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NCBI C++ ToolKit: src/algo/primer/primercheck.cpp File Reference

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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_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)   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 bool  SortHitByTopHspScores (TSortedHsp const &info1, TSortedHsp const &info2)   ◆ s_CountGaps() ◆ s_DoNWalign()

Definition at line 291 of file primercheck.cpp.

References CSeq_id::Assign(), CBioseq_Handle::eCoding_Iupac, eNa_strand_minus, eNa_strand_plus, CDense_seg::FromTranscript(), CAlnVec::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CRange_Base::GetFrom(), GetSeqData(), CAlnMap::GetSeqId(), CBioseq_Handle::GetSeqVector(), i, CAlnMap::IsPositiveStrand(), max(), min(), NULL, s_CountGaps(), and CDense_seg_Base::SetIds().

Referenced by COligoSpecificityCheck::x_NW_alignment().

◆ SeqLocAllowed() ◆ SortHitByTopHspScores() ◆ SortHspByMasterStartAscending() ◆ SortIndexListByScoreDescending() ◆ SortPrimerHitByMismatchAscending() ◆ SortPrimerHitInGroupByMismatchAscending() ◆ USING_SCOPE() [1/2] ◆ USING_SCOPE() [2/2] ◆ k_MaxReliableGapNum ◆ k_Min_Percent_Identity const double k_Min_Percent_Identity = 0.64999 static ◆ k_MinOverlapLenFactor const double k_MinOverlapLenFactor = 0.45 static ◆ USING_NCBI_SCOPE

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