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promptSysBiolAlg.R

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    readSBMLmod.R 42.41 KiB
    #------------------------------------------------------------------------------#
    #                          Link to libSBML for sybil                           #
    #------------------------------------------------------------------------------#
    
    #  readSBMLmod.R
    #  Link to libSBML for sybil.
    #
    #  Copyright (C) 2010-2013 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 sybilSBML.
    #
    #  SybilSBML 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.
    #
    #  SybilSBML 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 sybilSBML.  If not, see <http://www.gnu.org/licenses/>.
    
    
    ################################################
    # Function: readSBMLmod
    #
    #
    # The function readSBMLmod() is inspired by the function
    # readCbModel() contained in the COBRA Toolbox.
    # The algorithm is basically the same.
    
    
    readSBMLmod <- function(filename, description,
                            def_bnd = SYBIL_SETTINGS("MAXIMUM"),
                            validateSBML = FALSE,
                            extMetFlag = "b",
                            bndCond = TRUE,
                            ignoreNoAn = FALSE,
                            mergeMet = TRUE,
                            balanceReact = TRUE,
                            remUnusedMetReact = TRUE,
                            singletonMet = FALSE,
                            deadEndMet = FALSE,
                            remMet = FALSE,
                            constrMet = FALSE,
                            tol = SYBIL_SETTINGS("TOLERANCE")) {
    
    on.exit(expr = {
        if ( (exists("sbmldoc")) && (!isNULLpointerSBML(sbmldoc)) ) {
            closeSBMLfile(sbmldoc)
        }
    } )
    
    #------------------------------------------------------------------------------#
    # open the model file
    
    if ( file.exists(filename) == FALSE ) {
       stop("failed to open file ", sQuote(filename))
    }
    
    if (missing(description)) {
        mdesc <- filename
    }
    else {
        mdesc <- description