xtn.h File Reference

Listing of all shared data structures, constants, and exporting method. More...

#include <vector>

Go to the source code of this file.

Classes
struct	Int3
	12-byte integer representation for CDR3 string. More...
struct	Int2
	8-byte integer representation for pair of sequence index. More...
struct	SeqInfo
	Information related to a sequence. More...
struct	XTNArgs
	bundled representation for command line arguments. More...
struct	MemoryContext
	bundled representation for memory constraints and info. More...
struct	XTNOutput
	bundled representation for algorithm's output. More...
class	SeqArray

Enumerations
enum	ReturnCode { SUCCESS, ERROR, EXIT }
	control-flow representation. More...

Functions
void	xtn_perform (XTNArgs args, SeqArray seqArr, SeqInfo *seqInfo, void callback(XTNOutput))
	the algorithm's API. More...

Variables
const int	MAX_COMPRESSED_LENGTH = 18
	CDR3 length limit for compression. More...
int	verboseGlobal = 0
	control printing of each method More...
const char	LEVENSHTEIN = 0
	enum for distant type More...
const char	HAMMING = 1
	enum for distant type More...

Detailed Description

Listing of all shared data structures, constants, and exporting method.

Enumeration Type Documentation

ReturnCode

enum ReturnCode

control-flow representation.

Enumerator
SUCCESS
ERROR
EXIT

Function Documentation

xtn_perform()

void xtn_perform	(	XTNArgs	args,
		SeqArray	seqArr,
		SeqInfo *	seqInfo,
		void	callbackXTNOutput
	)

the algorithm's API.

Parameters

args	algorithm's bundled arguments
seqArr	list of CDR3 sequences
seqInfo	information of each CDR3 sequence, only used in overlap mode
callback	function to be invoked once a chunk of output is ready

Variable Documentation

HAMMING

const char HAMMING = 1

enum for distant type

LEVENSHTEIN

const char LEVENSHTEIN = 0

enum for distant type

MAX_COMPRESSED_LENGTH

const int MAX_COMPRESSED_LENGTH = 18

CDR3 length limit for compression.

verboseGlobal

int verboseGlobal = 0

control printing of each method