LSDynaln Member List

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

allocmem()	LSDynaln	[private]
allocmem()	LSDynaln	[private]
alnidx	Dynaln	[protected]
alntype	Dynaln	[protected]
buildAlnInfo()	Dynaln
buildAlnInfo()	Dynaln
buildResult()	LSDynaln
buildResult()	LSDynaln
buttomaln	Dynaln	[protected]
buttomBeginIndex() const	Dynaln	[inline]
buttomBeginIndex() const	Dynaln	[inline]
buttomEndIndex() const	Dynaln	[inline]
buttomEndIndex() const	Dynaln	[inline]
buttomruler	Dynaln	[protected]
C1	Dynaln	[protected]
C2	Dynaln	[protected]
clearResult()	Dynaln	[protected]
clearResult()	Dynaln	[protected]
computeScoreBW(int b1, int e1, int b2, int e2)	LSDynaln
computeScoreBW(int b1, int e1, int b2, int e2)	LSDynaln
computeScoreFW(int b1, int e1, int b2, int e2)	LSDynaln
computeScoreFW(int b1, int e1, int b2, int e2)	LSDynaln
countnumgaps()	Dynaln	[protected]
countnumgaps()	Dynaln	[protected]
debug_showmatrix(ostream &ous) const	Dynaln
debug_showmatrix(ostream &ous) const	Dynaln
debug_showmatrixBackward(pair< int, int > &rows, const int col)	LSDynaln
debug_showmatrixBackward(pair< int, int > &rows, const int col)	LSDynaln
debug_showmatrixForward(pair< int, int > &rows, const int col)	LSDynaln
debug_showmatrixForward(pair< int, int > &rows, const int col)	LSDynaln
Dynaln()	Dynaln	[inline]
Dynaln(const bioseq &s1, const bioseq &s2)	Dynaln	[inline]
Dynaln(const bioseq &s1, const bioseq &s2, const string &ma)	Dynaln	[inline]
Dynaln()	Dynaln	[inline]
Dynaln(const bioseq &s1, const bioseq &s2)	Dynaln	[inline]
Dynaln(const bioseq &s1, const bioseq &s2, const string &ma)	Dynaln	[inline]
findAlnBoundary()	Dynaln	[protected]
findAlnBoundary()	Dynaln	[protected]
gapchar	Dynaln	[static]
gape	Dynaln	[protected]
gapi	Dynaln	[protected]
gaplen1	Dynaln	[protected]
gaplen2	Dynaln	[protected]
getAlnlen() const	Dynaln	[inline]
getAlnlen() const	Dynaln	[inline]
getButtomAln() const	Dynaln	[inline]
getButtomAln() const	Dynaln	[inline]
getIdentity() const	Dynaln	[inline]
getIdentity() const	Dynaln	[inline]
getMatchArray(vector< int > &marr, bool countsim=true) const	Dynaln
getNgMatchArray(vector< int > &ngmarr, bool append=false, bool countsim=true) const	Dynaln
getScore()	Dynaln	[inline]
getScore()	Dynaln	[inline]
getScoringMatrix() const	Dynaln	[inline]
getScoringMatrix() const	Dynaln	[inline]
getSimilarity() const	Dynaln	[inline]
getSimilarity() const	Dynaln	[inline]
getTopAln() const	Dynaln	[inline]
getTopAln() const	Dynaln	[inline]
global()	LSDynaln
global()	LSDynaln
headers(const string &dl)	Dynaln	[static]
headers(const string &dl)	Dynaln	[static]
idenchar	Dynaln	[static]
idencnt	Dynaln	[protected]
IX	Dynaln	[protected]
IXR	LSDynaln	[private]
IY	Dynaln	[protected]
IYR	LSDynaln	[private]
local()	LSDynaln
local()	LSDynaln
LSDynaln()	LSDynaln	[inline]
LSDynaln(const bioseq &s1, const bioseq &s2)	LSDynaln	[inline]
LSDynaln(const bioseq &s1, const bioseq &s2, const string &mat)	LSDynaln	[inline]
LSDynaln()	LSDynaln	[inline]
LSDynaln(const bioseq &s1, const bioseq &s2)	LSDynaln	[inline]
LSDynaln(const bioseq &s1, const bioseq &s2, const string &mat)	LSDynaln	[inline]
M	Dynaln	[protected]
middle	Dynaln	[protected]
MR	LSDynaln	[private]
numcol	Dynaln	[protected]
numgaps() const	Dynaln	[inline]
numgaps() const	Dynaln	[inline]
numgaps1	Dynaln	[protected]
numgaps2	Dynaln	[protected]
path(int b1, int e1, int b2, int e2)	LSDynaln
path(int b1, int e1, int b2, int e2)	LSDynaln
printAlign(ostream &ous, const int w=70) const	Dynaln
printAlign(ostream &ous, const int w=70) const	Dynaln
PTRDIAG	Dynaln	[static]
PTRLEFT	Dynaln	[static]
PTRNULL	Dynaln	[static]
PTRTOP	Dynaln	[static]
runglobal()	Dynaln	[inline]
runglobal()	Dynaln	[inline]
runlocal()	LSDynaln	[inline]
runlocal()	LSDynaln	[inline]
S	Dynaln	[protected]
seq1	Dynaln	[protected]
seq1begin	Dynaln	[protected]
seq1end	Dynaln	[protected]
seq2	Dynaln	[protected]
seq2begin	Dynaln	[protected]
seq2end	Dynaln	[protected]
setAllParameter(const Matrix &mat, const int go, const int ge)	Dynaln	[inline]
setAllParameter(const Matrix &mat, const int go, const int ge)	Dynaln	[inline]
setGapExtend(int ext)	Dynaln	[inline]
setGapExtend(int ext)	Dynaln	[inline]
setGapInsert(int ins)	Dynaln	[inline]
setGapInsert(int ins)	Dynaln	[inline]
setGapParameter(const int go, const int ge)	Dynaln	[inline]
setGapParameter(const int go, const int ge)	Dynaln	[inline]
setMatrix(const string &mat)	Dynaln	[inline]
setMatrix(const Matrix &mat)	Dynaln	[inline]
setMatrix(const string &mat)	Dynaln	[inline]
setMatrix(const Matrix &mat)	Dynaln	[inline]
setseq(const bioseq &sq1, const bioseq &sq2)	Dynaln	[inline]
setseq(const bioseq &sq1, const bioseq &sq2)	Dynaln	[inline]
setSeq(const bioseq &sq1, const bioseq &sq2)	Dynaln	[inline]
setSeq(const bioseq &sq1, const bioseq &sq2)	Dynaln	[inline]
setSeq1(const bioseq &sq)	Dynaln	[inline]
setSeq1(const bioseq &sq)	Dynaln	[inline]
setSeq2(const bioseq &sq)	Dynaln	[inline]
setSeq2(const bioseq &sq)	Dynaln	[inline]
showseq() const	Dynaln	[inline]
showseq() const	Dynaln	[inline]
simchar	Dynaln	[static]
simcnt	Dynaln	[protected]
simcut	Dynaln	[static]
Smax	Dynaln	[protected]
Smaxi	Dynaln	[protected]
Smaxj	Dynaln	[protected]
Ssize	Dynaln	[protected]
ST	Dynaln	[protected]
toDelimitedString(const string &dl=",", int ibase=0) const	Dynaln
toDelimitedString(const string &dl=",") const	Dynaln
topaln	Dynaln	[protected]
topBeginIndex() const	Dynaln	[inline]
topBeginIndex() const	Dynaln	[inline]
topEndIndex() const	Dynaln	[inline]
topEndIndex() const	Dynaln	[inline]
topruler	Dynaln	[protected]
tracebackBW(pair< int, int > mrow, int b1, int &e1, int b2, int &e2)	LSDynaln
tracebackBW(pair< int, int > mrow, int b1, int &e1, int b2, int &e2)	LSDynaln
tracebackFW(pair< int, int > mrow, int b1, int &e1, int b2, int &e2)	LSDynaln
tracebackFW(pair< int, int > mrow, int b1, int &e1, int b2, int &e2)	LSDynaln
tracepointer(int &i, int &j)	Dynaln	[protected]
tracepointer(int &i, int &j)	Dynaln	[protected]
~Dynaln()	Dynaln
~Dynaln()	Dynaln
~LSDynaln()	LSDynaln
~LSDynaln()	LSDynaln