StochHMM::alignment Member List

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

_getGapScore(size_t, size_t, tracebackDirection)	StochHMM::alignment	private
_initTrellis(size_t, size_t)	StochHMM::alignment	private
_reset()	StochHMM::alignment	private
_resetSeqs()	StochHMM::alignment	private
align(alignment_type typ)	StochHMM::alignment
align(sequence &target, sequence &query, alignment_type typ)	StochHMM::alignment
align(sequence &target, sequence &query, alignment_type typ, double match, double mismatch, double gap, double gapext)	StochHMM::alignment
align(sequence &target, sequence &query, alignment_type typ, const mmMatrix &, double gap, double gapext)	StochHMM::alignment
alignment()	StochHMM::alignment
calc_pvalue()	StochHMM::alignment
calcLambda(std::vector< double > &)	StochHMM::alignment
end_position	StochHMM::alignment	private
estimateLambda()	StochHMM::alignment
gap	StochHMM::alignment	private
gap_ext	StochHMM::alignment	private
getAlignment()	StochHMM::alignment
getAlignmentSize()	StochHMM::alignment	inline
getHighScore()	StochHMM::alignment	inline
high_score	StochHMM::alignment	private
mMatrix	StochHMM::alignment	private
printAlignment()	StochHMM::alignment
printTrellis()	StochHMM::alignment
query	StochHMM::alignment	private
setGap(double value)	StochHMM::alignment	inline
setGapExt(double value)	StochHMM::alignment	inline
setMatch(double)	StochHMM::alignment
setMatrix(mmMatrix &)	StochHMM::alignment
setMismatch(double)	StochHMM::alignment
setQuery(sequence &)	StochHMM::alignment
setTarget(sequence &)	StochHMM::alignment
start_position	StochHMM::alignment	private
stochasticTraceback()	StochHMM::alignment
target	StochHMM::alignment	private
tr	StochHMM::alignment	private
traceback()	StochHMM::alignment
trellis	StochHMM::alignment	private