codec.cu File Reference

A collection of conversion operations turning CDR3 strings into numerical representation. More...

#include "util.cu"
#include <string.h>

Macros
#define	CODEC_DEF

Functions
int	char_encode (char amino_acid)
	encode character into 5 bit value (0-31). More...
Int3	str_encode (char *str)
	encode peptide string into int3 struct with 6 characters encoded into an integer. More...
char *	str_decode (Int3 binary)
	decode binary form into peptide string. More...
__device__ __host__ int	len_decode (Int3 binary)
	find the string length in original form. More...
__device__ __host__ Int3	remove_char (Int3 binary, int position)
	remove one character from the string in binary form (without turning it into the original string form). More...
void	print_int3_arr (Int3 *arr, int n)
	conviniently print Int3* in readable form. More...

Variables
const int	A_CHAR = (int)'A'
const int	BEFORE_A_CHAR = A_CHAR - 1
const int	Y_CHAR = (int) 'Y'
const int	ESTIMATE_LENGTH = 18
const int	MAX_INPUT_LENGTH = 500

Detailed Description

A collection of conversion operations turning CDR3 strings into numerical representation.

Also includes utilities to directly edit the representation.

Macro Definition Documentation

CODEC_DEF

#define CODEC_DEF

Function Documentation

char_encode()

int char_encode

(

char

amino_acid

)

encode character into 5 bit value (0-31).

-1 for non amino acid character

len_decode()

__device__ __host__ int len_decode

(

Int3

binary

)

find the string length in original form.

print_int3_arr()

void print_int3_arr	(	Int3 *	arr,
		int	n
	)

conviniently print Int3* in readable form.

remove_char()

__device__ __host__ Int3 remove_char	(	Int3	binary,
		int	position
	)

remove one character from the string in binary form (without turning it into the original string form).

str_decode()

char* str_decode

(

Int3

binary

)

decode binary form into peptide string.

str_encode()

Int3 str_encode

(

char *

str

)

encode peptide string into int3 struct with 6 characters encoded into an integer.

Variable Documentation

A_CHAR

const int A_CHAR = (int)'A'

BEFORE_A_CHAR

const int BEFORE_A_CHAR = A_CHAR - 1

ESTIMATE_LENGTH

const int ESTIMATE_LENGTH = 18

MAX_INPUT_LENGTH

const int MAX_INPUT_LENGTH = 500

Y_CHAR

const int Y_CHAR = (int) 'Y'