Class DomainArchitecture

    • Constructor Detail

      • DomainArchitecture

        public DomainArchitecture()
      • DomainArchitecture

        public DomainArchitecture​(java.util.List<PhylogenyData> domains,
                                  int total_length)
      • DomainArchitecture

        public DomainArchitecture​(java.lang.String da_str)
    • Method Detail

      • asText

        public java.lang.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
      • getDomains

        public java.util.SortedMap<java.math.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 java.lang.StringBuffer toNHX()
        Specified by:
        toNHX in interface PhylogenyData
      • toPhyloXML

        public void toPhyloXML​(java.io.Writer writer,
                               int level,
                               java.lang.String indentation)
                        throws java.io.IOException
        Description copied from interface: PhylogenyData
        Writes a phyloXML representation of this phylogeny data.
        Specified by:
        toPhyloXML in interface PhylogenyData
        Throws:
        java.io.IOException
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object