Nothing
######################################################
## INITIALIZE METHOD ##
######################################################
## Initialize method for class BCRANKmatch
setMethod("initialize", "BCRANKmatch",
function(.Object,
consensus,
bcrankScore,
matchVec){
## Check that consensus is in IUPAC coding
iupacMatch <- gregexpr("^[ACGTRYKMSWBVDHN]*$",consensus)[[1]]
if(attr(iupacMatch,"match.length") < 0){
stop(paste(consensus,"not in IUPAC coding."))
}
##callNextMethod()
.Object@consensus <- consensus
.Object@bcrankScore <- bcrankScore
.Object@matchVec <- matchVec
.Object
})
BCRANKmatch <- function(consensus, bcrankScore, matchVec){
new("BCRANKmatch", consensus=consensus, bcrankScore=bcrankScore, matchVec=matchVec)
}
######################################################
## DISPLAY METHODS ##
######################################################
setMethod("show", "BCRANKmatch", function(object){
cat("\nAn object of class \"BCRANKmatch\"\n\n")
cat("Consensus:",consensus(object),", bcrankScore:",bcrankScore(object))
cat("\n\nUse methods consensus(object), bcrankScore(object) and matchVector(object) to access object slots.\n\n")
})
######################################################
## ACCESSOR METHODS ##
######################################################
setMethod("consensus", "BCRANKmatch", function(object) object@consensus)
setMethod("bcrankScore", "BCRANKmatch", function(object) object@bcrankScore)
setMethod("matchVector", "BCRANKmatch", function(object){
matchVec <- object@matchVec
matchVec[which(matchVec>0)] <- 1
return(matchVec)
})
setMethod("nrMatch", "BCRANKmatch", function(object){
return(length(which(matchVector(object) != 0)))
})
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