static void PromoteToSeqEntry (Uint2 entityID, Uint2 datatype, Pointer dataptr)
{
BioseqPtr bsp;
BioseqSetPtr bssp;
SeqEntryPtr sep;
sep = GetTopSeqEntryForEntityID (entityID);
if (sep != NULL) return;
sep = SeqEntryNew ();
if (sep == NULL) return;
if (datatype == OBJ_BIOSEQ) {
bsp = (BioseqPtr) dataptr;
sep->choice = 1;
sep->data.ptrvalue = bsp;
SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep);
} else if (datatype == OBJ_BIOSEQSET) {
bssp = (BioseqSetPtr) dataptr;
sep->choice = 2;
sep->data.ptrvalue = bssp;
SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
} else {
sep = SeqEntryFree (sep);
}
}
extern void ExportSeqAnnotFeatureTable (FILE *fp, SeqAnnotPtr sap)
{
FeatureTableData ftd;
BioseqPtr fake_bsp;
SeqFeatPtr first_feat;
SeqEntryPtr sep;
if (fp == NULL || sap == NULL) return;
/* create fake bioseq to hold annotation */
fake_bsp = BioseqNew();
fake_bsp->annot = sap;
/* create SeqEntry for temporary bioseq to live in */
sep = SeqEntryNew ();
sep->choice = 1;
sep->data.ptrvalue = fake_bsp;
SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) fake_bsp, sep);
ftd.export_only_selected = FALSE;
ftd.fp = fp;
ftd.show_nucs = TRUE;
ftd.show_prots = TRUE;
ftd.suppress_protein_ids = FALSE;
/* show sources if there are any */
first_feat = (SeqFeatPtr) sap->data;
while (first_feat != NULL && first_feat->data.choice != SEQFEAT_BIOSRC) {
first_feat = first_feat->next;
}
if (first_feat != NULL) {
ftd.hide_sources = FALSE;
} else {
ftd.hide_sources = TRUE;
}
first_feat = (SeqFeatPtr) sap->data;
fake_bsp->id = SeqIdDup (SeqLocId (first_feat->location));
if (first_feat->data.choice == SEQFEAT_PROT) {
fake_bsp->mol = Seq_mol_aa;
} else {
fake_bsp->mol = Seq_mol_dna;
}
fake_bsp->repr = Seq_repr_raw;
fake_bsp->length = FindNecessaryBioseqLength (first_feat);
VisitBioseqsInSep (sep, &ftd, VSMExportFeatureTableBioseqCallback);
fake_bsp->annot = NULL;
fake_bsp->idx.deleteme = TRUE;
DeleteMarkedObjects (fake_bsp->idx.entityID, 0, NULL);
}
static Int2
VSMExportFeatureTable
(OMProcControlPtr ompcp,
Boolean show_nucs,
Boolean show_prots,
Boolean hide_sources,
Boolean suppress_protein_ids,
Boolean export_only_selected)
{
Char filename[255];
ValNode vn;
SeqEntryPtr sep = NULL;
FeatureTableData ftd;
SeqAnnotPtr sap = NULL;
BioseqPtr fake_bsp = NULL;
SeqFeatPtr first_feat = NULL;
switch(ompcp->input_itemtype)
{
case OBJ_SEQENTRY:
case OBJ_BIOSEQ:
case OBJ_BIOSEQSET:
case OBJ_SEQFEAT:
break;
case OBJ_SEQANNOT:
sap = (SeqAnnotPtr) ompcp->input_data;
if (sap== NULL) {
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can't write NULL Seq-annot");
return OM_MSG_RET_ERROR;
} else if (sap->type != 1) {
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Feature Table Seq-annot");
return OM_MSG_RET_ERROR;
} else if (sap->data == NULL) {
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can't write empty Feature Table Seq-annot");
return OM_MSG_RET_ERROR;
}
break;
default:
ErrPostEx(SEV_ERROR, 0,0,"ToFasta: Can only write Seq-entry, Feature Table Seq-annot, Bioseq, or Bioseq-set");
return OM_MSG_RET_ERROR;
}
ftd.show_nucs = show_nucs;
ftd.show_prots = show_prots;
ftd.hide_sources = hide_sources;
ftd.suppress_protein_ids = suppress_protein_ids;
ftd.export_only_selected = export_only_selected;
if (ompcp->input_itemtype == OBJ_SEQFEAT)
{
sep = GetTopSeqEntryForEntityID (ompcp->input_entityID);
}
else if (ompcp->input_choicetype == OBJ_SEQENTRY)
{
sep = (SeqEntryPtr)(ompcp->input_choice);
}
else if (ompcp->input_itemtype == OBJ_SEQANNOT) {
sep = GetTopSeqEntryForEntityID (ompcp->input_entityID);
if (sep == NULL) {
if (sap != NULL) {
fake_bsp = BioseqNew();
first_feat = (SeqFeatPtr) sap->data;
fake_bsp->id = SeqIdDup (SeqLocId (first_feat->location));
fake_bsp->annot = sap;
if (first_feat->data.choice == SEQFEAT_PROT) {
fake_bsp->mol = Seq_mol_aa;
} else {
fake_bsp->mol = Seq_mol_dna;
}
fake_bsp->repr = Seq_repr_raw;
fake_bsp->length = FindNecessaryBioseqLength (first_feat);
/* create SeqEntry for temporary bioseq to live in */
sep = SeqEntryNew ();
sep->choice = 1;
sep->data.ptrvalue = fake_bsp;
SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) fake_bsp, sep);
}
}
}
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
ftd.fp = FileOpen (filename, "r");
if (ftd.fp != NULL) {
FileClose (ftd.fp);
} else {
FileCreate (filename, "TEXT", "ttxt");
}
#endif
ftd.fp = FileOpen(filename, "w");
VisitBioseqsInSep (sep, &ftd, VSMExportFeatureTableBioseqCallback);
FileClose(ftd.fp);
ArrowCursor();
}
if (fake_bsp != NULL) {
fake_bsp->annot = NULL;
fake_bsp->idx.deleteme = TRUE;
DeleteMarkedObjects (fake_bsp->idx.entityID, 0, NULL);
}
return OM_MSG_RET_DONE;
}
static void ProcessSingleRecord (
CharPtr filename,
CSpeedFlagPtr cfp
)
{
AsnIoPtr aip;
BioseqPtr bsp;
ValNodePtr bsplist = NULL;
BioseqSetPtr bssp;
Pointer dataptr = NULL;
Uint2 datatype, entityID = 0;
FileCache fc;
FILE *fp;
Int1 iotype;
Char line [512];
Int4 maxio = 1;
SeqEntryPtr sep;
time_t starttime, stoptime, worsttime;
CharPtr str;
Int4 x;
if (cfp == NULL) return;
if (StringHasNoText (filename)) return;
if (StringChr (cfp->io, 'r') != NULL) {
maxio = cfp->maxcount;
}
starttime = GetSecs ();
for (x = 0; x < maxio; x++) {
if (entityID != 0) {
ObjMgrFreeByEntityID (entityID);
entityID = 0;
dataptr = NULL;
}
if (cfp->type == 1) {
fp = FileOpen (filename, "r");
if (fp == NULL) {
Message (MSG_POSTERR, "Failed to open '%s'", filename);
return;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, FALSE, FALSE);
FileClose (fp);
entityID = ObjMgrRegister (datatype, dataptr);
} else if (cfp->type >= 2 && cfp->type <= 5) {
aip = AsnIoOpen (filename, cfp->binary? "rb" : "r");
if (aip == NULL) {
Message (MSG_POSTERR, "AsnIoOpen failed for input file '%s'", filename);
return;
}
switch (cfp->type) {
case 2 :
dataptr = (Pointer) SeqEntryAsnRead (aip, NULL);
datatype = OBJ_SEQENTRY;
break;
case 3 :
dataptr = (Pointer) BioseqAsnRead (aip, NULL);
datatype = OBJ_BIOSEQ;
break;
case 4 :
dataptr = (Pointer) BioseqSetAsnRead (aip, NULL);
datatype = OBJ_BIOSEQSET;
break;
case 5 :
dataptr = (Pointer) SeqSubmitAsnRead (aip, NULL);
datatype = OBJ_SEQSUB;
break;
default :
break;
}
AsnIoClose (aip);
entityID = ObjMgrRegister (datatype, dataptr);
} else if (cfp->type == 6) {
fp = FileOpen (filename, "r");
if (fp == NULL) {
Message (MSG_POSTERR, "Failed to open '%s'", filename);
return;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, FALSE, FALSE);
FileClose (fp);
entityID = ObjMgrRegister (datatype, dataptr);
} else if (cfp->type == 7) {
fp = FileOpen (filename, "r");
if (fp == NULL) {
Message (MSG_POSTERR, "Failed to open '%s'", filename);
return;
}
FileCacheSetup (&fc, fp);
str = FileCacheReadLine (&fc, line, sizeof (line), NULL);
while (str != NULL) {
str = FileCacheReadLine (&fc, line, sizeof (line), NULL);
}
FileClose (fp);
return;
} else {
Message (MSG_POSTERR, "Input format type '%d' unrecognized", (int) cfp->type);
return;
}
}
if (entityID < 1 || dataptr == NULL) {
Message (MSG_POSTERR, "Data read failed for input file '%s'", filename);
return;
}
if (datatype == OBJ_SEQSUB || datatype == OBJ_SEQENTRY ||
datatype == OBJ_BIOSEQ || datatype == OBJ_BIOSEQSET) {
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "ASN reading time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
sep = GetTopSeqEntryForEntityID (entityID);
if (sep == NULL) {
sep = SeqEntryNew ();
if (sep != NULL) {
if (datatype == OBJ_BIOSEQ) {
bsp = (BioseqPtr) dataptr;
sep->choice = 1;
sep->data.ptrvalue = bsp;
SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep);
} else if (datatype == OBJ_BIOSEQSET) {
bssp = (BioseqSetPtr) dataptr;
sep->choice = 2;
sep->data.ptrvalue = bssp;
SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep);
} else {
sep = SeqEntryFree (sep);
}
}
sep = GetTopSeqEntryForEntityID (entityID);
}
if (sep != NULL) {
if (cfp->lock) {
starttime = GetSecs ();
bsplist = LockFarComponents (sep);
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "Far component locking time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
}
if (StringChr (cfp->io, 'w') != NULL) {
starttime = GetSecs ();
iotype = ASNIO_TEXT_OUT;
if (StringChr (cfp->io, 'b') != NULL) {
iotype = ASNIO_BIN_OUT;
}
for (x = 0; x < cfp->maxcount; x++) {
aip = AsnIoNew (iotype, cfp->ofp, NULL, NULL, NULL);
if (aip != NULL) {
SeqEntryAsnWrite (sep, aip, NULL);
AsnIoFree (aip, FALSE);
}
}
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "ASN writing time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
}
starttime = GetSecs ();
for (x = 0; x < cfp->maxcount; x++) {
DoProcess (sep, entityID, cfp);
}
stoptime = GetSecs ();
worsttime = stoptime - starttime;
if (cfp->logfp != NULL) {
fprintf (cfp->logfp, "Internal processing time %ld seconds\n", (long) worsttime);
fflush (cfp->logfp);
}
ObjMgrFreeByEntityID (entityID);
bsplist = UnlockFarComponents (bsplist);
}
} else {
Message (MSG_POSTERR, "Datatype %d not recognized", (int) datatype);
}
}
