Package org.forester.phylogeny.data

Class Accession

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      static class  Accession.Source  

    • Constructor Summary

      Constructors 
      Constructor Description
      Accession​(java.lang.String value)  
      Accession​(java.lang.String value, java.lang.String source)  
      Accession​(java.lang.String value, java.lang.String source, java.lang.String comment)  
      Accession​(java.lang.String value, Accession.Source source)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.StringBuffer asSimpleText()  
      java.lang.StringBuffer asText()  
      int compareTo​(Accession o)  
      PhylogenyData copy()
      Creates a new PhylogenyData object with identical values as this PhylogenyData.
      boolean equals​(java.lang.Object o)  
      java.lang.String getComment()  
      java.lang.String getSource()  
      java.lang.String getValue()  
      int hashCode()  
      boolean isEqual​(PhylogenyData data)
      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, finalize, getClass, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • Accession

        public Accession​(java.lang.String value)

      • Accession

        public Accession​(java.lang.String value,
                 java.lang.String source)

      • Accession

        public Accession​(java.lang.String value,
                 Accession.Source source)

      • Accession

        public Accession​(java.lang.String value,
                 java.lang.String source,
                 java.lang.String comment)

    • Method Detail

      • asText

        public java.lang.StringBuffer asText()
        Specified by:
        asText in interface PhylogenyData

      • compareTo

        public int compareTo​(Accession o)
        Specified by:
        compareTo in interface java.lang.Comparable<Accession>

      • 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

      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object

      • getComment

        public java.lang.String getComment()

      • getSource

        public java.lang.String getSource()

      • getValue

        public java.lang.String getValue()

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • isEqual

        public boolean isEqual​(PhylogenyData data)
        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