2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.msa;
28 import java.io.IOException;
29 import java.io.Writer;
30 import java.util.List;
32 import org.forester.sequence.Sequence;
33 import org.forester.sequence.Sequence.TYPE;
35 public interface Msa {
37 public static enum MSA_FORMAT {
41 public String getIdentifier( int row );
43 public void setIdentifier( int row, String identifier );
45 public int getLength();
47 public int getNumberOfSequences();
49 public char getResidueAt( int row, int col );
51 public boolean isGapAt( int row, int col );
53 public List<Character> getColumnAt( int col );
55 public Sequence getSequence( final String id );
57 public Sequence getSequence( final int row );
59 public List<Sequence> asSequenceList();
61 public StringBuffer getSequenceAsString( int row );
63 public abstract TYPE getType();
65 public void setResidueAt( final int row, final int col, final char residue );
67 public void write( Writer w, MSA_FORMAT format ) throws IOException;