NCBI C++ ToolKit
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Search Toolkit Book for DMAlignedOptimalScore
#include <algo/structure/cd_utils/cuDmAlignedOptimalScore.hpp>
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void | convertScoreToDistance () |
void | initDMAlignedScore (EScoreMatrixType type, int nTermExt, int cTermExt) |
Private Attributes | |
BlockExtender * | m_blockExtender |
Static Private Attributes | |
static const EDistMethod | DIST_METHOD = eScoreAlignedOptimal |
Definition at line 60 of file cuDmAlignedOptimalScore.hpp.
DMAlignedOptimalScore::DMAlignedOptimalScore | ( | EScoreMatrixType | type = GLOBAL_DEFAULT_SCORE_MATRIX | ) |
Definition at line 50 of file cuDmAlignedOptimalScore.cpp.
References initDMAlignedScore().
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Definition at line 46 of file cuDmAlignedOptimalScore.cpp.
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Implements AlignedDM.
Definition at line 73 of file cuDmAlignedOptimalScore.cpp.
References assert, convertScoreToDistance(), count, BlockExtender::extendOnePair(), AlignmentCollection::GetNumRows(), int, AMatrix_base::m_Array, m_blockExtender, DistanceMatrix::m_ConvertedSequences, DistanceMatrix::m_cTermExt, AlignedDM::m_maligns, DistanceMatrix::m_nTermExt, DistanceMatrix::m_scoreMatrix, BlockExtender::setAlignments(), BlockExtender::setCTermExt(), BlockExtender::setMatrixForExtensionScores(), BlockExtender::setNTermExt(), and BlockExtender::setScoringMatrix().
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Definition at line 132 of file cuDmAlignedOptimalScore.cpp.
References AlignedDM::FRACTIONAL_EXTRA_OFFSET, DistanceMatrix::GetMaxEntry(), AMatrix_base::GetNumRows(), i, AMatrix_base::m_Array, and max().
Referenced by ComputeMatrix().
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Definition at line 56 of file cuDmAlignedOptimalScore.cpp.
References DIST_METHOD, DistanceMatrix::m_cTermExt, DistanceMatrix::m_dMethod, DistanceMatrix::m_nTermExt, DistanceMatrix::m_scoreMatrix, and DistanceMatrix::m_useAligned.
Referenced by DMAlignedOptimalScore().
void DMAlignedOptimalScore::setBlockExtender | ( | BlockExtender * | be | ) |
Definition at line 68 of file cuDmAlignedOptimalScore.cpp.
References m_blockExtender.
Referenced by TreeFactory::makeTree().
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Definition at line 62 of file cuDmAlignedOptimalScore.hpp.
Referenced by initDMAlignedScore().
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Definition at line 81 of file cuDmAlignedOptimalScore.hpp.
Referenced by ComputeMatrix(), and setBlockExtender().