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/**
* \file addCVTerms.cpp
* \brief adds controlled vocabulary terms to a species in a model
* \author Sarah Keating
*
* <!--------------------------------------------------------------------------
* 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 libsbmlcs;
public class AddCVTerms
{
public static int Main(string[] args)
{
SBMLDocument d;
long errors, n;
Species s;
if (args.Length != 2)
{
Console.WriteLine(" usage: addCVTerms <input-filename> <output-filename>");
Console.WriteLine(" Adds controlled vocabulary term to a species");
return 2;
}
d = libsbml.readSBML(args[0]);
errors = d.getNumErrors();
if (errors > 0)
{
Console.WriteLine("Read Error(s):");
d.printErrors();
Console.WriteLine("Correct the above and re-run.");
}
else
{
n = d.getModel().getNumSpecies();
if (n <= 0)
{
Console.WriteLine("Model has no species.\n Cannot add CV terms\n");
}
else
{
s = d.getModel().getSpecies(0);
CVTerm cv = new CVTerm();
cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF);
cv.addResource("http://www.geneontology.org/#GO:0005892");
CVTerm cv2 = new CVTerm();
cv2.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
cv2.setBiologicalQualifierType(libsbml.BQB_IS);
cv2.addResource("http://www.geneontology.org/#GO:0005895");
CVTerm cv1 = new CVTerm();
cv1.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF);
cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
s.addCVTerm(cv);
s.addCVTerm(cv2);
s.addCVTerm(cv1);
libsbml.writeSBML(d, args[1]);
}
}
return (int)errors;
}
}
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