Field Detail

• DomainMidPositionComparator

  public static java.util.Comparator<Domain> DomainMidPositionComparator

Constructor Detail

• BasicProtein

  public BasicProtein​(java.lang.String id_str,
                      java.lang.String species_str,
                      int length)

Method Detail

• addProteinDomain

  public void addProteinDomain​(Domain protein_domain)

  Specified by:

  addProteinDomain in interface Protein

• contains

  public boolean contains​(java.util.List<java.lang.String> query_domain_ids,
                          boolean in_nc_order)

  Description copied from interface: Protein
  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).

  Specified by:

  contains in interface Protein

  Parameters:

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

  in_nc_order - to consider order

  Returns:

• getAccession

  public java.lang.String getAccession()

  Specified by:

  getAccession in interface Protein

• getDescription

  public java.lang.String getDescription()

  Specified by:

  getDescription in interface Protein

• getDomainsSortedByPosition

  public java.util.List<Domain> getDomainsSortedByPosition()

  Specified by:

  getDomainsSortedByPosition in interface Protein

• getLength

  public int getLength()

  Specified by:

  getLength in interface Protein

• getName

  public java.lang.String getName()

  Specified by:

  getName in interface Protein

• getNumberOfProteinDomains

  public int getNumberOfProteinDomains()

  Specified by:

  getNumberOfProteinDomains in interface Protein

• getProteinDomain

  public Domain getProteinDomain​(int index)

  Specified by:

  getProteinDomain in interface Protein

• getProteinDomainCount

  public int getProteinDomainCount​(java.lang.String domain_id)

  Specified by:

  getProteinDomainCount in interface Protein

• getProteinDomains

  public java.util.List<Domain> getProteinDomains()

  Specified by:

  getProteinDomains in interface Protein

• getProteinDomains

  public java.util.List<Domain> getProteinDomains​(java.lang.String domain_id)

  Specified by:

  getProteinDomains in interface Protein

• getProteinId

  public ProteinId getProteinId()

  Specified by:

  getProteinId in interface Protein

• getSpecies

  public Species getSpecies()

  Specified by:

  getSpecies in interface Protein

• setAccession

  public void setAccession​(java.lang.String accession)

• setDescription

  public void setDescription​(java.lang.String description)

• setName

  public void setName​(java.lang.String name)

• toDomainArchitectureString

  public java.lang.String toDomainArchitectureString​(java.lang.String separator)

• toDomainArchitectureString

  public java.lang.String toDomainArchitectureString​(java.lang.String separator,
                                                     int repeats_limit,
                                                     java.lang.String repeat_separator)

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object