Class DomainArchitecture

Method Details

• addDomain

  public void addDomain(ProteinDomain pd)

• asSimpleText

  public StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• asText

  public StringBuffer asText()

  Specified by:

  asText in interface PhylogenyData

• copy

  public PhylogenyData copy()

  Description copied from interface: PhylogenyData

  Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.

  Specified by:

  copy in interface PhylogenyData

  Returns:

  a ~deep~ copy of this PhylogenyData

• getDomain

  public ProteinDomain getDomain(int i)

• getDomains

  public SortedMap<BigDecimal,ProteinDomain> getDomains()

• getNumberOfDomains

  public int getNumberOfDomains()

• getTotalLength

  public int getTotalLength()

• isEqual

  public boolean isEqual(PhylogenyData domain_architecture)

  Returns true if the names and the order of the domains match (domain and linker lengths are ignored).

  Specified by:

  isEqual in interface PhylogenyData

  Returns:

  in general, true if and only if all fiels are exactly identical, false otherwise

• setTotalLength

  public void setTotalLength(int total_length)

• toNHX

  public StringBuffer toNHX()

  Specified by:

  toNHX in interface PhylogenyData

• toPhyloXML

  public void toPhyloXML(Writer writer, int level, String indentation) throws IOException

  Description copied from interface: PhylogenyData

  Writes a phyloXML representation of this phylogeny data.

  Specified by:

  toPhyloXML in interface PhylogenyData

  Throws:

  IOException

• toString

  public String toString()

  Overrides:

  toString in class Object