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NCBI C++ ToolKit: src/gui/packages/pkg_snp/ld/ld_ds.cpp Source File

->m_ObjectList.swap(glyphs);

}

(std::exception& ex) {

std::map<string, CLDBlockLine::TListFeats> TMapPopNames;

TMapPopNames mapPopName;

( ; feat; ++feat) {

mapPopName[pop].push_back(*feat);

(TMapPopNames, mapIter, mapPopName) {

& title = mapIter->first;

dmap.

(feat_iter->GetTotalRange());

(TMapPopNames, mapIter, mapPopName) {

the_feats.push_back(fref);

title = mapIter->first;

glyphs->push_back(ref_line);

&

=

&

(

.object.GetObject());

feat_iter(handle, range, sel);

(iter->IsNamed()) {

&

=

&

(

.object.GetObject());

(

.scope.GetObject(),

);

sid(

);

slabel(

);

User-defined methods of the data storage class.

const TAnnotNames & GetAnnotNames(void) const

size_t GetSize(void) const

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

void SetObjects(const CLayoutGroup::TObjectList &objs)

void SetAnnotName(const string &name)

virtual string GetExtensionLabel() const

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

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

CLDBlockDSType.

virtual string GetExtensionIdentifier() const

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

virtual bool IsSharable() const

check if the data source can be shared.

void SetName(const string &)

void LoadData(const SParams &param)

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

CLDBlockDS.

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

CLDBlockDS::SParams m_Params

CLDBlockJob(const CBioseq_Handle &handle, const CLDBlockDS::SParams &params)

virtual EJobState x_Execute()

method truly doing the job.

void x_LoadFtable(CFeat_CI &feats, CSeqGlyph::TObjects *glyphs)

void x_Load(CSeqGlyph::TObjects *)

std::list< objects::CMappedFeat > TListFeats

ILayoutPolicy::TObjectList TObjectList

void SetTitle(const string &label, const string &default_title=NcbiEmptyString)

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

CSGJobResult – the data structure holding the seqgraphic job results.

class CSeqGlyph defines an interface that wraps a rectilinear abstract object.

list< CRef< CSeqGlyph > > TObjects

CRef< CAppJobError > m_Error

namespace ncbi::objects::

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

container_type::value_type value_type

static const struct name_t names[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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.

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

EJobState

Job states (describe FSM)

TRange GetTotalRange(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

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.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

#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 TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

TReal GetReal(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TUser & GetUser(void) const

Get the variant data.

static bool s_PassesFilter(const CMappedFeat &feat, CLDBlockDS::SParams &params)

Static Helper functions.

CRenderingContext * r_cntx

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