NCBI C++ ToolKit
Functions | Variables
primercheck.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbistre.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
#include <objmgr/object_manager.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <algo/align/nw/nw_aligner.hpp>
#include <algo/align/nw/nw_formatter.hpp>
#include <algo/primer/primercheck.hpp>
+ Include dependency graph for primercheck.cpp:

Go to the source code of this file.

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 USING_SCOPE (objects)
 USING_SCOPE (sequence)
static void s_CountGaps (const string &xcript, TSeqPos &master_start_gap, TSeqPos &master_end_gap, TSeqPos &slave_start_gap, TSeqPos &slave_end_gap, char master_gap_char, char slave_gap_char)
CRef< CDense_segs_DoNWalign (const CRange< TSeqPos > &desired_align_range, string &master_seq, const CAlnVec &av, TSeqPos hit_full_start, TSeqPos hit_full_stop, ENa_strand hit_strand, string &xcript, bool &nw_align_modified)
static bool SeqLocAllowed (const list< CRef< CSeq_loc > > &allowed_seq, const CSeq_id &hit_id, const CRange< TSeqPos > &hit_range, CScope &scope)
static bool SortHspByMasterStartAscending (const SHspInfo *info1, const SHspInfo *info2)
static bool SortIndexListByScoreDescending (const COligoSpecificityCheck::SHspIndexInfo &info1, const COligoSpecificityCheck::SHspIndexInfo &info2)
static bool SortPrimerHitInGroupByMismatchAscending (const COligoSpecificityCheck::SPrimerHitInfo *info1, const COligoSpecificityCheck::SPrimerHitInfo *info2)
static bool SortPrimerHitByMismatchAscending (const vector< COligoSpecificityCheck::SPrimerHitInfo * > *info1, const vector< COligoSpecificityCheck::SPrimerHitInfo * > *info2)


static const double k_MinOverlapLenFactor = 0.45
static const double k_Min_Percent_Identity = 0.64999
static const int k_MaxReliableGapNum = 3

Function Documentation

◆ s_CountGaps()

static void s_CountGaps ( const string xcript,
TSeqPos master_start_gap,
TSeqPos master_end_gap,
TSeqPos slave_start_gap,
TSeqPos slave_end_gap,
char  master_gap_char,
char  slave_gap_char 

Definition at line 149 of file primercheck.cpp.

References i, and int.

Referenced by s_DoNWalign().

◆ s_DoNWalign()

CRef<CDense_seg> s_DoNWalign ( const CRange< TSeqPos > &  desired_align_range,
string master_seq,
const CAlnVec av,
TSeqPos  hit_full_start,
TSeqPos  hit_full_stop,
ENa_strand  hit_strand,
string xcript,
bool nw_align_modified 

◆ SeqLocAllowed()

static bool SeqLocAllowed ( const list< CRef< CSeq_loc > > &  allowed_seq,
const CSeq_id hit_id,
const CRange< TSeqPos > &  hit_range,
CScope scope 

◆ SortHspByMasterStartAscending()

static bool SortHspByMasterStartAscending ( const SHspInfo info1,
const SHspInfo info2 

◆ SortIndexListByScoreDescending()

static bool SortIndexListByScoreDescending ( const COligoSpecificityCheck::SHspIndexInfo info1,
const COligoSpecificityCheck::SHspIndexInfo info2 

◆ SortPrimerHitByMismatchAscending()

static bool SortPrimerHitByMismatchAscending ( const vector< COligoSpecificityCheck::SPrimerHitInfo * > *  info1,
const vector< COligoSpecificityCheck::SPrimerHitInfo * > *  info2 

Definition at line 1825 of file primercheck.cpp.

References ITERATE, and min().

Referenced by COligoSpecificityCheck::x_SortPrimerHit().

◆ SortPrimerHitInGroupByMismatchAscending()

static bool SortPrimerHitInGroupByMismatchAscending ( const COligoSpecificityCheck::SPrimerHitInfo info1,
const COligoSpecificityCheck::SPrimerHitInfo info2 

Definition at line 1803 of file primercheck.cpp.

References min().

Referenced by COligoSpecificityCheck::x_SortPrimerHit().

◆ USING_SCOPE() [1/2]

USING_SCOPE ( objects  )

◆ USING_SCOPE() [2/2]

USING_SCOPE ( sequence  )

Variable Documentation

◆ k_MaxReliableGapNum

const int k_MaxReliableGapNum = 3

Definition at line 68 of file primercheck.cpp.

Referenced by COligoSpecificityCheck::x_FindMatchInfoForAlignment().

◆ k_Min_Percent_Identity

const double k_Min_Percent_Identity = 0.64999

Definition at line 67 of file primercheck.cpp.

Referenced by COligoSpecificityCheck::x_FillGlobalAlignInfo().

◆ k_MinOverlapLenFactor

const double k_MinOverlapLenFactor = 0.45



Definition at line 61 of file primercheck.cpp.

Modified on Fri Mar 01 10:05:05 2024 by rev. 669887