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# optsol_blockedReactClass.R
# FBA and friends with R.
#
# Copyright (C) 2010-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
# All right reserved.
# Email: geliudie@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/>.
# optsol_blockedReactClass
#------------------------------------------------------------------------------#
# definition of the class optsol_blockedReact #
#------------------------------------------------------------------------------#
# slot obj_function is used here for the optimized reaction
setClass("optsol_blockedReact",
representation(
blocked = "logical", # blocked reaction (yes/no)
react = "reactId" # checked reaction id's
),
contains = "optsol"
)
#------------------------------------------------------------------------------#
# setters and getters #
#------------------------------------------------------------------------------#
# blocked
setMethod("blocked", signature(object = "optsol_blockedReact"),
function(object) {
return(object@blocked)
}
)
setReplaceMethod("blocked", signature(object = "optsol_blockedReact"),
function(object, value) {
object@blocked <- value
return(object)
}
)
# react
setMethod("react", signature(object = "optsol_blockedReact"),
function(object) {
return(object@react)
}
)
setReplaceMethod("react", signature(object = "optsol_blockedReact"),
function(object, value) {
object@react <- value
return(object)
}
)
#------------------------------------------------------------------------------#
# other methods #
#------------------------------------------------------------------------------#
setMethod("maxSol", signature(object = "optsol_blockedReact"),
function(object, slot) {
odds <- seq(1, num_of_prob(object), 2)
command <- paste(deparse(substitute(slot)), "(", deparse(substitute(object)), ")[odds]", sep = "")
minimalSolutions <- eval(parse(text = command))
return(minimalSolutions)
}
)
setMethod("minSol", signature(object = "optsol_blockedReact"),
function(object, slot) {
odds <- seq(2, num_of_prob(object), 2)
command <- paste(deparse(substitute(slot)), "(", deparse(substitute(object)), ")[odds]", sep = "")
minimalSolutions <- eval(parse(text = command))
return(minimalSolutions)
}
)
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