inference

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

diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java
index 6e407f8..d806c90 100644 (file)
--- a/forester/java/src/org/forester/msa/BasicMsa.java
+++ b/forester/java/src/org/forester/msa/BasicMsa.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2010 Christian M Zmasek
 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
 // 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
@@ -27,6 +27,7 @@ package org.forester.msa;
 
 import java.io.IOException;
 import java.io.Writer;
+import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.sequence.Sequence;
@@ -99,10 +100,12 @@ public class BasicMsa implements Msa {
         return _type;
     }
 
+    @Override
     public void setIdentifier( final int row, final Object id ) {
         _identifiers[ row ] = id;
     }
 
+    @Override
     public void setResidueAt( final int row, final int col, final char residue ) {
         _data[ row ][ col ] = residue;
     }
@@ -121,6 +124,7 @@ public class BasicMsa implements Msa {
         return sb.toString();
     }
 
+    @Override
     public void write( final Writer w ) throws IOException {
         final int max = determineMaxIdLength() + 1;
         for( int row = 0; row < _data.length; ++row ) {
@@ -153,4 +157,13 @@ public class BasicMsa implements Msa {
         }
         return msa;
     }
+
+    @Override
+    public List<Character> getColumnAt( final int col ) {
+        final List<Character> column = new ArrayList<Character>();
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            column.add( getResidueAt( row, col ) );
+        }
+        return column;
+    }
 }