inprogress

[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 60828bd..a172221 100644 (file)
--- 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;
@@ -87,8 +91,8 @@ public class BasicSequence implements Sequence {
     @Override
     public int getNumberOfGapResidues() {
         int gaps = 0;
-        for( int i = 0; i < _mol_sequence.length; ++i ) {
-            if ( _mol_sequence[ i ] == GAP ) {
+        for( final char element : _mol_sequence ) {
+            if ( element == GAP ) {
                 ++gaps;
             }
         }
@@ -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;
+    }
 }