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.List;
32 import org.forester.sequence.Sequence;
33 import org.forester.util.SystemCommandExecutor;
35 public abstract class MsaInferrer {
37 public abstract String getErrorDescription();
39 public abstract int getExitCode();
41 public static boolean isInstalled( final String path_to_prg ) {
42 return SystemCommandExecutor.isExecuteableFile( new File( path_to_prg ) );
46 public Object clone() {
47 throw new NoSuchMethodError();
50 public abstract Msa infer( File path_to_input_seqs, List<String> opts ) throws IOException, InterruptedException;
52 public abstract Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException,