info.bioinfweb.libralign.pherogram.provider

Class BioJavaPherogramProvider

java.lang.Object

info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider

All Implemented Interfaces:

DataModel, PherogramProvider

public class BioJavaPherogramProvider
extends java.lang.Object
implements PherogramProvider

Adapter class that provides the contents of any implementation of Chromatogram from BioJava 1 as a PherogramProvider.

You can use this class together with ChromatogramFactory to load ABI or SCF files into LibrAlign. Note that base call indices in LibrAlign start with 0 whereas the BioJava indices in the underlying Chromatogram instance start with 1. (This class converts the indices accordingly.)

Trace indices (x-values) start with 0 in LibrAlign and in BioJava.

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.biojava1

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	QUALITY_LABEL_PREFIX

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
BioJavaPherogramProvider(Chromatogram chromatogram) 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 a new instance of this class which uses the reverse complemented version of the underlying BioJava 1 chromatogram.

Methods inherited from class java.lang.Object

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

Field Detail

QUALITY_LABEL_PREFIX

public static final java.lang.String QUALITY_LABEL_PREFIX

See Also:

Constant Field Values

Constructor Detail

BioJavaPherogramProvider

public BioJavaPherogramProvider(Chromatogram chromatogram)

Creates a new instance of this class.

Parameters:

chromatogram - the BioJava pherogram instance

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 a new instance of this class which uses the reverse complemented version of the underlying BioJava 1 chromatogram.

Specified by:

reverseComplement in interface PherogramProvider

Returns:

a new instance of this class