Holds the whole search path from a single
bcrank run. Each individual search step
is stored in a
object. Several objects of this class are collected in a
Objects are not intended to be created directly but as a result from
a collection of
objects, ontaining all bcrank search steps from a start guess to a
locally optimal solution.
BCRANKmatch-class object for the
highest scoring consensus sequence (locally optimal solution) in this bcrank run.
position weight matrix for the highest scoring consensus sequence.
number of occurrences of the final consensus sequence in the fasta input file.
number of iterations required to move from the start guess to the final soloution in this bcrank run.
signature(object = "BCRANKsearch", i=NULL):
i is NULL, returns a data frame containing consensus and score
for the whole search path. Otherwise, the i'th
BCRANKmatch-class object in the search path is returned.
signature(object = "BCRANKsearch", normalize=TRUE): Returns
the position weight matrix (pwm) for the highest scoring consensus in
this bcrank run. Matrix positions are between between 0 and 1 when
is TRUE. When FALSE, the number of matching sequences is reported.
signature(x = "BCRANKsearch", y = "missing"):
A plot method for the searchPath.
Adam Ameur, email@example.com