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Searched refs:GetGapOpenPenalty (Results 1 – 4 of 4) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/
H A Drps.cpp124 m_Aligner.SetWg(kRpsScaleFactor * m_Options->GetGapOpenPenalty()); in x_RealignBlocks()
126 m_Aligner.SetStartWg(kRpsScaleFactor / 2 * m_Options->GetGapOpenPenalty()); in x_RealignBlocks()
128 m_Aligner.SetEndWg(kRpsScaleFactor / 2 * m_Options->GetGapOpenPenalty()); in x_RealignBlocks()
402 m_Aligner.SetWg(m_Options->GetGapOpenPenalty()); in x_RealignBlocks()
H A Dprog.cpp875 m_Aligner.SetWg(m_Options->GetGapOpenPenalty() * kScale); in x_AlignProfileProfile()
896 m_Aligner.SetWg(m_Options->GetGapOpenPenalty()); in x_AlignProfileProfile()
1015 m_Aligner.SetWg(m_Options->GetGapOpenPenalty() * kScale); in x_ComputeProfileRangeAlignment()
1043 m_Aligner.SetWg(m_Options->GetGapOpenPenalty()); in x_ComputeProfileRangeAlignment()
H A Dcobalt.cpp107 m_Aligner.SetWg(m_Options->GetGapOpenPenalty()); in x_InitAligner()
1017 m_Aligner.SetWg(m_Options->GetGapOpenPenalty()); in x_AlignInClusters()
1067 m_Aligner.SetWg(m_Options->GetGapOpenPenalty()); in x_AlignInClusters()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/cobalt/
H A Doptions.hpp620 TScore GetGapOpenPenalty(void) const {return m_GapOpen;} in GetGapOpenPenalty() function in CMultiAlignerOptions