org.biojava.bio.chromatogram
Interface Chromatogram

All Known Implementing Classes:

ABIFChromatogram, AbstractChromatogram, SCF, SimpleChromatogram

public interface Chromatogram

Encapsulates the basic information you would want from a chromatogram. Read-only.

Since:

1.3

Author:

Rhett Sutphin (UI CBCB), Matthew Pocock

Field Summary

static Object	DNA The sequence label for the list of called bases.
static 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

DNA

static final Object DNA

The sequence label for the list of called bases.

OFFSETS

static final Object OFFSETS

The sequence label for the trace offsets of the called bases.

Method Detail

getMax

int getMax()

Gets the max intensity from all the traces. Must be equivalent to the max of calling getMax(AtomicSymbol) on each of the four non-ambiguous DNA nucleotides.

Returns:

the max intensity

getMax

int getMax(AtomicSymbol nucleotide)
           throws IllegalSymbolException

Gets the max intensity on the trace for the specified nucleotide.

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

getTraceLength

int getTraceLength()

Returns the length of the trace of the Chromatogram.

Returns:

the number of samples in the trace

See Also:

getTrace(AtomicSymbol)

getTrace

int[] getTrace(AtomicSymbol nucleotide)
               throws IllegalSymbolException

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 getTraceLength() ints long.

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

getSignificantBits

int getSignificantBits()

Returns the number of bits of the traces which are significant. For instance, if the chromatogram were originally encoded with a single byte per trace sample, this method must return 8.

Returns:

the number of significant bits

getBaseCalls

Alignment getBaseCalls()

Returns an alignment that describes the base calls for this chromatogram. All of the SymbolLists in this alignment must be the same length and that length must equal getSequenceLength().

The alignment must contain, at the least, two sequences:

1. A sequence containing the called bases. The alphabet of this list must be DNATools.getDNA(). The label for this list in the alignment must be Chromatogram.DNA
2. A sequence containing the trace offsets at which the called bases were called. The alphabet of this list must be an 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.

Returns:

an alignment of at least two sequences, as described above.

getSequenceLength

int getSequenceLength()

Returns the number of bases called by whatever base-calling software analyzed the chromatogram as loaded. Must equal getBaseCalls().length().

Returns:

the number of bases

reverseComplement

Chromatogram reverseComplement()

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.

Returns:

a new chromatogram that is the reverse complement of this one