cleanup

[jalview.git] / forester / java / src / org / forester / sequence / BasicSequence.java

diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java
index 4cc03a7..786cc03 100644 (file)
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,7 +16,7 @@
 // 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
@@ -45,27 +45,43 @@ public class BasicSequence implements Sequence {
         _type = type;
     }
 
+    @Override
     public Object getIdentifier() {
         return _identifier;
     }
 
+    @Override
     public int getLength() {
         return _mol_sequence.length;
     }
 
+    @Override
     public char[] getMolecularSequence() {
         return _mol_sequence;
     }
 
+    @Override
     public char getResidueAt( final int position ) {
         return _mol_sequence[ position ];
     }
 
+    @Override
     public TYPE getType() {
         return _type;
     }
 
     @Override
+    public int getNumberOfGapResidues() {
+        int gaps = 0;
+        for( int i = 0; i < _mol_sequence.length; ++i ) {
+            if ( _mol_sequence[ i ] == GAP ) {
+                ++gaps;
+            }
+        }
+        return gaps;
+    }
+
+    @Override
     public String toString() {
         final StringBuffer sb = new StringBuffer();
         sb.append( _identifier.toString() );