Package org.forester.phylogeny.data

Class ProteinDomain

    • Constructor Summary

      Constructors 
      Constructor Description
      ProteinDomain​(java.lang.String name, int from, int to)  
      ProteinDomain​(java.lang.String name, int from, int to, double confidence)  
      ProteinDomain​(java.lang.String name, int from, int to, java.lang.String id)  
      ProteinDomain​(java.lang.String name, int from, int to, java.lang.String id, double confidence)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.StringBuffer asSimpleText()  
      java.lang.StringBuffer asText()  
      PhylogenyData copy()
      Creates a new PhylogenyData object with identical values as this PhylogenyData.
      double getConfidence()  
      int getFrom()  
      java.lang.String getId()  
      int getLength()  
      java.lang.String getName()  
      int getTo()  
      boolean isEqual​(PhylogenyData protein_domain)
      Compares this PhylogenyData to PhylogenyData data.
      java.lang.StringBuffer toNHX()  
      void toPhyloXML​(java.io.Writer writer, int level, java.lang.String indentation)
      Writes a phyloXML representation of this phylogeny data.
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • ProteinDomain

        public ProteinDomain​(java.lang.String name,
                     int from,
                     int to)

      • ProteinDomain

        public ProteinDomain​(java.lang.String name,
                     int from,
                     int to,
                     double confidence)

      • ProteinDomain

        public ProteinDomain​(java.lang.String name,
                     int from,
                     int to,
                     java.lang.String id)

      • ProteinDomain

        public ProteinDomain​(java.lang.String name,
                     int from,
                     int to,
                     java.lang.String id,
                     double confidence)

    • 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

      • getConfidence

        public double getConfidence()

      • getFrom

        public int getFrom()

      • getId

        public java.lang.String getId()

      • getLength

        public int getLength()

      • getName

        public java.lang.String getName()

      • getTo

        public int getTo()

      • isEqual

        public boolean isEqual​(PhylogenyData protein_domain)
        Description copied from interface: PhylogenyData
        Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.
        Specified by:
        isEqual in interface PhylogenyData
        Returns:
        in general, true if and only if all fiels are exactly identical, false otherwise

      • 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