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/**
* @file convertSBML.cpp
* @brief Converts SBML documents between levels
* @author Michael Hucka
* @author Sarah Keating
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* 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;
public class ConvertSBML
{
public static int Main(string[] args)
{
int latestLevel = (int)SBMLDocument.getDefaultLevel();
int latestVersion = (int)SBMLDocument.getDefaultVersion();
if (args.Length != 2)
{
Console.Write("Usage: convertSBML input-filename output-filename" + Environment.NewLine
+ "This program will attempt to convert a model either to" + Environment.NewLine
+ "SBML Level " + latestLevel + " Version " + latestVersion
+ " (if the model is not already) or, if " + Environment.NewLine
+ "the model is already expressed in Level " + latestLevel
+ " Version " + latestVersion + ", this" + Environment.NewLine
+ "program will attempt to convert the model to Level 1 Version 2."
+ Environment.NewLine);
return 1;
}
string inputFile = args[0];
string outputFile = args[1];
SBMLDocument document = libsbml.readSBML(inputFile);
long errors = document.getNumErrors();
if (errors > 0)
{
Console.Error.Write("Encountered the following SBML errors:" + Environment.NewLine);
document.printErrors();
Console.Error.Write("Conversion skipped. Please correct the problems above first."
+ Environment.NewLine);
return (int)errors;
}
/**
* If the given model is not already L2v4, assume that the user wants to
* convert it to the latest release of SBML (which is L2v4 currently).
* If the model is already L2v4, assume that the user wants to attempt to
* convert it down to Level 1 (specifically L1v2).
*/
int olevel = (int)document.getLevel();
int oversion = (int)document.getVersion();
bool success;
if (olevel < latestLevel || oversion < latestVersion)
{
Console.Write("Attempting to convert Level " + olevel + " Version " + oversion
+ " model to Level " + latestLevel
+ " Version " + latestVersion + "." + Environment.NewLine);
success = document.setLevelAndVersion(latestLevel, latestVersion);
}
else
{
Console.Write ("Attempting to convert Level " + olevel + " Version " + oversion
+ " model to Level 1 Version 2." + Environment.NewLine);
success = document.setLevelAndVersion(1, 2);
}
errors = document.getNumErrors();
if (!success)
{
Console.Error.Write("Unable to perform conversion due to the following:" + Environment.NewLine);
document.printErrors();
Console.Write(Environment.NewLine);
Console.Write("Conversion skipped. Either libSBML does not (yet)" + Environment.NewLine
+ "have the ability to convert this model or (automatic)" + Environment.NewLine
+ "conversion is not possible in this case." + Environment.NewLine);
return (int)errors;
}
else if (errors > 0)
{
Console.Write("Information may have been lost in conversion; but a valid model ");
Console.Write("was produced by the conversion.\nThe following information ");
Console.Write("was provided:\n");
document.printErrors();
libsbml.writeSBML(document, outputFile);
}
else
{
Console.Write("Conversion completed." + Environment.NewLine);
libsbml.writeSBML(document, outputFile);
}
return 0;
}
}
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