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
|
function Objective = Objective_create(varargin)
% Objective = Objective_create(level, version, pkgVersion)
%
% Takes
%
% 1. level, an integer representing an SBML level
% 2. version, an integer representing an SBML version
% 3. pkgVersion, an integer representing an SBML package version
%
% Returns
%
% 1. a MATLAB_SBML FBC Objective structure of the appropriate level, version and pkgVersion
%
%<!---------------------------------------------------------------------------
% 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 > 3)
error('too many input arguments');
end;
switch (nargin)
case 3
level = varargin{1};
version = varargin{2};
pkgVersion = varargin{3};
case 2
level = varargin{1};
version = varargin{2};
pkgVersion = 1;
case 1
level = varargin{1};
if (level == 1)
version = 2;
elseif (level == 2)
version = 4;
else
version = 1;
end;
pkgVersion = 1;
otherwise
level = 3;
version = 1;
pkgVersion = 1;
end;
if ~isValidLevelVersionCombination(level, version)
error('invalid level/version combination');
end;
%get fields and values and create the structure
[fieldnames, num] = getObjectiveFieldnames(level, version, pkgVersion);
if (num > 0)
values = getObjectiveDefaultValues(level, version, pkgVersion);
Objective = cell2struct(values, fieldnames, 2);
%add empty substructures
Objective.fbc_fluxObjective = FluxObjective_create(level, version, pkgVersion);
Objective.fbc_fluxObjective(1:end) = [];
%add level and version
Objective.level = level;
Objective.version = version;
Objective.fbc_version = pkgVersion;
%check correct structure
if ~isSBML_FBC_Objective(Objective, level, version)
Objective = struct();
warning('Warn:BadStruct', 'Failed to create Objective');
end;
else
Objective = [];
warning('Warn:InvalidLV', 'Objective not an element in SBML L%dV%d', level, version);
end;
|
