/*  Bonnie Berger, David Wilson and Theodore Tonchev 1992  */
/*      C Header File: modified Ethan Wolf 1995      */

/*  Defines function names called by sc2seq.c.       */

#ifndef __ScFreq_h__
#define __ScFreq_h__ 1

#include "scconst.h"
#include "sc.h"
#include "interface.h"


/* For Coil_Interface.  */
void PairCoilData (FILE *fgin, FILE **fpin,
		   int ProlineFree, int table_to_remove_from,
		   char *input_filename, int mode,
		   long pfreqp[MAX_TABLE_NUMBER][AANUM][AANUM][POSNUM][POSNUM]);
void switch_tables(int table);
void recalc_prob(Sequence sequence, int input_table, int mode, long pfreqp[MAX_TABLE_NUMBER][AANUM][AANUM][POSNUM][POSNUM]);
void average_many_pprob(int current_table);




void  preprocessor_score(char lib[MAXFUNCTNUM], 
			 char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
			 double *m, double *b, 
		       double *m_single, double *b_single, int mode, 
			 int Preprocessor_Method, int Offset_to_Use, 
	       double preprocessor_like[MAX_TABLE_NUMBER][MAXSEQLEN][POSNUM+1],
			 Sequence sequence,
		       char all_preproc_offsets[MAX_NUM_SCORE_DIM][MAXSEQLEN],
			 double bound);

double *ScoreSeq (char lib[MAXFUNCTNUM],
		  char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
		  double *m_paircoil, double *b_paircoil,
		  double *m_single, double *b_single,
		  int mode, int Table, int Method, 
		  int Preprocessor_Method, int Offset_to_Use,
		  double *maxscore, 
		  int rescore_seq, int rescore_preproc, double bound);

void DimerTrimerScore (int mode, Sequence sequence, 
			  double PairCoilLike[MAXSEQLEN][POSNUM+1],
			  double *maxscore,
			  int pairs, int coils, 
			  double m, double b, int offset_to_use,
		          double scores[MAXSEQLEN][POSNUM+1],int like2or3,
			  int CoilDiffMethod, int start_coil_at_reg_shift);

void PairCoilScore (int mode, Sequence sequence, char lib[MAXFUNCTNUM], 
		       double m, double b, 
		       double *maxscore, int table, char offsets[MAXSEQLEN],
		       double like[MAXSEQLEN][POSNUM+1], int offset_to_use,
		       int raw_score);
void PairCoilDiffer (int mode, Sequence sequence, char lib[MAXFUNCTNUM], 
		       double *maxscore,  char offsets[MAXSEQLEN],
		       double like[MAXSEQLEN][POSNUM+1], int offset_to_use,
		       int table,double scores[MAXSEQLEN][POSNUM+1],
		       int Avg_Coil_Score,
		       int CoilDiffMethod, int start_coil_at_reg_shift);
void SingleCoilScore(int mode, Sequence sequence, double m, double b,
			double *maxscore, int table, 
		        double scores[MAXSEQLEN][POSNUM+1],int offset_to_use,
		        int raw_score);
void NEWCOILSScore(int mode, Sequence sequence, double *maxscore,
		   double scores[MAXSEQLEN][POSNUM+1], int offset_to_use);

void ActualCoils (Sequence sequence,double scores[MAXSEQLEN][POSNUM+1],
		  int offset_to_use, int preprocessor); 
                /** Do "all offsets method" differently for a preprocessor **/
/***************************/


/* Proceduere in get_defaults.c. */
void get_defaults(char *command_line_config,
		  char *input_location, int *mode, double *bound, 
		    FILE **fgin, FILE **fpin,
                    FILE **ftotal_like, FILE **fout, 
		    FILE **flog,
		    FILE **fout_coils,  
		    int *by_coil_or_seq,
		    char likelihoods[MAX_TABLE_NUMBER][MAXLINE],
		    char *pir_name, char *lib, 
		    char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
		    int *functnum, 
		    int combine_dist[MAX_TABLE_NUMBER],
		    char *print, int *main_method, 
		    int *main_preprocessor_method, int *main_table, 
		    int *offset_to_use,
		    int *avg_max,
		    int *Coil_Score,
		    int *ps_res_per_line,
		    char class_sc_filenames[2][MAX_CLASS_NUMBER][MAXLINE],
		    char gaussian_parameters[2][MAXLINE],
		    int num_dist[MAX_TABLE_NUMBER],
		    double init_class_prob[MAX_CLASS_NUMBER],
		    int *table_to_remove_from,
		    char *command_line, 
		    int window_length[MAX_TABLE_NUMBER],
		    double scale0s[MAX_TABLE_NUMBER],
		    double scale0p[MAX_TABLE_NUMBER]);

/* Procedure Prototypes */
void init();

void done();

long calcseq(FILE* fgin, FILE* fpin, FILE* ftest, FILE* fout, FILE* flog,
	     FILE* regionfile, int ver_mode, double bound, double upper_bound,
	     char *lib);


/* These functions are def'd in scpos.c for reading sequences in the pos */
/* format (listing coiled region and registers) and for removing and     */
/* adding these sequences from the positive table when necessary.        */
void add_seq2(long pfreqs[AANUM][POSNUM], 
	long ptotals[POSNUM],
	long pfreqp[AANUM][AANUM][POSNUM][POSNUM], 
	long ptotalp[POSNUM][POSNUM],
        char reg[MAXSEQLEN],
	char seq[MAXSEQLEN], int seqlen, int bias);

int getpos (FILE *fl, Sequence *sequence);

/*****************************************************************************/

/* These functions are def'd in output.c for various forms of result output. */

void log_output_ver(int prog, double score, double stockscore, 
		    double scoresc2seq, int cnt, char *title, 
		    char *code, FILE *flog);

void log_output_prn(int mode, double score, double scs[MAXSEQLEN][POSNUM], 
		    char offsets[MAXSEQLEN], int seqlen, int cnt, 
		    Sequence sequence, double bound, 
		    double upper_bound, FILE *flog);

void txt_output(Sequence sequence, int mode, 
		FILE *fout, double scs[MAXSEQLEN][POSNUM], 
		double like[MAXSEQLEN][POSNUM +1],
		char offsets[MAXSEQLEN], double bound);

void print_coil(int mode, int seqlen, char reg[MAXSEQLEN], 
		double scs[MAXSEQLEN][POSNUM], double bound,
		double  upper_bound, char offsets[MAXSEQLEN], 
		char seq[MAXSEQLEN], FILE *flog);
/****************************************************************************/

void usage(char *prog_command);

int getpos (FILE *fl, Sequence *sequence);

void dumpvals (FILE *out, char seq[], char reg[], char offsets[], int seqlen,
               double scs[MAXSEQLEN][POSNUM], double bound);


#endif   /* __ScFreq_h__ */

/*       End of Code       */