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USING_SCOPE (objects) bool s_IsOverlapping (CAlignCompare::SAlignment const *lhs, CAlignCompare::SAlignment const *rhs, CAlignCompare::ERowComparison row) static void s_UpdateSpans (const TSeqRange &query_range, const TSeqRange &subject_range, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row) static void s_GetAlignmentSpans_Interval (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row) static void s_GetAlignmentMismatches (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row) static void s_GetAlignmentSpans_Exon (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row) static void s_GetAlignmentSpans_Intron (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row) static void s_GetAlignmentSpans_Span (const CSeq_align &align, CAlignCompare::SAlignment &align_info, CAlignCompare::ERowComparison row) template<typename T > void s_PopulateScores (const CSeq_align &align, const vector< string > &score_list, vector< T > &scores, bool required=true) static void s_PopulateScoreSet (const CSeq_align &align, const set< string > &score_set, bool score_set_as_blacklist, CAlignCompare::TIntegerScoreSet &integer_scores, CAlignCompare::TRealScoreSet &real_scores) static bool s_EquivalentScores (const CAlignCompare::TRealScoreSet &scores1, const CAlignCompare::TRealScoreSet &scores2, double real_score_tolerance) static void s_PopulateExtSet (const CSeq_align &align, const set< string > &ext_set, bool ext_set_as_blacklist, CAlignCompare::TExtSet &exts) string s_ConvertToHexString (unsigned char *ptr, unsigned int length) static bool s_EquivalentExts (const CAlignCompare::TExtSet &exts1, const CAlignCompare::TExtSet &exts2) ◆ TAlignPtrSet ◆ TComp ◆ TPtrPair ◆ s_ConvertToHexString() string s_ConvertToHexString ( unsigned char * ptr, unsigned int length ) ◆ s_EquivalentExts() ◆ s_EquivalentScores() ◆ s_GetAlignmentMismatches()Definition at line 148 of file align_compare.cpp.
References CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, CAlignCompare::e_Query, CAlignCompare::e_Subject, eNa_strand_minus, eUnknown, CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CSeq_align_Base::C_Segs::GetSpliced(), isdigit(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_exon_Base::IsSetParts(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, lookup(), match(), max(), min(), NCBI_THROW, CAlignCompare::SAlignment::query_mismatches, row, and CAlignCompare::SAlignment::subject_mismatches.
Referenced by CAlignCompare::SAlignment::SAlignment().
◆ s_GetAlignmentSpans_Exon()Definition at line 277 of file align_compare.cpp.
References CProduct_pos::AsSeqPos(), CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, eUnknown, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_start(), CStd_seg_Base::GetLoc(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_start(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeqRange(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, NCBI_THROW, row, s_UpdateSpans(), CRange_Base::SetFrom(), CRange_Base::SetTo(), and CSeq_align_Base::C_Segs::Which().
Referenced by CAlignCompare::SAlignment::SAlignment().
◆ s_GetAlignmentSpans_Interval()Definition at line 81 of file align_compare.cpp.
References ConvertSeqAlignToPairwiseAln(), CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Std, eUnknown, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align_Base::C_Segs::GetStd(), CSeq_loc::GetTotalRange(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsNull(), ITERATE, NCBI_THROW, r(), r0, r1, row, s_UpdateSpans(), and CSeq_align_Base::C_Segs::Which().
Referenced by CAlignCompare::SAlignment::SAlignment().
◆ s_GetAlignmentSpans_Intron()Definition at line 325 of file align_compare.cpp.
References CSpliced_seg_Base::CanGetGenomic_strand(), CSpliced_seg_Base::CanGetProduct_strand(), eUnknown, CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_seg_Base::GetProduct_strand(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, NCBI_THROW, row, s_UpdateSpans(), CRange_Base::SetFrom(), and CRange_Base::SetTo().
Referenced by CAlignCompare::SAlignment::SAlignment().
◆ s_GetAlignmentSpans_Span() ◆ s_IsOverlapping() ◆ s_PopulateExtSet() ◆ s_PopulateScores() ◆ s_PopulateScoreSet() ◆ s_UpdateSpans() ◆ USING_SCOPE()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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