// 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.surfacing;
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.species.Species;
import org.forester.util.ForesterUtil;
public final class DomainParsimonyCalculator {
private static final String TYPE_FORBINARY_CHARACTERS = "parsimony inferred";
- private CharacterStateMatrix<GainLossStates> _gain_loss_matrix;
private CharacterStateMatrix<BinaryStates> _binary_internal_states_matrix;
+ private int _cost;
+ private Map<String, Set<String>> _domain_id_to_secondary_features_map;
+ private CharacterStateMatrix<GainLossStates> _gain_loss_matrix;
private final List<GenomeWideCombinableDomains> _gwcd_list;
private final Phylogeny _phylogeny;
- private int _total_losses;
+ private SortedSet<String> _positive_filter;
private int _total_gains;
+ private int _total_losses;
private int _total_unchanged;
- private int _cost;
- private Map<DomainId, Set<String>> _domain_id_to_secondary_features_map;
- private SortedSet<DomainId> _positive_filter;
private DomainParsimonyCalculator( final Phylogeny phylogeny ) {
init();
private DomainParsimonyCalculator( final Phylogeny phylogeny,
final List<GenomeWideCombinableDomains> gwcd_list,
- final Map<DomainId, Set<String>> domain_id_to_secondary_features_map ) {
+ final Map<String, Set<String>> domain_id_to_secondary_features_map ) {
init();
_phylogeny = phylogeny;
_gwcd_list = gwcd_list;
setDomainIdToSecondaryFeaturesMap( domain_id_to_secondary_features_map );
}
- int calculateNumberOfBinaryDomainCombination() {
- if ( getGenomeWideCombinableDomainsList().isEmpty() ) {
- throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
- }
- final Set<BinaryDomainCombination> all_binary_combinations = new HashSet<BinaryDomainCombination>();
- for( final GenomeWideCombinableDomains gwcd : getGenomeWideCombinableDomainsList() ) {
- for( final BinaryDomainCombination bc : gwcd.toBinaryDomainCombinations() ) {
- all_binary_combinations.add( bc );
- }
- }
- return all_binary_combinations.size();
- }
-
- CharacterStateMatrix<BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence() {
- return createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
- }
-
- CharacterStateMatrix<BinaryStates> createMatrixOfDomainPresenceOrAbsence() {
- return createMatrixOfDomainPresenceOrAbsence( getGenomeWideCombinableDomainsList(), getPositiveFilter() );
- }
-
- CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeaturePresenceOrAbsence( final Map<Species, MappingResults> mapping_results_map ) {
- return createMatrixOfSecondaryFeaturePresenceOrAbsence( getGenomeWideCombinableDomainsList(),
- getDomainIdToSecondaryFeaturesMap(),
- mapping_results_map );
- }
-
- Phylogeny decoratePhylogenyWithDomains( final Phylogeny phylogeny ) {
- for( final PhylogenyNodeIterator it = phylogeny.iteratorPostorder(); it.hasNext(); ) {
- final PhylogenyNode node = it.next();
- final String node_identifier = node.getName();
- final BinaryCharacters bc = new BinaryCharacters( getUnitsOnNode( node_identifier ),
- getUnitsGainedOnNode( node_identifier ),
- getUnitsLostOnNode( node_identifier ),
- TYPE_FORBINARY_CHARACTERS,
- getSumOfPresentOnNode( node_identifier ),
- getSumOfGainsOnNode( node_identifier ),
- getSumOfLossesOnNode( node_identifier ) );
- node.getNodeData().setBinaryCharacters( bc );
- }
- return phylogeny;
- }
-
- private void executeDolloParsimony( final boolean on_domain_presence ) {
- reset();
- final DolloParsimony dollo = DolloParsimony.createInstance();
- dollo.setReturnGainLossMatrix( true );
- dollo.setReturnInternalStates( true );
- CharacterStateMatrix<BinaryStates> states = null;
- if ( on_domain_presence ) {
- states = createMatrixOfDomainPresenceOrAbsence();
- }
- else {
- states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence();
- }
- dollo.execute( getPhylogeny(), states );
- setGainLossMatrix( dollo.getGainLossMatrix() );
- setBinaryInternalStatesMatrix( dollo.getInternalStatesMatrix() );
- setCost( dollo.getCost() );
- setTotalGains( dollo.getTotalGains() );
- setTotalLosses( dollo.getTotalLosses() );
- setTotalUnchanged( dollo.getTotalUnchanged() );
- }
-
public void executeDolloParsimonyOnBinaryDomainCombintionPresence() {
executeDolloParsimony( false );
}
executeDolloParsimony( true );
}
- public void executeDolloParsimonyOnDomainPresence( final SortedSet<DomainId> positive_filter ) {
+ public void executeDolloParsimonyOnDomainPresence( final SortedSet<String> positive_filter ) {
setPositiveFilter( positive_filter );
executeDolloParsimony( true );
setPositiveFilter( null );
setTotalUnchanged( dollo.getTotalUnchanged() );
}
- private void executeFitchParsimony( final boolean on_domain_presence,
- 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 );
- CharacterStateMatrix<BinaryStates> states = null;
- if ( on_domain_presence ) {
- states = createMatrixOfDomainPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
- }
- else {
- states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
- }
- fitch.execute( getPhylogeny(), states );
- setGainLossMatrix( fitch.getGainLossMatrix() );
- setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
- setCost( fitch.getCost() );
- setTotalGains( fitch.getTotalGains() );
- setTotalLosses( fitch.getTotalLosses() );
- 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 );
}
+ public void executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( final boolean use_last ) {
+ executeFitchParsimonyOnSecondaryFeatures( use_last, false, 0 );
+ }
+
public void executeFitchParsimonyOnDomainPresence( final boolean use_last ) {
executeFitchParsimony( true, use_last, false, 0 );
}
return _cost;
}
- private Map<DomainId, Set<String>> getDomainIdToSecondaryFeaturesMap() {
- return _domain_id_to_secondary_features_map;
- }
-
public CharacterStateMatrix<Integer> getGainLossCountsMatrix() {
final CharacterStateMatrix<Integer> matrix = new BasicCharacterStateMatrix<Integer>( getGainLossMatrix()
.getNumberOfIdentifiers(), 3 );
return _gain_loss_matrix;
}
- private List<GenomeWideCombinableDomains> getGenomeWideCombinableDomainsList() {
- return _gwcd_list;
- }
-
public CharacterStateMatrix<BinaryStates> getInternalStatesMatrix() {
return _binary_internal_states_matrix;
}
return net;
}
- private Phylogeny getPhylogeny() {
- return _phylogeny;
- }
-
- private SortedSet<DomainId> getPositiveFilter() {
- return _positive_filter;
- }
-
public int getSumOfGainsOnNode( final String node_identifier ) {
return getStateSumDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.GAIN );
}
return getSumOfGainsOnNode( node_identifier ) + getSumOfUnchangedPresentOnNode( node_identifier );
}
+ public int getTotalGains() {
+ return _total_gains;
+ }
+
+ public int getTotalLosses() {
+ return _total_losses;
+ }
+
+ public int getTotalUnchanged() {
+ return _total_unchanged;
+ }
+
+ public SortedSet<String> getUnitsGainedOnNode( final String node_identifier ) {
+ return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.GAIN );
+ }
+
+ public SortedSet<String> getUnitsLostOnNode( final String node_identifier ) {
+ return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.LOSS );
+ }
+
+ public SortedSet<String> getUnitsOnNode( final String node_identifier ) {
+ final SortedSet<String> present = getUnitsGainedOnNode( node_identifier );
+ present.addAll( getUnitsUnchangedPresentOnNode( node_identifier ) );
+ return present;
+ }
+
+ int calculateNumberOfBinaryDomainCombination() {
+ if ( getGenomeWideCombinableDomainsList().isEmpty() ) {
+ throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
+ }
+ final Set<BinaryDomainCombination> all_binary_combinations = new HashSet<BinaryDomainCombination>();
+ for( final GenomeWideCombinableDomains gwcd : getGenomeWideCombinableDomainsList() ) {
+ for( final BinaryDomainCombination bc : gwcd.toBinaryDomainCombinations() ) {
+ all_binary_combinations.add( bc );
+ }
+ }
+ return all_binary_combinations.size();
+ }
+
+ CharacterStateMatrix<BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence() {
+ return createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
+ }
+
+ CharacterStateMatrix<BinaryStates> createMatrixOfDomainPresenceOrAbsence() {
+ return createMatrixOfDomainPresenceOrAbsence( getGenomeWideCombinableDomainsList(), getPositiveFilter() );
+ }
+
+ CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeaturePresenceOrAbsence( final Map<Species, MappingResults> mapping_results_map ) {
+ return createMatrixOfSecondaryFeaturePresenceOrAbsence( getGenomeWideCombinableDomainsList(),
+ getDomainIdToSecondaryFeaturesMap(),
+ mapping_results_map );
+ }
+
+ Phylogeny decoratePhylogenyWithDomains( final Phylogeny phylogeny ) {
+ for( final PhylogenyNodeIterator it = phylogeny.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode node = it.next();
+ final String node_identifier = node.getName();
+ final BinaryCharacters bc = new BinaryCharacters( getUnitsOnNode( node_identifier ),
+ getUnitsGainedOnNode( node_identifier ),
+ getUnitsLostOnNode( node_identifier ),
+ TYPE_FORBINARY_CHARACTERS,
+ getSumOfPresentOnNode( node_identifier ),
+ getSumOfGainsOnNode( node_identifier ),
+ getSumOfLossesOnNode( node_identifier ) );
+ node.getNodeData().setBinaryCharacters( bc );
+ }
+ return phylogeny;
+ }
+
int getSumOfUnchangedAbsentOnNode( final String node_identifier ) {
return getStateSumDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.UNCHANGED_ABSENT );
}
return getStateSumDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.UNCHANGED_PRESENT );
}
- public int getTotalGains() {
- return _total_gains;
+ SortedSet<String> getUnitsUnchangedAbsentOnNode( final String node_identifier ) {
+ return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.UNCHANGED_ABSENT );
}
- public int getTotalLosses() {
- return _total_losses;
+ SortedSet<String> getUnitsUnchangedPresentOnNode( final String node_identifier ) {
+ return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.UNCHANGED_PRESENT );
}
- public int getTotalUnchanged() {
- return _total_unchanged;
+ private void executeDolloParsimony( final boolean on_domain_presence ) {
+ reset();
+ final DolloParsimony dollo = DolloParsimony.createInstance();
+ dollo.setReturnGainLossMatrix( true );
+ dollo.setReturnInternalStates( true );
+ CharacterStateMatrix<BinaryStates> states = null;
+ if ( on_domain_presence ) {
+ states = createMatrixOfDomainPresenceOrAbsence();
+ }
+ else {
+ states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence();
+ }
+ dollo.execute( getPhylogeny(), states );
+ setGainLossMatrix( dollo.getGainLossMatrix() );
+ setBinaryInternalStatesMatrix( dollo.getInternalStatesMatrix() );
+ setCost( dollo.getCost() );
+ setTotalGains( dollo.getTotalGains() );
+ setTotalLosses( dollo.getTotalLosses() );
+ setTotalUnchanged( dollo.getTotalUnchanged() );
}
- public SortedSet<String> getUnitsGainedOnNode( final String node_identifier ) {
- return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.GAIN );
+ private void executeFitchParsimony( final boolean on_domain_presence,
+ 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 );
+ CharacterStateMatrix<BinaryStates> states = null;
+ if ( on_domain_presence ) {
+ states = createMatrixOfDomainPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
+ }
+ else {
+ states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
+ }
+ fitch.execute( getPhylogeny(), states, true );
+ setGainLossMatrix( fitch.getGainLossMatrix() );
+ setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
+ setCost( fitch.getCost() );
+ setTotalGains( fitch.getTotalGains() );
+ setTotalLosses( fitch.getTotalLosses() );
+ 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<String, Set<String>> map = getDomainIdToSecondaryFeaturesMap();
+ final Map<String, String> newmap = new HashMap<String, String>();
+ final Iterator<Entry<String, Set<String>>> it = map.entrySet().iterator();
+ while ( it.hasNext() ) {
+ final Map.Entry<String, Set<String>> pair = it.next();
+ if ( pair.getValue().size() != 1 ) {
+ throw new IllegalArgumentException( pair.getKey() + " 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, true );
+ setGainLossMatrix( fitch.getGainLossMatrix() );
+ setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
+ setCost( fitch.getCost() );
+ setTotalGains( fitch.getTotalGains() );
+ setTotalLosses( fitch.getTotalLosses() );
+ setTotalUnchanged( fitch.getTotalUnchanged() );
}
- public SortedSet<String> getUnitsLostOnNode( final String node_identifier ) {
- return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.LOSS );
+ private Map<String, Set<String>> getDomainIdToSecondaryFeaturesMap() {
+ return _domain_id_to_secondary_features_map;
}
- public SortedSet<String> getUnitsOnNode( final String node_identifier ) {
- final SortedSet<String> present = getUnitsGainedOnNode( node_identifier );
- present.addAll( getUnitsUnchangedPresentOnNode( node_identifier ) );
- return present;
+ private List<GenomeWideCombinableDomains> getGenomeWideCombinableDomainsList() {
+ return _gwcd_list;
}
- SortedSet<String> getUnitsUnchangedAbsentOnNode( final String node_identifier ) {
- return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.UNCHANGED_ABSENT );
+ private Phylogeny getPhylogeny() {
+ return _phylogeny;
}
- SortedSet<String> getUnitsUnchangedPresentOnNode( final String node_identifier ) {
- return getUnitsDeltaOnNode( node_identifier, getGainLossMatrix(), GainLossStates.UNCHANGED_PRESENT );
+ private SortedSet<String> getPositiveFilter() {
+ return _positive_filter;
}
private void init() {
_cost = cost;
}
- private void setDomainIdToSecondaryFeaturesMap( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map ) {
+ private void setDomainIdToSecondaryFeaturesMap( final Map<String, Set<String>> domain_id_to_secondary_features_map ) {
_domain_id_to_secondary_features_map = domain_id_to_secondary_features_map;
}
_gain_loss_matrix = gain_loss_matrix;
}
- private void setPositiveFilter( final SortedSet<DomainId> positive_filter ) {
+ private void setPositiveFilter( final SortedSet<String> positive_filter ) {
_positive_filter = positive_filter;
}
public static DomainParsimonyCalculator createInstance( final Phylogeny phylogeny,
final List<GenomeWideCombinableDomains> gwcd_list,
- final Map<DomainId, Set<String>> domain_id_to_secondary_features_map ) {
+ final Map<String, Set<String>> domain_id_to_secondary_features_map ) {
if ( phylogeny.getNumberOfExternalNodes() != gwcd_list.size() ) {
throw new IllegalArgumentException( "size of external nodes does not equal size of genome wide combinable domains list" );
}
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 ) {
+ public static CharacterStateMatrix<BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list ) {
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>();
+ final SortedSet<BinaryDomainCombination> all_binary_combinations = new TreeSet<BinaryDomainCombination>();
+ final Set<BinaryDomainCombination>[] binary_combinations_per_genome = new HashSet[ number_of_identifiers ];
+ int identifier_index = 0;
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 );
+ binary_combinations_per_genome[ identifier_index ] = new HashSet<BinaryDomainCombination>();
+ for( final BinaryDomainCombination bc : gwcd.toBinaryDomainCombinations() ) {
+ all_binary_combinations.add( bc );
+ binary_combinations_per_genome[ identifier_index ].add( bc );
}
+ ++identifier_index;
}
- final int number_of_characters = all_secondary_features.size();
+ final int number_of_characters = all_binary_combinations.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 );
+ for( final BinaryDomainCombination bc : all_binary_combinations ) {
+ matrix.setCharacter( character_index++, bc.toString() );
}
- int identifier_index = 0;
+ 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" );
+ throw new AssertionError( "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 ) ) ) {
+ BinaryDomainCombination bc = null;
+ if ( gwcd.getDomainCombinationType() == DomainCombinationType.DIRECTED_ADJACTANT ) {
+ bc = AdjactantDirectedBinaryDomainCombination.obtainInstance( matrix.getCharacter( ci ) );
+ }
+ else if ( gwcd.getDomainCombinationType() == DomainCombinationType.DIRECTED ) {
+ bc = DirectedBinaryDomainCombination.obtainInstance( matrix.getCharacter( ci ) );
+ }
+ else {
+ bc = BasicBinaryDomainCombination.obtainInstance( matrix.getCharacter( ci ) );
+ }
+ if ( binary_combinations_per_genome[ identifier_index ].contains( bc ) ) {
matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
}
else {
return matrix;
}
- public static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
- final Map<DomainId, String> domain_id_to_second_features_map ) {
+ public static CharacterStateMatrix<BinaryStates> createMatrixOfDomainPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
+ final SortedSet<String> positive_filter ) {
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" );
+ if ( ( positive_filter != null ) && ( positive_filter.size() < 1 ) ) {
+ throw new IllegalArgumentException( "positive filter is 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>();
+ final SortedSet<String> all_domain_ids = 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 );
+ for( final String domain : gwcd.getAllDomainIds() ) {
+ all_domain_ids.add( domain );
}
- ++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 );
+ int number_of_characters = all_domain_ids.size();
+ if ( positive_filter != null ) {
+ //number_of_characters = positive_filter.size(); -- bad if doms in filter but not in genomes
+ number_of_characters = 0;
+ for( final String id : all_domain_ids ) {
+ if ( positive_filter.contains( id ) ) {
+ number_of_characters++;
+ }
}
}
- 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() );
+ for( final String id : all_domain_ids ) {
+ if ( positive_filter == null ) {
+ matrix.setCharacter( character_index++, id );
+ }
+ else {
+ if ( positive_filter.contains( id ) ) {
+ matrix.setCharacter( character_index++, id );
+ }
+ }
}
- identifier_index = 0;
+ 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 AssertionError( "species [" + species_id + "] is not unique" );
+ throw new IllegalArgumentException( "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 ( ForesterUtil.isEmpty( matrix.getCharacter( ci ) ) ) {
+ throw new RuntimeException( "this should not have happened: problem with character #" + ci );
}
- if ( binary_combinations_per_genome_mapped[ identifier_index ].contains( bc ) ) {
+ final String id = matrix.getCharacter( ci );
+ if ( gwcd.contains( id ) ) {
matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
}
else {
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 ) {
+ public static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
+ final Map<String, 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 = new TreeSet<BinaryDomainCombination>();
- final Set<BinaryDomainCombination>[] binary_combinations_per_genome = new HashSet[ number_of_identifiers ];
+ 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[ identifier_index ] = new HashSet<BinaryDomainCombination>();
+ binary_combinations_per_genome_mapped[ identifier_index ] = new HashSet<BinaryDomainCombination>();
for( final BinaryDomainCombination bc : gwcd.toBinaryDomainCombinations() ) {
- all_binary_combinations.add( bc );
- binary_combinations_per_genome[ identifier_index ].add( bc );
+ 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;
}
- final int number_of_characters = all_binary_combinations.size();
+ 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 ) {
+ for( final BinaryDomainCombination bc : all_binary_combinations_mapped ) {
matrix.setCharacter( character_index++, bc.toString() );
}
identifier_index = 0;
for( int ci = 0; ci < matrix.getNumberOfCharacters(); ++ci ) {
BinaryDomainCombination bc = null;
if ( gwcd.getDomainCombinationType() == DomainCombinationType.DIRECTED_ADJACTANT ) {
- bc = AdjactantDirectedBinaryDomainCombination.createInstance( matrix.getCharacter( ci ) );
+ bc = AdjactantDirectedBinaryDomainCombination.obtainInstance( matrix.getCharacter( ci ) );
}
else if ( gwcd.getDomainCombinationType() == DomainCombinationType.DIRECTED ) {
- bc = DirectedBinaryDomainCombination.createInstance( matrix.getCharacter( ci ) );
+ bc = DirectedBinaryDomainCombination.obtainInstance( matrix.getCharacter( ci ) );
}
else {
- bc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( ci ) );
+ bc = BasicBinaryDomainCombination.obtainInstance( matrix.getCharacter( ci ) );
}
- if ( binary_combinations_per_genome[ identifier_index ].contains( bc ) ) {
+ if ( binary_combinations_per_genome_mapped[ identifier_index ].contains( bc ) ) {
matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
}
else {
return createMatrixOfDomainPresenceOrAbsence( gwcd_list, null );
}
- public static CharacterStateMatrix<BinaryStates> createMatrixOfDomainPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
- final SortedSet<DomainId> positive_filter ) {
+ /**
+ * For folds instead of Pfam-domains, for example
+ *
+ *
+ * @param gwcd_list
+ * @return
+ */
+ static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeaturePresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
+ final Map<String, 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 ( ( positive_filter != null ) && ( positive_filter.size() < 1 ) ) {
- throw new IllegalArgumentException( "positive filter 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<DomainId> all_domain_ids = new TreeSet<DomainId>();
+ final SortedSet<String> all_secondary_features = new TreeSet<String>();
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- for( final DomainId domain : gwcd.getAllDomainIds() ) {
- all_domain_ids.add( domain );
- }
- }
- int number_of_characters = all_domain_ids.size();
- if ( positive_filter != null ) {
- //number_of_characters = positive_filter.size(); -- bad if doms in filter but not in genomes
- number_of_characters = 0;
- for( final DomainId id : all_domain_ids ) {
- if ( positive_filter.contains( id ) ) {
- number_of_characters++;
+ int mapped = 0;
+ int not_mapped = 0;
+ for( final String 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 DomainId id : all_domain_ids ) {
- if ( positive_filter == null ) {
- matrix.setCharacter( character_index++, id.getId() );
- }
- else {
- if ( positive_filter.contains( id ) ) {
- matrix.setCharacter( character_index++, id.getId() );
- }
- }
+ 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>();
}
all_identifiers.add( species_id );
matrix.setIdentifier( identifier_index, species_id );
- for( int ci = 0; ci < matrix.getNumberOfCharacters(); ++ci ) {
- if ( ForesterUtil.isEmpty( matrix.getCharacter( ci ) ) ) {
- throw new RuntimeException( "this should not have happened: problem with character #" + ci );
+ final Set<String> all_second_per_gwcd = new HashSet<String>();
+ for( final String 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 ) );
}
- final DomainId id = new DomainId( matrix.getCharacter( ci ) );
- if ( gwcd.contains( id ) ) {
+ }
+ 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 {
}
return d;
}
+
+ private static BinaryDomainCombination mapBinaryDomainCombination( final Map<String, 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() );
+ id0 = bc.getId0();
+ }
+ 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() );
+ id1 = bc.getId1();
+ }
+ else {
+ id1 = domain_id_to_second_features_map.get( bc.getId1() );
+ }
+ // return new BasicBinaryDomainCombination( id0, id1 );
+ return BasicBinaryDomainCombination.obtainInstance( id0, id1 );
+ }
}
git://source.jalview.org / jalview.git / blobdiff