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/**
* @file qual_example1.java
* @brief SBML Qual example
* @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) 2013-2016 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.*;
public class qual_example1
{
public static void main(String[] args)
{
System.loadLibrary("sbmlj");
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "qual", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// mark qual as required
document.setPackageRequired("qual", true);
// create the Model
Model model = document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("c");
compartment.setConstant(true);
// Get a QualModelPlugin object plugged in the model object.
QualModelPlugin mplugin = (QualModelPlugin)(model.getPlugin("qual"));
// create the QualitativeSpecies
QualitativeSpecies qs = mplugin.createQualitativeSpecies();
qs.setId("s1");
qs.setCompartment("c");
qs.setConstant(false);
qs.setInitialLevel(1);
qs.setMaxLevel(4);
qs.setName("sss");
// create the Transition
Transition t = mplugin.createTransition();
t.setId("d");
t.setSBOTerm(1);
Input i = t.createInput();
i.setId("RD");
i.setQualitativeSpecies("s1");
i.setTransitionEffect(libsbml.INPUT_TRANSITION_EFFECT_NONE);
i.setSign(libsbml.INPUT_SIGN_NEGATIVE);
i.setThresholdLevel(2);
i.setName("aa");
Output o = t.createOutput();
o.setId("wd");
o.setQualitativeSpecies("s1");
o.setTransitionEffect(libsbml.OUTPUT_TRANSITION_EFFECT_PRODUCTION);
o.setOutputLevel(2);
o.setName("aa");
FunctionTerm ft = t.createFunctionTerm();
ASTNode math = libsbml.parseL3Formula("geq(s1, 2)");
ft.setResultLevel(1);
ft.setMath(math);
DefaultTerm dt = t.createDefaultTerm();
dt.setResultLevel(2);
libsbml.writeSBML(document, "qual_example1.xml");
}
}
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