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#
# Description of this R script:
# TODO
#
# Intended for use with R.
# Copyright (C) 2013 Martin Vincent
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>
#
#' print
#'
#' @param x
#' @param ...
#'
#' @author Martin Vincent
#' @method print epiG
#' @export
print.epiG <- function(x, ...) {
if("chunks" %in% class(x)) {
message(paste("Epigenotype model (estimated by epiG version ", x[[1]]$epiG_version, ")", sep=""))
message()
#TODO list chunks
# message(" ",paste(length(x), " chunks covering base position [", min(start(x)), ", ", max(end(x)), "]", " on ", x[[1]]$refname, ", ", sum(sapply(x, function(z) z$length)), " bases in total.", sep=""))
message()
message(" ",paste("Estimation was finalized ",x[[1]]$date, sep=""))
} else {
message(paste("Epigenotype model (estimated by epiG version ", x$epiG_version, ")", sep=""))
message()
message(paste(" Cover base position [", start(x), ", ", end(x), "]", " on ", x$refname, ", ", length(x), " bases in total.", sep=""))
message()
message(" ",paste("Estimation was finalized ",x$date, sep=""))
}
#TODO print number of reads
}
#' print config
#'
#' @param x
#' @param ...
#'
#' @author Martin Vincent
#' @method print epiG.config
#' @export
print.epiG.config <- function(x, ...) {
message("epiG config object:")
}
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