CMMAligner Class Reference
[Linear Space Global Alignment]

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#include <mm_aligner.hpp>

Inheritance diagram for CMMAligner:

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Collaboration diagram for CMMAligner:

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List of all members.

Detailed Description

Definition at line 60 of file mm_aligner.hpp.

Public Member Functions

 CMMAligner ()
 CMMAligner (const char *seq1, size_t len1, const char *seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0)
 CMMAligner (const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0)
virtual ~CMMAligner ()

Protected Types

enum  ETransitionType {
  eII = 0, eDI, eGI, eID,
  eDD, eGD, eIG, eDG,
  eGG
}

Protected Member Functions

virtual TScore x_Run ()
void x_DoSubmatrix (const SCoordRect &submatr, list< ETranscriptSymbol >::iterator translist_pos, bool left_top, bool right_bottom)
void x_RunTop (const SCoordRect &rect, vector< TScore > &vE, vector< TScore > &vF, vector< TScore > &vG, vector< unsigned char > &trace, bool lt) const
void x_RunBtm (const SCoordRect &rect, vector< TScore > &vE, vector< TScore > &vF, vector< TScore > &vG, vector< unsigned char > &trace, bool rb) const
TScore x_RunTerm (const SCoordRect &rect, bool left_top, bool right_bottom, list< ETranscriptSymbol > &subpath)
TScore 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 x_ExtendSubpath (vector< unsigned char >::const_iterator trace_it, bool direction, list< ETranscriptSymbol > &subpath) const
virtual bool x_CheckMemoryLimit ()

Protected Attributes

list< ETranscriptSymbol > m_TransList

Friends

class CThreadRunOnTop
class CThreadDoSM

Member Enumeration Documentation

enum CMMAligner::ETransitionType [protected]
 

Enumerator:
eII 
eDI 
eGI 
eID 
eDD 
eGD 
eIG 
eDG 
eGG 

Definition at line 98 of file mm_aligner.hpp.

Constructor & Destructor Documentation

CMMAligner::CMMAligner (   ) 
 

Definition at line 42 of file mm_aligner.cpp.

CMMAligner::CMMAligner (  const char *  seq1,
size_t  len1,
const char *  seq2,
size_t  len2,
const SNCBIPackedScoreMatrix *  scoremat = 0
) 
 

Definition at line 47 of file mm_aligner.cpp.

CMMAligner::CMMAligner (  const string &  seq1,
const string &  seq2,
const SNCBIPackedScoreMatrix *  scoremat = 0
) 
 

Definition at line 55 of file mm_aligner.cpp.

virtual CMMAligner::~CMMAligner (   )  [inline, virtual]
 

Definition at line 74 of file mm_aligner.hpp.

Member Function Documentation

bool CMMAligner::x_CheckMemoryLimit (   )  [protected, virtual]
 

Reimplemented from CNWAligner.

Definition at line 937 of file mm_aligner.cpp.

void CMMAligner::x_DoSubmatrix (  const SCoordRect &  submatr,
list< ETranscriptSymbol >::iterator  translist_pos,
bool  left_top,
bool  right_bottom
)  [protected]
 

Definition at line 113 of file mm_aligner.cpp.

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

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

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

Definition at line 368 of file mm_aligner.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, kMaskD, kMaskE, kMaskEc, and NCBI_THROW.

Referenced by x_DoSubmatrix().

CNWAligner::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 [protected]
 

Definition at line 328 of file mm_aligner.cpp.

References kMin_Int, CNWAligner::m_esf_L2, CNWAligner::m_esf_R2, CNWAligner::m_SeqLen2, and CNWAligner::m_Wg.

Referenced by x_DoSubmatrix().

CNWAligner::TScore CMMAligner::x_Run (   )  [protected, virtual]
 

Reimplemented from CNWAligner.

Definition at line 63 of file mm_aligner.cpp.

References CTrSequence< bitst, bitsc >::clear(), CNWAligner::eTS_None, kMin_Int, CNWAligner::m_prg_callback, CNWAligner::m_prg_info, CNWAligner::m_score, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, CNWAligner::m_Transcript, m_TransList, CTrSequence< bitst, bitsc >::resize(), and x_DoSubmatrix().

void CMMAligner::x_RunBtm (  const SCoordRect &  rect,
vector< TScore > &  vE,
vector< TScore > &  vF,
vector< TScore > &  vG,
vector< unsigned char > &  trace,
bool  rb
)  const [protected]
 

Definition at line 612 of file mm_aligner.cpp.

References SCoordRect::i1, SCoordRect::i2, SCoordRect::j1, SCoordRect::j2, kInfMinus(), CNWAligner::m_esf_L2, CNWAligner::m_esf_R1, CNWAligner::m_esf_R2, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, NCBI_FSM_DIM, and SNCBIFullScoreMatrix::s.

Referenced by x_DoSubmatrix().

CNWAligner::TScore CMMAligner::x_RunTerm (  const SCoordRect &  rect,
bool  left_top,
bool  right_bottom,
list< ETranscriptSymbol > &  subpath
)  [protected]
 

Definition at line 784 of file mm_aligner.cpp.

References SCoordRect::i1, SCoordRect::i2, SCoordRect::j1, SCoordRect::j2, kInfMinus(), kMaskE, kMaskEc, 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_SeqLen1, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, NCBI_FSM_DIM, and SNCBIFullScoreMatrix::s.

Referenced by x_DoSubmatrix().

void CMMAligner::x_RunTop (  const SCoordRect &  rect,
vector< TScore > &  vE,
vector< TScore > &  vF,
vector< TScore > &  vG,
vector< unsigned char > &  trace,
bool  lt
)  const [protected]
 

Definition at line 442 of file mm_aligner.cpp.

References SCoordRect::i1, SCoordRect::i2, SCoordRect::j1, SCoordRect::j2, kInfMinus(), CNWAligner::m_esf_L1, CNWAligner::m_esf_L2, CNWAligner::m_esf_R2, CNWAligner::m_ScoreMatrix, CNWAligner::m_Seq1, CNWAligner::m_Seq2, CNWAligner::m_SeqLen2, CNWAligner::m_terminate, CNWAligner::m_Wg, CNWAligner::m_Ws, NCBI_FSM_DIM, and SNCBIFullScoreMatrix::s.

Referenced by CThreadRunOnTop::Main(), and x_DoSubmatrix().

Friends And Related Function Documentation

friend class CThreadDoSM [friend]
 

Definition at line 119 of file mm_aligner.hpp.

Referenced by x_DoSubmatrix().

friend class CThreadRunOnTop [friend]
 

Definition at line 118 of file mm_aligner.hpp.

Referenced by x_DoSubmatrix().

Member Data Documentation

list<ETranscriptSymbol> CMMAligner::m_TransList [protected]
 

Definition at line 78 of file mm_aligner.hpp.

Referenced by x_DoSubmatrix(), and x_Run().

The documentation for this class was generated from the following files:
Generated on Mon Dec 7 12:55:55 2009 for NCBI C++ ToolKit by  doxygen 1.4.6
Modified on Mon Dec 07 16:23:28 2009 by modify_doxy.py rev. 173732