clean up

[jalview.git] / forester / java / src / org / forester / phylogeny / data / Sequence.java

diff --git a/forester/java/src/org/forester/phylogeny/data/Sequence.java b/forester/java/src/org/forester/phylogeny/data/Sequence.java
index 27b3b0c..39ff08a 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Sequence.java
+++ b/forester/java/src/org/forester/phylogeny/data/Sequence.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -70,6 +70,7 @@ public class Sequence implements PhylogenyData, MultipleUris {
         getAnnotations().add( annotation );
     }
 
+    @Override
     public void addUri( final Uri uri ) {
         if ( getUris() == null ) {
             setUris( new ArrayList<Uri>() );
@@ -81,6 +82,7 @@ public class Sequence implements PhylogenyData, MultipleUris {
         _seq_relations.add( sr );
     }
 
+    @Override
     public StringBuffer asSimpleText() {
         final StringBuffer sb = new StringBuffer();
         if ( getAccession() != null ) {
@@ -98,6 +100,7 @@ public class Sequence implements PhylogenyData, MultipleUris {
         return sb;
     }
 
+    @Override
     public StringBuffer asText() {
         return asSimpleText();
     }
@@ -106,6 +109,7 @@ public class Sequence implements PhylogenyData, MultipleUris {
      * Not a deep copy.
      * 
      */
+    @Override
     public PhylogenyData copy() {
         final Sequence seq = new Sequence();
         seq.setAnnotations( getAnnotations() );
@@ -213,10 +217,12 @@ public class Sequence implements PhylogenyData, MultipleUris {
         return _type;
     }
 
+    @Override
     public List<Uri> getUris() {
         return _uris;
     }
 
+    @Override
     public Uri getUri( final int index ) {
         return getUris().get( index );
     }
@@ -255,6 +261,7 @@ public class Sequence implements PhylogenyData, MultipleUris {
         setSourceId( null );
     }
 
+    @Override
     public boolean isEqual( final PhylogenyData data ) {
         if ( this == data ) {
             return true;
@@ -313,10 +320,12 @@ public class Sequence implements PhylogenyData, MultipleUris {
         _type = type;
     }
 
+    @Override
     public void setUris( final List<Uri> uris ) {
         _uris = uris;
     }
 
+    @Override
     public StringBuffer toNHX() {
         final StringBuffer sb = new StringBuffer();
         if ( getName().length() > 0 ) {
@@ -333,6 +342,7 @@ public class Sequence implements PhylogenyData, MultipleUris {
         return sb;
     }
 
+    @Override
     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
         if ( isEmpty() ) {
             return;