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# generateWT.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: .generateWT
#
#
#
.generateWT <- function(model, react = NULL, lb = NULL, ub = NULL, ...) {
# ca <- match.call()
#
# if ("solver" %in% names(ca)) {
# # It is necessary to test, whether argument solver has a variable,
# # or not. If it is a variable, it needs to be evaluated.
# testslv <- tryCatch(eval(parse(text = ca["solver"])),
# error = function(e) e)
# if (is(testslv, "simpleError")) {
# slv <- as.character(ca["solver"])
# }
# else {
# slv <- as.character(testslv)
# }
#
# }
# else {
# slv <- SYBIL_SETTINGS("SOLVER")
# }
# setting ... parameters into list
ca <- list(...)
if(is.null(ca[["solver"]])){
ca[["solver"]] <- SYBIL_SETTINGS("SOLVER")
}
me <- checkDefaultMethod(solver = ca[["solver"]],
method = "NA",
probType = "lp",
loadPackage = FALSE)
ca[["solver"]] <- me[["sol"]]
ca[["method"]] <- me[["met"]]
ca[["solverParm"]] <- as.data.frame(NA)
ca[["object"]] <- model
if(is.null(ca[["algorithm"]])) ca[["algorithm"]] <- "fba"
ca[["react"]] <- react
ca[["ub"]] <- ub
ca[["lb"]] <- lb
if (is(react, "list")) {
message("calculating fba solutions ... ", appendLF = FALSE)
suppressMessages({
ca[["lpdir"]] <- rep("max", length(react))
ca[["verboseMode"]] <- 0
tmp <- do.call(optimizer, ca)
# tmp <- optimizer(model, algorithm = algorithm,
# lpdir = rep("max", length(react)),
# react = react, lb = lb, ub = ub, verboseMode = 0,
# solver = me[["sol"]], method = me[["met"]],
# solverParm = as.data.frame(NA), ...)
})
message("OK")
}
else {
ca[["retOptSol"]] <- FALSE
ca[["lpdir"]] <- "max"
tmp <- do.call("optimizeProb", ca)
# tmp <- optimizeProb(model,
# react = react, lb = lb, ub = ub,
# retOptSol = FALSE,
# algorithm = algorithm,
# lpdir = "max",
# solver = me[["sol"]],
# method = me[["met"]],
# solverParm = as.data.frame(NA), ...)
}
return(tmp)
}
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