/usr/share/SBMLToolbox/Convenience/Substitute.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 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 | function value = Substitute(original_formula, model)
% value = Substitute(expression, SBMLModel)
%
% Takes
%
% 1. expression, a string representation of a math expression
% 2. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. the value of the expression when all variables within the model have
% been substituted
%
% *EXAMPLE:*
%
% Consider m to be an SBMLModel containing a species with
% id = 'g' and initialConcentration = '3'
%
% value = Substitute('g*2', m)
%
% value = 6
%
%<!---------------------------------------------------------------------------
% 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.
%----------------------------------------------------------------------- -->
% This function was radically improved by Pieter Pareit
if (model.SBML_level > 1 && ~isempty(model.time_symbol))
assert(exist(model.time_symbol,'var')==false);
assignin('caller',model.time_symbol,0);
end
% handle easy case where formula can be calculated without variables
value = str2double(original_formula);
if ~isnan(value)
return;
else
try
value = evalin('caller', original_formula);
if ~isnan(value)
return;
end;
catch
end;
end
% put everything in MATLAB and evaluate the formule
[Species, speciesValues] = GetSpecies(model);
[Parameters, paramValues] = GetAllParametersUnique(model);
[Compartments, compValues] = GetCompartments(model);
% if (model.SBML_level > 1 && ~isempty(model.time_symbol))
% assert(exist(model.time_symbol,'var')==false);
% assignin('caller',model.time_symbol,0);
% end
for i = 1:length(Species)
assert(exist(Species{i},'var')==false);
assignin('caller',Species{i}, speciesValues(i));
end;
for i = 1:length(Parameters)
assert(exist(Parameters{i},'var')==false);
assignin('caller',Parameters{i}, paramValues(i));
end;
for i = 1:length(Compartments)
assert(exist(Compartments{i},'var')==false);
assignin('caller',Compartments{i}, compValues(i));
end;
% this replaces all rules in the original formula
formula = original_formula;
rule_applied = 1;
iterations_left = Model_getNumAssignmentRules(model) + 1;
while rule_applied > 0 && iterations_left > 0
rule_applied = 0;
for rule = model.rule
if (strcmp(rule.typecode, 'SBML_ASSIGNMENT_RULE') ...
|| (isfield(rule, 'type') && strcmp(rule.type, 'scalar')))
str = formula;
exp = strcat('\<',rule.variable,'\>');
repstr = rule.formula;
formula = regexprep(str,exp,repstr);
for fd = 1:Model_getNumFunctionDefinitions(model)
newFormula = SubstituteFunction(formula, Model_getFunctionDefinition(model, fd));
if ~isempty(newFormula)
formula = newFormula;
end;
end;
rule_applied = rule_applied + strcmp(str, formula)==false;
end;
end
iterations_left = iterations_left - 1;
end
assert(rule_applied == 0, ...
'Substitute(): Cyclic dependency of rules dedected');
if model.SBML_level > 2 || (model.SBML_level == 2 && model.SBML_version > 1)
ia_applied = 1;
iterations_left = Model_getNumInitialAssignments(model) + 1;
while ia_applied > 0 && iterations_left > 0
ia_applied = 0;
for rule = model.initialAssignment
str = formula;
exp = strcat('\<',rule.symbol,'\>');
repstr = rule.math;
formula = regexprep(str,exp,repstr);
for fd = 1:Model_getNumFunctionDefinitions(model)
newFormula = SubstituteFunction(formula, Model_getFunctionDefinition(model, fd));
if ~isempty(newFormula)
formula = newFormula;
end;
end;
ia_applied = ia_applied + strcmp(str, formula)==false;
end
iterations_left = iterations_left - 1;
end
assert(ia_applied == 0, ...
'Substitute(): Cyclic dependency of rules dedected');
end;
try
value = evalin('caller',formula);
catch
error('Substitute(): Ill formed formula');
end
end
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