// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// 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
// 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
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.msa;
import java.io.IOException;
import java.io.Writer;
+import java.util.List;
-import org.forester.sequence.Sequence.TYPE;
+import org.forester.sequence.MolecularSequence;
+import org.forester.sequence.MolecularSequence.TYPE;
public interface Msa {
- public Object getIdentifier( int row );
+ public static enum MSA_FORMAT {
+ FASTA, PHYLIP, NEXUS;
+ }
- public void setIdentifier( int row, Object identifier );
+ public String getIdentifier( int row );
+
+ public void setIdentifier( int row, String identifier );
public int getLength();
public char getResidueAt( int row, int col );
+ public boolean isGapAt( int row, int col );
+
+ public List<Character> getColumnAt( int col );
+
+ public MolecularSequence getSequence( final String id );
+
+ public MolecularSequence getSequence( final int row );
+
+ public List<MolecularSequence> asSequenceList();
+
public StringBuffer getSequenceAsString( int row );
public abstract TYPE getType();
public void setResidueAt( final int row, final int col, final char residue );
- public void write( Writer w ) throws IOException;
+ public void write( Writer w, MSA_FORMAT format ) throws IOException;
}