18 #ifndef _BASE_ASCII_MAP_H
19 #define _BASE_ASCII_MAP_H
21 #include "StringBasics.h"
88 myBase2IntMapPtr = NULL;
96 if (myBase2IntMapPtr == NULL)
99 if (myPrimerCount < myNumPrimerBases)
115 if (myBase2IntMapPtr == NULL)
122 if ((myBase2IntMapPtr ==
color2int) && (myPrimerCount < myNumPrimerBases))
130 return myBase2IntMapPtr[(int)letter];
154 myNumPrimerBases = numPrimerBases;
166 myBase2IntMapPtr = NULL;
190 myBase2IntMapPtr = NULL;
196 unsigned int myNumPrimerBases;
200 unsigned int myPrimerCount;
202 unsigned char* myBase2IntMapPtr;
void setNumPrimerBases(int numPrimerBases)
Set the number of primer bases expected before the actual base/color space type occurs for the rest o...
static const int baseXIndex
Value associated with any non-base character in the ascii to base map (unknown, bad data).
static const int baseNIndex
Value associated with 'N' in the ascii to base map (bad read).
@ UNKNOWN
Base decision on the first raw seq character/type has yet to be determined.
void resetPrimerCount()
Reset the number of primers to 0.
Map between characters and the associated base type.
static unsigned char baseColor2int[256+1]
Map ASCII values to a 2 (or 3) bit encoding for the base pair value for both base and color space.
@ BASE_SPACE
Bases only (A,C,G,T,N).
static unsigned char color2int[256+1]
Map ASCII values to a 2 (or 3) bit encoding for the base pair value for just color space (0123).
SPACE_TYPE
The type of space (color or base) to use in the mapping.
void resetBaseMapType()
Reset the base mapping type to UNKNOWN.
static unsigned char base2int[256+1]
Map ASCII values to a 2 (or 3) bit encoding for the base pair value for just base space (ACTGNactgn).
int getBaseIndex(const char &letter)
Returns the baseIndex value for the character passed in.
void setBaseMapType(SPACE_TYPE spaceType)
Set the base type based on the passed in option.
static const char int2colorSpace[]
Convert from int representation to colorspace representation.
SPACE_TYPE getSpaceType()
Return the space type that is currently set.
static const char int2base[]
Convert from int representation to the base.
static unsigned char base2complement[]
This table maps 5' base space to the 3' complement base space values, as well as 5' color space value...
@ COLOR_SPACE
Color space only (0,1,2,3,.).