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

vector<string> info_fields{

,

,

,

,

,

,

,

,

,

,

,

,

};

&info_map =

->SetInfoColumns();

(

&field : info_fields) {

->ParseInfoColumns();

vector<unsigned> blob_pos;

variants((

*)vcf_blob->data(),

, data_cols);

(

pos: blob_pos) {

range_variants((

*)vcf_blob->data(), &variant_range, data_cols,

);

(variant_CI.

()) {

(vcf_object && vcf_object->GetID() == sSearchTerm) {

.push_back(vcf_object);

(

& annotdesc : prj_item.

()) {

(!annotdesc->IsSrc())

& prj_seq_id = annotdesc->GetSrc();

(seq_id.

() != prj_seq_id.AsFastaString()) {

sid(

);

(

);

token, shared_ptr<TDataBlob> &vcf_blob,

show_only_pathogenic);

TJobToken token,

max_feat,

&

=

&

(

.object.GetObject());

sid(

);

slabel(

);

shared_ptr<TDataBlob>& vcf_blob,

show_only_pathogenic)

, m_FeatLimit(max_feat)

, m_VcfBlob(vcf_blob)

, m_ShowOnlyPathogenic(show_only_pathogenic)

opt_start = chrono::steady_clock::now();

diff_opt = chrono::steady_clock::now() - opt_start;

exec_time_ms = chrono::duration_cast<chrono::milliseconds>(diff_opt).count();

&annot_name =

.GetIncludedAnnotsNames()[0].GetName();

hist_calc_time = CalculateHistogram(VCFHistogram);

(hist_calc_time > 50) {

->SetData(VCFHistogram);

->m_ObjectList.push_back(glyph);

(variant_CI.

()) {

(var->GetPos() ==

(-1)) {

(

<<

<< var->GetID());

&info_fields = var->GetInfoColumns();

clnsig_it = info_fields.find(

);

(clnsig_it == info_fields.end()) {

pathogens = {

,

,

};

clinsig = clnsig_it->second;

(0 == pathogens.count(clinsig)) {

->m_ObjectList.push_back(glyph);

}

(std::exception& ex) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

void SaveData(CRef< TData > data)

Clones TData, puts it into Save Queue for asynchroneous storage operation.

CRef< TData > GetData(const string &data_key)

Retrieves TData from in-memory cache or if not found calls TData::Init to initialize new TData instan...

static CGraphCache & GetInstance()

CRef< TData > GetCachedData(const string &data_key)

Retrieves TData from in-memory cache.

static int GetNearestLevel(const set< int > &levels, double zoom)

objects::SAnnotSelector m_Sel

our annotation selector

TSeqRange m_Range

target range

objects::CBioseq_Handle m_Handle

target sequence

TJobID x_LaunchJob(IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")

Launch either a background or foreground job.

objects::CBioseq_Handle & GetBioseqHandle(void)

Get the underlying bioseq handle.

TGraphLevels m_GraphLevels

Existing coverage graph levels.

objects::CBioseq_Handle m_Handle

CSGJobResult – the data structure holding the seqgraphic job results.

virtual void SetTaskTotal(int total)

virtual void SetTaskName(const string &name)

virtual void SetTaskCompleted(int completed)

set total finished task number.

void SetToken(TJobToken token)

CSeqGraphicJob inline methods.

TJobToken m_Token

Job token recognizable by job listener.

CRef< CAppJobError > m_Error

virtual bool GetPositionsForVariant(const string &variant_id, vector< unsigned > &positions)

string GetVariantID() const

string GetInfoField(const string &field_name) const

bool IsSetInfoField(const string &field_name) const

unsigned GetPosition() const

static const string sm_ALT

static const string sm_ID

static const string sm_INFO

static const string sm_REF

void GetHistogram(svector &hist, const svector::size_type &bin_width) const

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

create an instance of the layout track type using default settings.

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual bool IsSharable() const

check if the data source can be shared.

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

CConstIRef< INonAsnDataRegistry > m_DataRegistry

virtual void LoadFeatures(objects::SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, TJobToken token=-1, int max_feat=-1, ELinkedFeatDisplay LinkedFeatDisplay=ELinkedFeatDisplay::eLFD_Default, const string &="")

void SetNonAsnDataRegistry(const INonAsnDataRegistry *registry)

bool HasNonAsnData(const string &annot_name) const

CVcfFeatureDS(objects::CScope &scope, const objects::CSeq_id &id)

CVcfFeatureDS.

bool m_ShowOnlyPathogenic

virtual void DoSearch(const string &annot_name, const string &sSearchTerm, list< CRef< CObject >> &results) const

shared_ptr< TDataBlob > GetNonAsnDataBlob(const string &annot_name) const

size_t GetFeaturesCountInRange(const string &annot_name, const TSeqRange &range)

CVcfFeatureJob: a job class for loading annotated features from a given sequence and visible range.

CVcfFeatureJob(const string &desc, CBioseq_Handle handle, const SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, int max_feat, TJobToken token, shared_ptr< TDataBlob > &vcf_blob, bool show_only_pathogenic)

int m_FeatLimit

the maximum number of features allowed.

INonAsnTrackData::TDataBlob TDataBlob

shared_ptr< TDataBlob > m_VcfBlob

virtual EJobState x_Execute()

method truly doing the job.

TModelUnit m_Window

current window for smear bars

bool m_ShowOnlyPathogenic

static string GetCacheKey(const string &annot_name, const size_t bin_width)

static void InitHistogramGlyph(size_t bin_width, const TSeqRange &range, const THistogramVector &histogram, CHistogramGlyph::TMap &dmap)

INonAsnTrackData * CreateTrackData(const objects::CSeq_id &seq_id, const objects::CProjectItem &prj_item) const

string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

shared_ptr< TDataBlob > GetBlob() const

virtual void DoSearch(const objects::CSeq_id *seq_id, const string &sSearchTerm, list< CRef< CObject >> &results) const

const string GetDataSourceTypeName() const

succinct sparse vector with runtime compression using bit-slicing / transposition method

#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).

void Info(CExceptionArgs_Base &args)

EJobState

Job states (describe FSM)

const string AsFastaString(void) const

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

const TAnnotsNames & GetIncludedAnnotsNames(void) const

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Check if a string starts with a specified prefix value.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ eNocase

Case insensitive compare.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TType & GetType(void) const

Get the Type member data.

const TData & GetData(void) const

Get the Data member data.

const TItem & GetItem(void) const

Get the Item member data.

bool IsSetDescr(void) const

user-defined descriptors Check if a value has been assigned to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TOther & GetOther(void) const

Get the variant data.

bool IsOther(void) const

Check if variant Other is selected.

unsigned int

A callback function used to compare two keys in a database.

bm::id_t bvector_size_type

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

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

static CRef< CVcfVariant > s_CreateVcfGlyph(const objects::CSeq_id &seq_id, const CVCFVariant_CI &variant_CI)

static const float kMinScaleForMapping

static const size_t kMaxChildNum

static void s_DoSearch(const CSeq_id *seq_id, const shared_ptr< INonAsnTrackData::TDataBlob > &vcf_blob, const string &sSearchTerm, list< CRef< CObject >> &results)

static const int kMaxObjNum

static const int kMaxFeatures

static const float kSeqZoomLevel

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