|
|||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
Encapsulates the basic information you would want from a chromatogram. Read-only.
Field Summary | |
static java.lang.Object |
DNA
The sequence label for the list of called bases |
static java.lang.Object |
OFFSETS
The sequence label for the trace offsets of the called bases |
Method Summary | |
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. |
Field Detail |
public static final java.lang.Object DNA
public static final java.lang.Object OFFSETS
Method Detail |
public int getMax()
getMax(AtomicSymbol)
on each
of the four non-ambiguous DNA nucleotides.
public int getMax(AtomicSymbol nucleotide) throws IllegalSymbolException
nucleotide
- the trace to examine. Must be a concrete
(non-ambiguous) nucleotide from the DNA alphabet
IllegalSymbolException
- when the nucleotide isn't from the DNA
alphabetpublic int getTraceLength()
getTrace(AtomicSymbol)
public int[] getTrace(AtomicSymbol nucleotide) throws IllegalSymbolException
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()
int
s long.
nucleotide
- the trace to examine. Must be the symbol for A, C, G, or T
as provided by DNATools
IllegalSymbolException
- if nucleotide
isn't in the DNA alphabetpublic int getSignificantBits()
public Alignment getBaseCalls()
SymbolList
s in this alignment must be the same
length and that length must equal getSequenceLength()
.
The alignment must contain, at the least, two sequences:
DNATools.getDNA()
.
The label for this list in the alignment must be
Chromatogram.DNA
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.
public int getSequenceLength()
getBaseCalls()
.length()
.
public Chromatogram reverseComplement()
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.
|
|||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |