/* $Id: elecpcr.c,v 6.8 1999/07/27 18:43:04 shavirin Exp $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: $RCSfile: elecpcr.c,v $ * * Author: Sergei Shavirin * * Version Creation Date: 12/19/1996 * * $Revision: 6.8 $ * * File Description: * Main program for WWW and Command-Line Electronic PCR * * $Log: elecpcr.c,v $ * Revision 6.8 1999/07/27 18:43:04 shavirin * Fixed problems found on PC NT computer. * * Revision 6.7 1999/02/24 16:49:23 kans * use accutils copy of IS_ntdb_accession and IS_protdb_accession * * Revision 6.6 1999/02/23 17:28:11 shavirin * Replaced IS_ accession verification functions by it's "relaxed" * version * * Revision 6.5 1998/05/22 19:19:28 shavirin * Updated for porting to sunweb. Fixed bug with filtering of * organisms. * * Revision 6.4 1998/05/01 19:22:29 shavirin * Improved WWW page formating * * Revision 6.3 1998/05/01 18:22:58 shavirin * Next revision * * Revision 6.2 1998/04/28 19:32:13 shavirin * Fixed minor bugs detected by purify * * Revision 6.1 1997/09/03 17:19:45 shavirin * Added some debug information and sequence prevented from freeing * * Revision 6.0 1997/08/25 18:19:31 madden * Revision changed to 6.0 * * Revision 1.3 1997/05/23 15:32:18 shavirin * Added ability to use local database files (for remote users) * * Revision 1.2 1997/05/14 19:12:41 shavirin * Added define LF 10 * * Revision 1.1 1996/12/19 20:54:35 shavirin * Initial revision * * * ========================================================================== */ #include #include #include #include #include /****************************************************************************/ /* DEFINES */ /****************************************************************************/ #define BG_COLOR "#FDF5E6" #define PRIMER1_COLOR "#00BF00" #define PRIMER2_COLOR "red" #define LogFile "wwwsts.log" #define FASTA_IN 1 #define ACC_IN 2 #define MINSEQLEN 10 #define LF 10 /****************************************************************************/ /* TYPEDEFS */ /****************************************************************************/ typedef struct AccList { CharPtr acc; struct AccList *next; } AccList, PNTR AccListPtr; typedef struct StsPar { CharPtr sequence; Boolean html; Int4 organism; CharPtr orgname; Int4 intype; Boolean detailed; CharPtr sts_db_name; CharPtr org_db_name; CharPtr map_db_name; } StsPar, PNTR StsParPtr; /****************************************************************************/ /* STATIC FINCTIONS */ /****************************************************************************/ static Boolean GetSTSEntry(StsResultPtr result, FILE *fd, Boolean detailed); static StsResultPtr PrintSTSHeader(StsResultPtr result, CharPtr label, Boolean detailed, Boolean html); static Boolean PrintSTSDetailes(StsResultPtr result, Boolean html); static AccListPtr GetAccList(CharPtr buffer, Int4Ptr TotalItems); static void WWWSendSTSPage(CharPtr WWWSequence, Boolean NetscapeOK); static StsParPtr GetStsSearchParam(void); static FastaSeqPtr NextFastaFromBuff(CharPtr p, CharPtr PNTR next); static Int4 FilterNucSequence(CharPtr p); static StsParPtr StsParNew(void); static void StsParFree(StsParPtr param); static StsParPtr STSReadCommandLine(void); #define STS_WWW_DATABASE "/web/public/htdocs/STS/DB/sts.db" #define ORG_WWW_DATABASE "/web/public/htdocs/STS/DB/org.db" #define MAP_WWW_DATABASE "/web/public/htdocs/STS/DB/sts.map" static Boolean IS_NOT_accession (CharPtr word) { Int4 len, i; if(word == NULL) return TRUE; if((len = StringLen(word)) == 0) return TRUE; /* Testing, that this is 6 length accession */ if(len == 6 && isalpha(word[0])) { for(i = 1; i < len; i++) { if(!isdigit(word[i])) break; } if (i == len) return FALSE; /* This is accession */ } if(len == 8 && isalpha(word[0]) && isalpha(word[1])) { for(i = 2; i < len; i++) { if(!isdigit(word[i])) { break; } } if (i == len) return FALSE; /* This is accession */ } return TRUE; } Int2 Main(void) { StsParPtr stsp; Int4 NumBadChar, StsCount; CharPtr inbuff; FastaSeqPtr fseq; CharPtr NextChar; StsResultPtr result= NULL, newresult= NULL, tmpresult=NULL; Int4 NumAcc; AccListPtr MainAccList, AccTmp; STSDataPtr sts_data; STSDbNamesPtr db_name = NULL; putenv("USER=STSSearch"); if((stsp = GetStsSearchParam()) == NULL) { printf("Error getting Search data. Exiting ...\n"); exit(1); } if(stsp->html) { printf("Content-type: text/html\r\n\r\n"); printf("" "" " STS Match Program " "" "" " " " " "" "" "
 
\n", BG_COLOR); fflush(stdout); } #ifdef WWW_VERSION db_name = MemNew(sizeof(STSDbNames)); db_name->sts_db_name = StringSave(STS_WWW_DATABASE); db_name->sts_map_name = StringSave(MAP_WWW_DATABASE); db_name->sts_org_name = StringSave(ORG_WWW_DATABASE); #else if(stsp->sts_db_name != NULL || stsp->map_db_name != NULL || stsp->org_db_name) { db_name = MemNew(sizeof(STSDbNames)); db_name->sts_db_name = StringSave(stsp->sts_db_name); db_name->sts_map_name = StringSave(stsp->map_db_name); db_name->sts_org_name = StringSave(stsp->org_db_name); } #endif if((StsCount = InitSTSSearch_r(db_name, &sts_data)) < 0) { printf("Cannot initiate STS Search ... Exiting ...\n"); exit(1); } else if(stsp->html) { printf("STS database initialized with %d sequences, " "please wait for results ...
", StsCount 
               );
        fflush(stdout);
    }
    
    stsp->organism = STSGetOrganismIndex(sts_data, stsp->orgname);
    
    if(db_name != NULL) {
        MemFree(db_name->sts_db_name);
        MemFree(db_name->sts_map_name);
        MemFree(db_name);
    }
    
    if(stsp->intype != FASTA_IN) { 
        
        if (! EntrezInit("STSSearch", FALSE, NULL)) {
            printf("Cannot initialize Entrez
");
        }
        
        EntrezBioseqFetchEnable("STSSearch", TRUE);
    }

    printf(
"Location of STS              GenBank\n"
"within query                 accession\n"
"sequence          dbSTS id   number    Chromosome  STS marker name\n"
"================  ========  =========  ==========  ==============================\n\n");

    fflush(stdout);
    
    if(stsp->intype == FASTA_IN) {
        if(stsp->sequence[0] == NULLB) {
            printf("No sequence present in the search query.\n");
            exit(1);
        } else if(StringLen(inbuff = stsp->sequence) < MINSEQLEN) {
            printf("Length of entered sequence too small to start search\n");
            exit(1);
        }
        while(inbuff != NULL) {
            fseq = NextFastaFromBuff(inbuff, &NextChar);
            inbuff = NextChar;
            if((NumBadChar = FilterNucSequence(fseq->seq)) < 0) {
                printf("Error filtering nucleotide sequence\n");
                exit(1);
            } else if (NumBadChar >0 ) {
                printf("WARNING!!! %d bad characters found "
                       "in the input sequence\n\n", 
                       NumBadChar);
            }
            
            if(!STSSearch_r(sts_data, fseq->seq, stsp->organism, &newresult)) {
                printf("Error in STS Search. Exiting ...\n");
                return 1;
            }
            
            if(newresult != NULL) {
                tmpresult = newresult;
                newresult = PrintSTSHeader(newresult, fseq->label, 
                                           stsp->detailed, stsp->html);
                newresult->next = result;
                result = tmpresult;
            } else {
                printf("%s\n Did not return any hits ...\n\n", 
                       fseq->label);
                fflush(stdout);
            } 
            MemFree(fseq->label);
            MemFree(fseq->seq);
            MemFree(fseq);
        } /* while (inbuff != NULL) */
    } else  {  /* Type = Accession or GI */
        
        /* Here first we will fetch sequence from Entrez */
        
        MainAccList = GetAccList(stsp->sequence, &NumAcc);
        
        if(NumAcc == 0) {
            printf("ERROR: No valid gi/accessions found in input.
"); 
            exit(1);
        } 
        
        /*    printf("Retrieved %d valid accessions/gis\n", NumAcc);  */
        
        for (AccTmp = MainAccList; AccTmp != NULL; AccTmp = AccTmp->next) {  
            if((fseq = AccessionToFasta(AccTmp->acc)) == NULL) {
                printf("ERROR: No record was found "
                       "for %s - skipping..", 
                       AccTmp->acc);
                continue;
            }
            
            if(!STSSearch_r(sts_data, fseq->seq, stsp->organism, &newresult)) {
                printf("Error in STS Search. Exiting ...\n");
                return 1;
            }
            if(newresult != NULL) {
                tmpresult = newresult;
                newresult = PrintSTSHeader(newresult, fseq->label, 
                                           stsp->detailed, stsp->html);
                newresult->next = result;
                result = tmpresult;
            } else {
                printf("%s\n Did not return any hits ...\n\n", 
                       fseq->label);
                fflush(stdout);
            }
            
            MemFree(fseq->seq);
            MemFree(fseq->label);
            MemFree(fseq);
        }
    } 
    
    if(stsp->html)
        printf("
\n");  
    
    /* If detailed output requested */
    
    if(result && stsp->detailed)
        PrintSTSDetailes(result, stsp->html);
    
    if(stsp->detailed || stsp->intype != FASTA_IN) {  
        EntrezBioseqFetchDisable();
        EntrezFini();
    }
    
    StsResultFree(result);
    
    STSDataFree(sts_data);
    
    StsParFree(stsp);
    return 0;
}
static StsResultPtr PrintSTSHeader(StsResultPtr result, CharPtr label, 
                                   Boolean detailed, Boolean html) 
{
  Char TmpBuff[1024];
  Int4 tmplen;
  register Int4 i;

  printf("%s\n", label);

  while (TRUE) {
    
    /* Now printing short header information line */

    if(detailed && html) {
      sprintf(TmpBuff, " %d..%d ", 
              result->acc, 
              result->pos,  result->pos+result->real_len-1 
              );
    } else {
      sprintf(TmpBuff, " %d..%d ", 
              result->pos,  result->pos+result->real_len-1
              );
    }
    printf("%s", TmpBuff);

    if(detailed && html)
      tmplen = 41 - StringLen(TmpBuff);
    else
      tmplen = 19 - StringLen(TmpBuff);
    for(i =0; i < tmplen; i++)
      printf(" ");
    
    if(html) {
      sprintf(TmpBuff, "%d", 
              result->id_sts, result->id_sts);
    } else {
      sprintf(TmpBuff, "%d", result->id_sts);
    }

    printf("%s", TmpBuff);
    if(html)
      tmplen = 86 - StringLen(TmpBuff);
    else
      tmplen = 10 - StringLen(TmpBuff);

    for(i =0; i < tmplen; i++)
      printf(" ");
        
    if(html) {
      sprintf(TmpBuff, "%s",
              result->acc, result->acc);
    } else {
      sprintf(TmpBuff, "%s", result->acc);
    }
    
    printf("%s", TmpBuff);

    if(html)
      tmplen = 112 - StringLen(TmpBuff);
    else
      tmplen = 14 - StringLen(TmpBuff);

    for(i =0; i < tmplen; i++)
      printf(" ");

    sprintf(TmpBuff, "%s", 
            StringCmp(result->chrom, "0") ? result->chrom : " ");

    printf("%s", TmpBuff);

    tmplen = 9 - StringLen(TmpBuff);
    for(i =0; i < tmplen; i++)
      printf(" ");
    
    printf("%s\n", result->sts_name);
    
    fflush(stdout);
    if(result->next == NULL)
      break;
    result = result->next;
  }
  printf("\n"); 
  fflush(stdout);
  return result;
}

static Boolean PrintSTSDetailes(StsResultPtr result, Boolean html)
{
  register Int4 i;
  Int4 len1, len2, len_tot, len_end;
  Boolean ColorSet;
  
  printf("\n%sDetailed information...%s",
         html? ""  : "",  
         html? "\n\n" : ""
         );
  fflush(stdout);
  while(result) {

    if(html) {
      printf("
\n
%s
\n\n", 
             result->acc, result->sts_name);
      
      printf("dbSTS id: %d, "
             "GenBank Accession: "
             "%s
Organism: %s\n"
             "Primer1: %s\n"
             "Primer2: %s\n"
             "STS location: %d..%d Chromosome: %s\n"
             "Expected amplicon size: %d, Observed amplicon size: %d\n",
             result->id_sts, result->id_sts,
             result->acc, result->acc, 
             result->org,
             PRIMER1_COLOR, result->pr1,
             PRIMER2_COLOR, result->pr2,
             result->pos, result->pos+result->real_len, 
             StringCmp(result->chrom, "0") ? result->chrom : " ", 
             labs(result->exp_len), result->real_len
             );
    } else {
      printf("\n\n\n-------+= %s =+-------\n\n", 
             result->acc, result->sts_name);
      
      printf("dbSTS id: %d, GenBank Accession: %s\n"
             "Organism: %s\n"
             "Primer1: %s\n"
             "Primer2: %s\n"
             "STS location: %d..%d Chromosome: %s\n"
             "Expected amplicon size: %d, Observed amplicon size: %d\n",
             result->id_sts,
             result->acc,
             result->org,
             result->pr1,
             result->pr2,
             result->pos, result->pos+result->real_len-1, 
             StringCmp(result->chrom, "0") ? result->chrom : " ", 
             labs(result->exp_len), result->real_len
             );
    }
    
    fflush(stdout);
    printf("Primers match in %s orientation\n",
           result->exp_len > 0 ? "forward" : "backward");

    printf("\n%sQuery sequence:%s\n\n",
           html? ""  : "",  
           html? "" : ""
           );

    fflush(stdout);
    
    len1 = StringLen(result->pr1) + result->start;
    len2 = result->real_len - StringLen(result->pr2) + result->start; 
    len_tot = StringLen(result->sequence);
    len_end = result->real_len + result->start;
    
    printf("%6d  ", result->pos - result->start);
    fflush(stdout);
    ColorSet = FALSE;

    for(i = 0; i < len_tot; i++) {

      if(!(i%10) && i)
        printf(" ");

      if(i==result->start && html) {
        printf("",
               result->exp_len > 0 ? PRIMER1_COLOR : PRIMER2_COLOR); 
        ColorSet = (result->exp_len > 0 ? 1 : 2);
      }
      if(i == len_end && html) {
        printf("");
        ColorSet = FALSE;
      }
      if(i == len1 && html) {
        printf(""); 
        ColorSet = FALSE;
      }
      if(i == len2 && html) {
        printf("",
               result->exp_len > 0 ? PRIMER2_COLOR : PRIMER1_COLOR);       
        ColorSet = (result->exp_len > 0 ? 2 : 1);
      }
      if(!(i%60) && i) {
        if(ColorSet > 0 && html)
          printf("\n%6d  ", 
                 result->pos - result->start + i,
                 ColorSet == 1 ? PRIMER1_COLOR : PRIMER2_COLOR );
        else
          printf("\n%6d  ", result->pos - result->start + i );
      }
      printf("%c", result->sequence[i]);
    }
 
    fflush(stdout);

    result=result->next;
    fflush(stdout);
  }

  if(html) {
    printf("
"); for(i=0; i<25; i++) printf("
"); } else { printf("\n\n\n"); } fflush(stdout); return TRUE; } static AccListPtr GetAccList(CharPtr buffer, Int4Ptr TotalItems) { Char TmpBuff[256]; register Int4 i, j, k; Int4 FileLen = 0; AccListPtr acclist = NULL; AccListPtr acclistTmp, acclistlast; Int4 NumInvalid = 0; *TotalItems = 0; if(buffer == NULL || buffer[0] == NULLB) return NULL; MemSet(TmpBuff, '\0', sizeof(TmpBuff)); FileLen = StringLen(buffer); for(i = 0; i < FileLen; i++) { if(NumInvalid > 10) { printf("ERROR : Too many invalid Gi/Accession numbers
"); return NULL; } if(isspace(buffer[i])) /* Rolling spaces */ continue; j= 0; while (!isspace(buffer[i]) && j < 10 && i < FileLen) { TmpBuff[j] = buffer[i]; j++; i++; } TmpBuff[j] = NULLB; /* Now validating accession/gi */ for(k =0; k < j; k++) { if(!isdigit(TmpBuff[k])) { break; } } if(k != j) { if(IS_NOT_accession(TmpBuff)){ printf("WARNING: Gi/Accession \"%s\" " "is not valid
", TmpBuff); NumInvalid++; continue; } } /* It we come here - we got valid text ID */ if(acclist == NULL) { /* first element */ acclist = (AccListPtr) MemNew(sizeof(AccList)); acclistTmp = acclist; acclistTmp->acc = StringSave(TmpBuff); acclistTmp->next = NULL; acclistlast=acclistTmp; *TotalItems = *TotalItems +1; } else { acclistTmp = (AccListPtr) MemNew(sizeof(AccList)); acclistlast->next = acclistTmp; acclistTmp->acc = StringSave(TmpBuff); acclistTmp->next = NULL; acclistlast = acclistTmp; *TotalItems = *TotalItems +1; } } return acclist; } static void WWWSendSTSPage(CharPtr WWWSequence, Boolean NetscapeOK) { Int4 i; STSOrgPtr PNTR OrgTable; printf("Content-type: text/html\r\n\r\n"); printf("" "" " STS Match Program \n" "\n" "\n" " " " " "" "\n" "\n", BG_COLOR, getenv("SERVER_PORT")); if((OrgTable = STSGetOrgTable()) == NULL) { printf("ERROR: Cannot initiate Organism index " "Exiting...\n"); exit(1); } printf("
\n", getenv("SCRIPT_NAME") != NULL ? getenv("SCRIPT_NAME") : "NOT_SET", NetscapeOK? "ENCTYPE=\"multipart/form-data\"" : ""); printf("PCR-based sequence tagged sites (STSs) " "have been used as landmarks for " "construction of various types of genomic maps. " "Using \"electronic PCR\" (e-PCR), " "these sites can be detected in DNA sequences, " "potentially allowing their map " "locations to be determined.

\n"); printf("Enter here your input data as \n" "

\n" " \n", WWWSequence == NULL ? "" : WWWSequence); if(NetscapeOK) printf("
Or load your input data from file: " " \n"); printf("

\n"); printf("Retrieve STS from  " "

\n"); printf("Print detailed information " "

\n"); printf(" \n" " \n" "
\n" ); printf("%c
\n", LF); printf("Comments and suggestions to:" "< \n" "info@ncbi.nlm.nih.gov\n" " >
Credits to: \n" "" "Sergei B. Shavirin, \n" "\n" "" "Greg Schuler and \n" "" "Carolyn Tolstoshev\n"); printf("
\n"); } #define NUMARGS 9 Args pcr_args[NUMARGS] = { {"Input type\n" " 0 - FASTA file \n" " 1 - List of Gi/Accession numbers", NULL, NULL,NULL,FALSE,'t',ARG_INT,0.0,0,NULL}, {"Format of output \n" " 0 - Text \n" " 1 - HTML ", "0", NULL,NULL,FALSE,'f',ARG_INT, 0.0,0,NULL}, { "File with FASTA entries or GI/Accession numbers", "stdin", NULL, NULL, TRUE, 'i', ARG_FILE_IN, 0.0, 0, NULL}, {"Print detailed information \n" " 0 - Short \n" " 1 - Detailed ", "0", NULL,NULL,TRUE,'d',ARG_INT, 0.0,0,NULL}, { "GI/Accession number for quick look", NULL, NULL, NULL, TRUE, 'u', ARG_STRING, 0.0, 0, NULL}, {"STS database file name:", NULL, NULL,NULL,TRUE,'s',ARG_FILE_IN, 0.0,0,NULL}, {"ORG database file name:", NULL, NULL,NULL,TRUE,'o',ARG_FILE_IN, 0.0,0,NULL}, {"MAP database file name:", NULL, NULL,NULL,TRUE,'m',ARG_FILE_IN, 0.0,0,NULL}, {"Logfile name:", "elecpcr.log", NULL,NULL,TRUE,'l',ARG_FILE_OUT, 0.0,0,NULL} }; static StsParPtr STSReadCommandLine(void) { StsParPtr stsp; FILE *fd; if((stsp = StsParNew()) == NULL) return NULL; if ( !GetArgs ("elecpcr", NUMARGS, pcr_args) ) { exit(1); } if (!ErrSetLog (pcr_args[8].strvalue)) { ErrShow(); } else { ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON); } stsp->sts_db_name = StringSave(pcr_args[5].strvalue); stsp->org_db_name = StringSave(pcr_args[6].strvalue); stsp->map_db_name = StringSave(pcr_args[7].strvalue); if(pcr_args[1].intvalue == 1) stsp->html = TRUE; else stsp->html = FALSE; if(pcr_args[3].intvalue == 1) stsp->detailed = TRUE; else stsp->detailed = FALSE; if(pcr_args[0].intvalue == 1) stsp->intype = ACC_IN; else stsp->intype = FASTA_IN; if(pcr_args[4].strvalue != NULL) { /* Quick look ? */ stsp->sequence = pcr_args[4].strvalue; } else { /* Reading from file by default */ if((fd = FileOpen(pcr_args[2].strvalue, "rb")) == NULL) return NULL; if((stsp->sequence = WWWReadFileInMemory(fd, 0, TRUE)) == NULL) return NULL; } return stsp; } static StsParPtr GetStsSearchParam(void) { WWWInfoPtr info; CharPtr chptr; StsParPtr stsp; FILE *fd; time_t time_now; CharPtr TimeNowStr; WWWErrorCode error; Boolean SequenceOK = FALSE; if((fd = FileOpen(LogFile, "a")) == NULL) { if((fd = FileOpen("/tmp/wwwsts.log", "a")) == NULL) { printf("Cannot open logfile. Exiting...\n "); exit(1); } } if((error = WWWReadPosting(&info)) != WWWErrOk) return NULL; /* First check type of call to the program */ if(WWWGetMethod(info) == COMMAND_LINE) { /* Reading command line and create StsPar structure */ WWWInfoFree(info); return(STSReadCommandLine()); } if(WWWGetMethod(info) == WWW_GET) { if(WWWGetNumEntries(info) == 0) { time_now = time(NULL); TimeNowStr = ctime(&time_now); TimeNowStr[24] = '\0'; fprintf(fd, "\n%s|%s|%s|%s|%d", TimeNowStr, WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), 0); fclose(fd); WWWSendSTSPage(NULL, (Boolean)(WWWGetBrowser(info) == NETSCAPE)); exit(1); } else { /* Here is processing of link to Electronic PCR */ if((stsp = StsParNew()) == NULL) return NULL; /* Sequence Accession or GI */ stsp->intype = ACC_IN; if((chptr = WWWGetValueByName(info, "ID")) != NULL) { stsp->sequence = StringSave(chptr); } else { time_now = time(NULL); TimeNowStr = ctime(&time_now); TimeNowStr[24] = '\0'; fprintf(fd, "\n%s|%s|%s|%s|%d", TimeNowStr, WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), 0); fclose(fd); WWWSendSTSPage(NULL, (Boolean)(WWWGetBrowser(info) == NETSCAPE)); exit(1); } /* Detailed or short */ if((chptr = WWWGetValueByName(info, "D")) != NULL) { if(!StringICmp(chptr, "0") || !StringICmp(chptr, "FALSE") || !StringICmp(chptr, "OFF") || !StringICmp(chptr, "NO") ) stsp->detailed = FALSE; } else { stsp->detailed = TRUE; } /* Text or HTML */ if((chptr = WWWGetValueByName(info, "F")) != NULL) { if(!StringICmp(chptr, "0") || !StringICmp(chptr, "FALSE") || !StringICmp(chptr, "OFF") || !StringICmp(chptr, "TEXT") || !StringICmp(chptr, "NO") ) { stsp->html = FALSE; printf("Content-type: text/html\r\n\r\n"); printf("
", BG_COLOR);
                  printf(" STS Match Program ");
              }
          } else {
              stsp->html = TRUE;
          }
          return stsp;
          
      }  /* Link to Electronic PCR proccesing */
  }  /* Method == GET */
  
  if((stsp = StsParNew()) == NULL)
    return NULL;
 
#ifdef TEST
  printf("Content-type: text/html\r\n\r\n"); 
  info_data = (WWWInfoDataPtr) info;
  for(i=0; i < info_data->num_entries; i++) {
    printf("%s : %s\n 
%c", 
           info_data->entries[i]->name, 
           info_data->entries[i]->val, LF); 
  }
  exit(1);
#endif

  if((chptr = WWWGetValueByName(info, "ORGANISM")) != NULL)
      stsp->orgname = StringSave(chptr);

  if((chptr = WWWGetValueByName(info, "SEQUENCE")) != NULL) {
    if(chptr[0] != NULLB)
      SequenceOK = TRUE;
    stsp->sequence = StringSave(chptr);
  }
  if(((chptr = WWWGetValueByName(info, "SEQFILE")) != NULL) && 
     !SequenceOK) {
    stsp->sequence = StringSave(chptr);
  }

  if((chptr = WWWGetValueByName(info, "INPUT_TYPE")) != NULL) {
    if(StringStr(chptr, "Sequence")) {
      stsp->intype = FASTA_IN; 
    } else if(StringStr(chptr, "Accession")) {
      stsp->intype = ACC_IN; 
    } 
  }

  if((chptr = WWWGetValueByName(info, "DETAILED")) != NULL) {
    stsp->detailed = TRUE;
  }

  time_now = time(NULL);
  TimeNowStr = ctime(&time_now);
  TimeNowStr[24] = '\0'; 
  fprintf(fd, "\n%s|%s|%s|%s|%d|%d|%d",
          TimeNowStr, WWWGetAddress(info), 
          WWWGetHost(info), WWWGetAgent(info), 
          stsp->intype, 
          stsp->organism, 
          stsp->detailed);
  fclose(fd);

  WWWInfoFree(info);
  return stsp;
}
static StsParPtr StsParNew(void)
{
    StsParPtr param;
    param = (StsParPtr) MemNew(sizeof(StsPar));
    param->sequence = NULL;
    param->detailed = FALSE;
    param->intype = FASTA_IN; 
    param->html = TRUE;
    
    return param;
}

static void StsParFree(StsParPtr param) {
    MemFree(param->sequence);
    MemFree(param->sts_db_name);
    MemFree(param->org_db_name);
    MemFree(param->map_db_name);
    MemFree(param->orgname);

    MemFree(param);
}

static FastaSeqPtr NextFastaFromBuff(CharPtr p, CharPtr PNTR next)
{
  FastaSeqPtr fseq;
  CharPtr t;
  CharPtr str;
  Int4 i, SeqSize = INIT_BUFF_SIZE;

  *next = NULL;

  if(p == NULL | p[0] == NULLB)
    return NULL;

  t = p;

  while (isspace(*t)) /* Rolling spaces */
    *t++;

  fseq = (FastaSeqPtr) MemNew(sizeof(FastaSeq));
  fseq->label = NULL;
  fseq->seq = NULL;

  switch (*t) {
  case NULLB:
    return NULL;
  case '>':
    /* Reading label */
    str = (CharPtr) MemNew(SeqSize + 5);
    str[0] = NULLB;
    for(i=0; *t != NULLB; i++) {
      if((str[i] = *t) == '\n' || *t == '\r')
        break;
      if (i > SeqSize) {
        SeqSize = i + INIT_BUFF_SIZE;
        str = (CharPtr) Realloc(str, SeqSize + 5);
      }
      *t++;
    }
    str[i] = NULLB;
    fseq->label = StringSave(str);
    MemFree(str);

    /* Reading sequence */

    while (isspace(*t)) /* Rolling spaces */
      *t++;
    str = (CharPtr) MemNew(SeqSize + 5);
    str[0] = NULLB;

    for(i=0; *t != NULLB; i++) {
      if((str[i] = *t) == '>') {
        *next = t;
        break;
      }

      if (i > SeqSize) {
        SeqSize = i + INIT_BUFF_SIZE;
        str = (CharPtr) Realloc(str, SeqSize + 5);
      }
      *t++;
    }
    str[i] = NULLB;
    fseq->seq = StringSave(str);
    MemFree(str);
    break;
  default:

    /* Reading sequence */

    while (isspace(*t)) /* Rolling spaces */
      *t++;
    str = (CharPtr) MemNew(SeqSize + 5);
    str[0] = NULLB;

    for(i=0; *t != NULLB; i++) {
      if((str[i] = *t) == '>') {
        *next = t;
        break;
      }
      if (i > SeqSize) {
        SeqSize = i + INIT_BUFF_SIZE;
        str = (CharPtr) Realloc(str, SeqSize + 5);
      }
      *t++;
    }
    str[i] = NULLB;
    fseq->seq = StringSave(str);
    MemFree(str);
    break;
  }
  if(fseq->label == NULL)
    fseq->label = StringSave(">Your sequence");
  return fseq;
}

static Int4 FilterNucSequence(CharPtr p) 
{
  CharPtr t, s;
  Int4 len, i =0;
  Int4 NumBadChar=0;
  len = StringLen(p);
  
  s = p;

  for(t = p; i < len; i++){
    *p = toupper(*p);
    if (isalpha(*p)) {
      *t = *p;
      *t++;
    } else {
      if(!isspace(*p)) {
        NumBadChar++;
      }
    }
    *p++;
  }
  *t = NULLB;
  p = s;
  return NumBadChar;
}