FrequenciesView.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/analysis/TreeView.java b/src/main/java/es/uvigo/darwin/xprottest/analysis/TreeView.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/analysis/TreeWrapper.java b/src/main/java/es/uvigo/darwin/xprottest/analysis/TreeWrapper.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/analysis/consensus/Consensus.java b/src/main/java/es/uvigo/darwin/xprottest/analysis/consensus/Consensus.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/analysis/consensus/resources/Consensus.properties b/src/main/java/es/uvigo/darwin/xprottest/analysis/consensus/resources/Consensus.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/analysis/resources/FrequenciesView.properties b/src/main/java/es/uvigo/darwin/xprottest/analysis/resources/FrequenciesView.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/analysis/resources/TreeView.properties b/src/main/java/es/uvigo/darwin/xprottest/analysis/resources/TreeView.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/compute/OptionsView.java b/src/main/java/es/uvigo/darwin/xprottest/compute/OptionsView.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/compute/RunningFrame.java b/src/main/java/es/uvigo/darwin/xprottest/compute/RunningFrame.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/compute/resources/OptionsView.properties b/src/main/java/es/uvigo/darwin/xprottest/compute/resources/OptionsView.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/compute/resources/RunningFrame.properties b/src/main/java/es/uvigo/darwin/xprottest/compute/resources/RunningFrame.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/CreditsBox.properties b/src/main/java/es/uvigo/darwin/xprottest/resources/CreditsBox.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/PreferencesView.properties b/src/main/java/es/uvigo/darwin/xprottest/resources/PreferencesView.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestAboutBox.properties b/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestAboutBox.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestApp.properties b/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestApp.properties
old mode 100755
new mode 100644
index 2503ae5..d9198e8
--- a/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestApp.properties
+++ b/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestApp.properties
@@ -2,7 +2,7 @@
Application.name = XProtTest
Application.title = XProtTest
-Application.version = 3.3
+Application.version = 3.4.2
Application.vendor = Phylogenomics
Application.homepage = http://code.google.com/p/prottest3
Application.citation1 = Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection
@@ -34,5 +34,7 @@ button-accept=Accept
button-cancel=Cancel
Form.background=238, 238, 238
menu-manual=ProtTest Manual
+menu-homepage=ProtTest Homepage
+menu-discussiongroup=ProtTest Discussion Group
export-to-console=Export to main console
txtNCat.defaultText=4
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestView.properties b/src/main/java/es/uvigo/darwin/xprottest/resources/XProtTestView.properties
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/about.png b/src/main/java/es/uvigo/darwin/xprottest/resources/about.png
old mode 100755
new mode 100644
index c6dfe0a..cc25062
Binary files a/src/main/java/es/uvigo/darwin/xprottest/resources/about.png and b/src/main/java/es/uvigo/darwin/xprottest/resources/about.png differ
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon0.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon0.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon1.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon1.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon10.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon10.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon11.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon11.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon12.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon12.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon13.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon13.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon14.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon14.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon2.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon2.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon3.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon3.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon4.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon4.png
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon5.png b/src/main/java/es/uvigo/darwin/xprottest/resources/busyicons/busy-icon5.png
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@@ -1,583 +0,0 @@
-package es.uvigo.darwin.xprottest.util;
-
-import java.io.File;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-
-/**
- * BrowserLauncher is a class that provides one static method, openURL, which opens the default
- * web browser for the current user of the system to the given URL. It may support other
- * protocols depending on the system -- mailto, ftp, etc. -- but that has not been rigorously
- * tested and is not guaranteed to work.
- * <p>
- * Yes, this is platform-specific code, and yes, it may rely on classes on certain platforms
- * that are not part of the standard JDK. What we're trying to do, though, is to take something
- * that's frequently desirable but inherently platform-specific -- opening a default browser --
- * and allow programmers (you, for example) to do so without worrying about dropping into native
- * code or doing anything else similarly evil.
- * <p>
- * Anyway, this code is completely in Java and will run on all JDK 1.1-compliant systems without
- * modification or a need for additional libraries. All classes that are required on certain
- * platforms to allow this to run are dynamically loaded at runtime via reflection and, if not
- * found, will not cause this to do anything other than returning an error when opening the
- * browser.
- * <p>
- * There are certain system requirements for this class, as it's running through Runtime.exec(),
- * which is Java's way of making a native system call. Currently, this requires that a Macintosh
- * have a Finder which supports the GURL event, which is true for Mac OS 8.0 and 8.1 systems that
- * have the Internet Scripting AppleScript dictionary installed in the Scripting Additions folder
- * in the Extensions folder (which is installed by default as far as I know under Mac OS 8.0 and
- * 8.1), and for all Mac OS 8.5 and later systems. On Windows, it only runs under Win32 systems
- * (Windows 95, 98, and NT 4.0, as well as later versions of all). On other systems, this drops
- * back from the inherently platform-sensitive concept of a default browser and simply attempts
- * to launch Netscape via a shell command.
- * <p>
- * This code is Copyright 1999-2001 by Eric Albert (ejalbert at cs.stanford.edu) and may be
- * redistributed or modified in any form without restrictions as long as the portion of this
- * comment from this paragraph through the end of the comment is not removed. The author
- * requests that he be notified of any application, applet, or other binary that makes use of
- * this code, but that's more out of curiosity than anything and is not required. This software
- * includes no warranty. The author is not repsonsible for any loss of data or functionality
- * or any adverse or unexpected effects of using this software.
- * <p>
- * Credits:
- * <br>Steven Spencer, JavaWorld magazine (<a href="http://www.javaworld.com/javaworld/javatips/jw-javatip66.html">Java Tip 66</a>)
- * <br>Thanks also to Ron B. Yeh, Eric Shapiro, Ben Engber, Paul Teitlebaum, Andrea Cantatore,
- * Larry Barowski, Trevor Bedzek, Frank Miedrich, and Ron Rabakukk
- *
- * @author Eric Albert (<a href="mailto:ejalbert at cs.stanford.edu">ejalbert at cs.stanford.edu</a>)
- * @version 1.4b1 (Released June 20, 2001)
- */
-public class BrowserLauncher {
-
- /**
- * The Java virtual machine that we are running on. Actually, in most cases we only care
- * about the operating system, but some operating systems require us to switch on the VM. */
- private static int jvm;
-
- /** The browser for the system */
- private static Object browser;
-
- /**
- * Caches whether any classes, methods, and fields that are not part of the JDK and need to
- * be dynamically loaded at runtime loaded successfully.
- * <p>
- * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
- * IOException.
- */
- private static boolean loadedWithoutErrors;
-
- /** The com.apple.mrj.MRJFileUtils class */
- private static Class mrjFileUtilsClass;
-
- /** The com.apple.mrj.MRJOSType class */
- private static Class mrjOSTypeClass;
-
- /** The com.apple.MacOS.AEDesc class */
- private static Class aeDescClass;
-
- /** The <init>(int) method of com.apple.MacOS.AETarget */
- private static Constructor aeTargetConstructor;
-
- /** The <init>(int, int, int) method of com.apple.MacOS.AppleEvent */
- private static Constructor appleEventConstructor;
-
- /** The <init>(String) method of com.apple.MacOS.AEDesc */
- private static Constructor aeDescConstructor;
-
- /** The findFolder method of com.apple.mrj.MRJFileUtils */
- private static Method findFolder;
-
- /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
- private static Method getFileCreator;
-
- /** The getFileType method of com.apple.mrj.MRJFileUtils */
- private static Method getFileType;
-
- /** The openURL method of com.apple.mrj.MRJFileUtils */
- private static Method openURL;
-
- /** The makeOSType method of com.apple.MacOS.OSUtils */
- private static Method makeOSType;
-
- /** The putParameter method of com.apple.MacOS.AppleEvent */
- private static Method putParameter;
-
- /** The sendNoReply method of com.apple.MacOS.AppleEvent */
- private static Method sendNoReply;
-
- /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
- private static Object kSystemFolderType;
-
- /** The keyDirectObject AppleEvent parameter type */
- private static Integer keyDirectObject;
-
- /** The kAutoGenerateReturnID AppleEvent code */
- private static Integer kAutoGenerateReturnID;
-
- /** The kAnyTransactionID AppleEvent code */
- private static Integer kAnyTransactionID;
-
- /** The linkage object required for JDirect 3 on Mac OS X. */
- private static Object linkage;
-
- /** The framework to reference on Mac OS X */
- private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
-
- /** JVM constant for MRJ 2.0 */
- private static final int MRJ_2_0 = 0;
-
- /** JVM constant for MRJ 2.1 or later */
- private static final int MRJ_2_1 = 1;
-
- /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
- private static final int MRJ_3_0 = 3;
-
- /** JVM constant for MRJ 3.1 */
- private static final int MRJ_3_1 = 4;
-
- /** JVM constant for any Windows NT JVM */
- private static final int WINDOWS_NT = 5;
-
- /** JVM constant for any Windows 9x JVM */
- private static final int WINDOWS_9x = 6;
-
- /** JVM constant for any other platform */
- private static final int OTHER = -1;
-
- /**
- * The file type of the Finder on a Macintosh. Hardcoding "Finder" would keep non-U.S. English
- * systems from working properly.
- */
- private static final String FINDER_TYPE = "FNDR";
-
- /**
- * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
- * application.
- */
- private static final String FINDER_CREATOR = "MACS";
-
- /** The name for the AppleEvent type corresponding to a GetURL event. */
- private static final String GURL_EVENT = "GURL";
-
- /**
- * The first parameter that needs to be passed into Runtime.exec() to open the default web
- * browser on Windows.
- */
- private static final String FIRST_WINDOWS_PARAMETER = "/c";
-
- /** The second parameter for Runtime.exec() on Windows. */
- private static final String SECOND_WINDOWS_PARAMETER = "start";
-
- /**
- * The third parameter for Runtime.exec() on Windows. This is a "title"
- * parameter that the command line expects. Setting this parameter allows
- * URLs containing spaces to work.
- */
- private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
-
- /**
- * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
- * on many command-line systems.
- */
- private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
- private static final String NETSCAPE_OPEN_PARAMETER_START = "'openURL(";
- private static final String NETSCAPE_OPEN_PARAMETER_END = ")'";
-
- /**
- * The message from any exception thrown throughout the initialization process.
- */
- private static String errorMessage;
-
- /**
- * An initialization block that determines the operating system and loads the necessary
- * runtime data.
- */
- static {
- loadedWithoutErrors = true;
- String osName = System.getProperty("os.name");
- if (osName.startsWith("Mac OS")) {
- String mrjVersion = System.getProperty("mrj.version");
- String majorMRJVersion = mrjVersion.substring(0, 3);
- try {
- double version = Double.valueOf(majorMRJVersion).doubleValue();
- if (version == 2) {
- jvm = MRJ_2_0;
- } else if (version >= 2.1 && version < 3) {
- // Assume that all 2.x versions of MRJ work the same. MRJ 2.1 actually
- // works via Runtime.exec() and 2.2 supports that but has an openURL() method
- // as well that we currently ignore.
- jvm = MRJ_2_1;
- } else if (version == 3.0) {
- jvm = MRJ_3_0;
- } else if (version >= 3.1) {
- // Assume that all 3.1 and later versions of MRJ work the same.
- jvm = MRJ_3_1;
- } else {
- loadedWithoutErrors = false;
- errorMessage = "Unsupported MRJ version: " + version;
- }
- } catch (NumberFormatException nfe) {
- loadedWithoutErrors = false;
- errorMessage = "Invalid MRJ version: " + mrjVersion;
- }
- } else if (osName.startsWith("Windows")) {
- if (osName.indexOf("9") != -1) {
- jvm = WINDOWS_9x;
- } else {
- jvm = WINDOWS_NT;
- }
- } else {
- jvm = OTHER;
- }
-
- if (loadedWithoutErrors) { // if we haven't hit any errors yet
- loadedWithoutErrors = loadClasses();
- }
- }
-
- /**
- * This class should be never be instantiated; this just ensures so.
- */
- private BrowserLauncher() { }
-
- /**
- * Called by a static initializer to load any classes, fields, and methods required at runtime
- * to locate the user's web browser.
- * @return <code>true</code> if all intialization succeeded
- * <code>false</code> if any portion of the initialization failed
- */
- private static boolean loadClasses() {
- switch (jvm) {
- case MRJ_2_0:
- try {
- Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
- Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
- Class appleEventClass = Class.forName("com.apple.MacOS.AppleEvent");
- Class aeClass = Class.forName("com.apple.MacOS.ae");
- aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
-
- aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class [] { int.class });
- appleEventConstructor = appleEventClass.getDeclaredConstructor(new Class[] { int.class, int.class, aeTargetClass, int.class, int.class });
- aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[] { String.class });
-
- makeOSType = osUtilsClass.getDeclaredMethod("makeOSType", new Class [] { String.class });
- putParameter = appleEventClass.getDeclaredMethod("putParameter", new Class[] { int.class, aeDescClass });
- sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply", new Class[] { });
-
- Field keyDirectObjectField = aeClass.getDeclaredField("keyDirectObject");
- keyDirectObject = (Integer) keyDirectObjectField.get(null);
- Field autoGenerateReturnIDField = appleEventClass.getDeclaredField("kAutoGenerateReturnID");
- kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);
- Field anyTransactionIDField = appleEventClass.getDeclaredField("kAnyTransactionID");
- kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- } catch (NoSuchFieldException nsfe) {
- errorMessage = nsfe.getMessage();
- return false;
- } catch (IllegalAccessException iae) {
- errorMessage = iae.getMessage();
- return false;
- }
- break;
- case MRJ_2_1:
- try {
- mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
- mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
- Field systemFolderField = mrjFileUtilsClass.getDeclaredField("kSystemFolderType");
- kSystemFolderType = systemFolderField.get(null);
- findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder", new Class[] { mrjOSTypeClass });
- getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator", new Class[] { File.class });
- getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType", new Class[] { File.class });
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchFieldException nsfe) {
- errorMessage = nsfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- } catch (SecurityException se) {
- errorMessage = se.getMessage();
- return false;
- } catch (IllegalAccessException iae) {
- errorMessage = iae.getMessage();
- return false;
- }
- break;
- case MRJ_3_0:
- try {
- Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
- Constructor constructor = linker.getConstructor(new Class[]{ Class.class });
- linkage = constructor.newInstance(new Object[] { BrowserLauncher.class });
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- } catch (InvocationTargetException ite) {
- errorMessage = ite.getMessage();
- return false;
- } catch (InstantiationException ie) {
- errorMessage = ie.getMessage();
- return false;
- } catch (IllegalAccessException iae) {
- errorMessage = iae.getMessage();
- return false;
- }
- break;
- case MRJ_3_1:
- try {
- mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
- openURL = mrjFileUtilsClass.getDeclaredMethod("openURL", new Class[] { String.class });
- } catch (ClassNotFoundException cnfe) {
- errorMessage = cnfe.getMessage();
- return false;
- } catch (NoSuchMethodException nsme) {
- errorMessage = nsme.getMessage();
- return false;
- }
- break;
- default:
- break;
- }
- return true;
- }
-
- /**
- * Attempts to locate the default web browser on the local system. Caches results so it
- * only locates the browser once for each use of this class per JVM instance.
- * @return The browser for the system. Note that this may not be what you would consider
- * to be a standard web browser; instead, it's the application that gets called to
- * open the default web browser. In some cases, this will be a non-String object
- * that provides the means of calling the default browser.
- */
- private static Object locateBrowser() {
- if (browser != null) {
- return browser;
- }
- switch (jvm) {
- case MRJ_2_0:
- try {
- Integer finderCreatorCode = (Integer) makeOSType.invoke(null, new Object[] { FINDER_CREATOR });
- Object aeTarget = aeTargetConstructor.newInstance(new Object[] { finderCreatorCode });
- Integer gurlType = (Integer) makeOSType.invoke(null, new Object[] { GURL_EVENT });
- Object appleEvent = appleEventConstructor.newInstance(new Object[] { gurlType, gurlType, aeTarget, kAutoGenerateReturnID, kAnyTransactionID });
- // Don't set browser = appleEvent because then the next time we call
- // locateBrowser(), we'll get the same AppleEvent, to which we'll already have
- // added the relevant parameter. Instead, regenerate the AppleEvent every time.
- // There's probably a way to do this better; if any has any ideas, please let
- // me know.
- return appleEvent;
- } catch (IllegalAccessException iae) {
- browser = null;
- errorMessage = iae.getMessage();
- return browser;
- } catch (InstantiationException ie) {
- browser = null;
- errorMessage = ie.getMessage();
- return browser;
- } catch (InvocationTargetException ite) {
- browser = null;
- errorMessage = ite.getMessage();
- return browser;
- }
- case MRJ_2_1:
- File systemFolder;
- try {
- systemFolder = (File) findFolder.invoke(null, new Object[] { kSystemFolderType });
- } catch (IllegalArgumentException iare) {
- browser = null;
- errorMessage = iare.getMessage();
- return browser;
- } catch (IllegalAccessException iae) {
- browser = null;
- errorMessage = iae.getMessage();
- return browser;
- } catch (InvocationTargetException ite) {
- browser = null;
- errorMessage = ite.getTargetException().getClass() + ": " + ite.getTargetException().getMessage();
- return browser;
- }
- String[] systemFolderFiles = systemFolder.list();
- // Avoid a FilenameFilter because that can't be stopped mid-list
- for(int i = 0; i < systemFolderFiles.length; i++) {
- try {
- File file = new File(systemFolder, systemFolderFiles[i]);
- if (!file.isFile()) {
- continue;
- }
- // We're looking for a file with a creator code of 'MACS' and
- // a type of 'FNDR'. Only requiring the type results in non-Finder
- // applications being picked up on certain Mac OS 9 systems,
- // especially German ones, and sending a GURL event to those
- // applications results in a logout under Multiple Users.
- Object fileType = getFileType.invoke(null, new Object[] { file });
- if (FINDER_TYPE.equals(fileType.toString())) {
- Object fileCreator = getFileCreator.invoke(null, new Object[] { file });
- if (FINDER_CREATOR.equals(fileCreator.toString())) {
- browser = file.toString(); // Actually the Finder, but that's OK
- return browser;
- }
- }
- } catch (IllegalArgumentException iare) {
- browser = browser;
- errorMessage = iare.getMessage();
- return null;
- } catch (IllegalAccessException iae) {
- browser = null;
- errorMessage = iae.getMessage();
- return browser;
- } catch (InvocationTargetException ite) {
- browser = null;
- errorMessage = ite.getTargetException().getClass() + ": " + ite.getTargetException().getMessage();
- return browser;
- }
- }
- browser = null;
- break;
- case MRJ_3_0:
- case MRJ_3_1:
- browser = ""; // Return something non-null
- break;
- case WINDOWS_NT:
- browser = "cmd.exe";
- break;
- case WINDOWS_9x:
- browser = "command.com";
- break;
- case OTHER:
- default:
- browser = "netscape";
- break;
- }
- return browser;
- }
-
- /**
- * Attempts to open the default web browser to the given URL.
- * @param url The URL to open
- * @throws IOException If the web browser could not be located or does not run
- */
- public static void openURL(String url) throws IOException {
- if (!loadedWithoutErrors) {
- throw new IOException("Exception in finding browser: " + errorMessage);
- }
- Object browser = locateBrowser();
- if (browser == null) {
- throw new IOException("Unable to locate browser: " + errorMessage);
- }
-
- switch (jvm) {
- case MRJ_2_0:
- Object aeDesc = null;
- try {
- aeDesc = aeDescConstructor.newInstance(new Object[] { url });
- putParameter.invoke(browser, new Object[] { keyDirectObject, aeDesc });
- sendNoReply.invoke(browser, new Object[] { });
- } catch (InvocationTargetException ite) {
- throw new IOException("InvocationTargetException while creating AEDesc: " + ite.getMessage());
- } catch (IllegalAccessException iae) {
- throw new IOException("IllegalAccessException while building AppleEvent: " + iae.getMessage());
- } catch (InstantiationException ie) {
- throw new IOException("InstantiationException while creating AEDesc: " + ie.getMessage());
- } finally {
- aeDesc = null; // Encourage it to get disposed if it was created
- browser = null; // Ditto
- }
- break;
- case MRJ_2_1:
- Runtime.getRuntime().exec(new String[] { (String) browser, url } );
- break;
- case MRJ_3_0:
- int[] instance = new int[1];
- int result = ICStart(instance, 0);
- if (result == 0) {
- int[] selectionStart = new int[] { 0 };
- byte[] urlBytes = url.getBytes();
- int[] selectionEnd = new int[] { urlBytes.length };
- result = ICLaunchURL(instance[0], new byte[] { 0 }, urlBytes,
- urlBytes.length, selectionStart,
- selectionEnd);
- if (result == 0) {
- // Ignore the return value; the URL was launched successfully
- // regardless of what happens here.
- ICStop(instance);
- } else {
- throw new IOException("Unable to launch URL: " + result);
- }
- } else {
- throw new IOException("Unable to create an Internet Config instance: " + result);
- }
- break;
- case MRJ_3_1:
- try {
- openURL.invoke(null, new Object[] { url });
- } catch (InvocationTargetException ite) {
- throw new IOException("InvocationTargetException while calling openURL: " + ite.getMessage());
- } catch (IllegalAccessException iae) {
- throw new IOException("IllegalAccessException while calling openURL: " + iae.getMessage());
- }
- break;
- case WINDOWS_NT:
- case WINDOWS_9x:
- // Add quotes around the URL to allow ampersands and other special
- // characters to work.
- Process process = Runtime.getRuntime().exec(new String[] { (String) browser,
- FIRST_WINDOWS_PARAMETER,
- SECOND_WINDOWS_PARAMETER,
- THIRD_WINDOWS_PARAMETER,
- '"' + url + '"' });
- // This avoids a memory leak on some versions of Java on Windows.
- // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.
- try {
- process.waitFor();
- process.exitValue();
- } catch (InterruptedException ie) {
- throw new IOException("InterruptedException while launching browser: " + ie.getMessage());
- }
- break;
- case OTHER:
- // Assume that we're on Unix and that Netscape is installed
-
- // First, attempt to open the URL in a currently running session of Netscape
- process = Runtime.getRuntime().exec(new String[] { (String) browser,
- NETSCAPE_REMOTE_PARAMETER,
- NETSCAPE_OPEN_PARAMETER_START +
- url +
- NETSCAPE_OPEN_PARAMETER_END });
- try {
- int exitCode = process.waitFor();
- if (exitCode != 0) { // if Netscape was not open
- Runtime.getRuntime().exec(new String[] { (String) browser, url });
- }
- } catch (InterruptedException ie) {
- throw new IOException("InterruptedException while launching browser: " + ie.getMessage());
- }
- break;
- default:
- // This should never occur, but if it does, we'll try the simplest thing possible
- Runtime.getRuntime().exec(new String[] { (String) browser, url });
- break;
- }
- }
-
- /**
- * Methods required for Mac OS X. The presence of native methods does not cause
- * any problems on other platforms.
- */
- private native static int ICStart(int[] instance, int signature);
- private native static int ICStop(int[] instance);
- private native static int ICLaunchURL(int instance, byte[] hint, byte[] data, int len,
- int[] selectionStart, int[] selectionEnd);
-}
diff --git a/src/main/java/es/uvigo/darwin/xprottest/util/OptimizationStrategyWrapper.java b/src/main/java/es/uvigo/darwin/xprottest/util/OptimizationStrategyWrapper.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/util/TextAreaAppender.java b/src/main/java/es/uvigo/darwin/xprottest/util/TextAreaAppender.java
old mode 100755
new mode 100644
diff --git a/src/main/java/es/uvigo/darwin/xprottest/util/TextAreaWriter.java b/src/main/java/es/uvigo/darwin/xprottest/util/TextAreaWriter.java
old mode 100755
new mode 100644
diff --git a/src/main/resources/CHANGELOG b/src/main/resources/CHANGELOG
index ebe85ab..93e1697 100644
--- a/src/main/resources/CHANGELOG
+++ b/src/main/resources/CHANGELOG
@@ -1,5 +1,5 @@
-----------------------------------------------------------------------------
-ProtTest 3 Change Log - 25/Oct/2015
+ProtTest 3 Change Log - 8/May/2016
Diego Darriba (ddarriba at udc.es)
Guillermo L. Taboada (taboada at udc.es)
@@ -11,6 +11,15 @@ David Posada (dposada at uvigo.es)
-----------------------------------------------------------------------------
+ProtTest 3.4.2 (8/May/2016)
+
+ * Enhancement : Removed dependency on Netbeans libraries
+
+ * Enhancement : Check for global binaries on PATH env variable
+
+ * Enhancement : Added 'prottest3' script for running both GUi and console
+ interfaces (GUI if the script is called with no args)
+
ProtTest 3.4.1 (25/Oct/2015)
* Enhancement : Removed dependency on WriterOutputStream class.
diff --git a/src/main/resources/COPYING b/src/main/resources/COPYING
old mode 100755
new mode 100644
diff --git a/src/main/resources/README b/src/main/resources/README
old mode 100755
new mode 100644
index 045a2a2..f7e74dc
--- a/src/main/resources/README
+++ b/src/main/resources/README
@@ -1,5 +1,5 @@
-----------------------------------------------------------------------------
-ProtTest 3 Readme - 25/Oct/2015
+ProtTest 3 Readme - 8/May/2016
Diego Darriba (ddarriba at udc.es)
Guillermo L. Taboada (taboada at udc.es)
@@ -45,17 +45,17 @@ TOC
Console version
-$ tar zvxf prottest-3.4.1-yyyymmdd.tar.gz
+$ tar zvxf prottest-3.4.2-yyyymmdd.tar.gz
(Linux/Unix/OS X)
$ export PROTTEST_HOME=$PWD/prottest3
(Windows)
$ set PROTTEST_HOME=$CWD\prottest3
$ cd $PROTTEST_HOME
-$ java -jar prottest-3.4.1.jar -i examples/COX2_PF0016/alignment -all-matrices -all-distributions -threads 2
+$ java -jar prottest-3.4.2.jar -i examples/COX2_PF0016/alignment -all-matrices -all-distributions -threads 2
Graphical version
-$ tar zvxf prottest-3.4.1-yyyymmdd.tar.gz
+$ tar zvxf prottest-3.4.2-yyyymmdd.tar.gz
(Linux/Unix/OS X)
$ export PROTTEST_HOME=$PWD/prottest3
(Windows)
@@ -99,13 +99,14 @@ $PROTTEST_HOME/
# some test alignments and trees
|
| filecluster8.conf.template # machines file template for 8 node cluster
- | machines # machines file for cluster execution
- | prottest.properties # ProtTest3 configuration file (always required)
- | prottest-3.4.1.jar # ProtTest3 package
- | README # this README file
- | COPYING # ProtTest3 licese
- | runProtTestHPC.sh # basic script for ProtTest3 cluster execution
- | runXProtTestHPC.sh # basic script for ProtTest3 graphical version
+ | machines # machines file for cluster execution
+ | prottest3 # script for running ProtTest console or graphical
+ | prottest.properties # ProtTest3 configuration file (always required)
+ | prottest-3.4.2.jar # ProtTest3 package
+ | README # this README file
+ | COPYING # ProtTest3 licese
+ | runProtTestHPC.sh # basic script for ProtTest3 cluster execution
+ | runXProtTestHPC.sh # basic script for ProtTest3 graphical version
- The ProtTest properties (prottest.properties) file must be located in the
ProtTest root directory. It has the execution preferences. Please refer to such
@@ -210,7 +211,10 @@ These are the parameters of the sequential execution:
Basic execution example:
$ cd $PROTTEST_HOME
- $ java -jar prottest-3.4.1.jar -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc 0.5
+
+ $ java -jar prottest-3.4.2.jar -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc 0.5
+ or
+ $ ./prottest3 -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc 0.5
-----------------------------------------------------------------------------
@@ -222,7 +226,7 @@ can use up to the number of cores in your machine and beyond. Following the basi
execution example, a recommended multithread execution in a quad-core machine will be:
$ cd $PROTTEST_HOME
- $ java -jar prottest-3.4.1.jar -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc 0.5 -threads 4
+ $ java -jar prottest-3.4.2.jar -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc 0.5 -threads 4
It is remarkable that the substitution models will not be computed in a specific
order, so the full output will be shown once all models have been computed.
@@ -288,7 +292,10 @@ of the application, so it will be the best choice for running ProtTest on
a local multicore machine.
$ cd $PROTTEST_HOME
+
$ ./runXProtTestHPC.sh
+or
+$ ./prottest3
-----------------------------------------------------------------------------
5. Frequently Asked Questions
@@ -296,7 +303,7 @@ $ ./runXProtTestHPC.sh
5.1. I got this error when running ProtTest 3
- ./phyml-prottest-linux: /lib/libc.so.6: version `GLIBC_2.7' not found
+ ./PhyML_3.0_linux32: /lib/libc.so.6: version `GLIBC_2.7' not found
---
diff --git a/src/main/resources/THIRDPARTYLICENSES b/src/main/resources/THIRDPARTYLICENSES
old mode 100755
new mode 100644
diff --git a/src/main/resources/bin/README b/src/main/resources/bin/README
new file mode 100644
index 0000000..3b8ba49
--- /dev/null
+++ b/src/main/resources/bin/README
@@ -0,0 +1,10 @@
+Standard installation:
+
+ Place PhyML binary here, named 'phyml'
+
+ For multi-platform jModelTest distribution use the following names:
+
+ PhyML_3.0_linux32
+ PhyML_3.0_linux64
+ PhyML_3.0_macOS_i386
+ PhyML_3.0_win32.exe
diff --git a/src/main/resources/examples/COX2_PF0016/alignment b/src/main/resources/examples/COX2_PF0016/alignment
old mode 100755
new mode 100644
diff --git a/src/main/resources/examples/COX2_PF0016/tree b/src/main/resources/examples/COX2_PF0016/tree
old mode 100755
new mode 100644
diff --git a/src/main/resources/examples/HIV1.2008.pol.nex b/src/main/resources/examples/HIV1.2008.pol.nex
old mode 100755
new mode 100644
diff --git a/src/main/resources/examples/Ribosomal_L5_PF00673/alignment b/src/main/resources/examples/Ribosomal_L5_PF00673/alignment
old mode 100755
new mode 100644
diff --git a/src/main/resources/examples/Ribosomal_L5_PF00673/tree b/src/main/resources/examples/Ribosomal_L5_PF00673/tree
old mode 100755
new mode 100644
diff --git a/src/main/resources/filecluster8.conf.template b/src/main/resources/filecluster8.conf.template
old mode 100755
new mode 100644
diff --git a/src/main/resources/icon.png b/src/main/resources/icon.png
new file mode 100755
index 0000000..72abc83
Binary files /dev/null and b/src/main/resources/icon.png differ
diff --git a/src/main/resources/machines b/src/main/resources/machines
old mode 100755
new mode 100644
diff --git a/src/main/resources/models/FLU b/src/main/resources/models/FLU
old mode 100755
new mode 100644
diff --git a/src/main/resources/prottest.properties b/src/main/resources/prottest.properties
old mode 100755
new mode 100644
diff --git a/src/main/resources/prottest3 b/src/main/resources/prottest3
new file mode 100755
index 0000000..b1784ac
--- /dev/null
+++ b/src/main/resources/prottest3
@@ -0,0 +1,9 @@
+#!/bin/sh
+if [ $# -eq 0 ]; then
+ # Run ProtTest GUI
+ ./runXProtTestHPC.sh
+else
+ # Run ProtTest console interface
+ jarfile=`find . -name "prottest-3.*.jar" | sort | tail -n 1`
+ java -jar $jarfile $*
+fi
diff --git a/src/main/resources/runProtTestHPC.sh b/src/main/resources/runProtTestHPC.sh
index 801cb69..5d7864a 100755
--- a/src/main/resources/runProtTestHPC.sh
+++ b/src/main/resources/runProtTestHPC.sh
@@ -1,4 +1,5 @@
export MPJ_HOME=$PWD/mpj
export NP=$1
shift
-$MPJ_HOME/bin/mpjrun.sh -dev niodev -wdir $PWD/ -np $NP -jar prottest-3.4.1.jar $*
+jarfile=`find . -name "prottest-3.*.jar" | sort | tail -n 1`
+$MPJ_HOME/bin/mpjrun.sh -dev niodev -wdir $PWD/ -np $NP -jar $jarfile $*
diff --git a/src/main/resources/runXProtTestHPC.bat b/src/main/resources/runXProtTestHPC.bat
index e1bd4bf..2c3f971 100755
--- a/src/main/resources/runXProtTestHPC.bat
+++ b/src/main/resources/runXProtTestHPC.bat
@@ -1 +1 @@
-java -cp prottest-3.4.jar es.uvigo.darwin.xprottest.XProtTestApp
+java -cp prottest-3.4.2.jar es.uvigo.darwin.xprottest.XProtTestApp
diff --git a/src/main/resources/runXProtTestHPC.sh b/src/main/resources/runXProtTestHPC.sh
index 63127e6..1bf9193 100755
--- a/src/main/resources/runXProtTestHPC.sh
+++ b/src/main/resources/runXProtTestHPC.sh
@@ -1 +1,2 @@
-java -cp prottest-3.4.1.jar es.uvigo.darwin.xprottest.XProtTestApp
+jarfile=`find . -name "prottest-3.*.jar" | sort | tail -n 1`
+java -cp $jarfile es.uvigo.darwin.xprottest.XProtTestApp
--
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