0001 function newModel=addGenes(model,genesToAdd)
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0028 newModel=model;
0029
0030 if isempty(genesToAdd)
0031 return;
0032 end
0033
0034
0035 if ~isfield(genesToAdd,'genes')
0036 dispEM('genes is a required field in genesToAdd');
0037 end
0038
0039 if ~iscellstr(genesToAdd.genes)
0040 dispEM('genesToAdd.genes must be a cell array of strings');
0041 end
0042
0043 illegalCells=regexp(genesToAdd.genes,'[();:]', 'once');
0044 dispEM('Illegal character(s) in gene names:',true,genesToAdd.genes(~cellfun(@isempty,illegalCells)));
0045
0046
0047 nGenes=numel(genesToAdd.genes);
0048 nOldGenes=numel(model.genes);
0049 filler=cell(nGenes,1);
0050 filler(:)={''};
0051 largeFiller=cell(nOldGenes,1);
0052 largeFiller(:)={''};
0053
0054
0055 I=ismember(genesToAdd.genes,model.genes);
0056 if any(I)
0057 dispEM('One or more elements in genesToAdd.genes are already present in model.genes');
0058 else
0059 newModel.genes=[newModel.genes;genesToAdd.genes(:)];
0060 end
0061
0062
0063 if isfield(genesToAdd,'geneShortNames')
0064 if numel(genesToAdd.geneShortNames)~=nGenes
0065 dispEM('genesToAdd.geneShortNames must have the same number of elements as genesToAdd.genes');
0066 end
0067 if ~iscellstr(genesToAdd.geneShortNames)
0068 dispEM('genesToAdd.geneShortNames must be a cell array of strings');
0069 end
0070
0071 if ~isfield(newModel,'geneShortNames')
0072 newModel.geneShortNames=largeFiller;
0073 end
0074 newModel.geneShortNames=[newModel.geneShortNames;genesToAdd.geneShortNames(:)];
0075 else
0076
0077 if isfield(newModel,'geneShortNames')
0078 newModel.geneShortNames=[newModel.geneShortNames;filler];
0079 end
0080 end
0081
0082
0083 if isfield(genesToAdd,'geneMiriams')
0084 if numel(genesToAdd.geneMiriams)~=nGenes
0085 dispEM('genesToAdd.geneMiriams must have the same number of elements as genesToAdd.genes');
0086 end
0087
0088 if ~isfield(newModel,'geneMiriams')
0089 newModel.geneMiriams=cell(nOldGenes,1);
0090 end
0091 newModel.geneMiriams=[newModel.geneMiriams;genesToAdd.geneMiriams(:)];
0092 else
0093 if isfield(newModel,'geneMiriams')
0094 newModel.geneMiriams=[newModel.geneMiriams;cell(nGenes,1)];
0095 end
0096 end
0097
0098 if isfield(genesToAdd,'geneComps')
0099 if numel(genesToAdd.geneComps)~=nGenes
0100 dispEM('genesToAdd.geneComps must have the same number of elements as genesToAdd.genes');
0101 end
0102
0103 if ~isfield(newModel,'geneComps')
0104 newModel.geneComps=ones(nOldGenes,1);
0105 dispEM('Adding genes with compartment information to a model without such information. All existing genes will be assigned to the first compartment',false);
0106 end
0107 newModel.geneComps=[newModel.geneComps;genesToAdd.geneComps(:)];
0108 else
0109 if isfield(newModel,'geneComps')
0110 newModel.geneComps=[newModel.geneComps;ones(nGenes,1)];
0111 fprintf('NOTE: The added genes will be assigned to the first compartment\n');
0112 end
0113 end
0114
0115 if isfield(newModel,'geneFrom')
0116 newModel.geneFrom=[newModel.geneFrom;filler];
0117 end
0118
0119 if isfield(newModel,'rxnGeneMat')
0120 newModel.rxnGeneMat=[newModel.rxnGeneMat sparse(numel(model.rxns),nGenes)];
0121 end
0122 end