All Implemented Interfaces:

Chromatogram

public class SimpleChromatogram
extends AbstractChromatogram 

Since:

1.3

Author:

Rhett Sutphin (UI CBCB), Matthew Pocock

• Field Summary

  • Fields inherited from interface org.biojava.bio.chromatogram.Chromatogram

    DNA, OFFSETS

• Constructor Summary

  Constructors

  Constructor and Description
  SimpleChromatogram () Creates a new instance of SimpleChromatogram.

• Method Summary

  All Methods

  Modifier and Type	Method and Description
  void	clearTraceValues () Sets all the traces to null.
  protected AbstractChromatogram	reverseComplementInstance () Returns a new instance of this AbstractChromatogram subclass for use in AbstractChromatogram.reverseComplement().
  void	setSignificantBits (int bits) Sets the number of significant bits in the data.
  void	setSymbolLists (SymbolList dna, SymbolList offsets) Set the DNA and OFFSETS symbol lists for the basecall alignment.
  void	setTraceValues (AtomicSymbol nuc, int[] trace, int maxVal) Sets the trace array for one of the DNA nucleotides.

  • Methods inherited from class org.biojava.bio.chromatogram.AbstractChromatogram

    clearTraces, createImmutableAlignment, createImmutableSymbolList, getBaseCalls, getMax, getMax, getSequenceLength, getSignificantBits, getTrace, getTraceLength, reverse, reverseComplement, reverseComplementBaseCallList, reverseComplementBaseCalls, setBaseCallAlignment, setBits, setTrace

  • Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

• Constructor Detail

  • SimpleChromatogram

    public SimpleChromatogram()

    Creates a new instance of SimpleChromatogram.

• Method Detail

  • setSymbolLists

    public void setSymbolLists(SymbolList dna,
     SymbolList offsets)
     throws IllegalAlphabetException,
     IllegalArgumentException 

    Set the DNA and OFFSETS symbol lists for the basecall alignment. Beware: this method does no consistency checks to be sure that all the offsets are valid indices into the trace arrays.

    Parameters:

    dna - a symbol list in the DNA alphabet that contains the base calls for this chromatogram

    offsets - a symbol list in an integer or sub-integer alphabet that contains the locations in the chromatogram for the bases called in dna

    Throws:

    IllegalAlphabetException - when the alphabets aren't as specified

    IllegalArgumentException - when the lists aren't the same length

  • setTraceValues

    public void setTraceValues(AtomicSymbol nuc,
     int[] trace,
     int maxVal)
     throws IllegalArgumentException,
     IllegalSymbolException 

    Sets the trace array for one of the DNA nucleotides. The provided array will not be copied, so any modifications to it will be reflected in calls to AbstractChromatogram.getTrace(org.biojava.bio.symbol.AtomicSymbol).

    If you need to set a new set of traces whose length is different from the old set, you must call clearTraceValues() first, or you will provoke an IllegalArgumentException.

    Parameters:

    nuc - the nucleotide for which to set the trace

    trace - the sampled intensities along the trace

    maxVal - the maximum value on the trace, or Integer.MIN_VALUE to force this method to calculate it

    Throws:

    IllegalArgumentException - when trace.length is different from any of the existing (non-null) traces

    IllegalSymbolException - when nuc is not a concrete DNA nucleotide

  • clearTraceValues

    public void clearTraceValues()

    Sets all the traces to null.

  • setSignificantBits

    public void setSignificantBits(int bits)

    Sets the number of significant bits in the data.

    Parameters:

    bits - how many bits of the trace samples are significant

    See Also:

    Chromatogram.getSignificantBits()

  • reverseComplementInstance

    protected AbstractChromatogram reverseComplementInstance()

    Description copied from class: AbstractChromatogram
    Returns a new instance of this AbstractChromatogram subclass for use in AbstractChromatogram.reverseComplement().

    Specified by:

    reverseComplementInstance in class AbstractChromatogram

    Returns:

    a reverse-complemented AbstractChromatogram