Package org.biojava.bio.chromatogram

Class SimpleChromatogram

java.lang.Object

org.biojava.bio.chromatogram.AbstractChromatogram

org.biojava.bio.chromatogram.SimpleChromatogram

All Implemented Interfaces:

Chromatogram

public class SimpleChromatogram
extends AbstractChromatogram

A basic chromatogram implementation which provides public mutators for setting the various attributes of the chromatogram.

In general, new chromatogram implementations should be derived from AbstractChromatogram, not this class, as it is generally undesirable to allow the internal structures of a Chromatogram to be manipulated externally. This class could still be useful, however, for programatically generated "chromatograms".

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	Description
SimpleChromatogram()	Creates a new instance of SimpleChromatogram.

Method Summary

Modifier and Type	Method	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