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NCBI C++ ToolKit: src/misc/discrepancy/discrepancy_case.cpp Source File

& node = m_Objs[

].Info();

node.Add(*

.BioseqObjRef());

m_Objs[

];

& node = m_Objs[

].Info();

node.Add(*

.BioseqObjRef());

(

& id_it : seq.

()) {

& seq_id = *id_it;

m_Objs[

].Add(*

.BioseqObjRef()).Fatal();

(protein_id_prefix.

()) {

protein_id_prefix_lowercase = protein_id_prefix;

& canonical_forms_node = m_Objs[

][protein_id_prefix_lowercase];

canonical_protein_id_prefix;

(canonical_forms_node.

()) {

canonical_protein_id_prefix = protein_id_prefix;

canonical_forms_node[protein_id_prefix];

canonical_protein_id_prefix = canonical_forms_node.

().

()->first;

m_Objs[

][

+ canonical_protein_id_prefix].Fatal().Add(*

.BioseqObjRef());

( reports_collected.

().

() <= 1 ) {

(

& p: sum.

) {

details += (details.empty() ?

:

) + to_string(p.first) +

+ to_string(p.second);

m_Objs[

][sum.

+

+ details].Ext().Fatal().Add(*

.BioseqObjRef());

(!sum.

&& sum.

* 100. / sum.

> 5) {

m_Objs[

].Add(*

.BioseqObjRef());

*

[] = {

,

,

};

(INTERNAL_TRANSCRIBED_SPACER_RRNA, FEAT,

,

)

rna_name = feat.GetData().GetRna().GetRnaProductName();

m_Objs[

].Add(*

.SeqFeatObjRef(feat));

str1_has_similarity_word =

, str2_has_similarity_word =

;

str1_has_similarity_word =

;

str2_has_similarity_word =

;

(str1_has_similarity_word && str2_has_similarity_word) {

(

(product,

) != string::npos ||

(product,

) != string::npos) {

constraint.

(product);

*

=

;

*

=

;

*

=

;

(products.

(feat) == products.

()) {

name =

.GetProdForFeature(*feat);

products[feat];

& cds =

.FeatCDS();

(

= 0;

< cds.size();

++) {

& loc_i = cds[

]->GetLocation();

(

j =

+ 1; j < cds.size(); j++) {

& loc_j = cds[j]->GetLocation();

(prod_i.empty()) {

.ReplaceSeq_feat(*obj, *sf, *new_feat);

mol_info =

.GetMolinfo();

m_Objs[

].Add(*

.SeqFeatObjRef(feat));

(feat.GetData().IsRna() && !

.IsPseudo(feat)) {

(feat.GetData().GetSubtype()) {

& rna_ref = feat.GetData().GetRna();

& rna_ref = feat.GetData().GetRna();

(rna_ext.

()) {

(!feat.GetNamedQual(

).empty()) {

m_Objs[

].Add(*

.SeqFeatObjRef(feat),

);

*

=

;

*

=

;

*

=

;

*

=

;

& cds =

.FeatCDS();

(

= 0;

< cds.size();

++) {

& loc_i = cds[

]->GetLocation();

(

j =

+ 1; j < cds.size(); j++) {

& loc_j = cds[j]->GetLocation();

m_ReportItems = m_Objs[

].Export(*this)->GetSubitems();

new_feat->

().SetImp().SetKey(

);

(stringobj && !stringobj->

.empty()) {

.ReplaceSeq_feat(*obj, *sf, *new_feat);

* kMsg =

;

m_Objs[kMsg][

].Ext().Add(*

.BioseqObjRef());

m_Objs[kMsg][

].Ext().Add(*

.BioseqObjRef());

m_Objs[kMsg][

].Ext().Add(*

.BioseqObjRef());

m_Objs[kMsg][

].Ext().Add(*

.BioseqObjRef());

(

.IsSetClass()) {

(

.GetClass()) {

m_Objs[

].Add(*

.BioseqSetObjRef(

));

all_feat =

.GetAllFeat();

(all_feat.begin() == all_feat.end()) {

m_Objs[

].Add(*

.BioseqObjRef());

kSeqLength = 5000;

all_feat =

.GetAllFeat();

(all_feat.begin() == all_feat.end()) {

m_Objs[

].Add(*

.BioseqObjRef());

kSeqLength = 50000;

all_feat =

.GetAllFeat();

(all_feat.begin() == all_feat.end()) {

m_Objs[

].Add(*

.BioseqObjRef());

= 30;

(

= 0;

< seq_data.length();

++) {

(seq_data[

] ==

|| seq_data[

] ==

) {

stop = besh.GetInst_Length() - cut_from_end;

(start < stop && start + len > stop) {

seq_out = seq_in.substr(0, stop - start);

(start >= stop) {

seqmap_i = seqmap_i.

();

(feat.IsSetLocation()) {

(; loc_ci; ++loc_ci) {

m_Objs[

].Add(*

.SeqFeatObjRef(feat, &feat));

(new_loc_creator) {

new_loc_creator.

();

.ReplaceSeq_feat(*obj, *sf, *new_feat);

& gene_ref = feat->GetData().GetGene();

m_Objs[

].Fatal().Add(*

.SeqFeatObjRef(*feat));

(feat.IsSetData() && feat.GetData().IsGene()) {

& gene_ref = feat.GetData().GetGene();

m_Objs[

].Fatal().Add(*

.SeqFeatObjRef(feat));

& gene_ref = feat.GetData().GetGene();

(!locus_tag.empty() && !

.IsBadLocusTagFormat(locus_tag)) {

ss <<

<< prefix <<

;

m_Objs[ss.str()].Add(*

.SeqFeatObjRef(feat));

(m_Objs.GetMap().size() > 1) {

moltype =

;

(

&

: bioseq.

()) {

(id->Which()) {

& genes =

.FeatGenes();

& gene_ref = gene->GetData().GetGene();

(!locus_tag.empty() &&

.IsBadLocusTagFormat(locus_tag)) {

m_Objs[

].Fatal().Add(*

.SeqFeatObjRef(*gene));

m_Objs[

].Add(*

.BioseqSetObjRef());

m_Objs[

].Incr();

(

& ann : bioseq.

()) {

(ann->IsGraph()) {

m_Objs[

].Incr();

q = m_Objs[

].GetCount();

= m_Objs[

].GetCount() - q;

ret[

+ to_string(

) +

];

m_Objs[

].Add(*

.SeqFeatObjRef(feat));

=

;

(feat.GetExcept_text() ==

&& feat.IsSetComment() && feat.GetComment().find(

) != string::npos) {

& cdregion = feat.GetData().GetCdregion();

(feat.IsSetData() && feat.GetData().IsCdregion()) {

& locus = gene.

();

product =

.GetProdForFeature(feat);

genes[locus].push_back(make_pair(

.SeqFeatObjRef(feat), product));

(

& gene : genes) {

(gene.second.size() > 1) {

TGenesList::const_iterator cur_gene = gene.second.cbegin();

& product = cur_gene->second;

(++cur_gene; cur_gene != gene.second.cend(); ++cur_gene) {

& cur_product = cur_gene->second;

(product != cur_product) {

sub =

+ gene.first +

;

(

& rec : gene.second) {

m_Objs[

][sub].Ext().Add(*rec.first,

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ 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.

CBioseq_set_EditHandle –.

TSeqPos GetLength(void) const

bool IsSetLength(void) const

bool IsSkippable(void) const

TGeneLocusMap m_GeneLocusMap

static string GetBiomolName(CMolInfo::TBiomol biomol)

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

string GetRnaProductName(void) const

virtual vector< CRef< CReportItem > > GetSubitems() const =0

CRef< CReportItem > Export(CDiscrepancyCore &test, bool unique=true) const

Non-const iterator over CSeqMap (allows to edit the sequence).

namespace ncbi::objects::

static bool IsAa(EMol mol)

static string GetMoleculeClass(EMol mol)

static bool IsNa(EMol mol)

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

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

bool Match(const CMatchString &str) const

void SetMatch_text(const TMatch_text &value)

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

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

static const char * kRRNASpacer[]

static const char * kContainedOpps

static bool HasOverlapNote(const CSeq_feat &feat)

static bool HasContainedNote(const CSeq_feat &feat)

static const char * kIgnoreSimilarProductWords[]

static const string kDiscMessage

static bool SetOverlapNote(CSeq_feat &feat)

static const char * kContainedNote

static const char * kOverlap2

static const char * kOverlap1

static const char * kSimilarProductWords[]

static const size_t kNumIgnoreSimilarProductWords

static const string kInconsistent_Moltype

static bool ShouldIgnore(const string &product)

static const char * kOverlap0

static bool StrandsMatch(ENa_strand strand1, ENa_strand strand2)

static const char * kContainedSame

static const char * kContained

static const CSeq_id * GetProteinId(const CBioseq &seq)

static const size_t kRRNASpacer_len

static const string kOverlappingCDSNoteText

static bool ProductNamesAreSimilar(const string &product1, const string &product2)

static string GetProdName(const CSeq_feat *feat, map< const CSeq_feat *, string > &products, CDiscrepancyContext &context)

static const size_t kNumSimilarProductWords

#define DISCREPANCY_AUTOFIX(name)

#define DISCREPANCY_CASE(name, type, group, descr)

#define DISCREPANCY_SUMMARIZE(name)

unsigned int TSeqPos

Type for sequence locations and lengths.

constexpr size_t ArraySize(const Element(&)[Size])

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

Set object to copy of another one.

C * SerialClone(const C &src)

Create on heap a clone of the source object.

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

void Delete(void)

Delete current element, and make iterator to point to the next element.

ENa_strand GetStrand(void) const

Get the location's strand.

bool HasChanges(void) const

return true of any part was changed since initialization

const CSeq_loc & GetEmbeddingSeq_loc(void) const

Get the nearest seq-loc containing the current range.

@ eEmpty_Allow

ignore empty locations

@ eMake_PreserveType

use most compact Seq-loc type (default)

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

@ eNoOverlap

CSeq_locs do not overlap or abut.

void SetClass(TClass v) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

CSeqMap_I & Remove(void)

Remove current segment.

void GetSequence(string &buffer, CSeqUtil::ECoding buffer_coding) const

Get current sequence as a string with the selected encoding.

const CSeq_data & GetData(void) const

will allow only regular data segments (whole, plus strand)

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

void SetSequence(const string &buffer, CSeqUtil::ECoding buffer_coding, CSeq_data::E_Choice seq_data_coding)

Set sequence data.

TSeqPos GetLength(void) const

return length of current segment

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

#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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

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

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.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

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 SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

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 string & ToLower(string &str)

Convert string to lower case – string& version.

@ eNocase

Case insensitive compare.

bool IsSetPseudo(void) const

pseudogene Check if a value has been assigned to Pseudo data member.

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.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

void SetCase_sensitive(TCase_sensitive value)

Assign a value to Case_sensitive data member.

void SetWhole_word(TWhole_word value)

Assign a value to Whole_word data member.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetExt(void) const

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

const TGen & GetGen(void) const

Get the variant data.

const TName & GetName(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

@ e_Name

for naming "other" type

bool IsSetComment(void) const

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

bool IsSetData(void) const

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

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TAa & GetAa(void) const

Get the Aa member data.

TNcbieaa GetNcbieaa(void) const

Get the variant data.

const TComment & GetComment(void) const

Get the Comment member data.

const TGene & GetGene(void) const

Get the variant data.

ENa_strand

strand of nucleic acid

bool IsGeneral(void) const

Check if variant General is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_mut_set

set of mutations

@ eClass_eco_set

ecological sample study

@ eClass_genbank

converted genbank

@ eClass_segset

segmented sequence + parts

const TInst & GetInst(void) const

Get the Inst member data.

bool CanGetAnnot(void) const

Check if it is safe to call GetAnnot method.

bool IsSetMol(void) const

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

const TSource & GetSource(void) const

Get the variant data.

bool IsSetBiomol(void) const

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

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

TMol GetMol(void) const

Get the Mol member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

bool IsSetId(void) const

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

const TMolinfo & GetMolinfo(void) const

Get the variant data.

bool CanGetInst(void) const

Check if it is safe to call GetInst method.

E_Choice Which(void) const

Which variant is currently selected.

@ eCompleteness_complete

complete biological entity

void AddComment(CSeq_feat &feat, const string &comment)

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

GenericValue< UTF8<> > Value

GenericValue with UTF8 encoding.

#define FOR_EACH_CODEBREAK_ON_CDREGION(Itr, Var)

FOR_EACH_CODEBREAK_ON_CDREGION EDIT_EACH_CODEBREAK_ON_CDREGION.

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

#define RAW_FIELD_IS_EMPTY_OR_UNSET(Var, Fld)

RAW_FIELD_IS_EMPTY_OR_UNSET macro.

#define GET_FIELD_OR_DEFAULT(Var, Fld, Dflt)

GET_FIELD_OR_DEFAULT base macro.

#define FIELD_EQUALS(Var, Fld, Value)

FIELD_EQUALS base macro.

#define STRING_FIELD_NOT_EMPTY(Var, Fld)

STRING_FIELD_NOT_EMPTY base macro.

#define GET_STRING_FLD_OR_BLANK(Var, Fld)

GET_STRING_FLD_OR_BLANK base macro.

vector< pair< size_t, size_t > > NRuns

Selector used in CSeqMap methods returning iterators.

static CS_CONTEXT * context

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