org.forester.surfacing
Class BasicGenomeWideCombinableDomains

java.lang.Object
  extended by 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
 boolean contains(DomainId 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<DomainId,List<GoId>> domain_id_to_go_ids_map, BinaryDomainCombination.DomainCombinationType dc_type)
           
 CombinableDomains get(DomainId key_id)
           
 SortedMap<DomainId,CombinableDomains> getAllCombinableDomainsIds()
           
 SortedSet<DomainId> getAllDomainIds()
          This should return all domains ids present in the genome.
 BinaryDomainCombination.DomainCombinationType getDomainCombinationType()
           
 SortedSet<DomainId> 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(DomainId key_id)
Specified by:
contains in interface GenomeWideCombinableDomains

get

public CombinableDomains get(DomainId key_id)
Specified by:
get in interface GenomeWideCombinableDomains

getAllCombinableDomainsIds

public SortedMap<DomainId,CombinableDomains> getAllCombinableDomainsIds()
Specified by:
getAllCombinableDomainsIds in interface GenomeWideCombinableDomains

getAllDomainIds

public SortedSet<DomainId> 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<DomainId> 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<DomainId,List<GoId>> domain_id_to_go_ids_map,
                                                              BinaryDomainCombination.DomainCombinationType dc_type)