Class ABITools


  • public class ABITools
    extends java.lang.Object
    Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.
    Author:
    Matthew Pocock
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static AtomicSymbol _0
      The poorly supported symbol.
      static AtomicSymbol _1
      The well supported symbol.
      static FiniteAlphabet QUALITY
      The quality alphabet.
      static java.lang.Object SEQUENCE
      Alignment label for the DNA sequence row.
      static java.lang.Object SUPPORT
      Alignment label for the support row.
    • Constructor Summary

      Constructors 
      Constructor Description
      ABITools()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static Alignment getAlignment​(SymbolList abiSeq)
      View a symbol list over the QUALITY alphabet as an alignment.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • QUALITY

        public static final FiniteAlphabet QUALITY
        The quality alphabet. This is equivalent to DNA x [0,1] where 0 represents poorly supported (lower case) and 1 represents strongly supported (upper case).
      • _0

        public static final AtomicSymbol _0
        The poorly supported symbol.
      • SEQUENCE

        public static final java.lang.Object SEQUENCE
        Alignment label for the DNA sequence row.
      • SUPPORT

        public static final java.lang.Object SUPPORT
        Alignment label for the support row.
    • Method Detail

      • getAlignment

        public static Alignment getAlignment​(SymbolList abiSeq)
                                      throws IllegalAlphabetException

        View a symbol list over the QUALITY alphabet as an alignment.

        The alignment will have labels of SEQUENCE and SUPPORT that retrieve the DNA sequence and the binary support values respectively.

        Parameters:
        abiSeq - the SymbolList over the QUALITY alphabet to view
        Returns:
        an Alignment view of abiSeq
        Throws:
        IllegalAlphabetException - if abiSeq is not over QUALITY