// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.evoinference.parsimony;
+import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
public class FitchParsimony<STATE_TYPE> {
- final static private BinaryStates PRESENT = BinaryStates.PRESENT;
final static private BinaryStates ABSENT = BinaryStates.ABSENT;
- final static private GainLossStates LOSS = GainLossStates.LOSS;
final static private GainLossStates GAIN = GainLossStates.GAIN;
- final static private GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
- final static private GainLossStates UNCHANGED_ABSENT = GainLossStates.UNCHANGED_ABSENT;
- private static final boolean RETURN_INTERNAL_STATES_DEFAULT = false;
- private static final boolean RETURN_GAIN_LOSS_MATRIX_DEFAULT = false;
- private static final boolean RANDOMIZE_DEFAULT = false;
+ final static private GainLossStates LOSS = GainLossStates.LOSS;
+ final static private BinaryStates PRESENT = BinaryStates.PRESENT;
private static final long RANDOM_NUMBER_SEED_DEFAULT = 21;
+ private static final boolean RANDOMIZE_DEFAULT = false;
+ private static final boolean RETURN_GAIN_LOSS_MATRIX_DEFAULT = false;
+ private static final boolean RETURN_INTERNAL_STATES_DEFAULT = false;
+ final static private GainLossStates UNCHANGED_ABSENT = GainLossStates.UNCHANGED_ABSENT;
+ final static private GainLossStates UNCHANGED_PRESENT = GainLossStates.UNCHANGED_PRESENT;
private static final boolean USE_LAST_DEFAULT = false;
- private boolean _return_internal_states = false;
+ private int _cost;
+ private CharacterStateMatrix<GainLossStates> _gain_loss_matrix;
+ private CharacterStateMatrix<STATE_TYPE> _internal_states_matrix_after_traceback;
+ private CharacterStateMatrix<List<STATE_TYPE>> _internal_states_matrix_prior_to_traceback;
+ private Random _random_generator;
+ private long _random_number_seed;
+ private boolean _randomize;
private boolean _return_gain_loss = false;
+ private boolean _return_internal_states = false;
private int _total_gains;
private int _total_losses;
private int _total_unchanged;
- private CharacterStateMatrix<List<STATE_TYPE>> _internal_states_matrix_prior_to_traceback;
- private CharacterStateMatrix<STATE_TYPE> _internal_states_matrix_after_traceback;
- private CharacterStateMatrix<GainLossStates> _gain_loss_matrix;
- private boolean _randomize;
private boolean _use_last;
- private int _cost;
- private long _random_number_seed;
- private Random _random_generator;
+ private boolean _verbose = false;
public FitchParsimony() {
init();
}
- private int determineIndex( final SortedSet<STATE_TYPE> current_node_states, int i ) {
- if ( isRandomize() ) {
- i = getRandomGenerator().nextInt( current_node_states.size() );
- }
- else if ( isUseLast() ) {
- i = current_node_states.size() - 1;
- }
- return i;
+ public void execute( final Phylogeny p, final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
+ execute( p, external_node_states_matrix, false );
}
- public void execute( final Phylogeny p, final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix ) {
+ public void execute( final Phylogeny p,
+ final CharacterStateMatrix<STATE_TYPE> external_node_states_matrix,
+ final boolean verbose ) {
if ( !p.isRooted() ) {
throw new IllegalArgumentException( "attempt to execute Fitch parsimony on unroored phylogeny" );
}
+ p.getNumberOfExternalNodes() + "] and number of indentifiers ["
+ external_node_states_matrix.getNumberOfIdentifiers() + "] in matrix are not equal" );
}
+ setVerbose( verbose );
reset();
if ( isReturnInternalStates() ) {
initializeInternalStates( p, external_node_states_matrix );
if ( isReturnGainLossMatrix() ) {
initializeGainLossMatrix( p, external_node_states_matrix );
}
+ final DecimalFormat pf = new java.text.DecimalFormat( "000000" );
+ if ( isVerbose() ) {
+ System.out.println( "Number of characters: " + external_node_states_matrix.getNumberOfCharacters() );
+ }
for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
+ if ( isVerbose() ) {
+ ForesterUtil.updateProgress( character_index, pf );
+ }
executeForOneCharacter( p,
getStatesForCharacter( p, external_node_states_matrix, character_index ),
getStatesForCharacterForTraceback( p, external_node_states_matrix, character_index ),
character_index );
}
+ if ( isVerbose() ) {
+ System.out.println();
+ }
if ( external_node_states_matrix.getState( 0, 0 ) instanceof BinaryStates ) {
if ( ( external_node_states_matrix.getNumberOfCharacters() * p.getNumberOfBranches() ) != ( getTotalGains()
+ getTotalLosses() + getTotalUnchanged() ) ) {
}
}
- private void executeForOneCharacter( final Phylogeny p,
- final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
- final Map<PhylogenyNode, STATE_TYPE> traceback_states,
- final int character_state_column ) {
- postOrderTraversal( p, states );
- preOrderTraversal( p, states, traceback_states, character_state_column );
- }
-
public int getCost() {
return _cost;
}
return _internal_states_matrix_prior_to_traceback;
}
+ public int getTotalGains() {
+ return _total_gains;
+ }
+
+ public int getTotalLosses() {
+ return _total_losses;
+ }
+
+ public int getTotalUnchanged() {
+ return _total_unchanged;
+ }
+
+ public boolean isVerbose() {
+ return _verbose;
+ }
+
+ public void setRandomize( final boolean randomize ) {
+ if ( randomize && isUseLast() ) {
+ throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
+ }
+ _randomize = randomize;
+ }
+
+ public void setRandomNumberSeed( final long random_number_seed ) {
+ if ( !isRandomize() ) {
+ throw new IllegalArgumentException( "attempt to set random number generator seed without randomization enabled" );
+ }
+ _random_number_seed = random_number_seed;
+ }
+
+ public void setReturnGainLossMatrix( final boolean return_gain_loss ) {
+ _return_gain_loss = return_gain_loss;
+ }
+
+ public void setReturnInternalStates( final boolean return_internal_states ) {
+ _return_internal_states = return_internal_states;
+ }
+
+ /**
+ * This sets whether to use the first or last state in the sorted
+ * states at the undecided internal nodes.
+ * For randomized choices set randomize to true (and this to false).
+ *
+ * Note. It might be advisable to set this to false
+ * for BinaryStates if absence at the root is preferred
+ * (given the enum BinaryStates sorts in the following order:
+ * ABSENT, UNKNOWN, PRESENT).
+ *
+ *
+ * @param use_last
+ */
+ public void setUseLast( final boolean use_last ) {
+ if ( use_last && isRandomize() ) {
+ throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
+ }
+ _use_last = use_last;
+ }
+
+ public void setVerbose( final boolean verbose ) {
+ _verbose = verbose;
+ }
+
+ private int determineIndex( final SortedSet<STATE_TYPE> current_node_states, int i ) {
+ if ( isRandomize() ) {
+ i = getRandomGenerator().nextInt( current_node_states.size() );
+ }
+ else if ( isUseLast() ) {
+ i = current_node_states.size() - 1;
+ }
+ return i;
+ }
+
+ private void executeForOneCharacter( final Phylogeny p,
+ final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
+ final Map<PhylogenyNode, STATE_TYPE> traceback_states,
+ final int character_state_column ) {
+ postOrderTraversal( p, states );
+ preOrderTraversal( p, states, traceback_states, character_state_column );
+ }
+
private SortedSet<STATE_TYPE> getIntersectionOfStatesOfChildNodes( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
final PhylogenyNode node ) throws AssertionError {
final SortedSet<STATE_TYPE> states_in_child_nodes = new TreeSet<STATE_TYPE>();
private Map<PhylogenyNode, STATE_TYPE> getStatesForCharacterForTraceback( final Phylogeny p,
final CharacterStateMatrix<STATE_TYPE> matrix,
final int character_index ) {
- final Map<PhylogenyNode, STATE_TYPE> states = new HashMap<PhylogenyNode, STATE_TYPE>( matrix
- .getNumberOfIdentifiers() );
+ final Map<PhylogenyNode, STATE_TYPE> states = new HashMap<PhylogenyNode, STATE_TYPE>( matrix.getNumberOfIdentifiers() );
for( int indentifier_index = 0; indentifier_index < matrix.getNumberOfIdentifiers(); ++indentifier_index ) {
final STATE_TYPE state = matrix.getState( indentifier_index, character_index );
if ( state == null ) {
return states;
}
- public int getTotalGains() {
- return _total_gains;
- }
-
- public int getTotalLosses() {
- return _total_losses;
- }
-
- public int getTotalUnchanged() {
- return _total_unchanged;
- }
-
private SortedSet<STATE_TYPE> getUnionOfStatesOfChildNodes( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
final PhylogenyNode node ) throws AssertionError {
final SortedSet<STATE_TYPE> states_in_child_nodes = new TreeSet<STATE_TYPE>();
.getName() );
getInternalStatesMatrixPriorToTraceback().setIdentifier( identifier_index,
ForesterUtil.isEmpty( node.getName() ) ? node
- .getId()
- + "" : node.getName() );
+ .getId() + "" : node.getName() );
++identifier_index;
}
for( int character_index = 0; character_index < external_node_states_matrix.getNumberOfCharacters(); ++character_index ) {
return _use_last;
}
- private void postOrderTraversal( final Phylogeny p, final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states )
- throws AssertionError {
+ private void postOrderTraversal( final Phylogeny p, final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states ) {
for( final PhylogenyNodeIterator postorder = p.iteratorPostorder(); postorder.hasNext(); ) {
final PhylogenyNode node = postorder.next();
if ( !node.isExternal() ) {
private void preOrderTraversal( final Phylogeny p,
final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
final Map<PhylogenyNode, STATE_TYPE> traceback_states,
- final int character_state_column ) throws AssertionError {
+ final int character_state_column ) {
for( final PhylogenyNodeIterator preorder = p.iteratorPreorder(); preorder.hasNext(); ) {
final PhylogenyNode current_node = preorder.next();
final SortedSet<STATE_TYPE> current_node_states = states.get( current_node );
else if ( current_binary_state == ABSENT ) {//new
setGainLossState( character_state_column, current_node, UNCHANGED_ABSENT );//new
}//new
- // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
+ // setGainLossState( character_state_column, current_node, UNKNOWN_GAIN_LOSS );
}
}
}
private void setInternalNodeStatePriorToTraceback( final Map<PhylogenyNode, SortedSet<STATE_TYPE>> states,
final int character_state_column,
final PhylogenyNode node ) {
- getInternalStatesMatrixPriorToTraceback().setState( ForesterUtil.isEmpty( node.getName() ) ? node.getId() + ""
- : node.getName(),
- character_state_column,
- toListSorted( states.get( node ) ) );
+ getInternalStatesMatrixPriorToTraceback()
+ .setState( ForesterUtil.isEmpty( node.getName() ) ? String.valueOf( node.getId() ) : node.getName(),
+ character_state_column,
+ toListSorted( states.get( node ) ) );
}
private void setInternalStatesMatrixPriorToTraceback( final CharacterStateMatrix<List<STATE_TYPE>> internal_states_matrix_prior_to_traceback ) {
_random_generator = random_generator;
}
- public void setRandomize( final boolean randomize ) {
- if ( randomize && isUseLast() ) {
- throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
- }
- _randomize = randomize;
- }
-
- public void setRandomNumberSeed( final long random_number_seed ) {
- if ( !isRandomize() ) {
- throw new IllegalArgumentException( "attempt to set random number generator seed without randomization enabled" );
- }
- _random_number_seed = random_number_seed;
- }
-
- public void setReturnGainLossMatrix( final boolean return_gain_loss ) {
- _return_gain_loss = return_gain_loss;
- }
-
- public void setReturnInternalStates( final boolean return_internal_states ) {
- _return_internal_states = return_internal_states;
- }
-
private void setTotalGains( final int total_gains ) {
_total_gains = total_gains;
}
_total_unchanged = total_unchanged;
}
- /**
- * This sets whether to use the first or last state in the sorted
- * states at the undecided internal nodes.
- * For randomized choices set randomize to true (and this to false).
- *
- * Note. It might be advisable to set this to false
- * for BinaryStates if absence at the root is preferred
- * (given the enum BinaryStates sorts in the following order:
- * ABSENT, UNKNOWN, PRESENT).
- *
- *
- * @param use_last
- */
- public void setUseLast( final boolean use_last ) {
- if ( use_last && isRandomize() ) {
- throw new IllegalArgumentException( "attempt to allways use last state (ordered) if more than one choices and randomization at the same time" );
- }
- _use_last = use_last;
- }
-
private List<STATE_TYPE> toListSorted( final SortedSet<STATE_TYPE> states ) {
final List<STATE_TYPE> l = new ArrayList<STATE_TYPE>( states.size() );
for( final STATE_TYPE state : states ) {
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