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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__AlgoAlignRoot.html below:

NCBI C++ ToolKit: Generic Global(Needleman-Wunsch) Alignment

Definition at line 189 of file nw_aligner.hpp.

◆ EUnique_type

Multiple-sequences greedy alignment uniquification algorithm.

Parameters: hri_begin Input hit range start hri_end Input hit range stop phits_new An external hit vector to keep any extra hits created during the call min_hit_len Minimum alignment length to keep min_hit_idty Minimum alignment identity to keep margin Speed/memory trade-off (0 will use max memory; >0 will slow down a bit but retain_overlap Minimum length of overlaps to keep (0 = no overlaps)

Enumerator e_Strict e_Query e_Subject

Definition at line 228 of file hit_filter.hpp.

◆ BestPos() size_t CNWAligner::CBacktraceMatrix4::BestPos ( ) const inline ◆ BestScore() TNCBIScore CNWAligner::CBacktraceMatrix4::BestScore ( ) const inline ◆ CBacktraceMatrix4() CNWAligner::CBacktraceMatrix4::CBacktraceMatrix4 ( size_t dim ) inline

Definition at line 337 of file nw_aligner.hpp.

◆ CBandAligner() [1/3] ◆ CBandAligner() [2/3] ◆ CBandAligner() [3/3] ◆ CHitCoverageAccumulator() ◆ CNWAligner() [1/3] ◆ CNWAligner() [2/3] ◆ CNWAligner() [3/3] CNWAligner::CNWAligner ( void ) ◆ CPSSMAligner() [1/3] ◆ CPSSMAligner() [2/3] ◆ CPSSMAligner() [3/3] ◆ EnableMultipleThreads() void CNWAligner::EnableMultipleThreads ( bool enable = true ) ◆ FillEdgeGaps() void CNWAligner::SAlignInOut::FillEdgeGaps ( size_t len, bool seq1_gap_fist ) inline ◆ GetBand() size_t CBandAligner::GetBand ( void ) const inline ◆ GetDefaultSpaceLimit() static size_t CNWAligner::GetDefaultSpaceLimit ( void ) inlinestatic ◆ GetDefaultWg() ◆ GetDefaultWm() ◆ GetDefaultWms() ◆ GetDefaultWs() ◆ GetDense_seg() [1/2] ◆ GetDense_seg() [2/2] ◆ GetElemSize() virtual size_t CNWAligner::GetElemSize ( void ) const inlinevirtual ◆ GetEndSpaceFree() void CNWAligner::GetEndSpaceFree ( bool * L1, bool * R1, bool * L2, bool * R2 ) const ◆ GetEndWg() TScore CPSSMAligner::GetEndWg ( ) const inline ◆ GetEndWs() TScore CPSSMAligner::GetEndWs ( ) const inline ◆ GetFreq1() const double** CPSSMAligner::GetFreq1 ( ) const inline ◆ GetFreq2() const double** CPSSMAligner::GetFreq2 ( ) const inline ◆ GetFreqScale() int CPSSMAligner::GetFreqScale ( ) const inline ◆ GetGapPreference() ◆ GetLeftSeg() size_t CNWAligner::GetLeftSeg ( size_t * q0, size_t * q1, size_t * s0, size_t * s1, size_t min_size ) const ◆ GetLongestSeg() size_t CNWAligner::GetLongestSeg ( size_t * q0, size_t * q1, size_t * s0, size_t * s1 ) const ◆ GetMatrix() ◆ GetPositivesAsMatches() bool CNWAligner::GetPositivesAsMatches ( void ) const inline

Definition at line 214 of file nw_aligner.hpp.

◆ GetPssm1() ◆ GetRightSeg() size_t CNWAligner::GetRightSeg ( size_t * q0, size_t * q1, size_t * s0, size_t * s1, size_t min_size ) const

Definition at line 1556 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g_msg_InvalidTranscriptSymbol, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_Transcript, and NCBI_THROW.

◆ GetScore() ◆ GetScoreMatrix() ◆ GetSeq1() [1/2] const char* CPSSMAligner::GetSeq1 ( void ) const inline ◆ GetSeq1() [2/2] const char* CNWAligner::GetSeq1 ( void ) const inline ◆ GetSeq2() const char* CNWAligner::GetSeq2 ( void ) const inline ◆ GetSeqLen1() size_t CNWAligner::GetSeqLen1 ( void ) const inline

Definition at line 170 of file nw_aligner.hpp.

◆ GetSeqLen2() size_t CNWAligner::GetSeqLen2 ( void ) const inline ◆ GetShift() pair< Uint1, size_t > CBandAligner::GetShift ( void ) const ◆ GetSpace() size_t CNWAligner::SAlignInOut::GetSpace ( void ) const inline ◆ GetSpaceLimit() size_t CNWAligner::GetSpaceLimit ( void ) const inline

Definition at line 183 of file nw_aligner.hpp.

◆ GetStartWg() TScore CPSSMAligner::GetStartWg ( ) const inline ◆ GetStartWs() TScore CPSSMAligner::GetStartWs ( ) const inline ◆ GetTranscript() ◆ GetTranscriptString() string CNWAligner::GetTranscriptString ( void ) const

Definition at line 931 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Intron, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CNWAligner::eTS_SlackDelete, CNWAligner::eTS_SlackInsert, g_msg_InvalidTranscriptSymbol, i, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_Transcript, NCBI_THROW, and CNWAligner::x_GetDiagTS().

Referenced by CNWFormatter::AsDenseSeg(), CNWFormatter::AsSeqAlign(), and CContigAssembly::BandedGlobalAlignment().

◆ GetWg() TScore CNWAligner::GetWg ( void ) const inline ◆ GetWm() TScore CNWAligner::GetWm ( void ) const inline ◆ GetWms() ◆ GetWs() TScore CNWAligner::GetWs ( void ) const inline ◆ IsSmithWaterman() bool CNWAligner::IsSmithWaterman ( ) const ◆ MakePattern() size_t CNWAligner::MakePattern ( const size_t hit_size = 100, const size_t core_size = 28 )

Definition at line 1462 of file nw_aligner.cpp.

References fp, g_msg_NullParameter, i, CNWAligner::m_guides, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, NCBI_THROW, CNWAligner::x_CalcFingerPrint64(), and CNWAligner::x_FindFingerPrint64().

◆ operator()() ◆ operator<() ◆ operator[]() Uint1 CNWAligner::CBacktraceMatrix4::operator[] ( size_t i ) const inline ◆ PSpace() ◆ Purge() void CNWAligner::CBacktraceMatrix4::Purge ( size_t i ) inline ◆ Run() [1/4] CRef<objects::CSeq_align> CNWAligner::Run ( objects::CScope & scope, const objects::CSeq_id & id1, const objects::CSeq_id & id2, bool trim_end_gaps = true ) ◆ Run() [2/4] CRef<objects::CSeq_align> CNWAligner::Run ( objects::CScope & scope, const objects::CSeq_loc & loc1, const objects::CSeq_loc & loc2, bool trim_end_gaps = true ) ◆ Run() [3/4]

Reimplemented in CPSSMAligner.

Definition at line 503 of file nw_aligner.cpp.

References g_msg_DataNotAvailable, g_msg_HitSpaceLimit, CNWAligner::m_guides, CNWAligner::m_score, CNWAligner::m_ScoreMatrixInvalid, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SmithWaterman, NCBI_THROW, CNWAligner::x_CheckMemoryLimit(), and CNWAligner::x_Run().

Referenced by CContigAssembly::BandedGlobalAlignment(), CInstancedAligner::x_RunMMGlobal(), and CSplign::x_SetPattern().

◆ Run() [4/4] ◆ s_GetCoverage()

Collect coverage for the range of hits on the specified source sequence.

Parameters: where Accumulation source sequence (0 = query, 1 = subject) from Hit range start to Hit range stop

Returns: The number of residues on the source sequences covered by at least one alignment

Definition at line 139 of file hit_filter.hpp.

◆ s_GetOverlap() ◆ s_GetSpan() ◆ s_MergeAbutting()

template<class THit >

static void CHitFilter< THit >::s_MergeAbutting ( typename THitRefs::iterator hri_beg, typename THitRefs::iterator hri_end, const double & maxlenfr, THitRefs * pout ) inlinestatic ◆ s_PNullRef() ◆ s_RunGreedy()

Definition at line 234 of file hit_filter.hpp.

Referenced by RemoveOverlaps(), CCleanupAlignmentsJob::x_CreateProjectItems(), CAppHitFilter::x_DoMultiple(), and CAppHitFilter::x_DoPairwise().

◆ s_TrackHit() ◆ SAlignInOut() [1/2] CNWAligner::SAlignInOut::SAlignInOut ( ) inline

Definition at line 406 of file nw_aligner.hpp.

◆ SAlignInOut() [2/2] CNWAligner::SAlignInOut::SAlignInOut ( size_t offset1, size_t len1, bool esfL1, bool esfR1, size_t offset2, size_t len2, bool esfL2, bool esfR2 ) inline ◆ ScoreFromTranscript() [1/2]

Reimplemented from CNWAligner.

Definition at line 692 of file nw_pssm_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g_msg_InvalidTranscriptSymbol, i, CPSSMAligner::kPSSM_ColumnSize, CPSSMAligner::m_EndWg, CPSSMAligner::m_EndWs, CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_FreqScale, CPSSMAligner::m_Pssm1, CNWAligner::m_ScoreMatrix, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CPSSMAligner::m_StartWg, CPSSMAligner::m_StartWs, CNWAligner::m_Wg, CNWAligner::m_Ws, n, NCBI_FSM_DIM, NCBI_THROW, SNCBIFullScoreMatrix::s, and CNWAligner::ScoreFromTranscript().

◆ ScoreFromTranscript() [2/2]

Reimplemented in CSplicedAligner32, CSplicedAligner16, and CPSSMAligner.

Definition at line 1141 of file nw_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g(), g_msg_InconsistentArguments, g_msg_InvalidTranscriptSymbol, i, CNWAligner::IsSmithWaterman(), kMax_UInt, CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_Wg, CNWAligner::m_Wm, CNWAligner::m_Wms, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, and SNCBIFullScoreMatrix::s.

Referenced by CPSSMAligner::ScoreFromTranscript(), CNWAligner::SetTranscript(), CNWAligner::x_Align(), and CNWAligner::x_Run().

◆ SetAt() void CNWAligner::CBacktraceMatrix4::SetAt ( size_t i, Uint1 v ) inline ◆ SetBand() void CBandAligner::SetBand ( size_t band ) inline ◆ SetBestPos() void CNWAligner::CBacktraceMatrix4::SetBestPos ( size_t k ) inline ◆ SetBestScore() void CNWAligner::CBacktraceMatrix4::SetBestScore ( TNCBIScore score ) inline ◆ SetEndSpaceFree() void CNWAligner::SetEndSpaceFree ( bool Left1, bool Right1, bool Left2, bool Right2 ) ◆ SetEndWg() void CPSSMAligner::SetEndWg ( TScore value ) inline ◆ SetEndWs() void CPSSMAligner::SetEndWs ( TScore value ) inline ◆ SetFreqScale() void CPSSMAligner::SetFreqScale ( const int scale ) inline ◆ SetGapPreference() ◆ SetPattern() void CNWAligner::SetPattern ( const vector< size_t > & pattern ) ◆ SetPositivesAsMatches() void CNWAligner::SetPositivesAsMatches ( bool positives_as_matches = true ) inline

Definition at line 211 of file nw_aligner.hpp.

◆ SetProgressCallback() ◆ SetScoreMatrix() [1/2]

Definition at line 1036 of file nw_aligner.cpp.

References SNCBIPackedScoreMatrix::defscore, CNWAligner::m_abc, CNWAligner::m_ScoreMatrix, CNWAligner::m_ScoreMatrixInvalid, CNWAligner::m_Wm, CNWAligner::m_Wms, NCBISM_Unpack(), SNCBIPackedScoreMatrix::scores, and SNCBIPackedScoreMatrix::symbols.

Referenced by CNWAligner::CNWAligner(), CSplign::s_CreateDefaultAligner(), CPSSMAligner::SetScoreMatrix(), and CInstancedAligner::x_RunMMGlobal().

◆ SetScoreMatrix() [2/2] ◆ SetSequences() [1/5] void CNWAligner::SetSequences ( const char * seq1, size_t len1, const char * seq2, size_t len2, bool verify = true ) virtual

Reimplemented in CPSSMAligner.

Definition at line 140 of file nw_aligner.cpp.

References g_msg_NullParameter, CNWAligner::m_Seq1, CNWAligner::m_Seq1Vec, CNWAligner::m_Seq2, CNWAligner::m_Seq2Vec, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_Transcript, NCBI_THROW, verify, and CNWAligner::x_CheckSequence().

Referenced by CNWAligner::CNWAligner(), CPSSMAligner::SetSequences(), CNWAligner::SetSequences(), and CSplign::x_SetPattern().

◆ SetSequences() [2/5] void CPSSMAligner::SetSequences ( const char * seq1, size_t len1, const char * seq2, size_t len2, bool verify = true ) virtual

Reimplemented from CNWAligner.

Definition at line 89 of file nw_pssm_aligner.cpp.

References CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_Pssm1, CPSSMAligner::m_Seq2, CNWAligner::SetSequences(), and verify.

Referenced by CPSSMAligner::CPSSMAligner(), CMultiAligner::x_AlignInClusters(), x_AlignProfileProfile(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_ComputeProfileRangeAlignment(), and CMultiAligner::x_RealignBlocks().

◆ SetSequences() [3/5]

Definition at line 101 of file nw_pssm_aligner.cpp.

References g_msg_InvalidSequenceChars, g_msg_NullParameter, i, CPSSMAligner::kPSSM_ColumnSize, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_Pssm1, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, NCBI_THROW, and verify.

◆ SetSequences() [4/5] void CPSSMAligner::SetSequences ( const double ** freq1, size_t len1, const double ** freq2, size_t len2, const int scale = 1 )

Definition at line 129 of file nw_pssm_aligner.cpp.

References g_msg_NullParameter, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_FreqScale, CPSSMAligner::m_Pssm1, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, and NCBI_THROW.

◆ SetSequences() [5/5] ◆ SetShift() void CBandAligner::SetShift ( Uint1 where, size_t offset ) ◆ SetSmithWaterman() void CNWAligner::SetSmithWaterman ( bool SW ) ◆ SetSpaceLimit() void CNWAligner::SetSpaceLimit ( const size_t & maxmem ) inline ◆ SetStartWg() void CPSSMAligner::SetStartWg ( TScore value ) inline ◆ SetStartWs() void CPSSMAligner::SetStartWs ( TScore value ) inline ◆ SetTranscript() ◆ SetWg() [1/2] void CNWAligner::SetWg ( TScore value ) inline ◆ SetWg() [2/2] void CPSSMAligner::SetWg ( TScore value ) inline ◆ SetWm() void CNWAligner::SetWm ( TScore value ) ◆ SetWms() void CNWAligner::SetWms ( TScore value ) ◆ SetWs() [1/2] void CNWAligner::SetWs ( TScore value ) inline ◆ SetWs() [2/2] void CPSSMAligner::SetWs ( TScore value ) inline ◆ SProgressInfo() CNWAligner::SProgressInfo::SProgressInfo ( void ) inline

Definition at line 147 of file nw_aligner.hpp.

◆ sx_AddMidIfNeeded() ◆ sx_AddMidPoints() ◆ sx_Cleave() ◆ sx_GetEndsInRange()

Definition at line 645 of file hit_filter.hpp.

References a, b, multiset< Key, Compare >::begin(), multiset< Key, Compare >::lower_bound(), CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, CHitFilter< THit >::SHitEnd::m_X, max(), and multiset< Key, Compare >::upper_bound().

Referenced by CHitFilter< THit >::s_RunGreedy(), and CHitFilter< THit >::sx_AddMidPoints().

◆ sx_Merge() ◆ sx_TestAndMerge() ◆ sx_TM()

Definition at line 919 of file hit_filter.hpp.

References map_checker< Container >::end(), map_checker< Container >::find(), multiset< Key, Compare >::lower_bound(), CHitFilter< THit >::SHitEnd::m_Point, CHitFilter< THit >::SHitEnd::m_Ptr, CHitFilter< THit >::SHitEnd::m_X, min(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::NotNull(), CHitFilter< THit >::sx_Merge(), and multiset< Key, Compare >::upper_bound().

Referenced by CHitFilter< THit >::sx_TestAndMerge().

◆ x_Align() [1/3]

Reimplemented from CNWAligner.

Reimplemented in CSplicedAligner32, and CSplicedAligner16.

Definition at line 110 of file nw_band_aligner.cpp.

References data, E, G, g_msg_UnexpectedTermIndex, i, kMaskD(), kMaskE(), kMaskEc(), kMaskFc(), kMax_size_t, CBandAligner::m_band, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CBandAligner::m_LastCoordSeq1, CBandAligner::m_LastCoordSeq2, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CBandAligner::m_Shift, CNWAligner::m_terminate, CBandAligner::m_TermK, CNWAligner::m_Wg, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, CNWAligner::CBacktraceMatrix4::Purge(), SNCBIFullScoreMatrix::s, CNWAligner::CBacktraceMatrix4::SetAt(), CBandAligner::x_CheckParameters(), and CBandAligner::x_DoBackTrace().

Referenced by CSplicedAligner32::x_Align().

◆ x_Align() [2/3]

Reimplemented in CPSSMAligner, CSplicedAligner32, CSplicedAligner16, and CBandAligner.

Definition at line 229 of file nw_aligner.cpp.

References copy(), data, E, CNWAligner::eLater, F, G, kMaskD, kMaskE, kMaskEc, kMaskFc, CNWAligner::m_GapPreference, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_SmithWaterman, CNWAligner::m_terminate, CNWAligner::m_Wg, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, CNWAligner::CBacktraceMatrix4::Purge(), SNCBIFullScoreMatrix::s, CNWAligner::ScoreFromTranscript(), CNWAligner::CBacktraceMatrix4::SetAt(), CNWAligner::CBacktraceMatrix4::SetBestPos(), CNWAligner::CBacktraceMatrix4::SetBestScore(), and CNWAligner::x_SWDoBackTrace().

Referenced by CNWAlignerThread_Align::Main(), CPSSMAligner::x_Align(), and CNWAligner::x_Run().

◆ x_Align() [3/3] ◆ x_AlignProfile()

Definition at line 409 of file nw_pssm_aligner.cpp.

References data, E, G, i, kMaskD, kMaskE, kMaskEc, kMaskFc, CPSSMAligner::kPSSM_ColumnSize, CPSSMAligner::m_DScoreMatrix, CPSSMAligner::m_EndWg, CPSSMAligner::m_EndWs, CPSSMAligner::m_Freq1, CPSSMAligner::m_Freq2, CPSSMAligner::m_FreqScale, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CPSSMAligner::m_StartWg, CPSSMAligner::m_StartWs, CNWAligner::m_terminate, CNWAligner::m_Wg, CNWAligner::m_Ws, n, CNWAligner::CBacktraceMatrix4::Purge(), CNWAligner::CBacktraceMatrix4::SetAt(), and CNWAligner::x_DoBackTrace().

Referenced by CPSSMAligner::x_Align().

◆ x_AlignPSSM()

Definition at line 220 of file nw_pssm_aligner.cpp.

References data, E, G, i, kMaskD, kMaskE, kMaskEc, kMaskFc, CPSSMAligner::m_EndWg, CPSSMAligner::m_EndWs, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CPSSMAligner::m_Pssm1, CPSSMAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CPSSMAligner::m_StartWg, CPSSMAligner::m_StartWs, CNWAligner::m_terminate, CNWAligner::m_Wg, CNWAligner::m_Ws, CNWAligner::CBacktraceMatrix4::Purge(), CNWAligner::CBacktraceMatrix4::SetAt(), and CNWAligner::x_DoBackTrace().

Referenced by CPSSMAligner::x_Align().

◆ x_CalcFingerPrint64() unsigned char CNWAligner::x_CalcFingerPrint64 ( const char * beg, const char * end, size_t & err_index ) protected ◆ x_CheckMemoryLimit() [1/2] bool CNWAligner::x_CheckMemoryLimit ( void ) protectedvirtual ◆ x_CheckMemoryLimit() [2/2] bool CBandAligner::x_CheckMemoryLimit ( void ) protectedvirtual ◆ x_CheckParameters() ◆ x_CheckSequence() size_t CNWAligner::x_CheckSequence ( const char * seq, size_t len ) const protected ◆ x_DoBackTrace() [1/2]

Definition at line 359 of file nw_band_aligner.cpp.

References abs, data, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, g_msg_InvalidBacktraceData, kMaskD(), kMaskE(), kMaskEc(), kMaskFc(), kMax, kMax_size_t, CBandAligner::m_band, CBandAligner::m_LastCoordSeq1, CBandAligner::m_LastCoordSeq2, CBandAligner::m_Shift, CBandAligner::m_TermK, NCBI_THROW, and CNWAligner::x_GetDiagTS().

Referenced by CBandAligner::x_Align().

◆ x_DoBackTrace() [2/2] ◆ x_FindFingerPrint64() const char * CNWAligner::x_FindFingerPrint64 ( const char * beg, const char * end, unsigned char fingerprint, size_t size, size_t & err_index ) protected ◆ x_GetDiagTS() [1/2]

Reimplemented in CPSSMAligner.

Definition at line 707 of file nw_aligner.cpp.

References CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CNWAligner::m_PositivesAsMatches, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, SNCBIFullScoreMatrix::s, and toupper().

Referenced by CNWAligner::GetTranscriptString(), CBandAligner::x_DoBackTrace(), CNWAligner::x_DoBackTrace(), CSplicedAligner16::x_DoBackTrace(), CSplicedAligner32::x_DoBackTrace(), CPSSMAligner::x_GetDiagTS(), and CNWAligner::x_SWDoBackTrace().

◆ x_GetDiagTS() [2/2] ◆ x_Run()

Reimplemented in CMMAligner.

Definition at line 533 of file nw_aligner.cpp.

References CNWAligner::CNWAlignerThread_Align, copy(), data, CNWAligner::eTS_Match, g_msg_OutOfSpace, CNWAligner::GetTranscript(), i, ITERATE, CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, CNWAligner::m_guides, CNWAligner::m_maxthreads, CNWAligner::m_mt, CNWAligner::m_score, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, CNWAligner::m_Transcript, NCBI_THROW, NON_CONST_ITERATE, NW_RequestNewThread(), CNWAligner::SAlignInOut::PSpace(), CThread::Run(), CNWAligner::ScoreFromTranscript(), and CNWAligner::x_Align().

Referenced by CNWAligner::Run(), and CPSSMAligner::Run().

◆ x_SWDoBackTrace()

Definition at line 778 of file nw_aligner.cpp.

References CNWAligner::CBacktraceMatrix4::BestPos(), CNWAligner::CBacktraceMatrix4::BestScore(), data, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, kMaskD, kMaskE, kMaskEc, kMaskFc, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SmithWaterman, CNWAligner::m_Wg, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, SNCBIFullScoreMatrix::s, and CNWAligner::x_GetDiagTS().

Referenced by CNWAligner::x_Align().

◆ ~CBacktraceMatrix4() CNWAligner::CBacktraceMatrix4::~CBacktraceMatrix4 ( ) inline

Definition at line 344 of file nw_aligner.hpp.

◆ ~CBandAligner() virtual CBandAligner::~CBandAligner ( void ) inlinevirtual

Definition at line 71 of file nw_band_aligner.hpp.

◆ ~CNWAligner() virtual CNWAligner::~CNWAligner ( void ) inlinevirtual

Definition at line 88 of file nw_aligner.hpp.

◆ ~CPSSMAligner() virtual CPSSMAligner::~CPSSMAligner ( void ) inlinevirtual

Definition at line 76 of file nw_pssm_aligner.hpp.

◆ kPSSM_ColumnSize const int CPSSMAligner::kPSSM_ColumnSize = 28 staticprotected ◆ m_abc const char* CNWAligner::m_abc protected ◆ m_band size_t CBandAligner::m_band protected ◆ m_BestPos size_t CNWAligner::CBacktraceMatrix4::m_BestPos private

Definition at line 383 of file nw_aligner.hpp.

◆ m_BestScore ◆ m_Buf ◆ m_data void* CNWAligner::SProgressInfo::m_data ◆ m_DScoreMatrix ◆ m_Elem ◆ m_EndWg ◆ m_EndWs ◆ m_esf_L1 [1/2] bool CNWAligner::m_esf_L1 protected ◆ m_esf_L1 [2/2] ◆ m_esf_L2 [1/2] bool CNWAligner::m_esf_L2 protected

Definition at line 274 of file nw_aligner.hpp.

Referenced by CNWAligner::GetEndSpaceFree(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetEndSpaceFree(), CNWAligner::SetSmithWaterman(), CMMAligner::x_FindBestJ(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

◆ m_esf_L2 [2/2] ◆ m_esf_R1 [1/2] bool CNWAligner::m_esf_R1 protected ◆ m_esf_R1 [2/2] ◆ m_esf_R2 [1/2] bool CNWAligner::m_esf_R2 protected

Definition at line 274 of file nw_aligner.hpp.

◆ m_esf_R2 [2/2] ◆ m_Finish ◆ m_Freq1 const double** CPSSMAligner::m_Freq1 protected ◆ m_Freq2 const double** CPSSMAligner::m_Freq2 protected ◆ m_FreqScale int CPSSMAligner::m_FreqScale protected ◆ m_GapPreference ◆ m_guides vector<size_t> CNWAligner::m_guides protected ◆ m_i1 ◆ m_i2 ◆ m_iter_done size_t CNWAligner::SProgressInfo::m_iter_done ◆ m_iter_total size_t CNWAligner::SProgressInfo::m_iter_total ◆ m_LastCoordSeq1 size_t CBandAligner::m_LastCoordSeq1 protected ◆ m_LastCoordSeq2 size_t CBandAligner::m_LastCoordSeq2 protected ◆ m_len1 size_t CNWAligner::SAlignInOut::m_len1 ◆ m_len2 size_t CNWAligner::SAlignInOut::m_len2 ◆ m_MaxMem size_t CNWAligner::m_MaxMem protected ◆ m_maxthreads size_t CNWAligner::m_maxthreads protected ◆ m_mt ◆ m_offset1 size_t CNWAligner::SAlignInOut::m_offset1

Definition at line 419 of file nw_aligner.hpp.

◆ m_offset2 size_t CNWAligner::SAlignInOut::m_offset2

Definition at line 424 of file nw_aligner.hpp.

◆ m_Point ◆ m_PositivesAsMatches bool CNWAligner::m_PositivesAsMatches protected ◆ m_prg_callback ◆ m_prg_info ◆ m_Pssm1 ◆ m_Ptr ◆ m_score ◆ m_ScoreMatrix

Definition at line 281 of file nw_aligner.hpp.

Referenced by CPSSMAligner::GetMatrix(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetScoreMatrix(), CPSSMAligner::SetScoreMatrix(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CNWAligner::x_GetDiagTS(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

◆ m_ScoreMatrixInvalid bool CNWAligner::m_ScoreMatrixInvalid protected ◆ m_Seq1 const char* CNWAligner::m_Seq1 protected

Definition at line 295 of file nw_aligner.hpp.

Referenced by CNWAligner::GetLeftSeg(), CNWAligner::GetLongestSeg(), CNWAligner::GetRightSeg(), CPSSMAligner::GetSeq1(), CNWAligner::GetTranscriptString(), CNWAligner::MakePattern(), CNWAligner::Run(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CNWAligner::x_GetDiagTS(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

◆ m_Seq1Vec vector<char> CNWAligner::m_Seq1Vec protected ◆ m_Seq2 [1/2] const char* CNWAligner::m_Seq2 protected

Definition at line 298 of file nw_aligner.hpp.

Referenced by CNWAligner::GetLeftSeg(), CNWAligner::GetLongestSeg(), CNWAligner::GetRightSeg(), CNWAligner::GetTranscriptString(), CNWAligner::MakePattern(), CNWAligner::Run(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CNWAligner::x_GetDiagTS(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

◆ m_Seq2 [2/2] const char* CPSSMAligner::m_Seq2 protected ◆ m_Seq2Vec vector<char> CNWAligner::m_Seq2Vec protected ◆ m_SeqLen1 size_t CNWAligner::m_SeqLen1 protected

Definition at line 296 of file nw_aligner.hpp.

Referenced by CNWAligner::GetRightSeg(), CNWAligner::MakePattern(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::SetPattern(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CNWAligner::x_CheckMemoryLimit(), CBandAligner::x_CheckMemoryLimit(), CMMAligner::x_DoSubmatrix(), CMMAligner::x_Run(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), and CMMAligner::x_RunTerm().

◆ m_SeqLen2 size_t CNWAligner::m_SeqLen2 protected

Definition at line 299 of file nw_aligner.hpp.

Referenced by CNWAligner::GetRightSeg(), CNWAligner::MakePattern(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::SetPattern(), CNWAligner::SetSequences(), CPSSMAligner::SetSequences(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CNWAligner::x_CheckMemoryLimit(), CBandAligner::x_CheckMemoryLimit(), CMMAligner::x_DoSubmatrix(), CMMAligner::x_FindBestJ(), CMMAligner::x_Run(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

◆ m_Shift long CBandAligner::m_Shift protected ◆ m_SmithWaterman bool CNWAligner::m_SmithWaterman protected ◆ m_space size_t CNWAligner::SAlignInOut::m_space private ◆ m_StartWg TScore CPSSMAligner::m_StartWg protected ◆ m_StartWs TScore CPSSMAligner::m_StartWs protected ◆ m_terminate bool CNWAligner::m_terminate mutableprotected

Definition at line 291 of file nw_aligner.hpp.

Referenced by CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_DoSubmatrix(), CMMAligner::x_Run(), CNWAligner::x_Run(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

◆ m_TermK size_t CBandAligner::m_TermK protected ◆ m_text_buffer char CNWAligner::SProgressInfo::m_text_buffer[1024]

Definition at line 151 of file nw_aligner.hpp.

◆ m_Transcript

Definition at line 314 of file nw_aligner.hpp.

Referenced by CSplicedAligner::CheckPreferences(), CNWAligner::GetLeftSeg(), CNWAligner::GetLongestSeg(), CNWAligner::GetRightSeg(), CNWAligner::GetScore(), CNWAligner::GetTranscript(), CNWAligner::GetTranscriptString(), CNWAligner::SetSequences(), CNWAligner::SetTranscript(), CMMAligner::x_Run(), and CNWAligner::x_Run().

◆ m_transcript ◆ m_Wg

Definition at line 270 of file nw_aligner.hpp.

Referenced by CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CPSSMAligner::SetWg(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_FindBestJ(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

◆ m_Where ◆ m_Wm ◆ m_Wms ◆ m_Ws

Definition at line 271 of file nw_aligner.hpp.

Referenced by CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CPSSMAligner::SetWs(), CBandAligner::x_Align(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CNWAligner::x_Align(), CPSSMAligner::x_AlignProfile(), CPSSMAligner::x_AlignPSSM(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), CMMAligner::x_RunTop(), and CNWAligner::x_SWDoBackTrace().

◆ m_X ◆ CNWAlignerThread_Align ◆ operator<<

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