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
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
|
/**
* @file addCustomValidator.cpp
* @brief Example creating a custom validator to be called during validation
* @author Frank T. Bergmann
*
* <!--------------------------------------------------------------------------
* 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.SBMLDocument;
import org.sbml.libsbml.SBMLError;
import org.sbml.libsbml.SBMLValidator;
import org.sbml.libsbml.libsbml;
/**
* Declares a custom validator to be called. This allows you to validate any
* aspect of an SBML Model that you want to be notified about. You could use
* this to notify your application that a model contains an unsupported feature
* of SBML (either as warning).
*
* In this example the validator will go through the model and test for the
* presence of 'fast' reactions and algebraic rules. If either is used a warning
* will be added to the error log.
*/
public class addCustomValidator extends SBMLValidator {
public addCustomValidator() {
super();
}
public addCustomValidator(addCustomValidator orig) {
super(orig);
}
public @Override
SBMLValidator clone() {
return new addCustomValidator(this);
}
public @Override
long validate() {
// if we don't have a model we don't apply this validator.
if (getDocument() == null || getModel() == null)
return 0;
// if we have no rules and reactions we don't apply this validator
// either
if (getModel().getNumReactions() == 0 && getModel().getNumRules() == 0)
return 0;
int numErrors = 0;
// test for algebraic rules
for (int i = 0; i < getModel().getNumRules(); i++) {
if (getModel().getRule(i).getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE) {
getErrorLog()
.add(new SBMLError(
99999,
3,
1,
"This model uses algebraic rules, however this application does not support them.",
0, 0, libsbml.LIBSBML_SEV_WARNING, // or
// LIBSBML_SEV_ERROR
// if you
// want to
// stop
libsbml.LIBSBML_CAT_SBML // or whatever category
// you prefer
));
numErrors++;
}
}
// test for fast reactions
for (int i = 0; i < getModel().getNumReactions(); i++) {
// test whether value is set, and true
if (getModel().getReaction(i).isSetFast()
&& getModel().getReaction(i).getFast()) {
getErrorLog()
.add(new SBMLError(
99999,
3,
1,
"This model uses fast reactions, however this application does not support them.",
0, 0, libsbml.LIBSBML_SEV_WARNING, // or
// LIBSBML_SEV_ERROR
// if you
// want to
// stop
libsbml.LIBSBML_CAT_SBML // or whatever category
// you prefer
));
numErrors++;
}
}
return numErrors;
}
public static void main(String[] args) {
if (args.length != 1) {
System.out.println("Usage: addCustomValidator filename");
System.exit(1);
}
System.loadLibrary("sbmlj");
// read the file name
SBMLDocument document = libsbml.readSBML(args[0]);
// add a custom validator
document.addValidator(new addCustomValidator());
// check consistency like before
int numErrors = (int) document.checkConsistency();
// print errors and warnings
document.printErrors();
// return number of errors
System.exit(numErrors);
}
};
|
