modelorg2ExPA.R

#  modelorg2ExPA.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: modelorg2ExPA
#
#
#
#
# original function buildExpaFileFromModelorg by C. Jonathan Fritzemeier


modelorg2ExPA <- function(model,
                          fname = NULL,
                          exIntReact = NULL,
                          filepath = ".",
                          suffix = "expa",
                          tol = SYBIL_SETTINGS("TOLERANCE")) {
    
    if (!is(model, "modelorg")) {
        stop("needs an object of class modelorg!")
    }
	
	#expa <- ifelse (missing(fname), mod_id(model), fname)
	if (is.null(fname)) {
	    expa <- paste(mod_id(model), suffix, sep = ".")
	}
	else {
	    expa <- fname
	}
	
    tofile <- file.path(filepath, expa)
    
    fh <- try(file(tofile, "wt"), silent = TRUE)
    
    if (is(fh, "try-error")) {
        stop("cannot write ExPA file ", sQuote(fh))
    } else {
        on.exit(close(fh))
    }
    
    # exclude reactions
    if (is.null(exIntReact)) {
        exInt <- NA
    }
    else {
        exInt <- checkReactId(model, exIntReact)
    }