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

NCBI C++ ToolKit: Linear Space Global Alignment

CMMAligner::CMMAligner () CMMAligner::CMMAligner (const char *seq1, size_t len1, const char *seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0) CMMAligner::CMMAligner (const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0) virtual CMMAligner::~CMMAligner () virtual TScore CMMAligner::x_Run () void CMMAligner::x_DoSubmatrix (const SCoordRect &submatr, list< ETranscriptSymbol >::iterator translist_pos, bool left_top, bool right_bottom) void CMMAligner::x_RunTop (const SCoordRect &rect, vector< TScore > &vE, vector< TScore > &vF, vector< TScore > &vG, vector< unsigned char > &trace, bool lt) const void CMMAligner::x_RunBtm (const SCoordRect &rect, vector< TScore > &vE, vector< TScore > &vF, vector< TScore > &vG, vector< unsigned char > &trace, bool rb) const TScore CMMAligner::x_RunTerm (const SCoordRect &rect, bool left_top, bool right_bottom, list< ETranscriptSymbol > &subpath) TScore CMMAligner::x_FindBestJ (const vector< TScore > &vEtop, const vector< TScore > &vFtop, const vector< TScore > &vGtop, const vector< TScore > &vEbtm, const vector< TScore > &vFbtm, const vector< TScore > &vGbtm, size_t &pos, ETransitionType &trans_type) const size_t CMMAligner::x_ExtendSubpath (vector< unsigned char >::const_iterator trace_it, bool direction, list< ETranscriptSymbol > &subpath) const virtual bool CMMAligner::x_CheckMemoryLimit () SCoordRect::SCoordRect () SCoordRect::SCoordRect (size_t l, size_t t, size_t r, size_t b) unsigned int SCoordRect::GetArea () ◆ ETransitionType Enumerator eII eDI eGI eID eDD eGD eIG eDG eGG

Definition at line 98 of file mm_aligner.hpp.

◆ CMMAligner() [1/3] ◆ CMMAligner() [2/3] ◆ CMMAligner() [3/3] ◆ GetArea() unsigned int SCoordRect::GetArea ( ) inline ◆ SCoordRect() [1/2] ◆ SCoordRect() [2/2] SCoordRect::SCoordRect ( size_t l, size_t t, size_t r, size_t b ) inline

Definition at line 128 of file mm_aligner.hpp.

◆ x_CheckMemoryLimit() bool CMMAligner::x_CheckMemoryLimit ( void ) protectedvirtual ◆ x_DoSubmatrix()

Definition at line 113 of file mm_aligner.cpp.

References CMMAligner::CThreadDoSM, CMMAligner::CThreadRunOnTop, CMMAligner::eDD, CMMAligner::eGG, CMMAligner::eII, CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, SCoordRect::GetArea(), SCoordRect::i1, SCoordRect::i2, SCoordRect::j1, SCoordRect::j2, CThread::Join(), kMaskE, kMaskEc, kMaskFc, lt, CNWAligner::m_maxthreads, CNWAligner::m_mt, CNWAligner::m_score, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, CMMAligner::m_TransList, MM_RequestNewThread(), NCBI_THROW, CThread::Run(), CMMAligner::x_ExtendSubpath(), CMMAligner::x_FindBestJ(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

Referenced by CThreadDoSM::Main(), and CMMAligner::x_Run().

◆ x_ExtendSubpath() size_t CMMAligner::x_ExtendSubpath ( vector< unsigned char >::const_iterator trace_it, bool direction, list< ETranscriptSymbol > & subpath ) const protected ◆ x_FindBestJ() ◆ x_Run()

Reimplemented from CNWAligner.

Definition at line 63 of file mm_aligner.cpp.

References CNWAligner::eTS_None, kMin_Int, CNWAligner::SProgressInfo::m_iter_done, CNWAligner::SProgressInfo::m_iter_total, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_score, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, CNWAligner::m_Transcript, CMMAligner::m_TransList, and CMMAligner::x_DoSubmatrix().