Method Detail

• contains

  public boolean contains​(java.lang.String key_id)

  Specified by:

  contains in interface GenomeWideCombinableDomains

• get

  public CombinableDomains get​(java.lang.String key_id)

  Specified by:

  get in interface GenomeWideCombinableDomains

• getAllCombinableDomainsIds

  public java.util.SortedMap<java.lang.String,​CombinableDomains> getAllCombinableDomainsIds()

  Specified by:

  getAllCombinableDomainsIds in interface GenomeWideCombinableDomains

• getAllDomainIds

  public java.util.SortedSet<java.lang.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 java.util.SortedSet<java.lang.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 java.util.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 java.lang.String toString()

  Overrides:

  toString in class java.lang.Object

• toStringBuilder

  public java.lang.StringBuilder toStringBuilder​(GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder sort_order)

  Specified by:

  toStringBuilder in interface GenomeWideCombinableDomains

• createInstance

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

• createInstance

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

• createInstance

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