inprogress

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

diff --git a/forester/java/src/org/forester/msa/ResampleableMsa.java b/forester/java/src/org/forester/msa/ResampleableMsa.java
index 7476cad..4427ea7 100644 (file)
--- a/forester/java/src/org/forester/msa/ResampleableMsa.java
+++ b/forester/java/src/org/forester/msa/ResampleableMsa.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
@@ -15,16 +15,19 @@
 // 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 org.forester.sequence.BasicSequence;
+import org.forester.sequence.Sequence;
+
 public final class ResampleableMsa extends BasicMsa {
 
     private int[] _resampled_column_positions = null;
@@ -33,9 +36,16 @@ public final class ResampleableMsa extends BasicMsa {
         super( msa );
     }
 
-    public void resample( final int[] resampled_column_positions ) {
+    @Override
+    final public char getResidueAt( final int row, final int col ) {
+        if ( _resampled_column_positions != null ) {
+            return super.getResidueAt( row, _resampled_column_positions[ col ] );
+        }
+        return super.getResidueAt( row, col );
+    }
+
+    final public void resample( final int[] resampled_column_positions ) {
         if ( resampled_column_positions.length != getLength() ) {
-            _resampled_column_positions = null;
             throw new IllegalArgumentException( "illegal attempt to use " + resampled_column_positions.length
                     + " resampled column positions on msa of length " + getLength() );
         }
@@ -43,15 +53,12 @@ public final class ResampleableMsa extends BasicMsa {
     }
 
     @Override
-    public char getResidueAt( final int row, final int col ) {
-        if ( _resampled_column_positions != null ) {
-            return super.getResidueAt( row, _resampled_column_positions[ col ] );
-        }
-        return super.getResidueAt( row, col );
+    final public void setResidueAt( final int row, final int col, final char residue ) {
+        throw new NoSuchMethodError( "illegal attempt to set residue in resampleable msa" );
     }
 
     @Override
-    public void setResidueAt( final int row, final int col, final char residue ) {
-        throw new NoSuchMethodError( "illegal attempt to set residue in resampleable msa" );
+    public Sequence getSequence( final int row ) {
+        return new BasicSequence( getIdentifier( row ), getSequenceAsString( row ).toString(), getType() );
     }
 }