BaseAsciiMap Class Reference

Map between characters and the associated base type. More...

#include <BaseAsciiMap.h>

List of all members.

Public Types
enum	SPACE_TYPE { UNKNOWN, BASE_SPACE, COLOR_SPACE }
	The type of space (color or base) to use in the mapping. More...
Public Member Functions
void	setBaseMapType (SPACE_TYPE spaceType)
	Set the base type based on the passed in option.
int	getBaseIndex (const char &letter)
	Returns the baseIndex value for the character passed in.
SPACE_TYPE	getSpaceType ()
	Return the space type that is currently set.
void	setNumPrimerBases (int numPrimerBases)
	Set the number of primer bases expected before the actual base/color space type occurs for the rest of the entries.
void	resetPrimerCount ()
	Reset the number of primers to 0.
void	resetBaseMapType ()
	Reset the base mapping type to UNKNOWN.
Static Public Attributes
static const int	baseNIndex = 004
	Value associated with 'N' in the ascii to base map (bad read).
static const int	baseXIndex = 005
	Value associated with any non-base character in the ascii to base map (unknown, bad data).
static const char	int2base [] = "ACGTNMXXXXXXXXXX"
	Convert from int representation to the base.
static const char	int2colorSpace [] = "0123NXXXXXXXXXXX"
	Convert from int representation to colorspace representation.
static unsigned char	base2complement [] = "NNNNNNNNNNNNNNNN"
	This table maps 5' base space to the 3' complement base space values, as well as 5' color space values to the corresponding 3' complement color space values.
static unsigned char	baseColor2int [256+1] = "\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005"
	Map ASCII values to a 2 (or 3) bit encoding for the base pair value for both base and color space.
static unsigned char	base2int [256+1] = "\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005"
	Map ASCII values to a 2 (or 3) bit encoding for the base pair value for just base space (ACTGNactgn).
static unsigned char	color2int [256+1] = "\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005"
	Map ASCII values to a 2 (or 3) bit encoding for the base pair value for just color space (0123).

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Detailed Description

Map between characters and the associated base type.

Definition at line 24 of file BaseAsciiMap.h.

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Member Enumeration Documentation

enum BaseAsciiMap::SPACE_TYPE

The type of space (color or base) to use in the mapping.

Enumerator:

UNKNOWN	Base decision on the first raw seq character/type has yet to be determined.
BASE_SPACE	Bases only (A,C,G,T,N).
COLOR_SPACE	Color space only (0,1,2,3,.).

Definition at line 44 of file BaseAsciiMap.h.

                    {
        /// Base decision on the first raw seq character/type has yet 
        /// to be determined.
        UNKNOWN,
        BASE_SPACE, ///< Bases only (A,C,G,T,N).
        COLOR_SPACE ///< Color space only (0,1,2,3,.).
    };

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Member Function Documentation

void BaseAsciiMap::setNumPrimerBases

(

int

numPrimerBases

)

[inline]

Set the number of primer bases expected before the actual base/color space type occurs for the rest of the entries.

Definition at line 152 of file BaseAsciiMap.h.

    {
        myNumPrimerBases = numPrimerBases;
    }

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Member Data Documentation

unsigned char BaseAsciiMap::base2complement = "NNNNNNNNNNNNNNNN" [static]

This table maps 5' base space to the 3' complement base space values, as well as 5' color space values to the corresponding 3' complement color space values.

In both cases, invalids are mapped to 'N', which isn't accurate for ABI SOLiD, but internally it shouldn't matter (on output it will).

Definition at line 41 of file BaseAsciiMap.h.

unsigned char BaseAsciiMap::base2int = "\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" [static]

Map ASCII values to a 2 (or 3) bit encoding for the base pair value for just base space (ACTGNactgn).

'A'/'a' -> 0; 'C'/'c' -> 1; 'G'/'g' -> 2; 'T'/'t' -> 3; 'N'/'n' -> 4; anything else -> 5.

Definition at line 61 of file BaseAsciiMap.h.

Referenced by getBaseIndex(), getSpaceType(), and setBaseMapType().

unsigned char BaseAsciiMap::baseColor2int = "\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" [static]

Map ASCII values to a 2 (or 3) bit encoding for the base pair value for both base and color space.

'A'/'a'/'0' -> 0; 'C'/'c'/'1' -> 1; 'G'/'g'/'2' -> 2; 'T'/'t'/'3' -> 3; 'N'/'n'/'4' -> 4; anything else -> 5.

Definition at line 56 of file BaseAsciiMap.h.

const int BaseAsciiMap::baseXIndex = 005 [static]

Value associated with any non-base character in the ascii to base map (unknown, bad data).

Definition at line 31 of file BaseAsciiMap.h.

Referenced by getBaseIndex().

unsigned char BaseAsciiMap::color2int = "\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" [static]

Map ASCII values to a 2 (or 3) bit encoding for the base pair value for just color space (0123).

'0' -> 0; '1' -> 1; '2' -> 2; '3' -> 3; '4' -> 4; anything else -> 5.

Definition at line 65 of file BaseAsciiMap.h.

Referenced by getBaseIndex(), getSpaceType(), and setBaseMapType().

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The documentation for this class was generated from the following files:

• general/BaseAsciiMap.h
• general/BaseAsciiMap.cpp