/*
 * This program takes in one or more .ms2 files and writes .mgf files
 * The TITLE line conforms to TPP expected format
 */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>


void WRITE_SPECTRUM(FILE *fp,
     FILE *fpout,
     char *szTitle,
     char *szMZ,
     int iCharge)
{
   char szBuf[4096];

   fprintf(fpout, "BEGIN IONS\n");
   fprintf(fpout, "PEPMASS=%s\n", szMZ);
   fprintf(fpout, "CHARGE=%d+\n", iCharge);
   fprintf(fpout, "%s\n", szTitle);

   /* write out mz/int pairs */
   while (fgets(szBuf, 4096, fp))
   {
      if (szBuf[0]=='S')
         break;
      else if (!isalpha(szBuf[0]))
         fprintf(fpout, "%s", szBuf);
   }

   fprintf(fpout, "END IONS\n");
}


int main(int argc, char *argv[])
{
   int i;

   if (argc<2)
   {
      printf("\n");
      printf(" USAGE: %s *.ms2\n", argv[0]);
      printf(" This program converts .ms2 files to .mgf files\n");
      printf("\n");
   }

   /* loop through all input files */
   for (i=1; i<argc; i++)
   {
      char szInput[500];
      char szOutput[500];

      strcpy(szInput, argv[i]);

      /* handle only .ms2 files */
      if (!strncasecmp(szInput+strlen(szInput)-4, ".ms2", 4))
      {
         FILE *fp;
         FILE *fpout;

         if ((fp=fopen(szInput, "r"))!=NULL)
         {
            char szBaseName[500];
            char szBuf[4096];

            strcpy(szBaseName, szInput);
            szBaseName[strlen(szBaseName)-4]='\0';
            sprintf(szOutput, "%s.mgf", szBaseName);

            if ((fpout=fopen(szOutput, "w"))==NULL)
            {
               printf(" Error - cannot write file %s\n\n", szOutput);
               exit(1);
            }

            printf(" writing %s\n", szOutput);

            while (fgets(szBuf, 4096, fp))
            {
               long lFilePos;

               /* start of a new spectrum */
               if (szBuf[0]=='S')
               {
                  char szTitle[512];
                  char szMZ[48];
                  char szTmp[48];
                  int iStartScan=0;
                  int iEndScan=0;

                  /* grab start & end scan here */
                  sscanf(szBuf, "%s %d %d %s", szTmp, &iStartScan, &iEndScan, szMZ);

                  while (fgets(szBuf, 4096, fp))
                  {
                     /* now grab all charge state lines, search until fragment ion lines */
                     if (szBuf[0]=='Z')
                     {
                        int iCharge=0;
                        char szMH[48];
                        long lFilePos;

                        lFilePos=ftell(fp);
   
                        sscanf(szBuf, "%s %d %s", szTmp, &iCharge, szMH);
                        sprintf(szTitle, "TITLE=%s.%0.5d.%0.5d.%d", szBaseName, iStartScan, iEndScan, iCharge);
   
                        WRITE_SPECTRUM(fp, fpout, szTitle, szMZ, iCharge);

                        fseek(fp, lFilePos, SEEK_SET); /* my logic tells me this should not work */
                     }
                     else if (isdigit(szBuf[0]))
                     {
                        break;
                     }
                  }
               }
            }
            fclose(fp);
            fclose(fpout);
         }
         else
            printf(" skipping: %s (cannot read)\n", szInput);

      }
      else
         printf(" skipping: %s\n", szInput);
   }

   printf(" Done.\n\n");
   return 0;
}