org.forester.surfacing

Class BasicGenomeWideCombinableDomains

java.lang.Object

org.forester.surfacing.BasicGenomeWideCombinableDomains

All Implemented Interfaces:

GenomeWideCombinableDomains

public class BasicGenomeWideCombinableDomains
extends Object
implements GenomeWideCombinableDomains

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.surfacing.GenomeWideCombinableDomains

GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder

Method Summary

Modifier and Type	Method and Description
boolean	contains(String key_id)
static BasicGenomeWideCombinableDomains	createInstance(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species)
static BasicGenomeWideCombinableDomains	createInstance(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, BinaryDomainCombination.DomainCombinationType dc_type)
static BasicGenomeWideCombinableDomains	createInstance(List<Protein> protein_list, boolean ignore_combination_with_same_domain, Species species, Map<String,List<GoId>> domain_id_to_go_ids_map, BinaryDomainCombination.DomainCombinationType dc_type, Map<String,DescriptiveStatistics> protein_length_stats_by_dc, Map<String,DescriptiveStatistics> domain_number_stats_by_dc)
CombinableDomains	get(String key_id)
SortedMap<String,CombinableDomains>	getAllCombinableDomainsIds()
SortedSet<String>	getAllDomainIds() This should return all domains ids present in the genome.
BinaryDomainCombination.DomainCombinationType	getDomainCombinationType()
SortedSet<String>	getMostPromiscuosDomain()
DescriptiveStatistics	getPerGenomeDomainPromiscuityStatistics() This should return a statistic for per domain promiscuity in a genome.
int	getSize()
Species	getSpecies()
SortedSet<BinaryDomainCombination>	toBinaryDomainCombinations() This should return all binary domain combinations present in the genome.
String	toString()
StringBuilder	toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder sort_order)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

contains

public boolean contains(String key_id)

Specified by:

contains in interface GenomeWideCombinableDomains

get

public CombinableDomains get(String key_id)

Specified by:

get in interface GenomeWideCombinableDomains

getAllCombinableDomainsIds

public SortedMap<String,CombinableDomains> getAllCombinableDomainsIds()

Specified by:

getAllCombinableDomainsIds in interface GenomeWideCombinableDomains

getAllDomainIds

public SortedSet<String> getAllDomainIds()

Description copied from interface: GenomeWideCombinableDomains

This should return all domains ids present in the genome.

Specified by:

getAllDomainIds in interface GenomeWideCombinableDomains

Returns:

a sorted set of domains ids

getDomainCombinationType

public BinaryDomainCombination.DomainCombinationType getDomainCombinationType()

Specified by:

getDomainCombinationType in interface GenomeWideCombinableDomains

getMostPromiscuosDomain

public SortedSet<String> getMostPromiscuosDomain()

Specified by:

getMostPromiscuosDomain in interface GenomeWideCombinableDomains

getPerGenomeDomainPromiscuityStatistics

public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics()

Description copied from interface: GenomeWideCombinableDomains

This should return a statistic for per domain promiscuity in a genome.

Specified by:

getPerGenomeDomainPromiscuityStatistics in interface GenomeWideCombinableDomains

Returns:

descriptive statistics for per domain promiscuity in a genome

getSize

public int getSize()

Specified by:

getSize in interface GenomeWideCombinableDomains

getSpecies

public Species getSpecies()

Specified by:

getSpecies in interface GenomeWideCombinableDomains

toBinaryDomainCombinations

public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations()

Description copied from interface: GenomeWideCombinableDomains

This should return all binary domain combinations present in the genome.

Specified by:

toBinaryDomainCombinations in interface GenomeWideCombinableDomains

Returns:

a sorted set of binary domain combinations

toString

public String toString()

Overrides:

toString in class Object

toStringBuilder

public StringBuilder toStringBuilder(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder sort_order)

Specified by:

toStringBuilder in interface GenomeWideCombinableDomains

createInstance

public static BasicGenomeWideCombinableDomains createInstance(List<Protein> protein_list,
                                                              boolean ignore_combination_with_same_domain,
                                                              Species species)

createInstance

public static BasicGenomeWideCombinableDomains createInstance(List<Protein> protein_list,
                                                              boolean ignore_combination_with_same_domain,
                                                              Species species,
                                                              BinaryDomainCombination.DomainCombinationType dc_type)

createInstance

public static BasicGenomeWideCombinableDomains createInstance(List<Protein> protein_list,
                                                              boolean ignore_combination_with_same_domain,
                                                              Species species,
                                                              Map<String,List<GoId>> domain_id_to_go_ids_map,
                                                              BinaryDomainCombination.DomainCombinationType dc_type,
                                                              Map<String,DescriptiveStatistics> protein_length_stats_by_dc,
                                                              Map<String,DescriptiveStatistics> domain_number_stats_by_dc)