removeIdentifierPrefix

 removeIdentifierPrefix
   This function removes identifier prefixes:
       "R_" for model.rxns, model.rxnNames and model.id,
       "M_" for model.mets and model.metNames,
       "C_" for model.comps;
       "G_" for model.genes (and also represented in model.grRules).
   By default, the prefixes are only removed if all entries in a
   particular field has the prefix. The prefixes might have been present
   because one or more identifiers do not start with a letter or _, which
   conflicts with SBML specifications.

 Input:
   model           model whose identifiers should be modified
   fields          cell array with model field names from which the
                   identifiers should be removed, possible values: 
                   'rxns', 'mets', 'comps', 'genes', 'metNames', 
                   'rxnNames', 'id'. (optional, by default all listed
                   model fields will be checked).
   forceRemove     if prefixes should be removed even if not all entries
                   in a model field have the prefix (optional, default
                   false)

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

 Usage: model=removeIdentifierPrefix(model,fields,forceRemove)

0001 function [model, hasChanged]=removeIdentifierPrefix(model,fields,forceRemove)
0002 % removeIdentifierPrefix
0003 %   This function removes identifier prefixes:
0004 %       "R_" for model.rxns, model.rxnNames and model.id,
0005 %       "M_" for model.mets and model.metNames,
0006 %       "C_" for model.comps;
0007 %       "G_" for model.genes (and also represented in model.grRules).
0008 %   By default, the prefixes are only removed if all entries in a
0009 %   particular field has the prefix. The prefixes might have been present
0010 %   because one or more identifiers do not start with a letter or _, which
0011 %   conflicts with SBML specifications.
0012 %
0013 % Input:
0014 %   model           model whose identifiers should be modified
0015 %   fields          cell array with model field names from which the
0016 %                   identifiers should be removed, possible values:
0017 %                   'rxns', 'mets', 'comps', 'genes', 'metNames',
0018 %                   'rxnNames', 'id'. (optional, by default all listed
0019 %                   model fields will be checked).
0020 %   forceRemove     if prefixes should be removed even if not all entries
0021 %                   in a model field have the prefix (optional, default
0022 %                   false)
0023 %
0024 % Output:
0025 %   model           modified model
0026 %   hasChanged      cell array with fields and prefixes that are removed
0027 %
0028 % Usage: model=removeIdentifierPrefix(model,fields,forceRemove)
0029 
0030 if nargin<2 || isempty(fields)
0031     fields = {'rxns','mets','comps','genes','metNames','rxnNames','id'};
0032 end
0033 if nargin<3 || isempty(forceRemove)
0034     forceRemove = false;
0035 end
0036 
0037 modelFields = {'rxns',      'R_';
0038     'mets',      'M_';
0039     'comps',     'C_';
0040     'genes',     'G_';
0041     'metNames',  'M_';
0042     'rxnNames',  'R_';
0043     'id',        'M_'};
0044 
0045 toChangeIdx = find(ismember(modelFields(:,1),fields));
0046 hasChanged  = false(numel(modelFields(:,1)),1);
0047 for i=1:numel(toChangeIdx)
0048     currName    = modelFields{toChangeIdx(i),1};
0049     currPrefix  = modelFields{toChangeIdx(i),2};
0050     currField   = model.(currName);
0051 
0052     if forceRemove && any(startsWith(currField,currPrefix))
0053         hasPrefix = true;
0054     else
0055         hasPrefix = all(startsWith(currField,currPrefix));
0056     end
0057     if hasPrefix
0058         currField = regexprep(currField,['^' currPrefix],'');
0059         hasChanged(toChangeIdx(i)) = true;
0060         if strcmp(currName,'genes')
0061             model.grRules=regexprep(model.grRules,'^G_','');
0062             model.grRules=regexprep(model.grRules,'\(G_','(');
0063             model.grRules=regexprep(model.grRules,' G_',' ');
0064         end
0065     end
0066     model.(currName) = currField;
0067 end
0068 hasChanged = modelFields(hasChanged,:);
0069 hasChanged = append('model.', hasChanged(:,1), ' (', hasChanged(:,2), ' prefix)');
0070 end