sources/multicoil/sc2seq.h

   1 /*  Bonnie Berger, David Wilson and Theodore Tonchev 1992  */
   2 /*      C Header File: modified Ethan Wolf 1995      */
   3
   4 /*  Defines function names called by sc2seq.c.       */
   5
   6 #ifndef __ScFreq_h__
   7 #define __ScFreq_h__ 1
   8
   9 #include "scconst.h"
  10 #include "sc.h"
  11 #include "interface.h"
  12
  13
  14 /* For Coil_Interface.  */
  15 void PairCoilData (FILE *fgin, FILE **fpin,
  16                    int ProlineFree, int table_to_remove_from,
  17                    char *input_filename, int mode,
  18                    long pfreqp[MAX_TABLE_NUMBER][AANUM][AANUM][POSNUM][POSNUM]);
  19 void switch_tables(int table);
  20 void recalc_prob(Sequence sequence, int input_table, int mode, long pfreqp[MAX_TABLE_NUMBER][AANUM][AANUM][POSNUM][POSNUM]);
  21 void average_many_pprob(int current_table);
  22
  23
  24
  25
  26 void  preprocessor_score(char lib[MAXFUNCTNUM],
  27                          char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  28                          double *m, double *b,
  29                        double *m_single, double *b_single, int mode,
  30                          int Preprocessor_Method, int Offset_to_Use,
  31                double preprocessor_like[MAX_TABLE_NUMBER][MAXSEQLEN][POSNUM+1],
  32                          Sequence sequence,
  33                        char all_preproc_offsets[MAX_NUM_SCORE_DIM][MAXSEQLEN],
  34                          double bound);
  35
  36 double *ScoreSeq (char lib[MAXFUNCTNUM],
  37                   char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  38                   double *m_paircoil, double *b_paircoil,
  39                   double *m_single, double *b_single,
  40                   int mode, int Table, int Method,
  41                   int Preprocessor_Method, int Offset_to_Use,
  42                   double *maxscore,
  43                   int rescore_seq, int rescore_preproc, double bound);
  44
  45 void DimerTrimerScore (int mode, Sequence sequence,
  46                           double PairCoilLike[MAXSEQLEN][POSNUM+1],
  47                           double *maxscore,
  48                           int pairs, int coils,
  49                           double m, double b, int offset_to_use,
  50                           double scores[MAXSEQLEN][POSNUM+1],int like2or3,
  51                           int CoilDiffMethod, int start_coil_at_reg_shift);
  52
  53 void PairCoilScore (int mode, Sequence sequence, char lib[MAXFUNCTNUM],
  54                        double m, double b,
  55                        double *maxscore, int table, char offsets[MAXSEQLEN],
  56                        double like[MAXSEQLEN][POSNUM+1], int offset_to_use,
  57                        int raw_score);
  58 void PairCoilDiffer (int mode, Sequence sequence, char lib[MAXFUNCTNUM],
  59                        double *maxscore,  char offsets[MAXSEQLEN],
  60                        double like[MAXSEQLEN][POSNUM+1], int offset_to_use,
  61                        int table,double scores[MAXSEQLEN][POSNUM+1],
  62                        int Avg_Coil_Score,
  63                        int CoilDiffMethod, int start_coil_at_reg_shift);
  64 void SingleCoilScore(int mode, Sequence sequence, double m, double b,
  65                         double *maxscore, int table,
  66                         double scores[MAXSEQLEN][POSNUM+1],int offset_to_use,
  67                         int raw_score);
  68 void NEWCOILSScore(int mode, Sequence sequence, double *maxscore,
  69                    double scores[MAXSEQLEN][POSNUM+1], int offset_to_use);
  70
  71 void ActualCoils (Sequence sequence,double scores[MAXSEQLEN][POSNUM+1],
  72                   int offset_to_use, int preprocessor);
  73                 /** Do "all offsets method" differently for a preprocessor **/
  74 /***************************/
  75
  76
  77 /* Proceduere in get_defaults.c. */
  78 void get_defaults(char *command_line_config,
  79                   char *input_location, int *mode, double *bound,
  80                     FILE **fgin, FILE **fpin,
  81                     FILE **ftotal_like, FILE **fout,
  82                     FILE **flog,
  83                     FILE **fout_coils,
  84                     int *by_coil_or_seq,
  85                     char likelihoods[MAX_TABLE_NUMBER][MAXLINE],
  86                     char *pir_name, char *lib,
  87                     char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  88                     int *functnum,
  89                     int combine_dist[MAX_TABLE_NUMBER],
  90                     char *print, int *main_method,
  91                     int *main_preprocessor_method, int *main_table,
  92                     int *offset_to_use,
  93                     int *avg_max,
  94                     int *Coil_Score,
  95                     int *ps_res_per_line,
  96                     char class_sc_filenames[2][MAX_CLASS_NUMBER][MAXLINE],
  97                     char gaussian_parameters[2][MAXLINE],
  98                     int num_dist[MAX_TABLE_NUMBER],
  99                     double init_class_prob[MAX_CLASS_NUMBER],
 100                     int *table_to_remove_from,
 101                     char *command_line,
 102                     int window_length[MAX_TABLE_NUMBER],
 103                     double scale0s[MAX_TABLE_NUMBER],
 104                     double scale0p[MAX_TABLE_NUMBER]);
 105
 106 /* Procedure Prototypes */
 107 void init();
 108
 109 void done();
 110
 111 long calcseq(FILE* fgin, FILE* fpin, FILE* ftest, FILE* fout, FILE* flog,
 112              FILE* regionfile, int ver_mode, double bound, double upper_bound,
 113              char *lib);
 114
 115
 116 /* These functions are def'd in scpos.c for reading sequences in the pos */
 117 /* format (listing coiled region and registers) and for removing and     */
 118 /* adding these sequences from the positive table when necessary.        */
 119 void add_seq2(long pfreqs[AANUM][POSNUM],
 120         long ptotals[POSNUM],
 121         long pfreqp[AANUM][AANUM][POSNUM][POSNUM],
 122         long ptotalp[POSNUM][POSNUM],
 123         char reg[MAXSEQLEN],
 124         char seq[MAXSEQLEN], int seqlen, int bias);
 125
 126 int getpos (FILE *fl, Sequence *sequence);
 127
 128 /*****************************************************************************/
 129
 130 /* These functions are def'd in output.c for various forms of result output. */
 131
 132 void log_output_ver(int prog, double score, double stockscore,
 133                     double scoresc2seq, int cnt, char *title,
 134                     char *code, FILE *flog);
 135
 136 void log_output_prn(int mode, double score, double scs[MAXSEQLEN][POSNUM],
 137                     char offsets[MAXSEQLEN], int seqlen, int cnt,
 138                     Sequence sequence, double bound,
 139                     double upper_bound, FILE *flog);
 140
 141 void txt_output(Sequence sequence, int mode,
 142                 FILE *fout, double scs[MAXSEQLEN][POSNUM],
 143                 double like[MAXSEQLEN][POSNUM +1],
 144                 char offsets[MAXSEQLEN], double bound);
 145
 146 void print_coil(int mode, int seqlen, char reg[MAXSEQLEN],
 147                 double scs[MAXSEQLEN][POSNUM], double bound,
 148                 double  upper_bound, char offsets[MAXSEQLEN],
 149                 char seq[MAXSEQLEN], FILE *flog);
 150 /****************************************************************************/
 151
 152 void usage(char *prog_command);
 153
 154 int getpos (FILE *fl, Sequence *sequence);
 155
 156 void dumpvals (FILE *out, char seq[], char reg[], char offsets[], int seqlen,
 157                double scs[MAXSEQLEN][POSNUM], double bound);
 158
 159
 160 #endif   /* __ScFreq_h__ */
 161
 162 /*       End of Code       */
 163
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 166