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
|
function Model = Model_create(varargin)
% Model = Model_create(level(optional), version(optional) )
%
% Takes
%
% 1. level, an integer representing an SBML level (optional)
% 2. version, an integer representing an SBML version (optional)
%
% Returns
%
% 1. a MATLAB_SBML Model structure of the appropriate level and version
%
% *NOTE:* the optional level and version preserve backwards compatibility
% a missing version argument will default to L1V2; L2V4 or L3V1
% missing both arguments will default to L3V1
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox 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.
%----------------------------------------------------------------------- -->
%check the input arguments are appropriate
if (nargin > 2)
error('too many input arguments');
end;
switch (nargin)
case 2
level = varargin{1};
version = varargin{2};
case 1
level = varargin{1};
if (level == 1)
version = 2;
elseif (level == 2)
version = 4;
else
version = 1;
end;
otherwise
level = 3;
version = 1;
end;
if ~isValidLevelVersionCombination(level, version)
error('invalid level/version combination');
end;
% note state of the Level version warning
ss = warning('query', 'Warn:InvalidLV');
warnLV = strcmp(ss.state, 'off');
%get fields and values and create the structure
[fieldnames, num] = getModelFieldnames(level, version);
if (num > 0)
values = getModelDefaultValues(level, version);
Model = cell2struct(values, fieldnames, 2);
%add empty substructures
Model.unitDefinition = UnitDefinition_create(level, version);
Model.unitDefinition(1:end) = [];
Model.compartment = Compartment_create(level, version);
Model.compartment(1:end) = [];
Model.species = Species_create(level, version);
Model.species(1:end) = [];
Model.parameter = Parameter_create(level, version);
Model.parameter(1:end) = [];
Model.rule = Rule_create(level, version);
Model.rule(1:end) = [];
Model.reaction = Reaction_create(level, version);
Model.reaction(1:end) = [];
warning('off', 'Warn:InvalidLV');
t = FunctionDefinition_create(level, version);
if ~isempty(t)
Model.functionDefinition = t;
Model.functionDefinition(1:end) = [];
end;
t = Event_create(level, version);
if ~isempty(t)
Model.event = t;
Model.event(1:end) = [];
end;
warning('off', 'Warn:InvalidLV');
t = CompartmentType_create(level, version);
if ~isempty(t)
Model.compartmentType = t;
Model.compartmentType(1:end) = [];
end;
t = SpeciesType_create(level, version);
if ~isempty(t)
Model.speciesType = t;
Model.speciesType(1:end) = [];
end;
t = InitialAssignment_create(level, version);
if ~isempty(t)
Model.initialAssignment = t;
Model.initialAssignment(1:end) = [];
end;
t = Constraint_create(level, version);
if ~isempty(t)
Model.constraint = t;
Model.constraint(1:end) = [];
end;
if warnLV == 0
warning('on', 'Warn:InvalidLV');
else
warning('off', 'Warn:InvalidLV');
end;
if level > 1
Model.time_symbol = '';
Model.delay_symbol = '';
end;
if level > 2
Model.avogadro_symbol = '';
end;
ns = struct('prefix', [], 'uri', []);
Model.namespaces = ns;
Model.namespaces(1:end) = [];
%check correct structure
if ~isValidSBML_Model(Model)
Model = struct();
warning('Warn:BadStruct', 'Failed to create Model');
end;
else
Model = [];
warning('Warn:InvalidLV', 'Model not an element in SBML L%dV%d', level, version);
end;
|
