addIdentifierPrefix

 addIdentifierPrefix
   If reaction, metabolite, compartment, gene or model identifiers do not
   start with a letter or _, which conflicts with SBML specifications,
   prefixes are added for all identifiers in the respective model field.
   The prefixes are:
       "R_" for model.rxns,
       "M_" for model.mets,
       "C_" for model.comps;
       "G_" for model.genes (and also represented in model.grRules)

 Input:
   model           model whose identifiers should be modified
   fields          cell array with model field names that should be
                   checked if prefixes should be added, possible values: 
                   'rxns', 'mets', 'comps', 'genes', 'id'. (optional, by
                   default all listed model fields will be checked).

 Output:
   model           modified model
   hasChanged      cell array with fields and prefixes that are added

 Usage: [model, hasChanged]=addIdentifierPrefix(model,fields)

0001 function [model, hasChanged]=addIdentifierPrefix(model,fields)
0002 % addIdentifierPrefix
0003 %   If reaction, metabolite, compartment, gene or model identifiers do not
0004 %   start with a letter or _, which conflicts with SBML specifications,
0005 %   prefixes are added for all identifiers in the respective model field.
0006 %   The prefixes are:
0007 %       "R_" for model.rxns,
0008 %       "M_" for model.mets,
0009 %       "C_" for model.comps;
0010 %       "G_" for model.genes (and also represented in model.grRules)
0011 %
0012 % Input:
0013 %   model           model whose identifiers should be modified
0014 %   fields          cell array with model field names that should be
0015 %                   checked if prefixes should be added, possible values:
0016 %                   'rxns', 'mets', 'comps', 'genes', 'id'. (optional, by
0017 %                   default all listed model fields will be checked).
0018 %
0019 % Output:
0020 %   model           modified model
0021 %   hasChanged      cell array with fields and prefixes that are added
0022 %
0023 % Usage: [model, hasChanged]=addIdentifierPrefix(model,fields)
0024 
0025 if nargin<2 || isempty(fields)
0026     fields = {'rxns','mets','comps','genes','id'};
0027 end
0028 
0029 modelFields = {'rxns','R_';
0030                'mets','M_';
0031                'comps','C_';
0032                'genes','G_';
0033                'id','M_'};
0034 
0035 toChangeIdx = find(ismember(modelFields(:,1),fields));
0036 hasChanged  = false(numel(modelFields(:,1)),1);
0037 for i=1:numel(toChangeIdx)
0038     currName    = modelFields{toChangeIdx(i),1};
0039     currPrefix  = modelFields{toChangeIdx(i),2};
0040     if isfield(model,currName)
0041         currField   = model.(currName);
0042     else
0043         continue;
0044     end
0045     if ~all(startsWith(currField,regexpPattern('^[a-zA-Z_]')))
0046         currField = strcat(currPrefix, currField);
0047         hasChanged(toChangeIdx(i)) = true;
0048 
0049         if strcmp(currName,'genes')
0050                 model.grRules = regexprep(model.grRules, '(\<[0-9_a-zA-Z])', 'G_$1');
0051                 model.grRules = regexprep(model.grRules, ' G_or ', ' or ');
0052                 model.grRules = regexprep(model.grRules, ' G_and ', ' and ');
0053         end
0054         model.(currName) = currField;
0055     end
0056 end
0057 
0058 hasChanged = modelFields(hasChanged,:);
0059 hasChanged = append('model.', hasChanged(:,1), ' (', hasChanged(:,2), ' prefix)');
0060 end