Class BasicGenomeWideCombinableDomains

Method Details

• 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)