tn93_shared.h

#ifndef     __TN93SHARED__
#define     __TN93SHARED__
 
#include <iostream>
#include <cstdlib>
#include <cstdio>
#include <iomanip>
#include <math.h>
#include <string.h>
#include <unistd.h>
#include <climits>
#include <cstdint>
#include "stringBuffer.h"
 
using namespace std;
 
#define MIN(a,b) (a) < (b) ? (a) : (b)
#define MAX(a,b) (a) > (b) ? (a) : (b)

int readFASTA (FILE* F, char& automatonState, StringBuffer &names, StringBuffer& sequences, long& firstSequenceLength);
void initAlphabets(bool doAminoAcid = false);
int    reverseComplement (StringBuffer& sequence, unsigned long from, unsigned long to);
 
extern int8_t validFlags[];
 
#endif