/usr/share/SBMLToolbox/Convenience/PairBrackets.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 | function pairs = PairBrackets(formula)
% pairs = PairBrackets(expression)
%
% Takes
%
% 1. expression, a string representation of a math expression
%
% Returns
%
% 1. an array of the indices of each pair of brackets ordered from
% the opening bracket index
%
% *EXAMPLE:*
%
% pairs = PairBrackets('(a+((b*c)/(a+b)))')
%
% pairs =
% 1 17
% 4 16
% 5 9
% 11 15
%
%<!---------------------------------------------------------------------------
% 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.
%----------------------------------------------------------------------- -->
if (~ischar(formula))
error(sprintf('%s\n%s', 'PairBrackets(formula)', 'first argument must be a string'));
end;
OpeningBracketIndex = strfind(formula, '(');
ClosingBracketIndex = strfind(formula, ')');
% check that the number of brackets matches
if (length(OpeningBracketIndex) ~= length(ClosingBracketIndex))
error('Bracket mismatch');
end;
if (isempty(OpeningBracketIndex))
pairs = 0;
return;
end;
for i = 1:length(OpeningBracketIndex)
j = length(OpeningBracketIndex);
while(j > 0)
if (OpeningBracketIndex(j) < ClosingBracketIndex(i))
pairs(i,1) = OpeningBracketIndex(j);
pairs(i,2) = ClosingBracketIndex(i);
OpeningBracketIndex(j) = max(ClosingBracketIndex);
j = 0;
else
j = j - 1;
end;
end;
end;
% order the pairs so that the opening bracket index is in ascending order
OriginalPairs = pairs;
% function 'sort' changes in version 7.0.1
v = version;
v_num = str2num(v(1));
if (v_num < 7)
TempPairs = sort(pairs, 1);
else
TempPairs = sort(pairs, 1, 'ascend');
end;
for i = 1:length(OpeningBracketIndex)
pairs(i, 1) = TempPairs(i, 1);
j = find(OriginalPairs == pairs(i, 1));
pairs(i, 2) = OriginalPairs(j, 2);
end;
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