alignment_glyph.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objmgr/util/sequence.hpp>
#include <algo/sequence/consensus_splice.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Splice_site.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <gui/widgets/seq_graphic/seqgraphic_utils.hpp>
#include <gui/widgets/seq_graphic/alignment_glyph.hpp>
#include <gui/widgets/seq_graphic/rendering_ctx.hpp>
#include <gui/objutils/obj_fingerprint.hpp>
#include <gui/widgets/seq_graphic/gui_object_info_seq_align.hpp>
#include <gui/objutils/tooltip.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/opengl/irender.hpp>
#include <gui/opengl/glutils.hpp>
#include <gui/opengl/rasterizer.hpp>
#include <gui/opengl/gltexturefont.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <gui/widgets/gl/attrib_menu.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <math.h>

Include dependency graph for alignment_glyph.cpp:

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Classes
struct	SScPix
	represents a pixel with a score, if several intervals cover a pixel, the interval with the maximum coverage will "own" the pixel (i.e. More...
struct	SScPix2
	represents a pixel with two scores, one corresponds to a gap interval, another - to an aligned segment. More...

Functions
	USING_SCOPE (objects)
double	CompressLength (double len)
static void	FSetPixMaxCoverage (SScPix &dst, const SScPix &src, float fraction, bool)
	a pixel with the Max coverage (fraction) overrides all attributes More...
static void	FSetPix2 (SScPix2 &dst, const SScPix2 &src, float fraction, bool long_seg)
	accumulate weighted scores More...

Variables
static const TModelUnit	kPWAlignPackLevel = 0.333
static const TSeqPos	kTailGlyphLen = 12
static const TSeqPos	kCompactTailGlyphLen = 2
static const int	kAlignRowSpace = 3
static const int	kLabelSpace_v = 2
static const int	kLabelSpace_h = 5
static const int	kCompactLabelSpace_h = 1
static float	kMinSegDistance = 1.5f

Function Documentation

CompressLength()

double CompressLength ( double  len )

inline

Definition at line 237 of file alignment_glyph.cpp.

References len, log, and log10().

Referenced by CAlignGlyph::x_DrawInserts(), and CAlignGlyph::x_DrawMultiAlign().

FSetPix2()

static void FSetPix2 ( SScPix2 &  dst, const SScPix2 &  src, float  fraction, bool  long_seg  )

static

accumulate weighted scores

Definition at line 2184 of file alignment_glyph.cpp.

References SScPix2::m_GapLen, SScPix2::m_GapScore, SScPix2::m_Init, SScPix2::m_IntLen, SScPix2::m_IntScore, SScPix2::m_MinScore, and min().

FSetPixMaxCoverage()

static void FSetPixMaxCoverage ( SScPix &  dst, const SScPix &  src, float  fraction, bool    )

static

a pixel with the Max coverage (fraction) overrides all attributes

Definition at line 2035 of file alignment_glyph.cpp.

References SScPix::m_Gap, SScPix::m_MaxCoverage, and SScPix::m_Score.

Referenced by CAlignGlyph::x_RenderNonAveragableScores().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

kAlignRowSpace

const int kAlignRowSpace = 3

static

Definition at line 72 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_DrawMultiAlign(), and CAlignGlyph::x_UpdateBoundingBox().

kCompactLabelSpace_h

const int kCompactLabelSpace_h = 1

static

Definition at line 76 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_DrawTailGlyphs(), and CAlignGlyph::x_GetTailWidth().

kCompactTailGlyphLen

const TSeqPos kCompactTailGlyphLen = 2

static

Definition at line 70 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_DrawTailGlyphs(), and CAlignGlyph::x_GetTailWidth().

kLabelSpace_h

const int kLabelSpace_h = 5

static

Definition at line 75 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_GetTailWidth(), and CAlignGlyph::x_UpdateBoundingBox().

kLabelSpace_v

const int kLabelSpace_v = 2

static

Definition at line 73 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_DrawMultiAlign(), and CAlignGlyph::x_UpdateBoundingBox().

kMinSegDistance

float kMinSegDistance = 1.5f

static

Definition at line 2384 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_CalcIntervals().

kPWAlignPackLevel

const TModelUnit kPWAlignPackLevel = 0.333

static

Definition at line 68 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_DrawAlignRowSequence(), and CAlignGlyph::x_DrawUnalignedRowSequence().

kTailGlyphLen

const TSeqPos kTailGlyphLen = 12

static

Definition at line 69 of file alignment_glyph.cpp.

Referenced by CAlignGlyph::x_DrawTailGlyphs(), CAlignGlyph::x_GetTailWidth(), and CAlignGlyph::x_ShowUnalignedTails().