checkReactId.R

#  checkReactId.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: checkReactId
#
# 
# 
#

checkReactId <- function(model, react) {

  if (is(react, "reactId")) {
      return(react)
  }

  if (!is(model, "modelorg")) {
    stop("needs an object of class modelorg!")
  }

  checkedIds <- NULL

 
#------------------------------------------------------------------------------#
#                           if "react" is numeric                              #
#------------------------------------------------------------------------------#

# If react is numeric (or integer), we only need to check, whether no element of
# react is larger than the number of reactions and if all elements are positive.

  if (is.numeric(react) || is.integer(react)) {

      if ( (max(react) > react_num(model)) || (min(react) < 1) ) {
      #if ( (max(react) > react_num(model)) || (!all(react > 0)) ) {
          warning("reaction numbers must be in between 1 and ", react_num(model))
      }
      else {
          checkedIds <- new("reactId",
                            mod_id  = mod_id(model),
                            mod_key = mod_key(model),
                            pnt     = react,
                            id      = react_id(model)[react])
      }
      #return(checkedIds)

  }

#------------------------------------------------------------------------------#
#                          if "react" is character                             #