#include "pseud.h"

void
ReadOneSequencePair(FILE *fseq, OptionsBlkPtr options, FILE *fout)
{
   int   i, p, len;
   char  *seq_line;
   char  *seq;
	Uint1Ptr orig_seq;
	Uint1Ptr target_seq;
   double   t;

   /*read sequence*/
   seq_line = (char *)calloc(MaxSeqLen+1,sizeof(char));
   seq = (char *)calloc(MaxSeqLen+1,sizeof(char));

   fgets(seq_line, MaxSeqLen, fseq);
   fprintf(fout,"%s",seq_line);
   fscanf(fseq,"%lf, ",&t);
   options->branch_length = t /(options->num_t);
   /*fprintf(fout,"branch_length=%lf, \n",(options->branch_length)); */
   fscanf(fseq,"%d, ",&(options->orig_len));
   printf("%d, \n",(options->orig_len));
   /*fprintf(fout,"%d, \n",(options->orig_len)); */
   if((options->orig_len)>=MaxSeqLen){
   	printf("Warning!orig_len(%d)>=MaxSeqLen(%d)\n",options->orig_len, MaxSeqLen);
      getch();
      options->orig_len = MaxSeqLen;
   }
   len=0;
   while(len<(options->orig_len)){
   	fgets(seq_line,MaxSeqLen,fseq);
      for(i=0;seq_line[i]!='\0';i++){
      	if((seq_line[i]!=' ')&&(seq_line[i]!='\n')){seq[len]=seq_line[i];len++;}
      	if(len>(options->orig_len)){
         	printf("Warning!orig_len(%d)!=seqlen(%d)\n",options->orig_len, len);
            getch(); options->orig_len=len;
         }
      }
   }

   len = options->orig_len;
   for(i=0;i<len;i++)fprintf(fout,"%c",seq[i]);
   fprintf(fout,"(end)\n");
   orig_seq = options->orig_seq;
   for(i=0;i<len;i++)
   {
   	orig_seq[i] = ASCIIToBASEs(seq[i]);
   }
   orig_seq[len] = '\0';

   fscanf(fseq,"%d, ",&(options->target_len));
   printf("%d, \n",(options->target_len));
   /*fprintf(fout,"%d, \n",(options->target_len));  */
   if((options->target_len)>MaxSeqLen){
   	printf("Warning!target_len(%d)>MaxSeqLen(%d)\n",options->target_len, MaxSeqLen);
      getch(); options->target_len=len;
   }

   len=0;
   while(len<(options->target_len)){
   	fgets(seq_line,MaxSeqLen,fseq);
      for(i=0;seq_line[i]!='\0';i++){
      	if((seq_line[i]!=' ')&&(seq_line[i]!='\n')){seq[len]=seq_line[i];len++;}
      	if(len>(options->target_len)){
         	printf("Warning!taret_len(%d)!=seqlen(%d)\n",options->target_len, len);
            getch(); options->target_len=len;
         }
      }
   }
   len = options->target_len;
   for(i=0;i<len;i++)fprintf(fout,"%c",seq[i]);
   fprintf(fout,"(end)\n");
   target_seq = options->target_seq;
   for(i=0;i<len;i++)
   {
   	target_seq[i] = ASCIIToBASEs(seq[i]);
   }
   target_seq[len] = '\0';

   free(seq_line);
   free(seq);


   return;


}

void
ReCalculateOptionsForNewPair(OptionsBlkPtr options, FILE *fout)
{
   double *PMat;
   int    **MRC, i, j;

   /*Re-calculate PMat for new branch_length*/
   PMat = options->PMat;
   /*fprintf(fout,"re-calculate PMat\n"); */
   CalculatePMat(PMat,options,fout);

   if((options->orig_len<20)&&(abs(options->target_len-options->orig_len)<5)){
   	options->lmax=5;
   }
   else{options->lmax=options->lmax0;}
   if(abs(options->target_len-options->orig_len)>(options->lmax)){
   	fprintf(fout,"!!target_len(%d)-orig_len(%d)>lmax(%d)\n",options->target_len, options->orig_len, options->lmax);
   }

   MRC = options->MRC;

	CountModuloCenterFilter(options->orig_seq, options->orig_len, MRC, options->lmax, options->filter/*, fout*/);
   printf("MRC count\n");
   fprintf(fout,"MRC count\n");
   for(i=0;i<3;i++){
   	for(j=0;j<(options->lmax);j++){
      	printf("%d, ",MRC[i][j]);
      	fprintf(fout, "%d, ",MRC[i][j]);
      }
      printf("\n");
      fprintf(fout,"\n");
   }


   return;
}