Package org.biojava.bio.program.scf
Class SCF
- java.lang.Object
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- org.biojava.bio.chromatogram.AbstractChromatogram
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- org.biojava.bio.program.scf.SCF
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- All Implemented Interfaces:
Chromatogram
public class SCF extends AbstractChromatogram
AChromatogram
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 thePROB_
* constants in this class. The values areIntegerAlphabet.IntegerSymbol
objects in the range 0 to 255.- Author:
- Rhett Sutphin (UI CBCB)
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Field Summary
Fields Modifier and Type Field Description static int
BYTE_MAX_VALUE
Represents the maximum unsigned value of a byte for wrapping purposesstatic 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
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Constructor Summary
Constructors Modifier Constructor Description protected
SCF()
Creates a new, completely empty SCF.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static SCF
create(File f)
static SCF
create(InputStream in, long alreadyRead)
Properties
getComments()
Returns the comments fields as aProperties
mapping.static IntegerAlphabet.SubIntegerAlphabet
getProbabilityAlphabet()
protected void
load(File f)
protected void
load(InputStream in, long initOffset)
protected SymbolList
reverseComplementBaseCallList(String label)
OverridesAbstractChromatogram.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 inAbstractChromatogram.reverseComplement()
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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
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Field Detail
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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
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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
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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
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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
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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
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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
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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].
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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].
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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].
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Constructor Detail
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SCF
protected SCF()
Creates a new, completely empty SCF.
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Method Detail
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create
public static SCF create(File f) throws IOException, UnsupportedChromatogramFormatException
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create
public static SCF create(InputStream in, long alreadyRead) throws IOException, UnsupportedChromatogramFormatException
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load
protected void load(File f) throws IOException, UnsupportedChromatogramFormatException
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load
protected void load(InputStream in, long initOffset) throws IOException, UnsupportedChromatogramFormatException
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getComments
public Properties getComments()
Returns the comments fields as aProperties
mapping.
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reverseComplementInstance
protected AbstractChromatogram reverseComplementInstance()
Description copied from class:AbstractChromatogram
Returns a new instance of this AbstractChromatogram subclass for use inAbstractChromatogram.reverseComplement()
.- Specified by:
reverseComplementInstance
in classAbstractChromatogram
- Returns:
- a reverse-complemented AbstractChromatogram
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getProbabilityAlphabet
public static IntegerAlphabet.SubIntegerAlphabet getProbabilityAlphabet()
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reverseComplementBaseCallList
protected SymbolList reverseComplementBaseCallList(String label)
OverridesAbstractChromatogram.reverseComplementBaseCallList(java.lang.Object)
to support the 7 quality values from the SCF. These are handled thus:PROB_SUBSTITUTION
,PROB_OVERCALL
, andPROB_UNDERCALL
are just reversed &returned.PROB_NUC_
* returns the reverse of the quality sequence for the complement base.
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