Search Toolkit Book for SAlignmentScoringModel
Definition at line 84 of file best_placement.cpp.
◆ as_logodds() static double SAlignmentScoringModel::as_logodds ( double ratio ) inlinestaticprivate ◆ clamp() static double SAlignmentScoringModel::clamp ( double x, double lo, double hi ) inlinestaticprivate ◆ GetCoverage() ◆ GetExonsOdds() ◆ GetGapLengthOnRow() ◆ GetIdentOdds()Definition at line 395 of file best_placement.cpp.
References GET_SCORE, CSeq_align::GetAlignLength(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::IsDisc(), isProtSS(), CSeq_align_Base::C_Segs::IsSpliced(), MSerial_AsnText, NCBI_USER_THROW, s_GetIdentOdds_disc(), s_GetIdentOdds_nucSS(), and s_GetIdentOdds_protSS().
Referenced by GetScore(), and s_GetIdentOdds_disc().
◆ GetLongestMatchrunLen() ◆ GetNumGapopensBetweenExons() ◆ GetPolyA_length() ◆ GetScore()Definition at line 137 of file best_placement.cpp.
References as_logodds(), SAlignmentScoringModel::odds::AsString(), clamp(), CSeq_align::GetAlignLength(), GetCoverage(), GetExonsOdds(), GetIdentOdds(), GetLongestMatchrunLen(), CSeq_align::GetNumFrameshifts(), CSeq_align::GetNumGapOpenings(), GetNumGapopensBetweenExons(), GetPolyA_length(), GetSplicesOdds(), isProtSS(), SAlignmentScoringModel::odds::logodds(), SAlignmentScoringModel::odds::neg, and round().
Referenced by operator()().
◆ GetSpliceConsensusScore() ◆ GetSplicesOdds() ◆ isProtSS() ◆ operator()() ◆ s_GetIdentOdds_disc() ◆ s_GetIdentOdds_nucSS() ◆ s_GetIdentOdds_protSS()The documentation for this struct was generated from the following file:
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