1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
///**
// * @file createNormalExample.java
// * @brief SBML distrib example
// * @author Sarah Keating
// *
// *
// * <!--------------------------------------------------------------------------
// * This file is part of libSBML. Please visit http://sbml.org for more
// * information about SBML, and the latest version of libSBML.
// *
// * Copyright (C) 2009-2013 jointly by the following organizations:
// * 1. California Institute of Technology, Pasadena, CA, USA
// * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
// *
// * Copyright (C) 2006-2008 by the California Institute of Technology,
// * Pasadena, CA, USA
// *
// * Copyright (C) 2002-2005 jointly by the following organizations:
// * 1. California Institute of Technology, Pasadena, CA, USA
// * 2. Japan Science and Technology Agency, Japan
// *
// * This library is free software; you can redistribute it and/or modify it
// * under the terms of the GNU Lesser General Public License as published by
// * the Free Software Foundation. A copy of the license agreement is provided
// * in the file named "LICENSE.txt" included with this software distribution
// * and also available online as http://sbml.org/software/libsbml/license.html
// * ------------------------------------------------------------------------ -->
// */
import org.sbml.libsbml.*;
public class createNormalExample
{
public static void main(String[] args)
{
System.loadLibrary("sbmlj");
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "distrib", 1);
SBMLDocument document = new SBMLDocument(sbmlns);
// set the required attribute to true
DistribSBMLDocumentPlugin docPlug = (DistribSBMLDocumentPlugin)
(document->getPlugin("distrib"));
docPlug.setRequired(true);
// create the Model
Model model = document.createModel();
// create the FunctionDefintion
FunctionDefinition fd = model.createFunctionDefinition();
fd.setId("mynormal");
ASTNode math = libsbml.parseFormula("lambda(param1, param2, 0)");
fd.setMath(math);
//
// Get a DistribFunctionDefinitionPlugin object plugged in the fd 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.
//
DistribFunctionDefinitionPlugin fdPlugin =
(DistribFunctionDefinitionPlugin)(fd.getPlugin("distrib"));
// create a DrawFromDistribution object
DrawFromDistribution draw = fdPlugin.createDrawFromDistribution();
// create the distribInputs
DistribInput input1 = draw.createDistribInput();
input1.setId("mu");
input1.setIndex(0);
DistribInput input2 = draw.createDistribInput();
input2.setId("sigma");
input2.setIndex(1);
// create the UncertMLNode object
UncertMLNode uncert = libsbml.createDistributionNode
("NormalDistribution", "mean, variance", "mu,sigma");
draw.setUncertML(uncert);
libsbml.writeSBMLToFile(document, "distrib_example1.xml");
}
}
|
