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NCBI C++ ToolKit: src/algo/sequence/project_exons.cpp File Reference

USING_SCOPE (objects) void Canonicalize (CSeq_loc &loc) Recursively convert empty container-locs to null-locs, drop null sublocs from containers, and unwrap singleton containers. More...
bool AreAbuttingOnProduct (const CSpliced_exon &exon1, const CSpliced_exon &exon2) retrun true iff abutting on query (in nucpos-coords) More...
T53Partialness GetExonPartialness (const CSeq_align &spliced_aln, const CSpliced_exon &target_exon) Return whether 5' and/or 3' end of exon is partial based on consensus splicing with upstream/downstream exons. More...
size_t GetUnalignedLength_3p (const CSeq_align &spliced_aln) size_t GetUnalignedLength_5p (const CSeq_align &spliced_aln) T53Partialness GetTerminalPartialness (const CSeq_align &spliced_aln, CConstRef< CSeq_loc > product_cds_loc, size_t unaligned_ends_partialness_thr) Return whether 5' and/or 3' end of exons-loc is partial based on unaligned tails in case of RNA, or overlap of product-cds-loc with unaligned tails, in case of CDS. More...
void AugmentPartialness (CSeq_loc &loc, T53Partialness partialness) static CRef< CSeq_loc > ProjectExon_oldlogic (const CSpliced_exon &spliced_exon, const CSeq_id &aln_genomic_id, ENa_strand aln_genomic_strand, bool convert_overlaps) static TSeqPos as_nucpos (const CProduct_pos &pos) static CRef< CSeq_loc > ProjectExon_newlogic (const CSpliced_exon &exon, const CSeq_id &aln_genomic_id, ENa_strand aln_genomic_strand) static CRef< CSeq_loc > ProjectExon (const CSpliced_exon &exon, const CSeq_id &aln_genomic_id, ENa_strand aln_genomic_strand, bool convert_overlaps) CRef< CSpliced_exon > CollapseExonStructure (const CSpliced_exon &orig_exon) Create an exon with the structure consisting of two diags extending inwards from the exon terminals with a single gap of required length in the middle. More...
CRef< CPacked_seqint > ProjectAndCollapseCDS (const CSeq_align &spliced_aln, CConstRef< CSeq_loc > product_cds_loc) void TransferPartialness (const CSeq_loc &src, CSeq_loc &dest) CRef< CSeq_loc > TruncateToCDS (CRef< CSeq_loc > detailed_rna_exon, CConstRef< CPacked_seqint > collapsed_genomic_cds) CRef< CSeq_loc > ProjectExons (const CSeq_align &spliced_aln, CConstRef< CSeq_loc > product_cds_loc, bool convert_overlaps, size_t unaligned_ends_partialness_thr=0) CRef< CSeq_loc > CollapseDiscontinuitiesInUTR (const CSeq_loc &loc, TSeqPos cds_start, TSeqPos cds_stop) Precondition: input loc is discontinuity-preserving RNA loc Postcontition: adjacent packed-ints having the discontinuity between them entirely outside of cds-range are merged into single interval. More...
static CRef< CSeq_loc > PreserveTerminalCodons (CRef< CSeq_loc > exons_loc, TSeqPos cds_start, TSeqPos cds_stop) ◆ T53Partialness

first and ::second indicate partialness for of a loc or an exon, 5' and 3' end respectively.

Definition at line 124 of file project_exons.cpp.

◆ AreAbuttingOnProduct() ◆ as_nucpos() ◆ AugmentPartialness() ◆ Canonicalize()

Recursively convert empty container-locs to null-locs, drop null sublocs from containers, and unwrap singleton containers.

Definition at line 75 of file project_exons.cpp.

References CSeq_loc::Assign(), CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsPacked_int(), NON_CONST_ITERATE, CSeq_loc::SetInt(), CSeq_loc::SetMix(), and CSeq_loc::SetNull().

Referenced by CollapseDiscontinuitiesInUTR(), and ProjectExons().

◆ CollapseDiscontinuitiesInUTR()

Precondition: input loc is discontinuity-preserving RNA loc Postcontition: adjacent packed-ints having the discontinuity between them entirely outside of cds-range are merged into single interval.

Definition at line 1620 of file project_exons.cpp.

References CSeq_loc::Assign(), CSerialObject::Assign(), Canonicalize(), CSeq_loc_Base::e_Null, CSerialObject::Equals(), CSeq_loc::fMerge_SingleRange, CPacked_seqint_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsPacked_int(), ITERATE, MSerial_AsnText, NcbiCerr, NULL, Seq_loc_Add(), SerialClone(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), and CSeq_loc::SetPacked_int().

Referenced by CFeatureGenerator::s_ProjectRNA().

◆ CollapseExonStructure()

Create an exon with the structure consisting of two diags extending inwards from the exon terminals with a single gap of required length in the middle.

This is used for projecting cds-exons consisting entirely of gaps (see ProjectExons)

Definition at line 1224 of file project_exons.cpp.

References as_nucpos(), max(), min(), and SerialClone().

◆ GetExonPartialness() ◆ GetTerminalPartialness()

Return whether 5' and/or 3' end of exons-loc is partial based on unaligned tails in case of RNA, or overlap of product-cds-loc with unaligned tails, in case of CDS.

Definition at line 201 of file project_exons.cpp.

References CProduct_pos::AsSeqPos(), eExtreme_Positional, eNa_strand_minus, CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), CSpliced_seg_Base::GetProduct_type(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqStrand(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetUnalignedLength_3p(), GetUnalignedLength_5p(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), ITERATE, and swap().