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mawdefs.h
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mawdefs.h
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/**
MAW: Minimal Absent Words
Copyright (C) 2014 Alice Heliou and Solon P. Pissis.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
**/
#include <sdsl/bit_vectors.hpp>
#define ALLOC_SIZE 1048576
#define DEL '$'
#define DEL_STR "$"
#define DNA "ACGTN" //DNA alphabet
#define PROT "ARNDCQEGHILKMFPSTWYV" //Proteins alphabet
#define IUPAC "ACGTUWSMKRYBDHVN" //IUPAC alphabet
#define max(a,b) ((a) > (b)) ? (a) : (b)
#define min(a,b) ((a) < (b)) ? (a) : (b)
using namespace sdsl;
using namespace std;
#ifdef _USE_64
typedef int64_t INT;
#endif
#ifdef _USE_32
typedef int32_t INT;
#endif
struct TSwitch
{
char * alphabet;
char * input_filename;
char * output_filename;
unsigned int k;
unsigned int K;
unsigned int r;
unsigned int total_length;
};
double gettime( void );
int decode_switches ( int argc, char * argv [], struct TSwitch * sw );
void usage ( void );
unsigned int RevComStr ( unsigned char * str, unsigned char * str2, INT iLen );
unsigned int compute_maw ( unsigned char * seq, unsigned char * seq_id, struct TSwitch sw );
unsigned char Mapping( int a );
int RevMapping ( unsigned char b );
unsigned int LCParray ( unsigned char *text, INT n, INT * SA, INT * ISA, INT * LCP );
unsigned int GetBefore (
unsigned char * seq,
INT n,
int sigma,
INT * SA,
INT * LCP,
bit_vector * Before,
bit_vector * Beforelcp );
unsigned int GetMaws(
unsigned char * seq,
unsigned char * seq_id,
INT * SA,
INT n,
int sigma,
INT * LCP,
bit_vector * Before,
bit_vector * Beforelcp,
unsigned int k,
unsigned int K,
char * out_file );