Interface Protein

Method Details

• addProteinDomain

  void addProteinDomain(Domain protein_domain)

• contains

  boolean contains(List<String> domains, boolean in_nc_order)

  If in_nc_order is set to true, this should return true only and only if the order in List 'domains' and this protein (as determined by the start positions of the domains of this proteins, _not_ by their index) are the same (interspersing, 'other', domains in this are ignored). If in_nc_order is set to false, this should return true only and only if this contains all domains listed in 'domains' (order and count do not matter).

  Parameters:

  domains - a list of domain ids in a certain order.

  in_nc_order - to consider order

  Returns:

• getAccession

  String getAccession()

• getDescription

  String getDescription()

• getName

  String getName()

• getNumberOfProteinDomains

  int getNumberOfProteinDomains()

• getProteinDomain

  Domain getProteinDomain(int index)

• getProteinDomainCount

  int getProteinDomainCount(String domain_id)

• getProteinDomains

  List<Domain> getProteinDomains()

• getProteinDomains

  List<Domain> getProteinDomains(String domain_id)

• getProteinId

  ProteinId getProteinId()

• getLength

  int getLength()

• getSpecies

  Species getSpecies()

• getDomainsSortedByPosition

  List<Domain> getDomainsSortedByPosition()