2 // forester -- software libraries and applications
3 // for genomics and evolutionary biology research.
5 // Copyright (C) 2010 Christian M Zmasek
6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.msa;
29 import java.io.IOException;
30 import java.util.ArrayList;
31 import java.util.List;
33 import org.forester.io.parsers.FastaParser;
34 import org.forester.util.ForesterUtil;
35 import org.forester.util.SystemCommandExecutor;
37 public final class Mafft implements MsaInferrer {
39 private final static String DEFAULT_PARAMETERS = "--maxiterate 1000 --localpair";
40 private String _error;
41 private int _exit_code;
42 private final String _path_to_prg;
44 public static MsaInferrer createInstance( final String path_to_prg ) {
45 return new Mafft( path_to_prg );
48 private static String getPathToCmd() {
49 //TODO this needs to come from env variable, etc.
51 final String os = ForesterUtil.OS_NAME.toLowerCase();
52 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
53 path = "/usr/local/bin/mafft";
55 else if ( os.indexOf( "win" ) >= 0 ) {
56 path = "C:\\Program Files\\mafft-win\\mafft.bat";
59 path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-6.832-without-extensions/scripts/mafft";
64 public static boolean isInstalled() {
65 return SystemCommandExecutor.isExecuteableFile( new File( getPathToCmd() ) );
68 public static MsaInferrer createInstance() {
69 return createInstance( getPathToCmd() );
72 private Mafft( final String path_to_prg ) {
73 if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
74 throw new IllegalArgumentException( "cannot execute MAFFT via [" + path_to_prg + "]" );
76 _path_to_prg = new String( path_to_prg );
80 public static String getDefaultParameters() {
81 return DEFAULT_PARAMETERS;
85 public Object clone() {
86 throw new NoSuchMethodError();
90 public String getErrorDescription() {
95 public int getExitCode() {
100 public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
102 final List<String> my_opts = new ArrayList<String>();
103 my_opts.add( _path_to_prg );
104 for( int i = 0; i < opts.size(); i++ ) {
105 my_opts.add( opts.get( i ) );
107 my_opts.add( path_to_input_seqs.getAbsolutePath() );
108 final SystemCommandExecutor commandExecutor = new SystemCommandExecutor( my_opts );
109 final int _exit_code = commandExecutor.executeCommand();
110 if ( _exit_code != 0 ) {
111 throw new IOException( "MAFFT failed, exit code: " + _exit_code );
113 final StringBuilder stdout = commandExecutor.getStandardOutputFromCommand();
114 final StringBuilder stderr = commandExecutor.getStandardErrorFromCommand();
115 System.out.println( stdout );
116 System.out.println();
117 System.out.println( stderr );
118 _error = stderr.toString();
119 final Msa msa = FastaParser.parseMsa( stdout.toString() );
123 private void init() {