static void DoFastaFeat (
SeqFeatPtr sfp,
Pointer userdata
)
{
CSpeedFlagPtr cfp;
CharPtr str;
if (sfp == NULL) return;
cfp = (CSpeedFlagPtr) userdata;
if (cfp == NULL) return;
if (cfp->ofp != NULL) {
str = SeqLocPrint (sfp->location);
if (str != NULL) {
fprintf (cfp->ofp, "> [%s]\n", str);
MemFree (str);
}
SeqLocFastaStream (sfp->location, cfp->ofp, STREAM_EXPAND_GAPS, 70, 0, 0);
} else {
SeqPortStreamLoc (sfp->location, STREAM_EXPAND_GAPS, NULL, EmptyStreamProc);
}
}
Int2 LIBCALLBACK VSMFastaProtSaveWithProduct ( Pointer data )
{
Char filename[255];
FastaExportOptionsData fe;
ValNode vn;
SeqEntryPtr sep = NULL;
SeqFeatPtr sfp;
SeqLocPtr slp;
Uint1 code;
BioseqPtr bsp;
OMProcControlPtr ompcp;
if ((ompcp = (OMProcControlPtr) data) == NULL) {
return OM_MSG_RET_ERROR;
}
sfp = NULL;
switch(ompcp->input_itemtype)
{
case OBJ_SEQENTRY:
case OBJ_BIOSEQ:
case OBJ_BIOSEQSET:
break;
case OBJ_SEQFEAT:
sfp = (SeqFeatPtr) ompcp->input_data;
if (sfp == NULL || (sfp->data.choice != SEQFEAT_CDREGION && sfp->data.choice != SEQFEAT_PROT)) return OM_MSG_RET_ERROR;
break;
default:
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Seq-entry, Bioseq, or Bioseq-set");
return OM_MSG_RET_ERROR;
}
if (sfp != NULL) {
} else if (ompcp->input_choicetype == OBJ_SEQENTRY)
sep = (SeqEntryPtr)(ompcp->input_choice);
else
{
vn.next = NULL;
vn.data.ptrvalue = ompcp->input_data;
if (ompcp->input_itemtype == OBJ_BIOSEQ)
vn.choice = 1;
else
vn.choice = 2;
sep = &vn;
}
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
fe.fp = FileOpen (filename, "r");
if (fe.fp != NULL) {
FileClose (fe.fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
fe.fp = FileOpen(filename, "w");
if (sfp != NULL) {
code = Seq_code_ncbieaa;
slp = sfp->location;
if (sfp->data.choice == SEQFEAT_CDREGION) {
slp = sfp->product;
}
bsp = GetBioseqGivenSeqLoc (slp, ompcp->input_entityID);
if (slp != NULL && bsp != NULL) {
SeqLocFastaStream (slp, fe.fp, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, 70, 0, 0);
}
} else {
fe.flags = STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL;
fe.linelen = 70;
fe.blocklen = 0;
fe.grouplen = 0;
VisitBioseqsInSep (sep, &fe, WriteOneProteinWithProduct);
}
FileClose(fe.fp);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
static Int2 LIBCALLBACK VSMGenericFastaSave (OMProcControlPtr ompcp, Boolean is_na)
{
Char filename[255];
FILE * fp;
ValNode vn;
SeqEntryPtr sep = NULL;
SeqFeatPtr sfp;
SeqLocPtr slp;
Uint1 code;
BioseqPtr bsp;
sfp = NULL;
switch(ompcp->input_itemtype)
{
case OBJ_SEQENTRY:
case OBJ_BIOSEQ:
case OBJ_BIOSEQSET:
break;
case OBJ_SEQFEAT:
sfp = (SeqFeatPtr) ompcp->input_data;
if (sfp == NULL) return OM_MSG_RET_ERROR;
break;
default:
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Seq-entry, Bioseq, or Bioseq-set");
return OM_MSG_RET_ERROR;
}
if (sfp != NULL) {
} else if (ompcp->input_choicetype == OBJ_SEQENTRY)
sep = (SeqEntryPtr)(ompcp->input_choice);
else
{
vn.next = NULL;
vn.data.ptrvalue = ompcp->input_data;
if (ompcp->input_itemtype == OBJ_BIOSEQ)
vn.choice = 1;
else
vn.choice = 2;
sep = &vn;
}
filename[0] = '\0';
if (GetOutputFileName(filename, (size_t)254, NULL))
{
WatchCursor();
#ifdef WIN_MAC
fp = FileOpen (filename, "r");
if (fp != NULL) {
FileClose (fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
fp = FileOpen(filename, "w");
if (sfp != NULL) {
if (is_na)
code = Seq_code_iupacna;
else
code = Seq_code_ncbieaa;
slp = sfp->location;
if (sfp->data.choice == SEQFEAT_CDREGION && (! is_na)) {
slp = sfp->product;
}
/*
spp = SeqPortNewByLoc (slp, code);
*/
bsp = GetBioseqGivenSeqLoc (slp, ompcp->input_entityID);
/*
if (spp != NULL && bsp != NULL) {
while (FastaSeqLine(spp, buf, 70, is_na))
FastaFileFunc(bsp, FASTA_SEQLINE, buf, sizeof (buf), (Pointer)fp);
SeqPortFree(spp);
FastaFileFunc(bsp, FASTA_EOS, buf, sizeof (buf), (Pointer)fp);
}
*/
if (slp != NULL && bsp != NULL) {
SeqLocFastaStream (slp, fp, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, 70, 0, 0);
}
} else {
/*
SeqEntryToFasta(sep, fp, is_na);
*/
SeqEntryFastaStreamEx (sep, fp, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, 70, 0, 0, is_na, !is_na, FALSE, !is_na, FALSE);
}
FileClose(fp);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
