sysBiolAlg_fvClass.R

#  sysBiolAlg_fvClass.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_fv                     #
#------------------------------------------------------------------------------#

setClass(Class = "sysBiolAlg_fv",
         contains = "sysBiolAlg"
)


#------------------------------------------------------------------------------#
#                            default constructor                               #
#------------------------------------------------------------------------------#

# contructor for class sysBiolAlg_fv
setMethod(f = "initialize",
          signature = "sysBiolAlg_fv",
          definition = function(.Object,
                                model,
                                percentage = 100,
                                Zopt = NULL,
                                fixObjVal = TRUE,
                                tol = SYBIL_SETTINGS("TOLERANCE"),
                                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.null(Zopt) || is(Zopt, "numeric")),
                            is(tol, "numeric"),
                            is(percentage, "numeric"),
                            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),