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NCBI C++ ToolKit: src/objtools/validator/validerror_format.cpp Source File

rval =

;

rval =

;

rval =

;

rval =

;

rval =

;

rval =

;

rval =

;

rval =

;

(use_geo_loc_name) {

rval =

;

rval =

;

(

.GetErrIndex()) {

(

(

,

) != string::npos) {

(

(

,

) != string::npos) {

}

(

(

,

) != string::npos) {

rval =

;

}

(

(

,

) != string::npos) {

rval =

;

position_pos =

(

,

);

(position_pos == string::npos || other_clue == string::npos) {

(position_pos != string::npos) {

pos_str =

.substr(position_pos);

(sscanf(pos_str.c_str(),

, &pos) == 1) {

seq_pos =

(pos_str,

);

(seq_pos != string::npos) {

rval = pos_str.substr(seq_pos + 4) +

+ rval;

pos_str =

.substr(position_pos);

(sscanf(pos_str.c_str(),

, &pos1, &pos2) == 2) {

seq_pos =

(pos_str,

);

(seq_pos != string::npos) {

rval = pos_str.substr(seq_pos + 4) +

+ rval;

obj_desc =

.GetObjDesc();

type_pos =

(obj_desc,

);

(type_pos != string::npos) {

obj_desc = obj_desc.substr(type_pos + 9);

space_pos =

(obj_desc,

);

(space_pos != string::npos) {

obj_desc = obj_desc.substr(0, space_pos);

rval = obj_desc +

+ rval;

(type_pos != string::npos) {

=

.substr(type_pos + prefix.length());

(type_pos != string::npos) {

=

.substr(0, type_pos);

obj_desc =

.GetObjDesc();

obj_desc =

.GetObj_content();

(

.IsSetLocation()) {

obj_desc +=

+

.GetLocation();

(

.IsSetLocus_tag()) {

obj_desc +=

+

.GetLocus_tag();

}

(

.IsSetObject() &&

.GetObject().GetThisTypeInfo() == CSeq_feat:: GetTypeInfo()) {

close_pos =

(obj_desc,

);

(close_pos != string::npos) {

obj_desc = obj_desc.substr(0, close_pos);

rval =

.GetAccession() +

+ obj_desc;

(

.GetObject().GetThisTypeInfo() != CSeq_feat::GetTypeInfo()) {

((*it)->IsSetQual() &&

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

ec_numbers =

;

rval =

.GetAccnver() +

+ ec_numbers +

+ locus_tag +

+ prot_name;

((*it)->IsSetSubtype() &&

(*it)->IsSetSubname() &&

rval += (*it)->GetSubname();

kAlternateName =

;

spec_host =

.GetMsg().substr(kAlternateName.length());

}

(

.GetObject().GetThisTypeInfo() == CSeqdesc::GetTypeInfo()) {

}

(

.GetObject().GetThisTypeInfo() == CSeq_feat::GetTypeInfo()) {

rval =

.GetAccession() +

+ spec_host;

((*it)->IsSetSubtype() &&

(*it)->IsSetSubname() &&

pos =

((*it)->GetSubname(),

);

(pos != string::npos) {

= (*it)->GetSubname().substr(0, pos);

(

.GetObject().GetThisTypeInfo() == CSeqdesc::GetTypeInfo()) {

(

.GetObject().GetThisTypeInfo() == CSeq_feat::GetTypeInfo()) {

rval =

.GetAccession() +

+ codes;

(err_code == vit->GetErrIndex()) {

rval += this_val +

;

rval += this_val +

;

rval =

.GetAccession() +

+

.GetMsg();

vector<CValidErrItem::TErrIndex> list;

list.push_back(vit->GetErrIndex());

(list.begin(), list.end());

list.erase(unique(list.begin(), list.end()), list.end());

list.push_back(this_val);

(vector<CValidErrItem::TErrIndex>, it, codes) {

list.push_back(this_val);

(object_id.

()) {

}

(object_id.

()) {

feature_id = object_id.

();

(

& id_it : ft.

()) {

(pos != string::npos &&

.c_str()[pos + 1] != 0 &&

.c_str()[pos + 1] !=

) {

=

.substr(0, pos + 1) +

+

.substr(pos + 1);

(pos != string::npos &&

.c_str()[pos + 1] != 0 &&

.c_str()[pos + 1] !=

) {

=

.substr(0, pos + 1) +

+

.substr(pos + 1);

org.

().front()->GetLabel(&content);

prefix(

);

tlabel += prefix + (**it).GetQual();

(!(**it).GetVal().empty()) {

tlabel +=

+ (**it).GetVal();

(tlabel.empty()) {

content_label;

content_label =

;

=

+

+

;

content_label =

+ content_label.substr(

.length());

content_label =

;

content_label =

+ content_label.substr(6);

content_label =

+ content_label.substr(6);

content_label =

+ content_label.substr(6);

content_label;

(! suppress_context && scope) {

(li && ! hnd) {

}

(

std::exception&) {

(suppress_context) {

(loc_label.size() > 800) {

loc_label.replace(797,

,

);

(!loc_label.empty()) {

(suppress_context) {

(loc_label.size() > 800) {

loc_label.replace(795,

,

);

desc =

;

desc += content_label;

desc +=

+ feature_id +

;

desc +=

+ loc_label +

;

desc += bioseq_label;

desc += product_label;

(ds.

()) {

content =

+ content.substr(8);

content =

+ content.substr(10);

content =

;

content =

;

= content.substr(0, 1);

content =

+ content.substr(1);

colon_pos =

(content,

);

(colon_pos != string::npos) {

dash_pos =

(content.substr(0, colon_pos),

);

(dash_pos != string::npos) {

after_dash = content.substr(dash_pos + 1, 1);

content = content.substr(0, dash_pos) + after_dash + content.substr(dash_pos + 2);

content =

+ content.substr(10);

content =

+ content.substr(6);

content =

+ content.substr(5);

content =

+ content.substr(4);

desc(

);

(

.IsSeq()) {

isSetClass =

.IsSetClass();

suppress_context = suppress_context || !isSetClass;

=

;

(!suppress_context) {

&

= tv->FindName(setClass,

);

+=

;

temporary(accession);

=

;

(

: suppressedCodes) {

(

: suppressedCodes) {

(

: suppressedCodes) {

(

: suppressedCodes) {

(

it : errors.

()) {

(it->IsSetLocus_tag()) {

(it->IsSetObjectType() &&

it->IsSetObject() &&

it->GetObject().GetThisTypeInfo() == CSeq_feat::GetTypeInfo()) {

(

&&

->IsSetLocus_tag()) {

rval = &

->GetLocus_tag();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eErr_SEQ_FEAT_NotSpliceConsensusAcceptor

@ eErr_SEQ_FEAT_EcNumberProblem

@ eErr_SEQ_FEAT_NotSpliceConsensusDonor

@ eErr_SEQ_DESCR_LatLonWater

@ eErr_SEQ_DESCR_LatLonCountry

@ eErr_SEQ_FEAT_NotSpliceConsensusAcceptorTerminalIntron

@ eErr_SEQ_FEAT_ReplacedEcNumber

@ eErr_SEQ_FEAT_NotSpliceConsensusDonorTerminalIntron

@ eErr_SEQ_FEAT_BadEcNumberValue

@ eErr_SEQ_DESCR_BadInstitutionCode

@ eErr_SEQ_FEAT_NotSpliceConsensus

@ eErr_SEQ_DESCR_LatLonGeoLocName

@ eErr_SEQ_FEAT_SplitEcNumber

@ eErr_SEQ_FEAT_RareSpliceConsensusDonor

@ eErr_SEQ_FEAT_DeletedEcNumber

@ eErr_SEQ_FEAT_BadEcNumberFormat

@ eErr_SEQ_DESCR_BadSpecificHost

void GetLabel(string *label, ELabelType type, bool worst=false) const

void GetLabel(string *label) const

Exceptions for objmgr/util library.

void GetLabel(string *label) const

bool GetLabel(string *label, TLabelFlags flags=0, ELabelVersion version=eLabel_DefaultVersion) const override

Append a label to "label" based on content.

ESubtype GetSubtype(void) const

namespace ncbi::objects::

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

void GetLabel(string *const label, ELabelType label_type) const

static bool NCBI_UseGeoLocNameForCountry(void)

Template class for iteration on objects of class C (non-medifiable version)

static const string & ConvertErrCode(unsigned int)

string x_FormatBadSpecificHostForSubmitterReport(const CValidErrItem &error) const

static void AddSuppression(CUser_object &user, CValidErrItem::TErrIndex err_code)

string FormatCategoryForSubmitterReport(const CValidError &errors, CScope &scope, ESubmitterFormatErrorGroup grp) const

string x_FormatBadInstCodeForSubmitterReport(const CValidErrItem &error) const

ESubmitterFormatErrorGroup GetSubmitterFormatErrorGroup(CValidErrItem::TErrIndex err_code) const

static string GetFeatureBioseqLabel(const CSeq_feat &ft, CRef< CScope > scope, bool suppress_context)

static string GetDescriptorContent(const CSeqdesc &ds)

static string GetFeatureLocationLabel(const CSeq_feat &ft, CRef< CScope > scope, bool suppress_context)

static string GetFeatureProductLocLabel(const CSeq_feat &ft, CRef< CScope > scope, bool suppress_context)

static string GetDescriptorLabel(const CSeqdesc &ds, const CSeq_entry &ctx, CRef< CScope > scope, bool suppress_context)

string x_FormatConsensusSpliceForSubmitterReport(const CValidErrItem &error) const

string x_FormatLatLonCountryForSubmitterReport(const CValidErrItem &error) const

string GetSubmitterFormatErrorGroupTitle(CValidErrItem::TErrIndex err_code) const

vector< string > FormatCompleteSubmitterReport(const CValidError &errors, CScope &scope) const

static void SetSuppressionRules(const CUser_object &user, CValidError &errors)

vector< CValidErrItem::TErrIndex > GetListOfErrorCodes(const CValidError &errors) const

static string GetFeatureContentLabel(const CSeq_feat &feat, CRef< CScope > scope)

static string GetObjectLabel(const CObject &obj, const CSeq_entry &ctx, CRef< CScope > scope, bool suppress_context)

string x_FormatECNumberForSubmitterReport(const CValidErrItem &error, CScope &scope) const

static const string & x_GetLocusTag(const CSeq_feat &sf, CScope &scope)

static string GetFeatureLabel(const CSeq_feat &ft, CRef< CScope > scope, bool suppress_context)

static void AddLocusTags(CValidError &errors, CScope &scope)

static string GetFeatureIdLabel(const CSeq_feat &ft)

string FormatForSubmitterReport(const CValidErrItem &error, CScope &scope) const

static string GetBioseqLabel(CBioseq_Handle bh)

static string GetBioseqSetLabel(const CBioseq_set &st, CRef< CScope > scope, bool suppress_context)

string x_FormatGenericForSubmitterReport(const CValidErrItem &error, CScope &scope) const

static void AddSuppression(CUser_object &user, TErrCode errCode)

static void SetSuppressedCodes(const CUser_object &user, TCodes &errCodes)

void SuppressError(unsigned int ec)

Include a standard set of the NCBI C++ Toolkit most basic headers.

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ENUM_METHOD_NAME(EnumName)

string GetLabel(const CSeq_id &id)

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

Override Assign() to incorporate cache invalidation.

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

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,...

void ChangeSeqLocId(CSeq_loc *loc, bool best, CScope *scope)

Change each of the CSeq_ids embedded in a CSeq_loc to the best or worst CSeq_id accoring to the value...

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.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

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

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

Check if a string starts with a specified prefix value.

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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

static const char label[]

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org 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...

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member 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.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetClass(void) const

endeavor which designed this object Check if a value has been assigned to Class data member.

const TClass & GetClass(void) const

Get the Class member data.

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.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

TId GetId(void) const

Get the variant data.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

bool IsSetCommon(void) const

common name Check if a value has been assigned to Common data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TCommon & GetCommon(void) const

Get the Common member data.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetMod(void) const

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

list< CRef< COrgMod > > TMod

bool IsSetOrgname(void) const

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

bool IsSetTaxname(void) const

preferred formal name Check if a value has been assigned to Taxname data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_nat_host

natural host of this specimen

@ eSubtype_specimen_voucher

@ eSubtype_culture_collection

const TName & GetName(void) const

Get the Name member data.

bool IsSetEc(void) const

E.C.

TProcessed GetProcessed(void) const

Get the Processed member data.

bool IsSetProcessed(void) const

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

bool IsSetName(void) const

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

const TEc & GetEc(void) const

Get the Ec member data.

@ eProcessed_signal_peptide

@ eProcessed_transit_peptide

const TKey & GetKey(void) const

Get the Key member data.

bool IsSetComment(void) const

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

const TData & GetData(void) const

Get the Data member data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data 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 IsProt(void) const

Check if variant Prot is selected.

const TIds & GetIds(void) const

Get the Ids member data.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetKey(void) const

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

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

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.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsSetIds(void) const

set of Ids; will replace 'id' field Check if a value has been assigned to Ids data member.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsSetId(void) const

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

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

bool IsGeneral(void) const

Check if variant General is selected.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

const TImp & GetImp(void) const

Get the variant data.

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

@ e_Pub

publication applies to this seq

const TUser & GetUser(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

E_Choice Which(void) const

Which variant is currently selected.

const TPub & GetPub(void) const

Get the Pub member data.

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Comment

a more extensive comment

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

TErrs & SetErrs(void)

Assign a value to Errs data member.

constexpr auto sort(_Init &&init)

const string version

version string

const struct ncbi::grid::netcache::search::fields::KEY key

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

static string s_GetFeatureIdLabel(const CObject_id &object_id)

string s_GetInstCodeFromBioSource(const CBioSource &biosrc)

static void s_FixBioseqLabelProblems(string &str)

static const string kSuppressFieldLabel

static bool s_IsSuppressField(const CUser_field &field)

void RemoveSuffix(string &str, const string &suffix)

void RemovePrefix(string &str, const string &prefix)

static string s_GetOrgRefContentLabel(const COrg_ref &org)

string s_GetSpecificHostFromBioSource(const CBioSource &biosrc)

static string s_GetFeatureContentLabelExtras(const CSeq_feat &feat)

static string s_GetCdregionContentLabel(const CSeq_feat &feat, CRef< CScope > scope)

static string s_GetBioSourceContentLabel(const CBioSource &bsrc)

ESubmitterFormatErrorGroup

@ eSubmitterFormatErrorGroup_BadInstitutionCode

@ eSubmitterFormatErrorGroup_BadEcNumberValue

@ eSubmitterFormatErrorGroup_ConsensusSplice

@ eSubmitterFormatErrorGroup_BadEcNumberProblem

@ eSubmitterFormatErrorGroup_BadEcNumberFormat

@ eSubmitterFormatErrorGroup_Default

@ eSubmitterFormatErrorGroup_LatLonCountry

@ eSubmitterFormatErrorGroup_BadSpecificHost

static CS_CONTEXT * context

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