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sysBiolAlg_fbaClass.R 6.87 KiB
# sysBiolAlg_fbaClass.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/>.
#------------------------------------------------------------------------------#
# definition of the class sysBiolAlg_fba #
#------------------------------------------------------------------------------#
setClass(Class = "sysBiolAlg_fba",
contains = "sysBiolAlg"
)
#------------------------------------------------------------------------------#
# default constructor #
#------------------------------------------------------------------------------#
# contructor for class sysBiolAlg_fba
setMethod(f = "initialize",
signature = "sysBiolAlg_fba",
definition = function(.Object,
model,
lpdir = SYBIL_SETTINGS("OPT_DIRECTION"),
useNames = SYBIL_SETTINGS("USE_NAMES"),
cnames = NULL,
rnames = NULL,
pname = NULL,
scaling = NULL,
writeProbToFileName = NULL, ...) {
if ( ! missing(model) ) {
stopifnot(is(model, "modelorg"),
is(lpdir, "character"))
# problem dimensions
nCols <- react_num(model)
nRows <- met_num(model)
# row and column names for the problem object
if (isTRUE(useNames)) {
if (is.null(cnames)) {
colNames <- .makeLPcompatible(react_id(model),
prefix = "x")
}
else {
stopifnot(is(cnames, "character"),
length(cnames) == nCols)
colNames <- cnames
}
if (is.null(rnames)) {
rowNames <- .makeLPcompatible(met_id(model),
prefix = "r")
}
else {
stopifnot(is(rnames, "character"),
length(rnames) == nRows)
rowNames <- rnames
}
if (is.null(pname)) {
probName <- .makeLPcompatible(
paste("FBA", mod_id(model), sep = "_"),
prefix = "")
}
else {
stopifnot(is(pname, "character"),
length(pname) == 1)
probName <- pname
}
}
else {
colNames <- NULL
rowNames <- NULL
probName <- NULL
}
# generate problem object
.Object <- callNextMethod(.Object,
sbalg = "fba",
pType = "lp",
scaling = scaling,
fi = 1:nCols,
nCols = nCols,
nRows = nRows,
mat = S(model),
ub = uppbnd(model),
lb = lowbnd(model),
obj = obj_coef(model),
rlb = rep(0, nRows),
rtype = rep("E", nRows),
lpdir = lpdir,
rub = NULL,
ctype = NULL,
cnames = colNames,
rnames = rowNames,
pname = probName,
...)
if (!is.null(writeProbToFileName)) {
writeProb(problem(.Object),
fname = as.character(writeProbToFileName))
}
#
# # make problem object
# lp <- optObj(solver = solver, method = method)
# lp <- initProb(lp, nrows = nRows, ncols = nCols)
#
# # set parameters
# if (!any(is.na(solverParm))) {
# setSolverParm(lp, solverParm)
# }
#
# loadLPprob(lp,
# nCols = nCols,
# nRows = nRows,
# mat = S(model),
# ub = uppbnd(model),
# lb = lowbnd(model),# obj = obj_coef(model),
# rlb = rep(0, nRows),
# rub = NULL,
# rtype = rep("E", nRows),
# lpdir = lpdir
# )
#
# if (!is.null(scaling)) {
# scaleProb(lp, scaling)
# }
#
# .Object@problem <- lp
# .Object@algorithm <- "fba"
# .Object@nr <- as.integer(nRows)
# .Object@nc <- as.integer(nCols)
# .Object@fldind <- as.integer(c(1:nCols))
# validObject(.Object)
}
return(.Object)
}
)
#------------------------------------------------------------------------------#