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# upgradeModelorg.R
# FBA and friends with R.
#
# Copyright (C) 2010-2016 Claus Jonathan Fritzemeier, Dpt. for Bioinformatics,
# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
# All right reserved.
# Email: clausjonathan.fritzemeier@uni-duesseldorf.de
#
# This file is part of sybil.
#
# Sybil 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.
#
# Sybil 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 sybil. If not, see <http://www.gnu.org/licenses/>.
################################################
# Function: upgradeModelorg
#
# Takes an instance of a old modelorg version and returns one updated to the
# current version.
#
upgradeModelorg <- function(object){
stopifnot(is(object, "modelorg"))
if(!.hasSlot(object, "version") || compareVersion(version(object), "2.0") == -1){
# object is from a time before versions were introduced.
# just add version slot
object@version <- "2.0"
# update gprRules to new format
rules <- lapply(gpr(object), .parseBoolean)
if(length(rules) == 0){
genes(object) <- list()
gprRules(object) <- character(0)
}else{
genes(object) <- lapply(rules, "[[", "gene")
gprRules(object) <- sapply(rules, "[[", "rule")
}
# set attribute slots
react_attr(object) <- data.frame()
comp_attr(object) <- data.frame()
met_attr(object) <- data.frame()
mod_attr(object) <- data.frame()
#recursively upgrade to latest version.
return(upgradeModelorg(object))
}
if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == 0){
stopifnot(validObject(object))
return(object)
}
stop("unsupported version of modelorg")
}
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