Nothing
setClass("CGHoptions",
representation=list(
select = 'character',
calling = 'logical',
wavenorm = 'character',
GCnorm = 'character',
nblevels = 'numeric',
alpha = 'numeric',
beta = 'numeric',
nbprocs = 'numeric',
itermax = 'numeric'),
prototype(select = "mBIC",
calling = FALSE,
wavenorm = "none",
GCnorm = "none",
nblevels = 3,
alpha = 0.2,
beta = 0.5,
nbprocs = 1,
itermax = Inf)
)
setMethod(
f = "[",
signature = "CGHoptions",
definition = function(x,i,j,drop){
if (i=="select") {return(x@select)} else {}
if (i=="calling") {return(x@calling)} else {}
if (i=="wavenorm") {return(x@wavenorm)} else {}
if (i=="GCnorm") {return(x@GCnorm)} else {}
if (i=="nblevels") {return(x@nblevels)} else {}
if (i=="alpha") {return(x@alpha)} else {}
if (i=="beta") {return(x@beta)} else {}
if (i=="nbprocs") {return(x@nbprocs)} else {}
if (i=="itermax") {return(x@itermax)} else {}
}
)
setMethod(
f = "print",
signature = "CGHoptions",
definition = function(x){
cat("****** CGHoption print ******\n")
A = data.frame(options = rep(NA,9), value = rep(NA,9),row.names=NULL)
A[1,1] = "select"
A[1,2] = x@select
A[2,1] = "calling"
A[2,2] = x@calling
A[3,1] = "wavenorm"
A[3,2] = x@wavenorm
A[4,1] = "GCnorm"
A[4,2] = x@GCnorm
A[5,1] = "nblevels"
A[5,2] = x@nblevels
A[6,1] = "alpha"
A[6,2] = x@alpha
A[7,1] = "beta"
A[7,2] = x@beta
A[8,1] = "nbprocs"
A[8,2] = x@nbprocs
A[9,1] = "itermax"
A[9,2] = x@itermax
print(A)
}
)
setMethod(
f = "show",
signature = "CGHoptions",
definition = function(object){
cat("****** CGHoption show ******\n")
A = data.frame(options = rep(NA,9), value = rep(NA,9))
A[1,1] = "select"
A[1,2] = object@select
A[2,1] = "calling"
A[2,2] = object@calling
A[3,1] = "wavenorm"
A[3,2] = object@wavenorm
A[4,1] = "GCnorm"
A[4,2] = object@GCnorm
A[5,1] = "nblevels"
A[5,2] = object@nblevels
A[6,1] = "alpha"
A[6,2] = object@alpha
A[7,1] = "beta"
A[7,2] = object@beta
A[8,1] = "nbprocs"
A[8,2] = object@nbprocs
A[9,1] = "itermax"
A[9,2] = object@itermax
print(A)
}
)
setGeneric("select<-",function(object,value){standardGeneric("select<-")})
setReplaceMethod(
f="select",
signature="CGHoptions",
definition=function(object,value){
object@select =value
return (object)
}
)
setGeneric("calling<-",function(object,value){standardGeneric("calling<-")})
setReplaceMethod(
f="calling",
signature="CGHoptions",
definition=function(object,value){
object@calling =value
return (object)
}
)
setGeneric("wavenorm<-",function(object,value){standardGeneric("wavenorm<-")})
setReplaceMethod(
f="wavenorm",
signature="CGHoptions",
definition=function(object,value){
object@wavenorm =value
return (object)
}
)
setGeneric("GCnorm<-",function(object,value){standardGeneric("GCnorm<-")})
setReplaceMethod(
f="GCnorm",
signature="CGHoptions",
definition=function(object,value){
object@GCnorm =value
return (object)
}
)
setGeneric("nblevels<-",function(object,value){standardGeneric("nblevels<-")})
setReplaceMethod(
f="nblevels",
signature="CGHoptions",
definition=function(object,value){
object@nblevels =value
return (object)
}
)
setGeneric("alpha<-",function(object,value){standardGeneric("alpha<-")})
setReplaceMethod(
f="alpha",
signature="CGHoptions",
definition=function(object,value){
object@alpha =value
return (object)
}
)
setGeneric("beta<-",function(object,value){standardGeneric("beta<-")})
setReplaceMethod(
f="beta",
signature="CGHoptions",
definition=function(object,value){
object@beta =value
return (object)
}
)
setGeneric("nbprocs<-",function(object,value){standardGeneric("nbprocs<-")})
setReplaceMethod(
f="nbprocs",
signature="CGHoptions",
definition=function(object,value){
object@nbprocs =value
return (object)
}
)
setGeneric("itermax<-",function(object,value){standardGeneric("itermax<-")})
setReplaceMethod(
f="itermax",
signature="CGHoptions",
definition=function(object,value){
object@itermax =value
return (object)
}
)
setGeneric( name = "fun2run" ,def = function(.Object){standardGeneric("fun2run")})
setMethod(
f = "fun2run",
signature = "CGHoptions",
definition = function(.Object){
if (.Object@calling==TRUE & (.Object@wavenorm!="none" | .Object@GCnorm!="none") ){
instr = parse(text = "Res = ILSclust(.Object,CGHo,uniKmax,multiKmax)")
cat("[multiseg] ILSclust running \n")
} else if (.Object@calling==TRUE & .Object@wavenorm=="none" & .Object@GCnorm=="none" ){
instr = parse(text = "Res = multisegclust(.Object,CGHo,uniKmax,multiKmax)")
cat("[multiseg] multisegclust running \n")
} else if (.Object@calling==FALSE & .Object@wavenorm=="none" & .Object@GCnorm=="none"){
instr = parse(text = "Res = multisegmean(.Object,CGHo,uniKmax,multiKmax)")
cat("[multiseg] multisegmean running \n")
} else if (.Object@calling==FALSE & (.Object@wavenorm!="none" | .Object@GCnorm!="none") ){
instr = parse(text = "Res = ILS(.Object,CGHo,uniKmax,multiKmax)")
cat("[multiseg] ILS running \n")
}
return(instr)
}
)
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