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);
}
Int2 Main (void)
{
AsnIoPtr aip;
Boolean convertgis;
Boolean extractmrnas;
CharPtr infile, outfile;
SeqEntryPtr sep;
/* standard setup */
ErrSetFatalLevel (SEV_MAX);
ErrClearOptFlags (EO_SHOW_USERSTR);
UseLocalAsnloadDataAndErrMsg ();
ErrPathReset ();
/* finish resolving internal connections in ASN.1 parse tables */
if (! AllObjLoad ()) {
Message (MSG_FATAL, "AllObjLoad failed");
return 1;
}
if (! SubmitAsnLoad ()) {
Message (MSG_FATAL, "SubmitAsnLoad failed");
return 1;
}
if (! FeatDefSetLoad ()) {
Message (MSG_FATAL, "FeatDefSetLoad failed");
return 1;
}
if (! SeqCodeSetLoad ()) {
Message (MSG_FATAL, "SeqCodeSetLoad failed");
return 1;
}
if (! GeneticCodeTableLoad ()) {
Message (MSG_FATAL, "GeneticCodeTableLoad failed");
return 1;
}
/* process command line arguments */
if (! GetArgs ("gi2accn", sizeof (myargs) / sizeof (Args), myargs)) {
return 0;
}
infile = (CharPtr) myargs [i_argInputFile].strvalue;
outfile = (CharPtr) myargs [o_argOutputFile].strvalue;
convertgis = (Boolean) myargs [c_argConvertGIs].intvalue;
extractmrnas = (Boolean) myargs [x_argExtractMrnas].intvalue;
aip = AsnIoOpen (infile, "r");
if (aip == NULL) {
Message (MSG_FATAL, "AsnIoOpen input file failed");
return 1;
}
sep = SeqEntryAsnRead (aip, NULL);
AsnIoClose (aip);
if (sep == NULL) {
Message (MSG_FATAL, "SeqEntryAsnRead failed");
return 1;
}
PubSeqFetchEnable ();
LookupFarSeqIDs (sep, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE);
/* Extract mRNA hits from BLAST against nr */
if (extractmrnas) {
VisitAnnotsInSep (sep, NULL, FindBlastNR);
DeleteMarkedObjects (0, OBJ_SEQENTRY, (Pointer) sep);
}
/* convert gi numbers to accession.version */
if (convertgis) {
VisitAlignmentsInSep (sep, NULL, UpdateAligns);
}
PubSeqFetchDisable ();
BasicSeqEntryCleanup (sep);
aip = AsnIoOpen (outfile, "w");
if (aip == NULL) {
Message (MSG_FATAL, "AsnIoOpen output file failed");
return 1;
}
SeqEntryAsnWrite (sep, aip, NULL);
AsnIoClose (aip);
return 0;
}
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 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);
}
}
