M8MatchEX Member List

This is the complete list of members for M8MatchEX, including all inherited members.

_score	M8Match	[protected]
after	M8MatchEX	[private]
alnlen() const	M8Match	[inline]
asDelimitedString(const char delimiter[]=",") const	M8Match
attachTo(M8MatchEX &m)	M8MatchEX	[inline]
before	M8MatchEX	[private]
Boxchain class	M8MatchEX	[friend]
combine(const M8Match &m)	M8Match
Match::combine(const Match &m)	Match	[inline]
contain(const M8Match &m, bool sameDirection=true, float factor=0.8) const	M8Match
Match::contain(const Match &m, bool sameDirection=true) const	Match	[inline]
coveredBy(const Match &m, bool sd=true, float fraction=0.8) const	Match
e	M8Match	[protected]
expect() const	M8Match	[inline]
gap	M8Match	[protected]
getMaxScore() const	M8MatchEX	[inline]
iden	M8Match	[protected]
identity() const	M8Match	[inline]
isNull() const	Match	[inline]
len	M8Match	[protected]
M8Match()	M8Match	[inline]
M8Match(const M8Match &m)	M8Match	[inline]
M8Match(float identity, int alnlen, int mismatches, int gaps, int qbegin, int qend, int tbegin, int tend, double expect, double score)	M8Match	[inline]
M8MatchEX()	M8MatchEX	[inline]
M8MatchEX(const M8MatchEX &m)	M8MatchEX	[inline]
M8MatchEX(const M8Match &m)	M8MatchEX	[inline]
Match()	Match	[inline]
Match(const Match &m)	Match	[inline]
Match(int qb, int qe, int tb, int te)	Match	[inline]
maxScore	M8MatchEX	[private]
mis	M8Match	[protected]
next() const	M8MatchEX	[inline]
onMinus() const	Match	[inline]
onPlus() const	Match	[inline]
operator<(const Match &m) const	Match
operator<<(ostream &ous, const M8MatchEX &m)	M8MatchEX	[friend]
M8Match::operator<<(ostream &ous, M8Match &m)	M8Match	[friend]
Match::operator<<(ostream &ous, const Match &m)	Match	[friend]
operator=(const M8MatchEX &m)	M8MatchEX
operator=(const M8Match &m)	M8MatchEX
Match::operator=(const Match &m)	Match
operator==(const Match &m) const	Match	[inline]
output(ostream &ous, const char delimiter[]="\t") const	M8Match
overlap(const Match &m, bool sd=true) const	Match	[inline]
overlay(const Match &m) const	Match	[inline]
overlayFraction(const Match &m) const	Match	[inline]
plusContain(const Match &m) const	Match	[inline]
previous() const	M8MatchEX	[inline]
q	Match	[protected]
qcontain(const Match &m, bool sd=true) const	Match	[inline]
qoverlap(const Match &m, bool sameDirection=true) const	Match	[inline]
qplustminusContain(const Match &m) const	Match	[inline]
queryBegin() const	Match	[inline]
queryDistance(const Match &m)	Match	[inline]
queryEnd() const	Match	[inline]
queryLength() const	Match	[inline]
queryOverlapFraction(const Match &m, bool sameDirection=true) const	Match
queryOverlapFractionMax(const Match &m, bool sameDirection=true) const	Match	[inline]
queryOverlapFractionMerge(const Match &m, bool sameDirection=true) const	Match	[inline]
queryRange() const	Match	[inline]
score() const	M8Match	[inline]
set(int qb, int qe, int tb, int te)	Match	[inline]
setDefault()	M8MatchEX	[inline]
setMaxScore(double sc)	M8MatchEX	[inline]
setNext(M8MatchEX *p)	M8MatchEX	[inline]
setNull()	Match	[inline]
setPrevious(M8MatchEX *p)	M8MatchEX	[inline]
setTargetRange(int b, int e)	Match	[inline]
similar(const Match &m, bool sd=true) const	Match	[inline]
t	Match	[protected]
targetBegin() const	Match	[inline]
targetDirection() const	Match	[inline]
targetDistance(const Match &m)	Match	[inline]
targetEnd() const	Match	[inline]
targetLength() const	Match	[inline]
targetOnMinus() const	Match	[inline]
targetOnPlus() const	Match	[inline]
targetOverlapFraction(const Match &m, bool sameDirection=true) const	Match
targetOverlapFractionMax(const Match &m, bool sameDirection=true) const	Match	[inline]
targetOverlapFractionMerge(const Match &m, bool sameDirection=true) const	Match	[inline]
targetRange() const	Match	[inline]
tcontain(const Match &m, bool sd=true) const	Match	[inline]
toverlap(const Match &m, bool sameDirection=true) const	Match	[inline]
~Match()	Match	[inline]