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 throw(MException('','genes is a required field in genesToAdd'));
0037 end
0038
0039 if ~iscellstr(genesToAdd.genes)
0040 throw(MException('','genesToAdd.genes must be a cell array of strings'));
0041 end
0042
0043 illegalCells=regexp(genesToAdd.genes,'[();:]', 'once');
0044 if ~isempty(cell2mat(illegalCells))
0045 errorText='Illegal character(s) in gene names:\n';
0046 for i=1:length(illegalCells)
0047 if ~isempty(illegalCells{i})
0048 errorText=[errorText genesToAdd.genes{i} '\n'];
0049 end
0050 end
0051 throw(MException('',errorText));
0052 end
0053
0054
0055 nGenes=numel(genesToAdd.genes);
0056 nOldGenes=numel(model.genes);
0057 filler=cell(nGenes,1);
0058 filler(:)={''};
0059 largeFiller=cell(nOldGenes,1);
0060 largeFiller(:)={''};
0061
0062
0063 I=ismember(genesToAdd.genes,model.genes);
0064 if any(I)
0065 throw(MException('','One or more elements in genesToAdd.genes are already present in model.genes'));
0066 else
0067 newModel.genes=[newModel.genes;genesToAdd.genes(:)];
0068 end
0069
0070
0071 if isfield(genesToAdd,'geneShortNames')
0072 if numel(genesToAdd.geneShortNames)~=nGenes
0073 throw(MException('','genesToAdd.geneShortNames must have the same number of elements as genesToAdd.genes'));
0074 end
0075 if ~iscellstr(genesToAdd.geneShortNames)
0076 throw(MException('','genesToAdd.geneShortNames must be a cell array of strings'));
0077 end
0078
0079 if ~isfield(newModel,'geneShortNames')
0080 newModel.geneShortNames=largeFiller;
0081 end
0082 newModel.geneShortNames=[newModel.geneShortNames;genesToAdd.geneShortNames(:)];
0083 else
0084
0085 if isfield(newModel,'geneShortNames')
0086 newModel.geneShortNames=[newModel.geneShortNames;filler];
0087 end
0088 end
0089
0090
0091 if isfield(genesToAdd,'geneMiriams')
0092 if numel(genesToAdd.geneMiriams)~=nGenes
0093 throw(MException('','genesToAdd.geneMiriams must have the same number of elements as genesToAdd.genes'));
0094 end
0095
0096 if ~isfield(newModel,'geneMiriams')
0097 newModel.geneMiriams=cell(nOldGenes,1);
0098 end
0099 newModel.geneMiriams=[newModel.geneMiriams;genesToAdd.geneMiriams(:)];
0100 else
0101 if isfield(newModel,'geneMiriams')
0102 newModel.geneMiriams=[newModel.geneMiriams;cell(nGenes,1)];
0103 end
0104 end
0105
0106 if isfield(newModel,'geneFrom')
0107 newModel.geneFrom=[newModel.geneFrom;filler];
0108 end
0109
0110 if isfield(newModel,'rxnGeneMat')
0111 newModel.rxnGeneMat=[newModel.rxnGeneMat sparse(numel(model.rxns),nGenes)];
0112 end
0113 end