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/**
* \file addingEvidenceCodes_1.cpp
* \brief adds controlled vocabulary terms to a reaction 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.
* ------------------------------------------------------------------------ -->
*/
import org.sbml.libsbml.CVTerm;
import org.sbml.libsbml.Reaction;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.libsbml;
public class addingEvidenceCodes_1 {
public static void main(String[] args) {
System.loadLibrary("sbmlj");
SBMLDocument d;
long errors, n;
Reaction r;
if (args.length != 2) {
System.out
.print("\n"
+ " usage: addingEvidenceCodes_1 <input-filename> <output-filename>"
+ "\n"
+ " Adds controlled vocabulary term to a reaction"
+ "\n" + "\n");
System.exit(2);
}
d = libsbml.readSBML(args[0]);
errors = d.getNumErrors();
if (errors > 0) {
System.out.print("Read Error(s):" + "\n");
d.printErrors();
System.out.print("Correct the above and re-run." + "\n");
} else {
n = d.getModel().getNumReactions();
if (n <= 0) {
System.out
.print("Model has no reactions.\n Cannot add CV terms\n");
} else {
r = d.getModel().getReaction(0);
/*
* check that the reaction has a metaid no CVTerms will be added
* if there is no metaid to reference
*/
if (!r.isSetMetaId())
r.setMetaId("metaid_0000052");
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_IS_DESCRIBED_BY);
cv1.addResource("urn:miriam:obo.eco:ECO%3A0000183");
r.addCVTerm(cv1);
CVTerm cv2 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv2.setBiologicalQualifierType(libsbml.BQB_IS);
cv2.addResource("urn:miriam:kegg.reaction:R00756");
cv2.addResource("urn:miriam:reactome:REACT_736");
r.addCVTerm(cv2);
libsbml.writeSBML(d, args[1]);
}
}
System.exit( (int) errors);
}
}
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