/*
* do something to try to introduce more noise into the 'GetNoise' call
*/
static void rng_systemJitter(void)
{
static int fileToRead = 1;
if (ReadOneFile(fileToRead)) {
fileToRead = 1;
} else {
fileToRead++;
}
}
static void ProcessOneRecord (
CharPtr directory,
CharPtr base,
CharPtr organism,
Boolean findorf,
Boolean altstart,
Boolean validate,
Boolean flatfile
)
{
BioSourcePtr biop = NULL;
BioseqPtr bsp;
Uint2 datatype, entityID;
Int2 genCode;
MolInfoPtr mip;
SeqAnnotPtr sap;
SeqEntryPtr sep;
SeqFeatPtr sfp;
SqnTagPtr stp;
CharPtr ttl;
ValNodePtr vnp;
Message (MSG_POST, "Processing %s\n", base);
bsp = (BioseqPtr) ReadOneFile (directory, base, "fsa", &datatype);
if (bsp == NULL || datatype != OBJ_BIOSEQ) {
ObjMgrFree (datatype, (Pointer) bsp);
return;
}
if (bsp->mol == Seq_mol_na) {
bsp->mol = Seq_mol_dna;
}
vnp = ValNodeExtract (&(bsp->descr), Seq_descr_title);
if (vnp != NULL) {
ttl = (CharPtr) vnp->data.ptrvalue;
if (ttl != NULL) {
stp = SqnTagParse (ttl);
if (stp != NULL) {
biop = OldParseTitleIntoBioSource (stp, bsp, organism);
}
SqnTagFree (stp);
}
ValNodeFreeData (vnp);
}
if (biop == NULL) {
biop = OldParseTitleIntoBioSource (NULL, bsp, organism);
}
if (biop != NULL) {
SeqDescrAddPointer (&(bsp->descr), Seq_descr_source, (Pointer) biop);
}
mip = MolInfoNew ();
if (mip != NULL) {
mip->biomol = MOLECULE_TYPE_GENOMIC;
SeqDescrAddPointer (&(bsp->descr), Seq_descr_molinfo, (Pointer) mip);
}
entityID = ObjMgrRegister (datatype, (Pointer) bsp);
sep = GetBestTopParentForData (entityID, bsp);
genCode = SeqEntryToGeneticCode (sep, NULL, NULL, 0);
if (findorf) {
AnnotateBestOrf (bsp, genCode, altstart);
}
sap = (SeqAnnotPtr) ReadOneFile (directory, base, "tbl", &datatype);
if (sap != NULL && datatype == OBJ_SEQANNOT && sap->type == 1) {
sap->next = bsp->annot;
bsp->annot = sap;
} else {
ObjMgrFree (datatype, (Pointer) sap);
}
/* for parsed in features or best ORF, promote CDS products to protein bioseq */
for (sap = bsp->annot; sap != NULL; sap = sap->next) {
if (sap->type == 1) {
SetEmptyGeneticCodes (sap, genCode);
sfp = (SeqFeatPtr) sap->data;
PromoteXrefs (sfp, bsp, entityID);
}
}
sep = GetTopSeqEntryForEntityID (entityID);
if (sep != NULL) {
SeriousSeqEntryCleanup (sep, NULL, NULL);
WriteOneFile (directory, base, "sqn", sep);
if (validate || flatfile) {
SeqMgrIndexFeatures (entityID, 0);
}
if (validate) {
Message (MSG_POST, "Validating %s\n", base);
ValidateOneFile (directory, base, "val", sep);
}
if (flatfile) {
Message (MSG_POST, "Flatfile %s\n", base);
sep = FindNucSeqEntry (sep);
FlatfileOneFile (directory, base, "gbf", sep);
}
}
ObjMgrFreeByEntityID (entityID);
}
