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 4a4662a..dccc191 100644 (file)
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -31,10 +31,14 @@ 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 ) {
+    /**
+     * Only use if you know what you are doing!
+     * 
+     */
+    public BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
         if ( ForesterUtil.isEmpty( identifier ) ) {
             throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
         }
@@ -46,7 +50,10 @@ public class BasicSequence implements Sequence {
         _type = type;
     }
 
-    // Only use if you know what you are doing!
+    /**
+     * Only use if you know what you are doing!
+     * 
+     */
     public BasicSequence( final String identifier, final char[] mol_sequence, final TYPE type ) {
         if ( ForesterUtil.isEmpty( identifier ) ) {
             throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
@@ -59,6 +66,10 @@ public class BasicSequence implements Sequence {
         _type = type;
     }
 
+    public void setIdentifier( final String id ) {
+        _identifier = id;
+    }
+
     @Override
     public String getIdentifier() {
         return _identifier;
@@ -151,4 +162,9 @@ public class BasicSequence implements Sequence {
     public String getMolecularSequenceAsString() {
         return new String( getMolecularSequence() );
     }
+
+    @Override
+    public boolean isGapAt( final int position ) {
+        return getResidueAt( position ) == GAP;
+    }
 }