forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: www.phylosoft.org/forester
  26
  27 package org.forester.evoinference.parsimony;
  28
  29 import java.util.ArrayList;
  30 import java.util.HashMap;
  31 import java.util.Iterator;
  32 import java.util.List;
  33 import java.util.Map;
  34 import java.util.Random;
  35 import java.util.SortedSet;
  36 import java.util.TreeSet;
  37
  38 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  39 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  40 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  41 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  42 import org.forester.phylogeny.Phylogeny;
  43 import org.forester.phylogeny.PhylogenyNode;
  44 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  45 import org.forester.util.FailedConditionCheckException;
  46 import org.forester.util.ForesterUtil;
  47
  48 public class FitchParsimony<STATE_TYPE> {
  49
  50     final static private BinaryStates              PRESENT                         = BinaryStates.PRESENT;
  51     final static private BinaryStates              ABSENT                          = BinaryStates.ABSENT;
  52     final static private GainLossStates            LOSS                            = GainLossStates.LOSS;
  53     final static private GainLossStates            GAIN                            = GainLossStates.GAIN;
  54     final static private GainLossStates            UNCHANGED_PRESENT               = GainLossStates.UNCHANGED_PRESENT;
  55     final static private GainLossStates            UNCHANGED_ABSENT                = GainLossStates.UNCHANGED_ABSENT;
  56     private static final boolean                   RETURN_INTERNAL_STATES_DEFAULT  = false;
  57     private static final boolean                   RETURN_GAIN_LOSS_MATRIX_DEFAULT = false;
  58     private static final boolean                   RANDOMIZE_DEFAULT               = false;
  59     private static final long                      RANDOM_NUMBER_SEED_DEFAULT      = 21;
  60     private static final boolean                   USE_LAST_DEFAULT                = false;
  61     private boolean                                _return_internal_states         = false;
  62     private boolean                                _return_gain_loss               = false;
  63     private int                                    _total_gains;
  64     private int                                    _total_losses;
  65     private int                                    _total_unchanged;
  66     private CharacterStateMatrix<List<STATE_TYPE>> _internal_states_matrix_prior_to_traceback;
  67     private CharacterStateMatrix<STATE_TYPE>       _internal_states_matrix_after_traceback;
  68     private CharacterStateMatrix<GainLossStates>   _gain_loss_matrix;
  69     private boolean                                _randomize;
  70     private boolean                                _use_last;
  71     private int                                    _cost;
  72     private long                                   _random_number_seed;
  73     private Random                                 _random_generator;
  74
  75     public FitchParsimony() {
  76         init();
  77     }
  78
  79     private int determineIndex( final SortedSet<STATE_TYPE> current_node_states, int i ) {
  80         if ( isRandomize() ) {
  81             i = getRandomGenerator().nextInt( current_node_states.size() );
  82         }
  83         else if ( isUseLast() ) {
  84             i = current_node_states.size() - 1;
  85         }
  86         return i;
  87     }
  88
  89     public void execute( final Phylogeny p, final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
  90         if ( !p.isRooted() ) {
  91             throw new IllegalArgumentException( "attempt to execute Fitch parsimony on unroored phylogeny" );
  92         }
  93         if ( external_node_states_matrix.isEmpty() ) {
  94             throw new IllegalArgumentException( "character matrix is empty" );
  95         }
  96         if ( external_node_states_matrix.getNumberOfIdentifiers() != p.getNumberOfExternalNodes() ) {
  97             throw new IllegalArgumentException( "number of external nodes in phylogeny ["
  98                     + p.getNumberOfExternalNodes() + "] and number of indentifiers ["
  99                     + external_node_states_matrix.getNumberOfIdentifiers() + "] in matrix are not equal" );
 100         }
 101         reset();
 102         if ( isReturnInternalStates() ) {
 103             initializeInternalStates( p, external_node_states_matrix );
 104         }
 105         if ( isReturnGainLossMatrix() ) {
 106             initializeGainLossMatrix( p, external_node_states_matrix );
 107         }
 108         for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
 109             executeForOneCharacter( p,
 110                                     getStatesForCharacter( p, external_node_states_matrix, character_index ),
 111                                     getStatesForCharacterForTraceback( p, external_node_states_matrix, character_index ),
 112                                     character_index );
 113         }
 114         if ( external_node_states_matrix.getState( 0, 0 ) instanceof BinaryStates ) {
 115             if ( ( external_node_states_matrix.getNumberOfCharacters() * p.getNumberOfBranches() ) != ( getTotalGains()
 116                     + getTotalLosses() + getTotalUnchanged() ) ) {
 117                 throw new FailedConditionCheckException( "this should not have happened: something is deeply wrong with Fitch parsimony implementation" );
 118             }
 119         }
 120     }
 121
 122     private void executeForOneCharacter( final Phylogeny p,
 123                                          final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 124                                          final Map<PhylogenyNode, STATE_TYPE> traceback_states,
 125                                          final int character_state_column ) {
 126         postOrderTraversal( p, states );
 127         preOrderTraversal( p, states, traceback_states, character_state_column );
 128     }
 129
 130     public int getCost() {
 131         return _cost;
 132     }
 133
 134     public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix() {
 135         if ( !isReturnGainLossMatrix() ) {
 136             throw new RuntimeException( "creation of gain-loss matrix has not been enabled" );
 137         }
 138         return _gain_loss_matrix;
 139     }
 140
 141     public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix() {
 142         if ( !isReturnInternalStates() ) {
 143             throw new RuntimeException( "creation of internal state matrix has not been enabled" );
 144         }
 145         return _internal_states_matrix_after_traceback;
 146     }
 147
 148     /**
 149      * Returns a view of the internal states prior to trace-back.
 150      *
 151      * @return
 152      */
 153     public CharacterStateMatrix<List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback() {
 154         if ( !isReturnInternalStates() ) {
 155             throw new RuntimeException( "creation of internal state matrix has not been enabled" );
 156         }
 157         return _internal_states_matrix_prior_to_traceback;
 158     }
 159
 160     private SortedSet<STATE_TYPE> getIntersectionOfStatesOfChildNodes( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 161                                                                        final PhylogenyNode node ) throws AssertionError {
 162         final SortedSet<STATE_TYPE> states_in_child_nodes = new TreeSet<STATE_TYPE>();
 163         for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
 164             final PhylogenyNode node_child = node.getChildNode( i );
 165             if ( !states.containsKey( node_child ) ) {
 166                 throw new AssertionError( "this should not have happened: node [" + node_child.getName()
 167                         + "] not found in node state map" );
 168             }
 169             if ( i == 0 ) {
 170                 states_in_child_nodes.addAll( states.get( node_child ) );
 171             }
 172             else {
 173                 states_in_child_nodes.retainAll( states.get( node_child ) );
 174             }
 175         }
 176         return states_in_child_nodes;
 177     }
 178
 179     private Random getRandomGenerator() {
 180         return _random_generator;
 181     }
 182
 183     private long getRandomNumberSeed() {
 184         return _random_number_seed;
 185     }
 186
 187     private STATE_TYPE getStateAt( final int i, final SortedSet<STATE_TYPE> states ) {
 188         final Iterator<STATE_TYPE> it = states.iterator();
 189         for( int j = 0; j < i; ++j ) {
 190             it.next();
 191         }
 192         return it.next();
 193     }
 194
 195     private Map<PhylogenyNode, SortedSet<STATE_TYPE>> getStatesForCharacter( final Phylogeny p,
 196                                                                              final CharacterStateMatrix<STATE_TYPE> matrix,
 197                                                                              final int character_index ) {
 198         final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states = new HashMap<PhylogenyNode, SortedSet<STATE_TYPE>>( matrix
 199                 .getNumberOfIdentifiers() );
 200         for( int indentifier_index = 0; indentifier_index < matrix.getNumberOfIdentifiers(); ++indentifier_index ) {
 201             final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
 202             if ( state == null ) {
 203                 throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index
 204                         + "] is null" );
 205             }
 206             final SortedSet<STATE_TYPE> l = new TreeSet<STATE_TYPE>();
 207             l.add( state );
 208             states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), l );
 209         }
 210         return states;
 211     }
 212
 213     private Map<PhylogenyNode, STATE_TYPE> getStatesForCharacterForTraceback( final Phylogeny p,
 214                                                                               final CharacterStateMatrix<STATE_TYPE> matrix,
 215                                                                               final int character_index ) {
 216         final Map<PhylogenyNode, STATE_TYPE> states = new HashMap<PhylogenyNode, STATE_TYPE>( matrix.getNumberOfIdentifiers() );
 217         for( int indentifier_index = 0; indentifier_index < matrix.getNumberOfIdentifiers(); ++indentifier_index ) {
 218             final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
 219             if ( state == null ) {
 220                 throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index
 221                         + "] is null" );
 222             }
 223             states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state );
 224         }
 225         return states;
 226     }
 227
 228     public int getTotalGains() {
 229         return _total_gains;
 230     }
 231
 232     public int getTotalLosses() {
 233         return _total_losses;
 234     }
 235
 236     public int getTotalUnchanged() {
 237         return _total_unchanged;
 238     }
 239
 240     private SortedSet<STATE_TYPE> getUnionOfStatesOfChildNodes( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 241                                                                 final PhylogenyNode node ) throws AssertionError {
 242         final SortedSet<STATE_TYPE> states_in_child_nodes = new TreeSet<STATE_TYPE>();
 243         for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
 244             final PhylogenyNode node_child = node.getChildNode( i );
 245             if ( !states.containsKey( node_child ) ) {
 246                 throw new AssertionError( "this should not have happened: node [" + node_child.getName()
 247                         + "] not found in node state map" );
 248             }
 249             states_in_child_nodes.addAll( states.get( node_child ) );
 250         }
 251         return states_in_child_nodes;
 252     }
 253
 254     private void increaseCost() {
 255         ++_cost;
 256     }
 257
 258     private void init() {
 259         setReturnInternalStates( RETURN_INTERNAL_STATES_DEFAULT );
 260         setReturnGainLossMatrix( RETURN_GAIN_LOSS_MATRIX_DEFAULT );
 261         setRandomize( RANDOMIZE_DEFAULT );
 262         setUseLast( USE_LAST_DEFAULT );
 263         _random_number_seed = RANDOM_NUMBER_SEED_DEFAULT;
 264         reset();
 265     }
 266
 267     private void initializeGainLossMatrix( final Phylogeny p,
 268                                            final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
 269         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
 270         for( final PhylogenyNodeIterator postorder = p.iteratorPostorder(); postorder.hasNext(); ) {
 271             nodes.add( postorder.next() );
 272         }
 273         setGainLossMatrix( new BasicCharacterStateMatrix<CharacterStateMatrix.GainLossStates>( nodes.size(),
 274                                                                                                external_node_states_matrix
 275                                                                                                        .getNumberOfCharacters() ) );
 276         int identifier_index = 0;
 277         for( final PhylogenyNode node : nodes ) {
 278             getGainLossMatrix().setIdentifier( identifier_index++,
 279                                                ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node
 280                                                        .getName() );
 281         }
 282         for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
 283             getGainLossMatrix().setCharacter( character_index,
 284                                               external_node_states_matrix.getCharacter( character_index ) );
 285         }
 286     }
 287
 288     private void initializeInternalStates( final Phylogeny p,
 289                                            final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
 290         final List<PhylogenyNode> internal_nodes = new ArrayList<PhylogenyNode>();
 291         for( final PhylogenyNodeIterator postorder = p.iteratorPostorder(); postorder.hasNext(); ) {
 292             final PhylogenyNode node = postorder.next();
 293             if ( node.isInternal() ) {
 294                 internal_nodes.add( node );
 295             }
 296         }
 297         setInternalStatesMatrixPriorToTraceback( new BasicCharacterStateMatrix<List<STATE_TYPE>>( internal_nodes.size(),
 298                                                                                                   external_node_states_matrix
 299                                                                                                           .getNumberOfCharacters() ) );
 300         setInternalStatesMatrixTraceback( new BasicCharacterStateMatrix<STATE_TYPE>( internal_nodes.size(),
 301                                                                                      external_node_states_matrix
 302                                                                                              .getNumberOfCharacters() ) );
 303         int identifier_index = 0;
 304         for( final PhylogenyNode node : internal_nodes ) {
 305             getInternalStatesMatrix().setIdentifier( identifier_index,
 306                                                      ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node
 307                                                              .getName() );
 308             getInternalStatesMatrixPriorToTraceback().setIdentifier( identifier_index,
 309                                                                      ForesterUtil.isEmpty( node.getName() ) ? node
 310                                                                              .getId() + "" : node.getName() );
 311             ++identifier_index;
 312         }
 313         for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
 314             getInternalStatesMatrix().setCharacter( character_index,
 315                                                     external_node_states_matrix.getCharacter( character_index ) );
 316             getInternalStatesMatrixPriorToTraceback().setCharacter( character_index,
 317                                                                     external_node_states_matrix
 318                                                                             .getCharacter( character_index ) );
 319         }
 320     }
 321
 322     private boolean isRandomize() {
 323         return _randomize;
 324     }
 325
 326     private boolean isReturnGainLossMatrix() {
 327         return _return_gain_loss;
 328     }
 329
 330     private boolean isReturnInternalStates() {
 331         return _return_internal_states;
 332     }
 333
 334     private boolean isUseLast() {
 335         return _use_last;
 336     }
 337
 338     private void postOrderTraversal( final Phylogeny p, final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states )
 339             throws AssertionError {
 340         for( final PhylogenyNodeIterator postorder = p.iteratorPostorder(); postorder.hasNext(); ) {
 341             final PhylogenyNode node = postorder.next();
 342             if ( !node.isExternal() ) {
 343                 SortedSet<STATE_TYPE> states_in_children = getIntersectionOfStatesOfChildNodes( states, node );
 344                 if ( states_in_children.isEmpty() ) {
 345                     states_in_children = getUnionOfStatesOfChildNodes( states, node );
 346                 }
 347                 states.put( node, states_in_children );
 348             }
 349         }
 350     }
 351
 352     private void preOrderTraversal( final Phylogeny p,
 353                                     final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 354                                     final Map<PhylogenyNode, STATE_TYPE> traceback_states,
 355                                     final int character_state_column ) throws AssertionError {
 356         for( final PhylogenyNodeIterator preorder = p.iteratorPreorder(); preorder.hasNext(); ) {
 357             final PhylogenyNode current_node = preorder.next();
 358             final SortedSet<STATE_TYPE> current_node_states = states.get( current_node );
 359             STATE_TYPE parent_state = null;
 360             if ( current_node.isRoot() ) {
 361                 int i = 0;
 362                 i = determineIndex( current_node_states, i );
 363                 traceback_states.put( current_node, getStateAt( i, current_node_states ) );
 364             }
 365             else {
 366                 parent_state = traceback_states.get( current_node.getParent() );
 367                 if ( current_node_states.contains( parent_state ) ) {
 368                     traceback_states.put( current_node, parent_state );
 369                 }
 370                 else {
 371                     increaseCost();
 372                     int i = 0;
 373                     i = determineIndex( current_node_states, i );
 374                     traceback_states.put( current_node, getStateAt( i, current_node_states ) );
 375                 }
 376             }
 377             if ( isReturnInternalStates() ) {
 378                 if ( !current_node.isExternal() ) {
 379                     setInternalNodeStatePriorToTraceback( states, character_state_column, current_node );
 380                     setInternalNodeState( traceback_states, character_state_column, current_node );
 381                 }
 382             }
 383             if ( isReturnGainLossMatrix() && !current_node.isRoot() ) {
 384                 if ( !( parent_state instanceof BinaryStates ) ) {
 385                     throw new RuntimeException( "attempt to create gain loss matrix for not binary states" );
 386                 }
 387                 final BinaryStates parent_binary_state = ( BinaryStates ) parent_state;
 388                 final BinaryStates current_binary_state = ( BinaryStates ) traceback_states.get( current_node );
 389                 if ( ( parent_binary_state == PRESENT ) && ( current_binary_state == ABSENT ) ) {
 390                     ++_total_losses;
 391                     setGainLossState( character_state_column, current_node, LOSS );
 392                 }
 393                 else if ( ( ( parent_binary_state == ABSENT ) || ( parent_binary_state == null ) )
 394                         && ( current_binary_state == PRESENT ) ) {
 395                     ++_total_gains;
 396                     setGainLossState( character_state_column, current_node, GAIN );
 397                 }
 398                 else {
 399                     ++_total_unchanged;
 400                     if ( current_binary_state == PRESENT ) {
 401                         setGainLossState( character_state_column, current_node, UNCHANGED_PRESENT );
 402                     }
 403                     else if ( current_binary_state == ABSENT ) {
 404                         setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );
 405                     }
 406                 }
 407             }
 408             else if ( isReturnGainLossMatrix() && current_node.isRoot() ) {
 409                 final BinaryStates current_binary_state = ( BinaryStates ) traceback_states.get( current_node );
 410                 ++_total_unchanged; //new
 411                 if ( current_binary_state == PRESENT ) {//new
 412                     setGainLossState( character_state_column, current_node, UNCHANGED_PRESENT );//new
 413                 }//new
 414                 else if ( current_binary_state == ABSENT ) {//new
 415                     setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new
 416                 }//new
 417                  // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
 418             }
 419         }
 420     }
 421
 422     private void reset() {
 423         setCost( 0 );
 424         setTotalLosses( 0 );
 425         setTotalGains( 0 );
 426         setTotalUnchanged( 0 );
 427         setRandomGenerator( new Random( getRandomNumberSeed() ) );
 428     }
 429
 430     private void setCost( final int cost ) {
 431         _cost = cost;
 432     }
 433
 434     private void setGainLossMatrix( final CharacterStateMatrix<GainLossStates> gain_loss_matrix ) {
 435         _gain_loss_matrix = gain_loss_matrix;
 436     }
 437
 438     private void setGainLossState( final int character_state_column,
 439                                    final PhylogenyNode node,
 440                                    final GainLossStates state ) {
 441         getGainLossMatrix().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
 442                                       character_state_column,
 443                                       state );
 444     }
 445
 446     private void setInternalNodeState( final Map<PhylogenyNode, STATE_TYPE> states,
 447                                        final int character_state_column,
 448                                        final PhylogenyNode node ) {
 449         getInternalStatesMatrix()
 450                 .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
 451                            character_state_column,
 452                            states.get( node ) );
 453     }
 454
 455     private void setInternalNodeStatePriorToTraceback( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 456                                                        final int character_state_column,
 457                                                        final PhylogenyNode node ) {
 458         getInternalStatesMatrixPriorToTraceback().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + ""
 459                                                                     : node.getName(),
 460                                                             character_state_column,
 461                                                             toListSorted( states.get( node ) ) );
 462     }
 463
 464     private void setInternalStatesMatrixPriorToTraceback( final CharacterStateMatrix<List<STATE_TYPE>> internal_states_matrix_prior_to_traceback ) {
 465         _internal_states_matrix_prior_to_traceback = internal_states_matrix_prior_to_traceback;
 466     }
 467
 468     private void setInternalStatesMatrixTraceback( final CharacterStateMatrix<STATE_TYPE> internal_states_matrix_after_traceback ) {
 469         _internal_states_matrix_after_traceback = internal_states_matrix_after_traceback;
 470     }
 471
 472     private void setRandomGenerator( final Random random_generator ) {
 473         _random_generator = random_generator;
 474     }
 475
 476     public void setRandomize( final boolean randomize ) {
 477         if ( randomize && isUseLast() ) {
 478             throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
 479         }
 480         _randomize = randomize;
 481     }
 482
 483     public void setRandomNumberSeed( final long random_number_seed ) {
 484         if ( !isRandomize() ) {
 485             throw new IllegalArgumentException( "attempt to set random number generator seed without randomization enabled" );
 486         }
 487         _random_number_seed = random_number_seed;
 488     }
 489
 490     public void setReturnGainLossMatrix( final boolean return_gain_loss ) {
 491         _return_gain_loss = return_gain_loss;
 492     }
 493
 494     public void setReturnInternalStates( final boolean return_internal_states ) {
 495         _return_internal_states = return_internal_states;
 496     }
 497
 498     private void setTotalGains( final int total_gains ) {
 499         _total_gains = total_gains;
 500     }
 501
 502     private void setTotalLosses( final int total_losses ) {
 503         _total_losses = total_losses;
 504     }
 505
 506     private void setTotalUnchanged( final int total_unchanged ) {
 507         _total_unchanged = total_unchanged;
 508     }
 509
 510     /**
 511      * This sets whether to use the first or last state in the sorted
 512      * states at the undecided internal nodes.
 513      * For randomized choices set randomize to true (and this to false).
 514      *
 515      * Note. It might be advisable to set this to false
 516      * for BinaryStates if absence at the root is preferred
 517      * (given the enum BinaryStates sorts in the following order:
 518      * ABSENT, UNKNOWN, PRESENT).
 519      *
 520      *
 521      * @param use_last
 522      */
 523     public void setUseLast( final boolean use_last ) {
 524         if ( use_last && isRandomize() ) {
 525             throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
 526         }
 527         _use_last = use_last;
 528     }
 529
 530     private List<STATE_TYPE> toListSorted( final SortedSet<STATE_TYPE> states ) {
 531         final List<STATE_TYPE> l = new ArrayList<STATE_TYPE>( states.size() );
 532         for( final STATE_TYPE state : states ) {
 533             l.add( state );
 534         }
 535         return l;
 536     }
 537 }