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function varargout = GetCompartments(SBMLModel)
% [names, values] = GetCompartments(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. an array of strings representing the identifiers of all compartments within the model
% 2. an array of the size/volume values of each compartment
%
% *NOTE:* the value returned will be (in order)
%
% - determined from assignmentRules/initialAssignments where appropriate
% - the attribute 'size' ('volume' in L1) for the given compartment
% - NaN, if the value is not specified in any way within the model
%<!---------------------------------------------------------------------------
% 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 input is an SBML model
if (~isValidSBML_Model(SBMLModel))
error('GetCompartments(SBMLModel)\n%s', 'input must be an SBMLModel structure');
end;
%------------------------------------------------------------
% determine the number of compartments within the model
NumCompartments = length(SBMLModel.compartment);
%------------------------------------------------------------
% loop through the list of compartments
for i = 1:NumCompartments
%determine the name or id of the compartment
if (SBMLModel.SBML_level == 1)
name = SBMLModel.compartment(i).name;
else
if (isempty(SBMLModel.compartment(i).id))
name = SBMLModel.compartment(i).name;
else
name = SBMLModel.compartment(i).id;
end;
end;
% and array of the character names
CharArray{i} = name;
% get the volume/size
% add to an array
if (SBMLModel.SBML_level == 1)
Values(i) = SBMLModel.compartment(i).volume;
else
Values(i) = SBMLModel.compartment(i).size;
end;
AR = Model_getAssignmentRuleByVariable(SBMLModel, name);
if (~isempty(AR))
newSBMLModel = SBMLModel;
newSBMLModel.compartment(i) = [];
for fd = 1:Model_getNumFunctionDefinitions(SBMLModel)
newFormula = SubstituteFunction(AR.formula, Model_getFunctionDefinition(SBMLModel, fd));
if (~isempty(newFormula))
AR.formula = newFormula;
end;
end;
Values(i) = Substitute(AR.formula, newSBMLModel);
end;
% might be an initial assignment in l2v2
if ((SBMLModel.SBML_level == 2 && SBMLModel.SBML_version > 1) ...
|| SBMLModel.SBML_level == 3)
IA = Model_getInitialAssignmentBySymbol(SBMLModel, name);
if (~isempty(IA))
% remove this from the substtution
newSBMLModel = SBMLModel;
newSBMLModel.compartment(i) = [];
for fd = 1:Model_getNumFunctionDefinitions(SBMLModel)
newFormula = SubstituteFunction(IA.math, Model_getFunctionDefinition(SBMLModel, fd));
if (~isempty(newFormula))
IA.math = newFormula;
end;
end;
Values(i) = Substitute(IA.math, newSBMLModel);
end;
end;
end;
%--------------------------------------------------------------------------
% assign output
if (NumCompartments ~= 0)
varargout{1} = CharArray;
varargout{2} = Values;
else
varargout{1} = [];
varargout{2} = [];
end;
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