HalfAlignPile Member List

This is the complete list of members for HalfAlignPile, including all inherited members.

add(Interval *i)	IntervalPile
after(const Interval &iv) const	Interval	[inline]
before(const Interval &iv) const	Interval	[inline]
begin() const	Interval	[inline]
computeIntermediateResult() const	HalfAlignPile	[private]
end() const	Interval	[inline]
getBegin() const	Interval	[inline]
getCov() const	HalfAlignPile	[inline]
getEnd() const	Interval	[inline]
getIdentity() const	HalfAlignPile
getQcov() const	HalfAlignPile
getTcov() const	HalfAlignPile
HalfAlignPile()	HalfAlignPile	[inline]
HalfAlignPile(const HalfAlignPile &p)	HalfAlignPile	[inline]
HalfAlignPile(HalfAlignInterval *hp)	HalfAlignPile	[inline]
identity	HalfAlignPile	[mutable, private]
Interval()	Interval	[inline]
Interval(const int bb, const int ee)	Interval	[inline]
Interval(const Interval &iv)	Interval	[inline]
Interval(const string &str)	Interval
IntervalPile()	IntervalPile	[inline]
IntervalPile(Interval *ip)	IntervalPile	[inline]
isNull() const	Interval	[inline]
length() const	Interval	[inline]
less(const Interval &iv) const	Interval	[inline]
members	IntervalPile	[protected]
merge(Interval *ip, const int cut=5)	IntervalPile	[virtual]
operator<(const Interval &iv) const	Interval	[inline]
operator<<(ostream &ous, const Interval &iv)	Interval	[friend]
overlap(const Interval &i) const	Interval
overlap(const int bb, const int ee) const	Interval
qcov	HalfAlignPile	[mutable, private]
set(const Interval &iv)	Interval	[inline]
setBegin(const int bb)	Interval	[inline]
setEnd(const int ee)	Interval	[inline]
size() const	IntervalPile	[inline, virtual]
tcov	HalfAlignPile	[mutable, private]
toDelimitedString(const string &dl="\t") const	HalfAlignPile	[virtual]
~Interval()	Interval	[inline, virtual]
~IntervalPile()	IntervalPile