NCBI C++ ToolKit
Functions | Variables
vectorscreen.cpp File Reference
#include <ncbi_pch.hpp>
#include <objtools/align_format/vectorscreen.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 <html/html.hpp>
+ Include dependency graph for vectorscreen.cpp:

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Functions

 USING_SCOPE (objects)
 
static void s_RestoreHspPos (CSeq_align_set &seqalign)
 group hsp with same id togather More...
 
static bool AlnFromRangeAscendingSort (CRef< CSeq_align > const &info1, CRef< CSeq_align > const &info2)
 Sort on seqalign range from. More...
 
static bool AlnScoreDescendingSort (CRef< CSeq_align > const &info1, CRef< CSeq_align > const &info2)
 Sort on sealign score. More...
 

Variables

static const int kNumSeqalignMatchTypes = 3
 
static const int kTerminalMatchScore [kNumSeqalignMatchTypes] = {24, 19, 16}
 
static const int kInternalMatchScore [kNumSeqalignMatchTypes] = {30, 25, 23}
 
static const string kGif [kNumSeqalignMatchTypes+2]
 
static const string kGifLegend []
 
static const string kMatchUrlLegend []
 
static const TSeqPos kSupectLength = 50
 
static const TSeqPos kMasterPixel = 600
 
static const TSeqPos kBarHeight = 20
 
static const TSeqPos kNumScales = 5
 

Function Documentation

◆ AlnFromRangeAscendingSort()

static bool AlnFromRangeAscendingSort ( CRef< CSeq_align > const info1,
CRef< CSeq_align > const info2 
)
static

Sort on seqalign range from.

Parameters
info1the first seqalign
info2the second seqalign

Definition at line 130 of file vectorscreen.cpp.

References CAlignFormatUtil::GetAlnScores(), CRange_Base::GetFrom(), and CSeq_align::GetSeqRange().

Referenced by CVecscreen::x_MergeSeqalign().

◆ AlnScoreDescendingSort()

static bool AlnScoreDescendingSort ( CRef< CSeq_align > const info1,
CRef< CSeq_align > const info2 
)
static

Sort on sealign score.

Parameters
info1the first seqalign
info2the second seqalign

Definition at line 156 of file vectorscreen.cpp.

References CAlignFormatUtil::GetAlnScores().

Referenced by CVecscreen::ProcessSeqAlign(), CVecscreen::x_MergeLowerRankSeqalign(), and CVecscreen::x_MergeSeqalign().

◆ s_RestoreHspPos()

static void s_RestoreHspPos ( CSeq_align_set seqalign)
static

group hsp with same id togather

Parameters
seqalignthe seqalign

Definition at line 89 of file vectorscreen.cpp.

References CSeq_id::Match(), and CSeq_align_set_Base::Set().

Referenced by CVecscreen::ProcessSeqAlign().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kBarHeight

const TSeqPos kBarHeight = 20
static

Definition at line 70 of file vectorscreen.cpp.

Referenced by CVecscreen::x_BuildHtmlBar().

◆ kGif

Initial value:
=
{"red.gif", "purple.gif", "green.gif", "yellow.gif", "white.gif"}

Definition at line 60 of file vectorscreen.cpp.

Referenced by CVecscreen::x_BuildHtmlBar().

◆ kGifLegend

const string kGifLegend[]
static
Initial value:
=
{"Strong", "Moderate", "Weak", "Suspect"}

Definition at line 62 of file vectorscreen.cpp.

Referenced by CVecscreen::GetStrengthString(), and CVecscreen::x_BuildHtmlBar().

◆ kInternalMatchScore

const int kInternalMatchScore[kNumSeqalignMatchTypes] = {30, 25, 23}
static

Definition at line 58 of file vectorscreen.cpp.

Referenced by CVecscreen::x_GetMatchType().

◆ kMasterPixel

const TSeqPos kMasterPixel = 600
static

Definition at line 69 of file vectorscreen.cpp.

Referenced by CVecscreen::x_BuildHtmlBar().

◆ kMatchUrlLegend

const string kMatchUrlLegend[]
static
Initial value:
=
{"Strong match", "Moderate match", "Weak match", "Suspect origin"}

Definition at line 64 of file vectorscreen.cpp.

Referenced by CVecscreen::x_BuildHtmlBar().

◆ kNumScales

const TSeqPos kNumScales = 5
static

Definition at line 71 of file vectorscreen.cpp.

Referenced by CVecscreen::x_BuildHtmlBar().

◆ kNumSeqalignMatchTypes

const int kNumSeqalignMatchTypes = 3
static

Definition at line 54 of file vectorscreen.cpp.

Referenced by CVecscreen::x_BuildHtmlBar(), and CVecscreen::x_MergeSeqalign().

◆ kSupectLength

const TSeqPos kSupectLength = 50
static

Definition at line 67 of file vectorscreen.cpp.

Referenced by CVecscreen::x_BuildNonOverlappingRange().

◆ kTerminalMatchScore

const int kTerminalMatchScore[kNumSeqalignMatchTypes] = {24, 19, 16}
static

Definition at line 57 of file vectorscreen.cpp.

Referenced by CVecscreen::x_GetEdgeRanges(), and CVecscreen::x_GetMatchType().

Modified on Fri Mar 01 10:06:48 2024 by modify_doxy.py rev. 669887