Class DomainArchitecture

java.lang.Object
org.forester.phylogeny.data.DomainArchitecture
All Implemented Interfaces:
PhylogenyData
Direct Known Subclasses:
RenderableDomainArchitecture

public class DomainArchitecture extends Object implements PhylogenyData
  • Field Details

  • Constructor Details

    • DomainArchitecture

      public DomainArchitecture()
    • DomainArchitecture

      public DomainArchitecture(List<PhylogenyData> domains, int total_length)
    • DomainArchitecture

      public DomainArchitecture(String da_str)
  • 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
      Parameters:
      writer -
      level -
      indentation -
      Throws:
      IOException
    • toString

      public String toString()
      Overrides:
      toString in class Object