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nw.h
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nw.h
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/*
* nw.h for program nw.
*
*/
#include <iostream>
#include <string>
#include <algorithm>
#include <stdlib.h>
#include <stdio.h>
#include <vector>
#define DEBUG 0
using namespace std;
/*
struct record{
int mRNAs;
int mRNAe;
int gRNAs;
int gRNAe;
string gRNA;
int score;
int L;
string gname;
string mname;
int prefixL;
string seq_1_al;
string seq_2_al;
string mid;
};
*/
/*
extern void nw_LCS(
string, string, int, int, int,
string, char*, string, int, bool,
vector< struct record>&
);
*/
extern int nw(
string, string,
string&, string&,
bool, int&, int&, int&, int&
);
extern int nw_align(
int **, char **,
string, string,
string&, string&,
int, int&, int&, int&, int&
);
extern void dpm_init ( int **, char **, int, int, int );
//extern void dpm_init_LCS(int ***, char **, int, int);
//extern void print_al ( string&, string&, int, int, int, int, int );
extern string print_al ( string&, string&, int, int, int, int, int );
extern void print_matrix ( int ** const, string, string );
extern void print_traceback ( char ** const, string, string );
extern int max ( int, int, int, char * );
//extern void print_3Dmatrix (int *** const, string, string );