Class PhredSequence

    • Constructor Detail

      • PhredSequence

        public PhredSequence​(SymbolList phredSequence,
                             java.lang.String name,
                             java.lang.String urn,
                             Annotation anno)
                      throws IllegalAlphabetException
        Constructs a new PhredSequence.
        Parameters:
        phredSequence - - a SymbolList over the Phred Alphabet.
        name - - the name for the sequence.
        urn - - the URN for the sequence.
        anno - - the Annotation object for the sequence.
        Throws:
        IllegalAlphabetException
    • Method Detail

      • getQuality

        public SymbolList getQuality()
        Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
        Specified by:
        getQuality in interface Qualitative
      • getDNA

        public SymbolList getDNA()
        Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
      • getQualityAt

        public Symbol getQualityAt​(int index)
                            throws java.lang.IndexOutOfBoundsException
        Description copied from interface: Qualitative
        Retreives the quality symbol for the specified index.
        Specified by:
        getQualityAt in interface Qualitative
        Parameters:
        index - - Must be greater than zero.
        Throws:
        java.lang.IndexOutOfBoundsException - if index is outside of the quality symbol list.
      • getDNAAt

        public Symbol getDNAAt​(int index)
                        throws java.lang.IndexOutOfBoundsException
        Throws:
        java.lang.IndexOutOfBoundsException