/usr/share/SBMLToolbox/AccessModel/GetAllParameters.m is in sbmltoolbox 4.1.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | function varargout = GetAllParameters(SBMLModel)
% [names, values] = GetAllParameters(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. an array of strings representing the identifiers of all parameters
% (both global and embedded) within the model
% 2. an array of the values of each parameter
%
% *NOTE:* the value returned will be (in order)
%
% - determined from assignmentRules/initialAssignments where appropriate
% - the attribute 'value' for the given parameter
% - 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('GetAllParameters(SBMLModel)\n%s', 'input must be an SBMLModel structure');
end;
%------------------------------------------------------------
% get the global parameters
[ParamChar, ParamValues] = GetGlobalParameters(SBMLModel);
% get number of parameters
NumParams = length(ParamChar);
%------------------------------------------------------------
% get the number of reactions within the model
NumReactions = length(SBMLModel.reaction);
%------------------------------------------------------------
% loop through the list of reactions
for i = 1:NumReactions
% get parameters within each reaction
[Char, Value] = GetParameterFromReaction(SBMLModel.reaction(i));
% add to existing arrays
for j = 1:length(Char)
NumParams = NumParams + 1;
ParamValues(NumParams) = Value(j);
ParamChar{NumParams} = Char{j};
end;
end;
%--------------------------------------------------------------------------
% assign output
varargout{1} = ParamChar;
varargout{2} = ParamValues;
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