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NCBI C++ ToolKit: src/gui/packages/pkg_snp/bins/bins_ds.cpp Source File

objects::CSeq_loc &loc,

->listObjs.swap(glyphs);

(std::exception& ex) {

pos_start, pos_end;

title, comment;

hasResult =

;

hasPvalue(

);

window = scale*binWidth;

col_sub_type.

(annot, 0, subType);

(pos_end - pos_start > 500) {

(

= pos_start;

< pos_end; ++

) {

(!BinEntry.

()) {

(BinEntry->

!= 0) {

bin.

->count = 1;

bin.

->range = range;

bin.

->m_EntryList.push_back(BinEntry);

bin.

->m_SigEntry = BinEntry;

obj->m_SigEntry = BinEntry;

gene_markers.push_back(obj);

iBin->SequentialNumber = binCount++;

scatter_plot->SetTitle(title);

objs->push_back(sref);

bins->SetTitle(title);

bins->SetType(

);

objs->push_back(fref);

gene_marker_glyph->SetTitle(title);

objs->push_back(fref);

pos_start, pos_end;

(iter.

()!=1) {

title, comment;

(

= pos_start;

< pos_end; ++

) {

( col_pos.

(annot,

, pos)) {

&

=

&

(

.object.GetObject());

(iter->IsNamed()) {

&

=

&

(

.object.GetObject());

(

.scope.GetObject(),

);

sid(

);

slabel(

);

User-defined methods of the data storage class.

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.

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 bool IsSharable() const

check if the data source can be shared.

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

CBinsDSType.

void SetName(const string &)

static void GetTrackNames(SConstScopedObject &object, TAnnotNameTitleMap &names, const TSeqRange &range, const ILayoutTrackFactory::SExtraParams &)

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

CBinsDS.

void LoadData(const TSeqRange &range, TModelUnit scale, bool isSeqView)

bool x_PreFetchFtable(const SAnnotSelector &sel, const objects::CSeq_loc &loc, CSeqGlyph::TObjects *glyphs)

SBinsJobResult::EDataType m_eDataType

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

virtual EJobState x_Execute()

method truly doing the job.

CBinsJob(const CBioseq_Handle &handle, const TSeqRange &range, const SParams &params)

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

list< CRef< objects::NSnpBins::SBin > > TGeneMarkers

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

the only requerement to TDataType is that it has a method GetValue() that returns some kind of float-...

list< CRef< CSeqGlyph > > TObjects

CRef< CAppJobError > m_Error

bool TryGet(const CFeat_CI &feat_ci, Value &v) const

static void GetBinSelector(const string &sTrackAccession, bool isAdaptive, int depth, objects::SAnnotSelector &sel)

get a selector for a bin from a NA track accession

static bool GetBinHandle(objects::CScope &scope, const objects::SAnnotSelector &sel, const objects::CSeq_loc &loc, objects::CSeq_annot_Handle &annot)

get an annotation handle that is needed to load a singular bin on range

static void ReadAnnotDesc(const objects::CSeq_annot_Handle &handle, string &title, string &comment)

get title and comment out of annot.desc

@ eGAP

dbGaP analysis files

@ eGCAT

NHGRI GWAS Catalog Track (AKA Association Results)

static bool isGeneMarker(const string &trackSubType)

determine whether a string in TrackSubType describes a Gene Marker ("102_1" or "102_3")

static void FindPosIndexRange(const objects::CSeq_annot_Handle &annot, int pos_value_from, int pos_value_to, int &pos_index_begin, int &pos_index_end)

Perform iterative binary search to find table indexes (rows) 'pos_index_begin' and 'pos_index_end' in...

static CRef< SBinEntry > GetEntry(const objects::CSeq_annot_Handle &annot, int row)

get a bin entry corresponding to a row position in the table presumed contained within the handle

container_type::value_type value_type

static const struct name_t names[]

#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_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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

request an annotation selector for a given type

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

help function for setting selector resolve depth.

static const int c_BinWidth

standard width and height of a bin

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

EJobState

Job states (describe FSM)

size_t size(void) const

Get number of collected Seq-annots.

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

SAnnotSelector & SetCollectNames(bool value=true)

Collect available annot names rather than annots.

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

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.

#define row(bind, expected)

CRef< objects::NSnpBins::SBin > obj

TSeqPos pos_end

gene end when trackSubType is (Gene association)

TSeqPos pos

! arrange member names as in the dumped file

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