X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa%2FMsa.java;h=066b10ff2d41784c33ac77251eec5b4198439272;hb=88718609970e490e94727d12ebbca1270ba2c0a7;hp=2867989f30d8c2674a638b870464ea37e9b93144;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java
index 2867989..066b10f 100644
--- a/forester/java/src/org/forester/msa/Msa.java
+++ b/forester/java/src/org/forester/msa/Msa.java
@@ -5,7 +5,7 @@
 // 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
@@ -15,26 +15,32 @@
 // 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();
 
@@ -42,11 +48,21 @@ public interface Msa {
 
     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;
 }