X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsequence%2FBasicSequence.java;h=a172221a6494463255f827f258212081ffb36612;hb=9a7395cfe0de3a3405ac9e6105d0577bc45d30ff;hp=6b76f92941f2c66428f1c6d43e999a88b87698e6;hpb=03e51d179caedf757b09e2872f9500318bd85a53;p=jalview.git

diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java
index 6b76f92..a172221 100644
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -22,7 +22,7 @@
 // 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.sequence;
 
@@ -31,7 +31,7 @@ import org.forester.util.ForesterUtil;
 public class BasicSequence implements Sequence {
 
     private final char[] _mol_sequence;
-    private final String _identifier;
+    private String       _identifier;
     private final TYPE   _type;
 
     private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
@@ -59,6 +59,10 @@ public class BasicSequence implements Sequence {
         _type = type;
     }
 
+    public void setIdentifier( final String id ) {
+        _identifier = id;
+    }
+
     @Override
     public String getIdentifier() {
         return _identifier;
@@ -151,4 +155,9 @@ public class BasicSequence implements Sequence {
     public String getMolecularSequenceAsString() {
         return new String( getMolecularSequence() );
     }
+
+    @Override
+    public boolean isGapAt( final int position ) {
+        return getResidueAt( position ) == GAP;
+    }
 }