Search Toolkit Book for CFeatureGenerator
#include <algo/sequence/gene_model.hpp>
Definition at line 75 of file gene_model.hpp.
◆ TFeatureGeneratorFlags ◆ EGeneModelCreateFlags Enumerator fTrimEnds fMaximizeTranslation fCreateGene fCreateMrna fCreateCdregion fPromoteAllFeatures fPropagateOnly fForceTranslateCds fForceTranscribeMrna fDensegAsExon fGenerateLocalIds fGenerateStableLocalIds fPropagateNcrnaFeats fTrustProteinSeq fDeNovoProducts fAddTranslatedCDSAssembly fDropManeMarkup fSkipLocationCheck fDefaultsDefinition at line 84 of file gene_model.hpp.
◆ EIntronStitchThresholdFlags ◆ EProductPositionsModeAdjust alignment to the specified range (cross-the-origin range on circular chromosome is indicated by range.from > range.to) Will add necessary 'diags' at ends.
Throws an exception on attempt to shink past an indel in CDS Works on Spliced-seg alignments only. Note: for a protein alignment do not expand it to include stop codon.
Enumerator eForceProductFrom0 eTryToPreserveProductPositionsDefinition at line 151 of file gene_model.hpp.
◆ CFeatureGenerator() [1/2] CFeatureGenerator::CFeatureGenerator ( CRef< objects::CScope > scope ) ◆ CFeatureGenerator() [2/2] CFeatureGenerator::CFeatureGenerator ( objects::CScope & scope ) ◆ ~CFeatureGenerator() CFeatureGenerator::~CFeatureGenerator ( )Definition at line 191 of file gene_model.cpp.
◆ AdjustAlignment() ◆ CleanAlignment() ◆ ConvertAlignToAnnot() [1/2] void CFeatureGenerator::ConvertAlignToAnnot ( const list< CRef< objects::CSeq_align > > & aligns, objects::CSeq_annot & annot, objects::CBioseq_set & seqs ) ◆ ConvertAlignToAnnot() [2/2] CRef<objects::CSeq_feat> CFeatureGenerator::ConvertAlignToAnnot ( const objects::CSeq_align & align, objects::CSeq_annot & annot, objects::CBioseq_set & seqs, Int8 gene_id =0, const objects::CSeq_feat * cdregion_on_mrna = NULL ) ◆ ConvertLocToAnnot() void CFeatureGenerator::ConvertLocToAnnot ( const objects::CSeq_loc & loc, objects::CSeq_annot & annot, objects::CBioseq_set & seqs, objects::CCdregion::EFrame frame = objects::CCdregion::eFrame_one, CRef< objects::CSeq_id > prot_id = CRef<objects::CSeq_id>(), CRef< objects::CSeq_id > rna_id = CRef<objects::CSeq_id>() )
Convert genomic location to an annotation.
Populates seqs with mRna and protein sequences, and populates annot with gene, mRna and cdretgion features
Definition at line 243 of file gene_model.cpp.
References CAtomicCounter::Add(), CTime::AsString(), CTime::eCurrent, eExtreme_Biological, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eNa_strand_plus, CSpliced_seg_Base::eProduct_type_transcript, CSeq_align_Base::eType_not_set, eUnknown, fCreateCdregion, fGenerateLocalIds, flags, GetFlags(), fg::GetGeneticCode(), GetOrg_refOrNull(), ITERATE, m_impl, match(), NCBI_THROW, NStr::NumericToString(), CRef< C, Locker >::Reset(), CSeq_feat_Base::SetData(), CSeq_align_Base::SetDim(), SetFlags(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_feat_Base::SetProduct(), CSeq_align_Base::SetSegs(), CSeq_align_Base::SetType(), and str().
Referenced by BOOST_AUTO_TEST_CASE().
◆ CreateMicroIntrons() void CFeatureGenerator::CreateMicroIntrons ( objects::CScope & scope, objects::CBioseq_Handle bsh, const string & annot_name ="", TSeqRange * range = NULL, bool ignore_errors = false ) static
Definition at line 137 of file micro_introns.cpp.
References CSerialObject::Assign(), CSeq_id_Handle::AsString(), map_checker< Container >::begin(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Rna, map_checker< Container >::end(), GetAlignmentForRna(), CSeq_feat_Handle::GetAnnot(), CScope::GetBioseqHandle(), CScope::GetEditHandle(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), CSeq_feat_Handle::GetOriginalSeq_feat(), CSeq_feat_Handle::GetProductId(), SAnnotSelector::IncludeFeatType(), InheritPartialness(), NCBI_THROW, s_ProjectCDS(), s_ProjectRNA(), SAnnotSelector::SetAdaptiveDepth(), CSeq_feat_Base::SetLocation(), SAnnotSelector::SetResolveAll(), and x_SetAnnotName().
Referenced by CGeneModelTrack::GenerateAsn1(), and CAnnotWriterApp::xProcessBioseqHandle().
◆ GetFlags() ◆ RecomputePartialFlags() void CFeatureGenerator::RecomputePartialFlags ( objects::CSeq_annot & annot ) ◆ s_ProjectCDS() CRef< CSeq_loc > CFeatureGenerator::s_ProjectCDS ( const objects::CSeq_align & spliced_aln, const objects::CSeq_loc & product_cds_loc, bool convert_overlaps =true ) static ◆ s_ProjectRNA()
Project RNA, preserving discontinuities in the CDS.
Postcondition: Output is a mix of packed-ints, where each sub-loc in the mix is an exon, and each subloc in the exon packed-int is an exon chunk. The chunks may have gaps between them or overlap as to preserve the translation frame of the CDS.
The discontinuities (gaps and overlaps of chunks) that are outside of the CDS are collapsed.
Singleton container locs (comprised of single element) are canonicalized: unbroken exons are represented as a single interval single-exon locs are represented as a single packed-int (or int, as per above)
Definition at line 1773 of file project_exons.cpp.
References CollapseDiscontinuitiesInUTR(), eExtreme_Positional, CSeq_loc::fMerge_SingleRange, CSeq_loc::GetStart(), CSeq_loc::GetStop(), kInvalidSeqPos, CSeq_loc_Mapper_Base::Map(), NULL, PreserveTerminalCodons(), ProjectExons(), Seq_loc_Merge(), and CSeq_loc_Mapper_Base::SetTrimSplicedSeg().
Referenced by BOOST_AUTO_TEST_CASE(), and CreateMicroIntrons().
◆ SetAllowedUnaligned() void CFeatureGenerator::SetAllowedUnaligned ( TSeqPos value ) ◆ SetFeatureExceptions() void CFeatureGenerator::SetFeatureExceptions ( objects::CSeq_feat & feat, const objects::CSeq_align * align =NULL ) ◆ SetFlags() ◆ SetIntronStitchThresholdFlags() ◆ SetMinIntron() void CFeatureGenerator::SetMinIntron ( TSeqPos value ) ◆ SetPartialFlags() void CFeatureGenerator::SetPartialFlags ( CRef< objects::CSeq_feat > gene_feat, CRef< objects::CSeq_feat > mrna_feat, CRef< objects::CSeq_feat > cds_feat ) ◆ x_SetAnnotName() void CFeatureGenerator::x_SetAnnotName ( objects::SAnnotSelector & sel, const string & annot_name ) staticprivate ◆ kDefaultAllowedUnaligned const TSeqPos CFeatureGenerator::kDefaultAllowedUnaligned = 10 static ◆ kDefaultMinIntron ◆ m_impl
Definition at line 233 of file gene_model.hpp.
Referenced by AdjustAlignment(), CleanAlignment(), ConvertLocToAnnot(), GetFlags(), RecomputePartialFlags(), SetAllowedUnaligned(), SetFeatureExceptions(), SetFlags(), SetIntronStitchThresholdFlags(), SetMinIntron(), and SetPartialFlags().
The documentation for this class was generated from the following files:
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