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

NCBI C++ ToolKit: Spliced cDna-to-Genomic Alignment

void  CSplicedAligner::SetWi (unsigned char splice_type, TScore value)   TScore  CSplicedAligner::GetWi (unsigned char splice_type)   void  CSplicedAligner::SetCDS (size_t cds_start, size_t cds_stop)   void  CSplicedAligner::SetIntronMinSize (size_t s)   size_t  CSplicedAligner::GetIntronMinSize (void) const   static size_t  CSplicedAligner::GetDefaultIntronMinSize (void)   void  CSplicedAligner::CheckPreferences (void)   virtual size_t  CSplicedAligner::GetSpliceTypeCount (void)=0     CSplicedAligner::CSplicedAligner ()     CSplicedAligner::CSplicedAligner (const char *seq1, size_t len1, const char *seq2, size_t len2)     CSplicedAligner::CSplicedAligner (const string &seq1, const string &seq2)   virtual bool  CSplicedAligner::x_CheckMemoryLimit (void)   virtual TScore *  CSplicedAligner::x_GetSpliceScores ()=0     CSplicedAligner::SAllocator< T >::SAllocator (size_t N)     CSplicedAligner::SAllocator< T >::~SAllocator ()   T *  CSplicedAligner::SAllocator< T >::GetPointer (void)     CSplicedAligner16::CSplicedAligner16 (void)     CSplicedAligner16::CSplicedAligner16 (const char *seq1, size_t len1, const char *seq2, size_t len2)     CSplicedAligner16::CSplicedAligner16 (const string &seq1, const string &seq2)   static TScore  CSplicedAligner16::GetDefaultWi (unsigned char splice_type)   virtual size_t  CSplicedAligner16::GetElemSize (void) const   virtual size_t  CSplicedAligner16::GetSpliceTypeCount (void)   virtual TScore  CSplicedAligner16::ScoreFromTranscript (const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const   virtual TScore *  CSplicedAligner16::x_GetSpliceScores (void)   virtual TScore  CSplicedAligner16::x_Align (CNWAligner::SAlignInOut *data)   void  CSplicedAligner16::x_DoBackTrace (const Uint2 *backtrace_matrix, CNWAligner::SAlignInOut *data, size_t i_global_max, size_t j_global_max)     CSplicedAligner32::CSplicedAligner32 (void)     CSplicedAligner32::CSplicedAligner32 (const char *seq1, size_t len1, const char *seq2, size_t len2)     CSplicedAligner32::CSplicedAligner32 (const string &seq1, const string &seq2)   static TScore  CSplicedAligner32::GetDefaultWi (unsigned char splice_type)   static TScore  CSplicedAligner32::GetDefaultWd1 (void)   static TScore  CSplicedAligner32::GetDefaultWd2 (void)   virtual size_t  CSplicedAligner32::GetElemSize (void) const   virtual size_t  CSplicedAligner32::GetSpliceTypeCount (void)   virtual TScore  CSplicedAligner32::ScoreFromTranscript (const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const   virtual TScore *  CSplicedAligner32::x_GetSpliceScores (void)   virtual TScore  CSplicedAligner32::x_Align (CNWAligner::SAlignInOut *data)   void  CSplicedAligner32::x_DoBackTrace (const Uint4 *backtrace_matrix, CNWAligner::SAlignInOut *data)   ◆ CheckPreferences() void CSplicedAligner::CheckPreferences ( void  )

Definition at line 208 of file nw_spliced_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_NoAlignment, CNWAligner::GetSeq1(), CNWAligner::GetSeq2(), GetSplicePriority(), CNWAligner::m_Transcript, NCBI_THROW, CNWFormatter::SSegment::s_IsConsensusSplice(), swap(), and t.

◆ CSplicedAligner() [1/3] CSplicedAligner::CSplicedAligner ( ) protected ◆ CSplicedAligner() [2/3] CSplicedAligner::CSplicedAligner ( const char *  seq1, size_t  len1, const char *  seq2, size_t  len2  ) protected ◆ CSplicedAligner() [3/3] ◆ CSplicedAligner16() [1/3] CSplicedAligner16::CSplicedAligner16 ( const char *  seq1, size_t  len1, const char *  seq2, size_t  len2  ) ◆ CSplicedAligner16() [2/3] ◆ CSplicedAligner16() [3/3] CSplicedAligner16::CSplicedAligner16 ( void  ) ◆ CSplicedAligner32() [1/3] CSplicedAligner32::CSplicedAligner32 ( const char *  seq1, size_t  len1, const char *  seq2, size_t  len2  ) ◆ CSplicedAligner32() [2/3] ◆ CSplicedAligner32() [3/3] CSplicedAligner32::CSplicedAligner32 ( void  ) ◆ GetDefaultIntronMinSize() ◆ GetDefaultWd1() ◆ GetDefaultWd2() ◆ GetDefaultWi() [1/2] ◆ GetDefaultWi() [2/2] ◆ GetElemSize() [1/2] virtual size_t CSplicedAligner16::GetElemSize ( void  ) const inlinevirtual ◆ GetElemSize() [2/2] virtual size_t CSplicedAligner32::GetElemSize ( void  ) const inlinevirtual ◆ GetIntronMinSize() size_t CSplicedAligner::GetIntronMinSize ( void  ) const inline ◆ GetPointer() ◆ GetSpliceTypeCount() [1/3] virtual size_t CSplicedAligner16::GetSpliceTypeCount ( void  ) inlinevirtual ◆ GetSpliceTypeCount() [2/3] virtual size_t CSplicedAligner32::GetSpliceTypeCount ( void  ) inlinevirtual ◆ GetSpliceTypeCount() [3/3] virtual size_t CSplicedAligner::GetSpliceTypeCount ( void  ) pure virtual ◆ GetWi() ◆ SAllocator() ◆ ScoreFromTranscript() [1/2]

Reimplemented from CNWAligner.

Definition at line 606 of file nw_spliced_aligner16.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Intron, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CNWAligner::eTS_SlackDelete, CNWAligner::eTS_SlackInsert, g(), g_msg_InconsistentArguments, g_msg_InvalidTranscriptSymbol, i, 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, CSplicedAligner16::m_Wi, CNWAligner::m_Wm, CNWAligner::m_Wms, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, SNCBIFullScoreMatrix::s, and splice_type_count_16.

◆ ScoreFromTranscript() [2/2]

Reimplemented from CNWAligner.

Definition at line 528 of file nw_spliced_aligner32.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Intron, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, g(), g_msg_InconsistentArguments, g_msg_InvalidTranscriptSymbol, g_nwspl32_donor, i, 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, CSplicedAligner32::m_Wi, CNWAligner::m_Wm, CNWAligner::m_Wms, CNWAligner::m_Ws, NCBI_FSM_DIM, NCBI_THROW, SNCBIFullScoreMatrix::s, and splice_type_count_32.

◆ SetCDS() void CSplicedAligner::SetCDS ( size_t  cds_start, size_t  cds_stop  ) inline ◆ SetIntronMinSize() void CSplicedAligner::SetIntronMinSize ( size_t  s ) inline ◆ SetWi() void CSplicedAligner::SetWi ( unsigned char  splice_type, TScore  value  ) ◆ x_Align() [1/2]

Reimplemented from CBandAligner.

Definition at line 137 of file nw_spliced_aligner16.cpp.

References data, E, G, CSplicedAligner::SAllocator< T >::GetPointer(), i, kMaskD, kMaskE, kMaskEc, kMaskFc, CSplicedAligner::m_cds_start, CSplicedAligner::m_cds_stop, 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_terminate, CNWAligner::m_Wg, CSplicedAligner16::m_Wi, CNWAligner::m_Ws, min(), NCBI_FSM_DIM, NCBI_RESTRICT, NW_DON_EVAL, NW_NDON_EVAL, NW_SIG_EVAL, NWSPL_DETECTDONOR, SNCBIFullScoreMatrix::s, splice_type_count_16, st(), and CSplicedAligner16::x_DoBackTrace().

◆ x_Align() [2/2]

Reimplemented from CBandAligner.

Definition at line 160 of file nw_spliced_aligner32.cpp.

References abs, data, E, G, g_nwspl32_acceptor, g_nwspl32_donor, CSplicedAligner::SAllocator< T >::GetPointer(), i, kMax_UI4, kTypeDiag, kTypeGap, kTypeIntron, CSplicedAligner::m_cds_start, CSplicedAligner::m_cds_stop, CSplicedAligner::m_IntronMinSize, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CSplicedAligner32::m_Wd1, CSplicedAligner32::m_Wd2, CNWAligner::m_Wg, CSplicedAligner32::m_Wi, CNWAligner::m_Ws, max(), NCBI_FSM_DIM, SNCBIFullScoreMatrix::s, CBandAligner::SetBand(), CBandAligner::SetShift(), splice_type_count_32, st(), type, CBandAligner::x_Align(), and CSplicedAligner32::x_DoBackTrace().

◆ x_CheckMemoryLimit() bool CSplicedAligner::x_CheckMemoryLimit ( void  ) protectedvirtual ◆ x_DoBackTrace() [1/2]

Definition at line 519 of file nw_spliced_aligner16.cpp.

References data, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Intron, CNWAligner::eTS_SlackDelete, CNWAligner::eTS_SlackInsert, kMaskD, kMaskE, kMaskEc, kMaskFc, CSplicedAligner::m_IntronMinSize, and CNWAligner::x_GetDiagTS().

Referenced by CSplicedAligner16::x_Align().

◆ x_DoBackTrace() [2/2] ◆ x_GetSpliceScores() [1/3] virtual TScore* CSplicedAligner::x_GetSpliceScores ( ) protectedpure virtual ◆ x_GetSpliceScores() [2/3] virtual TScore* CSplicedAligner16::x_GetSpliceScores ( void  ) inlineprotectedvirtual ◆ x_GetSpliceScores() [3/3] virtual TScore* CSplicedAligner32::x_GetSpliceScores ( void  ) inlineprotectedvirtual ◆ ~SAllocator() ◆ m_Buf ◆ m_cds_start size_t CSplicedAligner::m_cds_start protected ◆ m_cds_stop size_t CSplicedAligner::m_cds_stop protected ◆ m_IntronMinSize size_t CSplicedAligner::m_IntronMinSize protected ◆ m_Wd1 TScore CSplicedAligner32::m_Wd1 protected ◆ m_Wd2 TScore CSplicedAligner32::m_Wd2 protected ◆ m_Wi [1/2] ◆ m_Wi [2/2] ◆ splice_type_count_16 const size_t splice_type_count_16 = 4 ◆ splice_type_count_32 const size_t splice_type_count_32 = 3

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