0.9916 beta

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

diff --git a/forester/java/src/org/forester/phylogeny/data/Event.java b/forester/java/src/org/forester/phylogeny/data/Event.java
index 22dacc9..afccbcd 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Event.java
+++ b/forester/java/src/org/forester/phylogeny/data/Event.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.phylogeny.data;
 
@@ -107,6 +107,7 @@ public class Event implements PhylogenyData {
         }
     }
 
+    @Override
     public StringBuffer asSimpleText() {
         final StringBuffer sb = new StringBuffer();
         if ( isUnassigned() ) {
@@ -140,6 +141,7 @@ public class Event implements PhylogenyData {
         return sb;
     }
 
+    @Override
     public StringBuffer asText() {
         final StringBuffer sb = new StringBuffer();
         if ( isUnassigned() || isSpeciationOrDuplication() || isOther() || isRoot() || isTransfer() || isFusion() ) {
@@ -179,6 +181,7 @@ public class Event implements PhylogenyData {
         return sb;
     }
 
+    @Override
     public PhylogenyData copy() {
         if ( isUnassigned() ) {
             return new Event();
@@ -213,13 +216,14 @@ public class Event implements PhylogenyData {
 
     /**
      * Returns true if this event contains one or more duplications events only
-     * 
+     *
      * @return true if this event contains one or more duplications events only
      */
     public boolean isDuplication() {
         return ( _duplications > 0 ) && ( _gene_losses < 1 ) && ( _speciations < 1 );
     }
 
+    @Override
     public boolean isEqual( final PhylogenyData event ) {
         if ( ( event == null ) || !( event instanceof Event ) ) {
             return false;
@@ -246,7 +250,7 @@ public class Event implements PhylogenyData {
 
     /**
      * Returns true if this event contains one or more gene loss events only
-     * 
+     *
      * @return true if this event contains one or more gene loss events only
      */
     public boolean isGeneLoss() {
@@ -263,7 +267,7 @@ public class Event implements PhylogenyData {
 
     /**
      * Returns true if this event contains one or more speciation events only
-     * 
+     *
      * @return true if this event contains one or more speciation events only
      */
     public boolean isSpeciation() {
@@ -301,6 +305,7 @@ public class Event implements PhylogenyData {
         _event_type = EventType.mixed;
     }
 
+    @Override
     public StringBuffer toNHX() {
         final StringBuffer sb = new StringBuffer();
         if ( !isUnassigned() && ( isSpeciationOrDuplication() || isDuplication() || isSpeciation() ) ) {
@@ -319,13 +324,14 @@ public class Event implements PhylogenyData {
         return sb;
     }
 
+    @Override
     public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
         writer.write( ForesterUtil.LINE_SEPARATOR );
         writer.write( indentation );
         PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.EVENTS );
         if ( ( getEventType() != EventType.unassigned ) && ( getEventType() != EventType.mixed ) ) {
             PhylogenyDataUtil
-                    .appendElement( writer, PhyloXmlMapping.EVENT_TYPE, getEventType().toString(), indentation );
+            .appendElement( writer, PhyloXmlMapping.EVENT_TYPE, getEventType().toString(), indentation );
         }
         if ( getNumberOfDuplications() > 0 ) {
             PhylogenyDataUtil.appendElement( writer,