alignment_track.cpp File Reference

#include <ncbi_pch.hpp>
#include <gui/widgets/seq_graphic/alignment_track.hpp>
#include <gui/widgets/seq_graphic/seqgraphic_ds_manager.hpp>
#include <gui/widgets/seq_graphic/seqgraphic_graph_ds.hpp>
#include <gui/widgets/seq_graphic/gene_model_track.hpp>
#include <gui/widgets/seq_graphic/gene_model_group.hpp>
#include <gui/widgets/seq_graphic/feature_track.hpp>
#include <gui/widgets/seq_graphic/config_utils.hpp>
#include <gui/widgets/seq_graphic/layout_track_proxy.hpp>
#include <gui/widgets/seq_graphic/rendering_ctx.hpp>
#include <gui/widgets/seq_graphic/alignment_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/histogram_glyph.hpp>
#include <gui/widgets/seq_graphic/coord_mapper.hpp>
#include <gui/widgets/seq_graphic/named_group.hpp>
#include <gui/widgets/seq_graphic/alignment_sorter_factory.hpp>
#include <gui/widgets/seq_graphic/alignment_sorter.hpp>
#include <gui/widgets/seq_graphic/alignment_quality_score.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <gui/widgets/seq/feature_check_dialog.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/objutils/na_utils.hpp>
#include <gui/objutils/label.hpp>
#include <gui/objutils/registry.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/impl/scope_info.hpp>
#include <wx/event.h>
#include <wx/menu.h>
#include "wx_aln_stat_dlg.hpp"

Include dependency graph for alignment_track.cpp:

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Classes
class	CAlnContentEvtHandler

Typedefs
typedef SStaticPair< const char *, CAlignmentConfig::ELabelPosition >	TLabelPosStr
typedef CStaticArrayMap< string, CAlignmentConfig::ELabelPosition >	TLabelPosMap
typedef SStaticPair< const char *, CAlignmentConfig::EHideSraAlignments >	THideSraStr
typedef CStaticArrayMap< string, CAlignmentConfig::EHideSraAlignments >	THideSraMap
typedef SStaticPair< const char *, CAlignmentConfig::EUnalignedTailsMode >	TUnalignedTailsModeStr
typedef CStaticArrayMap< string, CAlignmentConfig::EUnalignedTailsMode >	TUnalignedTailsModeMap

Enumerations
enum	{ CONFIG_SRA = 1 , CONFIG_NUC = 2 , CONFIG_PROT = 3 , CONFIG_ALL = 4 }

Functions
	USING_SCOPE (objects)
const string &	s_LayoutToDisplayName (CAlignmentTrack::ELayout layout)
	DEFINE_STATIC_ARRAY_MAP (TLabelPosMap, sm_LabelPosMap, s_LabelPosStrs)
	DEFINE_STATIC_ARRAY_MAP (THideSraMap, sm_HideSraMap, s_HideSraStrs)
	DEFINE_STATIC_ARRAY_MAP (TUnalignedTailsModeMap, sm_UnalignedTailsModeMap, s_UnalignedTailsModeStrs)
IAlnExplorer::EAlignType	s_ParseAlignType (const string &align_type)
CSGAlignmentDS::EDataLoader	s_ParseAlignDataLoader (const string &align_loader)

Variables
static const size_t	kProjectedFeatID = 10000
static const size_t	kContentBaseID = 10001
static const int	kMaxID = 100
static const double	kMinCoverageZoomLevel = 250.
	Scale at which we unconditionally switch to coverage graph. More...
static const int	kShowPileUpRange = 10000
	Range length for unconditional swith to pieup. More...
static const string	kGeneModelBaseKey = "GBPlugins.SeqGraphicGeneModel"
static const map< CAlignmentTrack::ELayout, string >	sm_LayoutDispMap
	layout style to layout display name More...
static const map< string, CAlignmentTrack::ELayout >	sm_LayoutMap
static const TLabelPosStr	s_LabelPosStrs []
static const THideSraStr	s_HideSraStrs []
static const TUnalignedTailsModeStr	s_UnalignedTailsModeStrs []
static const string	kAlignGlyphKey = "GBPlugins.SeqGraphicAlignGlyphs"
static const string	kMatePairKey = "GBPlugins.SeqGraphicMatePair"
static const string	kBaseKey = "GBPlugins.SeqGraphicAlignment"
static const string	kTrackName = "Alignments"
static const string	kDefProfile = "Default"
static const string	kReadsProfile = "BAM"
static const char *	kDefaultSraFilter = "none"
static const char *	kDefaultUnalignedTailsMode = "glyph"
static const char *	kDefaultScoringMethod = "Show Differences"

Typedef Documentation

THideSraMap

typedef CStaticArrayMap<string, CAlignmentConfig::EHideSraAlignments> THideSraMap

Definition at line 306 of file alignment_track.cpp.

THideSraStr

typedef SStaticPair<const char*, CAlignmentConfig::EHideSraAlignments> THideSraStr

Definition at line 298 of file alignment_track.cpp.

TLabelPosMap

typedef CStaticArrayMap<string, CAlignmentConfig::ELabelPosition> TLabelPosMap

Definition at line 271 of file alignment_track.cpp.

TLabelPosStr

typedef SStaticPair<const char*, CAlignmentConfig::ELabelPosition> TLabelPosStr

Definition at line 264 of file alignment_track.cpp.

TUnalignedTailsModeMap

typedef CStaticArrayMap<string, CAlignmentConfig::EUnalignedTailsMode> TUnalignedTailsModeMap

Definition at line 337 of file alignment_track.cpp.

TUnalignedTailsModeStr

typedef SStaticPair<const char*, CAlignmentConfig::EUnalignedTailsMode> TUnalignedTailsModeStr

Definition at line 330 of file alignment_track.cpp.

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
CONFIG_SRA
CONFIG_NUC
CONFIG_PROT
CONFIG_ALL	special setting for TMS tracks that did not go through complete alignment type discovery in seqconfig (IAlnExplorer::fHomogenous) this will create all possible kinds of scoring methods, in other respects will look like _NUC this is temporary until TMS will start to serve a real alignment type

Definition at line 2502 of file alignment_track.cpp.

Function Documentation

DEFINE_STATIC_ARRAY_MAP() [1/3]

DEFINE_STATIC_ARRAY_MAP	(	THideSraMap	,
		sm_HideSraMap	,
		s_HideSraStrs
	)

DEFINE_STATIC_ARRAY_MAP() [2/3]

DEFINE_STATIC_ARRAY_MAP	(	TLabelPosMap	,
		sm_LabelPosMap	,
		s_LabelPosStrs
	)

DEFINE_STATIC_ARRAY_MAP() [3/3]

DEFINE_STATIC_ARRAY_MAP	(	TUnalignedTailsModeMap	,
		sm_UnalignedTailsModeMap	,
		s_UnalignedTailsModeStrs
	)

s_LayoutToDisplayName()

const string& s_LayoutToDisplayName

(

CAlignmentTrack::ELayout

layout

)

Definition at line 220 of file alignment_track.cpp.

References kEmptyStr, and sm_LayoutDispMap.

Referenced by CAlignmentTrackFactory::GetSettings().

s_ParseAlignDataLoader()

CSGAlignmentDS::EDataLoader s_ParseAlignDataLoader

(

const string &

align_loader

)

Definition at line 2279 of file alignment_track.cpp.

References CSGAlignmentDS::eLoader_BAM, CSGAlignmentDS::eLoader_CSRA, and CSGAlignmentDS::eLoader_Unknown.

Referenced by CAlignmentTrackFactory::CreateTracks().

s_ParseAlignType()

IAlnExplorer::EAlignType s_ParseAlignType

(

const string &

align_type

)

Definition at line 2264 of file alignment_track.cpp.

References IAlnExplorer::fDNA, IAlnExplorer::fInvalid, IAlnExplorer::fMixed, and IAlnExplorer::fProtein.

Referenced by CAlignmentTrackFactory::CreateTracks().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

kAlignGlyphKey

const string kAlignGlyphKey = "GBPlugins.SeqGraphicAlignGlyphs"

static

Definition at line 360 of file alignment_track.cpp.

Referenced by CAlignmentTrack::x_LoadAlignmentSettings(), and CAlignmentTrack::x_SaveAlignmentSettings().

kBaseKey

const string kBaseKey = "GBPlugins.SeqGraphicAlignment"

static

Definition at line 362 of file alignment_track.cpp.

Referenced by CAlignmentTrackFactory::GetSettings(), CAlignmentTrack::x_LoadSettings(), and CAlignmentTrack::x_SaveConfiguration().

kContentBaseID

const size_t kContentBaseID = 10001

static

Definition at line 117 of file alignment_track.cpp.

Referenced by CAlignmentTrack::x_OnContentIconClicked(), CAlignmentTrack::x_OnTailsIconClicked(), and CAlnContentEvtHandler::x_OnToggleContent().

kDefaultScoringMethod

const char* kDefaultScoringMethod = "Show Differences"

static

Definition at line 2501 of file alignment_track.cpp.

Referenced by CAlignmentTrackFactory::GetSettings(), and CUpdateSeqAlignWidget::OnDSChanged().

kDefaultSraFilter

const char* kDefaultSraFilter = "none"

static

Definition at line 2499 of file alignment_track.cpp.

Referenced by CAlignmentTrackFactory::GetSettings().

kDefaultUnalignedTailsMode

const char* kDefaultUnalignedTailsMode = "glyph"

static

Definition at line 2500 of file alignment_track.cpp.

Referenced by CAlignmentTrackFactory::GetSettings().

kDefProfile

const string kDefProfile = "Default"

static

Definition at line 365 of file alignment_track.cpp.

Referenced by CAlignmentTrackFactory::GetSettings(), CAlignmentTrack::x_LoadAlignmentSettings(), CAlignmentTrack::x_LoadMatePairSettings(), CAlignmentTrack::x_LoadSettings(), CAlignmentTrack::x_SaveAlignmentSettings(), CAlignmentTrack::x_SaveConfiguration(), and CAlignmentTrack::x_SaveMatePairSettings().

kGeneModelBaseKey

const string kGeneModelBaseKey = "GBPlugins.SeqGraphicGeneModel"

static

Definition at line 130 of file alignment_track.cpp.

Referenced by CAlignmentTrack::x_LoadSettings().

kMatePairKey

const string kMatePairKey = "GBPlugins.SeqGraphicMatePair"

static

Definition at line 361 of file alignment_track.cpp.

Referenced by CAlignmentTrack::x_LoadMatePairSettings(), and CAlignmentTrack::x_SaveMatePairSettings().

kMaxID

const int kMaxID = 100

static

Definition at line 120 of file alignment_track.cpp.

kMinCoverageZoomLevel

const double kMinCoverageZoomLevel = 250.

static

Scale at which we unconditionally switch to coverage graph.

Definition at line 123 of file alignment_track.cpp.

Referenced by CAlignmentTrack::x_UpdateData().

kProjectedFeatID

const size_t kProjectedFeatID = 10000

static

Definition at line 115 of file alignment_track.cpp.

Referenced by CAlignmentTrack::x_OnContentIconClicked().

kReadsProfile

const string kReadsProfile = "BAM"

static

Definition at line 366 of file alignment_track.cpp.

Referenced by CAlignmentTrackFactory::CreateTracks().

kShowPileUpRange

const int kShowPileUpRange = 10000

static

Range length for unconditional swith to pieup.

Definition at line 125 of file alignment_track.cpp.

Referenced by CAlignmentTrack::x_UpdateData().

kTrackName

const string kTrackName = "Alignments"

static

Definition at line 364 of file alignment_track.cpp.

s_HideSraStrs

const THideSraStr s_HideSraStrs[]

static

Initial value:

= {
    { "bad",        CAlignmentConfig::eHide_BadReads },
    { "both",       CAlignmentConfig::eHide_Both },
    { "duplicates", CAlignmentConfig::eHide_Duplicates },
    { "none",       CAlignmentConfig::eHide_None },
}

Definition at line 299 of file alignment_track.cpp.

s_LabelPosStrs

const TLabelPosStr s_LabelPosStrs[]

static

Initial value:

= {
    { "above",    CAlignmentConfig::ePos_Above },
    { "no label", CAlignmentConfig::ePos_NoLabel },
    { "side",     CAlignmentConfig::ePos_Side },
}

Definition at line 265 of file alignment_track.cpp.

s_UnalignedTailsModeStrs

const TUnalignedTailsModeStr s_UnalignedTailsModeStrs[]

static

Initial value:

= {
    { "glyph",      CAlignmentConfig::eTails_ShowGlyph },
    { "hide",       CAlignmentConfig::eTails_Hide },
    { "sequence",   CAlignmentConfig::eTails_ShowSequence },
}

Definition at line 331 of file alignment_track.cpp.

sm_LayoutDispMap

const map<CAlignmentTrack::ELayout, string> sm_LayoutDispMap

static

Initial value:

= {
    { CAlignmentTrack::eLayout_Packed,          "Packed" },
    { CAlignmentTrack::eLayout_Adaptive,    "Adaptive" },
    { CAlignmentTrack::eLayout_ExpandedByPos,  "Ladder (one alignment per row)" },
    { CAlignmentTrack::eLayout_Full,  "Show All" }
}

layout style to layout display name

Definition at line 213 of file alignment_track.cpp.

Referenced by s_LayoutToDisplayName(), and CAlignmentTrack::x_OnLayoutIconClicked().

sm_LayoutMap

const map<string, CAlignmentTrack::ELayout> sm_LayoutMap

static

Initial value:

= {
    { "Adaptive",           CAlignmentTrack::eLayout_Adaptive },
    { "Full",               CAlignmentTrack::eLayout_Full },
    { "Expanded",           CAlignmentTrack::eLayout_ExpandedByPos },
    { "Smear",              CAlignmentTrack::eLayout_Packed },
    { "Packed",             CAlignmentTrack::eLayout_Packed }
}

Definition at line 231 of file alignment_track.cpp.

Referenced by CAlignmentTrack::LayoutStrToValue(), CFeatureTrack::LayoutStrToValue(), CAlignmentTrack::LayoutValueToStr(), CFeatureTrack::LayoutValueToStr(), s_LayoutStrToValue(), s_LayoutValueToStr(), and CFeatureTrack::x_OnLayoutIconClicked().