NCBI C++ ToolKit
Functions | Variables
alngraphic.cpp File Reference
#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:

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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

◆ 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

◆ 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 = "" 
)
static

◆ s_MapSeqInfoTemplate()

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

◆ USING_SCOPE() [1/2]

USING_SCOPE ( align_format  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( sequence  )

Variable Documentation

◆ kBlack

const char* kBlack = "black"

Definition at line 119 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_FormatGraphOverview().

◆ kBlankBarHeight

const TSeqPos kBlankBarHeight = 4

Definition at line 66 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_BuildHtmlTable().

◆ kDeflineLength

const int kDeflineLength = 55

Definition at line 83 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_GetAlnInfo().

◆ kDigitGif

const char* kDigitGif[]
Initial value:
= {"0.gif", "1.gif", "2.gif", "3.gif", "4.gif",
"5.gif", "6.gif", "7.gif", "8.gif", "9.gif"}

Definition at line 59 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_DisplayMaster().

◆ kDigitHeight

const TSeqPos kDigitHeight = 13

Definition at line 77 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_DisplayMaster().

◆ kDigitWidth

const TSeqPos kDigitWidth = 10

◆ kGapHeight

const TSeqPos kGapHeight = 1

◆ kGifBlack

const char* kGifBlack = "black.gif"

Definition at line 95 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_BuildHtmlTable().

◆ kGifGrey

const char* kGifGrey = "grey.gif"

Definition at line 93 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_BuildHtmlTable().

◆ kGifMaster

const char* kGifMaster ="query_no_scale.gif"

Definition at line 91 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_PrintTop().

◆ kGifScale

const char* kGifScale = "scale.gif"

Definition at line 94 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_DisplayMaster().

◆ kGifScore

const char* kGifScore = "score.gif"

Definition at line 92 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_PrintTop().

◆ kGifWhite

const char* kGifWhite = "white.gif"

◆ kGreakHeight

const TSeqPos kGreakHeight = 6

◆ kGrey

const char* kGrey = "grey"

Definition at line 118 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_FormatGraphOverview().

◆ kMasterBarLength

const TSeqPos kMasterBarLength = 550

Definition at line 70 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_PrintTop().

◆ kMasterHeight

const TSeqPos kMasterHeight = 10

Definition at line 68 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_PrintTop().

◆ kMasterPixel

const TSeqPos kMasterPixel = kScoreLength

◆ kNumMark

const TSeqPos kNumMark = 6

Definition at line 81 of file alngraphic.cpp.

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

◆ kOverlapDiff

const int kOverlapDiff = 5
static

Definition at line 87 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_MergeDifferentSeq().

◆ kScaleHeight

const TSeqPos kScaleHeight = 10

Definition at line 74 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_DisplayMaster().

◆ kScaleMarginAdj

const TSeqPos kScaleMarginAdj = 1

Definition at line 72 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_DisplayMaster().

◆ kScaleWidth

const TSeqPos kScaleWidth = 2

Definition at line 73 of file alngraphic.cpp.

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

◆ kScoreHeight

const TSeqPos kScoreHeight = 40

Definition at line 64 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_PrintTop().

◆ kScoreLength

const TSeqPos kScoreLength = 500

Definition at line 63 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_BuildHtmlTable(), and CAlnGraphic::x_PrintTop().

◆ kScoreMargin

const TSeqPos kScoreMargin = 50

◆ kWhite

const char* kWhite = "white"

Definition at line 117 of file alngraphic.cpp.

Referenced by CAlnGraphic::x_FormatGraphOverview().

Modified on Wed Feb 21 09:57:48 2024 by modify_doxy.py rev. 669887