#include <ncbi_pch.hpp>
#include <objtools/align_format/align_format_util.hpp>
#include <objtools/align/alngraphic.hpp>
#include <util/range.hpp>
#include <serial/iterator.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Std_seg.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objects/seqalign/seqalign_exception.hpp>
#include <objects/general/Object_id.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/create_defline.hpp>
#include <html/html.hpp>

Include dependency graph for alngraphic.cpp:

Go to the SVN repository for this file.

Functions
	USING_SCOPE (sequence)

	USING_SCOPE (align_format)

static string	s_GetGif (int bits)

static string	s_GetScoreColor (int bits)

static int	s_GetRoundNumber (int number)

template<class container >
static bool	s_GetBlastScore (const container &scoreList, int &score, double &bits, double &evalue)

static void	s_GetAlnScores (const CSeq_align &aln, int &score, double &bits, double &evalue)

static string	s_MapSeqInfoTemplate (string seqTemplate, string score, string seq, string defline, string acc, string eval)

static string	s_MapBarTemplate (string imageTemplate, int width, string imgType, string cssClass, string score="", string seq="", string defline="", string acc="", string eval="")

Variables
const char *	kDigitGif []

const TSeqPos	kScoreMargin = 50

const TSeqPos	kScoreLength = 500

const TSeqPos	kScoreHeight = 40

const TSeqPos	kBlankBarHeight = 4

const TSeqPos	kMasterHeight = 10

const TSeqPos	kMasterPixel = kScoreLength

const TSeqPos	kMasterBarLength = 550

const TSeqPos	kScaleMarginAdj = 1

const TSeqPos	kScaleWidth = 2

const TSeqPos	kScaleHeight = 10

const TSeqPos	kDigitWidth = 10

const TSeqPos	kDigitHeight = 13

const TSeqPos	kGapHeight = 1

const TSeqPos	kGreakHeight = 6

const TSeqPos	kNumMark = 6

const int	kDeflineLength = 55

static const int	kOverlapDiff = 5

const char *	kGifWhite = "white.gif"

const char *	kGifMaster ="query_no_scale.gif"

const char *	kGifScore = "score.gif"

const char *	kGifGrey = "grey.gif"

const char *	kGifScale = "scale.gif"

const char *	kGifBlack = "black.gif"

const char *	kWhite = "white"

const char *	kGrey = "grey"

const char *	kBlack = "black"

Function Documentation

◆ s_GetAlnScores()

static void s_GetAlnScores	(	const CSeq_align &	aln,
		int &	score,
		double &	bits,
		double &	evalue
	)

static

Definition at line 293 of file alngraphic.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Std, CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetScore(), CDense_seg_Base::GetScores(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetStd(), s_GetBlastScore(), and CSeq_align_Base::C_Segs::Which().

Referenced by CAlnGraphic::x_GetAlnInfo().

◆ s_GetBlastScore()

template<class container >

static bool s_GetBlastScore	(	const container &	scoreList,
		int &	score,
		double &	bits,
		double &	evalue
	)

static

Definition at line 270 of file alngraphic.cpp.

References CObject_id_Base::GetId(), and ITERATE.

Referenced by s_GetAlnScores().

◆ s_GetGif()

static string s_GetGif ( int bits )

static

Definition at line 97 of file alngraphic.cpp.

References NcbiEmptyString.

Referenced by CAlnGraphic::x_BuildHtmlTable().

◆ s_GetRoundNumber()

static int s_GetRoundNumber ( int number )

static

Definition at line 142 of file alngraphic.cpp.

References NStr::IntToString(), number, round(), and NStr::StringToInt().

Referenced by CAlnGraphic::Init(), and CAlnGraphic::x_DisplayMaster().

◆ s_GetScoreColor()

static string s_GetScoreColor ( int bits )

static

Definition at line 121 of file alngraphic.cpp.

References NcbiEmptyString.

Referenced by CAlnGraphic::x_FormatGraphOverview().

◆ s_MapBarTemplate()

static string s_MapBarTemplate	(	string	imageTemplate,
		int	width,
		string	imgType,
		string	cssClass,
		string	score = `""`,
		string	seq = `""`,
		string	defline = `""`,
		string	acc = `""`,
		string	eval = `""`
	)