// 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
package org.forester.surfacing;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import org.forester.application.surfacing;
import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.surfacing.BinaryDomainCombination.DomainCombinationType;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
+import org.forester.protein.DomainId;
+import org.forester.species.Species;
import org.forester.util.ForesterUtil;
public final class DomainParsimonyCalculator {
setTotalUnchanged( fitch.getTotalUnchanged() );
}
+ private void executeFitchParsimonyOnSecondaryFeatures( final boolean use_last,
+ final boolean randomize,
+ final long random_number_seed ) {
+ reset();
+ if ( use_last ) {
+ System.out.println( " Fitch parsimony: use_last = true" );
+ }
+ final FitchParsimony<BinaryStates> fitch = new FitchParsimony<BinaryStates>();
+ fitch.setRandomize( randomize );
+ if ( randomize ) {
+ fitch.setRandomNumberSeed( random_number_seed );
+ }
+ fitch.setUseLast( use_last );
+ fitch.setReturnGainLossMatrix( true );
+ fitch.setReturnInternalStates( true );
+ final Map<DomainId, Set<String>> map = getDomainIdToSecondaryFeaturesMap();
+ final Map<DomainId, String> newmap = new HashMap<DomainId, String>();
+ final Iterator<Entry<DomainId, Set<String>>> it = map.entrySet().iterator();
+ while ( it.hasNext() ) {
+ final Map.Entry<DomainId, Set<String>> pair = it.next();
+ if ( pair.getValue().size() != 1 ) {
+ throw new IllegalArgumentException( pair.getKey().getId() + " mapps to " + pair.getValue().size()
+ + " items" );
+ }
+ newmap.put( pair.getKey(), ( String ) pair.getValue().toArray()[ 0 ] );
+ }
+ final CharacterStateMatrix<BinaryStates> states = createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(),
+ newmap );
+ fitch.execute( getPhylogeny(), states );
+ setGainLossMatrix( fitch.getGainLossMatrix() );
+ setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
+ setCost( fitch.getCost() );
+ setTotalGains( fitch.getTotalGains() );
+ setTotalLosses( fitch.getTotalLosses() );
+ setTotalUnchanged( fitch.getTotalUnchanged() );
+ }
+
public void executeFitchParsimonyOnBinaryDomainCombintion( final boolean use_last ) {
executeFitchParsimony( false, use_last, false, 0 );
}
+ public void executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( final boolean use_last ) {
+ executeFitchParsimonyOnSecondaryFeatures( use_last, false, 0 );
+ }
+
public void executeFitchParsimonyOnBinaryDomainCombintion( final long random_number_seed ) {
executeFitchParsimony( false, false, true, random_number_seed );
}
return new DomainParsimonyCalculator( phylogeny, gwcd_list, domain_id_to_secondary_features_map );
}
+ /**
+ * For folds instead of Pfam-domains, for example
+ *
+ *
+ * @param gwcd_list
+ * @return
+ */
+ static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeaturePresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
+ final Map<DomainId, Set<String>> domain_id_to_second_features_map,
+ final Map<Species, MappingResults> mapping_results_map ) {
+ if ( gwcd_list.isEmpty() ) {
+ throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
+ }
+ if ( ( domain_id_to_second_features_map == null ) || domain_id_to_second_features_map.isEmpty() ) {
+ throw new IllegalArgumentException( "domain id to secondary features map is null or empty" );
+ }
+ final int number_of_identifiers = gwcd_list.size();
+ final SortedSet<String> all_secondary_features = new TreeSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ int mapped = 0;
+ int not_mapped = 0;
+ for( final DomainId domain : gwcd.getAllDomainIds() ) {
+ if ( domain_id_to_second_features_map.containsKey( domain ) ) {
+ all_secondary_features.addAll( domain_id_to_second_features_map.get( domain ) );
+ mapped++;
+ }
+ else {
+ not_mapped++;
+ }
+ }
+ if ( mapping_results_map != null ) {
+ final MappingResults mr = new MappingResults();
+ mr.setDescription( gwcd.getSpecies().getSpeciesId() );
+ mr.setSumOfSuccesses( mapped );
+ mr.setSumOfFailures( not_mapped );
+ mapping_results_map.put( gwcd.getSpecies(), mr );
+ }
+ }
+ final int number_of_characters = all_secondary_features.size();
+ final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> matrix = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( number_of_identifiers,
+ number_of_characters );
+ int character_index = 0;
+ for( final String second_id : all_secondary_features ) {
+ matrix.setCharacter( character_index++, second_id );
+ }
+ int identifier_index = 0;
+ final Set<String> all_identifiers = new HashSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ final String species_id = gwcd.getSpecies().getSpeciesId();
+ if ( all_identifiers.contains( species_id ) ) {
+ throw new IllegalArgumentException( "species [" + species_id + "] is not unique" );
+ }
+ all_identifiers.add( species_id );
+ matrix.setIdentifier( identifier_index, species_id );
+ final Set<String> all_second_per_gwcd = new HashSet<String>();
+ for( final DomainId domain : gwcd.getAllDomainIds() ) {
+ if ( domain_id_to_second_features_map.containsKey( domain ) ) {
+ all_second_per_gwcd.addAll( domain_id_to_second_features_map.get( domain ) );
+ }
+ }
+ for( int ci = 0; ci < matrix.getNumberOfCharacters(); ++ci ) {
+ if ( all_second_per_gwcd.contains( matrix.getCharacter( ci ) ) ) {
+ matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
+ }
+ else {
+ matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.ABSENT );
+ }
+ }
+ ++identifier_index;
+ }
+ return matrix;
+ }
+
+ public static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
+ final Map<DomainId, String> domain_id_to_second_features_map ) {
+ if ( gwcd_list.isEmpty() ) {
+ throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
+ }
+ if ( ( domain_id_to_second_features_map == null ) || domain_id_to_second_features_map.isEmpty() ) {
+ throw new IllegalArgumentException( "domain id to secondary features map is null or empty" );
+ }
+ final int number_of_identifiers = gwcd_list.size();
+ final SortedSet<BinaryDomainCombination> all_binary_combinations_mapped = new TreeSet<BinaryDomainCombination>();
+ final Set<BinaryDomainCombination>[] binary_combinations_per_genome_mapped = new HashSet[ number_of_identifiers ];
+ int identifier_index = 0;
+ final SortedSet<String> no_mappings = new TreeSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ binary_combinations_per_genome_mapped[ identifier_index ] = new HashSet<BinaryDomainCombination>();
+ for( final BinaryDomainCombination bc : gwcd.toBinaryDomainCombinations() ) {
+ final BinaryDomainCombination mapped_bc = mapBinaryDomainCombination( domain_id_to_second_features_map,
+ bc,
+ no_mappings );
+ all_binary_combinations_mapped.add( mapped_bc );
+ binary_combinations_per_genome_mapped[ identifier_index ].add( mapped_bc );
+ }
+ ++identifier_index;
+ }
+ if ( !no_mappings.isEmpty() ) {
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "No mappings for the following (" + no_mappings.size()
+ + "):" );
+ for( final String id : no_mappings ) {
+ ForesterUtil.programMessage( surfacing.PRG_NAME, id );
+ }
+ }
+ final int number_of_characters = all_binary_combinations_mapped.size();
+ final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> matrix = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( number_of_identifiers,
+ number_of_characters );
+ int character_index = 0;
+ for( final BinaryDomainCombination bc : all_binary_combinations_mapped ) {
+ matrix.setCharacter( character_index++, bc.toString() );
+ }
+ identifier_index = 0;
+ final Set<String> all_identifiers = new HashSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ final String species_id = gwcd.getSpecies().getSpeciesId();
+ if ( all_identifiers.contains( species_id ) ) {
+ throw new AssertionError( "species [" + species_id + "] is not unique" );
+ }
+ all_identifiers.add( species_id );
+ matrix.setIdentifier( identifier_index, species_id );
+ for( int ci = 0; ci < matrix.getNumberOfCharacters(); ++ci ) {
+ BinaryDomainCombination bc = null;
+ if ( gwcd.getDomainCombinationType() == DomainCombinationType.DIRECTED_ADJACTANT ) {
+ bc = AdjactantDirectedBinaryDomainCombination.createInstance( matrix.getCharacter( ci ) );
+ }
+ else if ( gwcd.getDomainCombinationType() == DomainCombinationType.DIRECTED ) {
+ bc = DirectedBinaryDomainCombination.createInstance( matrix.getCharacter( ci ) );
+ }
+ else {
+ bc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( ci ) );
+ }
+ if ( binary_combinations_per_genome_mapped[ identifier_index ].contains( bc ) ) {
+ matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
+ }
+ else {
+ matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.ABSENT );
+ }
+ }
+ ++identifier_index;
+ }
+ return matrix;
+ }
+
+ private static BinaryDomainCombination mapBinaryDomainCombination( final Map<DomainId, String> domain_id_to_second_features_map,
+ final BinaryDomainCombination bc,
+ final SortedSet<String> no_mappings ) {
+ String id0 = "";
+ String id1 = "";
+ if ( !domain_id_to_second_features_map.containsKey( bc.getId0() ) ) {
+ no_mappings.add( bc.getId0().getId() );
+ id0 = bc.getId0().getId();
+ }
+ else {
+ id0 = domain_id_to_second_features_map.get( bc.getId0() );
+ }
+ if ( !domain_id_to_second_features_map.containsKey( bc.getId1() ) ) {
+ no_mappings.add( bc.getId1().getId() );
+ id1 = bc.getId1().getId();
+ }
+ else {
+ id1 = domain_id_to_second_features_map.get( bc.getId1() );
+ }
+ return new BasicBinaryDomainCombination( id0, id1 );
+ }
+
public static CharacterStateMatrix<BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list ) {
if ( gwcd_list.isEmpty() ) {
throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
return matrix;
}
- /**
- * For folds instead of Pfam-domains, for example
- *
- *
- * @param gwcd_list
- * @return
- */
- static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeaturePresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
- final Map<DomainId, Set<String>> domain_id_to_second_features_map,
- final Map<Species, MappingResults> mapping_results_map ) {
- if ( gwcd_list.isEmpty() ) {
- throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
- }
- if ( ( domain_id_to_second_features_map == null ) || domain_id_to_second_features_map.isEmpty() ) {
- throw new IllegalArgumentException( "domain id to secondary features map is null or empty" );
- }
- final int number_of_identifiers = gwcd_list.size();
- final SortedSet<String> all_secondary_features = new TreeSet<String>();
- for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- int mapped = 0;
- int not_mapped = 0;
- for( final DomainId domain : gwcd.getAllDomainIds() ) {
- if ( domain_id_to_second_features_map.containsKey( domain ) ) {
- all_secondary_features.addAll( domain_id_to_second_features_map.get( domain ) );
- mapped++;
- }
- else {
- not_mapped++;
- }
- }
- if ( mapping_results_map != null ) {
- final MappingResults mr = new MappingResults();
- mr.setDescription( gwcd.getSpecies().getSpeciesId() );
- mr.setSumOfSuccesses( mapped );
- mr.setSumOfFailures( not_mapped );
- mapping_results_map.put( gwcd.getSpecies(), mr );
- }
- }
- final int number_of_characters = all_secondary_features.size();
- final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> matrix = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( number_of_identifiers,
- number_of_characters );
- int character_index = 0;
- for( final String second_id : all_secondary_features ) {
- matrix.setCharacter( character_index++, second_id );
- }
- int identifier_index = 0;
- final Set<String> all_identifiers = new HashSet<String>();
- for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- final String species_id = gwcd.getSpecies().getSpeciesId();
- if ( all_identifiers.contains( species_id ) ) {
- throw new IllegalArgumentException( "species [" + species_id + "] is not unique" );
- }
- all_identifiers.add( species_id );
- matrix.setIdentifier( identifier_index, species_id );
- final Set<String> all_second_per_gwcd = new HashSet<String>();
- for( final DomainId domain : gwcd.getAllDomainIds() ) {
- if ( domain_id_to_second_features_map.containsKey( domain ) ) {
- all_second_per_gwcd.addAll( domain_id_to_second_features_map.get( domain ) );
- }
- }
- for( int ci = 0; ci < matrix.getNumberOfCharacters(); ++ci ) {
- if ( all_second_per_gwcd.contains( matrix.getCharacter( ci ) ) ) {
- matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
- }
- else {
- matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.ABSENT );
- }
- }
- ++identifier_index;
- }
- return matrix;
- }
-
private static int getStateSumDeltaOnNode( final String node_identifier,
final CharacterStateMatrix<GainLossStates> gain_loss_matrix,
final GainLossStates state ) {
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