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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/search_utils.cpp Source File

vector<CMappedFeatOrObject>& search_results)

(; sub_it != subtypes.

().cend(); ++sub_it)

(

& annot : subtypes.

())

unordered_map<string, CConstIRef<INonAsnDataSource>> NonAsnDSs(subtypes.

());

(

vcf_ds : NonAsnDSs) {

vcf_ds.second->DoSearch(vcf_ds.first,

,

);

search_results.push_back(mfo);

(!search_results.empty()) {

unordered_map<string, set<CSeqFeatData::ESubtype>> named_annot_subtypes = subtypes.

();

re_snp(

);

re_var(

);

named_annot_subtypes.clear();

(exception&) {}

((*iSNPSearchResult)->CanGetPlacements(),

);

(!(*iSNPSearchResult)->CanGetPlacements())

(Placements.size(),

);

(Placements.empty())

pPlacement = Placements.front();

annot =

.GetAnnot().IsNamed() ?

.GetAnnot().GetName() :

;

(named_annot_subtypes.find(annot) == named_annot_subtypes.end() ||

named_annot_subtypes[annot].find(

.GetFeatSubtype()) == named_annot_subtypes[annot].end())

vector<string> feat_labels;

it = find_if(feat_labels.begin(), feat_labels.end(),

[&

, &case_sens](

& elem) { return (NStr::Find(elem, text, case_sens) != NPOS); });

(it != feat_labels.end()) {

search_results.push_back(mfo);

multiplier = 1000000;

(NStr::StringToNumeric<TSeqPos>(pos) * multiplier, NStr::StringToNumeric<TSeqPos>(pos) * multiplier);

multiplier0 = 1000000;

multiplier1 = 1000000;

(NStr::StringToNumeric<TSeqPos>(pos0) * multiplier0, NStr::StringToNumeric<TSeqPos>(pos1) * multiplier1);

got_label =

;

= (*it)->GetVal();

got_label =

;

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

feat_labels.push_back(aux_label);

feat_labels.push_back(

);

vector<string> quals{

,

,

,

,

,

,

,

,

,

,

,

,

};

(

& qual_name : quals) {

vector<string> class_quals{

,

,

,

,

,

,

,

};

(

& qual_name : class_quals) {

&

= feat.GetNamedQual(qual_name);

(!

.empty())

pos = second_part.find(

);

(pos != string::npos)

second_part = second_part.substr(0, pos);

(!second_part.empty()) {

(!

.empty())

+= second_part;

intervals = 0;

(loc.

()) {

intervals = loc.

().

().size();

(intervals != 0) {

(!extra_info.empty())

extra_info +=

;

(intervals != 1) {

(!extra_info.empty()) {

*

+= extra_info;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CDataTrack - a abstract base class for layout tracks which need to deal with background data retrieva...

virtual CRef< CSGGenBankDS > GetDataSource()=0

Method for accessing the data source.

void SetMappedFeat(const objects::CMappedFeat &mapped_feat)

void SetRange(const TSeqRange &range)

void SetObject(const CObject *object)

ESubtype GetSubtype(void) const

static E_Choice GetTypeFromSubtype(ESubtype subtype)

@ eSubtype_misc_structure

@ eSubtype_mobile_element

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

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

void Traverse(Tr &&tr, bool visible)

virtual bool IsVarTrack() const

virtual string GetAnnot() const =0

virtual void GetFeatSubtypes(set< objects::CSeqFeatData::ESubtype > &subtypes) const =0

virtual bool IsSnpTrack() const

unordered_map< string, CConstIRef< INonAsnDataSource > > GetNonAsnBlobs()

bool Track(const CTempTrackProxy *, const CLayoutTrack *t, bool visible)

set< objects::CSeqFeatData::ESubtype > m_subtypes

set< string > m_annots_snp

set< string > m_annots_var

const set< string > & GetAnnots()

const set< string > & GetAnnotsSnp()

unordered_map< string, set< objects::CSeqFeatData::ESubtype > > m_named_annot_subtypes

const set< string > & GetAnnotsVar()

unordered_map< string, CConstIRef< INonAsnDataSource > > m_NonAsnBlobs

unordered_map< string, set< objects::CSeqFeatData::ESubtype > > GetNamedAnnotSubtypes()

const set< objects::CSeqFeatData::ESubtype > & GetSubtypes()

static TRsid GetRsid(const CMappedFeat &mapped_feat)

Return rsid of SNP.

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

#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_ASSERT(expr, mess)

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

static TAnnotNameType NameTypeStrToValue(const string &type)

virtual bool HasNonAsnData(const string &annot_name) const =0

@ eAnnot_Unnamed

unnamed annotation

list< TSNPSearchCompoundResult > TSNPSearchCompoundResultList

results of a search for one or several ids

list< CRef< CVariation > > TSNPSearchResultList

various placements of a variation

static void Search(const std::string &sTerms, const std::string &sAssemblyAccession, TSNPSearchCompoundResultList &ResultList)

search for given SNP ID(s) and get a list of results

const objects::CSeq_loc & GetLocation() const

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

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

string GetLabel(const CSeq_id &id)

@ fLabel_Default

default options - always show the version

@ eContent

Untagged human-readable accession or the like.

TRange GetTotalRange(void) const

const CSeq_id * GetId(void) const

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

@ fFGL_NoComments

Leave out comments, even as fallbacks.

@ fFGL_NoQualifiers

Leave out qualifiers.

@ fFGL_Content

Include its content if there is any.

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,...

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

CConstRef< CSeq_id > GetSeqId(void) const

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

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & ExcludeAnnotType(TAnnotType type)

Exclude annotation type from the search.

SAnnotSelector & ResetAnnotsNames(void)

Select annotations from all Seq-annots.

TRange GetTotalRange(void) const

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

SAnnotSelector & AddUnnamedAnnots(void)

Add unnamed annots to set of annots names to look for.

TObjectType * GetPointerOrNull(void) const THROWS_NONE

Get pointer value.

position_type GetLength(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

bool IsMatch(CTempString str, TMatch flags=fMatch_default)

Check existence substring which match a specified pattern.

CTempString GetSub(CTempString str, size_t idx=0) const

Get pattern/subpattern from previous GetMatch().

CTempString GetMatch(CTempString str, size_t offset=0, size_t idx=0, TMatch flags=fMatch_default, bool noreturn=false)

Get matching pattern and subpatterns.

int NumFound() const

Get number of patterns + subpatterns.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert size_t to string.

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

Check if a string ends with a specified suffix value.

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

Convert int to string.

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

Case-sensitive equality of a substring with another 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 void TrimSuffixInPlace(string &str, const CTempString suffix, ECase use_case=eCase)

Trim suffix from a string (in-place)

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

Case-insensitive equality of a substring with another string.

ECase

Which type of string comparison.

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.

@ fWithCommas

Use commas as thousands separator.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From 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.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

bool IsSetTitle(void) const

for user defined label Check if a value has been assigned to Title data member.

bool IsSetComment(void) const

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

const TClone & GetClone(void) const

Get the variant data.

bool IsSetQual(void) const

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

const TRegion & GetRegion(void) const

Get the variant data.

const TTitle & GetTitle(void) const

Get the Title member data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetDescr(void) const

text description Check if a value has been assigned to Descr data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

const TData & GetData(void) const

Get the Data member data.

const TName & GetName(void) const

Get the Name member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

bool IsSetName(void) const

Official clone symbol Check if a value has been assigned to Name data member.

const TGene & GetGene(void) const

Get the variant data.

TSite GetSite(void) const

Get the variant data.

vector< CRef< CGb_qual > > TQual

bool IsSetProduct(void) const

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

const TVariation & GetVariation(void) const

Get the variant data.

bool IsRegion(void) const

Check if variant Region is selected.

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.

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

const TPoints & GetPoints(void) const

Get the Points member data.

const TMix & GetMix(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

@ e_Ids

used for communication between tools

@ e_not_set

No variant selected.

@ e_Locs

used for communication between tools

list< CRef< CVariantPlacement > > TPlacements

bool IsSetLoc(void) const

actual concrete placement we are considering Check if a value has been assigned to Loc data member.

const TLoc & GetLoc(void) const

Get the Loc member data.

const TId & GetId(void) const

Get the Id member data.

bool CanGetId(void) const

Check if it is safe to call GetId method.

static void text(MDB_val *v)

void s_GetSeqLabel(const CSeq_id &id, string *label, CScope *scope)

bool s_IncludeFeatureTypeInLabel(const objects::CSeq_feat &feat)

void s_GetSeq_TotalRangeLabel(const CSeq_loc &loc, string *label, CScope *scope)

void GetSubtypesForType(set< objects::CSeqFeatData::ESubtype > &subtypes, objects::CSeqFeatData::E_Choice feat)

void s_GetCustomLabel(const CSeq_feat &feat, string &label)

TSeqRange SplitPosOrRange(const string &text)

bool s_UseCustomLabel(const CSeq_feat &feat)

void GatherFeatures(const string &text, bool match_case, objects::CBioseq_Handle bsh, objects::CScope &scope, CFeaturePanel *panel, vector< CMappedFeatOrObject > &search_results)

void s_GetFeatureLabel(const CSeq_feat &feat, vector< string > &feat_labels, CScope *scope)

void s_LabelFromQualifiers(const CSeq_feat &feat, string &label)

const GenericPointer< typename T::ValueType > T2 value

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

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