HmmWeight Member List

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

align_type	Weight
allow_DI	Weight
allow_ID	Weight
AverageUIPAC() (defined in Weight)	Weight	[protected]
freq1	Weight
freq2	Weight
gap_extension	Weight
gap_open	Weight
GetAlphabet1() const	Weight	[inline]
GetAlphabet2() const	Weight	[inline]
HmmWeight(const Alphabet &, const Alphabet &, const std::string &name, double gap_open, double gap_extension, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false)	HmmWeight
HmmWeight(const ScoreMatrix &matrix, double _scale, const Frequencies &freq1, const Frequencies &freq2, double gap_open, double gap_extension, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false) (defined in HmmWeight)	HmmWeight
HmmWeight(const ScoreMatrix &matrix, const Sequence &seq1, const Sequence &seq2, double gap_open, double gap_extension, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false) (defined in HmmWeight)	HmmWeight
IsBoltzmann() const	Weight	[inline, virtual]
Normalize(bool setupUIPAC=false)	Weight	[protected]
scale	Weight
StreamOut(std::ostream &ost)	Weight	[virtual]
tDD (defined in Weight)	Weight
tDE (defined in Weight)	Weight
tDI (defined in Weight)	Weight
tDM (defined in Weight)	Weight
tID (defined in Weight)	Weight
tIE (defined in Weight)	Weight
tII (defined in Weight)	Weight
tIM (defined in Weight)	Weight
tMD (defined in Weight)	Weight
tME (defined in Weight)	Weight
tMI (defined in Weight)	Weight
tMM (defined in Weight)	Weight
tSD (defined in Weight)	Weight
tSI (defined in Weight)	Weight
tSM (defined in Weight)	Weight
Weight(const Alphabet &a1, const Alphabet &a2, AlignmentType t, bool _allow_DI=true, bool _allow_ID=false)	Weight
~Weight()	Weight	[inline, virtual]