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 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

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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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()`.

Methods inherited from class org.biojava.bio.chromatogram.AbstractChromatogram
clearTraces, createImmutableAlignment, createImmutableSymbolList, getBaseCalls, getMax, getMax, getSequenceLength, getSignificantBits, getTrace, getTraceLength, reverse, reverseComplement, 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 java.lang.Object PROB_NUC_A
```
    Base call alignment sequence label for the probability that call should be A.
  - PROB_NUC_C
```
public static final java.lang.Object PROB_NUC_C
```
    Base call alignment sequence label for the probability that call should be C.
  - PROB_NUC_G
```
public static final java.lang.Object PROB_NUC_G
```
    Base call alignment sequence label for the probability that call should be G.
  - PROB_NUC_T
```
public static final java.lang.Object PROB_NUC_T
```
    Base call alignment sequence label for the probability that call should be T.
  - PROB_SUBSTITUTION
```
public static final java.lang.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 java.lang.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 java.lang.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(java.io.File f)
                  throws java.io.IOException,
                         UnsupportedChromatogramFormatException
```
    Throws:
    
    java.io.IOException
    
    UnsupportedChromatogramFormatException
  - create
```
public static SCF create(java.io.InputStream in,
                         long alreadyRead)
                  throws java.io.IOException,
                         UnsupportedChromatogramFormatException
```
    Throws:
    
    java.io.IOException
    
    UnsupportedChromatogramFormatException
  - load
```
protected void load(java.io.File f)
             throws java.io.IOException,
                    UnsupportedChromatogramFormatException
```
    Throws:
    
    java.io.IOException
    
    UnsupportedChromatogramFormatException
  - load
```
protected void load(java.io.InputStream in,
                    long initOffset)
             throws java.io.IOException,
                    UnsupportedChromatogramFormatException
```
    Throws:
    
    java.io.IOException
    
    UnsupportedChromatogramFormatException
  - getComments
```
public java.util.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(java.lang.Object 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.
    Overrides:
    
    reverseComplementBaseCallList in class AbstractChromatogram
    
    Parameters:
    
    label - the label Object
    
    Returns:
    
    an appropriately reverse-complemented SymbolList, or null if the label is unhandled.

Class SCF

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

BYTE_MAX_VALUE

SHORT_MAX_VALUE

PROB_NUC_A

PROB_NUC_C

PROB_NUC_G

PROB_NUC_T

PROB_SUBSTITUTION

PROB_OVERCALL

PROB_UNDERCALL

Constructor Detail

SCF

Method Detail

create

create

load

load

getComments

reverseComplementInstance

getProbabilityAlphabet

reverseComplementBaseCallList