rio - gsdir work...

[jalview.git] / forester / java / src / org / forester / msa / Msa.java

diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java
index 2867989..790b674 100644 (file)
--- 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
@@ -15,7 +15,7 @@
 // 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
@@ -27,14 +27,20 @@ package org.forester.msa;
 
 import java.io.IOException;
 import java.io.Writer;
+import java.util.List;
 
+import org.forester.sequence.Sequence;
 import org.forester.sequence.Sequence.TYPE;
 
 public interface Msa {
 
-    public Object getIdentifier( int row );
+    public static enum MSA_FORMAT {
+        FASTA, PHYLIP;
+    }
 
-    public void setIdentifier( int row, Object identifier );
+    public String getIdentifier( int row );
+
+    public void setIdentifier( int row, String identifier );
 
     public int getLength();
 
@@ -42,11 +48,19 @@ public interface Msa {
 
     public char getResidueAt( int row, int col );
 
+    public List<Character> getColumnAt( int col );
+
+    public Sequence getSequence( final String id );
+
+    public Sequence getSequence( final int row );
+
+    public List<Sequence> 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;
 }