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NCBI C++ ToolKit: src/gui/packages/pkg_snp/track/snp_ds.cpp Source File

->listObjs.swap(glyphs);

}

(std::exception& ex) {

zoomAnnotName = sAnnotName;

(!name.IsNamed()) {

base_name != sAnnotName) {

(zoom_level <= max_zoom_level) {

(zoom_level > best_zoom_level || best_zoom_level > max_zoom_level) {

best_zoom_level = zoom_level;

(zoom_level < best_zoom_level) {

best_zoom_level = zoom_level;

(

<<

);

( ; graph_iter; ++graph_iter) {

TDMaps::iterator it = dmaps.find(title);

( it == dmaps.end()) {

& title = it->first;

glyphs->push_back(fref);

filter.

(bitfield);

ncbi::objects::CSeq_loc &loc,

glyphs->swap(tmpList);

glyphs->insert(glyphs->end(), tmpList.begin(), tmpList.end());

( ; feat_it; ++feat_it) {

glyphs.push_back(glyph);

( ; feat_it; ++feat_it) {

glyphs.push_back(glyph);

(

<<

<< srcFtable.size());

dmap.

( (*iter)->GetRange() );

&

=

&

(

.object.GetObject());

feat_iter(handle, range, sel);

annots[params.

] = iter->GetName();

annots[params.

] =

;

&

=

&

(

.object.GetObject());

(

.scope.GetObject(),

);

sid(

);

slabel(

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const TAnnotNames & GetAnnotNames(void) const

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

TIntervals & SetIntervals()

CFeatGlyph inline implementations.

void SetAnnotName(const string &name)

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.

bool m_Adaptive

adaptive/exact annot selector

int m_Depth

annotation resolving depth

objects::CBioseq_Handle m_Handle

virtual string GetExtensionIdentifier() const

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

virtual string GetExtensionLabel() const

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

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

CSGSnpDSType.

virtual bool IsSharable() const

check if the data source can be shared.

void LoadData(const TSeqRange &range, CSnpJob::SParams &p, SSnpFilter *filter)

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

CSGSnpDS.

static void GetAnnotNames(SConstScopedObject &object, map< string, string > &annots, const TSeqRange &range, const ILayoutTrackFactory::SExtraParams &params)

list< CRef< CSeqGlyph > > TObjects

CRef< CAppJobError > m_Error

namespace ncbi::objects::

CSnpBitfield is a facade for representing any version of the SNP bitfield.

CRef< SSnpFilter > m_Filter

void x_FetchFtableEx(const objects::SAnnotSelector &sel, const objects::CSeq_loc &loc, CSeqGlyph::TObjects *glyphs)

void x_FetchGraphs(const objects::CSeq_loc &, CSeqGlyph::TObjects *)

SSnpJobResult::EDataType m_eDataType

virtual EJobState x_Execute()

method truly doing the job.

void x_FetchFtable(const objects::CSeq_loc &, CSeqGlyph::TObjects *)

void x_MakeHistogramFromFtable(const CSeqGlyph::TObjects &srcFtable, CSeqGlyph::TObjects &glyphs)

static string s_AdjustAnnotName(const string &sAnnotName)

! this is a temporary function for an interim period when SNP filters are taken from !...

void x_PreFetchFtable(const objects::SAnnotSelector &sel, const ncbi::objects::CSeq_loc &loc, CSeqGlyph::TObjects &glyphs)

CSnpJob(const objects::CBioseq_Handle &handle, const TSeqRange &range, const SParams &params, SSnpFilter *filter)

CSnpJob.

vector< TSeqRange > TIntervals

const_iterator begin() const

const_iterator end() const

parent_type::const_iterator const_iterator

unsigned int TSeqPos

Type for sequence locations and lengths.

#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 LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

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)

static bool IsNAA(const string &annot, bool isStrict=false)

check if a given annotation is a named annotation accession[.version][number] when isSctrict == false...

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

request an annotation selector for a given type

static TAnnotNameType NameTypeStrToValue(const string &type)

static bool IsExtendedNAA(const string &annot, bool isStrict=false)

check if a given annotation is an extended NAA (named accession[.version][number],...

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

@ eAnnot_Unnamed

unnamed annotation

@ eAnnot_Other

any given named annots

virtual void AddRange(TSeqRange range, CntType score=1, bool expand=false)

EJobState

Job states (describe FSM)

TRange GetTotalRange(void) const

TSeqPos GetComp(void) const

const string & GetTitle(void) const

SAnnotSelector & ResetAnnotsNames(void)

Select annotations from all Seq-annots.

TRange GetTotalRange(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

string CombineWithZoomLevel(const string &acc, int zoom_level)

Combine accession string and zoom level into a string with separator.

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

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

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

bool ExtractZoomLevel(const string &full_name, string *acc_ptr, int *zoom_level_ptr)

Extract optional zoom level suffix from named annotation string.

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

const CSeq_loc & GetLoc(void) const

SAnnotSelector & AddUnnamedAnnots(void)

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

const CSeq_graph::C_Graph & GetGraph(void) const

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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TInt & GetInt(void) const

Get the variant data.

const TValues & GetValues(void) const

Get the Values member data.

const TByte & GetByte(void) const

Get the variant data.

const TValues & GetValues(void) const

Get the Values member data.

bool IsByte(void) const

Check if variant Byte is selected.

double value_type

The numeric datatype used by the parser.

const GenericPointer< typename T::ValueType > T2 value

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

static bool s_passes_bitfield(const CSeq_feat &or_feat, const SSnpFilter &filter)

bool bPreferFeat

Return feat glyphs instead of histogram glyphs.

bool bAdaptive

Only return feat glyphs when not overview.

virtual bool Passes(const CSnpBitfield &b) const

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