Lines Matching refs:alimits
1219 TSignedSeqRange alimits = ap->m_align->Limits(); in operator ()() local
1222 alimits.SetFrom(alimits.GetTo()); in operator ()()
1224 alimits.SetTo(alimits.GetFrom()); in operator ()()
1231 if(alimits == blimits) in operator ()()
1233 else if(alimits.GetFrom() == blimits.GetFrom()) in operator ()()
1234 return (alimits.GetTo() > blimits.GetTo()); in operator ()()
1236 return (alimits.GetFrom() < blimits.GetFrom()); in operator ()()
1728 TSignedSeqRange alimits = ap->m_align->Limits(); in operator ()() local
1731 alimits.SetFrom(alimits.GetTo()); in operator ()()
1733 alimits.SetTo(alimits.GetFrom()); in operator ()()
1741 if(alimits.GetTo() == blimits.GetTo()) in operator ()()
1742 return (alimits.GetFrom() > blimits.GetFrom()); in operator ()()
1744 return (alimits.GetTo() < blimits.GetTo()); in operator ()()
1752 TSignedSeqRange alimits = ap->m_align->Limits(); in operator ()() local
1755 alimits.SetFrom(alimits.GetTo()); in operator ()()
1757 alimits.SetTo(alimits.GetFrom()); in operator ()()
1765 if(alimits == blimits) in operator ()()
1767 else if(alimits.GetTo() == blimits.GetTo()) in operator ()()
1768 return (alimits.GetFrom() > blimits.GetFrom()); in operator ()()
1770 return (alimits.GetTo() < blimits.GetTo()); in operator ()()
1779 TSignedSeqRange alimits = ap->m_align->Limits(); in operator ()() local
1782 alimits.SetFrom(alimits.GetTo()); in operator ()()
1784 alimits.SetTo(alimits.GetFrom()); in operator ()()
1792 if(alimits.GetFrom() == blimits.GetFrom()) in operator ()()
1793 return (alimits.GetTo() < blimits.GetTo()); in operator ()()
1795 return (alimits.GetFrom() > blimits.GetFrom()); in operator ()()
1803 TSignedSeqRange alimits = ap->m_align->Limits(); in operator ()() local
1806 alimits.SetFrom(alimits.GetTo()); in operator ()()
1808 alimits.SetTo(alimits.GetFrom()); in operator ()()
1816 if(alimits == blimits) in operator ()()
1818 else if(alimits.GetFrom() == blimits.GetFrom()) in operator ()()
1819 return (alimits.GetTo() < blimits.GetTo()); in operator ()()
1821 return (alimits.GetFrom() > blimits.GetFrom()); in operator ()()
4316 TSignedSeqRange alimits = ai->Limits(); in CalculateSupportAndWeightFromMembers() local
4322 if(Include(exon.Limits(), alimits.GetFrom())) { in CalculateSupportAndWeightFromMembers()
4323 alimits.SetTo(min(alimits.GetTo(), exon.Limits().GetTo())); in CalculateSupportAndWeightFromMembers()
4324 matches = alimits.GetLength(); in CalculateSupportAndWeightFromMembers()
4329 if(alimits.GetFrom() < Limits().GetFrom()) { in CalculateSupportAndWeightFromMembers()
4330 alimits.SetTo(min(alimits.GetTo(), Exons().front().Limits().GetTo())); in CalculateSupportAndWeightFromMembers()
4331 matches = alimits.GetLength(); in CalculateSupportAndWeightFromMembers()
4341 if(Include(exon.Limits(), alimits.GetTo())) { in CalculateSupportAndWeightFromMembers()
4342 alimits.SetFrom(max(alimits.GetFrom(), exon.Limits().GetFrom())); in CalculateSupportAndWeightFromMembers()
4343 matches = alimits.GetLength(); in CalculateSupportAndWeightFromMembers()
4348 if(alimits.GetTo() > Limits().GetTo()) { in CalculateSupportAndWeightFromMembers()
4349 alimits.SetFrom(max(alimits.GetFrom(), Exons().back().Limits().GetFrom())); in CalculateSupportAndWeightFromMembers()
4350 matches = alimits.GetLength(); in CalculateSupportAndWeightFromMembers()
4360 if(intron.IntersectingWith(alimits)) in CalculateSupportAndWeightFromMembers()
4384 int left = (alimits&m_supported_range).GetFrom(); in CalculateSupportAndWeightFromMembers()
4389 int right = (alimits&m_supported_range).GetTo(); in CalculateSupportAndWeightFromMembers()
4872 TSignedSeqRange alimits = ai->Limits(); in ClipChain() local
4873 if(limits.IntersectingWith(alimits)) // not clipped in ClipChain()