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#!/usr/bin/env ruby
#
# @file flattenModel.rb
# @brief Flattens the comp code from the given SBML file.
# @author Frank T. Bergmann
#
# <!--------------------------------------------------------------------------
# This sample program is distributed under a different license than the rest
# of libSBML. This program uses the open-source MIT license, as follows:
#
# Copyright (c) 2013-2018 by the California Institute of Technology
# (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
# and the University of Heidelberg (Germany), with support from the National
# Institutes of Health (USA) under grant R01GM070923. All rights reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
#
# Neither the name of the California Institute of Technology (Caltech), nor
# of the European Bioinformatics Institute (EMBL-EBI), nor of the University
# of Heidelberg, nor the names of any contributors, may be used to endorse
# or promote products derived from this software without specific prior
# written permission.
# ------------------------------------------------------------------------ -->
require 'libSBML'
if ARGV.size < 2 || ARGV.size > 3
puts "Usage: flattenModel [-p] input-filename output-filename"
puts " -p : list unused ports"
exit(2)
end
inFile=""
outFile=""
listPorts = ARGV.size == 3
if listPorts then
inFile=ARGV[1]
outFile=ARGV[2]
else
inFile=ARGV[0]
outFile=ARGV[1]
end
d = LibSBML::readSBML(inFile)
if (d.getNumErrors() > 0)
d.printErrors
else
props = LibSBML::ConversionProperties.new
props.addOption("flatten comp", true, "Flatten Hierarchical model")
props.addOption("leavePorts", listPorts, "unused ports should be listed in the flattened model")
if d.convert(props) != 0
puts "[Error] conversion failed..."
d.printErrors
exit(3)
end
LibSBML::writeSBML(d,outFile)
end
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