Class ABITools

java.lang.Object
org.biojava.bio.program.abi.ABITools

public class ABITools extends 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 Details

    • 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.
    • _1

      public static final AtomicSymbol _1
      The well supported symbol.
    • SEQUENCE

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

      public static final Object SUPPORT
      Alignment label for the support row.
  • Constructor Details

  • Method Details

    • getAlignment

      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