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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/featedit_util.cpp Source File

vector<CConstRef<CObject> > objs;

(

->IsSetProduct()) {

objs.push_back(

);

.

(

->GetOriginalSeq_feat());

objs.push_back(

);

.

(

->GetOriginalSeq_feat());

objs.push_back(

);

.

(

->GetOriginalSeq_feat());

objs.push_back(

);

vector<CRef<CApplyObject> > objs;

vector<CConstRef<CObject> > feats =

(bsh);

vector<CRef<CApplyObject> > objs;

vector<CConstRef<CObject> > feats =

(bsh);

new_feat->

().SetGene();

(*it)->GetLabel(&

);

(!

.empty()) {

rval +=

+

;

:

);

rval = (

)

+ (partial3 ?

:

)

+

+ (partial5 ?

:

)

rval = (partial5 ?

:

)

+

+ (partial3 ?

:

)

( (*it)->IsInt()) {

(

);

((*it)->GetQual() ==

&& !((*it)->GetVal()).empty()) {

rval += (*it)->GetVal() +

;

member_name = sTitle;

(pos != string::npos) {

member_name = member_name.substr(0, pos);

member_name = member_name.substr(5);

member_name = member_name.substr(5);

current = (*iter)->GetVal();

(*iter)->SetVal(current);

in_out_feat.

().push_back(qual);

CSeq_feat::TQual::iterator it = in_out_feat.

().begin();

(it != in_out_feat.

().end()) {

it = in_out_feat.

().erase(it);

&& (*it)->IsSetVal()) {

+= (*it)->GetVal() +

;

vector<string> problems;

any_errors =

;

(vector<string>, it, values) {

problems.push_back(

);

(div == string::npos) {

=

;

start_str = (*it).substr(0, div);

end_str = (*it).substr(div + 2);

range_end =

(

[pos]);

=

;

(pos <

.size()) {

(range_start < 1 || range_end < 1) {

=

;

}

((

)range_start >

[pos]) {

=

;

}

((

)range_end >

[pos]) {

=

;

problems.push_back(

);

(!

(*it) && !

(*it) && *it !=

&& *it !=

&& *it !=

&& *it !=

) {

vector<string> problems;

any_errors =

;

(vector<string>, it, values) {

problems.push_back(

);

problems.push_back(

);

newValue(

);

type_added(

);

(newValue);

proper_type(

);

current_type, current_name;

(*iter)->SetVal(current_type +

+ current_name);

in_out_feat.

().push_back(qual);

current_type, current_name;

(*iter)->SetVal(current_type +

+ current_name);

in_out_feat.

().push_back(qual);

CSeq_feat::TQual::iterator it = in_out_feat.

().begin();

(it != in_out_feat.

().end()) {

(!(*it)->IsSetVal()) {

it = in_out_feat.

().erase(it);

(newValue.empty()) {

it = in_out_feat.

().erase(it);

(*it)->SetVal(newValue);

field.substr(0, pos);

field.substr(pos + 1,

);

+=

+ newValue;

in_out_feat.

().push_back(qual);

CSeq_feat::TQual::iterator it = in_out_feat.

().begin();

(it != in_out_feat.

().end()) {

it = in_out_feat.

().erase(it);

+= (*it)->GetVal() +

;

=

.substr(0,

.length() - 1);

vector<string> sorted;

sorted.assign(values.begin(), values.end());

stable_sort(sorted.begin(), sorted.end());

(sorted.size() < 2) {

vector<string>::iterator it_p = sorted.begin();

vector<string>::iterator it_n = it_p;

match_count = 0;

(it_n != sorted.end()) {

it_n = sorted.erase(it_n);

(match_count == 0) {

it_p = sorted.erase(it_p);

(match_count == 0) {

vector<string> sorted;

sorted.assign(values.begin(), values.end());

stable_sort(sorted.begin(), sorted.end());

(sorted.size() < 2) {

vector<string>::iterator it_p = sorted.begin();

vector<string>::iterator it_n = it_p;

(it_n != sorted.end()) {

it_n = sorted.erase(it_n);

vector<string> problems;

any_errors =

;

(vector<string>, it, values) {

problems.push_back(

+

());

=

;

(vector<string>, sit, sorted) {

problems.push_back(

+

());

problems.push_back(

);

.SetRnaProductName(product, remainder);

current =

.GetRnaProductName();

.SetRnaProductName(current, remainder);

vector<CRef<CApplyObject> > objs;

vector<CConstRef<CObject> > feats =

(bsh);

->Assign(*(bsh.

().front().GetSeqId()));

new_feat->

().SetProt();

(

->IsSetProduct()) {

objs.insert(objs.end(), p_objs.begin(), p_objs.end());

vector<CConstRef<CObject> > feats =

(bsh);

in_out_feat.

().SetProt().SetName().front() = current;

in_out_feat.

().SetProt().SetName().push_back(newValue);

in_out_feat.

().SetProt().SetName().push_back(newValue);

in_out_feat.

().SetProt().ResetName();

vector<CRef<CApplyObject> > objs;

edit::ApplyCDSFrame::ECdsFrame

= edit::ApplyCDSFrame::s_GetFrameFromName(newValue);

edit::ApplyCDSFrame::s_SetCDSFrame(in_out_feat,

, *

);

in_out_feat.

().SetCdregion().ResetFrame();

in_out_feat.

().SetCdregion().SetCode().SetId(gc);

(

exception&)

in_out_feat.

().SetCdregion().ResetCode();

in_out_feat.

().SetGene().SetDesc(current);

in_out_feat.

().SetProt().SetDesc(current);

in_out_feat.

().SetGene().ResetDesc();

in_out_feat.

().SetProt().ResetDesc();

in_out_feat.

().SetGene().SetLocus(current);

in_out_feat.

().SetGene().SetLocus_tag(current);

in_out_feat.

().SetGene().SetMaploc(current);

in_out_feat.

().SetGene().SetSyn().front() = newValue;

in_out_feat.

().SetGene().SetSyn().push_back(newValue);

in_out_feat.

().SetGene().SetAllele(current);

in_out_feat.

().SetLocus_tag(current);

in_out_feat.

().SetLocus_tag(newValue);

in_out_feat.

().SetSyn().front() = newValue;

in_out_feat.

().SetGene().ResetLocus();

in_out_feat.

().SetGene().ResetLocus_tag();

in_out_feat.

().SetGene().ResetMaploc();

in_out_feat.

().SetGene().ResetSyn();

in_out_feat.

().SetGene().ResetAllele();

}

( in_out_feat.

()) {

((*it)->IsSetData() && (*it)->GetData().IsGene()) {

gene_ref = &((*it)->GetData().GetGene());

vector<CRef<CApplyObject> > objs;

in_out_feat.

().SetProt().SetName().front() = current;

in_out_feat.

().SetProt().SetName().push_back(newValue);

current = *it;

in_out_feat.

().SetProt().SetEc().push_back(newValue);

current = *it;

in_out_feat.

().SetProt().SetActivity().push_back(newValue);

in_out_feat.

().SetProt().ResetName();

in_out_feat.

().SetProt().ResetEc();

in_out_feat.

().SetProt().ResetActivity();

in_out_feat.

().SetRna().SetExt().SetGen().SetClass(newValue);

in_out_feat.

().SetRna().SetExt().SetGen().ResetClass();

(

feat_it(entry); feat_it; ++feat_it) {

(feat_it->IsSetId()) {

&

= feat_it->GetId();

(

.IsLocal() &&

.GetLocal().IsId() &&

.GetLocal().

() > feat_id) {

}

(

exception& e) {

->SetColumns().push_back(id_col);

->SetColumns()[0]->SetData().SetId().push_back(

);

vector<CRef<CSeqTable_column> > column_list;

need_gene =

;

need_mrna =

;

need_prot =

;

(vector<string>, sit, fields) {

field_list.push_back(featcol);

id_string =

->GetColumns()[1]->GetData().GetString()[

];

=

->GetOriginalSeq_feat();

(

= 0;

< field_list.size();

++) {

= field_list[

]->GetFromFeat(*gene);

= field_list[

]->GetFromFeat(*mrna);

= field_list[

]->GetFromFeat(*

);

any_change =

;

need_gene =

;

need_mrna =

;

need_prot =

;

(

col = 2; col <

->GetColumns().

(); col++) {

title =

->GetColumns()[col]->GetHeader().GetTitle();

field_list.push_back(featcol);

id_string =

->GetColumns()[1]->GetData().GetString()[

];

=

->GetOriginalSeq_feat();

new_gene->

(*gene);

new_gene->

().SetGene();

new_mrna->

(*mrna);

changed_feat =

;

changed_gene =

;

changed_mrna =

;

changed_prot =

;

(

col = 2; col <

->GetColumns().

(); col++) {

title =

->GetColumns()[col]->GetHeader().GetTitle();

new_val =

->GetColumns()[col]->GetData().GetString()[

];

orig_val =

;

orig_val = field_list[col - 2]->GetFromFeat(*gene);

field_list[col - 2]->ClearInFeature(*new_gene);

changed_gene =

;

orig_val =

;

orig_val = field_list[col - 2]->GetFromFeat(*mrna);

field_list[col - 2]->ClearInFeature(*new_mrna);

changed_mrna =

;

orig_val =

;

orig_val = field_list[col - 2]->GetFromFeat(*

);

field_list[col - 2]->ClearInFeature(*new_prot);

changed_prot =

;

orig_val = field_list[col - 2]->GetFromFeat(*(orig_feat.

()));

field_list[col - 2]->ClearInFeature(*new_feat);

changed_feat =

;

loc->

().SetFrom(from);

loc->

().SetTo(to);

loc->

().SetId().Assign(*bioseq->

().front());

rna_ref->

().SetGen().SetProduct(name);

->SetData().SetRna().Assign(*rna_ref);

->SetLocation().Assign(*loc);

(ispartial5 || ispartial3)

->SetPartial(

);

rna_ref->

().SetName(name);

->SetData().SetRna().Assign(*rna_ref);

->SetLocation().Assign(*loc);

(ispartial5 || ispartial3)

->SetPartial(

);

( ; b_iter ; ++b_iter){

partial5 =

;

partial3 =

;

( ; b_iter ; ++b_iter){

new_feat->

().SetImp().SetKey(

);

partial5 =

;

partial3 =

;

( ; b_iter ; ++b_iter){

new_feat->

().SetImp().SetKey(

);

new_feat->

().push_back(qual1);

new_feat->

().push_back(qual2);

User-defined methods of the data storage class.

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat &new_prot, const CSeq_feat &cds)

AdjustProteinFeaturePartialsToMatchCDS A function to change an existing MolInfo to match a coding reg...

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(objects::CBioseq_Handle bsh)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

static CRef< CFeatureSeqTableColumnBase > Create(const string &sTitle, objects::CSeqFeatData::ESubtype subtype=objects::CSeqFeatData::eSubtype_any)

virtual vector< CConstRef< CObject > > GetObjects(objects::CBioseq_Handle bsh)

objects::CSeqFeatData::ESubtype m_Subtype

void SetMajorType(objects::CSeqFeatData::E_Choice major_type)

virtual vector< CRef< objects::edit::CApplyObject > > GetRelatedGeneApplyObjects(objects::CBioseq_Handle bsh)

objects::CSeqFeatData::E_Choice m_MajorType

void SetSubtype(objects::CSeqFeatData::ESubtype subtype)

virtual vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(objects::CBioseq_Handle bsh)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

@Gb_qual.hpp User-defined methods of the data storage class.

static string IndexToCodon(int index)

static bool IsGeneRefField(string qual)

static EFieldType x_GetFieldTypeFromString(string qual)

CGeneRefColumn(string qual)

virtual vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(objects::CBioseq_Handle bsh)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(objects::CBioseq_Handle bsh)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

static EFieldType x_GetFieldTypeFromString(string qual)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

static bool IsProtRefField(string qual)

CProtRefColumn(string qual)

@RNA_ref.hpp User-defined methods of the data storage class.

string GetRnaProductName(void) const

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

CRptUnitRangeColumn(const vector< size_t > lens)

virtual vector< string > IsValid(const vector< string > &values)

virtual vector< string > IsValid(const vector< string > &values)

string x_GetSatelliteName(const string &field) const

string x_AddSatellitePrefix(const string &value, objects::edit::EExistingText existing_text) const

bool x_AddSatelliteName(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

bool x_AddSatelliteType(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

CSatelliteColumn(const string &satellite_field)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

void x_ClearSatelliteSubFields(objects::CSeq_feat &in_out_feat) const

string x_GetSatelliteType(const string &field) const

bool x_IsQualAMatch(const CGb_qual &qual) const

virtual void ClearInFeature(objects::CSeq_feat &in_out_feat)

virtual string GetLabel() const

virtual bool RelaxedMatch(const objects::CSeq_feat &f1, const objects::CSeq_feat &f2) const

virtual vector< string > IsValid(const vector< string > &values)

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

virtual bool AddToFeature(objects::CSeq_feat &in_out_feat, const string &newValue, objects::edit::EExistingText existing_text)

ESubtype GetSubtype(void) const

static E_Choice GetTypeFromSubtype(ESubtype subtype)

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

CSeq_feat_EditHandle –.

namespace ncbi::objects::

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

void SetGeneXref(CGene_ref &value)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStart(ESeqLocExtremes ext) const

bool IsPartialStart(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

CSeq_feat_Handle GetFeatureWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

virtual string GetFromFeat(const objects::CSeq_feat &in_out_feat)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

vector< string > FindNonUniqueStrings(const vector< string > &values)

static const int kNumIgnoreColumns

vector< string > SortUniqueStrings(const vector< string > &values)

USING_SCOPE(ncbi::objects)

CRef< CSeq_feat > AddMiscRNA(const CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)

CRef< CSeq_feat > AddRibosomalRNA(const CBioseq_Handle &bsh, string name, int from, int to, bool ispartial5, bool ispartial3)

CRef< CSeq_loc > CreateFeatLocation(const CBioseq_Handle &bsh, int from, int to, bool ispartial5, bool ispartial3)

void SetRnaProductName(CRNA_ref &rna, const string &product, string &remainder, EExistingText existing_text)

CRef< CCmdComposite > ApplyFeatureSeqTableToSeqEntry(CRef< CSeq_table > table, CSeq_entry_Handle entry)

CRef< CCmdComposite > AddNamedrRna(CSeq_entry_Handle entry, string rna_name, bool ispartial5, bool ispartial3)

static const string kIgnoreColumns[]

CSeq_feat_Handle GetFeatureFromTableId(const string &id_string, CSeq_entry_Handle entry)

void AddToFeatureIdColumn(CSeq_feat_Handle feat, CRef< CSeqTable_column > column, size_t row, int &top_id)

static bool IsAllRptUnitSeqChars(string seq)

int FindHighestFeatureId(const CSeq_entry_Handle &entry)

CRef< CSeq_table > BuildFeatureSeqTableFromSeqEntry(CSeq_entry_Handle entry, const SAnnotSelector &sel)

CRef< CCmdComposite > CreateControlRegion(CSeq_entry_Handle entry)

CRef< CCmdComposite > CreateMicrosatellite(CSeq_entry_Handle entry)

void AddColumnsToFeatureTable(const vector< string > &fields, CRef< CSeq_table > table, CSeq_entry_Handle entry)

string GetIntervalString(const CSeq_interval &seq_int)

vector< CRef< CFeatureSeqTableColumnBase > > TFeatureSeqTableColumnList

static const int kNumSatelliteTypes

const string kPartialStart

static const string kSatelliteTypes[]

const string kPartialStop

const string kStopColLabel

const string kStartColLabel

const char * kSequenceIdColLabel

static const char * column

#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 LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

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,...

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

CConstRef< CSeq_feat > GetOverlappingmRNA(const CSeq_loc &loc, CScope &scope)

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

const CFeat_id & GetId(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

const CTSE_Handle & GetTSE_Handle(void) const

virtual const CSeq_loc & GetProduct(void) const

bool IsSetProduct(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

virtual const CSeq_loc & GetLocation(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from the TSE of this Seq-entry.

void SetFeatId(int id)

Set single feature id.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

const TId & GetId(void) const

const CSeq_loc & GetLocation(void) const

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

CTempString substr(size_type pos) const

Obtain a substring from this string, beginning at a given offset.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

@ fAllowTrailingSpaces

Ignore trailing whitespace characters.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

@ eNocase

Case insensitive compare.

static const char label[]

bool IsSetSyn(void) const

synonyms for locus Check if a value has been assigned to Syn data member.

const TSyn & GetSyn(void) const

Get the Syn member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

bool IsSetDesc(void) const

descriptive name Check if a value has been assigned to Desc data member.

bool IsSetAllele(void) const

Official allele designation Check if a value has been assigned to Allele data member.

bool IsSetMaploc(void) const

descriptive map location Check if a value has been assigned to Maploc data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

const TAllele & GetAllele(void) const

Get the Allele member data.

const TMaploc & GetMaploc(void) const

Get the Maploc member data.

bool IsId(void) const

Check if variant Id is selected.

TId GetId(void) const

Get the variant data.

bool IsSetDesc(void) const

description (instead of name) Check if a value has been assigned to Desc data member.

const TActivity & GetActivity(void) const

Get the Activity member data.

const TName & GetName(void) const

Get the Name member data.

bool IsSetEc(void) const

E.C.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetActivity(void) const

activities Check if a value has been assigned to Activity data member.

const TEc & GetEc(void) const

Get the Ec member data.

const TQuals & GetQuals(void) const

Get the Quals member data.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

const TCodon & GetCodon(void) const

Get the Codon member data.

bool IsTRNA(void) const

Check if variant TRNA is selected.

void SetExt(TExt &value)

Assign a value to Ext data member.

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

const Tdata & Get(void) const

Get the member data.

bool IsGen(void) const

Check if variant Gen is selected.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

bool CanGetAnticodon(void) const

Check if it is safe to call GetAnticodon method.

void SetType(TType value)

Assign a value to Type data member.

const TGen & GetGen(void) const

Get the variant data.

bool IsSetClass(void) const

for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value h...

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

bool CanGetCodon(void) const

Check if it is safe to call GetCodon method.

bool CanGetQuals(void) const

Check if it is safe to call GetQuals method.

const TClass & GetClass(void) const

Get the Class member data.

void SetHeader(THeader &value)

Assign a value to Header data member.

@ eField_id_location_id

location Seq-id

bool CanGetDbxref(void) const

Check if it is safe to call GetDbxref method.

bool CanGetExp_ev(void) const

Check if it is safe to call GetExp_ev method.

const TVal & GetVal(void) const

Get the Val member data.

bool IsSetComment(void) const

Check if a value has been assigned to Comment data member.

void ResetPartial(void)

Reset Partial data member.

bool IsSetQual(void) const

qualifiers Check if a value has been assigned to Qual data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TRegion & GetRegion(void) const

Get the variant data.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void ResetExcept(void)

Reset Except data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TLocal & GetLocal(void) const

Get the variant data.

void ResetExcept_text(void)

Reset Except_text data member.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

void SetExcept(TExcept value)

Assign a value to Except data member.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGene(void) const

Check if variant Gene is selected.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

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 TCode & GetCode(void) const

Get the Code member data.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

void SetData(TData &value)

Assign a value to Data data member.

void ResetComment(void)

Reset Comment data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetQual(void) const

Check if a value has been assigned to Qual data member.

const TComment & GetComment(void) const

Get the Comment member data.

const TGene & GetGene(void) const

Get the variant data.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

const TProt & GetProt(void) const

Get the variant data.

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

const TRna & GetRna(void) const

Get the variant data.

void ResetDbxref(void)

Reset Dbxref data member.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetVal(void) const

Check if a value has been assigned to Val data member.

bool IsRna(void) const

Check if variant Rna is selected.

TExp_ev GetExp_ev(void) const

Get the Exp_ev member data.

bool IsRegion(void) const

Check if variant Region is selected.

bool IsSetFrame(void) const

Check if a value has been assigned to Frame data member.

@ e_not_set

No variant selected.

@ eExp_ev_experimental

any reasonable experimental check

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

bool IsMix(void) const

Check if variant Mix is selected.

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

const Tdata & Get(void) const

Get the member data.

TStrand GetStrand(void) const

Get the Strand member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TMix & GetMix(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

@ eMol_na

just a nucleic acid

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

Utility macros and typedefs for exploring NCBI objects from seqset.asn.

bool QualifierNamesAreEquivalent(string name1, string name2)

CRef< CSeqTable_column > AddStringColumnToTable(CRef< CSeq_table > table, string label)

void AddValueToColumn(CRef< CSeqTable_column > column, string value, size_t row, edit::EExistingText existing_text=edit::eExistingText_replace_old)

void FillShortColumns(CRef< objects::CSeq_table > values_table)

#define row(bind, expected)

@ eExistingText_replace_old

bool AddValueToString(string &str, const string &value, EExistingText existing_text)

Add text to an existing string, using the "existing_text" directive to combine new text with existing...

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