Distribution

__init__ (
        self,
        alphabetX,
        alphabetY,
        offsetX,
        offsetY,
        )

construct a new DiscretePairDistribution @param alphabetX: Alphabet object for sequence X @param alphabetY: Alphabet object for sequence Y @param offsetX: number of characters the alphabet of sequence X consumes at a time @param offsetX: number of characters the alphabet of sequence Y consumes at a time

getCounts (
        self,
        sequenceX,
        sequenceY,
        )

extract the pair counts for aligned sequences sequenceX and sequenceY @param sequenceX: string for sequence X @param sequenceY: strinf for sequence Y @return: a list of counts

getEmptyProbabilityVector ( self )

get an empty probability vector for this distribution (filled with 0.0) @return: list of floats

getPairIndex (
        self,
        charX,
        charY,
        )

get the index of a pair of two characters in the probability vector (if you use the int representation both values must be ints) @param charX: character chain or int representation @param charY: character chain or int representation @return: the index of the pair in the probability vector

setPairProbability (
        self,
        charX,
        charY,
        probability,
        )

set the probability of the [air charX and charY to probability @param charX: character chain or int representation @param charY: character chain or int representation @param probability: probability (0<=float<=1)