NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Functions | Variables
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::ELabelPositionTLabelPosStr
 
typedef CStaticArrayMap< string, CAlignmentConfig::ELabelPositionTLabelPosMap
 
typedef SStaticPair< const char *, CAlignmentConfig::EHideSraAlignmentsTHideSraStr
 
typedef CStaticArrayMap< string, CAlignmentConfig::EHideSraAlignmentsTHideSraMap
 
typedef SStaticPair< const char *, CAlignmentConfig::EUnalignedTailsModeTUnalignedTailsModeStr
 
typedef CStaticArrayMap< string, CAlignmentConfig::EUnalignedTailsModeTUnalignedTailsModeMap
 

Enumerations

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

Functions

 USING_SCOPE (objects)
 
const strings_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, stringsm_LayoutDispMap
 layout style to layout display name More...
 
static const map< string, CAlignmentTrack::ELayoutsm_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

Definition at line 306 of file alignment_track.cpp.

◆ THideSraStr

Definition at line 298 of file alignment_track.cpp.

◆ TLabelPosMap

Definition at line 271 of file alignment_track.cpp.

◆ TLabelPosStr

Definition at line 264 of file alignment_track.cpp.

◆ TUnalignedTailsModeMap

Definition at line 337 of file alignment_track.cpp.

◆ 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)

◆ s_ParseAlignType()

IAlnExplorer::EAlignType s_ParseAlignType ( const string align_type)

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kAlignGlyphKey

const string kAlignGlyphKey = "GBPlugins.SeqGraphicAlignGlyphs"
static

◆ kBaseKey

const string kBaseKey = "GBPlugins.SeqGraphicAlignment"
static

◆ kContentBaseID

const size_t kContentBaseID = 10001
static

◆ kDefaultScoringMethod

const char* kDefaultScoringMethod = "Show Differences"
static

◆ 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

◆ 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

◆ 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

◆ s_LabelPosStrs

const TLabelPosStr s_LabelPosStrs[]
static
Initial value:
= {
}
@ ePos_Above
above the rendered bar
@ ePos_Side
always on 5' side
@ ePos_NoLabel
no label

Definition at line 265 of file alignment_track.cpp.

◆ s_UnalignedTailsModeStrs

const TUnalignedTailsModeStr s_UnalignedTailsModeStrs[]
static

◆ sm_LayoutDispMap

const map<CAlignmentTrack::ELayout, string> sm_LayoutDispMap
static
Initial value:
= {
{ CAlignmentTrack::eLayout_ExpandedByPos, "Ladder (one alignment per row)" },
}
@ eLayout_Adaptive
adaptive using loading costs to switch between rendering modes
@ eLayout_Full
one alignment per row sorted by pos
@ eLayout_ExpandedByPos
one alignment per row sorted by pos
@ eLayout_Packed
smear/pack all alignments into one smear bar

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
Modified on Thu May 30 12:21:13 2024 by modify_doxy.py rev. 669887