in progress

[jalview.git] / forester / java / src / org / forester / go / BasicGoTerm.java

diff --git a/forester/java/src/org/forester/go/BasicGoTerm.java b/forester/java/src/org/forester/go/BasicGoTerm.java
index 768de1c..ecf48f8 100644 (file)
--- a/forester/java/src/org/forester/go/BasicGoTerm.java
+++ b/forester/java/src/org/forester/go/BasicGoTerm.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
@@ -15,13 +15,13 @@
 // 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
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.go;
 
@@ -69,27 +69,31 @@ public class BasicGoTerm implements GoTerm {
         init();
     }
 
+    @Override
     public StringBuffer asSimpleText() {
         return new StringBuffer( getGoId().toString() );
     }
 
+    @Override
     public StringBuffer asText() {
         return new StringBuffer( toString() );
     }
 
     /**
      * Compares based on GO id.
-     * 
+     *
      */
+    @Override
     public int compareTo( final GoTerm go_term ) {
         return getGoId().compareTo( go_term.getGoId() );
     }
 
     /**
      * Makes a shallow copy.
-     * 
-     * 
+     *
+     *
      */
+    @Override
     public PhylogenyData copy() {
         final BasicGoTerm gt = new BasicGoTerm( getGoId(), getName(), getGoNameSpace(), isObsolete() );
         gt.setGoXrefs( getGoXRefs() );
@@ -102,7 +106,7 @@ public class BasicGoTerm implements GoTerm {
 
     /**
      * Return true if both GO id and namespace are equal.
-     * 
+     *
      */
     @Override
     public boolean equals( final Object o ) {
@@ -121,6 +125,7 @@ public class BasicGoTerm implements GoTerm {
         }
     }
 
+    @Override
     public List<GoId> getAltIds() {
         return _alt_ids;
     }
@@ -135,10 +140,12 @@ public class BasicGoTerm implements GoTerm {
         return _definition;
     }
 
+    @Override
     public GoId getGoId() {
         return _id;
     }
 
+    @Override
     public GoNameSpace getGoNameSpace() {
         return _namespace;
     }
@@ -153,22 +160,25 @@ public class BasicGoTerm implements GoTerm {
         return _go_subsets;
     }
 
+    @Override
     public List<GoXRef> getGoXRefs() {
         return _go_xrefs;
     }
 
+    @Override
     public String getName() {
         return _name;
     }
 
+    @Override
     public List<GoId> getSuperGoIds() {
         return _super_go_ids;
     }
 
     /**
      * Hashcode is based on hashcode of GO id.
-     * 
-     * 
+     *
+     *
      */
     @Override
     public int hashCode() {
@@ -185,10 +195,12 @@ public class BasicGoTerm implements GoTerm {
         setComment( "" );
     }
 
+    @Override
     public boolean isEqual( final PhylogenyData go_term ) {
         return equals( go_term );
     }
 
+    @Override
     public boolean isObsolete() {
         return _is_obsolete;
     }
@@ -221,10 +233,12 @@ public class BasicGoTerm implements GoTerm {
         _super_go_ids = super_terms;
     }
 
+    @Override
     public StringBuffer toNHX() {
         throw new UnsupportedOperationException();
     }
 
+    @Override
     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
         throw new UnsupportedOperationException();
     }