void CSeqMap_CI::x_Select(const CConstRef<CSeqMap>& seqMap, const SSeqMapSelector& selector, TSeqPos pos) { m_Selector = selector; if ( m_Selector.m_Length == kInvalidSeqPos ) { TSeqPos len = seqMap->GetLength(GetScope()); len -= min(len, m_Selector.m_Position); m_Selector.m_Length = len; } if ( pos < m_Selector.m_Position ) { pos = m_Selector.m_Position; } else if ( pos > m_Selector.m_Position + m_Selector.m_Length ) { pos = m_Selector.m_Position + m_Selector.m_Length; } x_Push(seqMap, m_Selector.m_TopTSE, m_Selector.m_Position, m_Selector.m_Length, m_Selector.m_MinusStrand, pos - m_Selector.m_Position); while ( !x_Found() && GetPosition() < m_SearchEnd ) { if ( !x_Push(pos - m_Selector.m_Position) ) { x_SettleNext(); break; } } }
pair<double, bool> CScoreUniqSeqCoverage::MakeScore(CBioseq_Handle const& query_handle, vector<CSeq_align const*>::const_iterator begin, vector<CSeq_align const*>::const_iterator end) { CConstRef<CBioseq> bioseq = query_handle.GetCompleteBioseq(); unsigned int qlen = 0; if ( !bioseq.Empty() && bioseq->IsSetLength()) { qlen = bioseq->GetLength(); } if ( !qlen ) { return make_pair(0, false); } bool isDenDiag = ( (*begin)->GetSegs().Which() == CSeq_align::C_Segs::e_Dendiag) ? true : false; CRangeCollection<TSeqPos> subj_rng_coll((*begin)->GetSeqRange(1)); CRange<TSeqPos> q_rng((*begin)->GetSeqRange(0)); CRangeCollection<TSeqPos> query_rng_coll(s_FixMinusStrandRange(q_rng)); for( ++begin; begin != end; ++begin ) { const CRange<TSeqPos> align_subj_rng((*begin)->GetSeqRange(1)); // subject range should always be on the positive strand assert(align_subj_rng.GetTo() > align_subj_rng.GetFrom()); CRangeCollection<TSeqPos> coll(align_subj_rng); coll.Subtract(subj_rng_coll); if ( coll.empty() ) { continue; } if(coll[0] == align_subj_rng) { CRange<TSeqPos> query_rng ((*begin)->GetSeqRange(0)); query_rng_coll += s_FixMinusStrandRange(query_rng); subj_rng_coll += align_subj_rng; } else { ITERATE (CRangeCollection<TSeqPos>, uItr, coll) { CRange<TSeqPos> query_rng; const CRange<TSeqPos> & subj_rng = (*uItr); CRef<CSeq_align> densegAln; if ( isDenDiag) { densegAln = CreateDensegFromDendiag(**begin); } CAlnMap map( (isDenDiag) ? densegAln->GetSegs().GetDenseg() : (*begin)->GetSegs().GetDenseg()); TSignedSeqPos subj_aln_start = map.GetAlnPosFromSeqPos(1,subj_rng.GetFrom()); TSignedSeqPos subj_aln_end = map.GetAlnPosFromSeqPos(1,subj_rng.GetTo()); query_rng.SetFrom(map.GetSeqPosFromAlnPos(0,subj_aln_start)); query_rng.SetTo(map.GetSeqPosFromAlnPos(0,subj_aln_end)); query_rng_coll += s_FixMinusStrandRange(query_rng); subj_rng_coll += subj_rng; } } }
bool CLocation_constraint :: x_DoesLocationMatchDistanceConstraint(CConstRef <CBioseq> bioseq, const CSeq_loc& loc) const { if (!CanGetEnd5() && !CanGetEnd3()) { return true; } unsigned pos = loc.GetStop(eExtreme_Positional); int pos2; if (bioseq.NotEmpty()) { pos2 = (bioseq->IsSetLength() ? bioseq->GetLength() : 0) - pos - 1; } if (loc.GetStrand() == eNa_strand_minus) { if (CanGetEnd5()) { if (bioseq.Empty()) { return false; } else { if (!GetEnd5().Match(pos2)) { return false; } } } if (CanGetEnd3()) { return GetEnd3().Match(pos); } } else { if (CanGetEnd5() && !GetEnd5().Match(pos)) { return false; } if (CanGetEnd3()) { if (bioseq.Empty()) { return false; } return GetEnd3().Match(pos2); } } return true; };
pair<double, bool> CScoreSeqCoverage::MakeScore(CBioseq_Handle const& query_handle, vector<CSeq_align const*>::const_iterator begin, vector<CSeq_align const*>::const_iterator end) { CConstRef<CBioseq> bioseq = query_handle.GetCompleteBioseq(); unsigned int qlen = 0; if ( !bioseq.Empty() && bioseq->IsSetLength()) { qlen = bioseq->GetLength(); } if ( !qlen ) { return make_pair(0, false); } // Subject coverage score CRangeCollection<TSeqPos> range_coll; for ( ; begin != end; ++begin ) { CRange<TSeqPos> range = (*begin)->GetSeqRange(0); s_FixMinusStrandRange(range); range_coll += range; } double score = ( 100.0 * range_coll.GetCoveredLength() ) / qlen; return make_pair(score, true); }