Package org.biojava.bio.chromatogram

Class AbstractChromatogram

    • Method Detail

      • getTrace

        public int[] getTrace​(AtomicSymbol nucleotide)
               throws IllegalSymbolException
        Description copied from interface: Chromatogram
        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 Chromatogram.getTraceLength() ints long.

        Specified by:
        getTrace in interface Chromatogram
        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

      • getMax

        public int getMax​(AtomicSymbol nucleotide)
           throws IllegalSymbolException
        Description copied from interface: Chromatogram
        Gets the max intensity on the trace for the specified nucleotide.
        Specified by:
        getMax in interface Chromatogram
        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

      • clearTraces

        protected final void clearTraces()
        Sets the trace data structures to null. If a subclass needs to replace the traces with new traces of a different length, this method must be called first to avoid provoking an IllegalArgumentException from setTrace due to a length mismatch.

      • setBits

        protected final void setBits​(int bits)
                      throws IllegalArgumentException
        Sets the number of significant bits in the trace samples.
        Parameters:
        bits - a non-negative integer indicating the number of significant bits in each trace sample
        Throws:
        IllegalArgumentException - when bits is negative

      • reverseComplement

        public Chromatogram reverseComplement()
        Description copied from interface: Chromatogram
        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.

        Specified by:
        reverseComplement in interface Chromatogram
        Returns:
        a new chromatogram that is the reverse complement of this one

      • reverseComplementBaseCalls

        protected Alignment reverseComplementBaseCalls()
        Returns a new base call alignment that is the reverse complement of one in this chromatogram. This is achieved by calling reverseComplementBaseCallList(java.lang.Object) for each label in the current base call alignment. When that method returns null, no list will appear in reverse complement base call alignment with the null-provoking label. For this reason, subclasses are encouraged to override reverseComplementBaseCallList(java.lang.Object) to handle any additional per-base metadata that they store.

        This implementation should be safely inheritable for all chromatogram implementations, unless one just doesn't want base calls on its reverse complement output. If this is the case, it should override this method to return null.

        Returns:
        a new Alignment that is the reverse complement of the one in the current chromatogram

      • reverseComplementBaseCallList

        protected SymbolList reverseComplementBaseCallList​(Object label)
        Return a symbol list containing the reverse complement of the base call data for the given label. The returned list will be stored in the reverse complement's base call alignment under the same label.

        Implementation note: subclasses which do not use an IntegerAlphabet for their offsets lists must override this method, at least for the case where label == Chromatogram.OFFSETS.

        Parameters:
        label - the label Object
        Returns:
        an appropriately reverse-complemented SymbolList, or null if the label is unhandled.

      • createImmutableSymbolList

        protected SymbolList createImmutableSymbolList​(Alphabet alpha,
                                               List syms)
                                        throws IllegalSymbolException,
                                               ClassCastException
        A factory method for creating new symbol lists with a given alphabet. The default implementation should be fine for nearly all cases, but the option is given in case a developer wishes to use a more memory efficient implementation.
        Parameters:
        alpha - the Alphabet for the new list
        syms - the symbols to put in the new list
        Returns:
        a new immutable SymbolList containing all the given symbols using the given Alphabet
        Throws:
        IllegalSymbolException - when alpha and syms are incompatible
        ClassCastException - when any object in syms isn't a Symbol

      • createImmutableAlignment

        protected Alignment createImmutableAlignment​(Map labelsToSymLists)
                                      throws IllegalArgumentException,
                                             ClassCastException
        A factory method for creating new immutable alignments, particularly for use as base call alignments. The default implementation should be fine for nearly all cases.
        Parameters:
        labelsToSymLists - a Map whose keys are desired labels for the alignment and whose values are the SymbolLists. All the SymbolLists must be the same length.
        Returns:
        a new Alignment
        Throws:
        IllegalArgumentException - if the lists aren't all the same length
        ClassCastException - if any of the values in the map aren't SymbolLists

      • reverse

        protected static final int[] reverse​(int[] src)
        Utility method for reversing an int[] array. Visible for subclass use.
        Parameters:
        src - the source array
        Returns:
        an array of the same length containing all values in src in reverse order