package org.forester.surfacing;
-import java.text.DecimalFormat;
-import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.TreeSet;
import org.forester.go.GoId;
-import org.forester.surfacing.BinaryDomainCombination.DomainCombinationType;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
+import org.forester.protein.Domain;
+import org.forester.protein.Protein;
+import org.forester.species.Species;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDomains {
- private final static NumberFormat FORMATTER = new DecimalFormat( "0.0E0" );
- private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER = new Comparator<CombinableDomains>() {
+ private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
- public int compare( final CombinableDomains d1,
- final CombinableDomains d2 ) {
- if ( d1
- .getKeyDomainCount() < d2
- .getKeyDomainCount() ) {
- return 1;
- }
- else if ( d1
- .getKeyDomainCount() > d2
- .getKeyDomainCount() ) {
- return -1;
- }
- else {
- return d1
- .getKeyDomain()
- .getId()
- .compareTo( d2
- .getKeyDomain()
- .getId() );
- }
- }
- };
- private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
+ @Override
+ public int compare( final CombinableDomains d1,
+ final CombinableDomains d2 ) {
+ if ( d1.getNumberOfCombinableDomains() < d2
+ .getNumberOfCombinableDomains() ) {
+ return 1;
+ }
+ else if ( d1
+ .getNumberOfCombinableDomains() > d2
+ .getNumberOfCombinableDomains() ) {
+ return -1;
+ }
+ else {
+ return d1
+ .getKeyDomain()
+ .compareTo( d2
+ .getKeyDomain() );
+ }
+ }
+ };
+ private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER = new Comparator<CombinableDomains>() {
- public int compare( final CombinableDomains d1,
- final CombinableDomains d2 ) {
- if ( d1
- .getKeyDomainProteinsCount() < d2
- .getKeyDomainProteinsCount() ) {
- return 1;
- }
- else if ( d1
- .getKeyDomainProteinsCount() > d2
- .getKeyDomainProteinsCount() ) {
- return -1;
- }
- else {
- return d1
- .getKeyDomain()
- .getId()
- .compareTo( d2
- .getKeyDomain()
- .getId() );
- }
- }
- };
- private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER = new Comparator<CombinableDomains>() {
+ @Override
+ public int compare( final CombinableDomains d1,
+ final CombinableDomains d2 ) {
+ if ( d1.getKeyDomainCount() < d2
+ .getKeyDomainCount() ) {
+ return 1;
+ }
+ else if ( d1
+ .getKeyDomainCount() > d2
+ .getKeyDomainCount() ) {
+ return -1;
+ }
+ else {
+ return d1
+ .getKeyDomain()
+ .compareTo( d2
+ .getKeyDomain() );
+ }
+ }
+ };
+ private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
- public int compare( final CombinableDomains d1,
- final CombinableDomains d2 ) {
- if ( d1
- .getNumberOfCombinableDomains() < d2
- .getNumberOfCombinableDomains() ) {
- return 1;
- }
- else if ( d1
- .getNumberOfCombinableDomains() > d2
- .getNumberOfCombinableDomains() ) {
- return -1;
- }
- else {
- return d1
- .getKeyDomain()
- .getId()
- .compareTo( d2
- .getKeyDomain()
- .getId() );
- }
- }
- };
- final private SortedMap<DomainId, CombinableDomains> _combinable_domains_map;
- final private Species _species;
- final private DomainCombinationType _dc_type;
+ @Override
+ public int compare( final CombinableDomains d1,
+ final CombinableDomains d2 ) {
+ if ( d1.getKeyDomainProteinsCount() < d2
+ .getKeyDomainProteinsCount() ) {
+ return 1;
+ }
+ else if ( d1
+ .getKeyDomainProteinsCount() > d2
+ .getKeyDomainProteinsCount() ) {
+ return -1;
+ }
+ else {
+ return d1
+ .getKeyDomain()
+ .compareTo( d2
+ .getKeyDomain() );
+ }
+ }
+ };
+ final private SortedMap<String, CombinableDomains> _combinable_domains_map;
+ final private DomainCombinationType _dc_type;
+ final private Species _species;
private BasicGenomeWideCombinableDomains( final Species species, final DomainCombinationType dc_type ) {
- _combinable_domains_map = new TreeMap<DomainId, CombinableDomains>();
+ _combinable_domains_map = new TreeMap<String, CombinableDomains>();
_species = species;
_dc_type = dc_type;
}
- private void add( final DomainId key, final CombinableDomains cdc ) {
- _combinable_domains_map.put( key, cdc );
- }
-
- public boolean contains( final DomainId key_id ) {
+ @Override
+ public boolean contains( final String key_id ) {
return _combinable_domains_map.containsKey( key_id );
}
- public CombinableDomains get( final DomainId key_id ) {
+ @Override
+ public CombinableDomains get( final String key_id ) {
return _combinable_domains_map.get( key_id );
}
- public SortedMap<DomainId, CombinableDomains> getAllCombinableDomainsIds() {
+ @Override
+ public SortedMap<String, CombinableDomains> getAllCombinableDomainsIds() {
return _combinable_domains_map;
}
@Override
- public SortedSet<DomainId> getAllDomainIds() {
- final SortedSet<DomainId> domains = new TreeSet<DomainId>();
- for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+ public SortedSet<String> getAllDomainIds() {
+ final SortedSet<String> domains = new TreeSet<String>();
+ for( final String key : getAllCombinableDomainsIds().keySet() ) {
final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
- final List<DomainId> ds = cb.getAllDomains();
- for( final DomainId d : ds ) {
+ final List<String> ds = cb.getAllDomains();
+ for( final String d : ds ) {
domains.add( d );
}
}
}
@Override
- public SortedSet<DomainId> getMostPromiscuosDomain() {
- final SortedSet<DomainId> doms = new TreeSet<DomainId>();
+ public SortedSet<String> getMostPromiscuosDomain() {
+ final SortedSet<String> doms = new TreeSet<String>();
final int max = ( int ) getPerGenomeDomainPromiscuityStatistics().getMax();
- for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+ for( final String key : getAllCombinableDomainsIds().keySet() ) {
final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
if ( cb.getNumberOfCombinableDomains() == max ) {
doms.add( key );
@Override
public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics() {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+ for( final String key : getAllCombinableDomainsIds().keySet() ) {
final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
stats.addValue( cb.getNumberOfCombinableDomains() );
}
return stats;
}
+ @Override
public int getSize() {
return _combinable_domains_map.size();
}
+ @Override
public Species getSpecies() {
return _species;
}
@Override
public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations() {
final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
- for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+ for( final String key : getAllCombinableDomainsIds().keySet() ) {
final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
for( final BinaryDomainCombination b : cb.toBinaryDomainCombinations() ) {
binary_combinations.add( b );
}
// Produces something like:
- // 2-oxoacid_dh 5 5 2 4.8E-67 Biotin_lipoyl [4], E3_binding [3]
+ // 2-oxoacid_dh 5 5 2 Biotin_lipoyl [4], E3_binding [3]
+ @Override
public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) {
final StringBuilder sb = new StringBuilder();
final List<CombinableDomains> combinable_domains = new ArrayList<CombinableDomains>();
- for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+ for( final String key : getAllCombinableDomainsIds().keySet() ) {
final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
combinable_domains.add( cb );
}
sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getKeyDomainCount() ), 8, ' ', false ) );
sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getKeyDomainProteinsCount() ), 8, ' ', false ) );
sb.append( ForesterUtil.pad( new StringBuffer( "" + cb.getNumberOfCombinableDomains() ), 8, ' ', false ) );
- sb
- .append( ForesterUtil
- .pad( new StringBuffer( ""
- + FORMATTER
- .format( cb.getKeyDomainConfidenceDescriptiveStatistics().median() ) ),
- 10,
- ' ',
- false ) );
sb.append( cb.getCombiningDomainIdsAsStringBuilder() );
sb.append( ForesterUtil.getLineSeparator() );
}
return sb;
}
- private static void countDomains( final Map<DomainId, Integer> domain_counts,
- final Map<DomainId, Integer> domain_protein_counts,
- final Map<DomainId, DescriptiveStatistics> stats,
- final Set<DomainId> saw_c,
- final DomainId id_i,
- final double support ) {
- if ( domain_counts.containsKey( id_i ) ) {
- domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
- if ( !saw_c.contains( id_i ) ) {
- domain_protein_counts.put( id_i, 1 + domain_protein_counts.get( ( id_i ) ) );
- }
- }
- else {
- stats.put( id_i, new BasicDescriptiveStatistics() );
- domain_counts.put( id_i, 1 );
- domain_protein_counts.put( id_i, 1 );
- }
- stats.get( id_i ).addValue( support );
- saw_c.add( id_i );
+ private void add( final String key, final CombinableDomains cdc ) {
+ _combinable_domains_map.put( key, cdc );
}
public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
ignore_combination_with_same_domain,
species,
null,
- DomainCombinationType.BASIC );
+ DomainCombinationType.BASIC,
+ null,
+ null );
}
public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
final boolean ignore_combination_with_same_domain,
final Species species,
final DomainCombinationType dc_type ) {
- return createInstance( protein_list, ignore_combination_with_same_domain, species, null, dc_type );
+ return createInstance( protein_list, ignore_combination_with_same_domain, species, null, dc_type, null, null );
}
public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
final boolean ignore_combination_with_same_domain,
final Species species,
- final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
- final DomainCombinationType dc_type ) {
+ final Map<String, List<GoId>> domain_id_to_go_ids_map,
+ final DomainCombinationType dc_type,
+ final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
+ final Map<String, DescriptiveStatistics> domain_number_stats_by_dc ) {
final BasicGenomeWideCombinableDomains instance = new BasicGenomeWideCombinableDomains( species, dc_type );
- final Map<DomainId, Integer> domain_counts = new HashMap<DomainId, Integer>();
- final Map<DomainId, Integer> domain_protein_counts = new HashMap<DomainId, Integer>();
- final Map<DomainId, DescriptiveStatistics> stats = new HashMap<DomainId, DescriptiveStatistics>();
+ final Map<String, Integer> domain_counts = new HashMap<String, Integer>();
for( final Protein protein : protein_list ) {
if ( !protein.getSpecies().equals( species ) ) {
throw new IllegalArgumentException( "species (" + protein.getSpecies()
+ ") does not match species of combinable domains collection (" + species + ")" );
}
- final Set<DomainId> saw_i = new HashSet<DomainId>();
- final Set<DomainId> saw_c = new HashSet<DomainId>();
+ final Set<String> saw_i = new HashSet<String>();
+ final Set<String> saw_c = new HashSet<String>();
for( int i = 0; i < protein.getProteinDomains().size(); ++i ) {
final Domain pd_i = protein.getProteinDomain( i );
- final DomainId id_i = pd_i.getDomainId();
+ final String id_i = pd_i.getDomainId();
final int current_start = pd_i.getFrom();
- BasicGenomeWideCombinableDomains.countDomains( domain_counts,
- domain_protein_counts,
- stats,
- saw_c,
- id_i,
- pd_i.getPerSequenceEvalue() );
+ BasicGenomeWideCombinableDomains.countDomains( domain_counts, saw_c, id_i );
if ( !saw_i.contains( id_i ) ) {
if ( dc_type == DomainCombinationType.BASIC ) {
saw_i.add( id_i );
else {
domain_combination = new BasicCombinableDomains( pd_i.getDomainId(), species );
}
- if ( ( domain_id_to_go_ids_map != null )
- && domain_id_to_go_ids_map.containsKey( pd_i.getDomainId() ) ) {
- final List<GoId> go_ids = domain_id_to_go_ids_map.get( pd_i.getDomainId() );
- for( final GoId go_id : go_ids ) {
- domain_combination.getKeyDomain().addGoId( go_id );
- }
- }
instance.add( id_i, domain_combination );
}
- final Set<DomainId> saw_j = new HashSet<DomainId>();
+ domain_combination.addKeyDomainProtein( protein.getProteinId().getId() );//^^^^^^^^^^^^^^
+ final Set<String> saw_j = new HashSet<String>();
if ( ignore_combination_with_same_domain ) {
saw_j.add( id_i );
}
continue;
}
if ( i != j ) {
- final DomainId id = protein.getProteinDomain( j ).getDomainId();
+ final String id = protein.getProteinDomain( j ).getDomainId();
if ( !saw_j.contains( id ) ) {
saw_j.add( id );
if ( dc_type != DomainCombinationType.DIRECTED_ADJACTANT ) {
if ( ( dc_type == DomainCombinationType.DIRECTED_ADJACTANT ) && ( closest != null ) ) {
domain_combination.addCombinableDomain( closest.getDomainId() );
}
+ if ( protein_length_stats_by_dc != null ) {
+ final List<BinaryDomainCombination> dcs = domain_combination.toBinaryDomainCombinations();
+ for( final BinaryDomainCombination dc : dcs ) {
+ final String dc_str = dc.toString();
+ if ( !protein_length_stats_by_dc.containsKey( dc_str ) ) {
+ protein_length_stats_by_dc.put( dc_str, new BasicDescriptiveStatistics() );
+ }
+ protein_length_stats_by_dc.get( dc_str ).addValue( protein.getLength() );
+ }
+ }
+ if ( domain_number_stats_by_dc != null ) {
+ final List<BinaryDomainCombination> dcs = domain_combination.toBinaryDomainCombinations();
+ for( final BinaryDomainCombination dc : dcs ) {
+ final String dc_str = dc.toString();
+ if ( !domain_number_stats_by_dc.containsKey( dc_str ) ) {
+ domain_number_stats_by_dc.put( dc_str, new BasicDescriptiveStatistics() );
+ }
+ domain_number_stats_by_dc.get( dc_str ).addValue( protein.getNumberOfProteinDomains() );
+ }
+ }
}
}
}
- for( final DomainId key_id : domain_counts.keySet() ) {
+ for( final String key_id : domain_counts.keySet() ) {
instance.get( key_id ).setKeyDomainCount( domain_counts.get( key_id ) );
- instance.get( key_id ).setKeyDomainProteinsCount( domain_protein_counts.get( key_id ) );
- instance.get( key_id ).setKeyDomainConfidenceDescriptiveStatistics( stats.get( key_id ) );
}
return instance;
}
+
+ private static void countDomains( final Map<String, Integer> domain_counts,
+ final Set<String> saw_c,
+ final String id_i ) {
+ if ( domain_counts.containsKey( id_i ) ) {
+ domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
+ }
+ else {
+ domain_counts.put( id_i, 1 );
+ }
+ saw_c.add( id_i );
+ }
}
git://source.jalview.org / jalview.git / blobdiff