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() {
45 return createInstance( getPathToCmd() );
48 public static MsaInferrer createInstance( final String path_to_prg ) {
49 return new Mafft( path_to_prg );
52 private static String getPathToCmd() {
53 //TODO this needs to come from env variable, etc.
55 //should not be in this class!
57 final String os = ForesterUtil.OS_NAME.toLowerCase();
58 if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) {
59 path = "/usr/local/bin/mafft";
61 else if ( os.indexOf( "win" ) >= 0 ) {
62 path = "C:\\Program Files\\mafft-win\\mafft.bat";
65 path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-6.864-without-extensions/scripts/mafft";
70 public static boolean isInstalled() {
71 return SystemCommandExecutor.isExecuteableFile( new File( getPathToCmd() ) );
74 private Mafft( final String path_to_prg ) {
75 if ( !SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) ) ) {
76 throw new IllegalArgumentException( "cannot execute MAFFT via [" + path_to_prg + "]" );
78 _path_to_prg = new String( path_to_prg );
82 public static String getDefaultParameters() {
83 return DEFAULT_PARAMETERS;
87 public Object clone() {
88 throw new NoSuchMethodError();
92 public String getErrorDescription() {
97 public int getExitCode() {
102 public Msa infer( final File path_to_input_seqs, final List<String> opts ) throws IOException, InterruptedException {
104 final List<String> my_opts = new ArrayList<String>();
105 my_opts.add( _path_to_prg );
106 for( int i = 0; i < opts.size(); i++ ) {
107 my_opts.add( opts.get( i ) );
109 my_opts.add( path_to_input_seqs.getAbsolutePath() );
110 final SystemCommandExecutor command_executor = new SystemCommandExecutor( my_opts );
111 final int _exit_code = command_executor.executeCommand();
112 if ( _exit_code != 0 ) {
113 throw new IOException( "MAFFT program failed, exit code: " + _exit_code + ", command: " + my_opts );
115 final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
116 final StringBuilder stderr = command_executor.getStandardErrorFromCommand();
117 if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {
118 throw new IOException( "MAFFT program did not produce any output, command: " + my_opts );
120 _error = stderr.toString();
121 final Msa msa = FastaParser.parseMsa( stdout.toString() );
125 private void init() {