Search Toolkit Book for CProSplign::CImplementation
Definition at line 756 of file prosplign.cpp.
◆ CImplementation() ◆ ~CImplementation() virtual CProSplign::CImplementation::~CImplementation ( ) inlinevirtualDefinition at line 761 of file prosplign.cpp.
◆ clone() ◆ create() ◆ FindGlobalAlignment() ◆ FindGlobalAlignment_stage1()Definition at line 1190 of file prosplign.cpp.
References CSeq_loc::Assign(), CProSplignOptions_Base::GetAltStarts(), CScope::GetBioseqHandle(), COrg_ref::GetGcode(), GetOrg_ref(), m_cnseq, m_genomic, m_matrix, m_protein, m_protseq, m_scope, m_scoring, CRef< C, Locker >::Reset(), CSubstMatrix::SetTranslationTable(), and stage1().
Referenced by FindGlobalAlignment().
◆ FindGlobalAlignment_stage2() CRef< CSeq_align > CProSplign::CImplementation::FindGlobalAlignment_stage2 ( ) ◆ GetExons() virtual const vector<pair<int, int> >& CProSplign::CImplementation::GetExons ( void ) const inlinevirtual ◆ GetFlanks() virtual void CProSplign::CImplementation::GetFlanks ( bool & , bool & ) const inlinevirtual ◆ GetScaleScoring() ◆ GetSubstMatrix() ◆ HasStartOnNuc()Definition at line 1265 of file prosplign.cpp.
References CSeq_id::Assign(), buf, CBioseq_Handle::eCoding_Iupac, CSpliced_exon_chunk_Base::GetDiag(), CSpliced_seg_Base::GetExons(), CProt_pos::GetFrame(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_start(), CProduct_pos_Base::GetProtpos(), CSeqVector_CI::GetSeqData(), CSpliced_exon_chunk_Base::IsDiag(), CSpliced_exon_chunk_Base::IsGenomic_ins(), CSpliced_exon_chunk_Base::IsMatch(), CSpliced_exon_chunk_Base::IsMismatch(), CSpliced_exon_chunk_Base::IsProduct_ins(), and len.
◆ HasStopOnNuc()Definition at line 1306 of file prosplign.cpp.
References CSeq_id::Assign(), buf, CBioseq_Handle::eCoding_Iupac, eNa_strand_minus, eNa_strand_plus, CSpliced_seg_Base::GetExons(), CProt_pos::GetFrame(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_seg_Base::GetGenomic_strand(), GetLength(), CSpliced_exon_Base::GetProduct_end(), CProduct_pos_Base::GetProtpos(), and CSeqVector_CI::GetSeqData().
◆ Interrupt() void CProSplign::CImplementation::Interrupt ( void ) inline ◆ SeekStartStop() void CProSplign::CImplementation::SeekStartStop ( CSeq_align & seq_align )Definition at line 1344 of file prosplign.cpp.
References _ASSERT, CSeq_id::Assign(), CProt_pos_Base::GetAmin(), CSpliced_seg_Base::GetModifiers(), CSpliced_seg_Base::GetProduct_id(), CSpliced_exon_Base::GetProduct_start(), CProduct_pos_Base::GetProtpos(), CPSeq::HasStart(), CSpliced_seg_Base::IsSetModifiers(), len, CRef< C, Locker >::Reset(), CSpliced_seg_Base::ResetModifiers(), CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetModifiers(), CSpliced_exon_Base::SetParts(), and CSeq_align_Base::SetSegs().
◆ SetExons() virtual vector<pair<int, int> >& CProSplign::CImplementation::SetExons ( void ) inlinevirtual ◆ SetFlanks() virtual void CProSplign::CImplementation::SetFlanks ( bool , bool ) inlinevirtual ◆ SetInterruptCallback() ◆ SetScope() void CProSplign::CImplementation::SetScope ( CScope & scope ) inline ◆ SetTranslationTable() void CProSplign::CImplementation::SetTranslationTable ( int gcode ) inline ◆ stage1() virtual int CProSplign::CImplementation::stage1 ( ) privatepure virtual ◆ stage2() ◆ m_cnseq shared_ptr<CNSeq> CProSplign::CImplementation::m_cnseq protected ◆ m_genomic ◆ m_Interrupt ◆ m_matrix ◆ m_protein ◆ m_protseq shared_ptr<CPSeq> CProSplign::CImplementation::m_protseq protected ◆ m_scope CScope* CProSplign::CImplementation::m_scope protected ◆ m_scoringThe documentation for this class was generated from the following file:
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