copyToComps

 copyToComps
   Copies reactions to new compartment(s)

   model           a model structure
   toComps         cell array of compartment ids. If there is no match
                   to model.comps then it is added as a new compartment
                   (see below for details)
   rxns            either a cell array of reaction IDs, a logical vector 
                   with the same number of elements as reactions in the model,
                   or a vector of indexes to remove (optional, default
                   model.rxns)
   deleteOriginal  true if the original reactions should be removed
                   (making it move the reactions instead) (optional, default
                   false)
   compNames       cell array of compartment names. This is used if new
                   compartments should be added (optional, default toComps)
   compOutside     cell array of the id (as in comps) for the compartment
                   surrounding each of the compartments. This is used if
                   new compartments should be added (optional, default all {''})

   model           an updated model structure

   NOTE: New reactions and metabolites will be named as "id_toComps(i)".

 Usage: model=copyToComps(model,toComps,rxns,deleteOriginal,compNames,compOutside)

0001 function model=copyToComps(model,toComps,rxns,deleteOriginal,compNames,compOutside)
0002 % copyToComps
0003 %   Copies reactions to new compartment(s)
0004 %
0005 %   model           a model structure
0006 %   toComps         cell array of compartment ids. If there is no match
0007 %                   to model.comps then it is added as a new compartment
0008 %                   (see below for details)
0009 %   rxns            either a cell array of reaction IDs, a logical vector
0010 %                   with the same number of elements as reactions in the model,
0011 %                   or a vector of indexes to remove (optional, default
0012 %                   model.rxns)
0013 %   deleteOriginal  true if the original reactions should be removed
0014 %                   (making it move the reactions instead) (optional, default
0015 %                   false)
0016 %   compNames       cell array of compartment names. This is used if new
0017 %                   compartments should be added (optional, default toComps)
0018 %   compOutside     cell array of the id (as in comps) for the compartment
0019 %                   surrounding each of the compartments. This is used if
0020 %                   new compartments should be added (optional, default all {''})
0021 %
0022 %   model           an updated model structure
0023 %
0024 %   NOTE: New reactions and metabolites will be named as "id_toComps(i)".
0025 %
0026 % Usage: model=copyToComps(model,toComps,rxns,deleteOriginal,compNames,compOutside)
0027 
0028 arguments
0029     model (1,1) struct
0030     toComps {emptyOrTextOrCellOfText}
0031     rxns = model.rxns
0032     deleteOriginal {emptyOrLogicalScalar} = false
0033     compNames {emptyOrTextOrCellOfText} = toComps
0034     compOutside {emptyOrTextOrCellOfText} = '';
0035 end
0036 
0037 if nargin >= 3 && ~islogical(rxns) && ~isnumeric(rxns)
0038     rxns = convertCharArray(rxns);
0039 end
0040 if nargin >= 5
0041     compNames=convertCharArray(compNames);
0042 end
0043 if nargin >= 6
0044     compOutside=convertCharArray(compOutside);
0045     if length(compOutside) ~= length(compNames)
0046         error('compOutside and compNames should be of equal size.');
0047     end
0048 end
0049 
0050 originalID=model.id;
0051 originalName=model.name;
0052 
0053 rxns=getIndexes(model,rxns,'rxns');
0054 
0055 for i=1:numel(toComps)
0056     %Check if the compartment exists, otherwise add it
0057     [I,J]=ismember(toComps(i),model.comps);
0058     if I==false
0059         model.comps=[model.comps;toComps(i)];
0060         model.compNames=[model.compNames;compNames(i)];
0061         if isfield(model,'compOutside')
0062             model.compOutside=[model.compOutside;compOutside(i)];
0063         end
0064         if isfield(model,'compMiriams')
0065             model.compMiriams=[model.compMiriams;cell(1,1)];
0066         end
0067         J=numel(model.comps);
0068     end
0069     %Copy the reactions by making a model structure with only them, then
0070     %change the localization, and finally merge with the original model
0071     modelToAdd=model;
0072     modelToAdd=removeReactions(modelToAdd,setdiff(1:numel(model.rxns),rxns),true,true);
0073     modelToAdd.rxns=strcat(modelToAdd.rxns,'_',toComps(i));
0074     modelToAdd.mets=strcat(modelToAdd.mets,'_',toComps(i));
0075     modelToAdd.comps=modelToAdd.comps(J);
0076     modelToAdd.compNames=modelToAdd.compNames(J);
0077     if isfield(modelToAdd,'compOutside')
0078         modelToAdd.compOutside=modelToAdd.compOutside(J);
0079     end
0080     if isfield(modelToAdd,'compMiriams')
0081         modelToAdd.compMiriams=modelToAdd.compMiriams(J);
0082     end
0083     modelToAdd.metComps=ones(numel(modelToAdd.mets),1);
0084     if isfield(modelToAdd,'metFrom')
0085         modelToAdd = rmfield(modelToAdd,'metFrom');
0086     end
0087     if isfield(modelToAdd,'rxnFrom')
0088         modelToAdd = rmfield(modelToAdd,'rxnFrom');
0089     end
0090     if isfield(modelToAdd,'geneFrom')
0091         modelToAdd = rmfield(modelToAdd,'geneFrom');
0092     end
0093   
0094     %Merge the models
0095     model=mergeModels({model;modelToAdd},'metNames',[],true);
0096 end
0097 
0098 if deleteOriginal==true
0099     model=removeReactions(model,rxns,true,true,true); %Also delete unused compartments
0100 end
0101 
0102 model.id=originalID;
0103 model.name=originalName;
0104 end