// 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 int _total_gains;
private int _total_unchanged;
private int _cost;
- private Map<DomainId, Set<String>> _domain_id_to_secondary_features_map;
- private SortedSet<DomainId> _positive_filter;
+ private Map<String, Set<String>> _domain_id_to_secondary_features_map;
+ private SortedSet<String> _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;
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 );
else {
states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
}
- fitch.execute( getPhylogeny(), states );
+ fitch.execute( getPhylogeny(), states, true );
setGainLossMatrix( fitch.getGainLossMatrix() );
setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
setCost( fitch.getCost() );
setTotalLosses( fitch.getTotalLosses() );
setTotalUnchanged( fitch.getTotalUnchanged() );
}
-
- private void executeFitchParsimonyOnSecondaryFeatures(
- final boolean use_last,
- final boolean randomize,
- final long random_number_seed ) {
+
+ 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" );
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 = (Map.Entry<DomainId, Set<String>>)it.next();
+ 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().getId() + " mapps to " + pair.getValue().size() + " items" );
+ throw new IllegalArgumentException( pair.getKey() + " mapps to " + pair.getValue().size() + " items" );
}
newmap.put( pair.getKey(), ( String ) pair.getValue().toArray()[ 0 ] );
}
-
- CharacterStateMatrix<BinaryStates> states =createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(),
- newmap );
-
- fitch.execute( getPhylogeny(), states );
+ final CharacterStateMatrix<BinaryStates> states = createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(),
+ newmap );
+ fitch.execute( getPhylogeny(), states, true );
setGainLossMatrix( fitch.getGainLossMatrix() );
setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
setCost( fitch.getCost() );
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 );
}
return _cost;
}
- private Map<DomainId, Set<String>> getDomainIdToSecondaryFeaturesMap() {
+ private Map<String, Set<String>> getDomainIdToSecondaryFeaturesMap() {
return _domain_id_to_secondary_features_map;
}
return _phylogeny;
}
- private SortedSet<DomainId> getPositiveFilter() {
+ private SortedSet<String> getPositiveFilter() {
return _positive_filter;
}
_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
*
* @return
*/
static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeaturePresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
- final Map<DomainId, Set<String>> domain_id_to_second_features_map,
+ 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" );
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
int mapped = 0;
int not_mapped = 0;
- for( final DomainId domain : gwcd.getAllDomainIds() ) {
+ 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++;
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() ) {
+ 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 ) );
}
}
return matrix;
}
-
-
+
public static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
- final Map<DomainId, String> domain_id_to_second_features_map) {
+ final Map<String, String> domain_id_to_second_features_map ) {
if ( gwcd_list.isEmpty() ) {
throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
}
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 );
}
++identifier_index;
}
-
if ( !no_mappings.isEmpty() ) {
- ForesterUtil.programMessage( surfacing.PRG_NAME, "No mappings for the following (" + no_mappings.size() + "):" );
+ 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);
+ 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 );
return matrix;
}
- private static BinaryDomainCombination mapBinaryDomainCombination( final Map<DomainId, String> domain_id_to_second_features_map,
+ 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().getId() );
- id0 = bc.getId0().getId();
+ no_mappings.add( bc.getId0() );
+ id0 = bc.getId0();
}
else {
- id0 = domain_id_to_second_features_map.get( bc.getId0());
+ 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();
+ no_mappings.add( bc.getId1() );
+ id1 = bc.getId1();
}
else {
- id1 = domain_id_to_second_features_map.get( bc.getId1());
+ 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" );
}
public static CharacterStateMatrix<BinaryStates> createMatrixOfDomainPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
- final SortedSet<DomainId> positive_filter ) {
+ final SortedSet<String> positive_filter ) {
if ( gwcd_list.isEmpty() ) {
throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
}
throw new IllegalArgumentException( "positive filter is empty" );
}
final int number_of_identifiers = gwcd_list.size();
- final SortedSet<DomainId> all_domain_ids = new TreeSet<DomainId>();
+ final SortedSet<String> all_domain_ids = new TreeSet<String>();
for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
- for( final DomainId domain : gwcd.getAllDomainIds() ) {
+ for( final String domain : gwcd.getAllDomainIds() ) {
all_domain_ids.add( domain );
}
}
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 ) {
+ for( final String id : all_domain_ids ) {
if ( positive_filter.contains( id ) ) {
number_of_characters++;
}
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 ) {
+ for( final String id : all_domain_ids ) {
if ( positive_filter == null ) {
- matrix.setCharacter( character_index++, id.getId() );
+ matrix.setCharacter( character_index++, id );
}
else {
if ( positive_filter.contains( id ) ) {
- matrix.setCharacter( character_index++, id.getId() );
+ matrix.setCharacter( character_index++, id );
}
}
}
if ( ForesterUtil.isEmpty( matrix.getCharacter( ci ) ) ) {
throw new RuntimeException( "this should not have happened: problem with character #" + ci );
}
- final DomainId id = new DomainId( matrix.getCharacter( ci ) );
+ final String id = matrix.getCharacter( ci );
if ( gwcd.contains( id ) ) {
matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
}
return matrix;
}
-
-
private static int getStateSumDeltaOnNode( final String node_identifier,
final CharacterStateMatrix<GainLossStates> gain_loss_matrix,
final GainLossStates state ) {
git://source.jalview.org / jalview.git / blobdiff