& strType )
67 constlist<CRef<CAnnotdesc> > descriptors = annot.
GetDesc().
Get();
68list<CRef<CAnnotdesc> >::const_iterator it;
69 for(it = descriptors.begin(); it != descriptors.end(); ++it) {
70 if(!(*it)->IsUser()) {
89 #define EMIT(str) { genome_str = str; return true; } 130 #define EMIT(str) { idType = str; return true; } 131 switch(seqId.
Which()) {
194 if(!
mod.IsSetSubtype() || !
mod.IsSetSubname()) {
209 #define EMIT(str) { subname = str; return true; } 218 EMIT(
"indeterminate");
238 static const char* AANames[] = {
239 "---",
"Ala",
"Asx",
"Cys",
"Asp",
"Glu",
"Phe",
"Gly",
"His",
"Ile",
240 "Lys",
"Leu",
"Met",
"Asn",
"Pro",
"Gln",
"Arg",
"Ser",
"Thr",
"Val",
241 "Trp",
"Other",
"Tyr",
"Glx",
"Sec",
"TERM",
"Pyl" 243 static const char* other =
"OTHER";
261aaName = ((aa <
ArraySize(AANames)) ? AANames[aa] : other);
268cbString =
"complement("+ cbString +
")";
274 autofrom = intv.
GetFrom()+1;
275 autoto = intv.
GetTo()+1;
311 const auto& points = packedPnt.
GetPoints();
313 for(
autoit = points.rbegin(); it != points.rend(); ++it) {
317 for(
const auto& point : points) {
321 if(cbString.empty()) {
324cbString.back() =
')';
325cbString =
"join("+ cbString +
")";
343}
else if(loc.
IsPnt()) {
355 if(! mix.
IsSet()) {
359 boolisOrdered{
false};
363 for(
autoit = mix.
Get().rbegin(); it != mix.
Get().rend(); ++it) {
367 for(
const auto& pLoc : mix.
Get()) {
372 if(mixString.empty()) {
375mixString.back() =
')';
378mixString =
"order("+ mixString;
380mixString =
"join("+ mixString;
393 if(! packedInt.
IsSet()) {
400 for(
autoit = packedInt.
Get().rbegin(); it != packedInt.
Get().rend(); ++it) {
404 for(
const auto& pInt : packedInt.
Get()) {
409 if(intsString.empty()) {
412intsString.back() =
')';
413intsString =
"join("+ intsString;
430 stringcb_str = (
"(pos:");
433 switch(loc.
Which()) {
454 "Unsupported code-break location type : "+
label);
464cb_str += aaName +
")";
481 static const charkIdxToSymbol[] =
"?ACMGRSVUWYHKDBN";
483vector<char> symbol_to_idx(256,
'\0');
484 for(
size_t i= 0;
i<
sizeof(kIdxToSymbol) - 1; ++
i) {
485symbol_to_idx[kIdxToSymbol[
i]] =
i;
488 size_tidx = symbol_to_idx[str1[2]] | symbol_to_idx[str2[2]];
489 returnkIdxToSymbol[idx];
506 if(!codon.empty()) {
517list<string>::iterator it =
codons.begin();
518list<string>::iterator
prev= it++;
519 while(it !=
codons.end()) {
520 string& codon1 = *
prev;
521 string& codon2 = *it;
522 if(codon1[0] == codon2[0] && codon1[1] == codon2[1]) {
572 static const char* sTrnaList[] = {
573 "tRNA-Gap",
"tRNA-Ala",
"tRNA-Asx",
"tRNA-Cys",
"tRNA-Asp",
"tRNA-Glu",
574 "tRNA-Phe",
"tRNA-Gly",
"tRNA-His",
"tRNA-Ile",
"tRNA-Xle",
"tRNA-Lys",
575 "tRNA-Leu",
"tRNA-Met",
"tRNA-Asn",
"tRNA-Pyl",
"tRNA-Pro",
"tRNA-Gln",
576 "tRNA-Arg",
"tRNA-Ser",
"tRNA-Thr",
"tRNA-Sec",
"tRNA-Val",
"tRNA-Trp",
577 "tRNA-OTHER",
"tRNA-Tyr",
"tRNA-Glx",
"tRNA-TERM" 579 static intsTrnaListSize =
static_cast<int>(
ArraySize(sTrnaList));
585(aa ==
'*') ? (aa = 25) : (aa -= 64);
586name = ((0 < aa && aa < sTrnaListSize) ? sTrnaList[aa] :
"");
601 switch( loc.
Which() ) {
614anticodon =
"complement("+ anticodon +
")";
619acStr =
string(
"(pos:") + anticodon +
")";
639 if(!
str.empty()) {
662 #define EMIT(str) { mol_str = str; return true; } 683 EMIT(
"genomic DNA");
685 EMIT(
"genomic RNA");
701 EMIT(
"transcribed RNA");
708 EMIT(
"other DNA");
710 EMIT(
"other RNA");
714 EMIT(
"viral cRNA");
717 EMIT(
"genomic RNA");
721 EMIT(
"unassigned");
723 EMIT(
"unassigned DNA");
725 EMIT(
"unassigned RNA");
738 switch( loc.
Which() ) {
774 for(
size_tu=0; u <
str.length(); ++u) {
775 if(
str[u] ==
'\"')
777 if(
str[u] ==
' '||
str[u] ==
';'||
str[u] ==
':'||
str[u] ==
'=') {
792 switch( loc.
Which() ) {
797vector<CRef<CSeq_loc> > sub_locs;
798sub_locs.reserve(loc.
GetMix().
Get().size());
804new_sub_loc->
Assign(**orig_sub_loc);
806sub_locs.push_back(new_sub_loc);
810 copy((*sub_loc)->GetPacked_int().Get().begin(),
811(*sub_loc)->GetPacked_int().Get().end(),
817 const auto& bond = loc.
GetBond();
818 const auto& aPoint = bond.
GetA();
819 const auto& bPoint = bond.IsSetB() ?
820bond.GetB() : bond.GetA();
822pSeqInt->SetId().Assign(aPoint.GetId());
823pSeqInt->SetFrom(aPoint.GetPoint());
824pSeqInt->SetTo(bPoint.GetPoint());
825 if(aPoint.IsSetStrand()) {
826pSeqInt->SetStrand(aPoint.GetStrand());
871 constlist< CRef< CSeqdesc > >& listDescr = descr.
Get();
873cit != listDescr.end(); ++cit) {
902 constlist< CRef< CSeqdesc > >& listDescr = descr.
Get();
904cit != listDescr.end(); ++cit) {
918 constlist< CRef< CSeqdesc > >& listDescr = descr.
Get();
920cit != listDescr.end(); ++cit) {
959 const string& strType)
967 for(CUser_object::TData::const_iterator it = fields.begin();
975 data.GetObject(), strType);
988 const string& strType)
992 typedeflist<CRef<CUser_object > >::const_iterator CIT;
993 for(CIT cit = uos.begin(); cit != uos.end(); ++cit) {
1062 size_tnumRna(0), numEst(0), numProtein(0), numLongSra(0),
1063rnaseqBaseCoverage(0), rnaseqBiosamplesIntronsFull(0);
1075 if(
label==
"Method") {
1079 if(
label==
"Counts") {
1089 if(
label==
"mRNA") {
1093 if(
label==
"EST") {
1097 if(
label==
"Protein") {
1101 if(
label==
"long SRA read") {
1107 if(
label==
"mRNA") {
1111 if(
label==
"EST") {
1115 if(
label==
"Protein") {
1119 if(
label==
"long SRA read") {
1123 if(
label==
"rnaseq_base_coverage") {
1129 if(
label==
"rnaseq_biosamples_introns_full") {
1138ostringstream
text;
1145 if(numRna > 0 || numEst > 0 || numProtein > 0 || numLongSra > 0 ||
1146rnaseqBaseCoverage > 0)
1148 text<<
"Supporting evidence includes similarity to:";
1150 stringsection_prefix =
" ";
1152 if(numRna > 0 || numEst > 0 || numProtein > 0 || numLongSra > 0)
1154 text<< section_prefix;
1157 text<< prefix << numRna <<
" mRNA";
1164 text<< prefix << numEst <<
" EST";
1170 if(numProtein > 0) {
1171 text<< prefix << numProtein <<
" Protein";
1172 if(numProtein > 1) {
1177 if(numLongSra > 0) {
1178 text<< prefix << numLongSra <<
" long SRA read";
1179 if(numLongSra > 1) {
1184section_prefix =
", and ";
1187 if(rnaseqBaseCoverage > 0)
1189 text<< section_prefix;
1191 text<< rnaseqBaseCoverage <<
"% coverage of the annotated genomic feature by RNAseq alignments";
1192 if(rnaseqBiosamplesIntronsFull > 0) {
1193 text<<
", including "<< rnaseqBiosamplesIntronsFull;
1195 if(rnaseqBiosamplesIntronsFull > 1) {
1198 text<<
" with support for all annotated introns";
1201section_prefix =
", and ";
1203mestr =
text.str();
1211 string& threeFeatType)
1218 if(!pUo || !pUo->HasField(
"location")) {
1221threeFeatType = pUo->GetField(
"location").GetString();
1236 if(!pUo || !pUo->HasField(
"score")) {
1239score = pUo->GetField(
"score").GetInt();
1254 if(!pUo || !pUo->HasField(
"color")) {
1257 color= pUo->GetField(
"color").GetString();
1267 usingFTABLE = list<CRef<CSeq_feat> >;
1273 autoremainingTests = 100;
1274 for(
autopFeat:
ftable) {
1279 if(--remainingTests == 0) {
1305vector<string>& goMarkup,
1310 for(
const auto& field: fields) {
1311 if(!field->IsSetLabel() || !field->GetLabel().IsId()
1312|| ( field->GetLabel().GetId() != 0 && ! relaxed)) {
1315 if(!field->IsSetData() || !field->GetData().IsFields()) {
1318 stringdescriptive, goId, pubmedId, evidence;
1319 const auto& subFields = field->GetData().GetFields();
1320 for(
const auto& subField: subFields) {
1321 if(!subField->IsSetLabel() || ! subField->GetLabel().IsStr()) {
1324 const auto& subLabel = subField->GetLabel().GetStr();
1325 if(subLabel ==
"text string") {
1326descriptive = subField->GetData().GetStr();
1329 if(subLabel ==
"go id") {
1330goId = subField->GetData().GetStr();
1333 if(subLabel ==
"pubmed id") {
1337 if(subLabel ==
"evidence") {
1338evidence = subField->GetData().GetStr();
1342goMarkup.push_back(descriptive +
"|"+ goId +
"|"+ pubmedId +
"|"+ evidence);
1350list<std::string>& goIds,
1354 for(
const auto& field: fields) {
1355 if(!field->IsSetLabel() || !field->GetLabel().IsId()
1356|| ( field->GetLabel().GetId() != 0 && ! relaxed)) {
1359 if(!field->IsSetData() || !field->GetData().IsFields()) {
1362 stringdescriptive, goId, pubmedId, evidence;
1363 const auto& subFields = field->GetData().GetFields();
1364 for(
const auto& subField: subFields) {
1365 if(!subField->IsSetLabel() || ! subField->GetLabel().IsStr()) {
1368 const auto& subLabel = subField->GetLabel().GetStr();
1369 if(subLabel ==
"go id") {
1370goId = subField->GetData().GetStr();
1371goIds.push_back(
string(
"GO:")+goId);
1391 if(lhs_id != rhs_id) {
1392 return(lhs_id < rhs_id);
1398 if(lhs_start != rhs_start) {
1399 return(lhs_start < rhs_start);
1404 if(lhs_stop != rhs_stop) {
1405 return(lhs_stop > rhs_stop);
1410 if(lhs_strand != rhs_strand) {
1411 returnlhs_strand > rhs_strand;
1417 if(lhs_subtype != rhs_subtype) {
1418 return(lhs_subtype > rhs_subtype);
1426 if(lhs_region != rhs_region) {
1427 return(lhs_region > rhs_region);
1441 if(loc.
GetId()) {
1466 for(
const auto& pDescr: descrs) {
1467 if(pDescr->IsMolinfo() && pDescr->GetMolinfo().CanGetBiomol()) {
1468 switch(pDescr->GetMolinfo().GetBiomol()) {
1503 for(
const auto& pDescr: descrs) {
1504 if(pDescr->IsMolinfo() && pDescr->GetMolinfo().CanGetBiomol()) {
1505 switch(pDescr->GetMolinfo().GetBiomol()) {
1541 unsigned int& inPoint,
1542 unsigned int& outPoint)
1547 typedeflist<CRef<CSeq_interval> >::const_iterator CIT;
1551 if(testLoc.
IsMix()) {
1560 constlist<CRef<CSeq_interval> >& intvs = packedInt.
Get();
1561 for(CIT cit = intvs.begin(); cit != intvs.end(); cit++) {
1563 if(intv.
GetFrom() < inPoint) {
1566 if(intv.
GetTo() > outPoint) {
1567outPoint = intv.
GetTo();
User-defined methods of the data storage class.
@ eExtreme_Positional
numerical value
@ eExtreme_Biological
5' and 3'
User-defined methods of the data storage class.
static string IndexToCodon(int index)
static CGenbankIdResolve & Get()
bool GetBestId(CSeq_id_Handle, CScope &, string &) const
bool m_bSequenceHasBioSource
void xAssignSequenceIsGenomicRecord()
void xAssignSequenceHasBioSource()
bool m_bSequenceIsGenomicRecord
CMappedFeat FindBestGeneParent(const CMappedFeat &mf)
@OrgMod.hpp User-defined methods of the data storage class.
static string GetSubtypeName(TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)
TSeqPos GetStop(ESeqLocExtremes ext) const
TSeqPos GetStart(ESeqLocExtremes ext) const
ENa_strand GetStrand(void) const
@ eSubtype_mobile_element
bool IsFtable(void) const
@Seq_descr.hpp User-defined methods of the data storage class.
namespace ncbi::objects::
ENa_strand GetStrand(void) const
static TIndex GetMapToIndex(CSeq_data::E_Choice from_type, CSeq_data::E_Choice to_type, TIndex from_idx)
static string GetSubtypeName(CSubSource::TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)
static bool IsTransspliced(const CSeq_feat &feature)
static void ChangeToPackedInt(CSeq_loc &loc)
static string GetStringId(const CSeq_loc &loc)
static bool IsSequenceCircular(CBioseq_Handle)
static bool IsProteinSequence(CBioseq_Handle)
static bool GetTrnaAntiCodon(const CTrna_ext &, string &)
static bool GetStringsForGoMarkup(const vector< CRef< CUser_field > > &fields, vector< string > &goMarkup, bool relaxed=false)
static bool GetSubSourceSubType(const CSubSource &, string &, string &)
static bool GetOrgModSubType(const COrgMod &, string &, string &)
static bool IsLocationOrdered(const CSeq_loc &)
static bool GetDbTag(const CDbtag &, string &)
static bool GetStringForGoMarkup(const vector< CRef< CUser_field > > &fields, string &goMarkup, bool relaxed=false)
static bool CompareFeatures(const CMappedFeat &lhs, const CMappedFeat &rhs)
static bool GetStringForModelEvidence(CMappedFeat mf, string &mestr)
static bool GetCodeBreak(const CCode_break &, string &)
static bool GetThreeFeatType(const CSeq_feat &, string &)
static bool GetThreeFeatRgb(const CSeq_feat &, string &)
static bool IsThreeFeatFormat(const CSeq_annot &)
static bool GetListOfGoIds(const vector< CRef< CUser_field > > &fields, list< std::string > &goIds, bool relaxed=false)
static CConstRef< CUser_object > GetUserObjectByType(const CUser_object &uo, const string &strType)
static CRef< CUser_object > GetDescriptor(const CSeq_annot &annot, const string &)
static ENa_strand GetEffectiveStrand(const CSeq_interval &)
static bool GetThreeFeatScore(const CSeq_feat &, int &)
static bool GetTranssplicedEndpoints(const CSeq_loc &loc, unsigned int &inPoint, unsigned int &outPoint)
static bool GetAaName(const CCode_break &, string &)
static bool GetBestId(CSeq_id_Handle, CScope &, string &)
static bool GetIdType(CBioseq_Handle, string &)
static bool GetTrnaCodons(const CTrna_ext &, string &)
static bool NeedsQuoting(const string &)
static bool IsNucleotideSequence(CBioseq_Handle)
static bool GetTrnaProductName(const CTrna_ext &, string &)
static CConstRef< CUser_object > GetModelEvidence(CMappedFeat)
static bool GetGenomeString(const CBioSource &, string &)
static bool GetBiomol(CBioseq_Handle, string &)
static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)
static const char * str(char *buf, int n)
static const char *const strings[]
const TResidue codons[4][4]
constexpr size_t ArraySize(const Element(&)[Size])
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
#define NON_CONST_ITERATE(Type, Var, Cont)
Non constant version of ITERATE macro.
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)
Set object to copy of another one.
const string AsFastaString(void) const
CConstRef< CSeq_id > GetSeqId(void) const
void SetPacked_int(TPacked_int &v)
ENa_strand GetStrand(void) const
Get the location's strand.
void ChangeToPackedInt(void)
Works only if location is currently an interval, point, packed-int (handled trivially),...
virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)
Override Assign() to incorporate cache invalidation.
TSeqPos GetStart(ESeqLocExtremes ext) const
Return start and stop positions of the seq-loc.
bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const
Check if strand is set for any/all part(s) of the seq-loc depending on the flag.
const CSeq_id * GetId(void) const
Get the id of the location return NULL if has multiple ids or no id at all.
void GetLabel(string *label) const
Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...
TSeqPos GetStop(ESeqLocExtremes ext) const
CMappedFeat GetBestGeneForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)
CMappedFeat GetBestGeneForFeat(const CMappedFeat &feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)
const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)
If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...
@ eGetId_Best
return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function
CBioseq_set_Handle GetParentBioseq_set(void) const
Return a handle for the parent Bioseq-set, or null handle.
CSeq_entry_Handle GetParentEntry(void) const
Get parent Seq-entry handle.
const CSeq_feat::TExts & GetExts(void) const
bool IsSetDescr(void) const
const CSeqFeatData & GetData(void) const
TInst_Mol GetInst_Mol(void) const
TInst_Topology GetInst_Topology(void) const
const CUser_object & GetExt(void) const
const TDescr & GetDescr(void) const
const TDescr & GetDescr(void) const
bool IsSetExts(void) const
CSeqFeatData::ESubtype GetFeatSubtype(void) const
bool IsSetDescr(void) const
bool IsSetInst_Topology(void) const
bool IsSetExt(void) const
TMol GetBioseqMolType(void) const
Get some values from core:
bool CanGetDescr(void) const
bool CanGetInst_Mol(void) const
const CSeq_loc & GetLocation(void) const
const CSeq_feat & GetMappedFeature(void) const
Feature mapped to the master sequence.
CRef< C > Ref(C *object)
Helper functions to get CRef<> and CConstRef<> objects.
void Reset(void)
Reset reference object.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
static string IntToString(int value, TNumToStringFlags flags=0, int base=10)
Convert int to string.
static string Join(const TContainer &arr, const CTempString &delim)
Join strings using the specified delimiter.
static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)
Convert UInt to string.
static string & ToUpper(string &str)
Convert string to upper case â string& version.
static const char label[]
TGenome GetGenome(void) const
Get the Genome member data.
TSubtype GetSubtype(void) const
Get the Subtype member data.
bool IsSetGenome(void) const
Check if a value has been assigned to Genome data member.
bool IsSetSubtype(void) const
Check if a value has been assigned to Subtype data member.
const TName & GetName(void) const
Get the Name member data.
bool IsSetName(void) const
Check if a value has been assigned to Name data member.
@ eSubtype_environmental_sample
@ eGenome_endogenous_virus
const TStr & GetStr(void) const
Get the variant data.
bool IsStr(void) const
Check if variant Str is selected.
bool IsSetDb(void) const
name of database or system Check if a value has been assigned to Db data member.
bool IsSetType(void) const
type of object within class Check if a value has been assigned to Type data member.
const TTag & GetTag(void) const
Get the Tag member data.
bool IsId(void) const
Check if variant Id is selected.
const TData & GetData(void) const
Get the Data member data.
bool CanGetData(void) const
Check if it is safe to call GetData method.
bool IsSetTag(void) const
appropriate tag Check if a value has been assigned to Tag data member.
const TFields & GetFields(void) const
Get the variant data.
const TDb & GetDb(void) const
Get the Db member data.
vector< CRef< CUser_field > > TFields
bool IsFields(void) const
Check if variant Fields is selected.
bool IsInt(void) const
Check if variant Int is selected.
bool IsSetLabel(void) const
field label Check if a value has been assigned to Label data member.
const TStr & GetStr(void) const
Get the variant data.
TInt GetInt(void) const
Get the variant data.
const TData & GetData(void) const
Get the Data member data.
const TLabel & GetLabel(void) const
Get the Label member data.
const TType & GetType(void) const
Get the Type member data.
bool IsSetData(void) const
Check if a value has been assigned to Data data member.
vector< CRef< CUser_field > > TData
TId GetId(void) const
Get the variant data.
@ e_Object
for using other definitions
const TAnticodon & GetAnticodon(void) const
Get the Anticodon member data.
const TAa & GetAa(void) const
Get the Aa member data.
const TCodon & GetCodon(void) const
Get the Codon member data.
bool IsSetAa(void) const
Check if a value has been assigned to Aa data member.
bool IsSetAnticodon(void) const
location of anticodon Check if a value has been assigned to Anticodon data member.
bool IsNcbieaa(void) const
Check if variant Ncbieaa is selected.
TNcbieaa GetNcbieaa(void) const
Get the variant data.
bool IsSetCodon(void) const
codon(s) as in Genetic-code Check if a value has been assigned to Codon data member.
const TExts & GetExts(void) const
Get the Exts member data.
TNcbi8aa GetNcbi8aa(void) const
Get the variant data.
E_Choice Which(void) const
Which variant is currently selected.
const TRegion & GetRegion(void) const
Get the variant data.
const TLoc & GetLoc(void) const
Get the Loc member data.
const TExcept_text & GetExcept_text(void) const
Get the Except_text member data.
bool IsSetExcept_text(void) const
explain if except=TRUE Check if a value has been assigned to Except_text data member.
const TAa & GetAa(void) const
Get the Aa member data.
TNcbieaa GetNcbieaa(void) const
Get the variant data.
bool IsSetExts(void) const
set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.
TNcbistdaa GetNcbistdaa(void) const
Get the variant data.
bool IsSetLoc(void) const
location of exception Check if a value has been assigned to Loc data member.
@ e_Ncbi8aa
NCBI8aa code.
@ e_Ncbieaa
ASCII value of NCBIeaa code.
bool IsSet(void) const
Check if a value has been assigned to data member.
bool IsMix(void) const
Check if variant Mix is selected.
ENa_strand
strand of nucleic acid
const Tdata & Get(void) const
Get the member data.
TStrand GetStrand(void) const
Get the Strand member data.
bool IsSetPoints(void) const
Check if a value has been assigned to Points data member.
const TPnt & GetPnt(void) const
Get the variant data.
TPoint GetPoint(void) const
Get the Point member data.
TFrom GetFrom(void) const
Get the From member data.
list< CRef< CSeq_loc > > Tdata
E_Choice Which(void) const
Which variant is currently selected.
E_Choice Which(void) const
Which variant is currently selected.
bool IsSet(void) const
Check if a value has been assigned to data member.
TStrand GetStrand(void) const
Get the Strand member data.
const Tdata & Get(void) const
Get the member data.
const TPacked_pnt & GetPacked_pnt(void) const
Get the variant data.
bool IsPacked_int(void) const
Check if variant Packed_int is selected.
const TA & GetA(void) const
Get the A member data.
bool IsSetStrand(void) const
Check if a value has been assigned to Strand data member.
bool IsSetStrand(void) const
Check if a value has been assigned to Strand data member.
const TPoints & GetPoints(void) const
Get the Points member data.
TStrand GetStrand(void) const
Get the Strand member data.
const TGeneral & GetGeneral(void) const
Get the variant data.
TTo GetTo(void) const
Get the To member data.
bool IsInt(void) const
Check if variant Int is selected.
const TInt & GetInt(void) const
Get the variant data.
bool IsNull(void) const
Check if variant Null is selected.
static string SelectionName(E_Choice index)
Retrieve selection name (for diagnostic purposes).
const TMix & GetMix(void) const
Get the variant data.
bool IsPnt(void) const
Check if variant Pnt is selected.
const TPacked_int & GetPacked_int(void) const
Get the variant data.
const TBond & GetBond(void) const
Get the variant data.
@ e_Gibbmt
Geninfo backbone moltype.
@ e_Giim
Geninfo import id.
@ e_Other
for historical reasons, 'other' = 'refseq'
@ e_Gpipe
Internal NCBI genome pipeline processing ID.
@ e_Tpe
Third Party Annot/Seq EMBL.
@ e_Tpd
Third Party Annot/Seq DDBJ.
@ e_Gibbsq
Geninfo backbone seqid.
@ e_General
for other databases
@ e_Gi
GenInfo Integrated Database.
@ e_Named_annot_track
Internal named annotation tracking ID.
@ e_Tpg
Third Party Annot/Seq Genbank.
const Tdata & Get(void) const
Get the member data.
bool IsMolinfo(void) const
Check if variant Molinfo is selected.
bool CanGet(void) const
Check if it is safe to call Get method.
bool IsSource(void) const
Check if variant Source is selected.
bool IsSetBiomol(void) const
Check if a value has been assigned to Biomol data member.
const Tdata & Get(void) const
Get the member data.
const TDesc & GetDesc(void) const
Get the Desc member data.
bool IsSetDesc(void) const
used only for stand alone Seq-annots Check if a value has been assigned to Desc data member.
TBiomol GetBiomol(void) const
Get the Biomol member data.
const TFtable & GetFtable(void) const
Get the variant data.
const TData & GetData(void) const
Get the Data member data.
const TMolinfo & GetMolinfo(void) const
Get the variant data.
@ e_Ncbieaa
extended ASCII 1 letter aa codes
@ e_Ncbistdaa
consecutive codes for std aas
@ eBiomol_pre_RNA
precursor RNA of any sort really
@ eBiomol_cRNA
viral RNA genome copy intermediate
@ eBiomol_snoRNA
small nucleolar RNA
@ eBiomol_genomic_mRNA
reported a mix of genomic and cdna sequence
@ eBiomol_transcribed_RNA
transcribed RNA other than existing classes
@ eBiomol_other_genetic
other genetic material
@ e_Molinfo
info on the molecule and techniques
@ eMol_na
just a nucleic acid
unsigned int
A callback function used to compare two keys in a database.
static void text(MDB_val *v)
const struct ncbi::grid::netcache::search::fields::SIZE size
void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)
static void s_AddComplement(string &cbString)
static size_t s_ComposeCodonRecognizedStr(const CTrna_ext &trna, string &recognized)
static void s_ReplaceUforT(string &codon)
static char s_MakeDegenerateBase(const string &str1, const string &str2)
size_t s_CountAccessions(const CUser_field &field)
static void s_MixStringAppend(const CSeq_loc &loc, string &mixString, bool &isOrdered)
static string s_GetCodeBreak(const CSeq_interval &intv, bool checkStrand=true)
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4