From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 3 Jul 2013 17:35:12 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e5997cf0185e43b0864767193c3cd89bde2fbacd;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/evoinference/matrix/character/DiscreteState.java b/forester/java/src/org/forester/evoinference/matrix/character/DiscreteState.java
deleted file mode 100644
index 7f80ceb..0000000
--- a/forester/java/src/org/forester/evoinference/matrix/character/DiscreteState.java
+++ /dev/null
@@ -1,80 +0,0 @@
-// $Id:
-//
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.evoinference.matrix.character;
-
-import org.forester.util.ForesterUtil;
-
-public class DiscreteState implements Comparable<DiscreteState> {
-
-    final private String _id;
-
-    public DiscreteState( final String id ) {
-        if ( ForesterUtil.isEmpty( id ) ) {
-            throw new IllegalArgumentException( "attempt to create new discrete state from empty or null string" );
-        }
-        _id = id.trim();
-    }
-
-    @Override
-    public int compareTo( final DiscreteState discrete_state ) {
-        if ( this == discrete_state ) {
-            return 0;
-        }
-        return getId().compareTo( discrete_state.getId() );
-    }
-
-    @Override
-    public boolean equals( final Object o ) {
-        if ( this == o ) {
-            return true;
-        }
-        else if ( o == null ) {
-            throw new IllegalArgumentException( "attempt to check discrete state equality to null" );
-        }
-        else if ( o.getClass() != this.getClass() ) {
-            throw new IllegalArgumentException( "attempt to check discrete stateequality to " + o + " [" + o.getClass()
-                    + "]" );
-        }
-        else {
-            return getId().equals( ( ( DiscreteState ) o ).getId() );
-        }
-    }
-
-    public String getId() {
-        return _id;
-    }
-
-    @Override
-    public int hashCode() {
-        return getId().hashCode();
-    }
-
-    @Override
-    public String toString() {
-        return getId();
-    }
-}
\ No newline at end of file
diff --git a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java
index fd51681..2f94bed 100644
--- a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java
+++ b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java
@@ -455,10 +455,10 @@ public class FitchParsimony<STATE_TYPE> {
     private void setInternalNodeStatePriorToTraceback( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
                                                        final int character_state_column,
                                                        final PhylogenyNode node ) {
-        getInternalStatesMatrixPriorToTraceback().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + ""
-                                                                    : node.getName(),
-                                                            character_state_column,
-                                                            toListSorted( states.get( node ) ) );
+        getInternalStatesMatrixPriorToTraceback()
+                .setState( ForesterUtil.isEmpty( node.getName() ) ? String.valueOf( node.getId() ) : node.getName(),
+                           character_state_column,
+                           toListSorted( states.get( node ) ) );
     }
 
     private void setInternalStatesMatrixPriorToTraceback( final CharacterStateMatrix<List<STATE_TYPE>> internal_states_matrix_prior_to_traceback ) {