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NCBI C++ ToolKit: CMultAlign Class Reference

#include <algo/gnomon/variations.hpp>

void SetDefaultParams () void SelectAligns (vector< const CLiteAlign * > &all_alignsp) void PrepareReads (const vector< const CLiteAlign * > &all_alignsp) void InsertDashesInBase () void InsertDashesInReads () void GetCounts () void PrepareStats () TSignedSeqRange LegitRange (int ir) string EmitSequenceFromRead (int ir, const TSignedSeqRange &word_range) string EmitSequenceFromBase (const TSignedSeqRange &word_range) bool CheckWord (const TSignedSeqRange &word_range, const string &word) int FindNextStrongWord (int nextp, const string &maximal_bases, string &strong_word, TSignedSeqRange &strong_word_range, int &first_gap) void SeqCountsBetweenTwoStrongWords (const TSignedSeqRange &prev_strong_word_range, const string &prev_strong_word, const TSignedSeqRange &strong_word_range, const string &strong_word, TSIMap &seq_counts, int &total_cross, int &accepted_cross)

Definition at line 91 of file variations.hpp.

◆ TCharIntMap ◆ TIntMap ◆ CMultAlign() [1/3] CMultAlign::CMultAlign ( ) inline ◆ CMultAlign() [2/3] ◆ CMultAlign() [3/3] ◆ AddAlignment() [1/2]

Definition at line 198 of file variations.cpp.

References count, CGeneModel::Exons(), CGeneModel::FrameShifts(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), GroupInDels(), i, int, ITERATE, m_aligns, m_indel_holder, m_maxNs, m_min_edge, CRange_Base::SetFrom(), CRange_Base::SetTo(), and CGeneModel::Weight().

◆ AddAlignment() [2/2] ◆ CheckWord() ◆ EmitSequenceFromBase() ◆ EmitSequenceFromRead() ◆ FindNextStrongWord() ◆ GetCounts() void CMultAlign::GetCounts ( void ) private ◆ GetVariationAlignList()

Definition at line 249 of file variations.cpp.

References a, count, delta(), CCigar::Distance(), CSeq_id_Base::e_Local, ePlus, CGeneModel::eSR, CRange_Base::GetFrom(), CCigar::GetInDels(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), GlbAlign(), i, NStr::IntToString(), ITERATE, m_contig_id, m_contigt, m_word, max(), and Variations().

◆ InsertDashesInBase() void CMultAlign::InsertDashesInBase ( ) private

Definition at line 348 of file variations.cpp.

References map_checker< Container >::begin(), map_checker< Container >::end(), map_checker< Container >::find(), i, int, ITERATE, l(), len, m_align_to_contig, m_alignsp, m_base, m_contig_to_align, m_contigt, m_reads, max(), n, NON_CONST_ITERATE, and prev().

Referenced by PrepareStats().

◆ InsertDashesInReads() void CMultAlign::InsertDashesInReads ( ) private

Definition at line 400 of file variations.cpp.

References _ASSERT, base_length, map_checker< Container >::insert(), int, ITERATE, len, m_alignsp, m_base, m_contig_to_align, m_reads, m_starts, n, r(), and map_checker< Container >::size().

Referenced by PrepareStats().

◆ LegitRange() ◆ PrepareReads() ◆ PrepareStats() void CMultAlign::PrepareStats ( ) private ◆ ProcessArgs() void CMultAlign::ProcessArgs ( const CArgs & args ) ◆ SelectAligns() void CMultAlign::SelectAligns ( vector< const CLiteAlign * > & all_alignsp ) private ◆ SeqCountsBetweenTwoStrongWords() ◆ SetDefaultParams() void CMultAlign::SetDefaultParams ( ) private ◆ SetGenomic()

Definition at line 171 of file variations.cpp.

References map_checker< Container >::clear(), set< Key, Compare >::clear(), CBioseq_Handle::eCoding_Iupac, CScope::GetBioseqHandle(), CSeqVector::GetSeqData(), CSeq_id::GetSeqIdString(), CBioseq_Handle::GetSeqVector(), m_align_to_contig, m_aligns, m_alignsp, m_base, m_contig_id, m_contig_to_align, m_contigt, m_counts, m_indel_holder, m_max_len, m_reads, m_starts, and CSeqVector::size().

Referenced by CMultAlign().

◆ SetupArgDescriptions() ◆ Variations()

Definition at line 547 of file variations.cpp.

References _ASSERT, map_checker< Container >::begin(), count, map_checker< Container >::empty(), COpenRange< Position >::Empty(), map_checker< Container >::end(), FindNextStrongWord(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), i, int, ITERATE, m_align_to_contig, m_aligns, m_base, m_contigt, m_counts, m_min_abs_support_for_variant, m_min_coverage, m_min_rel_support_for_variant, max(), COpenRange< Position >::NotEmpty(), PrepareStats(), SeqCountsBetweenTwoStrongWords(), CRange_Base::SetFrom(), CRange_Base::SetTo(), map_checker< Container >::size(), and t.

Referenced by GetVariationAlignList().

◆ m_align_to_contig TIntMap CMultAlign::m_align_to_contig private ◆ m_aligns ◆ m_alignsp ◆ m_base ◆ m_contig_id string CMultAlign::m_contig_id private ◆ m_contig_to_align TIntMap CMultAlign::m_contig_to_align private ◆ m_contigt ◆ m_counts ◆ m_indel_holder ◆ m_max_len int CMultAlign::m_max_len private ◆ m_maxNs ◆ m_min_abs_support_for_variant int CMultAlign::m_min_abs_support_for_variant private ◆ m_min_coverage int CMultAlign::m_min_coverage private ◆ m_min_edge int CMultAlign::m_min_edge private ◆ m_min_rel_support_for_variant double CMultAlign::m_min_rel_support_for_variant private ◆ m_reads vector<string> CMultAlign::m_reads private ◆ m_starts vector<int> CMultAlign::m_starts private ◆ m_strong_consensus double CMultAlign::m_strong_consensus private ◆ m_word

The documentation for this class was generated from the following files:

include/algo/gnomon/variations.hpp
src/algo/gnomon/variations.cpp

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