/usr/share/SBMLToolbox/Convenience/SubstituteFunction.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 | function Formula = SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)
% newExpression = SubstituteFunction(expression, SBMLFunctionDefinition)
%
% Takes
%
% 1. expression, a string representation of a math expression
% 2. SBMLFunctionDefinition, an SBML FunctionDefinition structure
%
% Returns
%
% 1. newExpression
% - the string representation of the expression when any instances of the
% functionDefinition have been substituted
% - an empty string if the functiondefinition is not in the original
% expression
%
% *EXAMPLE:*
%
% Consider fD to be an SBMLFunctionDefinition
% with id = 'g' and math = 'lambda(x,x+0.5)'
%
% formula = SubstituteFormula('g(y)', fD)
%
% formula = 'y+0.5'
%
%
% formula = SubstituteFormula('h(y)', fD)
%
% formula = ''
%
%<!---------------------------------------------------------------------------
% 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 arguments are appropriate
if (~isstruct(SBMLFunctionDefinition))
error(sprintf('%s', ...
'first argument must be an SBML functionDefinition structure'));
end;
[sbmlLevel, sbmlVersion] = GetLevelVersion(SBMLFunctionDefinition);
if (~ischar(OriginalFormula))
error('SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)\n%s', 'first argument must be a character array containing the id of the function definition');
elseif (~isSBML_FunctionDefinition(SBMLFunctionDefinition, sbmlLevel, sbmlVersion))
error('SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)\n%s', 'second argument must be an SBML function definition structure');
end;
OriginalFormula = LoseWhiteSpace(OriginalFormula);
startPoint = matchFunctionName(OriginalFormula, SBMLFunctionDefinition.id);
if (isempty(startPoint))
Formula = '';
return;
end;
ElementsOfFuncDef = GetArgumentsFromLambdaFunction(SBMLFunctionDefinition.math);
% get the arguments of the application of the formula
Formula = '';
index = length(startPoint);
StartFunctionInFormula = startPoint(index);
j = StartFunctionInFormula + length(SBMLFunctionDefinition.id);
pairs = PairBrackets(OriginalFormula);
for i=1:length(pairs)
if (pairs(i, 1) == j)
endPt = pairs(i, 2);
break;
end;
end;
[NoElements, ElementsInFormula] = GetElementsOfFunction(OriginalFormula(j:endPt));
OriginalFunction = '';
for i = StartFunctionInFormula:endPt
OriginalFunction = strcat(OriginalFunction, OriginalFormula(i));
end;
% check got right number
if (NoElements ~= length(ElementsOfFuncDef) - 1)
error('SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)\n%s', 'mismatch in number of arguments between formula and function');
end;
% check that same arguments have not been used
for i = 1:NoElements
for j = 1:NoElements
if (strcmp(ElementsInFormula{i}, ElementsOfFuncDef{j}))
newElem = strcat(ElementsInFormula{i}, '_new');
ElementsOfFuncDef{j} = newElem;
ElementsOfFuncDef{end} = strrep(ElementsOfFuncDef{end}, ElementsInFormula{i}, newElem);
end;
end;
end;
% replace the arguments in function definition with those in the formula
FuncFormula = '(';
FuncFormula = strcat(FuncFormula, ElementsOfFuncDef{end});
FuncFormula = strcat(FuncFormula, ')');
for i = 1:NoElements
FuncFormula = strrep(FuncFormula, ElementsOfFuncDef{i}, ElementsInFormula{i});
end;
Formula = strrep(OriginalFormula, OriginalFunction, FuncFormula);
% if the function occurred more than once
if (index - 1) > 0
Formula = SubstituteFunction(Formula, SBMLFunctionDefinition);
end;
function [NoElements, ElementsInFormula] = GetElementsOfFunction(OriginalFormula);
j = 2;
c = OriginalFormula(j);
element = '';
NoElements = 1;
ElementsInFormula = {};
while (j < length(OriginalFormula))
if (strcmp(c, ','))
ElementsInFormula{NoElements} = element;
element = '';
NoElements = NoElements + 1;
else
element = strcat(element, c);
end;
j = j + 1;
c = OriginalFormula(j);
end;
ElementsInFormula{NoElements} = element;
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