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/**
* @file replaceOneFD.cs
* @brief replaces a given function definition in a specific part of the model
* @author Frank 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.
* ------------------------------------------------------------------------ -->
*/
using System;
using System.Collections.Generic;
using System.IO;
using System.Text;
using libsbmlcs;
/**
* This example is not something you would normally do, what you would want to do is to
* call the inline function definition converter. However, if for example you would only
* want to expand one function definition, you could use the methods in SBMLTransform
* directly.
*/
internal class ReplaceFD
{
public static int Main(string[] args)
{
if (args.Length != 4)
{
Console.WriteLine("Usage: replaceOneFD filename functionDefinitionId reactionId outfile");
return 1;
}
string filename = args[0];
string outFile = args[3];
string functionDefinitionId = args[1];
string reactionId = args[2];
long current = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBML(filename);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0)
{
Console.WriteLine("The models contains errors, please correct them before continuing.");
document.printErrors();
return 1;
}
var model = document.getModel();
var functionDefinition = model.getFunctionDefinition(functionDefinitionId);
if (functionDefinition == null)
{
Console.WriteLine();
Console.WriteLine("No functiondefinition with the given id can be found.");
return 1;
}
var reaction = model.getReaction(reactionId);
if (reaction == null)
{
Console.WriteLine();
Console.WriteLine("No reaction with the given id can be found.");
return 1;
}
if (!reaction.isSetKineticLaw() || !reaction.getKineticLaw().isSetMath())
{
Console.WriteLine();
Console.WriteLine("The reaction has no math set. ");
return 1;
}
// Until here it was all setup, all we needed was an ASTNode, in which we wanted to
// replace calls to a function definition, with the function definitions content.
//
SBMLTransforms.replaceFD(reaction.getKineticLaw().getMath(), functionDefinition);
// finally write to file
libsbml.writeSBML(document, outFile);
return 0;
}
}
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