in progress

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

diff --git a/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java b/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java
index 4b3bdd1..0ee99bf 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java
+++ b/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.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;
 
@@ -94,7 +94,7 @@ public class BinaryCharacters implements PhylogenyData {
     public void addGainedCharacter( final String binary_character ) {
         if ( getLostCharacters().contains( binary_character ) ) {
             throw new IllegalArgumentException( "attempt to add binary character [" + binary_character
-                    + "] to gained characters but is already listed as lost" );
+                                                + "] to gained characters but is already listed as lost" );
         }
         getGainedCharacters().add( binary_character );
     }
@@ -102,11 +102,11 @@ public class BinaryCharacters implements PhylogenyData {
     public void addLostCharacter( final String binary_character ) {
         if ( getPresentCharacters().contains( binary_character ) ) {
             throw new IllegalArgumentException( "attempt to add binary character [" + binary_character
-                    + "] to lost characters but is already listed as present" );
+                                                + "] to lost characters but is already listed as present" );
         }
         if ( getGainedCharacters().contains( binary_character ) ) {
             throw new IllegalArgumentException( "attempt to add binary character [" + binary_character
-                    + "] to lost characters but is already listed as gained" );
+                                                + "] to lost characters but is already listed as gained" );
         }
         getLostCharacters().add( binary_character );
     }
@@ -114,7 +114,7 @@ public class BinaryCharacters implements PhylogenyData {
     public void addPresentCharacter( final String binary_character ) {
         if ( getLostCharacters().contains( binary_character ) ) {
             throw new IllegalArgumentException( "attempt to add binary character [" + binary_character
-                    + "] to present characters but is already listed as lost" );
+                                                + "] to present characters but is already listed as lost" );
         }
         getPresentCharacters().add( binary_character );
     }
@@ -148,7 +148,7 @@ public class BinaryCharacters implements PhylogenyData {
     @Override
     /**
      * Not a deep copy.
-     * 
+     *
      */
     public PhylogenyData copy() {
         validate();
@@ -238,10 +238,10 @@ public class BinaryCharacters implements PhylogenyData {
                                       getType(),
                                       PhyloXmlMapping.BINARY_CHARACTERS_GAINED_COUNT_ATTR,
                                       getGainedCount() != COUNT_DEFAULT ? String.valueOf( getGainedCount() ) : "",
-                                      PhyloXmlMapping.BINARY_CHARACTERS_LOST_COUNT_ATTR,
-                                      getLostCount() != COUNT_DEFAULT ? String.valueOf( getLostCount() ) : "",
-                                      PhyloXmlMapping.BINARY_CHARACTERS_PRESENT_COUNT_ATTR,
-                                      getPresentCount() != COUNT_DEFAULT ? String.valueOf( getPresentCount() ) : "" );
+                                              PhyloXmlMapping.BINARY_CHARACTERS_LOST_COUNT_ATTR,
+                                              getLostCount() != COUNT_DEFAULT ? String.valueOf( getLostCount() ) : "",
+                                                      PhyloXmlMapping.BINARY_CHARACTERS_PRESENT_COUNT_ATTR,
+                                                      getPresentCount() != COUNT_DEFAULT ? String.valueOf( getPresentCount() ) : "" );
         final String my_ind = indentation + PhylogenyWriter.PHYLO_XML_INTENDATION_BASE;
         if ( getGainedCharacters().size() > 0 ) {
             writer.write( ForesterUtil.LINE_SEPARATOR );