permuteModel

 permuteModel
   Changes the order of the reactions or metabolites in a model

   Input:
   model     a model structure
   indexes   a vector with the same length as the number of items in the
             model, which gives the new order of items
   type      'rxns' for reactions, 'mets' for metabolites, 'genes' for
             genes, 'comps' for compartments

     Output:
   newModel  an updated model structure

     Usage: newModel=permuteModel(model, indexes, type)

0001 function newModel=permuteModel(model, indexes, type)
0002 % permuteModel
0003 %   Changes the order of the reactions or metabolites in a model
0004 %
0005 %   Input:
0006 %   model     a model structure
0007 %   indexes   a vector with the same length as the number of items in the
0008 %             model, which gives the new order of items
0009 %   type      'rxns' for reactions, 'mets' for metabolites, 'genes' for
0010 %             genes, 'comps' for compartments
0011 %
0012 %     Output:
0013 %   newModel  an updated model structure
0014 %
0015 %     Usage: newModel=permuteModel(model, indexes, type)
0016 
0017 newModel=model;
0018 type=char(type);
0019 
0020 switch type
0021     case 'rxns'
0022         if isfield(newModel,'rxns')
0023             newModel.rxns=newModel.rxns(indexes);
0024         end
0025         if isfield(newModel,'lb')
0026             newModel.lb=newModel.lb(indexes);
0027         end
0028         if isfield(newModel,'ub')
0029             newModel.ub=newModel.ub(indexes);
0030         end
0031         if isfield(newModel,'rev')
0032             newModel.rev=newModel.rev(indexes);
0033         end
0034         if isfield(newModel,'c')
0035             newModel.c=newModel.c(indexes);
0036         end
0037         if isfield(newModel,'S')
0038             newModel.S=newModel.S(:,indexes);
0039         end
0040         if isfield(newModel,'rxnNames')
0041             newModel.rxnNames=newModel.rxnNames(indexes);
0042         end
0043         if isfield(newModel,'rxnGeneMat')
0044             newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:);
0045         end
0046         if isfield(newModel,'grRules')
0047             newModel.grRules=newModel.grRules(indexes);
0048         end
0049         if isfield(newModel,'subSystems')
0050             newModel.subSystems=newModel.subSystems(indexes);
0051         end
0052         if isfield(newModel,'eccodes')
0053             newModel.eccodes=newModel.eccodes(indexes);
0054         end
0055         if isfield(newModel,'equations')
0056             newModel.equations=newModel.equations(indexes);
0057         end
0058         if isfield(newModel,'rxnMiriams')
0059             newModel.rxnMiriams=newModel.rxnMiriams(indexes);
0060         end
0061         if isfield(newModel,'rxnComps')
0062             newModel.rxnComps=newModel.rxnComps(indexes);
0063         end
0064         if isfield(newModel,'rxnFrom')
0065             newModel.rxnFrom=newModel.rxnFrom(indexes);
0066         end
0067         if isfield(newModel,'rxnScores')
0068             newModel.rxnScores=newModel.rxnScores(indexes);
0069         end
0070         if isfield(newModel,'rxnNotes')
0071             newModel.rxnNotes=newModel.rxnNotes(indexes);
0072         end
0073         if isfield(newModel,'rxnReferences')
0074             newModel.rxnReferences=newModel.rxnReferences(indexes);
0075         end
0076         if isfield(newModel,'rxnConfidenceScores')
0077             newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes);
0078         end
0079         if isfield(newModel,'rxnDeltaG')
0080             newModel.rxnDeltaG=newModel.rxnDeltaG(indexes);
0081         end
0082     case 'mets'
0083         if isfield(newModel,'mets')
0084             newModel.mets=newModel.mets(indexes);
0085         end
0086         if isfield(newModel,'metNames')
0087             newModel.metNames=newModel.metNames(indexes);
0088         end
0089         if isfield(newModel,'b')
0090             newModel.b=newModel.b(indexes,:);
0091         end
0092         if isfield(newModel,'metComps')
0093             newModel.metComps=newModel.metComps(indexes);
0094         end
0095         if isfield(newModel,'S')
0096             newModel.S=newModel.S(indexes,:);
0097         end
0098         if isfield(newModel,'unconstrained')
0099             newModel.unconstrained=newModel.unconstrained(indexes);
0100         end
0101         if isfield(newModel,'metMiriams')
0102             newModel.metMiriams=newModel.metMiriams(indexes,:);
0103         end
0104         if isfield(newModel,'inchis')
0105             newModel.inchis=newModel.inchis(indexes);
0106         end
0107         if isfield(newModel,'metSmiles')
0108             newModel.metSmiles=newModel.metSmiles(indexes);
0109         end
0110         if isfield(newModel,'metFormulas')
0111             newModel.metFormulas=newModel.metFormulas(indexes);
0112         end
0113         if isfield(newModel,'metFrom')
0114             newModel.metFrom=newModel.metFrom(indexes);
0115         end
0116         if isfield(newModel,'metCharges')
0117             newModel.metCharges=newModel.metCharges(indexes);
0118         end
0119         if isfield(newModel,'metDeltaG')
0120             newModel.metDeltaG=newModel.metDeltaG(indexes);
0121         end
0122     case 'genes'
0123         if isfield(newModel,'genes')
0124             newModel.genes=newModel.genes(indexes);
0125         end
0126         if isfield(newModel,'geneComps')
0127             newModel.geneComps=newModel.geneComps(indexes);
0128         end
0129         if isfield(newModel,'geneMiriams')
0130             newModel.geneMiriams=newModel.geneMiriams(indexes);
0131         end
0132         if isfield(newModel,'geneShortNames')
0133             newModel.geneShortNames=newModel.geneShortNames(indexes);
0134         end
0135         if isfield(newModel,'proteins')
0136             newModel.proteins=newModel.proteins(indexes);
0137         end
0138         if isfield(newModel,'rxnGeneMat')
0139             newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes);
0140         end
0141     case 'comps'
0142         if isfield(newModel,'comps')
0143             newModel.comps=newModel.comps(indexes);
0144         end
0145         if isfield(newModel,'compNames')
0146             newModel.compNames=newModel.compNames(indexes);
0147         end
0148         if isfield(newModel,'compOutside')
0149             newModel.compOutside=newModel.compOutside(indexes);
0150         end
0151         if isfield(newModel,'compMiriams')
0152             newModel.compMiriams=newModel.compMiriams(indexes);
0153         end
0154         [~,J]=sort(indexes); % The *index* of compartment is used in next fields
0155         if isfield(newModel,'metComps')
0156             [toreplace, bywhat] = ismember(newModel.metComps,1:length(J));
0157             newModel.metComps(toreplace) = J(bywhat(toreplace));
0158         end
0159         if isfield(model,'rxnComps')
0160             [toreplace, bywhat] = ismember(model.rxnComps,1:length(J));
0161             model.rxnComps(toreplace) = J(bywhat(toreplace));
0162         end
0163         if isfield(model,'geneComps')
0164             [toreplace, bywhat] = ismember(model.geneComps,1:length(J));
0165             model.geneComps(toreplace) = J(bywhat(toreplace));
0166         end
0167 end
0168 end