Package org.biojava.bio.program.scf

Class SCF

java.lang.Object

org.biojava.bio.chromatogram.AbstractChromatogram

org.biojava.bio.program.scf.SCF

All Implemented Interfaces:

Chromatogram

public class SCF
extends AbstractChromatogram

A Chromatogram as loaded from an SCF v2 or v3 file. Also loads and exposes the SCF format's "private data" and "comments" sections. The quality values from the SCF are stored as additional sequences on the base call alignment. The labels are the PROB_* constants in this class. The values are IntegerAlphabet.IntegerSymbol objects in the range 0 to 255.

Author:

Rhett Sutphin (UI CBCB)

Field Summary

Fields

Modifier and Type	Field	Description
static int	BYTE_MAX_VALUE	Represents the maximum unsigned value of a byte for wrapping purposes
static String	PROB_NUC_A	Base call alignment sequence label for the probability that call should be A.
static String	PROB_NUC_C	Base call alignment sequence label for the probability that call should be C.
static String	PROB_NUC_G	Base call alignment sequence label for the probability that call should be G.
static String	PROB_NUC_T	Base call alignment sequence label for the probability that call should be T.
static Object	PROB_OVERCALL	Base call alignment sequence label for the overcall probability.
static Object	PROB_SUBSTITUTION	Base call alignment sequence label for the substitution probability.
static Object	PROB_UNDERCALL	Base call alignment sequence label for the undercall probability.
static int	SHORT_MAX_VALUE	Represents the maximum unsigned value of a short for wrapping purposes

Fields inherited from interface org.biojava.bio.chromatogram.Chromatogram

DNA, OFFSETS

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SCF()	Creates a new, completely empty SCF.

Method Summary

Modifier and Type	Method	Description
static SCF	create(File f)
static SCF	create(InputStream in, long alreadyRead)
Properties	getComments()	Returns the comments fields as a Properties mapping.
static IntegerAlphabet.SubIntegerAlphabet	getProbabilityAlphabet()
protected void	load(File f)
protected void	load(InputStream in, long initOffset)
protected SymbolList	reverseComplementBaseCallList(String label)	Overrides AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to support the 7 quality values from the SCF.
protected AbstractChromatogram	reverseComplementInstance()	Returns a new instance of this AbstractChromatogram subclass for use in AbstractChromatogram.reverseComplement().

Methods inherited from class org.biojava.bio.chromatogram.AbstractChromatogram

clearTraces, createImmutableAlignment, createImmutableSymbolList, getBaseCalls, getMax, getMax, getSequenceLength, getSignificantBits, getTrace, getTraceLength, reverse, reverseComplement, reverseComplementBaseCallList, reverseComplementBaseCalls, setBaseCallAlignment, setBits, setTrace

Methods inherited from class java.lang.Object

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

Field Detail

BYTE_MAX_VALUE

public static final int BYTE_MAX_VALUE

Represents the maximum unsigned value of a byte for wrapping purposes

See Also:

Constant Field Values

SHORT_MAX_VALUE

public static final int SHORT_MAX_VALUE

Represents the maximum unsigned value of a short for wrapping purposes

See Also:

Constant Field Values

PROB_NUC_A

public static final String PROB_NUC_A

Base call alignment sequence label for the probability that call should be A.

See Also:

Constant Field Values

PROB_NUC_C

public static final String PROB_NUC_C

Base call alignment sequence label for the probability that call should be C.

See Also:

Constant Field Values

PROB_NUC_G

public static final String PROB_NUC_G

Base call alignment sequence label for the probability that call should be G.

See Also:

Constant Field Values

PROB_NUC_T

public static final String PROB_NUC_T

Base call alignment sequence label for the probability that call should be T.

See Also:

Constant Field Values

PROB_SUBSTITUTION

public static final Object PROB_SUBSTITUTION

Base call alignment sequence label for the substitution probability. In versions of the SCF spec before 3.10, this is called spareQual[0].

PROB_OVERCALL

public static final Object PROB_OVERCALL

Base call alignment sequence label for the overcall probability. In versions of the SCF spec before 3.10, this is called spareQual[1].

PROB_UNDERCALL

public static final Object PROB_UNDERCALL

Base call alignment sequence label for the undercall probability. In versions of the SCF spec before 3.10, this is called spareQual[2].

Constructor Detail

SCF

protected SCF()

Creates a new, completely empty SCF.

Method Detail

create

public static SCF create(File f)
                  throws IOException,
                         UnsupportedChromatogramFormatException

Throws:

IOException

UnsupportedChromatogramFormatException

create

public static SCF create(InputStream in,
                         long alreadyRead)
                  throws IOException,
                         UnsupportedChromatogramFormatException

Throws:

IOException

UnsupportedChromatogramFormatException

load

protected void load(File f)
             throws IOException,
                    UnsupportedChromatogramFormatException

Throws:

IOException

UnsupportedChromatogramFormatException

load

protected void load(InputStream in,
                    long initOffset)
             throws IOException,
                    UnsupportedChromatogramFormatException

Throws:

IOException

UnsupportedChromatogramFormatException

getComments

public Properties getComments()

Returns the comments fields as a Properties mapping.

reverseComplementInstance

protected AbstractChromatogram reverseComplementInstance()

Description copied from class: AbstractChromatogram

Returns a new instance of this AbstractChromatogram subclass for use in AbstractChromatogram.reverseComplement().

Specified by:

reverseComplementInstance in class AbstractChromatogram

Returns:

a reverse-complemented AbstractChromatogram

getProbabilityAlphabet

public static IntegerAlphabet.SubIntegerAlphabet getProbabilityAlphabet()

reverseComplementBaseCallList

protected SymbolList reverseComplementBaseCallList(String label)

Overrides AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to support the 7 quality values from the SCF. These are handled thus:

• PROB_SUBSTITUTION, PROB_OVERCALL, and PROB_UNDERCALL are just reversed &returned.
• PROB_NUC_* returns the reverse of the quality sequence for the complement base.