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/forester
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.FailedConditionCheckException;
46 import org.forester.util.ForesterUtil;
48 public class FitchParsimony<STATE_TYPE> {
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;
72 private long _random_number_seed;
73 private Random _random_generator;
75 public FitchParsimony() {
79 private int determineIndex( final SortedSet<STATE_TYPE> current_node_states, int i ) {
80 if ( isRandomize() ) {
81 i = getRandomGenerator().nextInt( current_node_states.size() );
83 else if ( isUseLast() ) {
84 i = current_node_states.size() - 1;
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" );
93 if ( external_node_states_matrix.isEmpty() ) {
94 throw new IllegalArgumentException( "character matrix is empty" );
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" );
102 if ( isReturnInternalStates() ) {
103 initializeInternalStates( p, external_node_states_matrix );
105 if ( isReturnGainLossMatrix() ) {
106 initializeGainLossMatrix( p, external_node_states_matrix );
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 ),
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" );
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 );
130 public int getCost() {
134 public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix() {
135 if ( !isReturnGainLossMatrix() ) {
136 throw new RuntimeException( "creation of gain-loss matrix has not been enabled" );
138 return _gain_loss_matrix;
141 public CharacterStateMatrix<STATE_TYPE> getInternalStatesMatrix() {
142 if ( !isReturnInternalStates() ) {
143 throw new RuntimeException( "creation of internal state matrix has not been enabled" );
145 return _internal_states_matrix_after_traceback;
149 * Returns a view of the internal states prior to trace-back.
153 public CharacterStateMatrix<List<STATE_TYPE>> getInternalStatesMatrixPriorToTraceback() {
154 if ( !isReturnInternalStates() ) {
155 throw new RuntimeException( "creation of internal state matrix has not been enabled" );
157 return _internal_states_matrix_prior_to_traceback;
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" );
170 states_in_child_nodes.addAll( states.get( node_child ) );
173 states_in_child_nodes.retainAll( states.get( node_child ) );
176 return states_in_child_nodes;
179 private Random getRandomGenerator() {
180 return _random_generator;
183 private long getRandomNumberSeed() {
184 return _random_number_seed;
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 ) {
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
206 final SortedSet<STATE_TYPE> l = new TreeSet<STATE_TYPE>();
208 states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), l );
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
223 states.put( p.getNode( matrix.getIdentifier( indentifier_index ) ), state );
228 public int getTotalGains() {
232 public int getTotalLosses() {
233 return _total_losses;
236 public int getTotalUnchanged() {
237 return _total_unchanged;
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" );
249 states_in_child_nodes.addAll( states.get( node_child ) );
251 return states_in_child_nodes;
254 private void increaseCost() {
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;
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() );
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
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 ) );
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 );
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
308 getInternalStatesMatrixPriorToTraceback().setIdentifier( identifier_index,
309 ForesterUtil.isEmpty( node.getName() ) ? node
310 .getId() + "" : node.getName() );
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 ) );
322 private boolean isRandomize() {
326 private boolean isReturnGainLossMatrix() {
327 return _return_gain_loss;
330 private boolean isReturnInternalStates() {
331 return _return_internal_states;
334 private boolean isUseLast() {
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 );
347 states.put( node, states_in_children );
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() ) {
362 i = determineIndex( current_node_states, i );
363 traceback_states.put( current_node, getStateAt( i, current_node_states ) );
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 );
373 i = determineIndex( current_node_states, i );
374 traceback_states.put( current_node, getStateAt( i, current_node_states ) );
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 );
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" );
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 ) ) {
391 setGainLossState( character_state_column, current_node, LOSS );
393 else if ( ( ( parent_binary_state == ABSENT ) || ( parent_binary_state == null ) )
394 && ( current_binary_state == PRESENT ) ) {
396 setGainLossState( character_state_column, current_node, GAIN );
400 if ( current_binary_state == PRESENT ) {
401 setGainLossState( character_state_column, current_node, UNCHANGED_PRESENT );
403 else if ( current_binary_state == ABSENT ) {
404 setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );
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
414 else if ( current_binary_state == ABSENT ) {//new
415 setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new
417 // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
422 private void reset() {
426 setTotalUnchanged( 0 );
427 setRandomGenerator( new Random( getRandomNumberSeed() ) );
430 private void setCost( final int cost ) {
434 private void setGainLossMatrix( final CharacterStateMatrix<GainLossStates> gain_loss_matrix ) {
435 _gain_loss_matrix = gain_loss_matrix;
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,
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 ) );
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() + ""
460 character_state_column,
461 toListSorted( states.get( node ) ) );
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;
468 private void setInternalStatesMatrixTraceback( final CharacterStateMatrix<STATE_TYPE> internal_states_matrix_after_traceback ) {
469 _internal_states_matrix_after_traceback = internal_states_matrix_after_traceback;
472 private void setRandomGenerator( final Random random_generator ) {
473 _random_generator = random_generator;
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" );
480 _randomize = randomize;
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" );
487 _random_number_seed = random_number_seed;
490 public void setReturnGainLossMatrix( final boolean return_gain_loss ) {
491 _return_gain_loss = return_gain_loss;
494 public void setReturnInternalStates( final boolean return_internal_states ) {
495 _return_internal_states = return_internal_states;
498 private void setTotalGains( final int total_gains ) {
499 _total_gains = total_gains;
502 private void setTotalLosses( final int total_losses ) {
503 _total_losses = total_losses;
506 private void setTotalUnchanged( final int total_unchanged ) {
507 _total_unchanged = total_unchanged;
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).
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).
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" );
527 _use_last = use_last;
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 ) {