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java.lang.Objectorg.biojava.bio.chromatogram.AbstractChromatogram
org.biojava.bio.chromatogram.SimpleChromatogram
public class SimpleChromatogram
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".
Field Summary |
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Fields inherited from interface org.biojava.bio.chromatogram.Chromatogram |
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DNA, OFFSETS |
Constructor Summary | |
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SimpleChromatogram()
Creates a new instance of SimpleChromatogram. |
Method Summary | |
---|---|
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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SimpleChromatogram()
Method Detail |
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public void setSymbolLists(SymbolList dna, SymbolList offsets) throws IllegalAlphabetException, IllegalArgumentException
dna
- a symbol list in the DNA alphabet that contains the base calls
for this chromatogramoffsets
- a symbol list in an integer or sub-integer alphabet that
contains the locations in the chromatogram for the bases called
in dna
IllegalAlphabetException
- when the alphabets aren't as specified
IllegalArgumentException
- when the lists aren't the same lengthpublic void setTraceValues(AtomicSymbol nuc, int[] trace, int maxVal) throws IllegalArgumentException, IllegalSymbolException
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
.
nuc
- the nucleotide for which to set the tracetrace
- the sampled intensities along the tracemaxVal
- the maximum value on the trace, or Integer.MIN_VALUE
to force this method to calculate it
IllegalArgumentException
- when trace.length is different
from any of the existing (non-null) traces
IllegalSymbolException
- when nuc is not a concrete DNA nucleotidepublic void clearTraceValues()
public void setSignificantBits(int bits)
bits
- how many bits of the trace samples are significantChromatogram.getSignificantBits()
protected AbstractChromatogram reverseComplementInstance()
AbstractChromatogram
AbstractChromatogram.reverseComplement()
.
reverseComplementInstance
in class AbstractChromatogram
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