public class SCF extends AbstractChromatogram
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.Modifier and Type | Field and Description |
---|---|
static int |
BYTE_MAX_VALUE
Represents the maximum unsigned value
of a byte for wrapping purposes
|
static java.lang.Object |
PROB_NUC_A
Base call alignment sequence label for the probability that call
should be A.
|
static java.lang.Object |
PROB_NUC_C
Base call alignment sequence label for the probability that call
should be C.
|
static java.lang.Object |
PROB_NUC_G
Base call alignment sequence label for the probability that call
should be G.
|
static java.lang.Object |
PROB_NUC_T
Base call alignment sequence label for the probability that call
should be T.
|
static java.lang.Object |
PROB_OVERCALL
Base call alignment sequence label for the overcall probability.
|
static java.lang.Object |
PROB_SUBSTITUTION
Base call alignment sequence label for the substitution
probability.
|
static java.lang.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
|
DNA, OFFSETS
Modifier | Constructor and Description |
---|---|
protected |
SCF()
Creates a new, completely empty SCF.
|
Modifier and Type | Method and Description |
---|---|
static SCF |
create(java.io.File f) |
static SCF |
create(java.io.InputStream in,
long alreadyRead) |
java.util.Properties |
getComments()
Returns the comments fields as a
Properties mapping. |
static IntegerAlphabet.SubIntegerAlphabet |
getProbabilityAlphabet() |
protected void |
load(java.io.File f) |
protected void |
load(java.io.InputStream in,
long initOffset) |
protected SymbolList |
reverseComplementBaseCallList(java.lang.Object 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() . |
clearTraces, createImmutableAlignment, createImmutableSymbolList, getBaseCalls, getMax, getMax, getSequenceLength, getSignificantBits, getTrace, getTraceLength, reverse, reverseComplement, reverseComplementBaseCalls, setBaseCallAlignment, setBits, setTrace
public static final int BYTE_MAX_VALUE
public static final int SHORT_MAX_VALUE
public static final java.lang.Object PROB_NUC_A
public static final java.lang.Object PROB_NUC_C
public static final java.lang.Object PROB_NUC_G
public static final java.lang.Object PROB_NUC_T
public static final java.lang.Object PROB_SUBSTITUTION
public static final java.lang.Object PROB_OVERCALL
public static final java.lang.Object PROB_UNDERCALL
public static SCF create(java.io.File f) throws java.io.IOException, UnsupportedChromatogramFormatException
java.io.IOException
UnsupportedChromatogramFormatException
public static SCF create(java.io.InputStream in, long alreadyRead) throws java.io.IOException, UnsupportedChromatogramFormatException
java.io.IOException
UnsupportedChromatogramFormatException
protected void load(java.io.File f) throws java.io.IOException, UnsupportedChromatogramFormatException
java.io.IOException
UnsupportedChromatogramFormatException
protected void load(java.io.InputStream in, long initOffset) throws java.io.IOException, UnsupportedChromatogramFormatException
java.io.IOException
UnsupportedChromatogramFormatException
public java.util.Properties getComments()
Properties
mapping.protected AbstractChromatogram reverseComplementInstance()
AbstractChromatogram
AbstractChromatogram.reverseComplement()
.reverseComplementInstance
in class AbstractChromatogram
public static IntegerAlphabet.SubIntegerAlphabet getProbabilityAlphabet()
protected SymbolList reverseComplementBaseCallList(java.lang.Object label)
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.reverseComplementBaseCallList
in class AbstractChromatogram
label
- the label Object