/usr/share/SBMLToolbox/AccessModel/GetSpecies.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 | function varargout = GetSpecies(SBMLModel)
% [names, values] = GetSpecies(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. an array of strings representing the identifiers of all species within the model
% 2. an array of the initial concentration/amount values of each species
%
% *NOTE:* the value returned will be (in order)
%
% - determined from assignmentRules/initialAssignments where appropriate
% - the attribute 'initialAmount' or 'initialConcentration' 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('GetSpecies(SBMLModel)\n%s', 'input must be an SBMLModel structure');
end;
%------------------------------------------------------------
% determine the number of species within the model
NumSpecies = length(SBMLModel.species);
%------------------------------------------------------------
% loop through the list of species
for i = 1:NumSpecies
%determine the name or id of the species
if (SBMLModel.SBML_level == 1)
name = SBMLModel.species(i).name;
else
if (isempty(SBMLModel.species(i).id))
name = SBMLModel.species(i).name;
else
name = SBMLModel.species(i).id;
end;
end;
% and array of the character names
CharArray{i} = name;
% get the initial concentration values
% add to an array
Values(i) = SBMLModel.species(i).initialAmount;
if (SBMLModel.SBML_level > 1)
if (SBMLModel.species(i).isSetInitialConcentration)
Values(i) = SBMLModel.species(i).initialConcentration;
end;
end;
% might be set by assignment rule
AR = Model_getAssignmentRuleByVariable(SBMLModel, name);
if (~isempty(AR))
newSBMLModel = SBMLModel;
newSBMLModel.species(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.species(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 (NumSpecies ~= 0)
varargout{1} = CharArray;
varargout{2} = Values;
else
varargout{1} = [];
varargout{2} = [];
end;
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