_inference_manager = i;
}
- InferenceManager getInferenceManager() {
+ public InferenceManager getInferenceManager() {
return _inference_manager;
}
package org.forester.archaeopteryx.tools;
import java.io.File;
-import java.io.IOException;
import org.forester.archaeopteryx.Configuration;
-import org.forester.util.ForesterUtil;
public final class InferenceManager {
- private final File _path_to_local_mafft;
- private final File _path_to_local_kalign;
- private final File _path_to_local_fastme;
- private final File _path_to_local_raxml;
- private final File _path_to_local_clustalo;
+ private final static String DEFAULT_PATHS[] = { "C:\\Program Files\\", "C:\\Program Files (x86)\\", "/bin/",
+ "/usr/local/bin/", "/usr/bin/" };
+ private final File _path_to_local_mafft;
+ private final File _path_to_local_kalign;
+ private final File _path_to_local_fastme;
+ private final File _path_to_local_raxml;
+ private final File _path_to_local_clustalo;
public static InferenceManager createInstance( final Configuration c ) {
return new InferenceManager( c.getpathToLocalMafft(),
return _path_to_local_clustalo;
}
- private final static File createLocalPath( final File path ) {
- if ( path == null ) {
- return null;
+ private final static File createLocalPath( final File path, final String name ) {
+ if ( ( path != null ) && path.canExecute() && !path.isDirectory() ) {
+ return path;
}
- try {
- if ( path.getCanonicalFile().canExecute() && !path.getCanonicalFile().isDirectory() ) {
- return new File( path.getCanonicalFile().toString() );
- }
+ File p1 = new File( name );
+ if ( p1.canExecute() && !p1.isDirectory() ) {
+ return p1;
}
- catch ( final IOException e ) {
- return null;
+ for( final String path_str : DEFAULT_PATHS ) {
+ try {
+ final File p2 = new File( path_str + name );
+ if ( p2.canExecute() && !p2.isDirectory() ) {
+ return p2;
+ }
+ final File p3 = new File( path_str + name + ".exe" );
+ if ( p3.canExecute() && !p3.isDirectory() ) {
+ return p3;
+ }
+ final File p4 = new File( path_str + name + ".bat" );
+ if ( p4.canExecute() && !p4.isDirectory() ) {
+ return p4;
+ }
+ }
+ catch ( final Exception e ) {
+ }
}
return null;
}
final File path_to_local_fastme,
final File path_to_local_raxml,
final File path_to_local_clustalo ) {
- _path_to_local_mafft = createLocalPath( path_to_local_mafft ) != null ? createLocalPath( path_to_local_mafft )
- : createLocalPath( new File( "mafft" ) );
- _path_to_local_kalign = createLocalPath( path_to_local_kalign ) != null ? createLocalPath( path_to_local_kalign )
- : createLocalPath( new File( "kalign" ) );
- _path_to_local_fastme = createLocalPath( path_to_local_fastme ) != null ? createLocalPath( path_to_local_fastme )
- : createLocalPath( new File( "fastme" ) );
- _path_to_local_raxml = createLocalPath( path_to_local_raxml ) != null ? createLocalPath( path_to_local_raxml )
- : createLocalPath( new File( "raxml" ) );
- _path_to_local_clustalo = createLocalPath( path_to_local_clustalo ) != null ? createLocalPath( path_to_local_clustalo )
- : createLocalPath( new File( ForesterUtil.isWindowns() ? "clustalo.exe" : "clustalo" ) );
+ _path_to_local_mafft = createLocalPath( path_to_local_mafft, "mafft" );
+ _path_to_local_kalign = createLocalPath( path_to_local_kalign, "kalign" );
+ _path_to_local_fastme = createLocalPath( path_to_local_fastme, "fastme" );
+ _path_to_local_raxml = createLocalPath( path_to_local_raxml, "raxml" );
+ _path_to_local_clustalo = createLocalPath( path_to_local_clustalo, "clustalo" );
}
}
import org.forester.io.writers.SequenceWriter;
import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
import org.forester.msa.BasicMsa;
+import org.forester.msa.ClustalOmega;
import org.forester.msa.Mafft;
import org.forester.msa.Msa;
import org.forester.msa.MsaInferrer;
private Msa runMAFFT( final File input_seqs, final List<String> opts ) throws IOException, InterruptedException {
Msa msa = null;
- final MsaInferrer mafft = Mafft.createInstance();
+ final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft().getCanonicalPath());
try {
msa = mafft.infer( input_seqs, opts );
}
}
return msa;
}
+
+ private Msa runClustalOmega( final File input_seqs, final List<String> opts ) throws IOException, InterruptedException {
+ Msa msa = null;
+ final MsaInferrer clustalo = ClustalOmega.createInstance(_mf.getInferenceManager().getPathToLocalClustalo().getCanonicalPath());
+ try {
+ msa = clustalo.infer( input_seqs, opts );
+ }
+ catch ( final IOException e ) {
+ System.out.println( clustalo.getErrorDescription() );
+ }
+ return msa;
+ }
private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
--- /dev/null
+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// Copyright (C) 2010 Christian M Zmasek
+// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library 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
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.msa;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.io.parsers.FastaParser;
+import org.forester.util.SystemCommandExecutor;
+
+public final class ClustalOmega implements MsaInferrer {
+
+ private final static String DEFAULT_PARAMETERS = "";
+ private String _error;
+ private int _exit_code;
+ private final String _path_to_prg;
+
+
+
+ public static MsaInferrer createInstance( final String path_to_prg ) throws IOException {
+ return new ClustalOmega( path_to_prg );
+ }
+
+
+
+ private ClustalOmega( final String path_to_prg ) throws IOException {
+ if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
+ throw new IOException( "cannot execute MAFFT with \"" + path_to_prg + "\"" );
+ }
+ _path_to_prg = new String( path_to_prg );
+ init();
+ }
+
+ public static String getDefaultParameters() {
+ return DEFAULT_PARAMETERS;
+ }
+
+ @Override
+ public Object clone() {
+ throw new NoSuchMethodError();
+ }
+
+ @Override
+ public String getErrorDescription() {
+ return _error;
+ }
+
+ @Override
+ public int getExitCode() {
+ return _exit_code;
+ }
+
+ @Override
+ public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
+ init();
+ final List<String> my_opts = new ArrayList<String>();
+ my_opts.add( _path_to_prg );
+ for( int i = 0; i < opts.size(); i++ ) {
+ my_opts.add( opts.get( i ) );
+ }
+ my_opts.add( path_to_input_seqs.getAbsolutePath() );
+ final SystemCommandExecutor command_executor = new SystemCommandExecutor( my_opts );
+ final int _exit_code = command_executor.executeCommand();
+ final StringBuilder stderr = command_executor.getStandardErrorFromCommand();
+ _error = stderr.toString();
+ if ( _exit_code != 0 ) {
+ throw new IOException( "Clustal Omega program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts
+ + "\nError:\n" + stderr );
+ }
+ final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
+ if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {
+ throw new IOException( "Clustal Omega program did not produce any output\nCommand:\n" + my_opts + "\nError:\n"
+ + stderr );
+ }
+ final Msa msa = FastaParser.parseMsa( stdout.toString() );
+ return msa;
+ }
+
+ private void init() {
+ _error = null;
+ _exit_code = -100;
+ }
+}
private int _exit_code;
private final String _path_to_prg;
- public static MsaInferrer createInstance() throws IOException {
- return createInstance( getPathToCmd() );
- }
+
public static MsaInferrer createInstance( final String path_to_prg ) throws IOException {
return new Mafft( path_to_prg );
}
- private static String getPathToCmd() {
- //TODO this needs to come from config file!!
- //FIXME ..
- //should not be in this class!
- String path = "";
- final String os = ForesterUtil.OS_NAME.toLowerCase();
- if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
- path = "/usr/local/bin/mafft";
- }
- else if ( os.indexOf( "win" ) >= 0 ) {
- path = "C:\\Program Files\\mafft-win\\mafft.bat";
- }
- else {
- path = "/home/czmasek/bin/mafft";
- }
- return path;
- }
-
- public static boolean isInstalled() {
- return SystemCommandExecutor.isExecuteableFile( new File( getPathToCmd() ) );
- }
+
private Mafft( final String path_to_prg ) throws IOException {
if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
opts.add( "1000" );
opts.add( "--localpair" );
opts.add( "--quiet" );
+
+
+ String path = "";
+ final String os = ForesterUtil.OS_NAME.toLowerCase();
+ if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
+ path = "/usr/local/bin/mafft";
+ }
+ else if ( os.indexOf( "win" ) >= 0 ) {
+ path = "C:\\Program Files\\mafft-win\\mafft.bat";
+ }
+ else {
+ path = "/home/czmasek/bin/mafft";
+ }
+
Msa msa = null;
- final MsaInferrer mafft = Mafft.createInstance();
+ final MsaInferrer mafft = Mafft.createInstance( path );
msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts );
if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) {
return false;
git://source.jalview.org / jalview.git / commitdiff