SEXP r_cgiGet2Post() {
char *res=cgiGet2Post();
if(res) {
return mkString(res);
}
return R_NilValue;
}
int main (int argc, char *argv[])
{
char *queryString;
if ((Conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL)
return EXIT_FAILURE;
cgiInit();
cgiHeader("text/html");
queryString = cgiGet2Post();
if (queryString[0] == '\0') {
puts ("<html>");
puts ("<head>");
html_printGenericStyleSheet (12);
puts ("<title>geneFusions</title>\n");
puts ("</head>");
puts ("<body>");
puts ("<h1>Identification of potential gene fusions using paired-end reads</h1><br><br>");
printf ("<form action=%s/geneFusions_cgi method=get>", confp_get(Conf, "WEB_URL_CGI"));
puts ("<b>Data prefix</b>: ");
puts ("<input type=text name=prefix>");
puts ("<br><br><br>");
puts ("<b>Minimum number of paired-end reads connecting two genes</b>: ");
puts ("<select name=minNum>");
puts ("<option value=2>2");
puts ("<option value=3>3");
puts ("<option value=5 selected>5");
puts ("<option value=10>10");
puts ("</select>");
puts ("<br><br><br>");
puts ("<b>Type of gene fusion</b>: ");
puts ("<select name=type>");
puts ("<option value=read-through>Read-through events");
puts ("<option value=cis>Cis events");
puts ("<option value=intra>Intra-chromosomal events");
puts ("<option value=same>Genes on the same chromosome");
puts ("<option value=inter>Genes on different chromosomes");
puts ("<option value=all selected>All potential gene fusions");
puts ("</select>");
puts ("<br><br><br>");
puts ("<input type=submit value=Submit>");
puts ("<input type=reset value=Reset>");
puts ("</form>");
puts ("</body>");
puts ("</html>");
fflush (stdout);
}
else {
int first;
Stringa item = stringCreate (20);
Stringa value = stringCreate (20);
char *iPtr,*vPtr,*prefix,*type;
int minNum;
first = 1;
cgiGetInit ();
while (cgiGetNextPair (&first,item,value)) {
iPtr = string (item);
vPtr = string (value);
if (strEqual (iPtr,"prefix")) {
prefix = hlr_strdup (vPtr);
}
if (strEqual (iPtr,"type")) {
type = hlr_strdup (vPtr);
}
if (strEqual (iPtr,"minNum")) {
minNum = atoi (vPtr);
}
}
generateOutput (prefix,type,minNum);
}
confp_close(Conf);
return EXIT_SUCCESS;
}
