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# addExchReact.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/>.
################################################
# Function: addExchReact
#
#
# The function addExchReact() is inspired by the function
# addExchangeRxn() contained in the COBRA Toolbox.
# The algorithm is (more or less) the same.
addExchReact <- function(model, met, lb, ub) {
# ------------------------------------------------------------------------ #
# check arguments
# ------------------------------------------------------------------------ #
if (!is(model, "modelorg")) {
stop("needs an object of class modelorg")
}
#if ( (length(met) < 1) || (met == "") ) {
if ( (length(met) < 1) || (any(met == "")) ) {
stop("at least one metabolite is required and all metabolite character strings required to be non-empty")
}
if (missing(lb)) {
Clb <- rep(0, length(met))
}
else {
Clb <- lb
}
if (missing(ub)) {
Cub <- rep(SYBIL_SETTINGS("MAXIMUM"), length(met))
}
else {
Cub <- ub
}
if ( (length(met) != length(Clb)) || (length(met) != length(Cub)) ) {
stop("arguments 'met', 'lb' and 'ub' must have the same length")
}
Crev <- rep(FALSE, length(met))
Crev[Clb < 0] <- TRUE
exRid <- paste("Ex_", met, sep = "")
mod_out <- model
for (i in seq(along = met)) {
mod_out <- addReact(model = mod_out,
id = exRid[i],
met = met[i],
Scoef = -1,
reversible = Crev[i],
lb = Clb[i],
ub = Cub[i])
}
return(mod_out)
}
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