X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsequence%2FBasicSequence.java;h=42861fb227aba9cec109b26cb3828708878d1352;hb=b6366fd2ac865514d2ceacb63432dac532147a85;hp=dccc1911b5acbac4534d1f61bee1db83c539f551;hpb=db8b10baefc3e1b5fee9b8192657ecc97ca5b86d;p=jalview.git

diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java
index dccc191..42861fb 100644
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -28,7 +28,7 @@ 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 String       _identifier;
@@ -36,7 +36,7 @@ public class BasicSequence implements Sequence {
 
     /**
      * 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 ) ) {
@@ -52,7 +52,7 @@ public class BasicSequence implements Sequence {
 
     /**
      * 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 ) ) {
@@ -114,7 +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;
         }
@@ -135,7 +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 ];
@@ -143,19 +143,19 @@ 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 );
+                                  .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 );
+                                  .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 );
+                                  .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
     }
 
     @Override