info.bioinfweb.libralign.pherogram.provider

Class ReverseComplementPherogramProvider

java.lang.Object

info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider

All Implemented Interfaces:

DataModel, PherogramProvider

public class ReverseComplementPherogramProvider
extends java.lang.Object
implements PherogramProvider

Pherogram model that allows to view another model instance reverse complemented.

Author:

Ben Stöver

Field Summary

Fields inherited from interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider

LABEL_OVERCALL_PROBABILITY, LABEL_SUBSTITUTION_PROBABILITY, LABEL_UNDERCALL_PROBABILITY, PROBABILITY_LABELS, TRACE_CURVE_NUCLEOTIDES

Constructor Summary

Constructors

Constructor and Description
ReverseComplementPherogramProvider(PherogramProvider source) Creates a new instance of this class.

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 the source instance.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ReverseComplementPherogramProvider

public ReverseComplementPherogramProvider(PherogramProvider source)

Creates a new instance of this class.

Parameters:

source - the model to be viewed reverse complemented

Method Detail

getTraceValue

public double getTraceValue(char nucleotide,
                            int x)

Description copied from interface: PherogramProvider

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

Specified by:

getTraceValue in interface PherogramProvider

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 PherogramProvider.getTraceLength()- 1.)

Returns:

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

getTraceLength

public int getTraceLength()

Description copied from interface: PherogramProvider

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

Specified by:

getTraceLength in interface PherogramProvider

Returns:

an integer values >= 0

getMaxTraceValue

public double getMaxTraceValue(char nucleotide)

Description copied from interface: PherogramProvider

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

Specified by:

getMaxTraceValue in interface PherogramProvider

Parameters:

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

Returns:

a floating point value between 0 and 1

getBaseCall

public char getBaseCall(int baseIndex)

Description copied from interface: PherogramProvider

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

Specified by:

getBaseCall in interface PherogramProvider

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

public int getBaseCallPosition(int baseIndex)

Description copied from interface: PherogramProvider

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

Specified by:

getBaseCallPosition in interface PherogramProvider

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 PherogramProvider.getTraceLength()- 1

getQuality

public int getQuality(char nucleotide,
                      int baseIndex)

Description copied from interface: PherogramProvider

Returns the quality score associated with the specified nucleotide.

Specified by:

getQuality in interface PherogramProvider

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

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

Description copied from interface: PherogramProvider

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

Specified by:

getAnnotation in interface PherogramProvider

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

public int getSequenceLength()

Description copied from interface: PherogramProvider

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

Specified by:

getSequenceLength in interface PherogramProvider

Returns:

an integer value >= 0

reverseComplement

public PherogramProvider reverseComplement()

Returns the source instance.

Specified by:

reverseComplement in interface PherogramProvider

Returns:

the instance specified in the constructor