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Searched refs:hmm_params (Results 1 – 7 of 7) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_engine.cpp48 …eters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range) : m_seq(move(sequence)), m_range… in BEGIN_SCOPE()
51 …eters> hmm_params, const CResidueVec& sequence, TSignedSeqRange range) : m_seq(sequence), m_range(… in SGnomonEngineImplData() argument
55 CGnomonEngine::CGnomonEngine(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedS… in CGnomonEngine() argument
56 : m_data(new SGnomonEngineImplData(hmm_params,move(sequence),range)) in CGnomonEngine()
64 CGnomonEngine::CGnomonEngine(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSi… in CGnomonEngine() argument
65 : m_data(new SGnomonEngineImplData(hmm_params,sequence,range)) in CGnomonEngine()
H A Dgnomon_engine.hpp49 …SGnomonEngineImplData(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRang…
50 …SGnomonEngineImplData(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSe…
H A Dgnomon_objmgr.cpp678 double CCodingPropensity::GetScore(CConstRef<CHMMParameters> hmm_params, const CSeq_loc& cds, CScop… in GetScore() argument
699 …const CMC3_CodingRegion<5>& cdr = dynamic_cast<const CMC3_CodingRegion<5>&>(hmm_params->GetParam… in GetScore()
700 …const CMC_NonCodingRegion<5>& ncdr = dynamic_cast<const CMC_NonCodingRegion<5>&>(hmm_params->GetPa… in GetScore()
724 …const CWMM_Start& start = dynamic_cast<const CWMM_Start&>(hmm_params->GetParameter(CWMM_Start::cla… in GetScore()
H A Dchainer.cpp89 …CChainerImpl(CRef<CHMMParameters>& hmm_params, unique_ptr<CGnomonEngine>& gnomon, const CAlignMap&…
208 CChainer::CChainerImpl::CChainerImpl(CRef<CHMMParameters>& hmm_params, unique_ptr<CGnomonEngine>& g… in CChainerImpl() argument
209 …:m_hmm_params(hmm_params), m_gnomon(gnomon), m_edited_contig_map(edited_contig_map), m_limits(limi… in CChainerImpl()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon.hpp73 …CGnomonEngine(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange r…
74 …CGnomonEngine(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range …
122 …static double GetScore(CConstRef<CHMMParameters> hmm_params, const objects::CSeq_loc& cds, objects…
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/demo/
H A Dlocal_finder.cpp158 CRef<CHMMParameters> hmm_params(new CHMMParameters(myargs["model"].AsInputFile())); in Run() local
159 CGnomonEngine gnomon(hmm_params, seq, TSignedSeqRange(left, right)); in Run()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/seqqa/
H A Dxcript_tests.cpp318 CRef<CHMMParameters> hmm_params; in s_CodingPropensity() local
335 hmm_params = s_hmmparams_cache[model_file_name]; in s_CodingPropensity()
341 double score = CCodingPropensity::GetScore(hmm_params, cds, in s_CodingPropensity()