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 char *	kGif [kNumSeqalignMatchTypes+2]
static const char *	kGifLegend []
static const char *	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

info1	the first seqalign
info2	the second seqalign

Definition at line 128 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

info1	the first seqalign
info2	the second seqalign

Definition at line 154 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

seqalign

the seqalign

Definition at line 87 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

const char* kGif[kNumSeqalignMatchTypes+2]

static

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 char* 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 char* 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().