forester/java/src/org/forester/evoinference/parsimony/SankoffParsimony.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
  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.ForesterUtil;
  46
  47 /**
  48  *
  49  * IN PROGRESS!
  50  * DO NOT USE!
  51  *
  52  *
  53  * @param <STATE_TYPE>
  54  */
  55 public class SankoffParsimony<STATE_TYPE> {
  56
  57     final static private BinaryStates              PRESENT                         = BinaryStates.PRESENT;
  58     final static private BinaryStates              ABSENT                          = BinaryStates.ABSENT;
  59     final static private GainLossStates            LOSS                            = GainLossStates.LOSS;
  60     final static private GainLossStates            GAIN                            = GainLossStates.GAIN;
  61     final static private GainLossStates            UNCHANGED_PRESENT               = GainLossStates.UNCHANGED_PRESENT;
  62     final static private GainLossStates            UNCHANGED_ABSENT                = GainLossStates.UNCHANGED_ABSENT;
  63     private static final boolean                   RETURN_INTERNAL_STATES_DEFAULT  = false;
  64     private static final boolean                   RETURN_GAIN_LOSS_MATRIX_DEFAULT = false;
  65     private static final boolean                   RANDOMIZE_DEFAULT               = false;
  66     private static final long                      RANDOM_NUMBER_SEED_DEFAULT      = 21;
  67     private static final boolean                   USE_LAST_DEFAULT                = false;
  68     private boolean                                _return_internal_states         = false;
  69     private boolean                                _return_gain_loss               = false;
  70     private int                                    _total_gains;
  71     private int                                    _total_losses;
  72     private int                                    _total_unchanged;
  73     private CharacterStateMatrix<List<STATE_TYPE>> _internal_states_matrix_prior_to_traceback;
  74     private CharacterStateMatrix<STATE_TYPE>       _internal_states_matrix_after_traceback;
  75     private CharacterStateMatrix<GainLossStates>   _gain_loss_matrix;
  76     private boolean                                _randomize;
  77     private boolean                                _use_last;
  78     private int                                    _cost;
  79     private long                                   _random_number_seed;
  80     private Random                                 _random_generator;
  81
  82     public SankoffParsimony() {
  83         init();
  84     }
  85
  86     private int determineIndex( final SortedSet<STATE_TYPE> current_node_states, int i ) {
  87         if ( isRandomize() ) {
  88             i = getRandomGenerator().nextInt( current_node_states.size() );
  89         }
  90         else if ( isUseLast() ) {
  91             i = current_node_states.size() - 1;
  92         }
  93         return i;
  94     }
  95
  96     public void execute( final Phylogeny p, final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
  97         if ( !p.isRooted() ) {
  98             throw new IllegalArgumentException( "attempt to execute Fitch parsimony on unroored phylogeny" );
  99         }
 100         if ( external_node_states_matrix.isEmpty() ) {
 101             throw new IllegalArgumentException( "character matrix is empty" );
 102         }
 103         if ( external_node_states_matrix.getNumberOfIdentifiers() != p.getNumberOfExternalNodes() ) {
 104             throw new IllegalArgumentException( "number of external nodes in phylogeny ["
 105                     + p.getNumberOfExternalNodes() + "] and number of indentifiers ["
 106                     + external_node_states_matrix.getNumberOfIdentifiers() + "] in matrix are not equal" );
 107         }
 108         reset();
 109         if ( isReturnInternalStates() ) {
 110             initializeInternalStates( p, external_node_states_matrix );
 111         }
 112         if ( isReturnGainLossMatrix() ) {
 113             initializeGainLossMatrix( p, external_node_states_matrix );
 114         }
 115         for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
 116             executeForOneCharacter( p,
 117                                     getStatesForCharacter( p, external_node_states_matrix, character_index ),
 118                                     getStatesForCharacterForTraceback( p, external_node_states_matrix, character_index ),
 119                                     character_index );
 120         }
 121         if ( external_node_states_matrix.getState( 0, 0 ) instanceof BinaryStates ) {
 122             if ( ( external_node_states_matrix.getNumberOfCharacters() * p.getNumberOfBranches() ) != ( getTotalGains()
 123                     + getTotalLosses() + getTotalUnchanged() ) ) {
 124                 throw new RuntimeException( "this should not have happened: something is deeply wrong with Fitch parsimony implementation" );
 125             }
 126         }
 127     }
 128
 129     private void executeForOneCharacter( final Phylogeny p,
 130                                          final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 131                                          final Map<PhylogenyNode, STATE_TYPE> traceback_states,
 132                                          final int character_state_column ) {
 133         postOrderTraversal( p, states );
 134         preOrderTraversal( p, states, traceback_states, character_state_column );
 135     }
 136
 137     public int getCost() {
 138         return _cost;
 139     }
 140
 141     public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix() {
 142         if ( !isReturnGainLossMatrix() ) {
 143             throw new RuntimeException( "creation of gain-loss matrix has not been enabled" );
 144         }
 145         return _gain_loss_matrix;
 146     }
 147
 148     public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix() {
 149         if ( !isReturnInternalStates() ) {
 150             throw new RuntimeException( "creation of internal state matrix has not been enabled" );
 151         }
 152         return _internal_states_matrix_after_traceback;
 153     }
 154
 155     /**
 156      * Returns a view of the internal states prior to trace-back.
 157      *
 158      * @return
 159      */
 160     public CharacterStateMatrix<List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback() {
 161         if ( !isReturnInternalStates() ) {
 162             throw new RuntimeException( "creation of internal state matrix has not been enabled" );
 163         }
 164         return _internal_states_matrix_prior_to_traceback;
 165     }
 166
 167     private SortedSet<STATE_TYPE> getIntersectionOfStatesOfChildNodes( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 168                                                                        final PhylogenyNode node ) throws AssertionError {
 169         final SortedSet<STATE_TYPE> states_in_child_nodes = new TreeSet<STATE_TYPE>();
 170         for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
 171             final PhylogenyNode node_child = node.getChildNode( i );
 172             if ( !states.containsKey( node_child ) ) {
 173                 throw new AssertionError( "this should not have happened: node [" + node_child.getName()
 174                                           + "] not found in node state map" );
 175             }
 176             if ( i == 0 ) {
 177                 states_in_child_nodes.addAll( states.get( node_child ) );
 178             }
 179             else {
 180                 states_in_child_nodes.retainAll( states.get( node_child ) );
 181             }
 182         }
 183         return states_in_child_nodes;
 184     }
 185
 186     private Random getRandomGenerator() {
 187         return _random_generator;
 188     }
 189
 190     private long getRandomNumberSeed() {
 191         return _random_number_seed;
 192     }
 193
 194     private STATE_TYPE getStateAt( final int i, final SortedSet<STATE_TYPE> states ) {
 195         final Iterator<STATE_TYPE> it = states.iterator();
 196         for( int j = 0; j < i; ++j ) {
 197             it.next();
 198         }
 199         return it.next();
 200     }
 201
 202     private Map<PhylogenyNode, SortedSet<STATE_TYPE>> getStatesForCharacter( final Phylogeny p,
 203                                                                              final CharacterStateMatrix<STATE_TYPE> matrix,
 204                                                                              final int character_index ) {
 205         final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states = new HashMap<PhylogenyNode, SortedSet<STATE_TYPE>>( matrix
 206                 .getNumberOfIdentifiers() );
 207         for( int indentifier_index = 0; indentifier_index < matrix.getNumberOfIdentifiers(); ++indentifier_index ) {
 208             final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
 209             if ( state == null ) {
 210                 throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index
 211                                                     + "] is null" );
 212             }
 213             final SortedSet<STATE_TYPE> l = new TreeSet<STATE_TYPE>();
 214             l.add( state );
 215             states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), l );
 216         }
 217         return states;
 218     }
 219
 220     private Map<PhylogenyNode, STATE_TYPE> getStatesForCharacterForTraceback( final Phylogeny p,
 221                                                                               final CharacterStateMatrix<STATE_TYPE> matrix,
 222                                                                               final int character_index ) {
 223         final Map<PhylogenyNode, STATE_TYPE> states = new HashMap<PhylogenyNode, STATE_TYPE>( matrix.getNumberOfIdentifiers() );
 224         for( int indentifier_index = 0; indentifier_index < matrix.getNumberOfIdentifiers(); ++indentifier_index ) {
 225             final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
 226             if ( state == null ) {
 227                 throw new IllegalArgumentException( "value at [" + indentifier_index + ", " + character_index
 228                                                     + "] is null" );
 229             }
 230             states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state );
 231         }
 232         return states;
 233     }
 234
 235     public int getTotalGains() {
 236         return _total_gains;
 237     }
 238
 239     public int getTotalLosses() {
 240         return _total_losses;
 241     }
 242
 243     public int getTotalUnchanged() {
 244         return _total_unchanged;
 245     }
 246
 247     private SortedSet<STATE_TYPE> getUnionOfStatesOfChildNodes( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 248                                                                 final PhylogenyNode node ) throws AssertionError {
 249         final SortedSet<STATE_TYPE> states_in_child_nodes = new TreeSet<STATE_TYPE>();
 250         for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
 251             final PhylogenyNode node_child = node.getChildNode( i );
 252             if ( !states.containsKey( node_child ) ) {
 253                 throw new AssertionError( "this should not have happened: node [" + node_child.getName()
 254                                           + "] not found in node state map" );
 255             }
 256             states_in_child_nodes.addAll( states.get( node_child ) );
 257         }
 258         return states_in_child_nodes;
 259     }
 260
 261     private void increaseCost() {
 262         ++_cost;
 263     }
 264
 265     private void init() {
 266         setReturnInternalStates( RETURN_INTERNAL_STATES_DEFAULT );
 267         setReturnGainLossMatrix( RETURN_GAIN_LOSS_MATRIX_DEFAULT );
 268         setRandomize( RANDOMIZE_DEFAULT );
 269         setUseLast( USE_LAST_DEFAULT );
 270         _random_number_seed = RANDOM_NUMBER_SEED_DEFAULT;
 271         reset();
 272     }
 273
 274     private void initializeGainLossMatrix( final Phylogeny p,
 275                                            final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
 276         final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
 277         for( final PhylogenyNodeIterator postorder = p.iteratorPostorder(); postorder.hasNext(); ) {
 278             nodes.add( postorder.next() );
 279         }
 280         setGainLossMatrix( new BasicCharacterStateMatrix<CharacterStateMatrix.GainLossStates>( nodes.size(),
 281                 external_node_states_matrix
 282                 .getNumberOfCharacters() ) );
 283         int identifier_index = 0;
 284         for( final PhylogenyNode node : nodes ) {
 285             getGainLossMatrix().setIdentifier( identifier_index++,
 286                                                ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node
 287                                                        .getName() );
 288         }
 289         for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
 290             getGainLossMatrix().setCharacter( character_index,
 291                                               external_node_states_matrix.getCharacter( character_index ) );
 292         }
 293     }
 294
 295     private void initializeInternalStates( final Phylogeny p,
 296                                            final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
 297         final List<PhylogenyNode> internal_nodes = new ArrayList<PhylogenyNode>();
 298         for( final PhylogenyNodeIterator postorder = p.iteratorPostorder(); postorder.hasNext(); ) {
 299             final PhylogenyNode node = postorder.next();
 300             if ( node.isInternal() ) {
 301                 internal_nodes.add( node );
 302             }
 303         }
 304         setInternalStatesMatrixPriorToTraceback( new BasicCharacterStateMatrix<List<STATE_TYPE>>( internal_nodes.size(),
 305                 external_node_states_matrix
 306                 .getNumberOfCharacters() ) );
 307         setInternalStatesMatrixTraceback( new BasicCharacterStateMatrix<STATE_TYPE>( internal_nodes.size(),
 308                 external_node_states_matrix
 309                 .getNumberOfCharacters() ) );
 310         int identifier_index = 0;
 311         for( final PhylogenyNode node : internal_nodes ) {
 312             getInternalStatesMatrix().setIdentifier( identifier_index,
 313                                                      ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node
 314                                                              .getName() );
 315             getInternalStatesMatrixPriorToTraceback().setIdentifier( identifier_index,
 316                                                                      ForesterUtil.isEmpty( node.getName() ) ? node
 317                                                                              .getId() + "" : node.getName() );
 318             ++identifier_index;
 319         }
 320         for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
 321             getInternalStatesMatrix().setCharacter( character_index,
 322                                                     external_node_states_matrix.getCharacter( character_index ) );
 323             getInternalStatesMatrixPriorToTraceback().setCharacter( character_index,
 324                                                                     external_node_states_matrix
 325                                                                     .getCharacter( character_index ) );
 326         }
 327     }
 328
 329     private boolean isRandomize() {
 330         return _randomize;
 331     }
 332
 333     private boolean isReturnGainLossMatrix() {
 334         return _return_gain_loss;
 335     }
 336
 337     private boolean isReturnInternalStates() {
 338         return _return_internal_states;
 339     }
 340
 341     private boolean isUseLast() {
 342         return _use_last;
 343     }
 344
 345     private void postOrderTraversal( final Phylogeny p, final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states )
 346             throws AssertionError {
 347         for( final PhylogenyNodeIterator postorder = p.iteratorPostorder(); postorder.hasNext(); ) {
 348             final PhylogenyNode node = postorder.next();
 349             if ( !node.isExternal() ) {
 350                 SortedSet<STATE_TYPE> states_in_children = getIntersectionOfStatesOfChildNodes( states, node );
 351                 if ( states_in_children.isEmpty() ) {
 352                     states_in_children = getUnionOfStatesOfChildNodes( states, node );
 353                 }
 354                 states.put( node, states_in_children );
 355             }
 356         }
 357     }
 358
 359     private void preOrderTraversal( final Phylogeny p,
 360                                     final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 361                                     final Map<PhylogenyNode, STATE_TYPE> traceback_states,
 362                                     final int character_state_column ) throws AssertionError {
 363         for( final PhylogenyNodeIterator preorder = p.iteratorPreorder(); preorder.hasNext(); ) {
 364             final PhylogenyNode current_node = preorder.next();
 365             final SortedSet<STATE_TYPE> current_node_states = states.get( current_node );
 366             STATE_TYPE parent_state = null;
 367             if ( current_node.isRoot() ) {
 368                 int i = 0;
 369                 i = determineIndex( current_node_states, i );
 370                 traceback_states.put( current_node, getStateAt( i, current_node_states ) );
 371             }
 372             else {
 373                 parent_state = traceback_states.get( current_node.getParent() );
 374                 if ( current_node_states.contains( parent_state ) ) {
 375                     traceback_states.put( current_node, parent_state );
 376                 }
 377                 else {
 378                     increaseCost();
 379                     int i = 0;
 380                     i = determineIndex( current_node_states, i );
 381                     traceback_states.put( current_node, getStateAt( i, current_node_states ) );
 382                 }
 383             }
 384             if ( isReturnInternalStates() ) {
 385                 if ( !current_node.isExternal() ) {
 386                     setInternalNodeStatePriorToTraceback( states, character_state_column, current_node );
 387                     setInternalNodeState( traceback_states, character_state_column, current_node );
 388                 }
 389             }
 390             if ( isReturnGainLossMatrix() && !current_node.isRoot() ) {
 391                 if ( !( parent_state instanceof BinaryStates ) ) {
 392                     throw new RuntimeException( "attempt to create gain loss matrix for not binary states" );
 393                 }
 394                 final BinaryStates parent_binary_state = ( BinaryStates ) parent_state;
 395                 final BinaryStates current_binary_state = ( BinaryStates ) traceback_states.get( current_node );
 396                 if ( ( parent_binary_state == PRESENT ) && ( current_binary_state == ABSENT ) ) {
 397                     ++_total_losses;
 398                     setGainLossState( character_state_column, current_node, LOSS );
 399                 }
 400                 else if ( ( ( parent_binary_state == ABSENT ) || ( parent_binary_state == null ) )
 401                         && ( current_binary_state == PRESENT ) ) {
 402                     ++_total_gains;
 403                     setGainLossState( character_state_column, current_node, GAIN );
 404                 }
 405                 else {
 406                     ++_total_unchanged;
 407                     if ( current_binary_state == PRESENT ) {
 408                         setGainLossState( character_state_column, current_node, UNCHANGED_PRESENT );
 409                     }
 410                     else if ( current_binary_state == ABSENT ) {
 411                         setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );
 412                     }
 413                 }
 414             }
 415             else if ( isReturnGainLossMatrix() && current_node.isRoot() ) {
 416                 final BinaryStates current_binary_state = ( BinaryStates ) traceback_states.get( current_node );
 417                 ++_total_unchanged; //new
 418                 if ( current_binary_state == PRESENT ) {//new
 419                     setGainLossState( character_state_column, current_node, UNCHANGED_PRESENT );//new
 420                 }//new
 421                 else if ( current_binary_state == ABSENT ) {//new
 422                     setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new
 423                 }//new
 424                 // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
 425             }
 426         }
 427     }
 428
 429     private void reset() {
 430         setCost( 0 );
 431         setTotalLosses( 0 );
 432         setTotalGains( 0 );
 433         setTotalUnchanged( 0 );
 434         setRandomGenerator( new Random( getRandomNumberSeed() ) );
 435     }
 436
 437     private void setCost( final int cost ) {
 438         _cost = cost;
 439     }
 440
 441     private void setGainLossMatrix( final CharacterStateMatrix<GainLossStates> gain_loss_matrix ) {
 442         _gain_loss_matrix = gain_loss_matrix;
 443     }
 444
 445     private void setGainLossState( final int character_state_column,
 446                                    final PhylogenyNode node,
 447                                    final GainLossStates state ) {
 448         getGainLossMatrix().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
 449                 character_state_column,
 450                 state );
 451     }
 452
 453     private void setInternalNodeState( final Map<PhylogenyNode, STATE_TYPE> states,
 454                                        final int character_state_column,
 455                                        final PhylogenyNode node ) {
 456         getInternalStatesMatrix()
 457         .setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + "" : node.getName(),
 458                 character_state_column,
 459                 states.get( node ) );
 460     }
 461
 462     private void setInternalNodeStatePriorToTraceback( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
 463                                                        final int character_state_column,
 464                                                        final PhylogenyNode node ) {
 465         getInternalStatesMatrixPriorToTraceback().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + ""
 466                 : node.getName(),
 467                 character_state_column,
 468                 toListSorted( states.get( node ) ) );
 469     }
 470
 471     private void setInternalStatesMatrixPriorToTraceback( final CharacterStateMatrix<List<STATE_TYPE>> internal_states_matrix_prior_to_traceback ) {
 472         _internal_states_matrix_prior_to_traceback = internal_states_matrix_prior_to_traceback;
 473     }
 474
 475     private void setInternalStatesMatrixTraceback( final CharacterStateMatrix<STATE_TYPE> internal_states_matrix_after_traceback ) {
 476         _internal_states_matrix_after_traceback = internal_states_matrix_after_traceback;
 477     }
 478
 479     private void setRandomGenerator( final Random random_generator ) {
 480         _random_generator = random_generator;
 481     }
 482
 483     public void setRandomize( final boolean randomize ) {
 484         if ( randomize && isUseLast() ) {
 485             throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
 486         }
 487         _randomize = randomize;
 488     }
 489
 490     public void setRandomNumberSeed( final long random_number_seed ) {
 491         if ( !isRandomize() ) {
 492             throw new IllegalArgumentException( "attempt to set random number generator seed without randomization enabled" );
 493         }
 494         _random_number_seed = random_number_seed;
 495     }
 496
 497     public void setReturnGainLossMatrix( final boolean return_gain_loss ) {
 498         _return_gain_loss = return_gain_loss;
 499     }
 500
 501     public void setReturnInternalStates( final boolean return_internal_states ) {
 502         _return_internal_states = return_internal_states;
 503     }
 504
 505     private void setTotalGains( final int total_gains ) {
 506         _total_gains = total_gains;
 507     }
 508
 509     private void setTotalLosses( final int total_losses ) {
 510         _total_losses = total_losses;
 511     }
 512
 513     private void setTotalUnchanged( final int total_unchanged ) {
 514         _total_unchanged = total_unchanged;
 515     }
 516
 517     /**
 518      * This sets whether to use the first or last state in the sorted
 519      * states at the undecided internal nodes.
 520      * For randomized choices set randomize to true (and this to false).
 521      *
 522      * Note. It might be advisable to set this to false
 523      * for BinaryStates if absence at the root is preferred
 524      * (given the enum BinaryStates sorts in the following order:
 525      * ABSENT, UNKNOWN, PRESENT).
 526      *
 527      *
 528      * @param use_last
 529      */
 530     public void setUseLast( final boolean use_last ) {
 531         if ( use_last && isRandomize() ) {
 532             throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
 533         }
 534         _use_last = use_last;
 535     }
 536
 537     private List<STATE_TYPE> toListSorted( final SortedSet<STATE_TYPE> states ) {
 538         final List<STATE_TYPE> l = new ArrayList<STATE_TYPE>( states.size() );
 539         for( final STATE_TYPE state : states ) {
 540             l.add( state );
 541         }
 542         return l;
 543     }
 544 }