generateNewIds

 generateNewIds
   Generates a list of new metabolite or reaction ids, sequentially
   numbered with a defined prefix. The model is queried for the highest
   existing number of that type of id.

   model       model structure
   type        string specifying type of id, 'rxns' or 'mets'
   prefix      string specifying prefix to be used in all ids. E.g. 's_'
               or 'r_'.
   quantity    number of new ids that should be generated (optional, default 1)
   numLength   length of numerical part of id. E.g. 4 gives ids like
               r_0001 and 6 gives ids like r_000001. If the prefix is
               already used in the model, then the model-defined length
               will be used instead. (optional, default 4)

 Usage: newIds=generateNewIds(model,type,prefix,quantity,numLength)

0001 function newIds=generateNewIds(model,type,prefix,quantity,numLength)
0002 % generateNewIds
0003 %   Generates a list of new metabolite or reaction ids, sequentially
0004 %   numbered with a defined prefix. The model is queried for the highest
0005 %   existing number of that type of id.
0006 %
0007 %   model       model structure
0008 %   type        string specifying type of id, 'rxns' or 'mets'
0009 %   prefix      string specifying prefix to be used in all ids. E.g. 's_'
0010 %               or 'r_'.
0011 %   quantity    number of new ids that should be generated (optional, default 1)
0012 %   numLength   length of numerical part of id. E.g. 4 gives ids like
0013 %               r_0001 and 6 gives ids like r_000001. If the prefix is
0014 %               already used in the model, then the model-defined length
0015 %               will be used instead. (optional, default 4)
0016 %
0017 % Usage: newIds=generateNewIds(model,type,prefix,quantity,numLength)
0018 %
0019 type=char(type);
0020 prefix=char(prefix);
0021 
0022 if type=='rxns'
0023     existingIds=model.rxns;
0024 elseif type=='mets'
0025     existingIds=model.mets;
0026 else
0027     error('type should be either ''rxns'' or ''mets''.')
0028 end
0029 if nargin<4
0030     quantity=1;
0031 end
0032 if nargin<5
0033     numLength=4;
0034 end
0035 
0036 % Subset only existingIds that have the prefix
0037 existingIds=existingIds(~cellfun(@isempty,regexp(existingIds,['^' prefix])));
0038 
0039 if ~isempty(existingIds)
0040     existingIds=regexprep(existingIds,['^' prefix],'');
0041     existingIds=sort(existingIds);
0042     lastId=existingIds{end};
0043     numLength=length(lastId);
0044     lastId=str2double(lastId);
0045 else
0046     lastId=0;
0047     fprintf(['No ' type ' ids with prefix "' prefix ...
0048         '" currently exist in the model. The first new id will be "' ...
0049         [prefix,num2str(1,['%0' num2str(numLength) 'd'])] '"\n'],'%s')
0050 end
0051 
0052 if isnan(lastId)
0053     lastId = 0;
0054 end
0055 
0056 newIds=cell(quantity,1);
0057 
0058 for k=1:quantity
0059     newIds{k}=[prefix,num2str(k+lastId,['%0' num2str(numLength) 'd'])];
0060 end
0061 end