Searched refs:GetGapOpenPenalty (Results 1 – 4 of 4) sorted by relevance
124 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()
875 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()
107 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()
620 TScore GetGapOpenPenalty(void) const {return m_GapOpen;} in GetGapOpenPenalty() function in CMultiAlignerOptions