X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2Fparsimony%2FDolloParsimony.java;h=094621873d7c39d464eaf8bdb61881129dfc5449;hb=88718609970e490e94727d12ebbca1270ba2c0a7;hp=a10e8656f30491f6f808668f52f5f36fbbf372c6;hpb=eccc2fdb674f76be1815fd7984295661bff8a2be;p=jalview.git

diff --git a/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java
index a10e865..0946218 100644
--- a/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java
+++ b/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,13 +16,13 @@
 // 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.evoinference.parsimony;
 
@@ -130,13 +130,12 @@ public class DolloParsimony {
     private Map<PhylogenyNode, BinaryStates> getStatesForCharacter( final Phylogeny p,
                                                                     final CharacterStateMatrix<BinaryStates> matrix,
                                                                     final int character_index ) {
-        final Map<PhylogenyNode, BinaryStates> states = new HashMap<PhylogenyNode, BinaryStates>( matrix
-                .getNumberOfIdentifiers() );
+        final Map<PhylogenyNode, BinaryStates> states = new HashMap<PhylogenyNode, BinaryStates>( matrix.getNumberOfIdentifiers() );
         for( int indentifier_index = 0; indentifier_index < matrix.getNumberOfIdentifiers(); ++indentifier_index ) {
             final BinaryStates state = matrix.getState( indentifier_index, character_index );
             if ( state == null ) {
                 throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index
-                        + "] is null" );
+                                                    + "] is null" );
             }
             states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state );
         }
@@ -177,8 +176,8 @@ public class DolloParsimony {
             nodes.add( postorder.next() );
         }
         setGainLossMatrix( new BasicCharacterStateMatrix<CharacterStateMatrix.GainLossStates>( nodes.size(),
-                                                                                               external_node_states_matrix
-                                                                                                       .getNumberOfCharacters() ) );
+                external_node_states_matrix
+                .getNumberOfCharacters() ) );
         int identifier_index = 0;
         for( final PhylogenyNode node : nodes ) {
             getGainLossMatrix().setIdentifier( identifier_index++,
@@ -201,8 +200,8 @@ public class DolloParsimony {
             }
         }
         setInternalStatesMatrix( new BasicCharacterStateMatrix<BinaryStates>( internal_nodes.size(),
-                                                                              external_node_states_matrix
-                                                                                      .getNumberOfCharacters() ) );
+                external_node_states_matrix
+                .getNumberOfCharacters() ) );
         int identifier_index = 0;
         for( final PhylogenyNode node : internal_nodes ) {
             getInternalStatesMatrix().setIdentifier( identifier_index++,
@@ -315,17 +314,17 @@ public class DolloParsimony {
                                    final PhylogenyNode node,
                                    final GainLossStates state ) {
         getGainLossMatrix().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
-                                      character_state_column,
-                                      state );
+                character_state_column,
+                state );
     }
 
     private void setInternalNodeState( final Map<PhylogenyNode, BinaryStates> states,
                                        final int character_state_column,
                                        final PhylogenyNode node ) {
         getInternalStatesMatrix()
-                .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
-                           character_state_column,
-                           states.get( node ) );
+        .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
+                character_state_column,
+                states.get( node ) );
     }
 
     private void setInternalStatesMatrix( final CharacterStateMatrix<BinaryStates> internal_states_matrix ) {
@@ -369,7 +368,7 @@ public class DolloParsimony {
             final PhylogenyNode node_child = node.getChildNode( i );
             if ( !states.containsKey( node_child ) ) {
                 throw new RuntimeException( "this should not have happened: node [" + node_child.getName()
-                        + "] not found in node state map" );
+                                            + "] not found in node state map" );
             }
             if ( ( states.get( node_child ) == BinaryStates.PRESENT )
                     || ( states.get( node_child ) == BinaryStates.UNKNOWN ) ) {