3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.
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.
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
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org
27 package org.forester.evoinference.parsimony;
29 import java.util.ArrayList;
30 import java.util.HashMap;
31 import java.util.Iterator;
32 import java.util.List;
34 import java.util.Random;
35 import java.util.SortedSet;
36 import java.util.TreeSet;
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;
55 public class SankoffParsimony<STATE_TYPE> {
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;
79 private long _random_number_seed;
80 private Random _random_generator;
82 public SankoffParsimony() {
86 private int determineIndex( final SortedSet<STATE_TYPE> current_node_states, int i ) {
87 if ( isRandomize() ) {
88 i = getRandomGenerator().nextInt( current_node_states.size() );
90 else if ( isUseLast() ) {
91 i = current_node_states.size() - 1;
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" );
100 if ( external_node_states_matrix.isEmpty() ) {
101 throw new IllegalArgumentException( "character matrix is empty" );
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" );
109 if ( isReturnInternalStates() ) {
110 initializeInternalStates( p, external_node_states_matrix );
112 if ( isReturnGainLossMatrix() ) {
113 initializeGainLossMatrix( p, external_node_states_matrix );
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 ),
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" );
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 );
137 public int getCost() {
141 public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix() {
142 if ( !isReturnGainLossMatrix() ) {
143 throw new RuntimeException( "creation of gain-loss matrix has not been enabled" );
145 return _gain_loss_matrix;
148 public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix() {
149 if ( !isReturnInternalStates() ) {
150 throw new RuntimeException( "creation of internal state matrix has not been enabled" );
152 return _internal_states_matrix_after_traceback;
156 * Returns a view of the internal states prior to trace-back.
160 public CharacterStateMatrix<List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback() {
161 if ( !isReturnInternalStates() ) {
162 throw new RuntimeException( "creation of internal state matrix has not been enabled" );
164 return _internal_states_matrix_prior_to_traceback;
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" );
177 states_in_child_nodes.addAll( states.get( node_child ) );
180 states_in_child_nodes.retainAll( states.get( node_child ) );
183 return states_in_child_nodes;
186 private Random getRandomGenerator() {
187 return _random_generator;
190 private long getRandomNumberSeed() {
191 return _random_number_seed;
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 ) {
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
213 final SortedSet<STATE_TYPE> l = new TreeSet<STATE_TYPE>();
215 states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), l );
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
230 states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state );
235 public int getTotalGains() {
239 public int getTotalLosses() {
240 return _total_losses;
243 public int getTotalUnchanged() {
244 return _total_unchanged;
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" );
256 states_in_child_nodes.addAll( states.get( node_child ) );
258 return states_in_child_nodes;
261 private void increaseCost() {
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;
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() );
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
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 ) );
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 );
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
315 getInternalStatesMatrixPriorToTraceback().setIdentifier( identifier_index,
316 ForesterUtil.isEmpty( node.getName() ) ? node
317 .getId() + "" : node.getName() );
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 ) );
329 private boolean isRandomize() {
333 private boolean isReturnGainLossMatrix() {
334 return _return_gain_loss;
337 private boolean isReturnInternalStates() {
338 return _return_internal_states;
341 private boolean isUseLast() {
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 );
354 states.put( node, states_in_children );
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() ) {
369 i = determineIndex( current_node_states, i );
370 traceback_states.put( current_node, getStateAt( i, current_node_states ) );
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 );
380 i = determineIndex( current_node_states, i );
381 traceback_states.put( current_node, getStateAt( i, current_node_states ) );
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 );
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" );
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 ) ) {
398 setGainLossState( character_state_column, current_node, LOSS );
400 else if ( ( ( parent_binary_state == ABSENT ) || ( parent_binary_state == null ) )
401 && ( current_binary_state == PRESENT ) ) {
403 setGainLossState( character_state_column, current_node, GAIN );
407 if ( current_binary_state == PRESENT ) {
408 setGainLossState( character_state_column, current_node, UNCHANGED_PRESENT );
410 else if ( current_binary_state == ABSENT ) {
411 setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );
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
421 else if ( current_binary_state == ABSENT ) {//new
422 setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new
424 // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
429 private void reset() {
433 setTotalUnchanged( 0 );
434 setRandomGenerator( new Random( getRandomNumberSeed() ) );
437 private void setCost( final int cost ) {
441 private void setGainLossMatrix( final CharacterStateMatrix<GainLossStates> gain_loss_matrix ) {
442 _gain_loss_matrix = gain_loss_matrix;
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,
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 ) );
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() + ""
467 character_state_column,
468 toListSorted( states.get( node ) ) );
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;
475 private void setInternalStatesMatrixTraceback( final CharacterStateMatrix<STATE_TYPE> internal_states_matrix_after_traceback ) {
476 _internal_states_matrix_after_traceback = internal_states_matrix_after_traceback;
479 private void setRandomGenerator( final Random random_generator ) {
480 _random_generator = random_generator;
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" );
487 _randomize = randomize;
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" );
494 _random_number_seed = random_number_seed;
497 public void setReturnGainLossMatrix( final boolean return_gain_loss ) {
498 _return_gain_loss = return_gain_loss;
501 public void setReturnInternalStates( final boolean return_internal_states ) {
502 _return_internal_states = return_internal_states;
505 private void setTotalGains( final int total_gains ) {
506 _total_gains = total_gains;
509 private void setTotalLosses( final int total_losses ) {
510 _total_losses = total_losses;
513 private void setTotalUnchanged( final int total_unchanged ) {
514 _total_unchanged = total_unchanged;
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).
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).
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" );
534 _use_last = use_last;
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 ) {