alignment Member List

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

alignment()	alignment	[inline]
avgThick	alignment	[protected]
begin() const	alignment	[inline]
begin() const	alignment	[inline]
calBias(double &efflen, int psw=6) const	alignment
calBias(double &efflen, int psw=6) const	alignment
calcut(float top, float n, int iden)	alignment	[protected]
clusterid	alignment
consensus	alignment	[protected]
count()	alignment	[protected]
countDia()	alignment	[protected]
dumpaln()	alignment
dumpQuality(ostream &ou)	alignment
end() const	alignment	[inline]
end() const	alignment	[inline]
eValue() const	alignment	[inline]
eValue() const	alignment	[inline]
exp	alignment	[private]
getalnmodel() const	alignment
getIdentityCount() const	alignment	[inline]
getPosition() const	alignment
getqual(float base=0.08, float top=1.2)	alignment
getSimilarityCount() const	alignment	[inline]
goodSegment()	alignment
highQuality(float cut=0.2)	alignment
iden	alignment	[private]
idenCnt	alignment	[protected]
idenCut	alignment
identical_residue() const	alignment	[inline]
identical_residue() const	alignment	[inline]
identity() const	alignment	[inline]
identity() const	alignment	[inline]
identity() const	alignment	[inline]
iscompl() const	alignment	[inline]
iscompl() const	alignment	[inline]
isup() const	alignment	[inline]
isup() const	alignment	[inline]
len	alignment	[private]
length() const	alignment	[inline]
length() const	alignment	[inline]
length() const	alignment	[inline]
matchSeq() const	alignment	[inline]
matchSeq() const	alignment	[inline]
method	alignment
namearr	alignment	[protected]
nogapCol	alignment	[protected]
nogapcolcut	alignment	[static]
nogapIdentity() const	alignment	[inline]
nogapLength() const	alignment	[inline]
nogapsimCnt	alignment	[protected]
nogapSimilarity()	alignment	[inline]
operator<<(ostream &ou, const alignment &aln)	alignment	[friend]
partcol	alignment	[protected]
partialCount(float gapcut=0.51)	alignment
partialGood(float base)	alignment
partiden	alignment	[protected]
printPolymorphic(ostream &ous) const	alignment
qe	alignment	[private]
qs	alignment	[private]
qseq	alignment	[private]
querySeq() const	alignment	[inline]
querySeq() const	alignment	[inline]
read(istream &in)	alignment
read(istream &ins, char ln[], string &bf)	alignment
read(istream &ins, char ln[], string &bf)	alignment
readClustal(istream &in)	alignment
readDia(istream &in)	alignment
region class	alignment	[friend]
sbjbegin() const	alignment	[inline]
sbjbegin() const	alignment	[inline]
sbjend() const	alignment	[inline]
sbjend() const	alignment	[inline]
sbjseq	alignment	[private]
sco	alignment	[private]
score() const	alignment	[inline]
score() const	alignment	[inline]
se	alignment	[private]
seqarr	alignment	[protected]
seqCount() const	alignment	[inline]
simCnt	alignment	[protected]
simil	alignment	[private]
similarity() const	alignment	[inline]
size() const	alignment	[inline]
split(char ln[], int &s, string &seq, int &e)	alignment	[friend]
ss	alignment	[private]