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NCBI C++ ToolKit: include/gui/widgets/seq_graphic/alignment_job.hpp Source File

objects::SAnnotSelector& sel,

objects::SAnnotSelector& sel,

align_limit,

smear_if_overlimit,

objects::SAnnotSelector& sel,

& range,

SetSortBy(

& sort_by);

GetAnnotNames(

objects::CBioseq_Handle& handle,

& range, objects::SAnnotSelector& sel,

TAnnotNameTitleMap&

);

objects::CBioseq_Handle& handle,

objects::SAnnotSelector& sel,

& has_quality_map,

isFastConfig =

);

FilterDuplicatesAndBadReads(

objects::CSeq_align& mapped_align);

fAlign_LinkMatePairs = 0x1,

fAlign_MatedAlignsAsPwAlign = 0x2,

objects::CMappedFeat& mapped_feat,

& align)

;

x_CreateGeneModels(objects::CSeq_loc_Mapper& mapper,

objects::CAlign_CI& align_iter);

objects::CAlign_CI& align_iter,

sparseAln,

filterResults =

);

objects::CSeq_align& align,

objects::CSeq_align_Handle& align_handle,

x_BuildAlignDataSource(

objects::CSeq_align& align,

& align_ds,

sparseAln);

objects::CSeq_align& align,

objects::CSeq_align_Handle& align_handle,

m_SmearOverLimit =

;

m_ShowSecondPass =

;

vector< CConstRef<IAlnGraphicDataSource> >

;

objects::CBioseq_Handle handle,

objects::SAnnotSelector& aln_sel,

objects::SAnnotSelector& graph_sel,

& cache_key);

x_LoadAlignments(objects::CTSE_Handle& tse_handle);

vector<CConstRef<objects::CSeq_graph>>

;

pair< CRef< IAlnGraphicDataSource >, int > TAlnDS_Anchor

CSGAlignmentJob.

vector< TAlnDS_Anchor > TAlnDataSources

void GetAnchors(objects::CBioseq_Handle &handle, const objects::CSynonymsSet *synonyms, const objects::CSeq_align &align, vector< objects::CSeq_align::TDim > &anchors)

void BuildAlignDataSource(objects::CBioseq_Handle &handle, vector< objects::CSeq_align::TDim > &anchors, const objects::CSeq_align &align, bool sparseAln, TModelUnit window, TAlnDataSources &aln_datasources, CRange< TSeqPos > *range=nullptr)

CGraphStatCollector Helper class to use with CSGAlignStatJob::x_CollectAlignStats x_CollectAlignStats...

virtual bool ComputePileUp()

virtual void ClearRange(const TSeqRange &range)

CGraphStatCollector(double window)

virtual void AddStat(size_t index, CAlnStatGlyph::SStatStruct &stat)=0

virtual void UpdateGroup(size_t offset)

virtual ~CGraphStatCollector()=default

virtual void NewGroup(int batch_size)

const CSGAlignScoringJob & operator=(const CSGAlignScoringJob &)

pair< CConstRef< CObject >, int > TAlnAnchorPair

map< TAlnAnchorPair, CIRef< ISGAlnScore > > TAlnScoreMap

CSGAlignScoringJob(const CSGAlignScoringJob &)

TAlnScoreMap m_AlnScoreMap

vector< CConstRef< IAlnGraphicDataSource > > TAlnMgrVec

objects::SAnnotSelector m_GraphSel

pileup graph selector

string m_CacheKey

Graph cache key calculated by alignment ds.

TModelUnit m_Window

current zoom scale

CSGAlignStatJob(const CSGAlignStatJob &)

IAlnGraphicDataSource::TNumrow TNumrow

vector< CConstRef< objects::CSeq_graph > > TGraphs

const CSGAlignStatJob & operator=(const CSGAlignStatJob &)

pair< CRef< CAlignGlyph >, string > TMatedAlign

CIRef< ILayoutPolicy > m_LayoutPolicy

CAlignmentConfig::EUnalignedTailsMode m_UnalignedTailsMode

Flag, indicating whether and how to display unaligned tails.

CAlignmentConfig::EHideSraAlignments m_HideSra

Flag, indicating whether to hide duplicates and/or bad reads.

int m_AlignLimit

max number of alignments to load.

void SetLayoutPolicy(ILayoutPolicy *layout_policy)

void SetAnnotName(const string &name)

EAlignFlags

Request a list of alignments from a bioseq.

void SetShowSecondPass(bool value)

TModelUnit m_Window

current window for smear bars

TSignedSeqPos & m_MaxEndTail

Max length of unaligned tail at the end of the sequence.

vector< CRef< CAlignGlyph > > m_Aligns

alignments feature retrieval

void SetHideSra(CAlignmentConfig::EHideSraAlignments hideSra)

void SetUnalignedTailsMode(CAlignmentConfig::EUnalignedTailsMode tailsMode)

CIRef< IAlignSorter > m_Sorter

bool m_LinkPair

link mate pair aligns

TSignedSeqPos & m_MaxStartTail

> Flag to show second-pass alignments (relevant to assembly to assembly alignments)

list< CRef< CSeqGlyph > > TObjects

CSeqGraphicJob – the base class of seqgraphic job for handling the job status such as reporting the p...

virtual EJobState x_Execute()=0

method truly doing the job.

IAlnGraphicDataSource - interface to a data source representing an abstract alignment used in graphic...

IAlnExplorer::TNumrow TNumrow

class ILayoutPolicy defines the abstract interface required for generating layout based on a set of g...

static const struct name_t names[]

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

list< CRef< CLinkedFeature > > TLinkedFeats

EJobState

Job states (describe FSM)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT

const GenericPointer< typename T::ValueType > T2 value

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