[med-svn] [prottest] 01/08: Imported Upstream version 3.4.1+dfsg
Andreas Tille
tille at debian.org
Mon Nov 30 21:14:12 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository prottest.
commit d4f6421c5f36b67d21bd35efe79b28cb8682107e
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 26 08:08:56 2015 +0100
Imported Upstream version 3.4.1+dfsg
---
README.md | 49 +++++++++
buildconf/project.properties | 3 +-
.../java/es/uvigo/darwin/prottest/ProtTest.java | 2 +-
.../global/options/ApplicationOptions.java | 33 ++++---
.../java/es/uvigo/darwin/prottest/model/Model.java | 2 +-
.../darwin/prottest/util/WriterOutputStream.java | 87 ----------------
.../argumentparser/ProtTestArgumentParser.java | 2 +-
.../prottest/util/factory/ProtTestFactory.java | 4 +-
.../prottest/util/logging/ProtTestLogger.java | 109 ++++++++++++++++++++-
.../darwin/xprottest/results/ErrorLogView.java | 61 +++++++++++-
src/main/resources/CHANGELOG | 15 ++-
src/main/resources/README | 16 +--
src/main/resources/prottest.properties | 2 +-
src/main/resources/runProtTestHPC.sh | 2 +-
src/main/resources/runXProtTestHPC.sh | 2 +-
15 files changed, 263 insertions(+), 126 deletions(-)
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..399ffcc
--- /dev/null
+++ b/README.md
@@ -0,0 +1,49 @@
+# prottest3
+
+ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance(Posada [...]
+
+ProtTest is written in Java and uses the program PhyML (Guindon and Gascuel, 2003) for the maximum likelihood (ML) estimation of phylogenetic trees and model parameters. The current version of ProtTest (3.2) includes 15 different rate matrices that result in 120 different models when we consider rate variation among sites (+I: invariable sites; +G: gamma-distributed rates) and the observed amino acid frequencies (+F).
+
+--------
+Citation
+--------
+
+ Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27:1164-1165, 2011
+
+In addition, given that ProtTest uses Phyml intensively, we encourage users to cite this program as well when using ProtTest:
+
+ 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.
+
+--------
+Download
+--------
+
+New distributions of ProtTest will be hosted in google drive: ProtTest3 Downloads
+https://drive.google.com/folderview?id=0ByrkKOPtF_n_dVBBbDVBOEM5b1U
+
+--------
+News!
+--------
+
+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.
+ Removed dependency on WriterOutputStream class.
+
+23/01/2014 - ProtTest 3.4 is out. It includes the following updates:
+
+ Fixed problem while trying to execute ProtTest from outside its home directory.
+ Modified log files pattern to prottest3_YYYYMMDDhhmmss_randstring.log
+ Added configuration property for disable logging.
+ Added configuration property for using a system-wide installed PhyML.
+
+16/07/2013 - ProtTest 3.3 is out. This includes PhyML real-time logging and removes the sample size selection option.
+
+03/01/2013 - ProtTest 3.2.1 is out. A bug computing alpha and pInv parameters was fixed.
+Disclaimer
+
+This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have rec [...]
diff --git a/buildconf/project.properties b/buildconf/project.properties
index 1434886..1785c89 100755
--- a/buildconf/project.properties
+++ b/buildconf/project.properties
@@ -1,3 +1,4 @@
+application.version=3.4.1
application.homepage=http://darwin.uvigo.es
application.title=ProtTest
application.vendor=Diego Darriba
@@ -16,7 +17,7 @@ debug.test.classpath=\
${run.test.classpath}
# This directory is removed when the project is cleaned:
dist.dir=dist
-dist.jar=${dist.dir}/prottest-3.4.jar
+dist.jar=${dist.dir}/prottest-${application.version}.jar
dist.javadoc.dir=${dist.dir}/javadoc
excludes=
file.reference.AbsoluteLayout.jar=lib/AbsoluteLayout.jar
diff --git a/src/main/java/es/uvigo/darwin/prottest/ProtTest.java b/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
index 0077f8b..52a3d72 100755
--- a/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
+++ b/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
@@ -64,7 +64,7 @@ import pal.tree.Tree;
public class ProtTest {
/** The Constant versionNumber. */
- public static final String versionNumber = "3.4";
+ public static final String versionNumber = "3.4.1";
/** The Constant versionDate. */
public static final String versionDate = "23th January 2014";
/** The MPJ rank of the process. It is only useful if MPJ is running.*/
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
index b784f76..f4483e9 100755
--- a/src/main/java/es/uvigo/darwin/prottest/global/options/ApplicationOptions.java
+++ b/src/main/java/es/uvigo/darwin/prottest/global/options/ApplicationOptions.java
@@ -17,15 +17,33 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package es.uvigo.darwin.prottest.global.options;
-import static es.uvigo.darwin.prottest.global.AminoAcidApplicationGlobals.*;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_COMPARE_ALL;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_DEBUG;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_DISPLAY_ASCII_TREE;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_DISPLAY_CONSENSUS_TREE;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.DEFAULT_DISPLAY_NEWICK_TREE;
+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_NAMES;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.OPTIMIZE_USER;
+import static es.uvigo.darwin.prottest.global.ProtTestConstants.TREE_SEARCH_NNI;
+import static es.uvigo.darwin.prottest.util.logging.ProtTestLogger.info;
+import static es.uvigo.darwin.prottest.util.logging.ProtTestLogger.infoln;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.logging.Level;
import pal.alignment.Alignment;
import pal.tree.Tree;
+import es.uvigo.darwin.prottest.ProtTest;
import es.uvigo.darwin.prottest.model.Model;
import es.uvigo.darwin.prottest.util.ProtTestAlignment;
import es.uvigo.darwin.prottest.util.argumentparser.ProtTestArgumentParser;
@@ -36,13 +54,6 @@ import es.uvigo.darwin.prottest.util.factory.ProtTestFactory;
import es.uvigo.darwin.prottest.util.fileio.AlignmentReader;
import es.uvigo.darwin.prottest.util.logging.ProtTestLogger;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.logging.Level;
-import static es.uvigo.darwin.prottest.util.logging.ProtTestLogger.*;
-
/**
* The ProtTest application options models the common global options for the
* application execution. It is a singleton class which gathers all
@@ -687,7 +698,7 @@ public class ApplicationOptions {
println(" - Sequential version: ");
println(" java -jar prottest-2.1.jar -i alignm_file [OPTIONS]");
println(" - Parallel version: ");
- println(" mpjrun.sh -wdir $PWD/ -np [NUM_PROCS] -jar ModelTest-2.1.jar -i alignm_file [OPTIONS]");
+ println(" mpjrun.sh -wdir $PWD/ -np [NUM_PROCS] -jar prottest-"+ProtTest.versionNumber+".jar -i alignm_file [OPTIONS]");
println("OPTIONS:");
println(" -i alignment_filename");
println(" Alignment input file (required)");
@@ -757,9 +768,9 @@ public class ApplicationOptions {
println("-------------------------------------------------------------------------------------------------");
println("Example: ");
println("- Sequential version:");
- println(" java -jar ModelTest-2.1.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 alignm_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 ModelTest-2.1.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 alignm_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5");
}
public void reportModelOptimization() {
diff --git a/src/main/java/es/uvigo/darwin/prottest/model/Model.java b/src/main/java/es/uvigo/darwin/prottest/model/Model.java
index f7158f1..03d87b5 100755
--- a/src/main/java/es/uvigo/darwin/prottest/model/Model.java
+++ b/src/main/java/es/uvigo/darwin/prottest/model/Model.java
@@ -263,7 +263,7 @@ public abstract class Model implements Serializable {
numOfTransCategories = 1;
break;
case DISTRIBUTION_INVARIABLE:
- numOfTransCategories = 2;
+ numOfTransCategories = 1;
break;
case DISTRIBUTION_GAMMA:
numOfTransCategories = ncat;
diff --git a/src/main/java/es/uvigo/darwin/prottest/util/WriterOutputStream.java b/src/main/java/es/uvigo/darwin/prottest/util/WriterOutputStream.java
deleted file mode 100755
index 4e1e4e9..0000000
--- a/src/main/java/es/uvigo/darwin/prottest/util/WriterOutputStream.java
+++ /dev/null
@@ -1,87 +0,0 @@
-// ========================================================================
-// Copyright (c) 1999 Mort Bay Consulting (Australia) Pty. Ltd.
-// $Id: WriterOutputStream.java,v 1.1 2003/02/13 22:39:19 mpowers Exp $
-// ========================================================================
-
-package es.uvigo.darwin.prottest.util;
-
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.Writer;
-
-
-/* ------------------------------------------------------------ */
-/** Wrap a Writer as an OutputStream.
- * When all you have is a Writer and only an OutputStream will do.
- * Try not to use this as it indicates that your design is a dogs
- * breakfast (JSP made me write it).
- * @version 1.0 Tue Feb 12 2002
- * @author Greg Wilkins (gregw)
- */
-public class WriterOutputStream extends OutputStream
-{
- protected Writer _writer;
- protected String _encoding;
- private byte[] _buf=new byte[1];
-
- /* ------------------------------------------------------------ */
- public WriterOutputStream(Writer writer, String encoding)
- {
- _writer=writer;
- _encoding=encoding;
- }
-
- /* ------------------------------------------------------------ */
- public WriterOutputStream(Writer writer)
- {
- _writer=writer;
- }
-
- /* ------------------------------------------------------------ */
- @Override
- public void close()
- throws IOException
- {
- _writer.close();
- _writer=null;
- _encoding=null;
- }
-
- /* ------------------------------------------------------------ */
- @Override
- public void flush()
- throws IOException
- {
- _writer.flush();
- }
-
- /* ------------------------------------------------------------ */
- @Override
- public void write(byte[] b)
- throws IOException
- {
- if (_encoding==null)
- _writer.write(new String(b));
- else
- _writer.write(new String(b,_encoding));
- }
-
- /* ------------------------------------------------------------ */
- @Override
- public void write(byte[] b, int off, int len)
- throws IOException
- {
- if (_encoding==null)
- _writer.write(new String(b,off,len));
- else
- _writer.write(new String(b,off,len,_encoding));
- }
-
- /* ------------------------------------------------------------ */
- public synchronized void write(int b)
- throws IOException
- {
- _buf[0]=(byte)b;
- write(_buf);
- }
-}
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
index 8da7836..36f736d 100755
--- a/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/ProtTestArgumentParser.java
+++ b/src/main/java/es/uvigo/darwin/prottest/util/argumentparser/ProtTestArgumentParser.java
@@ -29,7 +29,7 @@ import java.util.Properties;
import es.uvigo.darwin.prottest.global.options.ApplicationOptions;
/**
- * The Class ModelTestArgumentParser.
+ * The Class ProtTestArgumentParser.
*/
public abstract class ProtTestArgumentParser
implements ProtTestConsoleParameters {
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
index d784a98..352a05c 100755
--- a/src/main/java/es/uvigo/darwin/prottest/util/factory/ProtTestFactory.java
+++ b/src/main/java/es/uvigo/darwin/prottest/util/factory/ProtTestFactory.java
@@ -115,7 +115,7 @@ public class ProtTestFactory {
instance = new ProtTestFactory(sort);
return args;
} else {
- throw new ProtTestInternalException("ModelTestFactory was already initialized");
+ throw new ProtTestInternalException("ProtTestFactory was already initialized");
}
}
@@ -128,7 +128,7 @@ public class ProtTestFactory {
if (instance == null) {
initialize(new String[0]);
}
-// throw new ProtTestInternalException("ModelTestFactory should be initialized");
+// throw new ProtTestInternalException("ProtTestFactory should be initialized");
return instance;
}
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
index 1d12961..9af9800 100755
--- a/src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogger.java
+++ b/src/main/java/es/uvigo/darwin/prottest/util/logging/ProtTestLogger.java
@@ -17,8 +17,9 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package es.uvigo.darwin.prottest.util.logging;
-import es.uvigo.darwin.prottest.util.WriterOutputStream;
import es.uvigo.darwin.prottest.util.exception.ProtTestInternalException;
+
+import java.io.IOException;
import java.io.OutputStream;
import java.io.Writer;
import java.util.ArrayList;
@@ -29,6 +30,7 @@ import java.util.logging.Level;
import java.util.logging.LogRecord;
import java.util.logging.StreamHandler;
+ at SuppressWarnings("rawtypes")
public class ProtTestLogger {
public static final String DEFAULT_LOGGER_NAME = "default";
@@ -135,22 +137,119 @@ public class ProtTestLogger {
return addHandler(out, DEFAULT_LEVEL);
}
- public Handler addHandler(Writer out, Level level) {
+ public Handler addHandler(final Writer out, Level level) {
if (out == null) {
throw new NullPointerException();
}
- Handler handler = new StreamHandler(new WriterOutputStream(out),
+ Handler handler = new StreamHandler(
+ new OutputStream()
+ {
+ protected Writer _writer = out;
+ protected String _encoding;
+ private byte[] _buf=new byte[1];
+
+ @Override
+ public void close()
+ throws IOException
+ {
+ _writer.close();
+ _writer=null;
+ _encoding=null;
+ }
+
+ @Override
+ public void flush()
+ throws IOException
+ {
+ _writer.flush();
+ }
+
+ @Override
+ public void write(byte[] b)
+ throws IOException
+ {
+ if (_encoding==null)
+ _writer.write(new String(b));
+ else
+ _writer.write(new String(b,_encoding));
+ }
+
+ @Override
+ public void write(byte[] b, int off, int len)
+ throws IOException
+ {
+ if (_encoding==null)
+ _writer.write(new String(b,off,len));
+ else
+ _writer.write(new String(b,off,len,_encoding));
+ }
+
+ public synchronized void write(int b)
+ throws IOException
+ {
+ _buf[0]=(byte)b;
+ write(_buf);
+ }
+ },
new ProtTestLogFormatter());
handler.setLevel(level);
this.handlers.add(handler);
return handler;
}
- public Handler addLowLevelHandler(Writer out) {
+ public Handler addLowLevelHandler(final Writer out) {
if (out == null) {
throw new NullPointerException();
}
- Handler handler = new StreamHandler(new WriterOutputStream(out),
+ Handler handler = new StreamHandler(new OutputStream()
+ {
+ protected Writer _writer = out;
+ protected String _encoding;
+ private byte[] _buf=new byte[1];
+
+ @Override
+ public void close()
+ throws IOException
+ {
+ _writer.close();
+ _writer=null;
+ _encoding=null;
+ }
+
+ @Override
+ public void flush()
+ throws IOException
+ {
+ _writer.flush();
+ }
+
+ @Override
+ public void write(byte[] b)
+ throws IOException
+ {
+ if (_encoding==null)
+ _writer.write(new String(b));
+ else
+ _writer.write(new String(b,_encoding));
+ }
+
+ @Override
+ public void write(byte[] b, int off, int len)
+ throws IOException
+ {
+ if (_encoding==null)
+ _writer.write(new String(b,off,len));
+ else
+ _writer.write(new String(b,off,len,_encoding));
+ }
+
+ public synchronized void write(int b)
+ throws IOException
+ {
+ _buf[0]=(byte)b;
+ write(_buf);
+ }
+ },
new ProtTestLogFormatter());
handler.setLevel(Level.ALL);
lowLevelHandler = handler;
diff --git a/src/main/java/es/uvigo/darwin/xprottest/results/ErrorLogView.java b/src/main/java/es/uvigo/darwin/xprottest/results/ErrorLogView.java
index c661541..92039ac 100755
--- a/src/main/java/es/uvigo/darwin/xprottest/results/ErrorLogView.java
+++ b/src/main/java/es/uvigo/darwin/xprottest/results/ErrorLogView.java
@@ -17,10 +17,15 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package es.uvigo.darwin.xprottest.results;
-import es.uvigo.darwin.prottest.util.WriterOutputStream;
import es.uvigo.darwin.prottest.util.logging.ProtTestLogFormatter;
+
+import java.io.IOException;
+import java.io.OutputStream;
import java.io.PrintWriter;
+import java.io.Writer;
+
import es.uvigo.darwin.xprottest.util.TextAreaAppender;
+
import java.util.logging.Filter;
import java.util.logging.Handler;
import java.util.logging.Level;
@@ -33,7 +38,9 @@ import java.util.logging.StreamHandler;
*/
public class ErrorLogView extends javax.swing.JFrame {
- private PrintWriter errorWriter;
+ private static final long serialVersionUID = -2022588731545645833L;
+
+ private PrintWriter errorWriter;
private Handler logHandler;
public Handler getLogHandler() {
@@ -44,7 +51,55 @@ public class ErrorLogView extends javax.swing.JFrame {
public ErrorLogView() {
initComponents();
errorWriter = new PrintWriter(new TextAreaAppender(errorTextArea));
- logHandler = new StreamHandler(new WriterOutputStream(errorWriter),
+ logHandler = new StreamHandler(new OutputStream()
+ {
+ protected Writer _writer = errorWriter;
+ protected String _encoding;
+ private byte[] _buf=new byte[1];
+
+ @Override
+ public void close()
+ throws IOException
+ {
+ _writer.close();
+ _writer=null;
+ _encoding=null;
+ }
+
+ @Override
+ public void flush()
+ throws IOException
+ {
+ _writer.flush();
+ }
+
+ @Override
+ public void write(byte[] b)
+ throws IOException
+ {
+ if (_encoding==null)
+ _writer.write(new String(b));
+ else
+ _writer.write(new String(b,_encoding));
+ }
+
+ @Override
+ public void write(byte[] b, int off, int len)
+ throws IOException
+ {
+ if (_encoding==null)
+ _writer.write(new String(b,off,len));
+ else
+ _writer.write(new String(b,off,len,_encoding));
+ }
+
+ public synchronized void write(int b)
+ throws IOException
+ {
+ _buf[0]=(byte)b;
+ write(_buf);
+ }
+ },
new ProtTestLogFormatter());
logHandler.setFilter(new Filter(){
diff --git a/src/main/resources/CHANGELOG b/src/main/resources/CHANGELOG
index 638c215..ebe85ab 100644
--- a/src/main/resources/CHANGELOG
+++ b/src/main/resources/CHANGELOG
@@ -1,5 +1,5 @@
-----------------------------------------------------------------------------
-ProtTest 3 Change Log - 23/Jan/2014
+ProtTest 3 Change Log - 25/Oct/2015
Diego Darriba (ddarriba at udc.es)
Guillermo L. Taboada (taboada at udc.es)
@@ -11,12 +11,21 @@ David Posada (dposada at uvigo.es)
-----------------------------------------------------------------------------
+ProtTest 3.4.1 (25/Oct/2015)
+
+ * Enhancement : Removed dependency on WriterOutputStream class.
+
+ * Fix : Fixed bug with number of categories which might induce an error with
+ certain PhyML versions.
+
ProtTest 3.4 (23/Jan/2014)
- * Fix : Fixed problem while trying to execute ProtTest from outside its home directory.
+ * Fix : Fixed problem while trying to execute ProtTest from outside its home
+ directory.
* Enhancement : Added configuration property for disable logging.
- Added configuration property for using a system-wide installed PhyML.
+ Added configuration property for using a system-wide installed
+ PhyML.
ProtTest 3.3 (16/Jul/2013)
diff --git a/src/main/resources/README b/src/main/resources/README
index 3368595..045a2a2 100755
--- a/src/main/resources/README
+++ b/src/main/resources/README
@@ -1,5 +1,5 @@
-----------------------------------------------------------------------------
-ProtTest 3 Readme - 23/Jan/2014
+ProtTest 3 Readme - 25/Oct/2015
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-yyyymmdd.tar.gz
+$ tar zvxf prottest-3.4.1-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.jar -i examples/COX2_PF0016/alignment -all-matrices -all-distributions -threads 2
+$ java -jar prottest-3.4.1.jar -i examples/COX2_PF0016/alignment -all-matrices -all-distributions -threads 2
Graphical version
-$ tar zvxf prottest-3.4-yyyymmdd.tar.gz
+$ tar zvxf prottest-3.4.1-yyyymmdd.tar.gz
(Linux/Unix/OS X)
$ export PROTTEST_HOME=$PWD/prottest3
(Windows)
@@ -101,7 +101,7 @@ $PROTTEST_HOME/
| 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.jar # ProtTest3 package
+ | prottest-3.4.1.jar # ProtTest3 package
| README # this README file
| COPYING # ProtTest3 licese
| runProtTestHPC.sh # basic script for ProtTest3 cluster execution
@@ -210,7 +210,7 @@ These are the parameters of the sequential execution:
Basic execution example:
$ cd $PROTTEST_HOME
- $ java -jar prottest-3.4.jar -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc
+ $ java -jar prottest-3.4.1.jar -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc 0.5
-----------------------------------------------------------------------------
@@ -222,7 +222,7 @@ 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.jar -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc -threads 4
+ $ java -jar prottest-3.4.1.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.
@@ -265,7 +265,7 @@ bash script: 'runProtTestHPC.sh'
The basic syntax is:
./runProtTestHPC.sh $NUMBER_OF_PROCESSORS $APPLICATION_PARAMETERS
-$ ./runProtTestHPC.sh 2 -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc
+$ ./runProtTestHPC.sh 2 -i examples/COX2_PF0016/alignment -all-distributions -F -AIC -BIC -tc 0.5
-----------------------------------------------------------------------------
4.2.4 Cluster hybrid execution
diff --git a/src/main/resources/prottest.properties b/src/main/resources/prottest.properties
index 2571159..1d154af 100755
--- a/src/main/resources/prottest.properties
+++ b/src/main/resources/prottest.properties
@@ -17,7 +17,7 @@ analyzer=phyml
# If an usable version of PhyML is installed system-wide
# (for example, from the Ubuntu/Debian repositories),
# the user can set 'global-phyml-exe' property to true
-# and jModelTest will use the global binary instead of
+# and ProtTest will use the global binary instead of
# local ones.
# ------------------------------------------------------------------
global-phyml-exe = false
diff --git a/src/main/resources/runProtTestHPC.sh b/src/main/resources/runProtTestHPC.sh
index 5d08a4a..801cb69 100755
--- a/src/main/resources/runProtTestHPC.sh
+++ b/src/main/resources/runProtTestHPC.sh
@@ -1,4 +1,4 @@
export MPJ_HOME=$PWD/mpj
export NP=$1
shift
-$MPJ_HOME/bin/mpjrun.sh -dev niodev -wdir $PWD/ -np $NP -jar prottest-3.4.jar $*
+$MPJ_HOME/bin/mpjrun.sh -dev niodev -wdir $PWD/ -np $NP -jar prottest-3.4.1.jar $*
diff --git a/src/main/resources/runXProtTestHPC.sh b/src/main/resources/runXProtTestHPC.sh
index e1bd4bf..63127e6 100755
--- a/src/main/resources/runXProtTestHPC.sh
+++ b/src/main/resources/runXProtTestHPC.sh
@@ -1 +1 @@
-java -cp prottest-3.4.jar es.uvigo.darwin.xprottest.XProtTestApp
+java -cp prottest-3.4.1.jar es.uvigo.darwin.xprottest.XProtTestApp
--
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