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NCBI C++ ToolKit: src/objtools/alnmgr/score_builder_base.cpp File Reference

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  USING_SCOPE (objects)   static TSeqPos  s_IntersectionLength (const CRangeCollection< TSeqPos > &ranges, const TSeqRange &range)   Get length of intersection between a range and a range collection. More...
  static void  s_GetNucIdentityMismatch (const vector< string > &data, int *identities, int *mismatches)   calculate mismatches and identities in a seq-align More...
  static void  s_GetSplicedSegIdentityMismatch (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, int *identities, int *mismatches)   static void  s_GetCountIdentityMismatch (CScope &scope, const CSeq_align &align, int *identities, int *mismatches, const CRangeCollection< TSeqPos > &ranges=CRangeCollection< TSeqPos >(TSeqRange::GetWhole()))   static void  s_GetPercentIdentity (CScope &scope, const CSeq_align &align, int *identities, int *mismatches, double *pct_identity, CScoreBuilderBase::EPercentIdentityType type, const CRangeCollection< TSeqPos > &ranges=CRangeCollection< TSeqPos >(TSeqRange::GetWhole()))   calculate the percent identity we also return the count of identities and mismatches More...
  static bool  s_SequenceIsProtein (CScope &scope, const CSeq_id &id)   calculate the percent coverage More...
  static bool  s_IsProteinToGenomic (CScope &scope, const CSeq_align &align)   static void  s_GetPercentCoverage (CScope &scope, const CSeq_align &align, const CRangeCollection< TSeqPos > &ranges, double *pct_coverage, unsigned query=0)   string  GetDonor (const objects::CSpliced_exon &exon)   string  GetAcceptor (const objects::CSpliced_exon &exon)   bool  IsConsSplice (const string &donor, const string acc)   ◆ GetAcceptor() string GetAcceptor ( const objects::CSpliced_exon &  exon ) ◆ GetDonor() string GetDonor ( const objects::CSpliced_exon &  exon ) ◆ IsConsSplice() ◆ s_GetCountIdentityMismatch()

Definition at line 285 of file score_builder_base.cpp.

References _ASSERT, CSeq_id::AsFastaString(), CProduct_pos::AsSeqPos(), data, CSeq_align_Base::C_Segs::e_Denseg, CSpliced_exon_chunk_Base::e_Diag, CSeq_align_Base::C_Segs::e_Disc, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, CSeq_align::eScore_IdentityCount, CSeq_align_set_Base::Get(), CSeq_align::GetAlignLength(), CSeq_align_Base::C_Segs::GetDenseg(), CSpliced_exon_chunk_Base::GetDiag(), CSeq_align_Base::C_Segs::GetDisc(), CSpliced_seg_Base::GetExons(), CRange_Base::GetFrom(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSeq_align::GetNamedScore(), CAlnMap::GetNumRows(), CAlnMap::GetNumSegs(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_chunk_Base::GetProduct_ins(), CSpliced_exon_Base::GetProduct_start(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CAlnVec::GetSeqString(), CSeq_align_Base::C_Segs::GetSpliced(), CAlnMap::GetStart(), CAlnMap::GetStop(), i, CRangeCollection< Position >::IntersectWith(), CSpliced_exon_Base::IsSetParts(), ITERATE, len, NCBI_RETHROW_SAME, NCBI_THROW, offset, s_GetNucIdentityMismatch(), s_GetSplicedSegIdentityMismatch(), s_IntersectionLength(), COpenRange< Position >::Set(), CSeq_align_Base::C_Segs::Which(), and CSpliced_exon_chunk_Base::Which().

Referenced by CScoreBuilderBase::GetIdentityCount(), CScoreBuilderBase::GetMismatchCount(), and s_GetPercentIdentity().

◆ s_GetNucIdentityMismatch() ◆ s_GetPercentCoverage()

Definition at line 537 of file score_builder_base.cpp.

References CRangeCollection< Position >::begin(), CRangeCollection< Position >::empty(), eNa_strand_minus, CSeq_align::eScore_PercentCoverage, CSeq_align::GetAlignLengthWithinRanges(), CScope::GetBioseqHandle(), CRangeCollection< Position >::GetCoveredLength(), CSeq_align::GetNamedScore(), CSpliced_seg_Base::GetPoly_a(), CSpliced_seg_Base::GetProduct_length(), CSpliced_seg_Base::GetProduct_strand(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align_Base::C_Segs::GetSpliced(), CSpliced_seg_Base::IsSetPoly_a(), CSpliced_seg_Base::IsSetProduct_length(), CSpliced_seg_Base::IsSetProduct_strand(), CSeq_align_Base::C_Segs::IsSpliced(), CSeq_align_Base::C_Segs::IsStd(), NCBI_THROW, query, and s_IsProteinToGenomic().

Referenced by CScoreBuilderBase::ComputeScore(), and CScoreBuilderBase::GetPercentCoverage().

◆ s_GetPercentIdentity() ◆ s_GetSplicedSegIdentityMismatch()

Definition at line 127 of file score_builder_base.cpp.

References CSeq_id::AsFastaString(), ConvertSeqAlignToPairwiseAln(), count, CSeqUtil::e_Iupacna, CBioseq_Handle::eCoding_Iupac, CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::eProduct_type_transcript, gen, CScope::GetBioseqHandle(), CTrans_table::GetCodonResidue(), CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetFirstTo(), COrgName_Base::GetGcode(), GetOrg_ref(), COrg_ref_Base::GetOrgname(), CSpliced_seg_Base::GetProduct_type(), CAlignRange< Position >::GetSecondFrom(), CAlignRange< Position >::GetSecondTo(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeqVector::GetSeqData(), CSeq_align_Base::C_Segs::GetSpliced(), CTrans_table::GetStartResidue(), CRange_Base::GetTo(), CGen_code_table::GetTransTable(), i, CRangeCollection< Position >::IntersectWith(), CAlignRange< Position >::IsReversed(), ITERATE, match(), NCBI_THROW, r1, r2, CSeqManip::ReverseComplement(), and CTrans_table::SetCodonState().

Referenced by s_GetCountIdentityMismatch().

◆ s_IntersectionLength() ◆ s_IsProteinToGenomic() ◆ s_SequenceIsProtein() ◆ USING_SCOPE()

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