Int2 LIBCALLBACK VSMDescriptorAsnSave (Pointer data)
{
OMProcControlPtr ompcp;
Char filename[255];
SelStructPtr ssp, sel;
SeqDescrPtr sdp;
BioseqPtr bsp;
SeqEntryPtr sep;
SeqMgrDescContext dcontext;
#ifdef WIN_MAC
FILE * fp;
#endif
ValNodePtr vnp;
SaveSetSdpData sd;
ValNodePtr obj_list = NULL;
ompcp = (OMProcControlPtr)data;
if (ompcp == NULL) return OM_MSG_RET_ERROR;
sd.already_have_molinfo = FALSE;
ssp = ObjMgrGetSelected();
if (ssp == NULL)
{
Message (MSG_ERROR, "You must select a sequence or set from which descriptors should be saved");
return OM_MSG_RET_DONE;
} else {
for (sel = ssp; sel != NULL; sel = sel->next)
{
GatherItem (sel->entityID, sel->itemID, sel->itemtype,
(Pointer) &obj_list, AddToSaveList);
}
}
/* get file name to use */
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
sd.aip = AsnIoOpen(filename, "w");
for (vnp = obj_list; vnp != NULL; vnp = vnp->next)
{
switch (vnp->choice) {
case OBJ_SEQDESC:
sdp = (SeqDescrPtr) vnp->data.ptrvalue;
SeqDescAsnWrite (sdp, sd.aip, NULL);
AsnPrintNewLine (sd.aip);
AsnIoFlush (sd.aip);
break;
case OBJ_BIOSEQ:
bsp = (BioseqPtr) vnp->data.ptrvalue;
for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext);
sdp != NULL;
sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext)) {
if (sdp->choice != Seq_descr_source
&& sdp->choice != Seq_descr_pub
&& sdp->choice != Seq_descr_molinfo
&& sdp->choice != Seq_descr_comment) continue;
SeqDescAsnWrite (sdp, sd.aip, NULL);
AsnPrintNewLine (sd.aip);
AsnIoFlush (sd.aip);
}
break;
case OBJ_BIOSEQSET:
sep = SeqMgrGetSeqEntryForData (vnp->data.ptrvalue);
VisitDescriptorsInSep (sep, &sd, SaveSetDescriptors);
break;
}
}
AsnIoClose(sd.aip);
ArrowCursor();
}
return OM_MSG_RET_DONE;
}
static void DoRecord (SeqEntryPtr sep, Pointer userdata)
{
BioseqPtr bsp;
SeqEntryPtr nsep;
ScanDataPtr sdp;
sdp = (ScanDataPtr) userdata;
(sdp->recordCount)++;
nsep = FindNthBioseq (sep, 1);
if (nsep != NULL && IS_Bioseq (nsep)) {
bsp = (BioseqPtr) nsep->data.ptrvalue;
if (bsp != NULL) {
SeqIdWrite (bsp->id, sdp->buf, PRINTID_FASTA_LONG, sizeof (sdp->buf));
}
}
#ifdef OS_UNIX
/* printf ("%s\n", sdp->buf); */
#endif
VisitPubdescsInSep (sep, (Pointer) sdp, DoThesis);
/* check for 'genomic DNA' in DoTitle suppressed for bulk submissions */
sdp->bulk = FALSE;
VisitDescriptorsInSep (sep, (Pointer) sdp, LookForBulk);
VisitDescriptorsInSep (sep, (Pointer) sdp, DoTitle);
VisitFeaturesInSep (sep, (Pointer) sdp, DoImpCDSandTrna);
/* index for pseudo cds, impfeat peptides codon frame */
SeqMgrIndexFeatures (0, sep->data.ptrvalue);
VisitFeaturesInSep (sep, (Pointer) sdp, DoPseudoCDS);
VisitFeaturesInSep (sep, (Pointer) sdp, DoPeptide);
/* now cleanup, index for overlapping peptides */
SeriousSeqEntryCleanup (sep, NULL, NULL);
SeqMgrIndexFeatures (0, sep->data.ptrvalue);
VisitBioseqsInSep (sep, (Pointer) sdp, DoProteins);
/*
VisitBioseqsInSep (sep, (Pointer) sdp, DoGraphs);
*/
#if 0
{
Boolean hasUser = FALSE;
VisitFeaturesInSep (sep, (Pointer) &hasUser, DoUser);
if (hasUser && sdp->aop != NULL && sdp->atp_se != NULL) {
SeqEntryAsnWrite (sep, sdp->aop, sdp->atp_se);
}
}
#endif
}
static void DoProcess (
SeqEntryPtr sep,
Uint2 entityID,
CSpeedFlagPtr cfp
)
{
Char id [64];
ErrSev oldErrSev;
ValidStructPtr vsp;
if (sep == NULL || cfp == NULL) return;
if (StringChr (cfp->clean, 't') != NULL) {
VisitDescriptorsInSep (sep, NULL, MarkTitles);
DeleteMarkedObjects (entityID, 0, NULL);
}
if (StringChr (cfp->clean, 'a') != NULL) {
AssignIDsInEntity (entityID, 0, NULL);
}
if (StringChr (cfp->clean, 'b') != NULL) {
BasicSeqEntryCleanup (sep);
}
if (StringChr (cfp->clean, 's') != NULL) {
SeriousSeqEntryCleanup (sep, NULL, NULL);
}
if (StringChr (cfp->index, 'f') != NULL) {
SeqMgrIndexFeatures (entityID, 0);
}
if (StringChr (cfp->seq, 'c') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaExist);
}
if (StringChr (cfp->seq, 'C') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaRegen);
}
if (StringChr (cfp->seq, 's') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaSeq);
}
if (StringChr (cfp->seq, 'S') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaSeq);
}
if (StringChr (cfp->seq, 'r') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaRaw);
}
if (StringChr (cfp->seq, 'd') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaDefline);
}
if (StringChr (cfp->seq, 'D') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaDefline);
}
if (StringChr (cfp->seq, 'T') != NULL) {
VisitDescriptorsInSep (sep, NULL, MarkTitles);
DeleteMarkedObjects (entityID, 0, NULL);
SeqMgrIndexFeatures (entityID, 0);
VisitBioseqsInSep (sep, (Pointer) cfp, DoFastaDefline);
}
if (StringChr (cfp->seq, 'x') != NULL) {
VisitBioseqsInSep (sep, (Pointer) cfp, DoNewFastaDefline);
}
if (StringChr (cfp->seq, 'X') != NULL) {
VisitDescriptorsInSep (sep, NULL, MarkTitles);
DeleteMarkedObjects (entityID, 0, NULL);
SeqMgrIndexFeatures (entityID, 0);
VisitBioseqsInSep (sep, (Pointer) cfp, DoNewFastaDefline);
}
if (StringChr (cfp->seq, 'f') != NULL) {
VisitFeaturesInSep (sep, (Pointer) cfp, DoFastaFeat);
}
if (StringChr (cfp->seq, 't') != NULL) {
VisitFeaturesInSep (sep, (Pointer) cfp, DoFastaTrans);
}
if (StringChr (cfp->feat, 'v') != NULL) {
VisitFeaturesInSep (sep, NULL, DoVisitFeaturesTest);
}
if (StringChr (cfp->feat, 'g') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitFeaturesInSep (sep, (Pointer) cfp, DoGeneOverlapPrintTest);
}
if (StringChr (cfp->feat, 'h') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
VisitFeaturesInSep (sep, (Pointer) cfp, DoGeneOverlapSpeedTest);
}
if (StringChr (cfp->feat, 'x') != NULL) {
}
if (StringChr (cfp->feat, 'o') != NULL) {
}
if (StringChr (cfp->feat, 'd') != NULL) {
}
if (StringChr (cfp->feat, 't') != NULL) {
SeqEntryToGnbk (sep, NULL, FTABLE_FMT, SEQUIN_MODE, NORMAL_STYLE,
0, 0, SHOW_PROT_FTABLE, NULL, cfp->ofp);
}
if (StringChr (cfp->feat, 's') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
cfp->nucbsp = FindNucBioseq (sep);
if (cfp->nucbsp != NULL) {
BioseqToGeneticCode (cfp->nucbsp, &(cfp->genCode), NULL, NULL, NULL, 0, NULL);
SeqIdWrite (cfp->nucbsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
fprintf (cfp->ofp, "%s\n", id);
VisitBioseqsInSep (sep, (Pointer) cfp, DoSuggestIntervals);
cfp->nucbsp = NULL;
cfp->genCode = 0;
}
}
if (StringChr (cfp->feat, 'S') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
cfp->nucbsp = FindNucBioseq (sep);
if (cfp->nucbsp != NULL) {
BioseqToGeneticCode (cfp->nucbsp, &(cfp->genCode), NULL, NULL, NULL, 0, NULL);
SetBatchSuggestNucleotide (cfp->nucbsp, cfp->genCode);
SeqIdWrite (cfp->nucbsp->id, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
fprintf (cfp->ofp, "%s\n", id);
VisitBioseqsInSep (sep, (Pointer) cfp, DoSuggestIntervals);
ClearBatchSuggestNucleotide ();
cfp->nucbsp = NULL;
cfp->genCode = 0;
}
}
if (StringChr (cfp->feat, 'c') != NULL) {
VisitFeaturesInSep (sep, (Pointer) cfp, DoVisitCodingRegions);
}
if (StringChr (cfp->desc, 'b') != NULL) {
}
if (StringChr (cfp->desc, 't') != NULL) {
}
if (StringChr (cfp->verify, 'v') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
vsp = ValidStructNew ();
if (vsp != NULL) {
vsp->useSeqMgrIndexes = TRUE;
vsp->suppressContext = TRUE;
vsp->seqSubmitParent = TRUE;
vsp->testLatLonSubregion = TRUE;
oldErrSev = ErrSetMessageLevel (SEV_NONE);
vsp->errfunc = ValidCallback;
vsp->userdata = (Pointer) cfp->ofp;
/* vsp->convertGiToAccn = FALSE; */
ValidateSeqEntry (sep, vsp);
ValidStructFree (vsp);
ErrSetMessageLevel (oldErrSev);
}
}
if (StringChr (cfp->verify, 'b') != NULL) {
if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
SeqMgrIndexFeatures (entityID, 0);
}
SeqEntryToGnbk (sep, NULL, GENBANK_FMT, SEQUIN_MODE, NORMAL_STYLE,
0, 0, 0, NULL, cfp->ofp);
}
if (cfp->ofp != NULL) {
fflush (cfp->ofp);
}
}
