info.bioinfweb.libralign.pherogram.provider

Interface PherogramProvider

All Superinterfaces:

DataModel

All Known Implementing Classes:

BioJavaPherogramProvider, ReverseComplementPherogramProvider

public interface PherogramProvider
extends DataModel

Interface that should be implemented by all classes providing pherogram data. Data provided by such implementations can be displayed by a PherogramArea.

Since:

0.1.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	LABEL_OVERCALL_PROBABILITY Label to be used with getAnnotation(String, int) to determine the overcall probability
static java.lang.String	LABEL_SUBSTITUTION_PROBABILITY Label to be used with getAnnotation(String, int) to determine the substitution probability
static java.lang.String	LABEL_UNDERCALL_PROBABILITY Label to be used with getAnnotation(String, int) to determine the undercall probability
static java.util.Set<java.lang.String>	PROBABILITY_LABELS A list that allows to iterate over all probability labels.
static java.util.Set<java.lang.Character>	TRACE_CURVE_NUCLEOTIDES A list of the nucleotides A, T, C and G to which trace curves exist in a trace file from Sanger sequencing.

Method Summary

Modifier and Type	Method and Description
int	getAnnotation(java.lang.String label, int baseIndex) Returns the specified annotation (e.g.
char	getBaseCall(int baseIndex) Returns a base from the DNA sequence associated with the stored trace.
int	getBaseCallPosition(int baseIndex) Returns the position in the trace where the base at the specified index was observed.
double	getMaxTraceValue(char nucleotide) Returns the maximum trace value the specified curve contains.
int	getQuality(char nucleotide, int baseIndex) Returns the quality score associated with the specified nucleotide.
int	getSequenceLength() Returns the length of the sequence associated with the stored trace.
int	getTraceLength() Returns the length of the stored trace.
double	getTraceValue(char nucleotide, int x) Returns the y value of the specified trace curve at the specified position.
PherogramProvider	reverseComplement() Returns a reverse complemented view of this model.

Field Detail

TRACE_CURVE_NUCLEOTIDES

static final java.util.Set<java.lang.Character> TRACE_CURVE_NUCLEOTIDES

A list of the nucleotides A, T, C and G to which trace curves exist in a trace file from Sanger sequencing.

LABEL_SUBSTITUTION_PROBABILITY

static final java.lang.String LABEL_SUBSTITUTION_PROBABILITY

Label to be used with getAnnotation(String, int) to determine the substitution probability

See Also:

Constant Field Values

LABEL_OVERCALL_PROBABILITY

static final java.lang.String LABEL_OVERCALL_PROBABILITY

Label to be used with getAnnotation(String, int) to determine the overcall probability

See Also:

Constant Field Values

LABEL_UNDERCALL_PROBABILITY

static final java.lang.String LABEL_UNDERCALL_PROBABILITY

Label to be used with getAnnotation(String, int) to determine the undercall probability

See Also:

Constant Field Values

PROBABILITY_LABELS

static final java.util.Set<java.lang.String> PROBABILITY_LABELS

A list that allows to iterate over all probability labels.

Method Detail

getTraceValue

double getTraceValue(char nucleotide,
                     int x)

Returns the y value of the specified trace curve at the specified position.

Parameters:

nucleotide - the type of trace curve (A, T, C or G)

x - the x position of the curve (The first position is 0 and the last is getTraceLength()- 1.)

Returns:

the stored trace value at this position normalized between 0 and 1

getTraceLength

int getTraceLength()

Returns the length of the stored trace. (The length depends on the read length and sampling rate.)

Returns:

an integer values >= 0

getMaxTraceValue

double getMaxTraceValue(char nucleotide)

Returns the maximum trace value the specified curve contains. (The normalization is the same as in #getTraceValue(TraceCurve, int).)

Parameters:

nucleotide - the type of trace curve (A, T, C or G)

Returns:

a floating point value between 0 and 1

getBaseCall

char getBaseCall(int baseIndex)

Returns a base from the DNA sequence associated with the stored trace.

Parameters:

baseIndex - the index of the base in the pherogram (base call) sequence (This might differ from the index of the base in the associated sequence in the alignment. Indices start with 0.)

Returns:

a DNA base or an ambiguity code

getBaseCallPosition

int getBaseCallPosition(int baseIndex)

Returns the position in the trace where the base at the specified index was observed.

Parameters:

baseIndex - the index of the base in the pherogram (base call) sequence (This might differ from the index of the base in the associated sequence in the alignment. Indices start with 0.)

Returns:

an integer value between 0 and getTraceLength()- 1

getQuality

int getQuality(char nucleotide,
               int baseIndex)

Returns the quality score associated with the specified nucleotide.

Parameters:

nucleotide - the nucleotide identifying the trace curve for the quality score

baseIndex - the index of the base call position to which the quality score belongs (Indices start with 0.)

Returns:

the quality score or -1 if no value is stored at the specified position for the specified nucleotide

getAnnotation

int getAnnotation(java.lang.String label,
                  int baseIndex)

Returns the specified annotation (e.g. substitution probability) associated with the base call at the specified position.

Parameters:

label - the name of the attachment to be returned

baseIndex - the index of base call to which the returned attachment score belongs (Indices start with 0.)

Returns:

the attached value or -1 if no value is stored at the specified position under the specified label

getSequenceLength

int getSequenceLength()

Returns the length of the sequence associated with the stored trace.

Returns:

an integer value >= 0

reverseComplement

PherogramProvider reverseComplement()

Returns a reverse complemented view of this model.

Returns:

another instance with a possibly shared data source