Package org.biojava.bio.chromatogram

Interface Chromatogram

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String DNA
      The sequence label for the list of called bases.
      static String OFFSETS
      The sequence label for the trace offsets of the called bases.

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      Alignment getBaseCalls()
      Returns an alignment that describes the base calls for this chromatogram.
      int getMax()
      Gets the max intensity from all the traces.
      int getMax​(AtomicSymbol nucleotide)
      Gets the max intensity on the trace for the specified nucleotide.
      int getSequenceLength()
      Returns the number of bases called by whatever base-calling software analyzed the chromatogram as loaded.
      int getSignificantBits()
      Returns the number of bits of the traces which are significant.
      int[] getTrace​(AtomicSymbol nucleotide)
      Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base nucleotide.
      int getTraceLength()
      Returns the length of the trace of the Chromatogram.
      Chromatogram reverseComplement()
      Returns a new Chromatogram representing the reverse complement of this one.

    • Method Detail

      • getMax

        int getMax()
        Gets the max intensity from all the traces. Must be equivalent to the max of calling getMax(AtomicSymbol) on each of the four non-ambiguous DNA nucleotides.
        Returns:
        the max intensity

      • getMax

        int getMax​(AtomicSymbol nucleotide)
    throws IllegalSymbolException
        Gets the max intensity on the trace for the specified nucleotide.
        Parameters:
        nucleotide - the trace to examine. Must be a concrete (non-ambiguous) nucleotide from the DNA alphabet
        Returns:
        the max intensity
        Throws:
        IllegalSymbolException - when the nucleotide isn't from the DNA alphabet

      • getTrace

        int[] getTrace​(AtomicSymbol nucleotide)
        throws IllegalSymbolException
        Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base nucleotide. This may be a reference the actual internal representation of the samples, so callers must not modify it.

        The resulting array for each nucleotide must be getTraceLength() ints long.

        Parameters:
        nucleotide - the trace to examine. Must be the symbol for A, C, G, or T as provided by DNATools
        Returns:
        an array of integers representing the values of a particular chromatogram trace.
        Throws:
        IllegalSymbolException - if nucleotide isn't in the DNA alphabet

      • getSignificantBits

        int getSignificantBits()
        Returns the number of bits of the traces which are significant. For instance, if the chromatogram were originally encoded with a single byte per trace sample, this method must return 8.
        Returns:
        the number of significant bits

      • getBaseCalls

        Alignment getBaseCalls()
        Returns an alignment that describes the base calls for this chromatogram. All of the SymbolLists in this alignment must be the same length and that length must equal getSequenceLength().

        The alignment must contain, at the least, two sequences:

        1. A sequence containing the called bases. The alphabet of this list must be DNATools.getDNA(). The label for this list in the alignment must be Chromatogram.DNA
        2. A sequence containing the trace offsets at which the called bases were called. The alphabet of this list must be an IntegerAlphabet or a IntegerAlphabet.SubIntegerAlphabet. The label for this list in the alignment must be Chromatogram.OFFSETS.

        Implementors may provide other sequences as they see fit.

        Returns:
        an alignment of at least two sequences, as described above.

      • getSequenceLength

        int getSequenceLength()
        Returns the number of bases called by whatever base-calling software analyzed the chromatogram as loaded. Must equal getBaseCalls().length().
        Returns:
        the number of bases

      • reverseComplement

        Chromatogram reverseComplement()
        Returns a new Chromatogram representing the reverse complement of this one.

        Implementors should copy the metadata about the chromatogram (i.e., base calls) as is appropriate to their formats.

        Returns:
        a new chromatogram that is the reverse complement of this one