/* $Id: translation.h 188718 2016-04-30 01:53:47Z twu $ */
#ifndef TRANSLATION_INCLUDED
#define TRANSLATION_INCLUDED

#include <stdio.h>
#include "bool.h"
#include "pair.h"
#include "filestring.h"


#define T Translation_T
typedef struct T *T;

extern void
Translation_setup (int translation_code);

#ifdef PMAP
extern void
Translation_via_cdna (int *translation_leftpos, int *translation_rightpos, int *translation_length,
		      int *relaastart, int *relaaend,
		      struct Pair_T *pairs, int npairs, char *queryaaseq_ptr, bool strictp);
#else
extern void
Translation_via_genomic (int *translation_leftpos, int *translation_rightpos, int *translation_length,
			 int *relaastart, int *relaaend,
			 struct Pair_T *pairs, int npairs, bool backwardp, bool revcompp, bool fulllengthp,
			 int cds_startpos, int querylength, bool strictp);
#endif

extern void
Translation_via_reference (int *relaastart, int *relaaend,
			   struct Pair_T *pairs, int npairs, bool watsonp, bool backwardp, bool revcompp,
			   struct Pair_T *refpairs, int nrefpairs, bool refwatsonp);

extern void
Translation_print_comparison (Filestring_T fp, struct Pair_T *pairs, int npairs,
			      int relaastart, int relaaend);

#undef T
#endif