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
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)
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
Represents the maximum unsigned value of a byte for wrapping purposesstatic final String
Base call alignment sequence label for the probability that call should be A.static final String
Base call alignment sequence label for the probability that call should be C.static final String
Base call alignment sequence label for the probability that call should be G.static final String
Base call alignment sequence label for the probability that call should be T.static final Object
Base call alignment sequence label for the overcall probability.static final Object
Base call alignment sequence label for the substitution probability.static final Object
Base call alignment sequence label for the undercall probability.static final int
Represents the maximum unsigned value of a short for wrapping purposesFields inherited from interface org.biojava.bio.chromatogram.Chromatogram
DNA, OFFSETS
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic SCF
static SCF
create
(InputStream in, long alreadyRead) Returns the comments fields as aProperties
mapping.protected void
protected void
load
(InputStream in, long initOffset) protected SymbolList
OverridesAbstractChromatogram.reverseComplementBaseCallList(java.lang.Object)
to support the 7 quality values from the SCF.protected AbstractChromatogram
Returns a new instance of this AbstractChromatogram subclass for use inAbstractChromatogram.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
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Field Details
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BYTE_MAX_VALUE
Represents the maximum unsigned value of a byte for wrapping purposes- See Also:
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SHORT_MAX_VALUE
Represents the maximum unsigned value of a short for wrapping purposes- See Also:
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PROB_NUC_A
Base call alignment sequence label for the probability that call should be A.- See Also:
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PROB_NUC_C
Base call alignment sequence label for the probability that call should be C.- See Also:
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PROB_NUC_G
Base call alignment sequence label for the probability that call should be G.- See Also:
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PROB_NUC_T
Base call alignment sequence label for the probability that call should be T.- See Also:
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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
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
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 Details
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SCF
protected SCF()Creates a new, completely empty SCF.
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Method Details
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create
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create
public static SCF create(InputStream in, long alreadyRead) throws IOException, UnsupportedChromatogramFormatException -
load
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load
protected void load(InputStream in, long initOffset) throws IOException, UnsupportedChromatogramFormatException -
getComments
Returns the comments fields as aProperties
mapping. -
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
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reverseComplementBaseCallList
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 invalid input: '&returned'.PROB_NUC_
* returns the reverse of the quality sequence for the complement base.
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