/*  Last edited: Jan 10 17:23 1997 (birney) */



%{
#include "wisebase.h"
#include "probability.h"

#define ComplexConsensiLISTLENGTH 64

%}


struct ComplexConsensusWord
char * pattern
Score score
Probability p

struct ComplexConsensi
ComplexConsensusWord ** ccw !list
char * name


%{
#include "complexconsensi.h"

%func
shows complexconsensi in vaguely human form
%arg
%%
void show_ComplexConsensi(ComplexConsensi * cc,FILE *ofp)
{
  register int i;

  for(i=0;i<cc->len;i++)
    show_ComplexConsensusWord(cc->ccw[i],ofp);

}

%func
shows an individual ccword
%type internal
%arg
%%
void show_ComplexConsensusWord(ComplexConsensusWord * ccw,FILE * ofp)
{
  fprintf(ofp,"%s %4.4f %d\n",ccw->pattern,ccw->p,ccw->score);
}


%func
Way of getting probabilities out of a consensus.
If it is in the Consensus, then gets prob, otherwise 0.
%arg
%%
Probability word_from_ComplexConsensi(char * word,ComplexConsensi * cc)
{
  ComplexConsensusWord * ccw;

  ccw = best_ComplexConsensusWord(word,cc);

  if( ccw == NULL )
    return 0.0;

  return ccw->p;
}

%func
Way of getting scores out of a consensus.
If it is in the Consensus, then gets score, otherwise NEGI.
%arg
%%
Score score_from_ComplexConsensi(char * word,ComplexConsensi * cc)
{
  ComplexConsensusWord * ccw;

  ccw = best_ComplexConsensusWord(word,cc);

  if( ccw == NULL )
    return NEGI;

  return ccw->score;
}

%func
Finds the best (highest) match to this word
%arg
%%
ComplexConsensusWord * best_ComplexConsensusWord(char * word,ComplexConsensi * cc)
{
  register int i;

  for(i=0;i<cc->len;i++) {
    if( word_matches_ComplexConsensusWord(word,cc->ccw[i]) == TRUE)
      return cc->ccw[i];
  }

  return NULL;
}
    

%func
Core of the matching system. Checks that word matches 
ComplexConsensusWord. This says that '-' matches anything.
Issues a warning if hits a '\0' in word
%arg
%%
boolean word_matches_ComplexConsensusWord(char * word,ComplexConsensusWord * ccw)
{
  return strcmp_with_dashes(word,ccw->pattern);
} 

%func
The matching 'function' used by
/word_matches_ComplexConsensusWord
%type internal
%%
boolean strcmp_with_dashes(char * word,char * pattern)
{
  char * runner;
  char * base = word;

  for(runner = pattern;*runner && *word;word++,runner++) {
    if( *runner == '-') {
      continue;
    }

    if( *runner != *word ) {
      break;
    }

  }

  if( *word == '\0' && *runner != '\0') {
    warn("Tried to match a word [%s] which is shorter than the pattern [%s]",base,pattern);
    return FALSE;
  }

  if( *runner == '\0') {
    /* end of pattern */
    return TRUE;
  }

  return FALSE;
}




 /************************/
 /* I/O                  */
 /************************/


%func
Reads a file containing the ComplexConsensi.
Not every useful, as most times these consensi
are in one file, with other things
%arg
%%
ComplexConsensi * read_ComplexConsensi_file(char * filename)
{
  FILE * ifp;
  ComplexConsensi * out;

  ifp = openfile(filename,"r");
  if( ifp == NULL ) {
    warn("Could not open file %s for ComplexConsensi",filename);
    return NULL;
  }

  out = read_ComplexConsensi(ifp);

  fclose(ifp);

  return out;
}


%func
Reads on ComplexConsensi from the FILE ifp.
%arg
ifp input filestream
%%
ComplexConsensi * read_ComplexConsensi(FILE * ifp)
{
  ComplexConsensi * out;
  ComplexConsensusWord * temp;
  char buffer[MAXLINE];


  out = ComplexConsensi_alloc_std();
  if( out == NULL )
    return NULL;


  while( fgets(buffer,MAXLINE,ifp) != NULL ) {
    if( buffer[0] == '#' ) 
      continue;
    temp = read_ComplexConsensusWord_line(buffer);
    if( temp != NULL ) 
      add_ComplexConsensi(out,temp);
  }

  return out;
}
    

%func
Reads a single ccword from a line
%type internal
%arg
%%
ComplexConsensusWord * read_ComplexConsensusWord_line(char * line)
{
  ComplexConsensusWord * out;
  char * pattern;
  char * score;


  pattern = strtok(line,spacestr);
  score   = strtok(NULL,spacestr);

  if( pattern == NULL || score == NULL ) {
    warn("Could not read a ComplexConsenusWord... ooops");
    return NULL;
  }


  out = ComplexConsensusWord_alloc();

  if( out == NULL)
    return NULL;

  out->pattern = stringalloc(pattern);
  out->score = (double) atof(score);

  return out;
}