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 if nargin<3
0029     rxns=model.rxns;
0030 elseif ~islogical(rxns) && ~isnumeric(rxns)
0031     rxns=convertCharArray(rxns);
0032 end
0033 if nargin<4
0034     deleteOriginal=false;
0035 end
0036 if nargin<5
0037     compNames=toComps;
0038 else
0039     compNames=convertCharArray(compNames);
0040 end
0041 if nargin<6
0042     compOutside=cell(numel(toComps),1);
0043     compOutside(:)={''};
0044 else
0045     compOutside=convertCharArray(compOutside);
0046 end
0047 
0048 originalID=model.id;
0049 originalName=model.name;
0050 
0051 rxns=getIndexes(model,rxns,'rxns');
0052 
0053 for i=1:numel(toComps)
0054     %Check if the compartment exists, otherwise add it
0055     [I,J]=ismember(toComps(i),model.comps);
0056     if I==false
0057         model.comps=[model.comps;toComps(i)];
0058         model.compNames=[model.compNames;compNames(i)];
0059         if isfield(model,'compOutside')
0060             model.compOutside=[model.compOutside;compOutside(i)];
0061         end
0062         if isfield(model,'compMiriams')
0063             model.compMiriams=[model.compMiriams;cell(1,1)];
0064         end
0065         J=numel(model.comps);
0066     end
0067     %Copy the reactions by making a model structure with only them, then
0068     %change the localization, and finally merge with the original model
0069     modelToAdd=model;
0070     modelToAdd=removeReactions(modelToAdd,setdiff(1:numel(model.rxns),rxns),true,true);
0071     modelToAdd.rxns=strcat(modelToAdd.rxns,'_',toComps(i));
0072     modelToAdd.mets=strcat(modelToAdd.mets,'_',toComps(i));
0073     modelToAdd.comps=modelToAdd.comps(J);
0074     modelToAdd.compNames=modelToAdd.compNames(J);
0075     if isfield(modelToAdd,'compOutside')
0076         modelToAdd.compOutside=modelToAdd.compOutside(J);
0077     end
0078     if isfield(modelToAdd,'compMiriams')
0079         modelToAdd.compMiriams=modelToAdd.compMiriams(J);
0080     end
0081     modelToAdd.metComps=ones(numel(modelToAdd.mets),1);
0082     
0083     %Merge the models
0084     model=mergeModels({model;modelToAdd},'metNames');
0085 end
0086 
0087 model=rmfield(model,'rxnFrom');
0088 model=rmfield(model,'metFrom');
0089 model=rmfield(model,'geneFrom');
0090 
0091 if deleteOriginal==true
0092     model=removeReactions(model,rxns,true,true,true); %Also delete unused compartments
0093 end
0094 
0095 model.id=originalID;
0096 model.name=originalName;
0097 end