libSBML C++ API
5.18.0
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Examples
qual_example1.cpp
An example of creating a model using SBML Level 3 Qualitative Models.
/**
* @file example1.cpp
* @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) 2013-2018 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.
* ------------------------------------------------------------------------ -->
*/
#include <iostream>
#include "
sbml/SBMLTypes.h
"
#include "
sbml/packages/qual/common/QualExtensionTypes.h
"
LIBSBML_CPP_NAMESPACE_USE
int
main(
int
argc,
char
** argv)
{
if
(argc != 2)
{
std::cout <<
"Usage: example1\n"
;
return
1;
}
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "qual") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"qual",1,"QUAL");
//
SBMLNamespaces
sbmlns(3,1,
"qual"
,1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a qual package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("qual",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(QualExtension::XmlnsL3V1V1,"qual");
//
// (2) Creates a QualPkgNamespaces object (SBMLNamespace derived class for
// qual package. The class is basically used for createing an SBase
// derived objects defined in the qual package) with the given SBML
// level, version, and package version
//
// QualPkgNamespaces sbmlns(3,1,1);
//
// 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.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
QualModelPlugin
* mplugin
=
static_cast<
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
(
INPUT_TRANSITION_EFFECT_NONE
);
i->
setSign
(
INPUT_SIGN_NEGATIVE
);
i->
setThresholdLevel
(2);
i->
setName
(
"aa"
);
Output
* o = t->
createOutput
();
o->
setId
(
"wd"
);
o->
setQualitativeSpecies
(
"s1"
);
o->
setTransitionEffect
(
OUTPUT_TRANSITION_EFFECT_PRODUCTION
);
o->
setOutputLevel
(2);
o->
setName
(
"aa"
);
DefaultTerm
* dt = t->
createDefaultTerm
();
dt->
setResultLevel
(2) ;
FunctionTerm
* ft = t->
createFunctionTerm
();
ASTNode
* math =
SBML_parseL3Formula
(
"geq(s1, 2)"
);
ft->
setResultLevel
(1);
ft->
setMath
(math);
writeSBML
(document,
"qual_example1.xml"
);
delete
document;
return
0;
}
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