X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsequence%2FBasicSequence.java;h=f7a8917fb87dd746c70bf7ae634e78cc759c22d8;hb=7a194f3da2c3a659ecc67bff021d9f64c845e923;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..f7a8917 100644
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -22,19 +22,23 @@
 // 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;
 
 import org.forester.util.ForesterUtil;
 
-public class BasicSequence implements Sequence {
+public class BasicSequence implements MolecularSequence {
 
     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;
@@ -103,7 +114,7 @@ public class BasicSequence implements Sequence {
         if ( obj.getClass() != getClass() ) {
             return false;
         }
-        final Sequence other = ( Sequence ) obj;
+        final MolecularSequence other = ( MolecularSequence ) obj;
         if ( getMolecularSequenceAsString().equals( other.getMolecularSequenceAsString() ) ) {
             return true;
         }
@@ -124,7 +135,7 @@ public class BasicSequence implements Sequence {
         return sb.toString();
     }
 
-    public static Sequence copySequence( final Sequence seq ) {
+    public static MolecularSequence copySequence( final MolecularSequence seq ) {
         final char[] s = new char[ seq.getMolecularSequence().length ];
         for( int i = 0; i < seq.getMolecularSequence().length; i++ ) {
             s[ i ] = seq.getMolecularSequence()[ i ];
@@ -132,17 +143,17 @@ public class BasicSequence implements Sequence {
         return new BasicSequence( new String( seq.getIdentifier() ), s, seq.getType() );
     }
 
-    public static Sequence createAaSequence( final String identifier, final String mol_sequence ) {
+    public static MolecularSequence createAaSequence( final String identifier, final String mol_sequence ) {
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
                 .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA );
     }
 
-    public static Sequence createDnaSequence( final String identifier, final String mol_sequence ) {
+    public static MolecularSequence createDnaSequence( final String identifier, final String mol_sequence ) {
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
                 .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA );
     }
 
-    public static Sequence createRnaSequence( final String identifier, final String mol_sequence ) {
+    public static MolecularSequence createRnaSequence( final String identifier, final String mol_sequence ) {
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
                 .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
     }
@@ -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;
+    }
 }