#include <ncbi_pch.hpp>
#include <gui/widgets/seq_graphic/alignment_job.hpp>
#include <gui/widgets/seq_graphic/graph_cache.hpp>
#include <gui/widgets/seq_graphic/sparse_graph.hpp>
#include <gui/widgets/seq_graphic/alignment_glyph.hpp>
#include <gui/widgets/seq_graphic/gene_model_group.hpp>
#include <gui/widgets/seq_graphic/cds_glyph.hpp>
#include <gui/widgets/seq_graphic/mate_pair_glyph.hpp>
#include <gui/widgets/seq_graphic/alignment_smear_glyph.hpp>
#include <gui/widgets/seq_graphic/alnvec_graphic_ds.hpp>
#include <gui/widgets/seq_graphic/sparsealn_graphic_ds.hpp>
#include <gui/widgets/seq_graphic/denseg_graphic_ds.hpp>
#include <gui/widgets/seq_graphic/simple_graphic_ds.hpp>
#include <gui/widgets/seq_graphic/alignment_sorter_factory.hpp>
#include <gui/widgets/seq_graphic/named_group.hpp>
#include <gui/widgets/seq_graphic/seqgraphic_utils.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/objutils/na_utils.hpp>
#include <objtools/alnmgr/aln_converters.hpp>
#include <objtools/alnmgr/aln_builders.hpp>
#include <objtools/alnmgr/aln_container.hpp>
#include <objtools/alnmgr/aln_generators.hpp>
#include <objmgr/align_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/graph_ci.hpp>
#include <objmgr/impl/synonyms.hpp>
#include <objmgr/impl/scope_info.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seqres/Byte_graph.hpp>
#include <objects/seqres/Int_graph.hpp>
#include <corelib/ncbiutil.hpp>
#include <gui/widgets/seq_graphic/layout_policy.hpp>
#include <math.h>
#include <gui/widgets/seq_graphic/column_layout_policy.hpp>
#include <future>
#include <corelib/rwstream.hpp>
#include <util/checksum.hpp>
#include <connect/services/grid_worker_app.hpp>
#include <corelib/ncbiapp.hpp>

Include dependency graph for alignment_job.cpp:

Go to the SVN repository for this file.

Classes
class	CGraphStatCollector_Graph

class	CGraphStatCollector_Glyph

Typedefs
typedef SStaticPair< const char *, CAlnStatConfig::EStatType >	TGraphTitle
	layout style to layout display name More...

typedef CStaticArrayMap< string, CAlnStatConfig::EStatType >	TGraphTitleMap

Functions
	USING_SCOPE (objects)

static void	s_ObjectIdToStr (const CObject_id &id, string &id_str)

static bool	s_CheckTraceMateAlign (bool match_id, bool is_bam_align, const CSeq_align &align, string &ti, string &mate_ti, const string &expect_mate_ti="")

static bool	s_IsMatchById (CConstRef< CSeq_annot > aln_annot)

static bool	s_IsSecondPassAlignment (const CSeq_align &align)

	DEFINE_STATIC_ARRAY_MAP (TGraphTitleMap, sm_GraphTitleMap, s_GraphTitles)

size_t	s_GraphTitleToIndex (const string &title)

const string &	s_GraphIndexToTitle (size_t idx)

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

static CRef< CSeq_align >	s_CompressDiscToDenseq (list< CRef< CSeq_align >> &aln_set, int anchor_row)

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

Variables
static const double	kSequenceZoomLevel = 1.0/8.
	always show individual alignments when zoom level is below this threshold. More...

static const double	kDetailsZoomLevel = 2
	Scale at which align details are made visible Align details: unaligned tails, mate pairs. More...

static const int	kMaxAlignmentLoaded = 250000
	maximal number of alignments allowed to load to avoid potential memery and performance problem. More...

static const TGraphTitle	s_GraphTitles []

Typedef Documentation

◆ TGraphTitle

typedef SStaticPair<const char*, CAlnStatConfig::EStatType> TGraphTitle

layout style to layout display name

Definition at line 1550 of file alignment_job.cpp.

◆ TGraphTitleMap

typedef CStaticArrayMap<string, CAlnStatConfig::EStatType> TGraphTitleMap

Definition at line 1561 of file alignment_job.cpp.

Function Documentation

◆ BuildAlignDataSource()

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

Definition at line 2252 of file alignment_job.cpp.

References _ASSERT, CAlnMix::Add(), BuildAln(), CSeq_align::CheckNumRows(), CDense_seg::CheckNumSegs(), CreateAnchoredAlnFromAln(), CAlnUserOptions::eBothDirections, CAlnUserOptions::eDefaultMergeAlgo, eNa_strand_minus, IAlnGraphicDataSource::ePartial_3prime, IAlnGraphicDataSource::ePartial_5prime, IAlnGraphicDataSource::ePartial_None, CAlnUserOptions::ePreserveRows, CSeq_align_Base::eType_disc, eUnknown, CAlnMix::fGapJoin, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fOverlap, CSeq_align_set_Base::Get(), CAlnStats< _TAlnIdVec >::GetAlnCount(), CSeq_align_Base::C_Segs::GetDenseg(), CAlnMix::GetDenseg(), CAnchoredAln::GetDim(), CSparseAln::GetDim(), CSeq_align_Base::C_Segs::GetDisc(), COpenRange< Position >::GetLength(), CAnchoredAln::GetPairwiseAlns(), CBioseq_Handle::GetScope(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqRange(), CSeq_align_Base::C_Segs::GetStd(), CAlnContainer::insert(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_align_Base::C_Segs::IsDisc(), CAlignRangeCollectionList< TAlnRange >::IsSet(), CDense_seg::IsSetWidths(), CSeq_align_Base::C_Segs::IsStd(), ITERATE, LOG_POST, CAlnUserOptions::m_Direction, CAlnUserOptions::m_MergeAlgo, CAlnMix::Merge(), NCBI_THROW, NON_CONST_ITERATE, prev(), CAlnIdMap< _TAlnVec, TAlnSeqIdExtract >::push_back(), r(), compile_time_bits::range(), Ref(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), row, s_CompressDiscToDenseq(), CAlnMap::SetAnchor(), CDensegGraphicDataSource::SetColoringAvailable(), CSimpleGraphicDataSource::SetRegularity(), CAnchoredAln::SetScore(), CAlnContainer::size(), swap(), and Warning().

Referenced by CSGAlignmentJob::x_BuildAlignDataSource(), CSGAlignmentJob::x_GetAlignments(), and CSGAlignStatJob::x_LoadAlignments().

◆ DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP	(	TGraphTitleMap	,
		sm_GraphTitleMap	,
		s_GraphTitles
	)

◆ GetAnchors()

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

Definition at line 2174 of file alignment_job.cpp.

References CSeq_align::CheckNumRows(), CBioseq_Handle::ContainsSegment(), eGetId_Best, eGetId_Canonical, eUnknown, GetId(), CBioseq_Handle::GetId(), CBioseq_Handle::GetScope(), CSeq_align::GetSeq_id(), GetSeqId(), NCBI_THROW, and row.

Referenced by CSGAlignmentJob::x_BuildAlignDataSource(), CSGAlignmentJob::x_CreateAlignGlyphsForCrossOriginAlign(), CSGAlignmentJob::x_GetAlignments(), and CSGAlignStatJob::x_LoadAlignments().

◆ s_CheckTraceMateAlign()

static bool s_CheckTraceMateAlign	(	bool	match_id,
		bool	is_bam_align,
		const CSeq_align &	align,
		string &	ti,
		string &	mate_ti,
		const string &	expect_mate_ti = `""`
	)

static

Definition at line 348 of file alignment_job.cpp.

References CUser_field_Base::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetExt(), CUser_field::GetFieldRef(), CSeq_id_Base::GetGeneral(), GetId(), CDense_seg_Base::GetIds(), CUser_field_Base::C_Data::GetInt(), CSeq_id_Base::GetLocal(), CSeq_align::GetNamedScore(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CUser_field_Base::C_Data::GetStr(), CDbtag_Base::GetTag(), i, NStr::IntToString(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_id_Base::IsGeneral(), CUser_field_Base::C_Data::IsInt(), CSeq_id_Base::IsLocal(), CSeq_align_Base::IsSetExt(), CUser_field_Base::C_Data::IsStr(), ITERATE, len, NStr::NumericToString(), s_ObjectIdToStr(), and NStr::SizetToString().

Referenced by CSGAlignmentJob::x_CreateCAlignGlyph(), and CSGAlignmentJob::x_GetAlignments().

◆ s_CompressDiscToDenseq()

static CRef<CSeq_align> s_CompressDiscToDenseq	(	list< CRef< CSeq_align >> &	aln_set,
		int	anchor_row
	)

static

Definition at line 2207 of file alignment_job.cpp.

References ERR_POST, Error(), CSeq_align_Base::eType_not_set, CDense_seg_Base::GetDim(), i, len, r(), CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CDense_seg_Base::SetStarts(), and CDense_seg_Base::SetStrands().

Referenced by BuildAlignDataSource().

◆ s_GraphIndexToTitle()

const string& s_GraphIndexToTitle ( size_t idx )

Definition at line 1574 of file alignment_job.cpp.

References _ASSERT, and kEmptyStr.

Referenced by CSGAlignStatJob::x_CreatePileUpGraphs().

◆ s_GraphTitleToIndex()

size_t s_GraphTitleToIndex ( const string & title )

Definition at line 1564 of file alignment_job.cpp.

Referenced by CSGAlignStatJob::x_CollectAlignStats().

◆ s_IsMatchById()

static bool s_IsMatchById ( CConstRef< CSeq_annot > aln_annot )

static

Definition at line 1089 of file alignment_job.cpp.

References CSeq_annot_Base::CanGetDesc(), CAnnot_descr_Base::Get(), CUser_field_Base::C_Data::GetBool(), CUser_field_Base::GetData(), CSeq_annot_Base::GetDesc(), CUser_field::GetFieldRef(), CUser_field_Base::C_Data::IsBool(), and ITERATE.

Referenced by CSGAlignmentJob::x_GetAlignments().

◆ s_IsSecondPassAlignment()

static bool s_IsSecondPassAlignment ( const CSeq_align & align )

static

Definition at line 1112 of file alignment_job.cpp.

References CSeq_align::GetNamedScore().

Referenced by CSGAlignmentJob::x_GetAlignments().

◆ s_ObjectIdToStr()

static void s_ObjectIdToStr	(	const CObject_id &	id,
		string &	id_str
	)

static

Definition at line 337 of file alignment_job.cpp.

References GetId(), and NStr::NumericToString().

Referenced by s_CheckTraceMateAlign().

◆ USING_SCOPE()

USING_SCOPE ( objects )

Variable Documentation

◆ kDetailsZoomLevel

const double kDetailsZoomLevel = 2

static

Scale at which align details are made visible Align details: unaligned tails, mate pairs.

Definition at line 96 of file alignment_job.cpp.

Referenced by CSGAlignmentJob::x_GetAlignments().

◆ kMaxAlignmentLoaded

const int kMaxAlignmentLoaded = 250000

static

maximal number of alignments allowed to load to avoid potential memery and performance problem.

Unit: number of alignments

Definition at line 101 of file alignment_job.cpp.

Referenced by CSGAlignmentJob::x_LoadAlignments(), and CSGAlignStatJob::x_LoadAlignments().

◆ kSequenceZoomLevel

const double kSequenceZoomLevel = 1.0/8.

static

always show individual alignments when zoom level is below this threshold.

Unit: bases per screen pixel (BPP)

Definition at line 92 of file alignment_job.cpp.

Referenced by CSGAlignmentJob::x_LoadAlignments().

◆ s_GraphTitles

const TGraphTitle s_GraphTitles[]

static

Initial value:

= {
    {"Number of A bases",  CAlnStatConfig::eStat_A},
    {"Number of C bases",  CAlnStatConfig::eStat_C},
    {"Number of G bases",  CAlnStatConfig::eStat_G},
    {"Number of T bases",  CAlnStatConfig::eStat_T},
    {"Number of inserts",  CAlnStatConfig::eStat_Gap},
    {"Number of introns",  CAlnStatConfig::eStat_Intron },
    {"Number of matches",  CAlnStatConfig::eStat_Match}
}

Definition at line 1551 of file alignment_job.cpp.

Classes

Typedefs

Functions

Variables

Typedef Documentation

◆ TGraphTitle

◆ TGraphTitleMap

Function Documentation

◆ BuildAlignDataSource()

◆ DEFINE_STATIC_ARRAY_MAP()

◆ GetAnchors()

◆ s_CheckTraceMateAlign()

◆ s_CompressDiscToDenseq()

◆ s_GraphIndexToTitle()

◆ s_GraphTitleToIndex()

◆ s_IsMatchById()

◆ s_IsSecondPassAlignment()

◆ s_ObjectIdToStr()

◆ USING_SCOPE()

Variable Documentation

◆ kDetailsZoomLevel

◆ kMaxAlignmentLoaded

◆ kSequenceZoomLevel

◆ s_GraphTitles