Int2 Nlm_Main(void) {
Boolean use_new_engine=FALSE;
char buf[256] = { '\0' };
StringCpy(buf, "mgblast ");
StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf)-1);
if (! GetArgs (buf, NUMARG, myargs))
return (1);
UseLocalAsnloadDataAndErrMsg ();
if (! SeqEntryLoad())
return 1;
ErrSetMessageLevel(SEV_WARNING);
/*
if (myargs[ARG_FORCE_OLD].intvalue == 0 &&
myargs[ARG_OUTTYPE].intvalue > 1 &&
myargs[ARG_GILIST].strvalue == NULL)
use_new_engine = readdb_use_new_blast(myargs[ARG_DB].strvalue);
if (myargs[ARG_MASKEDQUERY].strvalue)
use_new_engine = FALSE;
*/
/*if (use_new_engine)
return Main_new();
else */
return Main_old();
}
Int2 Main (void)
{
Char buf[256] = { '\0' }; /* Used below for name and version. */
Int2 status = 0; /* return value of function. */
StringCpy(buf, "bl2seq ");
StringNCat(buf, BlastGetVersionNumber(), sizeof(buf)-StringLen(buf)-1);
if (! GetArgs (buf, NUMARG, myargs)) {
return (1);
}
UseLocalAsnloadDataAndErrMsg ();
if (! SeqEntryLoad())
return 1;
ErrSetMessageLevel(SEV_WARNING);
if (myargs[ARG_FORCE_OLD].intvalue != 0)
status = Main_old();
else
status = Main_new();
FreeArgs(NUMARG, myargs);
return status;
}
/** Creates the header part of an XML report for a BLAST search.
* @param program Program name [in]
* @param database Database name [in]
* @param query_loc Query Seq-loc [in]
* @param flags Flag to indicate whether query sequence should be included in
* the output. [in]
* @param search_param Search parameters [in]
*/
static BlastOutput*
s_CreateBlastOutputHead(const char* program, const char* database,
SeqLoc* query_loc, Int4 flags,
const Blast_SearchParams* search_param)
{
BlastOutput* boutp;
Char buffer[1024];
char* program_to_use = NULL;
if((boutp = BlastOutputNew()) == NULL)
return FALSE;
if (strcmp(program, "rpsblast") == 0)
program_to_use = strdup("blastp");
else if (strcmp(program, "rpstblastn") == 0)
program_to_use = strdup("blastx");
else
program_to_use = strdup(program);
/* For optimization BLOSUM62 may be loaded ones */
if (query_loc) {
SeqId* sip = SeqLocId(query_loc);
Bioseq* bsp;
SeqIdWrite(sip, buffer, PRINTID_FASTA_LONG, sizeof(buffer));
boutp->query_ID = strdup(buffer);
bsp = BioseqLockById(sip);
if(bsp != NULL) {
if (BioseqGetTitle(bsp) != NULL)
boutp->query_def = strdup(BioseqGetTitle(bsp));
else
boutp->query_def = strdup("No definition line found");
}
BioseqUnlock(bsp);
boutp->query_len = SeqLocLen(query_loc);
if(flags & BXML_INCLUDE_QUERY) {
boutp->query_seq = (char *) calloc(boutp->query_len+1, 1);
SeqPortStreamLoc(query_loc,
STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL,
boutp->query_seq, NULL);
} else {
boutp->query_seq = NULL; /* Do we need sequence here??? */
}
}
/* Program name. Use the local version of the program. No need to copy it
since it was locally allocated. */
boutp->program = program_to_use;
/* Database name */
if (database)
boutp->db = strdup(database);
/* Version text */
sprintf(buffer, "%s %s [%s]", program_to_use, BlastGetVersionNumber(),
BlastGetReleaseDate());
boutp->version = strdup(buffer);
/* Reference */
boutp->reference = BlastGetReference(FALSE);
/* Filling parameters */
boutp->param = ParametersNew();
boutp->param->expect = search_param->expect;
boutp->param->gap_open = search_param->gap_open;
boutp->param->gap_extend = search_param->gap_extension;
if (search_param->matrix)
boutp->param->matrix = strdup(search_param->matrix);
boutp->param->sc_match = search_param->match;
boutp->param->sc_mismatch = search_param->mismatch;
boutp->param->include = search_param->ethresh;
if (search_param->filter_string)
boutp->param->filter = strdup(search_param->filter_string);
return boutp;
}
