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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/discrepancy__context_8cpp_source.html below:

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

*m_CurrentNode->m_BioseqSummary;

(

(taxname,

) ||

(taxname,

) ||

biosrc ?

(biosrc,

) :

;

biosrc ?

(biosrc,

) :

;

(

.empty()) {

(sum.

>= 10) {

q = sum.

;

(q > sum.

) {

(seq_data.

()) {

vector<char>::const_iterator it = seq_data.

().

().begin();

= 0xc0;

shift = 6;

(

= 0;

<

;

++, sum.

++) {

c = ((*it) &

) >> shift;

vector<char>::const_iterator it = seq_data.

().

().begin();

= 0xf0;

shift = 4;

(

= 0;

<

;

++, sum.

++) {

c = ((*it) &

) >> shift;

(

= 0;

<

;

++, sum.

++) {

(

= 0;

<

;

++, sum.

++) {

(

: bs.

()) {

(best_score > id->BaseBestRankScore()) {

(seq_iter.GetType()) {

(seq_iter.GetData(), seq_iter.GetPosition(), seq_iter.GetLength(), summary);

(summary.

) {

summary.

=

;

summary.

+= seq_iter.GetLength();

summary.

=

;

vector<string>

;

[

] = (

==

) ?

: ((

==

) ?

:

);

= aa.find_last_of(

);

(

!= string::npos) {

aa = aa.substr(

+ 1);

constexpr

locus_tag_re =

;

!ctre::match<locus_tag_re>(locus_tag);

(

&

: bioseq.

()) {

(; !IsBGPipe_is_bgpipe && user_desc_ci; ++user_desc_ci) {

IsBGPipe_is_bgpipe =

;

IsBGPipe_is_bgpipe;

IsBGPipe_is_bgpipe;

gene ?

*

(&*gene->m_Obj) :

;

(

& it : feat.

()) {

(

& it : feat.

()) {

(it->IsSetData() && it->GetData().IsGene() && it->GetData().GetGene().IsSetPseudo() && it->GetData().GetGene().GetPseudo()) {

(

.GetFrom() >=

.GetToOpen() ||

.GetFrom() >=

.GetToOpen()) {

(

node =

; node; node = node->m_Parent) {

(&*node->m_Obj == obj) {

(

node =

; node; node = node->m_Parent) {

(it != node->m_FeatureMap.end()) {

(

& child : node->m_Children) {

(

node =

; node; node = node->m_Parent) {

(it != node->m_DescriptorMap.end()) {

ret ? ret : ref.

.GetPointer();

(node->m_Ref->m_Text.empty()) {

fixref = &*node->m_Ref;

(node->m_Ref->m_Text.empty()) {

(node->m_Ref->m_Text.empty()) {

(

node =

; node; node = node->m_Parent) {

it = node->m_BiosourceMap.find(&biosrc);

(it != node->m_BiosourceMap.end()) {

(it->second->m_Ref->m_Text.empty()) {

(it->second->m_Type ==

) {

(it->second->m_Ref->m_Text.empty()) {

(it->second->m_Type ==

) {

(it->second->m_Type ==

) {

(it->second->m_Ref->m_Text.empty()) {

(it->second->m_Type ==

) {

(it->second->m_Type ==

) {

(

: testnames)

(

, filename);

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.

User-defined methods of the data storage class.

ncbi::TMaskedQueryRegions mask

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

const string & GetLineage(void) const

bool IsSetLineage(void) const

const CParseNode * GeneForFeature(const CParseNode &node)

string GetProdForFeature(const CSeq_feat &feat)

CSeqdesc_run GetAllSeqdesc()

void AddTest(eTestNames name) override

vector< const CSeq_feat * > m_Feat_RNAs

static bool HasLineage(const CBioSource &biosrc, const string &def_lineage, const string &type)

bool IsViral(const CBioSource *biosrc) const

CRef< CDiscrepancyObject > BiosourceObjRef(const CBioSource &biosrc, bool fix=false, const CObject *more=nullptr)

CRef< objects::CScope > m_Scope

CParseNode * FindNode(const CRefNode &obj)

CRef< CDiscrepancyObject > AuthorsObjRef(const CAuth_list &authors, bool fix=false, const CObject *more=nullptr)

TDiscrepancyCoreMap m_Tests

void Push(const CSerialObject &root, const string &fname) override

CRef< CParseNode > m_RootNode

CRef< CDiscrepancyObject > BioseqObjRef(EFixType fix=eFixNone, const CObject *more=nullptr)

const CPerson_id * GetPerson_id() const

CRef< CDiscrepancyObject > SeqFeatObjRef(const CSeq_feat &feat, EFixType fix=eFixNone, const CObject *more=nullptr)

static string GetGenomeName(unsigned n)

CConstRef< CSuspect_rule_set > GetOrganelleProductRules()

CRef< CParseNode > m_CurrentNode

vector< const CSeq_feat * > m_FeatAll

CRefNode * ContainingSet(CRefNode &ref)

static bool IsBadLocusTagFormat(string_view locus_tag)

vector< const CSeq_feat * > m_FeatRRNAs

objects::CScope & GetScope() const

vector< const CSeq_feat * > m_FeatCDS

CParseNode * FindLocalNode(const CParseNode &node, const CSeq_feat &feat) const

CRef< CDiscrepancyObject > StringObjRef(const CObject *fix=nullptr, const CObject *more=nullptr)

const CSeq_feat * GetGeneForFeature(const CSeq_feat &feat)

bool IsEukaryotic(const CBioSource *biosrc) const

const CBioseq & CurrentBioseq() const

vector< const CSeq_feat * > m_FeatGenes

const CSubmit_block * GetSubmit_block() const

void BuildSeqSummary(const CBioseq &bs, CSeqSummary &summary)

bool IsBacterial(const CBioSource *biosrc) const

vector< const CSeq_feat * > m_FeatMRNAs

void CollectFeature(const CSeq_feat &feat)

static bool IsOrganelle(const CBioSource *biosrc)

void SetSuspectRules(const string &name, bool read=true) override

CRef< CDiscrepancyObject > SubmitBlockObjRef(bool fix=false, const CObject *more=nullptr)

bool IsProkaryotic(const CBioSource *biosrc) const

friend class CDiscrepancyObject

CConstRef< CSuspect_rule_set > m_OrganelleProductRules

CRef< CDiscrepancyObject > SeqdescObjRef(const CSeqdesc &desc, const CObject *fix=nullptr, const CObject *more=nullptr)

CConstRef< CSuspect_rule_set > GetProductRules()

vector< const CSeq_feat * > m_FeatTRNAs

bool IsPseudo(const CSeq_feat &feat)

vector< const CSeq_feat * > m_FeatExons

void ParseAll(CParseNode &node)

CRef< CDiscrepancyObject > BioseqSetObjRef(bool fix=false, const CObject *more=nullptr)

CRef< CDiscrepancyProduct > GetProduct() override

CConstRef< CSuspect_rule_set > m_ProductRules

static bool IsUnculturedNonOrganelleName(const string &taxname)

vector< const CSeq_feat * > m_FeatIntrons

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2) const

vector< const CSeq_feat * > m_FeatPseudo

static string GetAminoacidName(const CSeq_feat &feat)

string ProdForFeature(const CParseNode &node)

static bool IsSeqSet(EObjType n)

CRef< CDiscrepancyObject > PubdescObjRef(const CPubdesc &pubdesc, bool fix=false, const CObject *more=nullptr)

vector< const CSeq_feat * > m_FeatMisc

static string GetTextObjectDescription(const CSeq_feat &seq_feat, CScope &scope)

const string & GetLineage() const

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

ESubtype GetSubtype(void) const

namespace ncbi::objects::

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

Base class for all serializable objects.

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

CConstRef< objects::CSuspect_rule_set > GetProductRules(const string &name="")

CConstRef< objects::CSuspect_rule_set > GetOrganelleProductRules(const string &name="")

static void _QualityScore(CSeqSummary &sum)

static void sA(CSeqSummary &sum)

static void sN(CSeqSummary &sum)

static void sG(CSeqSummary &sum)

static void sT(CSeqSummary &sum)

static void CountNucleotides(const CSeq_data &seq_data, TSeqPos pos, TSeqPos len, CSeqSummary &sum)

static void sC(CSeqSummary &sum)

static void sZ(CSeqSummary &sum)

static void _notN(CSeqSummary &sum)

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

unsigned int TSeqPos

Type for sequence locations and lengths.

const TPrim & Get(void) const

#define ENUM_METHOD_NAME(EnumName)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

int BaseBestRankScore(void) const

string GetLabel(const CSeq_id &id)

@ eContent

Untagged human-readable accession or the like.

TRange GetTotalRange(void) const

@ fFGL_Content

Include its content if there is any.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eNoOverlap

CSeq_locs do not overlap or abut.

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

Finds gene for feature, but obeys SeqFeatXref directives.

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

static CRef< CSeqMap > CreateSeqMapForBioseq(const CBioseq &seq)

@ eSeqData

real sequence data

@ eSeqRef

reference to Bioseq

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 END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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 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.

@ eNocase

Case insensitive compare.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

Author, Primary or Secondary Check if a value has been assigned to Name data member.

TGenome GetGenome(void) const

Get the Genome member data.

bool IsSetGenome(void) const

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

bool IsSetPseudo(void) const

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

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

ESource_location

Access to ESource_location's attributes (values, names) as defined in spec.

@ eSource_location_unknown

@ eSource_location_chromatophore

bool IsSetQual(void) const

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

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetXref(void) const

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

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

bool IsSetPseudo(void) const

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

const TGene & GetGene(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

bool IsRna(void) const

Check if variant Rna is selected.

@ e_Other

for historical reasons, 'other' = 'refseq'

const TUser & GetUser(void) const

Get the variant data.

const TInst & GetInst(void) const

Get the Inst member data.

const TIupacna & GetIupacna(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

TLength GetLength(void) const

Get the Length member data.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

const TNcbi2na & GetNcbi2na(void) const

Get the variant data.

bool IsSetId(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

@ e_Ncbipna

nucleic acid probabilities

@ e_Ncbi2na

2 bit nucleic acid code

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ e_Ncbi8na

8 bit extended nucleic acid code

@ e_Ncbi4na

4 bit nucleic acid code

@ e_User

user defined object

const TContact & GetContact(void) const

Get the Contact member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

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

const TContact & GetContact(void) const

Get the Contact member data.

bool IsSetContact(void) const

who to contact Check if a value has been assigned to Contact data member.

bool IsSetContact(void) const

WARNING: this will replace the above Check if a value has been assigned to Contact data member.

static string GetProductName(const CProt_ref &prot)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

static const sljit_gpr r1

static const sljit_gpr r2

CConstRef< CSerialObject > m_Obj

map< const CSeq_feat *, CParseNode * > m_FeatureMap

const CParseNode * m_Gene

map< const CSeqdesc *, CParseNode * > m_DescriptorMap

CRef< CRefNode > m_Parent

vector< pair< size_t, size_t > > NRuns

size_t _CBposition[WINDOW_SIZE]

static const size_t WINDOW_SIZE

size_t _CBscore[WINDOW_SIZE]

Selector used in CSeqMap methods returning iterators.

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