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function [valid, message] = isSBML_Reaction(varargin)
% [valid, message] = isSBML_Reaction(SBMLReaction, level, version(optional))
%
% Takes
%
% 1. SBMLReaction, an SBML Reaction structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
%
% Returns
%
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Reaction structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
% *NOTE:* the optional version defaults to a value of 1
%
% *NOTE:* The fields present in a MATLAB_SBML Reaction structure of the appropriate
% level and version can be found using getReactionFieldnames(level, version)
%<!---------------------------------------------------------------------------
% 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 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_REACTION';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_REACTION', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
%check that any nested structures are appropriate
% reactants
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.reactant))
[valid, message] = isSBML_SpeciesReference(SBMLStructure.reactant(index), ...
level, version);
index = index + 1;
end;
end;
% products
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.product))
[valid, message] = isSBML_SpeciesReference(SBMLStructure.product(index), ...
level, version);
index = index + 1;
end;
end;
% modifiers
if (valid == 1 && level > 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.modifier))
[valid, message] = isSBML_ModifierSpeciesReference( ...
SBMLStructure.modifier(index), ...
level, version);
index = index + 1;
end;
end;
% kineticLaw
if (valid == 1 && length(SBMLStructure.kineticLaw) == 1)
[valid, message] = isSBML_KineticLaw(SBMLStructure.kineticLaw, level, version);
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Reaction\n%s\n', message);
end;
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