diff --git a/core/permuteModel.m b/core/permuteModel.m index 15765f83..23a06cea 100755 --- a/core/permuteModel.m +++ b/core/permuteModel.m @@ -2,111 +2,155 @@ % 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 reactions in the -% model which gives the new order of reactions -% type 'rxns' for reactions and 'mets' for metabolites +% 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 % -% newModel an updated model structure +% Output: +% newModel an updated model structure % % Usage: newModel=permuteModel(model, indexes, type) newModel=model; indexes=indexes(:); -if strcmp(type,'rxns') - if isfield(newModel,'rxns') - newModel.rxns=newModel.rxns(indexes); - end - if isfield(newModel,'lb') - newModel.lb=newModel.lb(indexes); - end - if isfield(newModel,'ub') - newModel.ub=newModel.ub(indexes); - end - if isfield(newModel,'rev') - newModel.rev=newModel.rev(indexes); - end - if isfield(newModel,'c') - newModel.c=newModel.c(indexes); - end - if isfield(newModel,'S') - newModel.S=newModel.S(:,indexes); - end - if isfield(newModel,'rxnNames') - newModel.rxnNames=newModel.rxnNames(indexes); - end - if isfield(newModel,'rxnGeneMat') - newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:); - end - if isfield(newModel,'grRules') - newModel.grRules=newModel.grRules(indexes); - end - if isfield(newModel,'subSystems') - newModel.subSystems=newModel.subSystems(indexes); - end - if isfield(newModel,'eccodes') - newModel.eccodes=newModel.eccodes(indexes); - end - if isfield(newModel,'equations') - newModel.equations=newModel.equations(indexes); - end - if isfield(newModel,'rxnMiriams') - newModel.rxnMiriams=newModel.rxnMiriams(indexes); - end - if isfield(newModel,'rxnComps') - newModel.rxnComps=newModel.rxnComps(indexes); - end - if isfield(newModel,'rxnFrom') - newModel.rxnFrom=newModel.rxnFrom(indexes); - end - if isfield(newModel,'rxnScores') - newModel.rxnScores=newModel.rxnScores(indexes); - end - if isfield(newModel,'rxnNotes') - newModel.rxnNotes=newModel.rxnNotes(indexes); - end - if isfield(newModel,'rxnReferences') - newModel.rxnReferences=newModel.rxnReferences(indexes); - end - if isfield(newModel,'rxnConfidenceScores') - newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes); - end -end - -if strcmp(type,'mets') - if isfield(newModel,'mets') - newModel.mets=newModel.mets(indexes); - end - if isfield(newModel,'metNames') - newModel.metNames=newModel.metNames(indexes); - end - if isfield(newModel,'b') - newModel.b=newModel.b(indexes,:); - end - if isfield(newModel,'metComps') - newModel.metComps=newModel.metComps(indexes); - end - if isfield(newModel,'S') - newModel.S=newModel.S(indexes,:); - end - if isfield(newModel,'unconstrained') - newModel.unconstrained=newModel.unconstrained(indexes); - end - if isfield(newModel,'metMiriams') - newModel.metMiriams=newModel.metMiriams(indexes,:); - end - if isfield(newModel,'inchis') - newModel.inchis=newModel.inchis(indexes); - end - if isfield(newModel,'metFormulas') - newModel.metFormulas=newModel.metFormulas(indexes); - end - if isfield(newModel,'metFrom') - newModel.metFrom=newModel.metFrom(indexes); - end - if isfield(newModel,'metCharges') - newModel.metCharges=newModel.metCharges(indexes); - end +switch type + case 'rxns' + if isfield(newModel,'rxns') + newModel.rxns=newModel.rxns(indexes); + end + if isfield(newModel,'lb') + newModel.lb=newModel.lb(indexes); + end + if isfield(newModel,'ub') + newModel.ub=newModel.ub(indexes); + end + if isfield(newModel,'rev') + newModel.rev=newModel.rev(indexes); + end + if isfield(newModel,'c') + newModel.c=newModel.c(indexes); + end + if isfield(newModel,'S') + newModel.S=newModel.S(:,indexes); + end + if isfield(newModel,'rxnNames') + newModel.rxnNames=newModel.rxnNames(indexes); + end + if isfield(newModel,'rxnGeneMat') + newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:); + end + if isfield(newModel,'grRules') + newModel.grRules=newModel.grRules(indexes); + end + if isfield(newModel,'subSystems') + newModel.subSystems=newModel.subSystems(indexes); + end + if isfield(newModel,'eccodes') + newModel.eccodes=newModel.eccodes(indexes); + end + if isfield(newModel,'equations') + newModel.equations=newModel.equations(indexes); + end + if isfield(newModel,'rxnMiriams') + newModel.rxnMiriams=newModel.rxnMiriams(indexes); + end + if isfield(newModel,'rxnComps') + newModel.rxnComps=newModel.rxnComps(indexes); + end + if isfield(newModel,'rxnFrom') + newModel.rxnFrom=newModel.rxnFrom(indexes); + end + if isfield(newModel,'rxnScores') + newModel.rxnScores=newModel.rxnScores(indexes); + end + if isfield(newModel,'rxnNotes') + newModel.rxnNotes=newModel.rxnNotes(indexes); + end + if isfield(newModel,'rxnReferences') + newModel.rxnReferences=newModel.rxnReferences(indexes); + end + if isfield(newModel,'rxnConfidenceScores') + newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes); + end + case 'mets' + if isfield(newModel,'mets') + newModel.mets=newModel.mets(indexes); + end + if isfield(newModel,'metNames') + newModel.metNames=newModel.metNames(indexes); + end + if isfield(newModel,'b') + newModel.b=newModel.b(indexes,:); + end + if isfield(newModel,'metComps') + newModel.metComps=newModel.metComps(indexes); + end + if isfield(newModel,'S') + newModel.S=newModel.S(indexes,:); + end + if isfield(newModel,'unconstrained') + newModel.unconstrained=newModel.unconstrained(indexes); + end + if isfield(newModel,'metMiriams') + newModel.metMiriams=newModel.metMiriams(indexes,:); + end + if isfield(newModel,'inchis') + newModel.inchis=newModel.inchis(indexes); + end + if isfield(newModel,'metFormulas') + newModel.metFormulas=newModel.metFormulas(indexes); + end + if isfield(newModel,'metFrom') + newModel.metFrom=newModel.metFrom(indexes); + end + if isfield(newModel,'metCharges') + newModel.metCharges=newModel.metCharges(indexes); + end + case 'genes' + if isfield(newModel,'genes') + newModel.genes=newModel.genes(indexes); + end + if isfield(newModel,'geneComps') + newModel.geneComps=newModel.geneComps(indexes); + end + if isfield(newModel,'geneMiriams') + newModel.geneMiriams=newModel.geneMiriams(indexes); + end + if isfield(newModel,'geneShortNames') + newModel.geneShortNames=newModel.geneShortNames(indexes); + end + if isfield(newModel,'rxnGeneMat') + newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes); + end + case 'comps' + if isfield(newModel,'comps') + newModel.comps=newModel.comps(indexes); + end + if isfield(newModel,'compNames') + newModel.compNames=newModel.compNames(indexes); + end + if isfield(newModel,'compOutside') + newModel.compOutside=newModel.compOutside(indexes); + end + if isfield(newModel,'compMiriams') + newModel.compMiriams=newModel.compMiriams(indexes); + end + [~,J]=sort(indexes); % The *index* of compartment is used in next fields + if isfield(newModel,'metComps') + [toreplace, bywhat] = ismember(newModel.metComps,1:length(J)); + newModel.metComps(toreplace) = J(bywhat(toreplace)); + end + if isfield(model,'rxnComps') + [toreplace, bywhat] = ismember(model.rxnComps,1:length(J)); + model.rxnComps(toreplace) = J(bywhat(toreplace)); + end + if isfield(model,'geneComps') + [toreplace, bywhat] = ismember(model.geneComps,1:length(J)); + model.geneComps(toreplace) = J(bywhat(toreplace)); + end end end diff --git a/doc/core/permuteModel.html b/doc/core/permuteModel.html index e09feed4..32b608e1 100644 --- a/doc/core/permuteModel.html +++ b/doc/core/permuteModel.html @@ -30,12 +30,15 @@

DESCRIPTION ^
 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 reactions in the
-             model which gives the new order of reactions
-   type      'rxns' for reactions and 'mets' for metabolites
+   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
 
-     newModel  an updated model structure
+     Output:
+   newModel  an updated model structure
 
      Usage: newModel=permuteModel(model, indexes, type)
@@ -56,114 +59,158 @@

SOURCE CODE ^% permuteModel 0003 % Changes the order of the reactions or metabolites in a model 0004 % -0005 % model a model structure -0006 % indexes a vector with the same length as the number of reactions in the -0007 % model which gives the new order of reactions -0008 % type 'rxns' for reactions and 'mets' for metabolites -0009 % -0010 % newModel an updated model structure +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 % Usage: newModel=permuteModel(model, indexes, type) -0013 -0014 newModel=model; -0015 indexes=indexes(:); +0012 % Output: +0013 % newModel an updated model structure +0014 % +0015 % Usage: newModel=permuteModel(model, indexes, type) 0016 -0017 if strcmp(type,'rxns') -0018 if isfield(newModel,'rxns') -0019 newModel.rxns=newModel.rxns(indexes); -0020 end -0021 if isfield(newModel,'lb') -0022 newModel.lb=newModel.lb(indexes); -0023 end -0024 if isfield(newModel,'ub') -0025 newModel.ub=newModel.ub(indexes); -0026 end -0027 if isfield(newModel,'rev') -0028 newModel.rev=newModel.rev(indexes); -0029 end -0030 if isfield(newModel,'c') -0031 newModel.c=newModel.c(indexes); -0032 end -0033 if isfield(newModel,'S') -0034 newModel.S=newModel.S(:,indexes); -0035 end -0036 if isfield(newModel,'rxnNames') -0037 newModel.rxnNames=newModel.rxnNames(indexes); -0038 end -0039 if isfield(newModel,'rxnGeneMat') -0040 newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:); -0041 end -0042 if isfield(newModel,'grRules') -0043 newModel.grRules=newModel.grRules(indexes); -0044 end -0045 if isfield(newModel,'subSystems') -0046 newModel.subSystems=newModel.subSystems(indexes); -0047 end -0048 if isfield(newModel,'eccodes') -0049 newModel.eccodes=newModel.eccodes(indexes); -0050 end -0051 if isfield(newModel,'equations') -0052 newModel.equations=newModel.equations(indexes); -0053 end -0054 if isfield(newModel,'rxnMiriams') -0055 newModel.rxnMiriams=newModel.rxnMiriams(indexes); -0056 end -0057 if isfield(newModel,'rxnComps') -0058 newModel.rxnComps=newModel.rxnComps(indexes); -0059 end -0060 if isfield(newModel,'rxnFrom') -0061 newModel.rxnFrom=newModel.rxnFrom(indexes); -0062 end -0063 if isfield(newModel,'rxnScores') -0064 newModel.rxnScores=newModel.rxnScores(indexes); -0065 end -0066 if isfield(newModel,'rxnNotes') -0067 newModel.rxnNotes=newModel.rxnNotes(indexes); -0068 end -0069 if isfield(newModel,'rxnReferences') -0070 newModel.rxnReferences=newModel.rxnReferences(indexes); -0071 end -0072 if isfield(newModel,'rxnConfidenceScores') -0073 newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes); -0074 end -0075 end -0076 -0077 if strcmp(type,'mets') -0078 if isfield(newModel,'mets') -0079 newModel.mets=newModel.mets(indexes); -0080 end -0081 if isfield(newModel,'metNames') -0082 newModel.metNames=newModel.metNames(indexes); -0083 end -0084 if isfield(newModel,'b') -0085 newModel.b=newModel.b(indexes,:); -0086 end -0087 if isfield(newModel,'metComps') -0088 newModel.metComps=newModel.metComps(indexes); -0089 end -0090 if isfield(newModel,'S') -0091 newModel.S=newModel.S(indexes,:); -0092 end -0093 if isfield(newModel,'unconstrained') -0094 newModel.unconstrained=newModel.unconstrained(indexes); -0095 end -0096 if isfield(newModel,'metMiriams') -0097 newModel.metMiriams=newModel.metMiriams(indexes,:); -0098 end -0099 if isfield(newModel,'inchis') -0100 newModel.inchis=newModel.inchis(indexes); -0101 end -0102 if isfield(newModel,'metFormulas') -0103 newModel.metFormulas=newModel.metFormulas(indexes); -0104 end -0105 if isfield(newModel,'metFrom') -0106 newModel.metFrom=newModel.metFrom(indexes); -0107 end -0108 if isfield(newModel,'metCharges') -0109 newModel.metCharges=newModel.metCharges(indexes); -0110 end -0111 end -0112 end +0017 newModel=model; +0018 indexes=indexes(:); +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 case 'mets' +0080 if isfield(newModel,'mets') +0081 newModel.mets=newModel.mets(indexes); +0082 end +0083 if isfield(newModel,'metNames') +0084 newModel.metNames=newModel.metNames(indexes); +0085 end +0086 if isfield(newModel,'b') +0087 newModel.b=newModel.b(indexes,:); +0088 end +0089 if isfield(newModel,'metComps') +0090 newModel.metComps=newModel.metComps(indexes); +0091 end +0092 if isfield(newModel,'S') +0093 newModel.S=newModel.S(indexes,:); +0094 end +0095 if isfield(newModel,'unconstrained') +0096 newModel.unconstrained=newModel.unconstrained(indexes); +0097 end +0098 if isfield(newModel,'metMiriams') +0099 newModel.metMiriams=newModel.metMiriams(indexes,:); +0100 end +0101 if isfield(newModel,'inchis') +0102 newModel.inchis=newModel.inchis(indexes); +0103 end +0104 if isfield(newModel,'metFormulas') +0105 newModel.metFormulas=newModel.metFormulas(indexes); +0106 end +0107 if isfield(newModel,'metFrom') +0108 newModel.metFrom=newModel.metFrom(indexes); +0109 end +0110 if isfield(newModel,'metCharges') +0111 newModel.metCharges=newModel.metCharges(indexes); +0112 end +0113 case 'genes' +0114 if isfield(newModel,'genes') +0115 newModel.genes=newModel.genes(indexes); +0116 end +0117 if isfield(newModel,'geneComps') +0118 newModel.geneComps=newModel.geneComps(indexes); +0119 end +0120 if isfield(newModel,'geneMiriams') +0121 newModel.geneMiriams=newModel.geneMiriams(indexes); +0122 end +0123 if isfield(newModel,'geneShortNames') +0124 newModel.geneShortNames=newModel.geneShortNames(indexes); +0125 end +0126 if isfield(newModel,'rxnGeneMat') +0127 newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes); +0128 end +0129 case 'comps' +0130 if isfield(newModel,'comps') +0131 newModel.comps=newModel.comps(indexes); +0132 end +0133 if isfield(newModel,'compNames') +0134 newModel.compNames=newModel.compNames(indexes); +0135 end +0136 if isfield(newModel,'compOutside') +0137 newModel.compOutside=newModel.compOutside(indexes); +0138 end +0139 if isfield(newModel,'compMiriams') +0140 newModel.compMiriams=newModel.compMiriams(indexes); +0141 end +0142 [~,J]=sort(indexes); % The *index* of compartment is used in next fields +0143 if isfield(newModel,'metComps') +0144 [toreplace, bywhat] = ismember(newModel.metComps,1:length(J)); +0145 newModel.metComps(toreplace) = J(bywhat(toreplace)); +0146 end +0147 if isfield(model,'rxnComps') +0148 [toreplace, bywhat] = ismember(model.rxnComps,1:length(J)); +0149 model.rxnComps(toreplace) = J(bywhat(toreplace)); +0150 end +0151 if isfield(model,'geneComps') +0152 [toreplace, bywhat] = ismember(model.geneComps,1:length(J)); +0153 model.geneComps(toreplace) = J(bywhat(toreplace)); +0154 end +0155 end +0156 end
Generated by m2html © 2005
\ No newline at end of file diff --git a/doc/io/SBMLFromExcel.html b/doc/io/SBMLFromExcel.html index 9799b702..34b74dae 100644 --- a/doc/io/SBMLFromExcel.html +++ b/doc/io/SBMLFromExcel.html @@ -49,7 +49,7 @@

DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

This function calls: +
  • exportModel exportModel
  • importExcelModel importExcelModel
    • This function is called by: @@ -86,7 +86,7 @@

    SOURCE CODE ^importExcelModel(fileName,false,printWarnings); 0028 printModelStats(model,printWarnings,false); -0029 exportModel(model,outputFileName,toCOBRA,true); +0029 exportModel(model,outputFileName,toCOBRA,true); 0030 end
    Generated by m2html © 2005
    diff --git a/doc/io/exportForGit.html b/doc/io/exportForGit.html index 82d9dc3b..a7418a09 100644 --- a/doc/io/exportForGit.html +++ b/doc/io/exportForGit.html @@ -56,7 +56,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • exportModel exportModel
  • exportToExcelFormat exportToExcelFormat
  • getToolboxVersion getToolboxVersion
  • sortIdentifiers exportModel
  • writeYaml writeYaml
    • This function is called by: @@ -113,91 +113,94 @@

    SOURCE CODE ^'model'; 0047 end 0048 -0049 %Get versions or commits of toolboxes: -0050 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',masterFlag); -0051 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',masterFlag); -0052 -0053 %Retrieve libSBML version: -0054 try % 5.17.0 and newer -0055 libSBMLver=OutputSBML; -0056 libSBMLver=libSBMLver.libSBML_version_string; -0057 catch % before 5.17.0 -0058 fid = fopen('tempModelForLibSBMLversion.xml','w+'); -0059 fclose(fid); -0060 evalc('[~,~,libSBMLver]=TranslateSBML(''tempModelForLibSBMLversion.xml'',0,0)'); -0061 libSBMLver=libSBMLver.libSBML_version_string; -0062 delete('tempModelForLibSBMLversion.xml'); -0063 end -0064 -0065 % Make models folder, no warnings if folder already exists -0066 if subDirs -0067 path=fullfile(path,'model'); -0068 filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'}); -0069 [~,~,~]=mkdir(path); -0070 for i = 1:length(formats) -0071 [~,~,~]=mkdir(fullfile(path,formats{i})); -0072 end -0073 else -0074 filePath=cell(1,5); filePath(:)={path}; -0075 end -0076 -0077 -0078 % Write TXT format -0079 if ismember('txt', formats) -0080 fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w'); -0081 eqns=constructEquations(model,model.rxns,false,false,false,true); -0082 eqns=strrep(eqns,' => ',' -> '); -0083 eqns=strrep(eqns,' <=> ',' <=> '); -0084 eqns=regexprep(eqns,'> $','>'); -0085 grRules=regexprep(model.grRules,'\((?!\()','( '); -0086 grRules=regexprep(grRules,'(?<!\))\)',' )'); -0087 fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n'); -0088 for i = 1:numel(model.rxns) -0089 fprintf(fid, '%s\t', model.rxns{i}); -0090 fprintf(fid, '%s \t', eqns{i}); -0091 fprintf(fid, '%s\t', grRules{i}); -0092 fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i)); -0093 end -0094 fclose(fid); -0095 end -0096 -0097 % Write YML format -0098 if ismember('yml', formats) -0099 writeYaml(model,fullfile(filePath{2},strcat(prefix,'.yml'))); -0100 end -0101 -0102 % Write MAT format -0103 if ismember('mat', formats) -0104 save(fullfile(filePath{3},strcat(prefix,'.mat')),'model'); -0105 end -0106 -0107 % Write XLSX format -0108 if ismember('xlsx', formats) -0109 exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx'))); -0110 end -0111 -0112 % Write XML format -0113 if ismember('xml', formats) -0114 exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml'))); -0115 end -0116 -0117 %Save file with versions: -0118 fid = fopen(fullfile(path,'dependencies.txt'),'wt'); -0119 fprintf(fid,['MATLAB\t' version '\n']); -0120 fprintf(fid,['libSBML\t' libSBMLver '\n']); -0121 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']); -0122 if ~isempty(COBRAver) -0123 fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']); -0124 end -0125 if isfield(model,'modelVersion') -0126 fields = fieldnames(model.modelVersion); -0127 for i = 1:length(fields) -0128 value = model.modelVersion.(fields{i}); -0129 fprintf(fid,[fields{i} '\t' num2str(value) '\n']); -0130 end -0131 end -0132 fclose(fid); -0133 end +0049 %Sort reactions, metabolites and genes alphabetically +0050 model=sortIdentifiers(model); +0051 +0052 %Get versions or commits of toolboxes: +0053 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',masterFlag); +0054 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',masterFlag); +0055 +0056 %Retrieve libSBML version: +0057 try % 5.17.0 and newer +0058 libSBMLver=OutputSBML; +0059 libSBMLver=libSBMLver.libSBML_version_string; +0060 catch % before 5.17.0 +0061 fid = fopen('tempModelForLibSBMLversion.xml','w+'); +0062 fclose(fid); +0063 evalc('[~,~,libSBMLver]=TranslateSBML(''tempModelForLibSBMLversion.xml'',0,0)'); +0064 libSBMLver=libSBMLver.libSBML_version_string; +0065 delete('tempModelForLibSBMLversion.xml'); +0066 end +0067 +0068 % Make models folder, no warnings if folder already exists +0069 if subDirs +0070 path=fullfile(path,'model'); +0071 filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'}); +0072 [~,~,~]=mkdir(path); +0073 for i = 1:length(formats) +0074 [~,~,~]=mkdir(fullfile(path,formats{i})); +0075 end +0076 else +0077 filePath=cell(1,5); filePath(:)={path}; +0078 end +0079 +0080 +0081 % Write TXT format +0082 if ismember('txt', formats) +0083 fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w'); +0084 eqns=constructEquations(model,model.rxns,false,false,false,true); +0085 eqns=strrep(eqns,' => ',' -> '); +0086 eqns=strrep(eqns,' <=> ',' <=> '); +0087 eqns=regexprep(eqns,'> $','>'); +0088 grRules=regexprep(model.grRules,'\((?!\()','( '); +0089 grRules=regexprep(grRules,'(?<!\))\)',' )'); +0090 fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n'); +0091 for i = 1:numel(model.rxns) +0092 fprintf(fid, '%s\t', model.rxns{i}); +0093 fprintf(fid, '%s \t', eqns{i}); +0094 fprintf(fid, '%s\t', grRules{i}); +0095 fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i)); +0096 end +0097 fclose(fid); +0098 end +0099 +0100 % Write YML format +0101 if ismember('yml', formats) +0102 writeYaml(model,fullfile(filePath{2},strcat(prefix,'.yml'))); +0103 end +0104 +0105 % Write MAT format +0106 if ismember('mat', formats) +0107 save(fullfile(filePath{3},strcat(prefix,'.mat')),'model'); +0108 end +0109 +0110 % Write XLSX format +0111 if ismember('xlsx', formats) +0112 exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx'))); +0113 end +0114 +0115 % Write XML format +0116 if ismember('xml', formats) +0117 exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml'))); +0118 end +0119 +0120 %Save file with versions: +0121 fid = fopen(fullfile(path,'dependencies.txt'),'wt'); +0122 fprintf(fid,['MATLAB\t' version '\n']); +0123 fprintf(fid,['libSBML\t' libSBMLver '\n']); +0124 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']); +0125 if ~isempty(COBRAver) +0126 fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']); +0127 end +0128 if isfield(model,'modelVersion') +0129 fields = fieldnames(model.modelVersion); +0130 for i = 1:length(fields) +0131 value = model.modelVersion.(fields{i}); +0132 fprintf(fid,[fields{i} '\t' num2str(value) '\n']); +0133 end +0134 end +0135 fclose(fid); +0136 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/io/exportModel.html b/doc/io/exportModel.html index b4ee2aaf..e44d0db7 100644 --- a/doc/io/exportModel.html +++ b/doc/io/exportModel.html @@ -24,7 +24,7 @@

    PURPOSE ^exportModel

    SYNOPSIS ^

    -
    function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
    +
    function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)

    DESCRIPTION ^

     exportModel
@@ -38,15 +38,17 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
@@ -57,7 +59,7 @@ 
    SUBFUNCTIONS ^function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
  • function miriamString=getMiriam(miriamStruct)
  • function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
  • function vecT = columnVector(vec)
    • 
 
 
    SOURCE CODE ^
    
-
    0001 function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
+
    0001 function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
 0002 % exportModel
 0003 %   Exports a constraint-based model to an SBML file (L3V1 FBCv2)
 0004 %
@@ -69,795 +71,803 @@ 
    SOURCE CODE ^%                       (opt, default false)
 0011 %   supressWarnings     true if warnings should be supressed (opt, default
 0012 %                       false)
-0013 %
-0014 %
-0015 %   Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings)
-0016 if nargin<3
-0017     exportGeneComplexes=false;
-0018 end
-0019 if nargin<4
-0020     supressWarnings=false;
-0021 end
-0022 
-0023 %If no subSystems are defined, then no need to use groups package
-0024 if isfield(model,'subSystems')
-0025     modelHasSubsystems=true;
-0026 else
-0027     modelHasSubsystems=false;
-0028 end
-0029 
-0030 %The default SBML format settings, which are used as input for appropriate
-0031 %libSBML functions to generate the blank SBML model structure before using
-0032 %exporting in with OutputSBML to xml file
-0033 sbmlLevel=3;
-0034 sbmlVersion=1;
-0035 sbmlPackages={'fbc'};
-0036 sbmlPackageVersions=2;
-0037 if modelHasSubsystems
-0038     sbmlPackages={sbmlPackages,'groups'};
-0039     sbmlPackageVersions=[sbmlPackageVersions,1];
-0040 end
-0041 
-0042 %Check if the "unconstrained" field is still present. This shows if
-0043 %exchange metabolites have been removed
-0044 if ~isfield(model,'unconstrained')
-0045     if supressWarnings==false
-0046         EM='There is no unconstrained field in the model structure. This means that no metabolites are considered exchange metabolites';
-0047         dispEM(EM,false);
-0048     end
-0049     model.unconstrained=zeros(numel(model.mets),1);
-0050 end
-0051 
-0052 %If model id and name do not exist, make sure that default
-0053 %strings are included
-0054 if ~isfield(model,'id')
-0055     fprintf('WARNING: The model is missing the "id" field. Uses "blankID". \n');
-0056     model.id='blankID';
-0057 end
-0058 if ~isfield(model,'name')
-0059     fprintf('WARNING: The model is missing the "name" field. Uses "blankName". \n');
-0060     model.name='blankName';
-0061 end
-0062 
-0063 %Check the model structure
-0064 if supressWarnings==false
-0065     checkModelStruct(model,false);
-0066 end
-0067 
-0068 %Add several blank fields, if they do not exist already. This is to reduce
-0069 %the number of conditions below
-0070 if ~isfield(model,'compMiriams')
-0071     model.compMiriams=cell(numel(model.comps),1);
-0072 end
-0073 if ~isfield(model,'inchis')
-0074     model.inchis=cell(numel(model.mets),1);
-0075 end
-0076 if ~isfield(model,'metFormulas')
-0077     model.metFormulas=cell(numel(model.mets),1);
-0078 end
-0079 if ~isfield(model,'metMiriams')
-0080     model.metMiriams=cell(numel(model.mets),1);
-0081 end
-0082 if ~isfield(model,'geneMiriams') && isfield(model,'genes')
-0083     model.geneMiriams=cell(numel(model.genes),1);
-0084 end
-0085 if ~isfield(model,'geneShortNames') && isfield(model,'genes')
-0086     model.geneShortNames=cell(numel(model.genes),1);
-0087 end
-0088 if ~isfield(model,'subSystems')
-0089     model.subSystems=cell(numel(model.rxns),1);
-0090 end
-0091 if ~isfield(model,'eccodes')
-0092     model.eccodes=cell(numel(model.rxns),1);
-0093 end
-0094 if ~isfield(model,'rxnReferences')
-0095     model.rxnReferences=cell(numel(model.rxns),1);
-0096 end
-0097 if ~isfield(model,'rxnConfidenceScores')
-0098     model.rxnConfidenceScores=NaN(numel(model.rxns),1);
-0099 end
-0100 if ~isfield(model,'rxnNotes')
-0101     model.rxnNotes=cell(numel(model.rxns),1);
-0102 end
-0103 if ~isfield(model,'rxnMiriams')
-0104     model.rxnMiriams=cell(numel(model.rxns),1);
-0105 end
-0106 
-0107 if sbmlLevel<3
-0108     %Check if genes have associated compartments
-0109     if ~isfield(model,'geneComps') && isfield(model,'genes')
-0110         if supressWarnings==false
-0111             EM='There are no compartments specified for genes. All genes will be assigned to the first compartment. This is because the SBML structure requires all elements to be assigned to a compartment';
-0112             dispEM(EM,false);
-0113         end
-0114         model.geneComps=ones(numel(model.genes),1);
-0115     end
-0116 end
-0117 
-0118 %Convert ids to SBML-convenient format. This is to avoid the data loss when
-0119 %unsupported characters are included in ids. Here we are using part from
-0120 %convertSBMLID, originating from the COBRA Toolbox
-0121 model.rxns=regexprep(model.rxns,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0122 model.mets=regexprep(model.mets,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0123 model.comps=regexprep(model.comps,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0124 if isfield(model,'genes')
-0125     problemGenes=find(~cellfun('isempty',regexp(model.genes,'([^0-9_a-zA-Z])')));
-0126     originalGenes=model.genes(problemGenes);
-0127     replacedGenes=regexprep(model.genes(problemGenes),'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0128     model.genes(problemGenes)=replacedGenes;
-0129     for i=1:numel(problemGenes)
-0130         model.grRules = regexprep(model.grRules, ['(^|\s|\()' originalGenes{i} '($|\s|\))'], ['$1' replacedGenes{i} '$2']);
-0131     end
-0132 end
-0133 
-0134 %Generate an empty SBML structure
-0135 modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0136 modelSBML.metaid=model.id;
-0137 modelSBML.id=model.id;
-0138 modelSBML.name=model.name;
-0139 
-0140 if isfield(model,'annotation')
-0141     if isfield(model.annotation,'note')
-0142         modelSBML.notes=['<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>',regexprep(model.annotation.note,'<p>|</p>',''),'</p></body></notes>'];
-0143     end
-0144 else
-0145     modelSBML.notes='<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>This file was generated using the exportModel function in RAVEN Toolbox 2 and OutputSBML in libSBML </p></body></notes>';
-0146 end
+0013 %   sortIds             logical whether metabolites, reactions and genes
+0014 %                       should be sorted alphabetically by their
+0015 %                       identifiers (opt, default false)
+0016 %
+0017 %   Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
+0018 if nargin<3
+0019     exportGeneComplexes=false;
+0020 end
+0021 if nargin<4
+0022     supressWarnings=false;
+0023 end
+0024 if nargin<5
+0025     sortIds=false;
+0026 end
+0027 if sortIds==true
+0028     model=sortIdentifiers(model);
+0029 end
+0030 
+0031 %If no subSystems are defined, then no need to use groups package
+0032 if isfield(model,'subSystems')
+0033     modelHasSubsystems=true;
+0034 else
+0035     modelHasSubsystems=false;
+0036 end
+0037 
+0038 %The default SBML format settings, which are used as input for appropriate
+0039 %libSBML functions to generate the blank SBML model structure before using
+0040 %exporting in with OutputSBML to xml file
+0041 sbmlLevel=3;
+0042 sbmlVersion=1;
+0043 sbmlPackages={'fbc'};
+0044 sbmlPackageVersions=2;
+0045 if modelHasSubsystems
+0046     sbmlPackages={sbmlPackages,'groups'};
+0047     sbmlPackageVersions=[sbmlPackageVersions,1];
+0048 end
+0049 
+0050 %Check if the "unconstrained" field is still present. This shows if
+0051 %exchange metabolites have been removed
+0052 if ~isfield(model,'unconstrained')
+0053     if supressWarnings==false
+0054         EM='There is no unconstrained field in the model structure. This means that no metabolites are considered exchange metabolites';
+0055         dispEM(EM,false);
+0056     end
+0057     model.unconstrained=zeros(numel(model.mets),1);
+0058 end
+0059 
+0060 %If model id and name do not exist, make sure that default
+0061 %strings are included
+0062 if ~isfield(model,'id')
+0063     fprintf('WARNING: The model is missing the "id" field. Uses "blankID". \n');
+0064     model.id='blankID';
+0065 end
+0066 if ~isfield(model,'name')
+0067     fprintf('WARNING: The model is missing the "name" field. Uses "blankName". \n');
+0068     model.name='blankName';
+0069 end
+0070 
+0071 %Check the model structure
+0072 if supressWarnings==false
+0073     checkModelStruct(model,false);
+0074 end
+0075 
+0076 %Add several blank fields, if they do not exist already. This is to reduce
+0077 %the number of conditions below
+0078 if ~isfield(model,'compMiriams')
+0079     model.compMiriams=cell(numel(model.comps),1);
+0080 end
+0081 if ~isfield(model,'inchis')
+0082     model.inchis=cell(numel(model.mets),1);
+0083 end
+0084 if ~isfield(model,'metFormulas')
+0085     model.metFormulas=cell(numel(model.mets),1);
+0086 end
+0087 if ~isfield(model,'metMiriams')
+0088     model.metMiriams=cell(numel(model.mets),1);
+0089 end
+0090 if ~isfield(model,'geneMiriams') && isfield(model,'genes')
+0091     model.geneMiriams=cell(numel(model.genes),1);
+0092 end
+0093 if ~isfield(model,'geneShortNames') && isfield(model,'genes')
+0094     model.geneShortNames=cell(numel(model.genes),1);
+0095 end
+0096 if ~isfield(model,'subSystems')
+0097     model.subSystems=cell(numel(model.rxns),1);
+0098 end
+0099 if ~isfield(model,'eccodes')
+0100     model.eccodes=cell(numel(model.rxns),1);
+0101 end
+0102 if ~isfield(model,'rxnReferences')
+0103     model.rxnReferences=cell(numel(model.rxns),1);
+0104 end
+0105 if ~isfield(model,'rxnConfidenceScores')
+0106     model.rxnConfidenceScores=NaN(numel(model.rxns),1);
+0107 end
+0108 if ~isfield(model,'rxnNotes')
+0109     model.rxnNotes=cell(numel(model.rxns),1);
+0110 end
+0111 if ~isfield(model,'rxnMiriams')
+0112     model.rxnMiriams=cell(numel(model.rxns),1);
+0113 end
+0114 
+0115 if sbmlLevel<3
+0116     %Check if genes have associated compartments
+0117     if ~isfield(model,'geneComps') && isfield(model,'genes')
+0118         if supressWarnings==false
+0119             EM='There are no compartments specified for genes. All genes will be assigned to the first compartment. This is because the SBML structure requires all elements to be assigned to a compartment';
+0120             dispEM(EM,false);
+0121         end
+0122         model.geneComps=ones(numel(model.genes),1);
+0123     end
+0124 end
+0125 
+0126 %Convert ids to SBML-convenient format. This is to avoid the data loss when
+0127 %unsupported characters are included in ids. Here we are using part from
+0128 %convertSBMLID, originating from the COBRA Toolbox
+0129 model.rxns=regexprep(model.rxns,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0130 model.mets=regexprep(model.mets,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0131 model.comps=regexprep(model.comps,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0132 if isfield(model,'genes')
+0133     problemGenes=find(~cellfun('isempty',regexp(model.genes,'([^0-9_a-zA-Z])')));
+0134     originalGenes=model.genes(problemGenes);
+0135     replacedGenes=regexprep(model.genes(problemGenes),'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0136     model.genes(problemGenes)=replacedGenes;
+0137     for i=1:numel(problemGenes)
+0138         model.grRules = regexprep(model.grRules, ['(^|\s|\()' originalGenes{i} '($|\s|\))'], ['$1' replacedGenes{i} '$2']);
+0139     end
+0140 end
+0141 
+0142 %Generate an empty SBML structure
+0143 modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0144 modelSBML.metaid=model.id;
+0145 modelSBML.id=model.id;
+0146 modelSBML.name=model.name;
 0147 
-0148 modelSBML.annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.id '">'];
-0149 if isfield(model,'annotation')
-0150     nameString='';
-0151     if isfield(model.annotation,'familyName')
-0152         if ~isempty(model.annotation.familyName)
-0153             nameString=['<vCard:Family>' model.annotation.familyName '</vCard:Family>'];
-0154         end
-0155     end
-0156     if isfield(model.annotation,'givenName')
-0157         if ~isempty(model.annotation.givenName)
-0158             nameString=[nameString '<vCard:Given>' model.annotation.givenName '</vCard:Given>'];
-0159         end
-0160     end
-0161     email='';
-0162     if isfield(model.annotation,'email')
-0163         if ~isempty(model.annotation.email)
-0164             email=['<vCard:EMAIL>' model.annotation.email '</vCard:EMAIL>'];
-0165         end
-0166     end
-0167     org='';
-0168     if isfield(model.annotation,'organization')
-0169         if ~isempty(model.annotation.organization)
-0170             org=['<vCard:ORG rdf:parseType="Resource"><vCard:Orgname>' model.annotation.organization '</vCard:Orgname></vCard:ORG>'];
-0171         end
-0172     end
-0173     if ~isempty(nameString) || ~isempty(email) || ~isempty(org)
-0174         modelSBML.annotation=[modelSBML.annotation '<dc:creator><rdf:Bag><rdf:li rdf:parseType="Resource">'];
-0175         if ~isempty(nameString)
-0176             modelSBML.annotation=[modelSBML.annotation '<vCard:N rdf:parseType="Resource">' nameString '</vCard:N>'];
-0177         end
-0178         modelSBML.annotation=[modelSBML.annotation email org '</rdf:li></rdf:Bag></dc:creator>'];
-0179     end
-0180 end
-0181 modelSBML.annotation=[modelSBML.annotation '<dcterms:created rdf:parseType="Resource">'...
-0182     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
-0183     '</dcterms:created>'...
-0184     '<dcterms:modified rdf:parseType="Resource">'...
-0185     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
-0186     '</dcterms:modified>'];
-0187 
-0188 if isfield(model,'annotation')
-0189     if isfield(model.annotation,'taxonomy')
-0190         modelSBML.annotation=[modelSBML.annotation '<bqbiol:is><rdf:Bag><rdf:li rdf:resource="https://identifiers.org/taxonomy/' regexprep(model.annotation.taxonomy,'taxonomy/','') '"/></rdf:Bag></bqbiol:is>'];
-0191     end
-0192 end
-0193 modelSBML.annotation=[modelSBML.annotation '</rdf:Description></rdf:RDF></annotation>'];
-0194 
-0195 %Prepare compartments
-0196 for i=1:numel(model.comps)
-0197     %Add the default values, as these will be the same in all entries
-0198     if i==1
-0199         if isfield(modelSBML.compartment, 'sboTerm')
-0200             modelSBML.compartment(i).sboTerm=290;
-0201         end
-0202         if isfield(modelSBML.compartment, 'spatialDimensions')
-0203             modelSBML.compartment(i).spatialDimensions=3;
-0204         end
-0205         if isfield(modelSBML.compartment, 'size')
-0206             modelSBML.compartment(i).size=1;
-0207         end
-0208         if isfield(modelSBML.compartment, 'constant')
-0209             modelSBML.compartment(i).constant=1;
-0210         end
-0211         if isfield(modelSBML.compartment, 'isSetSize')
-0212             modelSBML.compartment(i).isSetSize=1;
-0213         end
-0214         if isfield(modelSBML.compartment, 'isSetSpatialDimensions')
-0215             modelSBML.compartment(i).isSetSpatialDimensions=1;
-0216         end
-0217     end
-0218     %Copy the default values to the next entry as long as it is not the
-0219     %last one
-0220     if i<numel(model.comps)
-0221         modelSBML.compartment(i+1)=modelSBML.compartment(i);
-0222     end
-0223     
-0224     if isfield(modelSBML.compartment,'metaid')
-0225         if regexp(model.comps{i},'^[^a-zA-Z_]')
-0226             EM='The compartment IDs are in numeric format. For the compliance with SBML specifications, compartment IDs will be preceded with "c_" string';
-0227             dispEM(EM,false);
-0228             model.comps(i)=strcat('c_',model.comps(i));
-0229         end
-0230         modelSBML.compartment(i).metaid=model.comps{i};
-0231     end
-0232     %Prepare Miriam strings
-0233     if ~isempty(model.compMiriams{i})
-0234         [~,sbo_ind] = ismember('sbo',model.compMiriams{i}.name);
-0235         if sbo_ind > 0
-0236             modelSBML.compartment(i).sboTerm=str2double(regexprep(model.compMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0237             % remove the SBO term from compMiriams so the information is
-0238             % not duplicated in the "annotation" field later on
-0239             model.compMiriams{i}.name(sbo_ind) = [];
-0240             model.compMiriams{i}.value(sbo_ind) = [];
-0241         end
-0242     end
-0243     if ~isempty(model.compMiriams{i}) && isfield(modelSBML.compartment(i),'annotation')
-0244         modelSBML.compartment(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.comps{i} '">'];
-0245         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation '<bqbiol:is><rdf:Bag>'];
-0246         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation getMiriam(model.compMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0247     end
-0248     if isfield(modelSBML.compartment, 'name')
-0249         modelSBML.compartment(i).name=model.compNames{i};
+0148 if isfield(model,'annotation')
+0149     if isfield(model.annotation,'note')
+0150         modelSBML.notes=['<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>',regexprep(model.annotation.note,'<p>|</p>',''),'</p></body></notes>'];
+0151     end
+0152 else
+0153     modelSBML.notes='<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>This file was generated using the exportModel function in RAVEN Toolbox 2 and OutputSBML in libSBML </p></body></notes>';
+0154 end
+0155 
+0156 modelSBML.annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.id '">'];
+0157 if isfield(model,'annotation')
+0158     nameString='';
+0159     if isfield(model.annotation,'familyName')
+0160         if ~isempty(model.annotation.familyName)
+0161             nameString=['<vCard:Family>' model.annotation.familyName '</vCard:Family>'];
+0162         end
+0163     end
+0164     if isfield(model.annotation,'givenName')
+0165         if ~isempty(model.annotation.givenName)
+0166             nameString=[nameString '<vCard:Given>' model.annotation.givenName '</vCard:Given>'];
+0167         end
+0168     end
+0169     email='';
+0170     if isfield(model.annotation,'email')
+0171         if ~isempty(model.annotation.email)
+0172             email=['<vCard:EMAIL>' model.annotation.email '</vCard:EMAIL>'];
+0173         end
+0174     end
+0175     org='';
+0176     if isfield(model.annotation,'organization')
+0177         if ~isempty(model.annotation.organization)
+0178             org=['<vCard:ORG rdf:parseType="Resource"><vCard:Orgname>' model.annotation.organization '</vCard:Orgname></vCard:ORG>'];
+0179         end
+0180     end
+0181     if ~isempty(nameString) || ~isempty(email) || ~isempty(org)
+0182         modelSBML.annotation=[modelSBML.annotation '<dc:creator><rdf:Bag><rdf:li rdf:parseType="Resource">'];
+0183         if ~isempty(nameString)
+0184             modelSBML.annotation=[modelSBML.annotation '<vCard:N rdf:parseType="Resource">' nameString '</vCard:N>'];
+0185         end
+0186         modelSBML.annotation=[modelSBML.annotation email org '</rdf:li></rdf:Bag></dc:creator>'];
+0187     end
+0188 end
+0189 modelSBML.annotation=[modelSBML.annotation '<dcterms:created rdf:parseType="Resource">'...
+0190     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
+0191     '</dcterms:created>'...
+0192     '<dcterms:modified rdf:parseType="Resource">'...
+0193     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
+0194     '</dcterms:modified>'];
+0195 
+0196 if isfield(model,'annotation')
+0197     if isfield(model.annotation,'taxonomy')
+0198         modelSBML.annotation=[modelSBML.annotation '<bqbiol:is><rdf:Bag><rdf:li rdf:resource="https://identifiers.org/taxonomy/' regexprep(model.annotation.taxonomy,'taxonomy/','') '"/></rdf:Bag></bqbiol:is>'];
+0199     end
+0200 end
+0201 modelSBML.annotation=[modelSBML.annotation '</rdf:Description></rdf:RDF></annotation>'];
+0202 
+0203 %Prepare compartments
+0204 for i=1:numel(model.comps)
+0205     %Add the default values, as these will be the same in all entries
+0206     if i==1
+0207         if isfield(modelSBML.compartment, 'sboTerm')
+0208             modelSBML.compartment(i).sboTerm=290;
+0209         end
+0210         if isfield(modelSBML.compartment, 'spatialDimensions')
+0211             modelSBML.compartment(i).spatialDimensions=3;
+0212         end
+0213         if isfield(modelSBML.compartment, 'size')
+0214             modelSBML.compartment(i).size=1;
+0215         end
+0216         if isfield(modelSBML.compartment, 'constant')
+0217             modelSBML.compartment(i).constant=1;
+0218         end
+0219         if isfield(modelSBML.compartment, 'isSetSize')
+0220             modelSBML.compartment(i).isSetSize=1;
+0221         end
+0222         if isfield(modelSBML.compartment, 'isSetSpatialDimensions')
+0223             modelSBML.compartment(i).isSetSpatialDimensions=1;
+0224         end
+0225     end
+0226     %Copy the default values to the next entry as long as it is not the
+0227     %last one
+0228     if i<numel(model.comps)
+0229         modelSBML.compartment(i+1)=modelSBML.compartment(i);
+0230     end
+0231     
+0232     if isfield(modelSBML.compartment,'metaid')
+0233         if regexp(model.comps(i),'^[^a-zA-Z_]')
+0234             EM='The compartment IDs are in numeric format. For the compliance with SBML specifications, compartment IDs will be preceded with "c_" string';
+0235             dispEM(EM,false);
+0236             model.comps(i)=strcat('c_',model.comps(i));
+0237         end
+0238         modelSBML.compartment(i).metaid=model.comps{i};
+0239     end
+0240     %Prepare Miriam strings
+0241     if ~isempty(model.compMiriams{i})
+0242         [~,sbo_ind] = ismember('sbo',model.compMiriams{i}.name);
+0243         if sbo_ind > 0
+0244             modelSBML.compartment(i).sboTerm=str2double(regexprep(model.compMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0245             % remove the SBO term from compMiriams so the information is
+0246             % not duplicated in the "annotation" field later on
+0247             model.compMiriams{i}.name(sbo_ind) = [];
+0248             model.compMiriams{i}.value(sbo_ind) = [];
+0249         end
 0250     end
-0251     if isfield(modelSBML.compartment, 'id')
-0252         modelSBML.compartment(i).id=model.comps{i};
-0253     end
-0254     
-0255 end
-0256 
-0257 %Begin writing species
-0258 for i=1:numel(model.mets)
-0259     %Add the default values, as these will be the same in all entries
-0260     if i==1
-0261         if isfield(modelSBML.species, 'sboTerm')
-0262             modelSBML.species(i).sboTerm=247;
-0263         end
-0264         if isfield(modelSBML.species, 'initialAmount')
-0265             modelSBML.species(i).initialAmount=1;
-0266         end
-0267         if isfield(modelSBML.species, 'initialConcentration')
-0268             modelSBML.species(i).initialConcentration=0;
-0269         end
-0270         if isfield(modelSBML.species, 'isSetInitialAmount')
-0271             modelSBML.species(i).isSetInitialAmount=1;
-0272         end
-0273         if isfield(modelSBML.species, 'isSetInitialConcentration')
-0274             modelSBML.species(i).isSetInitialConcentration=1;
-0275         end
-0276     end
-0277     %Copy the default values to the next entry as long as it is not the
-0278     %last one
-0279     if i<numel(model.mets)
-0280         modelSBML.species(i+1)=modelSBML.species(i);
-0281     end
-0282     
-0283     if isfield(modelSBML.species,'metaid')
-0284         modelSBML.species(i).metaid=['M_' model.mets{i}];
-0285     end
-0286     if isfield(modelSBML.species, 'name')
-0287         modelSBML.species(i).name=model.metNames{i};
-0288     end
-0289     if isfield(modelSBML.species, 'id')
-0290         modelSBML.species(i).id=['M_' model.mets{i}];
-0291     end
-0292     if isfield(modelSBML.species, 'compartment')
-0293         modelSBML.species(i).compartment=model.comps{model.metComps(i)};
-0294     end
-0295     if isfield(model,'unconstrained')
-0296         if model.unconstrained(i)
-0297             modelSBML.species(i).boundaryCondition=1;
-0298         end
+0251     if ~isempty(model.compMiriams{i}) && isfield(modelSBML.compartment(i),'annotation')
+0252         modelSBML.compartment(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.comps{i} '">'];
+0253         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation '<bqbiol:is><rdf:Bag>'];
+0254         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation getMiriam(model.compMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0255     end
+0256     if isfield(modelSBML.compartment, 'name')
+0257         modelSBML.compartment(i).name=model.compNames{i};
+0258     end
+0259     if isfield(modelSBML.compartment, 'id')
+0260         modelSBML.compartment(i).id=model.comps{i};
+0261     end
+0262     
+0263 end
+0264 
+0265 %Begin writing species
+0266 for i=1:numel(model.mets)
+0267     %Add the default values, as these will be the same in all entries
+0268     if i==1
+0269         if isfield(modelSBML.species, 'sboTerm')
+0270             modelSBML.species(i).sboTerm=247;
+0271         end
+0272         if isfield(modelSBML.species, 'initialAmount')
+0273             modelSBML.species(i).initialAmount=1;
+0274         end
+0275         if isfield(modelSBML.species, 'initialConcentration')
+0276             modelSBML.species(i).initialConcentration=0;
+0277         end
+0278         if isfield(modelSBML.species, 'isSetInitialAmount')
+0279             modelSBML.species(i).isSetInitialAmount=1;
+0280         end
+0281         if isfield(modelSBML.species, 'isSetInitialConcentration')
+0282             modelSBML.species(i).isSetInitialConcentration=1;
+0283         end
+0284     end
+0285     %Copy the default values to the next entry as long as it is not the
+0286     %last one
+0287     if i<numel(model.mets)
+0288         modelSBML.species(i+1)=modelSBML.species(i);
+0289     end
+0290     
+0291     if isfield(modelSBML.species,'metaid')
+0292         modelSBML.species(i).metaid=['M_' model.mets{i}];
+0293     end
+0294     if isfield(modelSBML.species, 'name')
+0295         modelSBML.species(i).name=model.metNames{i};
+0296     end
+0297     if isfield(modelSBML.species, 'id')
+0298         modelSBML.species(i).id=['M_' model.mets{i}];
 0299     end
-0300     if isfield(modelSBML.species, 'fbc_charge') && isfield(model,'metCharges')
-0301         if ~isnan(model.metCharges(i))
-0302             modelSBML.species(i).fbc_charge=model.metCharges(i);
-0303             modelSBML.species(i).isSetfbc_charge=1;
-0304         else
-0305             modelSBML.species(i).isSetfbc_charge=0;
+0300     if isfield(modelSBML.species, 'compartment')
+0301         modelSBML.species(i).compartment=model.comps{model.metComps(i)};
+0302     end
+0303     if isfield(model,'unconstrained')
+0304         if model.unconstrained(i)
+0305             modelSBML.species(i).boundaryCondition=1;
 0306         end
 0307     end
-0308     if ~isempty(model.metMiriams{i})
-0309         [~,sbo_ind] = ismember('sbo',model.metMiriams{i}.name);
-0310         if sbo_ind > 0
-0311             modelSBML.species(i).sboTerm=str2double(regexprep(model.metMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0312             % remove the SBO term from metMiriams so the information is
-0313             % not duplicated in the "annotation" field later on
-0314             model.metMiriams{i}.name(sbo_ind) = [];
-0315             model.metMiriams{i}.value(sbo_ind) = [];
-0316         end
-0317     end
-0318     if isfield(modelSBML.species,'annotation')
-0319         if ~isempty(model.metMiriams{i}) || ~isempty(model.metFormulas{i})
-0320             hasInchi=false;
-0321             if ~isempty(model.metFormulas{i})
-0322                 %Only export formula if there is no InChI. This is because
-0323                 %the metFormulas field is populated by InChIs if available
-0324                 if ~isempty(model.inchis{i})
-0325                     hasInchi=true;
-0326                 end
-0327                 if hasInchi==false
-0328                     modelSBML.species(i).fbc_chemicalFormula=model.metFormulas{i};
-0329                 end
-0330             end
-0331             if ~isempty(model.metMiriams{i}) || hasInchi==true
-0332                 modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_M_' model.mets{i} '">'];
-0333                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<bqbiol:is><rdf:Bag>'];
-0334                 if ~isempty(model.metMiriams{i})
-0335                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation getMiriam(model.metMiriams{i})];
-0336                 end
-0337                 if hasInchi==true
-0338                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<rdf:li rdf:resource="https://identifiers.org/inchi/InChI=' regexprep(model.inchis{i},'^InChI=','') '"/>'];
-0339                     modelSBML.species(i).fbc_chemicalFormula=char(regexp(model.inchis{i}, '/(\w+)/', 'tokens', 'once'));
-0340                 end
-0341                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0342             end
-0343         end
-0344     end
-0345 end
-0346 
-0347 if isfield(model,'genes')
-0348     for i=1:numel(model.genes)
-0349         %Add the default values, as these will be the same in all entries
-0350         if i==1
-0351             if isfield(modelSBML.fbc_geneProduct, 'sboTerm')
-0352                 modelSBML.fbc_geneProduct(i).sboTerm=243;
-0353             end
-0354         end
-0355         %Copy the default values to the next index as long as it is not the
-0356         %last one
-0357         if i<numel(model.genes)
-0358             modelSBML.fbc_geneProduct(i+1)=modelSBML.fbc_geneProduct(i);
-0359         end
-0360         
-0361         if isfield(modelSBML.fbc_geneProduct,'metaid')
-0362             modelSBML.fbc_geneProduct(i).metaid=model.genes{i};
-0363         end
-0364         if ~isempty(model.geneMiriams{i})
-0365             [~,sbo_ind] = ismember('sbo',model.geneMiriams{i}.name);
-0366             if sbo_ind > 0
-0367                 modelSBML.fbc_geneProduct(i).sboTerm=str2double(regexprep(model.geneMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0368                 % remove the SBO term from compMiriams so the information is
-0369                 % not duplicated in the "annotation" field later on
-0370                 model.geneMiriams{i}.name(sbo_ind) = [];
-0371                 model.geneMiriams{i}.value(sbo_ind) = [];
-0372             end
-0373         end
-0374         if ~isempty(model.geneMiriams{i}) && isfield(modelSBML.fbc_geneProduct(i),'annotation')
-0375             modelSBML.fbc_geneProduct(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.genes{i} '">'];
-0376             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation '<bqbiol:is><rdf:Bag>'];
-0377             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation getMiriam(model.geneMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0378         end
-0379         if isfield(modelSBML.fbc_geneProduct, 'fbc_id')
-0380             modelSBML.fbc_geneProduct(i).fbc_id=model.genes{i};
+0308     if isfield(modelSBML.species, 'fbc_charge') && isfield(model,'metCharges')
+0309         if ~isnan(model.metCharges(i))
+0310             modelSBML.species(i).fbc_charge=model.metCharges(i);
+0311             modelSBML.species(i).isSetfbc_charge=1;
+0312         else
+0313             modelSBML.species(i).isSetfbc_charge=0;
+0314         end
+0315     end
+0316     if ~isempty(model.metMiriams{i})
+0317         [~,sbo_ind] = ismember('sbo',model.metMiriams{i}.name);
+0318         if sbo_ind > 0
+0319             modelSBML.species(i).sboTerm=str2double(regexprep(model.metMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0320             % remove the SBO term from metMiriams so the information is
+0321             % not duplicated in the "annotation" field later on
+0322             model.metMiriams{i}.name(sbo_ind) = [];
+0323             model.metMiriams{i}.value(sbo_ind) = [];
+0324         end
+0325     end
+0326     if isfield(modelSBML.species,'annotation')
+0327         if ~isempty(model.metMiriams{i}) || ~isempty(model.metFormulas{i})
+0328             hasInchi=false;
+0329             if ~isempty(model.metFormulas{i})
+0330                 %Only export formula if there is no InChI. This is because
+0331                 %the metFormulas field is populated by InChIs if available
+0332                 if ~isempty(model.inchis{i})
+0333                     hasInchi=true;
+0334                 end
+0335                 if hasInchi==false
+0336                     modelSBML.species(i).fbc_chemicalFormula=model.metFormulas{i};
+0337                 end
+0338             end
+0339             if ~isempty(model.metMiriams{i}) || hasInchi==true
+0340                 modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_M_' model.mets{i} '">'];
+0341                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<bqbiol:is><rdf:Bag>'];
+0342                 if ~isempty(model.metMiriams{i})
+0343                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation getMiriam(model.metMiriams{i})];
+0344                 end
+0345                 if hasInchi==true
+0346                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<rdf:li rdf:resource="https://identifiers.org/inchi/InChI=' regexprep(model.inchis{i},'^InChI=','') '"/>'];
+0347                     modelSBML.species(i).fbc_chemicalFormula=char(regexp(model.inchis{i}, '/(\w+)/', 'tokens', 'once'));
+0348                 end
+0349                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0350             end
+0351         end
+0352     end
+0353 end
+0354 
+0355 if isfield(model,'genes')
+0356     for i=1:numel(model.genes)
+0357         %Add the default values, as these will be the same in all entries
+0358         if i==1
+0359             if isfield(modelSBML.fbc_geneProduct, 'sboTerm')
+0360                 modelSBML.fbc_geneProduct(i).sboTerm=243;
+0361             end
+0362         end
+0363         %Copy the default values to the next index as long as it is not the
+0364         %last one
+0365         if i<numel(model.genes)
+0366             modelSBML.fbc_geneProduct(i+1)=modelSBML.fbc_geneProduct(i);
+0367         end
+0368         
+0369         if isfield(modelSBML.fbc_geneProduct,'metaid')
+0370             modelSBML.fbc_geneProduct(i).metaid=model.genes{i};
+0371         end
+0372         if ~isempty(model.geneMiriams{i})
+0373             [~,sbo_ind] = ismember('sbo',model.geneMiriams{i}.name);
+0374             if sbo_ind > 0
+0375                 modelSBML.fbc_geneProduct(i).sboTerm=str2double(regexprep(model.geneMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0376                 % remove the SBO term from compMiriams so the information is
+0377                 % not duplicated in the "annotation" field later on
+0378                 model.geneMiriams{i}.name(sbo_ind) = [];
+0379                 model.geneMiriams{i}.value(sbo_ind) = [];
+0380             end
 0381         end
-0382         if isfield(modelSBML.fbc_geneProduct, 'fbc_label') && isfield(model,'geneShortNames')
-0383             if isempty(model.geneShortNames{i})
-0384                 modelSBML.fbc_geneProduct(i).fbc_label=model.genes{i};
-0385             else
-0386                 modelSBML.fbc_geneProduct(i).fbc_label=model.geneShortNames{i};
-0387             end
-0388         end
-0389     end
-0390     if exportGeneComplexes==true
-0391         %Also add the complexes as genes. This is done by splitting grRules
-0392         %on "or" and adding the ones which contain several genes
-0393         geneComplexes={};
-0394         if isfield(model,'grRules')
-0395             %Only grRules which contain " and " can be complexes
-0396             uniqueRules=unique(model.grRules);
-0397             I=cellfun(@any,strfind(uniqueRules,' and '));
-0398             uniqueRules(~I)=[];
-0399             uniqueRules=strrep(uniqueRules,'(','');
-0400             uniqueRules=strrep(uniqueRules,')','');
-0401             uniqueRules=strrep(uniqueRules,' and ',':');
-0402             for i=1:numel(uniqueRules)
-0403                 genes=regexp(uniqueRules(i),' or ','split');
-0404                 genes=genes{1}(:);
-0405                 %Check which ones are complexes
-0406                 I=cellfun(@any,strfind(genes,':'));
-0407                 geneComplexes=[geneComplexes;genes(I)];
-0408             end
-0409         end
-0410         geneComplexes=unique(geneComplexes);
-0411         if ~isempty(geneComplexes)
-0412             %Then add them as genes. There is a possiblity that a complex
-0413             %A&B is added as separate from B&A. This is not really an issue
-0414             %so this is not dealt with
-0415             for i=1:numel(geneComplexes)
-0416                 modelSBML.fbc_geneProduct(numel(model.genes)+i)=modelSBML.fbc_geneProduct(1);
-0417                 if isfield(modelSBML.fbc_geneProduct,'metaid')
-0418                     modelSBML.fbc_geneProduct(numel(model.genes)+i).metaid=geneComplexes{i};
-0419                 end
-0420                 if isfield(modelSBML.fbc_geneProduct,'fbc_id')
-0421                     modelSBML.fbc_geneProduct(numel(model.genes)+i).fbc_id=geneComplexes{i};
-0422                 else
-0423                     modelSBML.fbc_geneProduct(i).fbc_label=modelSBML.fbc_geneProduct(i).fbc_id;
-0424                 end
-0425             end
-0426         end
-0427     end
-0428 end
-0429 
-0430 %Generate a list of unique fbc_bound names
-0431 totalValues=[model.lb; model.ub];
-0432 totalNames=cell(size(totalValues,1),1);
-0433 
-0434 listUniqueValues=unique(totalValues);
-0435 
-0436 for i=1:length(listUniqueValues)
-0437     listUniqueNames{i,1}=['FB',num2str(i),'N',num2str(abs(round(listUniqueValues(i))))]; % create unique flux bound IDs.
-0438     ind=find(ismember(totalValues,listUniqueValues(i)));
-0439     totalNames(ind)=listUniqueNames(i,1);
-0440 end
+0382         if ~isempty(model.geneMiriams{i}) && isfield(modelSBML.fbc_geneProduct(i),'annotation')
+0383             modelSBML.fbc_geneProduct(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.genes{i} '">'];
+0384             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation '<bqbiol:is><rdf:Bag>'];
+0385             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation getMiriam(model.geneMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0386         end
+0387         if isfield(modelSBML.fbc_geneProduct, 'fbc_id')
+0388             modelSBML.fbc_geneProduct(i).fbc_id=model.genes{i};
+0389         end
+0390         if isfield(modelSBML.fbc_geneProduct, 'fbc_label') && isfield(model,'geneShortNames')
+0391             if isempty(model.geneShortNames{i})
+0392                 modelSBML.fbc_geneProduct(i).fbc_label=model.genes{i};
+0393             else
+0394                 modelSBML.fbc_geneProduct(i).fbc_label=model.geneShortNames{i};
+0395             end
+0396         end
+0397     end
+0398     if exportGeneComplexes==true
+0399         %Also add the complexes as genes. This is done by splitting grRules
+0400         %on "or" and adding the ones which contain several genes
+0401         geneComplexes={};
+0402         if isfield(model,'grRules')
+0403             %Only grRules which contain " and " can be complexes
+0404             uniqueRules=unique(model.grRules);
+0405             I=cellfun(@any,strfind(uniqueRules,' and '));
+0406             uniqueRules(~I)=[];
+0407             uniqueRules=strrep(uniqueRules,'(','');
+0408             uniqueRules=strrep(uniqueRules,')','');
+0409             uniqueRules=strrep(uniqueRules,' and ',':');
+0410             for i=1:numel(uniqueRules)
+0411                 genes=regexp(uniqueRules(i),' or ','split');
+0412                 genes=genes{1}(:);
+0413                 %Check which ones are complexes
+0414                 I=cellfun(@any,strfind(genes,':'));
+0415                 geneComplexes=[geneComplexes;genes(I)];
+0416             end
+0417         end
+0418         geneComplexes=unique(geneComplexes);
+0419         if ~isempty(geneComplexes)
+0420             %Then add them as genes. There is a possiblity that a complex
+0421             %A&B is added as separate from B&A. This is not really an issue
+0422             %so this is not dealt with
+0423             for i=1:numel(geneComplexes)
+0424                 modelSBML.fbc_geneProduct(numel(model.genes)+i)=modelSBML.fbc_geneProduct(1);
+0425                 if isfield(modelSBML.fbc_geneProduct,'metaid')
+0426                     modelSBML.fbc_geneProduct(numel(model.genes)+i).metaid=geneComplexes{i};
+0427                 end
+0428                 if isfield(modelSBML.fbc_geneProduct,'fbc_id')
+0429                     modelSBML.fbc_geneProduct(numel(model.genes)+i).fbc_id=geneComplexes{i};
+0430                 else
+0431                     modelSBML.fbc_geneProduct(i).fbc_label=modelSBML.fbc_geneProduct(i).fbc_id;
+0432                 end
+0433             end
+0434         end
+0435     end
+0436 end
+0437 
+0438 %Generate a list of unique fbc_bound names
+0439 totalValues=[model.lb; model.ub];
+0440 totalNames=cell(size(totalValues,1),1);
 0441 
-0442 for i=1:length(listUniqueNames)
-0443     %Add the default values, as these will be the same in all entries
-0444     if i==1
-0445         if isfield(modelSBML.parameter, 'constant')
-0446             modelSBML.parameter(i).constant=1;
-0447         end
-0448         if isfield(modelSBML.parameter, 'isSetValue')
-0449             modelSBML.parameter(i).isSetValue=1;
-0450         end
-0451     end
-0452     %Copy the default values to the next index as long as it is not the
-0453     %last one
-0454     if i<numel(listUniqueNames)
-0455         modelSBML.parameter(i+1)=modelSBML.parameter(i);
-0456     end
-0457     modelSBML.parameter(i).id=listUniqueNames{i};
-0458     modelSBML.parameter(i).value=listUniqueValues(i);
-0459 end
-0460 
-0461 for i=1:numel(model.rxns)
-0462     %Add the default values, as these will be the same in all entries
-0463     if i==1
-0464         if isfield(modelSBML.reaction, 'sboTerm')
-0465             modelSBML.reaction(i).sboTerm=176;
-0466         end
-0467         if isfield(modelSBML.reaction, 'isSetFast')
-0468             modelSBML.reaction(i).isSetFast=1;
-0469         end
-0470     end
-0471     %Copy the default values to the next index as long as it is not the
-0472     %last one
-0473     if i<numel(model.rxns)
-0474         modelSBML.reaction(i+1)=modelSBML.reaction(i);
-0475     end
-0476     
-0477     if isfield(modelSBML.reaction,'metaid')
-0478         modelSBML.reaction(i).metaid=['R_' model.rxns{i}];
-0479     end
-0480     
-0481     %Export notes information
-0482     if (~isnan(model.rxnConfidenceScores(i)) || ~isempty(model.rxnReferences{i}) || ~isempty(model.rxnNotes{i}))
-0483         modelSBML.reaction(i).notes='<notes><body xmlns="http://www.w3.org/1999/xhtml">';
-0484         if ~isnan(model.rxnConfidenceScores(i))
-0485             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>Confidence Level: ' num2str(model.rxnConfidenceScores(i)) '</p>'];
-0486         end
-0487         if ~isempty(model.rxnReferences{i})
-0488             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>AUTHORS: ' model.rxnReferences{i} '</p>'];
-0489         end
-0490         if ~isempty(model.rxnNotes{i})
-0491             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>NOTES: ' model.rxnNotes{i} '</p>'];
-0492         end
-0493         modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '</body></notes>'];
-0494     end
-0495     
-0496     % Export SBO terms from rxnMiriams
-0497     if ~isempty(model.rxnMiriams{i})
-0498         [~,sbo_ind] = ismember('sbo',model.rxnMiriams{i}.name);
-0499         if sbo_ind > 0
-0500             modelSBML.reaction(i).sboTerm=str2double(regexprep(model.rxnMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0501             % remove the SBO term from rxnMiriams so the information is not
-0502             % duplicated in the "annotation" field later on
-0503             model.rxnMiriams{i}.name(sbo_ind) = [];
-0504             model.rxnMiriams{i}.value(sbo_ind) = [];
-0505         end
-0506     end
-0507     
-0508     %Export annotation information from rxnMiriams
-0509     if (~isempty(model.rxnMiriams{i}) && isfield(modelSBML.reaction(i),'annotation')) || ~isempty(model.eccodes{i})
-0510         modelSBML.reaction(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_R_' model.rxns{i} '">'];
-0511         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation '<bqbiol:is><rdf:Bag>'];
-0512         if ~isempty(model.eccodes{i})
-0513             eccodes=regexp(model.eccodes{i},';','split');
-0514             for j=1:numel(eccodes)
-0515                 modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation  '<rdf:li rdf:resource="https://identifiers.org/ec-code/' regexprep(eccodes{j},'ec-code/|EC','') '"/>'];
-0516             end
-0517         end
-0518         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation getMiriam(model.rxnMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0519     end
-0520     
-0521     if isfield(modelSBML.reaction, 'name')
-0522         modelSBML.reaction(i).name=model.rxnNames{i};
-0523     end
-0524     if isfield(modelSBML.reaction, 'id')
-0525         modelSBML.reaction(i).id=['R_' model.rxns{i}];
-0526     end
-0527     
-0528     %Add the information about reactants and products
-0529     involvedMets=addReactantsProducts(model,modelSBML,i);
-0530     for j=1:numel(involvedMets.reactant)
-0531         if j<numel(involvedMets.reactant)
-0532             modelSBML.reaction(i).reactant(j+1)=modelSBML.reaction(i).reactant(j);
-0533         end
-0534         modelSBML.reaction(i).reactant(j).species=involvedMets.reactant(j).species;
-0535         modelSBML.reaction(i).reactant(j).stoichiometry=involvedMets.reactant(j).stoichiometry;
-0536         modelSBML.reaction(i).reactant(j).isSetStoichiometry=involvedMets.reactant(j).isSetStoichiometry;
-0537         modelSBML.reaction(i).reactant(j).constant=involvedMets.reactant(j).constant;
-0538     end
-0539     if numel(involvedMets.reactant)==0
-0540         modelSBML.reaction(i).reactant='';
-0541     end
-0542     for j=1:numel(involvedMets.product)
-0543         if j<numel(involvedMets.product)
-0544             modelSBML.reaction(i).product(j+1)=modelSBML.reaction(i).product(j);
-0545         end
-0546         modelSBML.reaction(i).product(j).species=involvedMets.product(j).species;
-0547         modelSBML.reaction(i).product(j).stoichiometry=involvedMets.product(j).stoichiometry;
-0548         modelSBML.reaction(i).product(j).isSetStoichiometry=involvedMets.product(j).isSetStoichiometry;
-0549         modelSBML.reaction(i).product(j).constant=involvedMets.product(j).constant;
-0550     end
-0551     if numel(involvedMets.product)==0
-0552         modelSBML.reaction(i).product='';
-0553     end
-0554     %Export reversibility information. Reactions are irreversible by
-0555     %default
-0556     if model.rev(i)==1
-0557         modelSBML.reaction(i).reversible=1;
+0442 listUniqueValues=unique(totalValues);
+0443 
+0444 for i=1:length(listUniqueValues)
+0445     listUniqueNames{i,1}=['FB',num2str(i),'N',num2str(abs(round(listUniqueValues(i))))]; % create unique flux bound IDs.
+0446     ind=find(ismember(totalValues,listUniqueValues(i)));
+0447     totalNames(ind)=listUniqueNames(i,1);
+0448 end
+0449 
+0450 for i=1:length(listUniqueNames)
+0451     %Add the default values, as these will be the same in all entries
+0452     if i==1
+0453         if isfield(modelSBML.parameter, 'constant')
+0454             modelSBML.parameter(i).constant=1;
+0455         end
+0456         if isfield(modelSBML.parameter, 'isSetValue')
+0457             modelSBML.parameter(i).isSetValue=1;
+0458         end
+0459     end
+0460     %Copy the default values to the next index as long as it is not the
+0461     %last one
+0462     if i<numel(listUniqueNames)
+0463         modelSBML.parameter(i+1)=modelSBML.parameter(i);
+0464     end
+0465     modelSBML.parameter(i).id=listUniqueNames{i};
+0466     modelSBML.parameter(i).value=listUniqueValues(i);
+0467 end
+0468 
+0469 for i=1:numel(model.rxns)
+0470     %Add the default values, as these will be the same in all entries
+0471     if i==1
+0472         if isfield(modelSBML.reaction, 'sboTerm')
+0473             modelSBML.reaction(i).sboTerm=176;
+0474         end
+0475         if isfield(modelSBML.reaction, 'isSetFast')
+0476             modelSBML.reaction(i).isSetFast=1;
+0477         end
+0478     end
+0479     %Copy the default values to the next index as long as it is not the
+0480     %last one
+0481     if i<numel(model.rxns)
+0482         modelSBML.reaction(i+1)=modelSBML.reaction(i);
+0483     end
+0484     
+0485     if isfield(modelSBML.reaction,'metaid')
+0486         modelSBML.reaction(i).metaid=['R_' model.rxns{i}];
+0487     end
+0488     
+0489     %Export notes information
+0490     if (~isnan(model.rxnConfidenceScores(i)) || ~isempty(model.rxnReferences{i}) || ~isempty(model.rxnNotes{i}))
+0491         modelSBML.reaction(i).notes='<notes><body xmlns="http://www.w3.org/1999/xhtml">';
+0492         if ~isnan(model.rxnConfidenceScores(i))
+0493             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>Confidence Level: ' num2str(model.rxnConfidenceScores(i)) '</p>'];
+0494         end
+0495         if ~isempty(model.rxnReferences{i})
+0496             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>AUTHORS: ' model.rxnReferences{i} '</p>'];
+0497         end
+0498         if ~isempty(model.rxnNotes{i})
+0499             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>NOTES: ' model.rxnNotes{i} '</p>'];
+0500         end
+0501         modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '</body></notes>'];
+0502     end
+0503     
+0504     % Export SBO terms from rxnMiriams
+0505     if ~isempty(model.rxnMiriams{i})
+0506         [~,sbo_ind] = ismember('sbo',model.rxnMiriams{i}.name);
+0507         if sbo_ind > 0
+0508             modelSBML.reaction(i).sboTerm=str2double(regexprep(model.rxnMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0509             % remove the SBO term from rxnMiriams so the information is not
+0510             % duplicated in the "annotation" field later on
+0511             model.rxnMiriams{i}.name(sbo_ind) = [];
+0512             model.rxnMiriams{i}.value(sbo_ind) = [];
+0513         end
+0514     end
+0515     
+0516     %Export annotation information from rxnMiriams
+0517     if (~isempty(model.rxnMiriams{i}) && isfield(modelSBML.reaction(i),'annotation')) || ~isempty(model.eccodes{i})
+0518         modelSBML.reaction(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_R_' model.rxns{i} '">'];
+0519         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation '<bqbiol:is><rdf:Bag>'];
+0520         if ~isempty(model.eccodes{i})
+0521             eccodes=regexp(model.eccodes{i},';','split');
+0522             for j=1:numel(eccodes)
+0523                 modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation  '<rdf:li rdf:resource="https://identifiers.org/ec-code/' regexprep(eccodes{j},'ec-code/|EC','') '"/>'];
+0524             end
+0525         end
+0526         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation getMiriam(model.rxnMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0527     end
+0528     
+0529     if isfield(modelSBML.reaction, 'name')
+0530         modelSBML.reaction(i).name=model.rxnNames{i};
+0531     end
+0532     if isfield(modelSBML.reaction, 'id')
+0533         modelSBML.reaction(i).id=['R_' model.rxns{i}];
+0534     end
+0535     
+0536     %Add the information about reactants and products
+0537     involvedMets=addReactantsProducts(model,modelSBML,i);
+0538     for j=1:numel(involvedMets.reactant)
+0539         if j<numel(involvedMets.reactant)
+0540             modelSBML.reaction(i).reactant(j+1)=modelSBML.reaction(i).reactant(j);
+0541         end
+0542         modelSBML.reaction(i).reactant(j).species=involvedMets.reactant(j).species;
+0543         modelSBML.reaction(i).reactant(j).stoichiometry=involvedMets.reactant(j).stoichiometry;
+0544         modelSBML.reaction(i).reactant(j).isSetStoichiometry=involvedMets.reactant(j).isSetStoichiometry;
+0545         modelSBML.reaction(i).reactant(j).constant=involvedMets.reactant(j).constant;
+0546     end
+0547     if numel(involvedMets.reactant)==0
+0548         modelSBML.reaction(i).reactant='';
+0549     end
+0550     for j=1:numel(involvedMets.product)
+0551         if j<numel(involvedMets.product)
+0552             modelSBML.reaction(i).product(j+1)=modelSBML.reaction(i).product(j);
+0553         end
+0554         modelSBML.reaction(i).product(j).species=involvedMets.product(j).species;
+0555         modelSBML.reaction(i).product(j).stoichiometry=involvedMets.product(j).stoichiometry;
+0556         modelSBML.reaction(i).product(j).isSetStoichiometry=involvedMets.product(j).isSetStoichiometry;
+0557         modelSBML.reaction(i).product(j).constant=involvedMets.product(j).constant;
 0558     end
-0559     if isfield(model, 'rxnComps')
-0560         modelSBML.reaction(i).compartment=model.comps{model.rxnComps(i)};
+0559     if numel(involvedMets.product)==0
+0560         modelSBML.reaction(i).product='';
 0561     end
-0562     if isfield(model, 'grRules')
-0563         modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association=model.grRules{i};
-0564     end
-0565     modelSBML.reaction(i).fbc_lowerFluxBound=totalNames{i};
-0566     modelSBML.reaction(i).fbc_upperFluxBound=totalNames{length(model.lb)+i};
-0567 end
-0568 
-0569 %Prepare subSystems Code taken from COBRA functions getModelSubSystems,
-0570 %writeSBML, findRxnsFromSubSystem under GNU General Public License v3.0,
-0571 %license file in readme/GPL.MD. Code modified for RAVEN
-0572 if modelHasSubsystems
-0573     modelSBML.groups_group.groups_kind = 'partonomy';
-0574     modelSBML.groups_group.sboTerm = 633;
-0575     tmpStruct=modelSBML.groups_group;
+0562     %Export reversibility information. Reactions are irreversible by
+0563     %default
+0564     if model.rev(i)==1
+0565         modelSBML.reaction(i).reversible=1;
+0566     end
+0567     if isfield(model, 'rxnComps')
+0568         modelSBML.reaction(i).compartment=model.comps{model.rxnComps(i)};
+0569     end
+0570     if isfield(model, 'grRules')
+0571         modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association=model.grRules{i};
+0572     end
+0573     modelSBML.reaction(i).fbc_lowerFluxBound=totalNames{i};
+0574     modelSBML.reaction(i).fbc_upperFluxBound=totalNames{length(model.lb)+i};
+0575 end
 0576 
-0577     rxns=strcat('R_',model.rxns);
-0578     if ~any(cellfun(@iscell,model.subSystems))
-0579         if ~any(~cellfun(@isempty,model.subSystems))
-0580             subSystems = {};
-0581         else
-0582             subSystems = setdiff(model.subSystems,'');
-0583         end
-0584     else
-0585         orderedSubs = cellfun(@(x) columnVector(x),model.subSystems,'UniformOUtput',false);
-0586         subSystems = setdiff(vertcat(orderedSubs{:}),'');
-0587     end
-0588     if isempty(subSystems)
-0589         subSystems = {};
-0590     end
-0591     if ~isempty(subSystems)
-0592         %Build the groups for the group package
-0593         groupIDs = strcat('group',cellfun(@num2str, num2cell(1:length(subSystems)),'UniformOutput',false));
-0594         for i = 1:length(subSystems)
-0595             cgroup = tmpStruct;
-0596             if ~any(cellfun(@iscell,model.subSystems))
-0597                 present = ismember(model.subSystems,subSystems{i});
-0598             else
-0599                 present = cellfun(@(x) any(ismember(x,subSystems{i})),model.subSystems);
-0600             end
-0601             groupMembers = rxns(present);
-0602             for j = 1:numel(groupMembers)
-0603                 cMember = tmpStruct.groups_member;
-0604                 cMember.groups_idRef = groupMembers{j};
-0605                 if j == 1
-0606                     cgroup.groups_member = cMember;
-0607                 else
-0608                     cgroup.groups_member(j) = cMember;
-0609                 end
-0610             end
-0611             cgroup.groups_id = groupIDs{i};
-0612             cgroup.groups_name = subSystems{i};
-0613             if i == 1
-0614                 modelSBML.groups_group = cgroup;
-0615             else
-0616                 modelSBML.groups_group(i) = cgroup;
-0617             end
-0618         end
-0619     end
-0620 end
-0621 
-0622 %Prepare fbc_objective subfield
-0623 
-0624 modelSBML.fbc_objective.fbc_type='maximize';
-0625 modelSBML.fbc_objective.fbc_id='obj';
-0626 
-0627 ind=find(model.c);
-0628 
-0629 if isempty(ind)
-0630     modelSBML.fbc_objective.fbc_fluxObjective.fbc_coefficient=0;
-0631     EM='The objective function is not defined. The model will be exported as it is. Notice that having undefined objective function may produce warnings related to "fbc:coefficient" and "fbc:reaction" in SBML Validator';
-0632     dispEM(EM,false);
-0633 else
-0634     for i=1:length(ind)
-0635         %Copy the default values to the next index as long as it is not the
-0636         %last one
-0637         if i<numel(ind)
-0638             modelSBML.reaction(i+1)=modelSBML.reaction(i);
-0639         end
-0640         values=model.c(model.c~=0);
-0641         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction=modelSBML.reaction(ind(i)).id;
-0642         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient=values(i);
-0643         modelSBML.fbc_objective(i).fbc_fluxObjective.isSetfbc_coefficient=1;
-0644     end
-0645 end
-0646 
-0647 modelSBML.fbc_activeObjective=modelSBML.fbc_objective.fbc_id;
-0648 
-0649 fbcStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/fbc/version',num2str(sbmlPackageVersions(1))];
-0650 if modelHasSubsystems
-0651     groupStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/groups/version',num2str(sbmlPackageVersions(2))];
-0652     modelSBML.namespaces=struct('prefix',{'','fbc','groups'},...
-0653     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
-0654     fbcStr,groupStr});
-0655 else
-0656     modelSBML.namespaces=struct('prefix',{'','fbc'},...
-0657     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
-0658     fbcStr});
-0659 end
-0660 
-0661 if sbmlPackageVersions(1) == 2
-0662     modelSBML.fbc_strict=1;
-0663 end
-0664 
-0665 modelSBML.rule=[];
-0666 modelSBML.constraint=[];
-0667 
-0668 OutputSBML(modelSBML,fileName,1,0,[1,0]);
-0669 end
-0670 
-0671 
-0672 function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
-0673 %Returns the blank SBML model structure by using appropriate libSBML
-0674 %functions. This creates structure by considering three levels
+0577 %Prepare subSystems Code taken from COBRA functions getModelSubSystems,
+0578 %writeSBML, findRxnsFromSubSystem under GNU General Public License v3.0,
+0579 %license file in readme/GPL.MD. Code modified for RAVEN
+0580 if modelHasSubsystems
+0581     modelSBML.groups_group.groups_kind = 'partonomy';
+0582     modelSBML.groups_group.sboTerm = 633;
+0583     tmpStruct=modelSBML.groups_group;
+0584 
+0585     rxns=strcat('R_',model.rxns);
+0586     if ~any(cellfun(@iscell,model.subSystems))
+0587         if ~any(~cellfun(@isempty,model.subSystems))
+0588             subSystems = {};
+0589         else
+0590             subSystems = setdiff(model.subSystems,'');
+0591         end
+0592     else
+0593         orderedSubs = cellfun(@(x) columnVector(x),model.subSystems,'UniformOUtput',false);
+0594         subSystems = setdiff(vertcat(orderedSubs{:}),'');
+0595     end
+0596     if isempty(subSystems)
+0597         subSystems = {};
+0598     end
+0599     if ~isempty(subSystems)
+0600         %Build the groups for the group package
+0601         groupIDs = strcat('group',cellfun(@num2str, num2cell(1:length(subSystems)),'UniformOutput',false));
+0602         for i = 1:length(subSystems)
+0603             cgroup = tmpStruct;
+0604             if ~any(cellfun(@iscell,model.subSystems))
+0605                 present = ismember(model.subSystems,subSystems{i});
+0606             else
+0607                 present = cellfun(@(x) any(ismember(x,subSystems{i})),model.subSystems);
+0608             end
+0609             groupMembers = rxns(present);
+0610             for j = 1:numel(groupMembers)
+0611                 cMember = tmpStruct.groups_member;
+0612                 cMember.groups_idRef = groupMembers{j};
+0613                 if j == 1
+0614                     cgroup.groups_member = cMember;
+0615                 else
+0616                     cgroup.groups_member(j) = cMember;
+0617                 end
+0618             end
+0619             cgroup.groups_id = groupIDs{i};
+0620             cgroup.groups_name = subSystems{i};
+0621             if i == 1
+0622                 modelSBML.groups_group = cgroup;
+0623             else
+0624                 modelSBML.groups_group(i) = cgroup;
+0625             end
+0626         end
+0627     end
+0628 end
+0629 
+0630 %Prepare fbc_objective subfield
+0631 
+0632 modelSBML.fbc_objective.fbc_type='maximize';
+0633 modelSBML.fbc_objective.fbc_id='obj';
+0634 
+0635 ind=find(model.c);
+0636 
+0637 if isempty(ind)
+0638     modelSBML.fbc_objective.fbc_fluxObjective.fbc_coefficient=0;
+0639     EM='The objective function is not defined. The model will be exported as it is. Notice that having undefined objective function may produce warnings related to "fbc:coefficient" and "fbc:reaction" in SBML Validator';
+0640     dispEM(EM,false);
+0641 else
+0642     for i=1:length(ind)
+0643         %Copy the default values to the next index as long as it is not the
+0644         %last one
+0645         if i<numel(ind)
+0646             modelSBML.reaction(i+1)=modelSBML.reaction(i);
+0647         end
+0648         values=model.c(model.c~=0);
+0649         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction=modelSBML.reaction(ind(i)).id;
+0650         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient=values(i);
+0651         modelSBML.fbc_objective(i).fbc_fluxObjective.isSetfbc_coefficient=1;
+0652     end
+0653 end
+0654 
+0655 modelSBML.fbc_activeObjective=modelSBML.fbc_objective.fbc_id;
+0656 
+0657 fbcStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/fbc/version',num2str(sbmlPackageVersions(1))];
+0658 if modelHasSubsystems
+0659     groupStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/groups/version',num2str(sbmlPackageVersions(2))];
+0660     modelSBML.namespaces=struct('prefix',{'','fbc','groups'},...
+0661     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
+0662     fbcStr,groupStr});
+0663 else
+0664     modelSBML.namespaces=struct('prefix',{'','fbc'},...
+0665     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
+0666     fbcStr});
+0667 end
+0668 
+0669 if sbmlPackageVersions(1) == 2
+0670     modelSBML.fbc_strict=1;
+0671 end
+0672 
+0673 modelSBML.rule=[];
+0674 modelSBML.constraint=[];
 0675 
-0676 sbmlFieldNames=getStructureFieldnames('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0677 sbmlDefaultValues=getDefaultValues('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0676 OutputSBML(modelSBML,fileName,1,0,[1,0]);
+0677 end
 0678 
-0679 for i=1:numel(sbmlFieldNames)
-0680     modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
-0681     sbmlSubfieldNames=getStructureFieldnames(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0682     sbmlSubfieldValues=getDefaultValues(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0683     if ~strcmp(sbmlFieldNames{1,i},'event') && ~strcmp(sbmlFieldNames{1,i},'functionDefinition') && ~strcmp(sbmlFieldNames{1,i},'initialAssignment')
-0684         for j=1:numel(sbmlSubfieldNames)
-0685             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j})=sbmlSubfieldValues{1,j};
-0686             sbmlSubsubfieldNames=getStructureFieldnames(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0687             sbmlSubsubfieldValues=getDefaultValues(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0688             if ~strcmp(sbmlSubfieldNames{1,j},'modifier') && ~strcmp(sbmlSubfieldNames{1,j},'kineticLaw')
-0689                 for k=1:numel(sbmlSubsubfieldNames)
-0690                     %'compartment' and 'species' fields are not supposed to
-0691                     %have their standalone structures if they are subfields
-0692                     %or subsubfields
-0693                     if ~strcmp(sbmlSubfieldNames{1,j},'compartment') && ~strcmp(sbmlSubfieldNames{1,j},'species')
-0694                         modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k})=sbmlSubsubfieldValues{1,k};
-0695                     end
-0696                     %If it is fbc_association in the third level, we need
-0697                     %to establish the fourth level, since libSBML requires
-0698                     %it
-0699                     if strcmp(sbmlSubsubfieldNames{1,k},'fbc_association')
-0700                         fbc_associationFieldNames=getStructureFieldnames('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0701                         fbc_associationFieldValues=getDefaultValues('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0702                         for l=1:numel(fbc_associationFieldNames)
-0703                             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k}).(fbc_associationFieldNames{1,l})=fbc_associationFieldValues{1,l};
-0704                         end
-0705                     end
-0706                 end
-0707             end
-0708         end
-0709     end
-0710     if ~isstruct(modelSBML.(sbmlFieldNames{1,i}))
-0711         modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
-0712     end
-0713 end
-0714 
-0715 modelSBML.unitDefinition.id='mmol_per_gDW_per_hr';
-0716 
-0717 unitFieldNames=getStructureFieldnames('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0718 unitDefaultValues=getDefaultValues('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0719 
-0720 kinds={'mole','gram','second'};
-0721 exponents=[1 -1 -1];
-0722 scales=[-3 0 0];
-0723 multipliers=[1 1 1*60*60];
+0679 
+0680 function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
+0681 %Returns the blank SBML model structure by using appropriate libSBML
+0682 %functions. This creates structure by considering three levels
+0683 
+0684 sbmlFieldNames=getStructureFieldnames('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0685 sbmlDefaultValues=getDefaultValues('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0686 
+0687 for i=1:numel(sbmlFieldNames)
+0688     modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
+0689     sbmlSubfieldNames=getStructureFieldnames(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0690     sbmlSubfieldValues=getDefaultValues(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0691     if ~strcmp(sbmlFieldNames{1,i},'event') && ~strcmp(sbmlFieldNames{1,i},'functionDefinition') && ~strcmp(sbmlFieldNames{1,i},'initialAssignment')
+0692         for j=1:numel(sbmlSubfieldNames)
+0693             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j})=sbmlSubfieldValues{1,j};
+0694             sbmlSubsubfieldNames=getStructureFieldnames(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0695             sbmlSubsubfieldValues=getDefaultValues(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0696             if ~strcmp(sbmlSubfieldNames{1,j},'modifier') && ~strcmp(sbmlSubfieldNames{1,j},'kineticLaw')
+0697                 for k=1:numel(sbmlSubsubfieldNames)
+0698                     %'compartment' and 'species' fields are not supposed to
+0699                     %have their standalone structures if they are subfields
+0700                     %or subsubfields
+0701                     if ~strcmp(sbmlSubfieldNames{1,j},'compartment') && ~strcmp(sbmlSubfieldNames{1,j},'species')
+0702                         modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k})=sbmlSubsubfieldValues{1,k};
+0703                     end
+0704                     %If it is fbc_association in the third level, we need
+0705                     %to establish the fourth level, since libSBML requires
+0706                     %it
+0707                     if strcmp(sbmlSubsubfieldNames{1,k},'fbc_association')
+0708                         fbc_associationFieldNames=getStructureFieldnames('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0709                         fbc_associationFieldValues=getDefaultValues('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0710                         for l=1:numel(fbc_associationFieldNames)
+0711                             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k}).(fbc_associationFieldNames{1,l})=fbc_associationFieldValues{1,l};
+0712                         end
+0713                     end
+0714                 end
+0715             end
+0716         end
+0717     end
+0718     if ~isstruct(modelSBML.(sbmlFieldNames{1,i}))
+0719         modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
+0720     end
+0721 end
+0722 
+0723 modelSBML.unitDefinition.id='mmol_per_gDW_per_hr';
 0724 
-0725 for i=1:numel(unitFieldNames)
-0726     modelSBML.unitDefinition.unit(1).(unitFieldNames{1,i})=unitDefaultValues{1,i};
-0727     for j=1:3
-0728         modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=unitDefaultValues{1,i};
-0729         if strcmp(unitFieldNames{1,i},'kind')
-0730             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=kinds{j};
-0731         elseif strcmp(unitFieldNames{1,i},'exponent')
-0732             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=exponents(j);
-0733         elseif strcmp(unitFieldNames{1,i},'scale')
-0734             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=scales(j);
-0735         elseif strcmp(unitFieldNames{1,i},'multiplier')
-0736             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=multipliers(j);
-0737         end
-0738     end
-0739 end
-0740 end
-0741 
-0742 function miriamString=getMiriam(miriamStruct)
-0743 %Returns a string with list elements for a miriam structure ('<rdf:li
-0744 %rdf:resource="https://identifiers.org/go/GO:0005739"/>' for example). This
-0745 %is just to speed up things since this is done many times during the
-0746 %exporting
-0747 
-0748 miriamString='';
-0749 if isfield(miriamStruct,'name')
-0750     for i=1:numel(miriamStruct.name)
-0751         miriamString=[miriamString '<rdf:li rdf:resource="https://identifiers.org/' miriamStruct.name{i} '/' miriamStruct.value{i} '"/>'];
-0752     end
-0753 end
-0754 end
+0725 unitFieldNames=getStructureFieldnames('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0726 unitDefaultValues=getDefaultValues('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0727 
+0728 kinds={'mole','gram','second'};
+0729 exponents=[1 -1 -1];
+0730 scales=[-3 0 0];
+0731 multipliers=[1 1 1*60*60];
+0732 
+0733 for i=1:numel(unitFieldNames)
+0734     modelSBML.unitDefinition.unit(1).(unitFieldNames{1,i})=unitDefaultValues{1,i};
+0735     for j=1:3
+0736         modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=unitDefaultValues{1,i};
+0737         if strcmp(unitFieldNames{1,i},'kind')
+0738             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=kinds{j};
+0739         elseif strcmp(unitFieldNames{1,i},'exponent')
+0740             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=exponents(j);
+0741         elseif strcmp(unitFieldNames{1,i},'scale')
+0742             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=scales(j);
+0743         elseif strcmp(unitFieldNames{1,i},'multiplier')
+0744             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=multipliers(j);
+0745         end
+0746     end
+0747 end
+0748 end
+0749 
+0750 function miriamString=getMiriam(miriamStruct)
+0751 %Returns a string with list elements for a miriam structure ('<rdf:li
+0752 %rdf:resource="https://identifiers.org/go/GO:0005739"/>' for example). This
+0753 %is just to speed up things since this is done many times during the
+0754 %exporting
 0755 
-0756 function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
-0757 %This function provides reactants and products for particular reaction. The
-0758 %function was 'borrowed' from writeSBML in COBRA toolbox, lines 663-679
-0759 
-0760 met_idx = find(model.S(:, i));
-0761 tmp_Rxn.product=[];
-0762 tmp_Rxn.reactant=[];
-0763 for j_met=1:size(met_idx,1)
-0764     tmp_idx = met_idx(j_met,1);
-0765     sbml_tmp_species_ref.species = sbmlModel.species(tmp_idx).id;
-0766     met_stoich = model.S(tmp_idx, i);
-0767     sbml_tmp_species_ref.stoichiometry = abs(met_stoich);
-0768     sbml_tmp_species_ref.isSetStoichiometry=1;
-0769     sbml_tmp_species_ref.constant=1;
-0770     if (met_stoich > 0)
-0771         tmp_Rxn.product = [ tmp_Rxn.product, sbml_tmp_species_ref ];
-0772     else
-0773         tmp_Rxn.reactant = [ tmp_Rxn.reactant, sbml_tmp_species_ref];
-0774     end
-0775 end
-0776 end
-0777 
-0778 function vecT = columnVector(vec)
-0779 % Code below taken from COBRA Toolbox under GNU General Public License v3.0
-0780 % license file in readme/GPL.MD.
-0781 %
-0782 % Converts a vector to a column vector
-0783 %
-0784 % USAGE:
-0785 %
-0786 %   vecT = columnVector(vec)
-0787 %
-0788 % INPUT:
-0789 %   vec:     a vector
-0790 %
-0791 % OUTPUT:
-0792 %   vecT:    a column vector
-0793 
-0794 [n, m] = size(vec);
-0795 
-0796 if n < m
-0797     vecT = vec';
-0798 else
-0799     vecT = vec;
-0800 end
-0801 end
    
+0756 miriamString='';
+0757 if isfield(miriamStruct,'name')
+0758     for i=1:numel(miriamStruct.name)
+0759         miriamString=[miriamString '<rdf:li rdf:resource="https://identifiers.org/' miriamStruct.name{i} '/' miriamStruct.value{i} '"/>'];
+0760     end
+0761 end
+0762 end
+0763 
+0764 function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
+0765 %This function provides reactants and products for particular reaction. The
+0766 %function was 'borrowed' from writeSBML in COBRA toolbox, lines 663-679
+0767 
+0768 met_idx = find(model.S(:, i));
+0769 tmp_Rxn.product=[];
+0770 tmp_Rxn.reactant=[];
+0771 for j_met=1:size(met_idx,1)
+0772     tmp_idx = met_idx(j_met,1);
+0773     sbml_tmp_species_ref.species = sbmlModel.species(tmp_idx).id;
+0774     met_stoich = model.S(tmp_idx, i);
+0775     sbml_tmp_species_ref.stoichiometry = abs(met_stoich);
+0776     sbml_tmp_species_ref.isSetStoichiometry=1;
+0777     sbml_tmp_species_ref.constant=1;
+0778     if (met_stoich > 0)
+0779         tmp_Rxn.product = [ tmp_Rxn.product, sbml_tmp_species_ref ];
+0780     else
+0781         tmp_Rxn.reactant = [ tmp_Rxn.reactant, sbml_tmp_species_ref];
+0782     end
+0783 end
+0784 end
+0785 
+0786 function vecT = columnVector(vec)
+0787 % Code below taken from COBRA Toolbox under GNU General Public License v3.0
+0788 % license file in readme/GPL.MD.
+0789 %
+0790 % Converts a vector to a column vector
+0791 %
+0792 % USAGE:
+0793 %
+0794 %   vecT = columnVector(vec)
+0795 %
+0796 % INPUT:
+0797 %   vec:     a vector
+0798 %
+0799 % OUTPUT:
+0800 %   vecT:    a column vector
+0801 
+0802 [n, m] = size(vec);
+0803 
+0804 if n < m
+0805     vecT = vec';
+0806 else
+0807     vecT = vec;
+0808 end
+0809 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/exportToExcelFormat.html b/doc/io/exportToExcelFormat.html
index df284072..be859c81 100644
--- a/doc/io/exportToExcelFormat.html
+++ b/doc/io/exportToExcelFormat.html
@@ -24,7 +24,7 @@ 
    PURPOSE ^exportToExcelFormat

    SYNOPSIS ^

    -
    function exportToExcelFormat(model,filename)
    +
    function exportToExcelFormat(model,filename,sortIds)

    DESCRIPTION ^

     exportToExcelFormat
@@ -36,6 +36,9 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • exportToTabDelimited	exportToTabDelimited
  • loadWorkbook	loadWorkbook
  • sortIdentifiers	exportModel
  • writeSheet	writeSheet
    • 
 This function is called by:
 
@@ -58,7 +61,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 
 
 <h2><a name=SOURCE CODE ^
    
-
    0001 function exportToExcelFormat(model,filename)
+
    0001 function exportToExcelFormat(model,filename,sortIds)
 0002 % exportToExcelFormat
 0003 %   Exports a model structure to the Microsoft Excel model format
 0004 %
@@ -68,369 +71,378 @@ 
    SOURCE CODE ^%               be only a path, in which case the model is exported to a set
 0009 %               of tab-delimited text files instead. See exportToTabDelimited
 0010 %               for details regarding that functionality
-0011 %
-0012 %   The resulting Excel file can be used with importExcelModel/SBMLFromExcel
-0013 %   for modelling or to generate a SBML file.
+0011 %   sortIds     logical whether metabolites, reactions and genes should be
+0012 %               sorted alphabetically by their identifiers (opt, default
+0013 %               false)
 0014 %
-0015 %   NOTE: No checks are made regarding the correctness of the model. Use
-0016 %         checkModelStruct to identify problems in the model structure
+0015 %   The resulting Excel file can be used with importExcelModel/SBMLFromExcel
+0016 %   for modelling or to generate a SBML file.
 0017 %
-0018 %   Usage: exportToExcelFormat(model,filename)
-0019 
-0020 [~, A, B]=fileparts(filename);
-0021 
-0022 %If a path was used call on exportToTabDelimited instead
-0023 if ~any(A) || ~any(B)
-0024     exportToTabDelimited(model,filename);
-0025     return;
-0026 end
-0027 
-0028 if ~strcmpi(B,'.xlsx')
-0029     EM='As of RAVEN version 1.9, only export to xlsx format is supported';
-0030     dispEM(EM);
-0031 end
-0032 
-0033 import java.io.File;
-0034 import java.io.FileOutputStream;
-0035 import java.io.IOException;
+0018 %   NOTE: No checks are made regarding the correctness of the model. Use
+0019 %         checkModelStruct to identify problems in the model structure
+0020 %
+0021 %   Usage: exportToExcelFormat(model,filename,sortIds)
+0022 if nargin<3
+0023     sortIds=false;
+0024 end
+0025 if sortIds==true
+0026     model=sortIdentifiers(model);
+0027 end
+0028 
+0029 [~, A, B]=fileparts(filename);
+0030 
+0031 %If a path was used call on exportToTabDelimited instead
+0032 if ~any(A) || ~any(B)
+0033     exportToTabDelimited(model,filename);
+0034     return;
+0035 end
 0036 
-0037 %Remove the output file if it already exists
-0038 if exist(filename,'file')
-0039     delete(filename);
+0037 if ~strcmpi(B,'.xlsx')
+0038     EM='As of RAVEN version 1.9, only export to xlsx format is supported';
+0039     dispEM(EM);
 0040 end
 0041 
-0042 %Load an empty workbook
-0043 wb=loadWorkbook(filename,true);
-0044 
-0045 %Construct equations
-0046 model.equations=constructEquations(model,model.rxns,true);
-0047 
-0048 %Check if it should print genes
-0049 if isfield(model,'grRules')
-0050     rules=model.grRules;
-0051 else
-0052     rules=[];
-0053 end
-0054 
-0055 %Check if the model has default upper/lower bounds. This determines if
-0056 %those values should be printed or not
-0057 hasDefaultLB=false;
-0058 hasDefaultUB=false;
-0059 if isfield(model,'annotation')
-0060     if isfield(model.annotation,'defaultLB')
-0061         hasDefaultLB=true;
-0062     end
-0063     if isfield(model.annotation,'defaultUB')
-0064         hasDefaultUB=true;
-0065     end
-0066 end
-0067 
-0068 %Add the RXNS sheet
-0069 
-0070 %Create the header row
-0071 headers={'#';'ID';'NAME';'EQUATION';'EC-NUMBER';'GENE ASSOCIATION';'LOWER BOUND';'UPPER BOUND';'OBJECTIVE';'COMPARTMENT';'MIRIAM';'SUBSYSTEM';'REPLACEMENT ID';'NOTE';'REFERENCE';'CONFIDENCE SCORE'};
-0072 
-0073 %Add empty comments
-0074 emptyColumn=cell(numel(model.rxns),1);
-0075 rxnSheet=emptyColumn;
+0042 import java.io.File;
+0043 import java.io.FileOutputStream;
+0044 import java.io.IOException;
+0045 
+0046 %Remove the output file if it already exists
+0047 if exist(filename,'file')
+0048     delete(filename);
+0049 end
+0050 
+0051 %Load an empty workbook
+0052 wb=loadWorkbook(filename,true);
+0053 
+0054 %Construct equations
+0055 model.equations=constructEquations(model,model.rxns,true);
+0056 
+0057 %Check if it should print genes
+0058 if isfield(model,'grRules')
+0059     rules=model.grRules;
+0060 else
+0061     rules=[];
+0062 end
+0063 
+0064 %Check if the model has default upper/lower bounds. This determines if
+0065 %those values should be printed or not
+0066 hasDefaultLB=false;
+0067 hasDefaultUB=false;
+0068 if isfield(model,'annotation')
+0069     if isfield(model.annotation,'defaultLB')
+0070         hasDefaultLB=true;
+0071     end
+0072     if isfield(model.annotation,'defaultUB')
+0073         hasDefaultUB=true;
+0074     end
+0075 end
 0076 
-0077 %Add the model fields
-0078 rxnSheet=[rxnSheet model.rxns];
-0079 
-0080 if isfield(model,'rxnNames')
-0081     rxnSheet=[rxnSheet model.rxnNames];
-0082 else
-0083     rxnSheet=[rxnSheet emptyColumn];
-0084 end
+0077 %Add the RXNS sheet
+0078 
+0079 %Create the header row
+0080 headers={'#';'ID';'NAME';'EQUATION';'EC-NUMBER';'GENE ASSOCIATION';'LOWER BOUND';'UPPER BOUND';'OBJECTIVE';'COMPARTMENT';'MIRIAM';'SUBSYSTEM';'REPLACEMENT ID';'NOTE';'REFERENCE';'CONFIDENCE SCORE'};
+0081 
+0082 %Add empty comments
+0083 emptyColumn=cell(numel(model.rxns),1);
+0084 rxnSheet=emptyColumn;
 0085 
-0086 rxnSheet=[rxnSheet model.equations];
-0087 
-0088 if isfield(model,'eccodes')
-0089     rxnSheet=[rxnSheet model.eccodes];
-0090 else
-0091     rxnSheet=[rxnSheet emptyColumn];
-0092 end
-0093 
-0094 if ~isempty(rules)
-0095     rxnSheet=[rxnSheet rules];
-0096 else
-0097     rxnSheet=[rxnSheet emptyColumn];
-0098 end
-0099 
-0100 lb=emptyColumn;
-0101 ub=emptyColumn;
-0102 objective=emptyColumn;
-0103 rxnMiriams=emptyColumn;
-0104 
-0105 for i=1:numel(model.rxns)
-0106     if isfield(model,'lb')
-0107         if hasDefaultLB==true
-0108             if model.rev(i)==1
-0109                 %If reversible, print only if different than defaultLB
-0110                 if model.lb(i) ~= model.annotation.defaultLB
-0111                     lb{i}=model.lb(i);
-0112                 end
-0113             else
-0114                 %If irreversible, print only for non-zero values
-0115                 if model.lb(i)~=0
-0116                     lb{i}=model.lb(i);
-0117                 end
-0118             end
-0119         else
-0120             lb{i}=model.lb(i);
-0121         end
-0122     end
-0123     
-0124     if isfield(model,'ub')
-0125         if hasDefaultUB==true
-0126             if model.ub(i) ~= model.annotation.defaultUB
-0127                 ub{i}=model.ub(i);
-0128             end
-0129         else
-0130             ub{i}=model.ub(i);
-0131         end
-0132     end
-0133     
-0134     if isfield(model,'c')
-0135         if model.c(i)~=0
-0136             objective{i}=model.c(i);
-0137         end
-0138     end
-0139     
-0140     if isfield(model,'rxnMiriams')
-0141         if ~isempty(model.rxnMiriams{i})
-0142             toPrint=[];
-0143             for j=1:numel(model.rxnMiriams{i}.name)
-0144                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
-0145             end
-0146             rxnMiriams{i}=toPrint(1:end-1);
-0147         end
-0148     end
-0149 end
-0150 
-0151 rxnSheet=[rxnSheet lb];
-0152 rxnSheet=[rxnSheet ub];
-0153 rxnSheet=[rxnSheet objective];
-0154 
-0155 if isfield(model,'rxnComps')
-0156     rxnSheet=[rxnSheet model.comps(model.rxnComps)];
-0157 else
-0158     rxnSheet=[rxnSheet emptyColumn];
-0159 end
-0160 
-0161 rxnSheet=[rxnSheet rxnMiriams];
-0162 
-0163 subsystems='';
-0164 if isfield(model,'subSystems')
-0165     for i=1:numel(model.subSystems)
-0166         if ~isempty(model.subSystems{i,1})
-0167             subsystems{i,1}=strjoin(model.subSystems{i,1},';');
-0168         else
-0169             subsystems{i,1}='';
-0170         end
-0171     end
-0172     rxnSheet=[rxnSheet subsystems];
-0173 else
-0174     rxnSheet=[rxnSheet emptyColumn];
-0175 end
-0176 
-0177 %For REPLACEMENT ID which isn't in the model
-0178 rxnSheet=[rxnSheet emptyColumn];
-0179 
-0180 if isfield(model,'rxnNotes')
-0181     rxnSheet=[rxnSheet model.rxnNotes];
+0086 %Add the model fields
+0087 rxnSheet=[rxnSheet model.rxns];
+0088 
+0089 if isfield(model,'rxnNames')
+0090     rxnSheet=[rxnSheet model.rxnNames];
+0091 else
+0092     rxnSheet=[rxnSheet emptyColumn];
+0093 end
+0094 
+0095 rxnSheet=[rxnSheet model.equations];
+0096 
+0097 if isfield(model,'eccodes')
+0098     rxnSheet=[rxnSheet model.eccodes];
+0099 else
+0100     rxnSheet=[rxnSheet emptyColumn];
+0101 end
+0102 
+0103 if ~isempty(rules)
+0104     rxnSheet=[rxnSheet rules];
+0105 else
+0106     rxnSheet=[rxnSheet emptyColumn];
+0107 end
+0108 
+0109 lb=emptyColumn;
+0110 ub=emptyColumn;
+0111 objective=emptyColumn;
+0112 rxnMiriams=emptyColumn;
+0113 
+0114 for i=1:numel(model.rxns)
+0115     if isfield(model,'lb')
+0116         if hasDefaultLB==true
+0117             if model.rev(i)==1
+0118                 %If reversible, print only if different than defaultLB
+0119                 if model.lb(i) ~= model.annotation.defaultLB
+0120                     lb{i}=model.lb(i);
+0121                 end
+0122             else
+0123                 %If irreversible, print only for non-zero values
+0124                 if model.lb(i)~=0
+0125                     lb{i}=model.lb(i);
+0126                 end
+0127             end
+0128         else
+0129             lb{i}=model.lb(i);
+0130         end
+0131     end
+0132     
+0133     if isfield(model,'ub')
+0134         if hasDefaultUB==true
+0135             if model.ub(i) ~= model.annotation.defaultUB
+0136                 ub{i}=model.ub(i);
+0137             end
+0138         else
+0139             ub{i}=model.ub(i);
+0140         end
+0141     end
+0142     
+0143     if isfield(model,'c')
+0144         if model.c(i)~=0
+0145             objective{i}=model.c(i);
+0146         end
+0147     end
+0148     
+0149     if isfield(model,'rxnMiriams')
+0150         if ~isempty(model.rxnMiriams{i})
+0151             toPrint=[];
+0152             for j=1:numel(model.rxnMiriams{i}.name)
+0153                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
+0154             end
+0155             rxnMiriams{i}=toPrint(1:end-1);
+0156         end
+0157     end
+0158 end
+0159 
+0160 rxnSheet=[rxnSheet lb];
+0161 rxnSheet=[rxnSheet ub];
+0162 rxnSheet=[rxnSheet objective];
+0163 
+0164 if isfield(model,'rxnComps')
+0165     rxnSheet=[rxnSheet model.comps(model.rxnComps)];
+0166 else
+0167     rxnSheet=[rxnSheet emptyColumn];
+0168 end
+0169 
+0170 rxnSheet=[rxnSheet rxnMiriams];
+0171 
+0172 subsystems='';
+0173 if isfield(model,'subSystems')
+0174     for i=1:numel(model.subSystems)
+0175         if ~isempty(model.subSystems{i,1})
+0176             subsystems{i,1}=strjoin(model.subSystems{i,1},';');
+0177         else
+0178             subsystems{i,1}='';
+0179         end
+0180     end
+0181     rxnSheet=[rxnSheet subsystems];
 0182 else
 0183     rxnSheet=[rxnSheet emptyColumn];
 0184 end
 0185 
-0186 if isfield(model,'rxnReferences')
-0187     rxnSheet=[rxnSheet model.rxnReferences];
-0188 else
-0189     rxnSheet=[rxnSheet emptyColumn];
-0190 end
-0191 
-0192 if isfield(model,'rxnConfidenceScores')
-0193     rxnSheet=[rxnSheet num2cell(model.rxnConfidenceScores)];
-0194 else
-0195     rxnSheet=[rxnSheet emptyColumn];
-0196 end
-0197 
-0198 wb=writeSheet(wb,'RXNS',0,headers,[],rxnSheet);
-0199 
-0200 headers={'#';'ID';'NAME';'UNCONSTRAINED';'MIRIAM';'COMPOSITION';'InChI';'COMPARTMENT';'REPLACEMENT ID';'CHARGE'};
-0201 
-0202 metSheet=cell(numel(model.mets),numel(headers));
-0203 
-0204 for i=1:numel(model.mets)
-0205     metSheet{i,2}=[model.metNames{i} '[' model.comps{model.metComps(i)} ']'];
-0206     
-0207     if isfield(model,'metNames')
-0208         metSheet(i,3)=model.metNames(i);
-0209     end
-0210     
-0211     if isfield(model,'unconstrained')
-0212         if model.unconstrained(i)~=0
-0213             metSheet{i,4}=true;
-0214         end
-0215     end
-0216     
-0217     if isfield(model,'metMiriams')
-0218         if ~isempty(model.metMiriams{i})
-0219             toPrint=[];
-0220             for j=1:numel(model.metMiriams{i}.name)
-0221                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
-0222             end
-0223             metSheet{i,5}=toPrint(1:end-1);
-0224         end
-0225     end
-0226     
-0227     % Making sure that only these metFormulas are exported, which don't
-0228     % have InChI strings
-0229     if isfield(model,'metFormulas')
-0230         if isfield(model,'inchis')
-0231             if isempty(model.inchis{i})
-0232                 metSheet(i,6)=model.metFormulas(i);
-0233             end
-0234         else
-0235             metSheet(i,6)=model.metFormulas(i);
-0236         end
-0237     end
-0238     
-0239     if isfield(model,'inchis')
-0240         metSheet(i,7)=model.inchis(i);
-0241     end
-0242     
-0243     if isfield(model,'metComps')
-0244         metSheet(i,8)=model.comps(model.metComps(i));
-0245     end
-0246     
-0247     metSheet(i,9)=model.mets(i);
-0248     
-0249     if isfield(model,'metCharges')
-0250         metSheet{i,10}=model.metCharges(i);
-0251     end
-0252 end
-0253 
-0254 wb=writeSheet(wb,'METS',1,headers,[],metSheet);
-0255 
-0256 %Add the COMPS sheet
-0257 
-0258 %Create the header row
-0259 headers={'#';'ABBREVIATION';'NAME';'INSIDE';'MIRIAM'};
-0260 
-0261 compSheet=cell(numel(model.comps),numel(headers));
+0186 %For REPLACEMENT ID which isn't in the model
+0187 rxnSheet=[rxnSheet emptyColumn];
+0188 
+0189 if isfield(model,'rxnNotes')
+0190     rxnSheet=[rxnSheet model.rxnNotes];
+0191 else
+0192     rxnSheet=[rxnSheet emptyColumn];
+0193 end
+0194 
+0195 if isfield(model,'rxnReferences')
+0196     rxnSheet=[rxnSheet model.rxnReferences];
+0197 else
+0198     rxnSheet=[rxnSheet emptyColumn];
+0199 end
+0200 
+0201 if isfield(model,'rxnConfidenceScores')
+0202     rxnSheet=[rxnSheet num2cell(model.rxnConfidenceScores)];
+0203 else
+0204     rxnSheet=[rxnSheet emptyColumn];
+0205 end
+0206 
+0207 wb=writeSheet(wb,'RXNS',0,headers,[],rxnSheet);
+0208 
+0209 headers={'#';'ID';'NAME';'UNCONSTRAINED';'MIRIAM';'COMPOSITION';'InChI';'COMPARTMENT';'REPLACEMENT ID';'CHARGE'};
+0210 
+0211 metSheet=cell(numel(model.mets),numel(headers));
+0212 
+0213 for i=1:numel(model.mets)
+0214     metSheet{i,2}=[model.metNames{i} '[' model.comps{model.metComps(i)} ']'];
+0215     
+0216     if isfield(model,'metNames')
+0217         metSheet(i,3)=model.metNames(i);
+0218     end
+0219     
+0220     if isfield(model,'unconstrained')
+0221         if model.unconstrained(i)~=0
+0222             metSheet{i,4}=true;
+0223         end
+0224     end
+0225     
+0226     if isfield(model,'metMiriams')
+0227         if ~isempty(model.metMiriams{i})
+0228             toPrint=[];
+0229             for j=1:numel(model.metMiriams{i}.name)
+0230                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
+0231             end
+0232             metSheet{i,5}=toPrint(1:end-1);
+0233         end
+0234     end
+0235     
+0236     % Making sure that only these metFormulas are exported, which don't
+0237     % have InChI strings
+0238     if isfield(model,'metFormulas')
+0239         if isfield(model,'inchis')
+0240             if isempty(model.inchis{i})
+0241                 metSheet(i,6)=model.metFormulas(i);
+0242             end
+0243         else
+0244             metSheet(i,6)=model.metFormulas(i);
+0245         end
+0246     end
+0247     
+0248     if isfield(model,'inchis')
+0249         metSheet(i,7)=model.inchis(i);
+0250     end
+0251     
+0252     if isfield(model,'metComps')
+0253         metSheet(i,8)=model.comps(model.metComps(i));
+0254     end
+0255     
+0256     metSheet(i,9)=model.mets(i);
+0257     
+0258     if isfield(model,'metCharges')
+0259         metSheet{i,10}=model.metCharges(i);
+0260     end
+0261 end
 0262 
-0263 for i=1:numel(model.comps)
-0264     compSheet(i,2)=model.comps(i);
-0265     
-0266     if isfield(model,'compNames')
-0267         compSheet(i,3)=model.compNames(i);
-0268     end
-0269     
-0270     if isfield(model,'compOutside')
-0271         compSheet(i,4)=model.compOutside(i);
-0272     end
-0273     
-0274     if isfield(model,'compMiriams')
-0275         if ~isempty(model.compMiriams{i})
-0276             toPrint=[];
-0277             for j=1:numel(model.compMiriams{i}.name)
-0278                 toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
-0279             end
-0280             compSheet{i,5}=toPrint(1:end-1);
-0281         end
-0282     end
-0283 end
-0284 
-0285 wb=writeSheet(wb,'COMPS',2,headers,[],compSheet);
-0286 
-0287 %Add the GENES sheet
-0288 if isfield(model,'genes')
-0289     %Create the header row
-0290     headers={'#';'NAME';'MIRIAM';'SHORT NAME';'COMPARTMENT'};
-0291     
-0292     geneSheet=cell(numel(model.genes),numel(headers));
-0293     
-0294     for i=1:numel(model.genes)
-0295         geneSheet(i,2)=model.genes(i);
-0296         
-0297         if isfield(model,'geneMiriams')
-0298             if ~isempty(model.geneMiriams{i})
-0299                 toPrint=[];
-0300                 for j=1:numel(model.geneMiriams{i}.name)
-0301                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
-0302                 end
-0303                 geneSheet{i,3}=toPrint(1:end-1);
-0304             end
-0305         end
-0306         if isfield(model,'geneShortNames')
-0307             geneSheet(i,4)=model.geneShortNames(i);
-0308         end
-0309         if isfield(model,'geneComps')
-0310             geneSheet(i,5)=model.comps(model.geneComps(i));
-0311         end
-0312     end
-0313     
-0314     wb=writeSheet(wb,'GENES',3,headers,[],geneSheet);
-0315 end
-0316 
-0317 %Add the MODEL sheet
-0318 
-0319 %Create the header row
-0320 headers={'#';'ID';'NAME';'TAXONOMY';'DEFAULT LOWER';'DEFAULT UPPER';'CONTACT GIVEN NAME';'CONTACT FAMILY NAME';'CONTACT EMAIL';'ORGANIZATION';'NOTES'};
-0321 
-0322 modelSheet=cell(1,numel(headers));
-0323 
-0324 if ~isfield(model,'annotation')
-0325     model.annotation = [];
-0326 end
+0263 wb=writeSheet(wb,'METS',1,headers,[],metSheet);
+0264 
+0265 %Add the COMPS sheet
+0266 
+0267 %Create the header row
+0268 headers={'#';'ABBREVIATION';'NAME';'INSIDE';'MIRIAM'};
+0269 
+0270 compSheet=cell(numel(model.comps),numel(headers));
+0271 
+0272 for i=1:numel(model.comps)
+0273     compSheet(i,2)=model.comps(i);
+0274     
+0275     if isfield(model,'compNames')
+0276         compSheet(i,3)=model.compNames(i);
+0277     end
+0278     
+0279     if isfield(model,'compOutside')
+0280         compSheet(i,4)=model.compOutside(i);
+0281     end
+0282     
+0283     if isfield(model,'compMiriams')
+0284         if ~isempty(model.compMiriams{i})
+0285             toPrint=[];
+0286             for j=1:numel(model.compMiriams{i}.name)
+0287                 toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
+0288             end
+0289             compSheet{i,5}=toPrint(1:end-1);
+0290         end
+0291     end
+0292 end
+0293 
+0294 wb=writeSheet(wb,'COMPS',2,headers,[],compSheet);
+0295 
+0296 %Add the GENES sheet
+0297 if isfield(model,'genes')
+0298     %Create the header row
+0299     headers={'#';'NAME';'MIRIAM';'SHORT NAME';'COMPARTMENT'};
+0300     
+0301     geneSheet=cell(numel(model.genes),numel(headers));
+0302     
+0303     for i=1:numel(model.genes)
+0304         geneSheet(i,2)=model.genes(i);
+0305         
+0306         if isfield(model,'geneMiriams')
+0307             if ~isempty(model.geneMiriams{i})
+0308                 toPrint=[];
+0309                 for j=1:numel(model.geneMiriams{i}.name)
+0310                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
+0311                 end
+0312                 geneSheet{i,3}=toPrint(1:end-1);
+0313             end
+0314         end
+0315         if isfield(model,'geneShortNames')
+0316             geneSheet(i,4)=model.geneShortNames(i);
+0317         end
+0318         if isfield(model,'geneComps')
+0319             geneSheet(i,5)=model.comps(model.geneComps(i));
+0320         end
+0321     end
+0322     
+0323     wb=writeSheet(wb,'GENES',3,headers,[],geneSheet);
+0324 end
+0325 
+0326 %Add the MODEL sheet
 0327 
-0328 if isfield(model,'id')
-0329     modelSheet{1,2}=model.id;
-0330 else
-0331     modelSheet{1,2}='blankID';
-0332 end
-0333 if isfield(model,'name')
-0334     modelSheet{1,3}=model.name;
-0335 else
-0336     modelSheet{1,3}='blankName';
-0337 end
-0338 if isfield(model.annotation,'taxonomy')
-0339     modelSheet{1,4}=model.annotation.taxonomy;
-0340 end
-0341 if isfield(model.annotation,'defaultLB')
-0342     modelSheet{1,5}=model.annotation.defaultLB;
-0343 end
-0344 if isfield(model.annotation,'defaultUB')
-0345     modelSheet{1,6}=model.annotation.defaultUB;
+0328 %Create the header row
+0329 headers={'#';'ID';'NAME';'TAXONOMY';'DEFAULT LOWER';'DEFAULT UPPER';'CONTACT GIVEN NAME';'CONTACT FAMILY NAME';'CONTACT EMAIL';'ORGANIZATION';'NOTES'};
+0330 
+0331 modelSheet=cell(1,numel(headers));
+0332 
+0333 if ~isfield(model,'annotation')
+0334     model.annotation = [];
+0335 end
+0336 
+0337 if isfield(model,'id')
+0338     modelSheet{1,2}=model.id;
+0339 else
+0340     modelSheet{1,2}='blankID';
+0341 end
+0342 if isfield(model,'name')
+0343     modelSheet{1,3}=model.name;
+0344 else
+0345     modelSheet{1,3}='blankName';
 0346 end
-0347 if isfield(model.annotation,'givenName')
-0348     modelSheet{1,7}=model.annotation.givenName;
+0347 if isfield(model.annotation,'taxonomy')
+0348     modelSheet{1,4}=model.annotation.taxonomy;
 0349 end
-0350 if isfield(model.annotation,'familyName')
-0351     modelSheet{1,8}=model.annotation.familyName;
+0350 if isfield(model.annotation,'defaultLB')
+0351     modelSheet{1,5}=model.annotation.defaultLB;
 0352 end
-0353 if isfield(model.annotation,'email')
-0354     modelSheet{1,9}=model.annotation.email;
+0353 if isfield(model.annotation,'defaultUB')
+0354     modelSheet{1,6}=model.annotation.defaultUB;
 0355 end
-0356 if isfield(model.annotation,'organization')
-0357     modelSheet{1,10}=model.annotation.organization;
+0356 if isfield(model.annotation,'givenName')
+0357     modelSheet{1,7}=model.annotation.givenName;
 0358 end
-0359 if isfield(model.annotation,'note')
-0360     modelSheet{1,11}=model.annotation.note;
+0359 if isfield(model.annotation,'familyName')
+0360     modelSheet{1,8}=model.annotation.familyName;
 0361 end
-0362 
-0363 if isfield(model,'genes')
-0364     wb=writeSheet(wb,'MODEL',4,headers,[],modelSheet);
-0365 else
-0366     wb=writeSheet(wb,'MODEL',3,headers,[],modelSheet);
+0362 if isfield(model.annotation,'email')
+0363     modelSheet{1,9}=model.annotation.email;
+0364 end
+0365 if isfield(model.annotation,'organization')
+0366     modelSheet{1,10}=model.annotation.organization;
 0367 end
-0368 
-0369 %Open the output stream
-0370 out = FileOutputStream(filename);
-0371 wb.write(out);
-0372 out.close();
-0373 end
    
+0368 if isfield(model.annotation,'note')
+0369     modelSheet{1,11}=model.annotation.note;
+0370 end
+0371 
+0372 if isfield(model,'genes')
+0373     wb=writeSheet(wb,'MODEL',4,headers,[],modelSheet);
+0374 else
+0375     wb=writeSheet(wb,'MODEL',3,headers,[],modelSheet);
+0376 end
+0377 
+0378 %Open the output stream
+0379 out = FileOutputStream(filename);
+0380 wb.write(out);
+0381 out.close();
+0382 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/exportToTabDelimited.html b/doc/io/exportToTabDelimited.html
index b35d6ca0..d570724b 100644
--- a/doc/io/exportToTabDelimited.html
+++ b/doc/io/exportToTabDelimited.html
@@ -24,7 +24,7 @@ 
    PURPOSE ^exportToTabDelimited

    SYNOPSIS ^

    -
    function exportToTabDelimited(model,path)
    +
    function exportToTabDelimited(model,path,sortIds)

    DESCRIPTION ^

     exportToTabDelimited
@@ -34,6 +34,8 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
+
  • exportToExcelFormat	exportToExcelFormat
    • 
 
 
 
 
 
    SOURCE CODE ^
    
-
    0001 function exportToTabDelimited(model,path)
+
    0001 function exportToTabDelimited(model,path,sortIds)
 0002 % exportToTabDelimited
 0003 %   Exports a model structure to a set of tab-delimited text files
 0004 %
@@ -65,330 +67,338 @@ 
    SOURCE CODE ^%   path    the path to export to. The resulting text files will be saved
 0007 %           under the names excelRxns.txt, excelMets.txt, excelGenes.txt,
 0008 %           excelModel.txt, and excelComps.txt
-0009 %
-0010 %   NOTE: This functionality was previously a part of exportToExcelFormat.
-0011 %         The naming of the resulting text files is to preserve backward
-0012 %         compatibility
-0013 %
-0014 %   NOTE: No checks are made regarding the correctness of the model. Use
-0015 %         checkModelStruct to identify problems in the model structure
-0016 %
-0017 %   Usage: exportToTabDelimited(model,path)
-0018 
-0019 if nargin<2
-0020     path='./';
-0021 end
-0022 
-0023 %If the folder doesn't exist then create it
-0024 if ~exist(path,'dir')
-0025     mkdir(path);
+0009 %   sortIds logical whether metabolites, reactions and genes should be
+0010 %           sorted alphabetically by their identifiers (opt, default false)
+0011 %
+0012 %   NOTE: This functionality was previously a part of exportToExcelFormat.
+0013 %         The naming of the resulting text files is to preserve backward
+0014 %         compatibility
+0015 %
+0016 %   NOTE: No checks are made regarding the correctness of the model. Use
+0017 %         checkModelStruct to identify problems in the model structure
+0018 %
+0019 %   Usage: exportToTabDelimited(model,path,sortIds)
+0020 
+0021 if nargin<2
+0022     path='./';
+0023 end
+0024 if nargin<3
+0025     sortIds=false;
 0026 end
-0027 
-0028 %Remove the files if they already exist
-0029 if exist(fullfile(path,'excelRxns.txt'),'file')
-0030     delete(fullfile(path,'excelRxns.txt'));
-0031 end
-0032 if exist(fullfile(path,'excelMets.txt'),'file')
-0033     delete(fullfile(path,'excelMets.txt'));
+0027 if sortIds==true
+0028     model=sortIdentifiers(model);
+0029 end
+0030 
+0031 %If the folder doesn't exist then create it
+0032 if ~exist(path,'dir')
+0033     mkdir(path);
 0034 end
-0035 if exist(fullfile(path,'excelGenes.txt'),'file')
-0036     delete(fullfile(path,'excelGenes.txt'));
-0037 end
-0038 if exist(fullfile(path,'excelModel.txt'),'file')
-0039     delete(fullfile(path,'excelModel.txt'));
-0040 end
-0041 if exist(fullfile(path,'excelComps.txt'),'file')
-0042     delete(fullfile(path,'excelComps.txt'));
-0043 end
-0044 
-0045 %Construct equations
-0046 model.equations=constructEquations(model,model.rxns,true);
-0047 
-0048 %Open for printing the rxn sheet
-0049 rxnFile=fopen(fullfile(path,'excelRxns.txt'),'wt');
-0050 
-0051 %Print header
-0052 fprintf(rxnFile,'#\tID\tNAME\tEQUATION\tEC-NUMBER\tGENE ASSOCIATION\tLOWER BOUND\tUPPER BOUND\tOBJECTIVE\tCOMPARTMENT\tMIRIAM\tSUBSYSTEM\tREPLACEMENT ID\tNOTE\tREFERENCE\tCONFIDENCE SCORE\n');
-0053 
-0054 %Loop through the reactions
-0055 for i=1:numel(model.rxns)
-0056     fprintf(rxnFile,['\t' model.rxns{i} '\t' model.rxnNames{i} '\t' model.equations{i} '\t']);
-0057     
-0058     if isfield(model,'eccodes')
-0059         fprintf(rxnFile,[model.eccodes{i} '\t']);
-0060     else
-0061         fprintf(rxnFile,'\t');
-0062     end
-0063     
-0064     if isfield(model,'grRules')
-0065         fprintf(rxnFile,[model.grRules{i} '\t']);
-0066     else
-0067         fprintf(rxnFile,'\t');
-0068     end
-0069     
-0070     %Print bounds and objectives
-0071     fprintf(rxnFile,[num2str(model.lb(i)) '\t' num2str(model.ub(i)) '\t']);
-0072     
-0073     if model.c(i)~=0
-0074         fprintf(rxnFile,[num2str(model.c(i)) '\t' ]);
-0075     else
-0076         fprintf(rxnFile,'\t');
-0077     end
-0078     
-0079     if isfield(model,'rxnComps')
-0080         fprintf(rxnFile,[model.comps{model.rxnComps(i)} '\t']);
-0081     else
-0082         fprintf(rxnFile,'\t');
-0083     end
-0084     
-0085     if isfield(model,'rxnMiriams')
-0086         if ~isempty(model.rxnMiriams{i})
-0087             toPrint=[];
-0088             for j=1:numel(model.rxnMiriams{i}.name)
-0089                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
-0090             end
-0091             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
-0092         else
-0093             fprintf(rxnFile,'\t');
-0094         end
-0095     else
-0096         fprintf(rxnFile,'\t');
-0097     end
-0098     
-0099     if isfield(model,'subSystems')
-0100         if ~isempty(model.subSystems{i})
-0101             fprintf(rxnFile,[strjoin(model.subSystems{i,1},';') '\t']);
-0102         else
-0103             fprintf(rxnFile,'\t');
-0104         end
+0035 
+0036 %Remove the files if they already exist
+0037 if exist(fullfile(path,'excelRxns.txt'),'file')
+0038     delete(fullfile(path,'excelRxns.txt'));
+0039 end
+0040 if exist(fullfile(path,'excelMets.txt'),'file')
+0041     delete(fullfile(path,'excelMets.txt'));
+0042 end
+0043 if exist(fullfile(path,'excelGenes.txt'),'file')
+0044     delete(fullfile(path,'excelGenes.txt'));
+0045 end
+0046 if exist(fullfile(path,'excelModel.txt'),'file')
+0047     delete(fullfile(path,'excelModel.txt'));
+0048 end
+0049 if exist(fullfile(path,'excelComps.txt'),'file')
+0050     delete(fullfile(path,'excelComps.txt'));
+0051 end
+0052 
+0053 %Construct equations
+0054 model.equations=constructEquations(model,model.rxns,true);
+0055 
+0056 %Open for printing the rxn sheet
+0057 rxnFile=fopen(fullfile(path,'excelRxns.txt'),'wt');
+0058 
+0059 %Print header
+0060 fprintf(rxnFile,'#\tID\tNAME\tEQUATION\tEC-NUMBER\tGENE ASSOCIATION\tLOWER BOUND\tUPPER BOUND\tOBJECTIVE\tCOMPARTMENT\tMIRIAM\tSUBSYSTEM\tREPLACEMENT ID\tNOTE\tREFERENCE\tCONFIDENCE SCORE\n');
+0061 
+0062 %Loop through the reactions
+0063 for i=1:numel(model.rxns)
+0064     fprintf(rxnFile,['\t' model.rxns{i} '\t' model.rxnNames{i} '\t' model.equations{i} '\t']);
+0065     
+0066     if isfield(model,'eccodes')
+0067         fprintf(rxnFile,[model.eccodes{i} '\t']);
+0068     else
+0069         fprintf(rxnFile,'\t');
+0070     end
+0071     
+0072     if isfield(model,'grRules')
+0073         fprintf(rxnFile,[model.grRules{i} '\t']);
+0074     else
+0075         fprintf(rxnFile,'\t');
+0076     end
+0077     
+0078     %Print bounds and objectives
+0079     fprintf(rxnFile,[num2str(model.lb(i)) '\t' num2str(model.ub(i)) '\t']);
+0080     
+0081     if model.c(i)~=0
+0082         fprintf(rxnFile,[num2str(model.c(i)) '\t' ]);
+0083     else
+0084         fprintf(rxnFile,'\t');
+0085     end
+0086     
+0087     if isfield(model,'rxnComps')
+0088         fprintf(rxnFile,[model.comps{model.rxnComps(i)} '\t']);
+0089     else
+0090         fprintf(rxnFile,'\t');
+0091     end
+0092     
+0093     if isfield(model,'rxnMiriams')
+0094         if ~isempty(model.rxnMiriams{i})
+0095             toPrint=[];
+0096             for j=1:numel(model.rxnMiriams{i}.name)
+0097                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
+0098             end
+0099             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
+0100         else
+0101             fprintf(rxnFile,'\t');
+0102         end
+0103     else
+0104         fprintf(rxnFile,'\t');
 0105     end
 0106     
-0107     %Print replacement IDs
-0108     fprintf(rxnFile,'\t');
-0109     
-0110     if isfield(model,'rxnNotes')
-0111         fprintf(rxnFile,[model.rxnNotes{i} '\t']);
-0112     else
-0113         fprintf(rxnFile,'\t');
-0114     end
-0115     
-0116     if isfield(model,'rxnReferences')
-0117         fprintf(rxnFile,[model.rxnReferences{i} '\t']);
-0118     else
-0119         fprintf(rxnFile,'\t');
-0120     end
-0121     
-0122     if isfield(model,'rxnConfidenceScores')
-0123         fprintf(rxnFile,[num2str(model.rxnConfidenceScores(i)) '\t' ]);
-0124     else
-0125         fprintf(rxnFile,'\t');
-0126     end
-0127     
-0128     fprintf(rxnFile,'\n');
-0129 end
-0130 
-0131 fclose(rxnFile);
-0132 
-0133 %Open for printing the metabolites sheet
-0134 metFile=fopen(fullfile(path,'excelMets.txt'),'wt');
-0135 
-0136 %Print header
-0137 fprintf(metFile,'#\tID\tNAME\tUNCONSTRAINED\tMIRIAM\tCOMPOSITION\tInChI\tCOMPARTMENT\tREPLACEMENT ID\tMETS FIELD\tCHARGE\n');
+0107     if isfield(model,'subSystems')
+0108         if ~isempty(model.subSystems{i})
+0109             fprintf(rxnFile,[strjoin(model.subSystems{i,1},';') '\t']);
+0110         else
+0111             fprintf(rxnFile,'\t');
+0112         end
+0113     end
+0114     
+0115     %Print replacement IDs
+0116     fprintf(rxnFile,'\t');
+0117     
+0118     if isfield(model,'rxnNotes')
+0119         fprintf(rxnFile,[model.rxnNotes{i} '\t']);
+0120     else
+0121         fprintf(rxnFile,'\t');
+0122     end
+0123     
+0124     if isfield(model,'rxnReferences')
+0125         fprintf(rxnFile,[model.rxnReferences{i} '\t']);
+0126     else
+0127         fprintf(rxnFile,'\t');
+0128     end
+0129     
+0130     if isfield(model,'rxnConfidenceScores')
+0131         fprintf(rxnFile,[num2str(model.rxnConfidenceScores(i)) '\t' ]);
+0132     else
+0133         fprintf(rxnFile,'\t');
+0134     end
+0135     
+0136     fprintf(rxnFile,'\n');
+0137 end
 0138 
-0139 %Loop through the metabolites
-0140 for i=1:numel(model.mets)
-0141     fprintf(metFile,['\t' model.metNames{i} '[' model.comps{model.metComps(i)} ']\t' model.metNames{i} '\t']);
-0142     
-0143     if isfield(model,'unconstrained')
-0144         if model.unconstrained(i)~=0
-0145             fprintf(metFile,'TRUE\t');
-0146         else
-0147             fprintf(metFile,'\t');
-0148         end
-0149     else
-0150         fprintf(metFile,'\t');
-0151     end
-0152     
-0153     if isfield(model,'metMiriams')
-0154         if ~isempty(model.metMiriams{i})
-0155             toPrint=[];
-0156             for j=1:numel(model.metMiriams{i}.name)
-0157                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
-0158             end
-0159             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
-0160         else
-0161             fprintf(metFile,'\t');
-0162         end
-0163     else
-0164         fprintf(metFile,'\t');
-0165     end
-0166     
-0167     if isfield(model,'metFormulas')
-0168         fprintf(metFile,[model.metFormulas{i} '\t']);
-0169     else
-0170         fprintf(metFile,'\t');
-0171     end
-0172     
-0173     if isfield(model,'inchis')
-0174         fprintf(metFile,[model.inchis{i} '\t']);
-0175     else
-0176         fprintf(metFile,'\t');
-0177     end
-0178     
-0179     fprintf(metFile,[model.comps{model.metComps(i)} '\t']);
+0139 fclose(rxnFile);
+0140 
+0141 %Open for printing the metabolites sheet
+0142 metFile=fopen(fullfile(path,'excelMets.txt'),'wt');
+0143 
+0144 %Print header
+0145 fprintf(metFile,'#\tID\tNAME\tUNCONSTRAINED\tMIRIAM\tCOMPOSITION\tInChI\tCOMPARTMENT\tREPLACEMENT ID\tMETS FIELD\tCHARGE\n');
+0146 
+0147 %Loop through the metabolites
+0148 for i=1:numel(model.mets)
+0149     fprintf(metFile,['\t' model.metNames{i} '[' model.comps{model.metComps(i)} ']\t' model.metNames{i} '\t']);
+0150     
+0151     if isfield(model,'unconstrained')
+0152         if model.unconstrained(i)~=0
+0153             fprintf(metFile,'TRUE\t');
+0154         else
+0155             fprintf(metFile,'\t');
+0156         end
+0157     else
+0158         fprintf(metFile,'\t');
+0159     end
+0160     
+0161     if isfield(model,'metMiriams')
+0162         if ~isempty(model.metMiriams{i})
+0163             toPrint=[];
+0164             for j=1:numel(model.metMiriams{i}.name)
+0165                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
+0166             end
+0167             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
+0168         else
+0169             fprintf(metFile,'\t');
+0170         end
+0171     else
+0172         fprintf(metFile,'\t');
+0173     end
+0174     
+0175     if isfield(model,'metFormulas')
+0176         fprintf(metFile,[model.metFormulas{i} '\t']);
+0177     else
+0178         fprintf(metFile,'\t');
+0179     end
 0180     
-0181     %There can be no replacement IDs in the structure, but it has to be
-0182     %something to give working met IDs.
-0183     fprintf(metFile,['m' int2str(i) '\t']);
-0184     
-0185     %Print the model.mets field. The reason for not putting this as
-0186     %replacement ID is that it's not guaranteed to be a valid SBML id.
-0187     fprintf(metFile,[model.mets{i} '\t']);
+0181     if isfield(model,'inchis')
+0182         fprintf(metFile,[model.inchis{i} '\t']);
+0183     else
+0184         fprintf(metFile,'\t');
+0185     end
+0186     
+0187     fprintf(metFile,[model.comps{model.metComps(i)} '\t']);
 0188     
-0189     if isfield(model,'metCharges')
-0190         fprintf(metFile,[num2str(model.metCharges(i)) '\t']);
-0191     else
-0192         fprintf(metFile,'\t');
-0193     end
-0194     
-0195     fprintf(metFile,'\n');
-0196 end
-0197 
-0198 fclose(metFile);
-0199 
-0200 if isfield(model,'genes')
-0201     %Open for printing the genes sheet
-0202     geneFile=fopen(fullfile(path,'excelGenes.txt'),'wt');
-0203     
-0204     %Print header
-0205     fprintf(geneFile,'#\tNAME\tMIRIAM\tSHORT NAME\tCOMPARTMENT\n');
-0206     
-0207     %Loop through the genes
-0208     for i=1:numel(model.genes)
-0209         fprintf(geneFile,['\t' model.genes{i} '\t']);
-0210         
-0211         if isfield(model,'geneMiriams')
-0212             if ~isempty(model.geneMiriams{i})
-0213                 toPrint=[];
-0214                 for j=1:numel(model.geneMiriams{i}.name)
-0215                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
-0216                 end
-0217                 fprintf(geneFile,[toPrint(1:end-1) '\t']);
-0218             else
-0219                 fprintf(geneFile,'\t');
-0220             end
-0221         else
-0222             fprintf(geneFile,'\t');
-0223         end
-0224         
-0225         if isfield(model,'geneShortNames')
-0226             fprintf(geneFile,[model.geneShortNames{i} '\t']);
-0227         else
-0228             fprintf(geneFile,'\t');
-0229         end
-0230         
-0231         if isfield(model,'geneComps')
-0232             fprintf(geneFile,[model.comps{model.geneComps(i)} '\t']);
-0233         else
-0234             fprintf(geneFile,'\t');
-0235         end
-0236         
-0237         fprintf(geneFile,'\n');
-0238     end
-0239     fclose(geneFile);
-0240 end
-0241 
-0242 if isfield(model,'id')
-0243     %Open for printing the model sheet
-0244     modelFile=fopen(fullfile(path,'excelModel.txt'),'wt');
-0245     
-0246     %Print header
-0247     fprintf(geneFile,'#\tID\tNAME\tDEFAULT LOWER\tDEFAULT UPPER\tCONTACT GIVEN NAME\tCONTACT FAMILY NAME\tCONTACT EMAIL\tORGANIZATION\tTAXONOMY\tNOTES\n');
-0248     
-0249     %Print model ID and name. It is assumed that the default lower/upper
-0250     %bound correspond to min/max of the bounds
-0251     toPrint=['\t' model.id '\t' model.name '\t'];
-0252     if isfield(model,'annotation')
-0253         if isfield(model.annotation,'defaultLB')
-0254             toPrint=[toPrint num2str(model.annotation.defaultLB) '\t'];
-0255         else
-0256             toPrint=[toPrint num2str(min(model.lb)) '\t'];
-0257         end
-0258         if isfield(model.annotation,'defaultUB')
-0259             toPrint=[toPrint num2str(model.annotation.defaultUB) '\t'];
-0260         else
-0261             toPrint=[toPrint num2str(max(model.ub)) '\t'];
-0262         end
-0263         if isfield(model.annotation,'givenName')
-0264             toPrint=[toPrint model.annotation.givenName '\t'];
-0265         else
-0266             toPrint=[toPrint '\t'];
-0267         end
-0268         if isfield(model.annotation,'familyName')
-0269             toPrint=[toPrint model.annotation.familyName '\t'];
-0270         else
-0271             toPrint=[toPrint '\t'];
-0272         end
-0273         if isfield(model.annotation,'email')
-0274             toPrint=[toPrint model.annotation.email '\t'];
-0275         else
-0276             toPrint=[toPrint '\t'];
-0277         end
-0278         if isfield(model.annotation,'organization')
-0279             toPrint=[toPrint model.annotation.organization '\t'];
-0280         else
-0281             toPrint=[toPrint '\t'];
-0282         end
-0283         if isfield(model.annotation,'taxonomy')
-0284             toPrint=[toPrint model.annotation.taxonomy '\t'];
-0285         else
-0286             toPrint=[toPrint '\t'];
-0287         end
-0288         if isfield(model.annotation,'note')
-0289             toPrint=[toPrint model.annotation.note '\t'];
-0290         else
-0291             toPrint=[toPrint '\t'];
-0292         end
-0293     else
-0294         toPrint=[toPrint num2str(min(model.lb)) '\t' num2str(max(model.ub)) '\t\t\t\t\t\t\n'];
-0295     end
-0296     fprintf(modelFile,toPrint);
-0297     fclose(modelFile);
-0298 end
-0299 
-0300 if isfield(model,'comps')
-0301     %Open for printing the model sheet
-0302     compsFile=fopen(fullfile(path,'excelComps.txt'),'wt');
-0303     
-0304     %Print header
-0305     fprintf(compsFile,'#\tABBREVIATION\tNAME\tINSIDE\tMIRIAM\n');
-0306     
-0307     for i=1:numel(model.comps)
-0308         toPrint=['\t' model.comps{i} '\t' model.compNames{i} '\t'];
-0309         if isfield(model,'compOutside')
-0310             toPrint=[toPrint model.compOutside{i} '\t'];
-0311         else
-0312             toPrint=[toPrint '\t'];
-0313         end
-0314         if isfield(model,'compMiriams')
-0315             if ~isempty(model.compMiriams{i})
-0316                 for j=1:numel(model.compMiriams{i}.name)
-0317                     toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
-0318                 end
-0319                 toPrint(end)=[];
-0320                 toPrint=[toPrint '\t'];
-0321             else
-0322                 toPrint=[toPrint '\t'];
-0323             end
-0324         else
-0325             toPrint=[toPrint '\t'];
-0326         end
-0327         toPrint=[toPrint '\n'];
-0328         fprintf(compsFile,toPrint);
-0329     end
-0330     fclose(compsFile);
-0331 end
-0332 end
    
+0189     %There can be no replacement IDs in the structure, but it has to be
+0190     %something to give working met IDs.
+0191     fprintf(metFile,['m' int2str(i) '\t']);
+0192     
+0193     %Print the model.mets field. The reason for not putting this as
+0194     %replacement ID is that it's not guaranteed to be a valid SBML id.
+0195     fprintf(metFile,[model.mets{i} '\t']);
+0196     
+0197     if isfield(model,'metCharges')
+0198         fprintf(metFile,[num2str(model.metCharges(i)) '\t']);
+0199     else
+0200         fprintf(metFile,'\t');
+0201     end
+0202     
+0203     fprintf(metFile,'\n');
+0204 end
+0205 
+0206 fclose(metFile);
+0207 
+0208 if isfield(model,'genes')
+0209     %Open for printing the genes sheet
+0210     geneFile=fopen(fullfile(path,'excelGenes.txt'),'wt');
+0211     
+0212     %Print header
+0213     fprintf(geneFile,'#\tNAME\tMIRIAM\tSHORT NAME\tCOMPARTMENT\n');
+0214     
+0215     %Loop through the genes
+0216     for i=1:numel(model.genes)
+0217         fprintf(geneFile,['\t' model.genes{i} '\t']);
+0218         
+0219         if isfield(model,'geneMiriams')
+0220             if ~isempty(model.geneMiriams{i})
+0221                 toPrint=[];
+0222                 for j=1:numel(model.geneMiriams{i}.name)
+0223                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
+0224                 end
+0225                 fprintf(geneFile,[toPrint(1:end-1) '\t']);
+0226             else
+0227                 fprintf(geneFile,'\t');
+0228             end
+0229         else
+0230             fprintf(geneFile,'\t');
+0231         end
+0232         
+0233         if isfield(model,'geneShortNames')
+0234             fprintf(geneFile,[model.geneShortNames{i} '\t']);
+0235         else
+0236             fprintf(geneFile,'\t');
+0237         end
+0238         
+0239         if isfield(model,'geneComps')
+0240             fprintf(geneFile,[model.comps{model.geneComps(i)} '\t']);
+0241         else
+0242             fprintf(geneFile,'\t');
+0243         end
+0244         
+0245         fprintf(geneFile,'\n');
+0246     end
+0247     fclose(geneFile);
+0248 end
+0249 
+0250 if isfield(model,'id')
+0251     %Open for printing the model sheet
+0252     modelFile=fopen(fullfile(path,'excelModel.txt'),'wt');
+0253     
+0254     %Print header
+0255     fprintf(geneFile,'#\tID\tNAME\tDEFAULT LOWER\tDEFAULT UPPER\tCONTACT GIVEN NAME\tCONTACT FAMILY NAME\tCONTACT EMAIL\tORGANIZATION\tTAXONOMY\tNOTES\n');
+0256     
+0257     %Print model ID and name. It is assumed that the default lower/upper
+0258     %bound correspond to min/max of the bounds
+0259     toPrint=['\t' model.id '\t' model.name '\t'];
+0260     if isfield(model,'annotation')
+0261         if isfield(model.annotation,'defaultLB')
+0262             toPrint=[toPrint num2str(model.annotation.defaultLB) '\t'];
+0263         else
+0264             toPrint=[toPrint num2str(min(model.lb)) '\t'];
+0265         end
+0266         if isfield(model.annotation,'defaultUB')
+0267             toPrint=[toPrint num2str(model.annotation.defaultUB) '\t'];
+0268         else
+0269             toPrint=[toPrint num2str(max(model.ub)) '\t'];
+0270         end
+0271         if isfield(model.annotation,'givenName')
+0272             toPrint=[toPrint model.annotation.givenName '\t'];
+0273         else
+0274             toPrint=[toPrint '\t'];
+0275         end
+0276         if isfield(model.annotation,'familyName')
+0277             toPrint=[toPrint model.annotation.familyName '\t'];
+0278         else
+0279             toPrint=[toPrint '\t'];
+0280         end
+0281         if isfield(model.annotation,'email')
+0282             toPrint=[toPrint model.annotation.email '\t'];
+0283         else
+0284             toPrint=[toPrint '\t'];
+0285         end
+0286         if isfield(model.annotation,'organization')
+0287             toPrint=[toPrint model.annotation.organization '\t'];
+0288         else
+0289             toPrint=[toPrint '\t'];
+0290         end
+0291         if isfield(model.annotation,'taxonomy')
+0292             toPrint=[toPrint model.annotation.taxonomy '\t'];
+0293         else
+0294             toPrint=[toPrint '\t'];
+0295         end
+0296         if isfield(model.annotation,'note')
+0297             toPrint=[toPrint model.annotation.note '\t'];
+0298         else
+0299             toPrint=[toPrint '\t'];
+0300         end
+0301     else
+0302         toPrint=[toPrint num2str(min(model.lb)) '\t' num2str(max(model.ub)) '\t\t\t\t\t\t\n'];
+0303     end
+0304     fprintf(modelFile,toPrint);
+0305     fclose(modelFile);
+0306 end
+0307 
+0308 if isfield(model,'comps')
+0309     %Open for printing the model sheet
+0310     compsFile=fopen(fullfile(path,'excelComps.txt'),'wt');
+0311     
+0312     %Print header
+0313     fprintf(compsFile,'#\tABBREVIATION\tNAME\tINSIDE\tMIRIAM\n');
+0314     
+0315     for i=1:numel(model.comps)
+0316         toPrint=['\t' model.comps{i} '\t' model.compNames{i} '\t'];
+0317         if isfield(model,'compOutside')
+0318             toPrint=[toPrint model.compOutside{i} '\t'];
+0319         else
+0320             toPrint=[toPrint '\t'];
+0321         end
+0322         if isfield(model,'compMiriams')
+0323             if ~isempty(model.compMiriams{i})
+0324                 for j=1:numel(model.compMiriams{i}.name)
+0325                     toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
+0326                 end
+0327                 toPrint(end)=[];
+0328                 toPrint=[toPrint '\t'];
+0329             else
+0330                 toPrint=[toPrint '\t'];
+0331             end
+0332         else
+0333             toPrint=[toPrint '\t'];
+0334         end
+0335         toPrint=[toPrint '\n'];
+0336         fprintf(compsFile,toPrint);
+0337     end
+0338     fclose(compsFile);
+0339 end
+0340 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/loadWorkbook.html b/doc/io/loadWorkbook.html
index 7c06b146..ebca57da 100644
--- a/doc/io/loadWorkbook.html
+++ b/doc/io/loadWorkbook.html
@@ -46,7 +46,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=addJavaPaths	addJavaPaths
  • getFullPath	getFullPath - Get absolute canonical path of a file or folder
    • 
 This function is called by:
 
+
  • exportToExcelFormat	exportToExcelFormat
  • importExcelModel	importExcelModel
    • 
 
 
 
diff --git a/doc/io/sortIdentifiers.html b/doc/io/sortIdentifiers.html
new file mode 100644
index 00000000..33ae0b7d
--- /dev/null
+++ b/doc/io/sortIdentifiers.html
@@ -0,0 +1,83 @@
+
+
+
+  Description of sortIdentifiers
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  io > sortIdentifiers.m
    
+
+
+
+
    sortIdentifiers
+
    
+
+
    PURPOSE ^
    
+
    exportModel
    
+
+
    SYNOPSIS ^
    
+
    function newModel = sortIdentifiers(model) 
    
+
+
    DESCRIPTION ^
    
+
     exportModel
+   Sort reactions, metabolites, genes and compartments alphabetically by
+   their identifier.
+
+   Input:
+   model       a model structure
+
+   Output:
+   newModel    an updated model structure with alphabetically sorted
+               identifiers
+
+   Usage: newModel=sortIdentifiers(model)
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
+
+
    SOURCE CODE ^
    
+
    0001 function newModel = sortIdentifiers(model)
+0002 % exportModel
+0003 %   Sort reactions, metabolites, genes and compartments alphabetically by
+0004 %   their identifier.
+0005 %
+0006 %   Input:
+0007 %   model       a model structure
+0008 %
+0009 %   Output:
+0010 %   newModel    an updated model structure with alphabetically sorted
+0011 %               identifiers
+0012 %
+0013 %   Usage: newModel=sortIdentifiers(model)
+0014 
+0015 [~,I]=sort(model.rxns);
+0016 newModel=permuteModel(model,I,'rxns');
+0017 [~,I]=sort(newModel.mets);
+0018 newModel=permuteModel(newModel,I,'mets');
+0019 if isfield(newModel,'genes')
+0020     [~,I]=sort(newModel.genes);
+0021     newModel=permuteModel(newModel,I,'genes');
+0022 end
+0023 [~,I]=sort(newModel.comps);
+0024 newModel=permuteModel(newModel,I,'comps');
+0025 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/io/writeSheet.html b/doc/io/writeSheet.html
index 10b1aa8c..04270560 100644
--- a/doc/io/writeSheet.html
+++ b/doc/io/writeSheet.html
@@ -48,7 +48,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=addJavaPaths	addJavaPaths
 This function is called by:
 
+
  • exportToExcelFormat	exportToExcelFormat
    • 
 
 
 
    SUBFUNCTIONS ^
    
diff --git a/doc/io/writeYaml.html b/doc/io/writeYaml.html
index c5a19c29..277e0b4b 100644
--- a/doc/io/writeYaml.html
+++ b/doc/io/writeYaml.html
@@ -45,7 +45,7 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
@@ -77,298 +77,282 @@ 
    SOURCE CODE ^if nargin < 4
 0020     sortIds = false;
 0021 end
-0022 
-0023 if ~endsWith(name,{'.yml','.yaml'})
-0024     name = strcat(name,'.yml');
-0025 end
-0026 
-0027 %Check that model is in RAVEN format:
-0028 if isfield(model,'rules')
-0029     model = ravenCobraWrapper(model);
-0030 end
-0031 
-0032 %Simplify Miriam fields:
-0033 if isfield(model,'metMiriams')
-0034     [model.newMetMiriams,model.newMetMiriamNames]   = extractMiriam(model.metMiriams);
-0035     model.newMetMiriams                             = regexprep(model.newMetMiriams,'^.+/','');
-0036 end
-0037 if isfield(model,'rxnMiriams')
-0038     [model.newRxnMiriams,model.newRxnMiriamNames]   = extractMiriam(model.rxnMiriams);
-0039     model.newRxnMiriams                             = regexprep(model.newRxnMiriams,'^.+/','');
+0022 if ~endsWith(name,{'.yml','.yaml'})
+0023     name = strcat(name,'.yml');
+0024 end
+0025 
+0026 %Check that model is in RAVEN format:
+0027 if isfield(model,'rules')
+0028     model = ravenCobraWrapper(model);
+0029 end
+0030 
+0031 %Sort identifiers alphabetically
+0032 if sortIds == true
+0033     model = sortIdentifiers(model);
+0034 end
+0035 
+0036 %Simplify Miriam fields:
+0037 if isfield(model,'metMiriams')
+0038     [model.newMetMiriams,model.newMetMiriamNames]   = extractMiriam(model.metMiriams);
+0039     model.newMetMiriams                             = regexprep(model.newMetMiriams,'^.+/','');
 0040 end
-0041 if isfield(model,'geneMiriams')
-0042     [model.newGeneMiriams,model.newGeneMiriamNames] = extractMiriam(model.geneMiriams);
-0043     model.newGeneMiriams                            = regexprep(model.newGeneMiriams,'^.+/','');
+0041 if isfield(model,'rxnMiriams')
+0042     [model.newRxnMiriams,model.newRxnMiriamNames]   = extractMiriam(model.rxnMiriams);
+0043     model.newRxnMiriams                             = regexprep(model.newRxnMiriams,'^.+/','');
 0044 end
-0045 if isfield(model,'compMiriams')
-0046     [model.newCompMiriams,model.newCompMiriamNames] = extractMiriam(model.compMiriams);
-0047     model.newCompMiriams                            = regexprep(model.newCompMiriams,'^.+/','');
+0045 if isfield(model,'geneMiriams')
+0046     [model.newGeneMiriams,model.newGeneMiriamNames] = extractMiriam(model.geneMiriams);
+0047     model.newGeneMiriams                            = regexprep(model.newGeneMiriams,'^.+/','');
 0048 end
-0049 
-0050 %Open file:
-0051 fid = fopen(name,'wt');
-0052 fprintf(fid,'---\n!!omap\n');
+0049 if isfield(model,'compMiriams')
+0050     [model.newCompMiriams,model.newCompMiriamNames] = extractMiriam(model.compMiriams);
+0051     model.newCompMiriams                            = regexprep(model.newCompMiriams,'^.+/','');
+0052 end
 0053 
-0054 %Insert file header (metadata)
-0055 writeMetadata(model,fid);
-0056 
-0057 %Metabolites:
-0058 fprintf(fid,'- metabolites:\n');
-0059 if sortIds==true
-0060     [~,pos] = sort(model.mets);
-0061 else
-0062     pos = 1:numel(model.mets);
-0063 end
-0064 for i = 1:length(model.mets)
-0065     fprintf(fid,'    - !!omap\n');
-0066     writeField(model, fid, 'mets',        'txt', pos(i), '  - id',          preserveQuotes)
-0067     writeField(model, fid, 'metNames',    'txt', pos(i), '  - name',        preserveQuotes)
-0068     writeField(model, fid, 'metComps',    'txt', pos(i), '  - compartment', preserveQuotes)
-0069     writeField(model, fid, 'metFormulas', 'txt', pos(i), '  - formula',     preserveQuotes)
-0070     writeField(model, fid, 'metCharges',  'num', pos(i), '  - charge',      preserveQuotes)
-0071     writeField(model, fid, 'inchis',      'txt', pos(i), '  - inchis',      preserveQuotes)
-0072     writeField(model, fid, 'metMiriams',  'txt', pos(i), '  - annotation',  preserveQuotes)
-0073     writeField(model, fid, 'metFrom',     'txt', pos(i), '  - metFrom',     preserveQuotes)
-0074 end
-0075 
-0076 %Reactions:
-0077 fprintf(fid,'- reactions:\n');
-0078 if sortIds==true
-0079     [~,pos] = sort(model.rxns);
-0080 else
-0081     pos = 1:numel(model.rxns);
-0082 end
-0083 for i = 1:length(model.rxns)
-0084     fprintf(fid,'    - !!omap\n');
-0085     writeField(model, fid, 'rxns',                 'txt', pos(i), '  - id',                    preserveQuotes)
-0086     writeField(model, fid, 'rxnNames',             'txt', pos(i), '  - name',                  preserveQuotes)
-0087     writeField(model, fid, 'S',                    'txt', pos(i), '  - metabolites',           preserveQuotes)
-0088     writeField(model, fid, 'lb',                   'num', pos(i), '  - lower_bound',           preserveQuotes)
-0089     writeField(model, fid, 'ub',                   'num', pos(i), '  - upper_bound',           preserveQuotes)
-0090     writeField(model, fid, 'grRules',              'txt', pos(i), '  - gene_reaction_rule',    preserveQuotes)
-0091     writeField(model, fid, 'rxnFrom',              'txt', pos(i), '  - rxnFrom',               preserveQuotes)
-0092     if model.c(i)~=0
-0093         writeField(model, fid, 'c',                    'num', pos(i), '  - objective_coefficient', preserveQuotes)    
-0094     end
-0095     writeField(model, fid, 'eccodes',              'txt', pos(i), '  - eccodes',               preserveQuotes)
-0096     writeField(model, fid, 'rxnReferences',        'txt', pos(i), '  - references',            preserveQuotes)
-0097     writeField(model, fid, 'subSystems',           'txt', pos(i), '  - subsystem',             preserveQuotes)
-0098     writeField(model, fid, 'rxnMiriams',           'txt', pos(i), '  - annotation',            preserveQuotes)
-0099     writeField(model, fid, 'rxnConfidenceScores',  'num', pos(i), '  - confidence_score',      preserveQuotes)
-0100 end
-0101 
-0102 %Genes:
-0103 fprintf(fid,'- genes:\n');
-0104 if sortIds==true
-0105     [~,pos] = sort(model.genes);
-0106 else
-0107     pos = 1:numel(model.genes);
-0108 end
-0109 for i = 1:length(model.genes)
-0110     fprintf(fid,'    - !!omap\n');
-0111     writeField(model, fid, 'genes',          'txt', pos(i), '  - id',         preserveQuotes)
-0112     writeField(model, fid, 'geneShortNames', 'txt', pos(i), '  - name',       preserveQuotes)
-0113     writeField(model, fid, 'geneMiriams',    'txt', pos(i), '  - annotation', preserveQuotes)
-0114 end
-0115 
-0116 %Compartments:
-0117 fprintf(fid,'- compartments: !!omap\n');
-0118 if sortIds==true
-0119     [~,pos] = sort(model.comps);
-0120 else
-0121     pos = 1:numel(model.comps);
-0122 end
-0123 for i = 1:length(model.comps)
-0124     writeField(model, fid, 'compNames',   'txt', pos(i), ['- ' model.comps{pos(i)}], preserveQuotes)
-0125     writeField(model, fid, 'compMiriams', 'txt', pos(i), '- annotation',             preserveQuotes)
-0126 end
-0127 
-0128 %Close file:
-0129 fclose(fid);
-0130 
-0131 end
-0132 
-0133 function writeField(model,fid,fieldName,type,pos,name,preserveQuotes)
-0134 %Writes a new line in the yaml file if the field exists and the field is
-0135 %not empty at the correspoinding position. It's recursive for some fields
-0136 %(metMiriams, rxnMiriams, and S)
-0137 
-0138 if isfield(model,fieldName)
-0139     if strcmp(fieldName,'metComps')
-0140         %metComps: write full name
-0141         fieldName = 'comps';
-0142         pos       = model.metComps(pos);
-0143     end
-0144     
-0145     field = eval(['model.' fieldName]);
-0146     
-0147     if strcmp(fieldName,'metMiriams')
-0148         if ~isempty(model.metMiriams{pos})
-0149             fprintf(fid,['    ' name ': !!omap\n']);
-0150             for i=1:size(model.newMetMiriams,2)
-0151                 %'i' represents the different miriam names, e.g.
-0152                 %kegg.compound or chebi
-0153                 if ~isempty(model.newMetMiriams{pos,i})
-0154                     %As during the following writeField call the value of
-0155                     %'i' would be lost, it is temporarily concatenated to
-0156                     %'name' parameter, which will be edited later
-0157                     writeField(model, fid, 'newMetMiriams', 'txt', pos, ['      - ' model.newMetMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0158                 end
-0159             end
-0160         end
-0161         
-0162     elseif strcmp(fieldName,'rxnMiriams')
-0163         if ~isempty(model.rxnMiriams{pos})
-0164             fprintf(fid,['    ' name ': !!omap\n']);
-0165             for i=1:size(model.newRxnMiriams,2)
-0166                 if ~isempty(model.newRxnMiriams{pos,i})
-0167                     writeField(model, fid, 'newRxnMiriams', 'txt', pos, ['      - ' model.newRxnMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0168                 end
-0169             end
-0170         end
-0171         
-0172     elseif strcmp(fieldName,'geneMiriams')
-0173         if ~isempty(model.geneMiriams{pos})
-0174             fprintf(fid,['    ' name ': !!omap\n']);
-0175             for i=1:size(model.newGeneMiriams,2)
-0176                 if ~isempty(model.newGeneMiriams{pos,i})
-0177                     writeField(model, fid, 'newGeneMiriams', 'txt', pos, ['      - ' model.newGeneMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0178                 end
-0179             end
-0180         end
-0181         
-0182     elseif strcmp(fieldName,'compMiriams')
-0183         if ~isempty(model.compMiriams{pos})
-0184             fprintf(fid,['    ' name ': !!omap\n']);
-0185             for i=1:size(model.newCompMiriams,2)
-0186                 if ~isempty(model.newCompMiriams{pos,i})
-0187                     writeField(model, fid, 'newCompMiriams', 'txt', pos, ['      - ' model.newCompMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0188                 end
-0189             end
-0190         end
-0191         
-0192     elseif strcmp(fieldName,'S')
-0193         %S: create header & write each metabolite in a new line
-0194         fprintf(fid,['    ' name ': !!omap\n']);
-0195         if sum(field(:,pos) ~= 0) > 0
-0196             model.mets   = model.mets(field(:,pos) ~= 0);
-0197             model.coeffs = field(field(:,pos) ~= 0,pos);
-0198             %Sort metabolites:
-0199             [model.mets,order] = sort(model.mets);
-0200             model.coeffs       = model.coeffs(order);
-0201             for i = 1:length(model.mets)
-0202                 writeField(model, fid, 'coeffs',  'num', i, ['      - ' model.mets{i}], preserveQuotes)
-0203             end
-0204         end
-0205         
-0206     elseif sum(strcmp({'subSystems','newMetMiriams','newRxnMiriams','newGeneMiriams','newCompMiriams','eccodes'},fieldName)) > 0
-0207         %eccodes/rxnNotes: if 1 write in 1 line, if more create header and list
-0208         if strcmp(fieldName,'subSystems')
-0209             list = field{pos};  %subSystems already comes in a cell array
-0210         elseif strcmp(fieldName,'newMetMiriams')
-0211             index = str2double(regexprep(name,'^.+_',''));
-0212             name  = regexprep(name,'_\d+$','');
-0213             list = strsplit(model.newMetMiriams{pos,index},'; ');
-0214         elseif strcmp(fieldName,'newRxnMiriams')
-0215             index = str2double(regexprep(name,'^.+_',''));
-0216             name  = regexprep(name,'_\d+$','');
-0217             list = strsplit(model.newRxnMiriams{pos,index},'; ');
-0218         elseif strcmp(fieldName,'newGeneMiriams')
-0219             index = str2double(regexprep(name,'^.+_',''));
-0220             name  = regexprep(name,'_\d+$','');
-0221             list = strsplit(model.newGeneMiriams{pos,index},'; ');
-0222         elseif strcmp(fieldName,'newCompMiriams')
-0223             index = str2double(regexprep(name,'^.+_',''));
-0224             name  = regexprep(name,'_\d+$','');
-0225             list = strsplit(model.newCompMiriams{pos,index},'; ');
-0226         else
-0227             list = strrep(field{pos},' ','');     %Exception for eccodes
-0228             list = strsplit(list,';');
-0229         end
-0230 
-0231         if length(list) == 1 && ~strcmp(list{1},'') && ~strcmp(fieldName,'subSystems')
-0232             if preserveQuotes
-0233                 list = strcat('"',list,'"');
-0234             end
-0235             fprintf(fid,['    ' name ': ' list{1} '\n']);
-0236         elseif length(list) > 1 || strcmp(fieldName,'subSystems')
-0237             if preserveQuotes
-0238                 list = strcat('"',list,'"');
-0239             end
-0240             fprintf(fid,['    ' name ':\n']);
-0241             for i = 1:length(list)
-0242                 fprintf(fid,[regexprep(name,'(^\s*).*','$1') '        - ' list{i} '\n']);
-0243             end
-0244         end
-0245         
-0246     elseif sum(pos) > 0
-0247         %All other fields:
-0248         if strcmp(type,'txt')
-0249             value = field{pos};
-0250             if preserveQuotes && ~isempty(value)
-0251                 value = strcat('"',value,'"');
-0252             end
-0253         elseif strcmp(type,'num')
-0254             if isnan(field(pos))
-0255                 value = [];
-0256             else
-0257                 value = num2str(field(pos),12);
-0258             end
-0259         end
-0260         if ~isempty(value)
-0261             fprintf(fid,['    ' name ': ' value '\n']);
-0262         end
-0263     end
-0264 end
-0265 
-0266 
-0267 end
-0268 
-0269 function writeMetadata(model,fid)
-0270 % Writes model metadata to the yaml file. This information will eventually
-0271 % be extracted entirely from the model, but for now, many of the entries
-0272 % are hard-coded defaults for HumanGEM.
-0273 
-0274 fprintf(fid, '- metaData:\n');
-0275 fprintf(fid, ['    id: "',          model.id,          '"\n']);
-0276 fprintf(fid, ['    name: "',        model.name, '"\n']);
-0277 if isfield(model,'version')
-0278     fprintf(fid, ['    version: "', model.version,     '"\n']);
-0279 end
-0280 fprintf(fid, ['    date: "',        datestr(now,29),   '"\n']);  % 29=YYYY-MM-DD
-0281 if isfield(model,'annotation')
-0282     if isfield(model.annotation,'defaultLB')
-0283         fprintf(fid, ['    defaultLB: "',    num2str(model.annotation.defaultLB), '"\n']);
-0284     end
-0285     if isfield(model.annotation,'defaultUB')
-0286         fprintf(fid, ['    defaultUB: "',    num2str(model.annotation.defaultUB), '"\n']);
-0287     end
-0288     if isfield(model.annotation,'givenName')
-0289         fprintf(fid, ['    givenName: "',    model.annotation.givenName,          '"\n']);
-0290     end
-0291     if isfield(model.annotation,'familyName')
-0292         fprintf(fid, ['    familyName: "',   model.annotation.familyName,         '"\n']);
-0293     end
-0294     if isfield(model.annotation,'authors')
-0295         fprintf(fid, ['    authors: "',      model.annotation.authors,            '"\n']);
-0296     end
-0297     if isfield(model.annotation,'email')
-0298         fprintf(fid, ['    email: "',        model.annotation.email,              '"\n']);
-0299     end
-0300     if isfield(model.annotation,'organization')
-0301         fprintf(fid, ['    organization: "', model.annotation.organization,       '"\n']);
-0302     end
-0303     if isfield(model.annotation,'taxonomy')
-0304         fprintf(fid, ['    taxonomy: "',     model.annotation.taxonomy,           '"\n']);
-0305     end
-0306     if isfield(model.annotation,'note')
-0307         fprintf(fid, ['    note: "',         model.annotation.note,               '"\n']);
-0308     end
-0309     if isfield(model.annotation,'sourceUrl')
-0310         fprintf(fid, ['    sourceUrl: "',    model.annotation.sourceUrl,          '"\n']);
-0311     end
-0312 end
-0313 end
    +0054 %Open file: +0055 fid = fopen(name,'wt'); +0056 fprintf(fid,'---\n!!omap\n'); +0057 +0058 %Insert file header (metadata) +0059 writeMetadata(model,fid); +0060 +0061 %Metabolites: +0062 fprintf(fid,'- metabolites:\n'); +0063 for i = 1:length(model.mets) +0064 fprintf(fid,' - !!omap\n'); +0065 writeField(model, fid, 'mets', 'txt', pos(i), ' - id', preserveQuotes) +0066 writeField(model, fid, 'metNames', 'txt', pos(i), ' - name', preserveQuotes) +0067 writeField(model, fid, 'metComps', 'txt', pos(i), ' - compartment', preserveQuotes) +0068 writeField(model, fid, 'metFormulas', 'txt', pos(i), ' - formula', preserveQuotes) +0069 writeField(model, fid, 'metCharges', 'num', pos(i), ' - charge', preserveQuotes) +0070 writeField(model, fid, 'inchis', 'txt', pos(i), ' - inchis', preserveQuotes) +0071 writeField(model, fid, 'metMiriams', 'txt', pos(i), ' - annotation', preserveQuotes) +0072 writeField(model, fid, 'metFrom', 'txt', pos(i), ' - metFrom', preserveQuotes) +0073 end +0074 +0075 %Reactions: +0076 fprintf(fid,'- reactions:\n'); +0077 for i = 1:length(model.rxns) +0078 fprintf(fid,' - !!omap\n'); +0079 writeField(model, fid, 'rxns', 'txt', pos(i), ' - id', preserveQuotes) +0080 writeField(model, fid, 'rxnNames', 'txt', pos(i), ' - name', preserveQuotes) +0081 writeField(model, fid, 'S', 'txt', pos(i), ' - metabolites', preserveQuotes) +0082 writeField(model, fid, 'lb', 'num', pos(i), ' - lower_bound', preserveQuotes) +0083 writeField(model, fid, 'ub', 'num', pos(i), ' - upper_bound', preserveQuotes) +0084 writeField(model, fid, 'grRules', 'txt', pos(i), ' - gene_reaction_rule', preserveQuotes) +0085 writeField(model, fid, 'rxnFrom', 'txt', pos(i), ' - rxnFrom', preserveQuotes) +0086 if model.c(i)~=0 +0087 writeField(model, fid, 'c', 'num', pos(i), ' - objective_coefficient', preserveQuotes) +0088 end +0089 writeField(model, fid, 'eccodes', 'txt', pos(i), ' - eccodes', preserveQuotes) +0090 writeField(model, fid, 'rxnReferences', 'txt', pos(i), ' - references', preserveQuotes) +0091 writeField(model, fid, 'subSystems', 'txt', pos(i), ' - subsystem', preserveQuotes) +0092 writeField(model, fid, 'rxnMiriams', 'txt', pos(i), ' - annotation', preserveQuotes) +0093 writeField(model, fid, 'rxnConfidenceScores', 'num', pos(i), ' - confidence_score', preserveQuotes) +0094 end +0095 +0096 %Genes: +0097 fprintf(fid,'- genes:\n'); +0098 for i = 1:length(model.genes) +0099 fprintf(fid,' - !!omap\n'); +0100 writeField(model, fid, 'genes', 'txt', pos(i), ' - id', preserveQuotes) +0101 writeField(model, fid, 'geneShortNames', 'txt', pos(i), ' - name', preserveQuotes) +0102 writeField(model, fid, 'geneMiriams', 'txt', pos(i), ' - annotation', preserveQuotes) +0103 end +0104 +0105 %Compartments: +0106 fprintf(fid,'- compartments: !!omap\n'); +0107 for i = 1:length(model.comps) +0108 writeField(model, fid, 'compNames', 'txt', pos(i), ['- ' model.comps{pos(i)}], preserveQuotes) +0109 writeField(model, fid, 'compMiriams', 'txt', pos(i), '- annotation', preserveQuotes) +0110 end +0111 +0112 %Close file: +0113 fclose(fid); +0114 +0115 end +0116 +0117 function writeField(model,fid,fieldName,type,pos,name,preserveQuotes) +0118 %Writes a new line in the yaml file if the field exists and the field is +0119 %not empty at the correspoinding position. It's recursive for some fields +0120 %(metMiriams, rxnMiriams, and S) +0121 +0122 if isfield(model,fieldName) +0123 if strcmp(fieldName,'metComps') +0124 %metComps: write full name +0125 fieldName = 'comps'; +0126 pos = model.metComps(pos); +0127 end +0128 +0129 field = eval(['model.' fieldName]); +0130 +0131 if strcmp(fieldName,'metMiriams') +0132 if ~isempty(model.metMiriams{pos}) +0133 fprintf(fid,[' ' name ': !!omap\n']); +0134 for i=1:size(model.newMetMiriams,2) +0135 %'i' represents the different miriam names, e.g. +0136 %kegg.compound or chebi +0137 if ~isempty(model.newMetMiriams{pos,i}) +0138 %As during the following writeField call the value of +0139 %'i' would be lost, it is temporarily concatenated to +0140 %'name' parameter, which will be edited later +0141 writeField(model, fid, 'newMetMiriams', 'txt', pos, [' - ' model.newMetMiriamNames{i} '_' num2str(i)], preserveQuotes) +0142 end +0143 end +0144 end +0145 +0146 elseif strcmp(fieldName,'rxnMiriams') +0147 if ~isempty(model.rxnMiriams{pos}) +0148 fprintf(fid,[' ' name ': !!omap\n']); +0149 for i=1:size(model.newRxnMiriams,2) +0150 if ~isempty(model.newRxnMiriams{pos,i}) +0151 writeField(model, fid, 'newRxnMiriams', 'txt', pos, [' - ' model.newRxnMiriamNames{i} '_' num2str(i)], preserveQuotes) +0152 end +0153 end +0154 end +0155 +0156 elseif strcmp(fieldName,'geneMiriams') +0157 if ~isempty(model.geneMiriams{pos}) +0158 fprintf(fid,[' ' name ': !!omap\n']); +0159 for i=1:size(model.newGeneMiriams,2) +0160 if ~isempty(model.newGeneMiriams{pos,i}) +0161 writeField(model, fid, 'newGeneMiriams', 'txt', pos, [' - ' model.newGeneMiriamNames{i} '_' num2str(i)], preserveQuotes) +0162 end +0163 end +0164 end +0165 +0166 elseif strcmp(fieldName,'compMiriams') +0167 if ~isempty(model.compMiriams{pos}) +0168 fprintf(fid,[' ' name ': !!omap\n']); +0169 for i=1:size(model.newCompMiriams,2) +0170 if ~isempty(model.newCompMiriams{pos,i}) +0171 writeField(model, fid, 'newCompMiriams', 'txt', pos, [' - ' model.newCompMiriamNames{i} '_' num2str(i)], preserveQuotes) +0172 end +0173 end +0174 end +0175 +0176 elseif strcmp(fieldName,'S') +0177 %S: create header & write each metabolite in a new line +0178 fprintf(fid,[' ' name ': !!omap\n']); +0179 if sum(field(:,pos) ~= 0) > 0 +0180 model.mets = model.mets(field(:,pos) ~= 0); +0181 model.coeffs = field(field(:,pos) ~= 0,pos); +0182 %Sort metabolites: +0183 [model.mets,order] = sort(model.mets); +0184 model.coeffs = model.coeffs(order); +0185 for i = 1:length(model.mets) +0186 writeField(model, fid, 'coeffs', 'num', i, [' - ' model.mets{i}], preserveQuotes) +0187 end +0188 end +0189 +0190 elseif sum(strcmp({'subSystems','newMetMiriams','newRxnMiriams','newGeneMiriams','newCompMiriams','eccodes'},fieldName)) > 0 +0191 %eccodes/rxnNotes: if 1 write in 1 line, if more create header and list +0192 if strcmp(fieldName,'subSystems') +0193 list = field{pos}; %subSystems already comes in a cell array +0194 elseif strcmp(fieldName,'newMetMiriams') +0195 index = str2double(regexprep(name,'^.+_','')); +0196 name = regexprep(name,'_\d+$',''); +0197 list = strsplit(model.newMetMiriams{pos,index},'; '); +0198 elseif strcmp(fieldName,'newRxnMiriams') +0199 index = str2double(regexprep(name,'^.+_','')); +0200 name = regexprep(name,'_\d+$',''); +0201 list = strsplit(model.newRxnMiriams{pos,index},'; '); +0202 elseif strcmp(fieldName,'newGeneMiriams') +0203 index = str2double(regexprep(name,'^.+_','')); +0204 name = regexprep(name,'_\d+$',''); +0205 list = strsplit(model.newGeneMiriams{pos,index},'; '); +0206 elseif strcmp(fieldName,'newCompMiriams') +0207 index = str2double(regexprep(name,'^.+_','')); +0208 name = regexprep(name,'_\d+$',''); +0209 list = strsplit(model.newCompMiriams{pos,index},'; '); +0210 else +0211 list = strrep(field{pos},' ',''); %Exception for eccodes +0212 list = strsplit(list,';'); +0213 end +0214 +0215 if length(list) == 1 && ~strcmp(list{1},'') && ~strcmp(fieldName,'subSystems') +0216 if preserveQuotes +0217 list = strcat('"',list,'"'); +0218 end +0219 fprintf(fid,[' ' name ': ' list{1} '\n']); +0220 elseif length(list) > 1 || strcmp(fieldName,'subSystems') +0221 if preserveQuotes +0222 list = strcat('"',list,'"'); +0223 end +0224 fprintf(fid,[' ' name ':\n']); +0225 for i = 1:length(list) +0226 fprintf(fid,[regexprep(name,'(^\s*).*','$1') ' - ' list{i} '\n']); +0227 end +0228 end +0229 +0230 elseif sum(pos) > 0 +0231 %All other fields: +0232 if strcmp(type,'txt') +0233 value = field{pos}; +0234 if preserveQuotes && ~isempty(value) +0235 value = strcat('"',value,'"'); +0236 end +0237 elseif strcmp(type,'num') +0238 if isnan(field(pos)) +0239 value = []; +0240 else +0241 value = num2str(field(pos),12); +0242 end +0243 end +0244 if ~isempty(value) +0245 fprintf(fid,[' ' name ': ' value '\n']); +0246 end +0247 end +0248 end +0249 +0250 +0251 end +0252 +0253 function writeMetadata(model,fid) +0254 % Writes model metadata to the yaml file. This information will eventually +0255 % be extracted entirely from the model, but for now, many of the entries +0256 % are hard-coded defaults for HumanGEM. +0257 +0258 fprintf(fid, '- metaData:\n'); +0259 fprintf(fid, [' id: "', model.id, '"\n']); +0260 fprintf(fid, [' name: "', model.name, '"\n']); +0261 if isfield(model,'version') +0262 fprintf(fid, [' version: "', model.version, '"\n']); +0263 end +0264 fprintf(fid, [' date: "', datestr(now,29), '"\n']); % 29=YYYY-MM-DD +0265 if isfield(model,'annotation') +0266 if isfield(model.annotation,'defaultLB') +0267 fprintf(fid, [' defaultLB: "', num2str(model.annotation.defaultLB), '"\n']); +0268 end +0269 if isfield(model.annotation,'defaultUB') +0270 fprintf(fid, [' defaultUB: "', num2str(model.annotation.defaultUB), '"\n']); +0271 end +0272 if isfield(model.annotation,'givenName') +0273 fprintf(fid, [' givenName: "', model.annotation.givenName, '"\n']); +0274 end +0275 if isfield(model.annotation,'familyName') +0276 fprintf(fid, [' familyName: "', model.annotation.familyName, '"\n']); +0277 end +0278 if isfield(model.annotation,'authors') +0279 fprintf(fid, [' authors: "', model.annotation.authors, '"\n']); +0280 end +0281 if isfield(model.annotation,'email') +0282 fprintf(fid, [' email: "', model.annotation.email, '"\n']); +0283 end +0284 if isfield(model.annotation,'organization') +0285 fprintf(fid, [' organization: "', model.annotation.organization, '"\n']); +0286 end +0287 if isfield(model.annotation,'taxonomy') +0288 fprintf(fid, [' taxonomy: "', model.annotation.taxonomy, '"\n']); +0289 end +0290 if isfield(model.annotation,'note') +0291 fprintf(fid, [' note: "', model.annotation.note, '"\n']); +0292 end +0293 if isfield(model.annotation,'sourceUrl') +0294 fprintf(fid, [' sourceUrl: "', model.annotation.sourceUrl, '"\n']); +0295 end +0296 end +0297 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/testing/unit_tests/sortIdentifiers_and_permuteModelTests.html b/doc/testing/unit_tests/sortIdentifiers_and_permuteModelTests.html new file mode 100644 index 00000000..c719b047 --- /dev/null +++ b/doc/testing/unit_tests/sortIdentifiers_and_permuteModelTests.html @@ -0,0 +1,103 @@ + + + + Description of sortIdentifiers_and_permuteModelTests + + + + + + + + + +
    Home > testing > unit_tests > sortIdentifiers_and_permuteModelTests.m
    + + + +

    sortIdentifiers_and_permuteModelTests +

    + +

    PURPOSE ^

    +
    run this test case with the command
    + +

    SYNOPSIS ^

    +
    function tests = sortIdentifiers_and_permuteModelTests
    + +

    DESCRIPTION ^

    +
    run this test case with the command
+results = runtests('sortIdentifiers_and_permuteModelTests.m')
    + + +

    CROSS-REFERENCE INFORMATION ^

    +This function calls: + +This function is called by: + + + +

    SUBFUNCTIONS ^

    + + +

    SOURCE CODE ^

    +
    0001 %run this test case with the command
+0002 %results = runtests('sortIdentifiers_and_permuteModelTests.m')
+0003 function tests = sortIdentifiers_and_permuteModelTests
+0004 tests = functiontests(localfunctions);
+0005 end
+0006 
+0007 function sortRandomizedModelTest(testCase)
+0008 
+0009 %Load the expected (i.e. sorted) model
+0010 sourceDir = fileparts(which(mfilename));
+0011 load([sourceDir,'/test_data/ecoli_textbook.mat'], expModel);
+0012 
+0013 %Create the actual model that will be permuted and sorted
+0014 actModel = expModel;
+0015 
+0016 %Randomly permutate model, do not use RAVEN functions
+0017 rndIdx = randperm(numel(actModel.rxns));
+0018 fieldsToChange = {'rxns','lb','ub','rev','c','rxnNames','grRules','eccodes'};
+0019 for i=1:numel(fieldsToChange)
+0020     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0021 end
+0022 actModel.S          = actModel.S(:,rndIdx);
+0023 actModel.rxnGeneMat = actModel.rxnGeneMat(rndIdx,:);
+0024 
+0025 rndIdx = randperm(numel(actModel.mets));
+0026 fieldsToChange = {'mets','metNames','metComps','metFormulas'};
+0027 for i=1:numel(fieldsToChange)
+0028     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0029 end
+0030 actModel.S     = actModel.S(rndIdx,:);
+0031 
+0032 rndIdx = randperm(numel(actModel.genes));
+0033 fieldsToChange = {'genes','geneShortNames'};
+0034 for i=1:numel(fieldsToChange)
+0035     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0036 end
+0037 actModel.rxnGeneMat = actModel.rxnGeneMat(:,rndIdx);
+0038 
+0039 rndIdx = randperm(numel(actModel.comps));
+0040 fieldsToChange = {'comps','compNames'};
+0041 for i=1:numel(fieldsToChange)
+0042     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0043 end
+0044 [~,J]=sort(rndIdx);
+0045 [toreplace, bywhat] = ismember(actModel.metComps,1:length(J));
+0046 actModel.metComps(toreplace) = J(bywhat(toreplace));
+0047 
+0048 %Sort randomly permuted model
+0049 actModel = sortIdentifiers(actModel);
+0050 
+0051 %Check that the actual model is the same as the expected model
+0052 verifyEqual(testCase,actModel,expModel)
+0053 end
    +
    Generated by m2html © 2005
    + + \ No newline at end of file diff --git a/io/exportForGit.m b/io/exportForGit.m index e7da5112..1f80068b 100755 --- a/io/exportForGit.m +++ b/io/exportForGit.m @@ -46,6 +46,9 @@ prefix='model'; end +%Sort reactions, metabolites and genes alphabetically +model=sortIdentifiers(model); + %Get versions or commits of toolboxes: RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',masterFlag); COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',masterFlag); diff --git a/io/exportModel.m b/io/exportModel.m index b51c0b12..be5b64ea 100755 --- a/io/exportModel.m +++ b/io/exportModel.m @@ -1,4 +1,4 @@ -function exportModel(model,fileName,exportGeneComplexes,supressWarnings) +function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds) % exportModel % Exports a constraint-based model to an SBML file (L3V1 FBCv2) % @@ -10,15 +10,23 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings) % (opt, default false) % supressWarnings true if warnings should be supressed (opt, default % false) +% sortIds logical whether metabolites, reactions and genes +% should be sorted alphabetically by their +% identifiers (opt, default false) % -% -% Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings) +% Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds) if nargin<3 exportGeneComplexes=false; end if nargin<4 supressWarnings=false; end +if nargin<5 + sortIds=false; +end +if sortIds==true + model=sortIdentifiers(model); +end %If no subSystems are defined, then no need to use groups package if isfield(model,'subSystems') diff --git a/io/exportToExcelFormat.m b/io/exportToExcelFormat.m index d15a006b..75a6cd34 100755 --- a/io/exportToExcelFormat.m +++ b/io/exportToExcelFormat.m @@ -1,4 +1,4 @@ -function exportToExcelFormat(model,filename) +function exportToExcelFormat(model,filename,sortIds) % exportToExcelFormat % Exports a model structure to the Microsoft Excel model format % @@ -8,6 +8,9 @@ function exportToExcelFormat(model,filename) % be only a path, in which case the model is exported to a set % of tab-delimited text files instead. See exportToTabDelimited % for details regarding that functionality +% sortIds logical whether metabolites, reactions and genes should be +% sorted alphabetically by their identifiers (opt, default +% false) % % The resulting Excel file can be used with importExcelModel/SBMLFromExcel % for modelling or to generate a SBML file. @@ -15,7 +18,13 @@ function exportToExcelFormat(model,filename) % NOTE: No checks are made regarding the correctness of the model. Use % checkModelStruct to identify problems in the model structure % -% Usage: exportToExcelFormat(model,filename) +% Usage: exportToExcelFormat(model,filename,sortIds) +if nargin<3 + sortIds=false; +end +if sortIds==true + model=sortIdentifiers(model); +end [~, A, B]=fileparts(filename); diff --git a/io/exportToTabDelimited.m b/io/exportToTabDelimited.m index b015bad1..137f7601 100755 --- a/io/exportToTabDelimited.m +++ b/io/exportToTabDelimited.m @@ -1,4 +1,4 @@ -function exportToTabDelimited(model,path) +function exportToTabDelimited(model,path,sortIds) % exportToTabDelimited % Exports a model structure to a set of tab-delimited text files % @@ -6,6 +6,8 @@ function exportToTabDelimited(model,path) % path the path to export to. The resulting text files will be saved % under the names excelRxns.txt, excelMets.txt, excelGenes.txt, % excelModel.txt, and excelComps.txt +% sortIds logical whether metabolites, reactions and genes should be +% sorted alphabetically by their identifiers (opt, default false) % % NOTE: This functionality was previously a part of exportToExcelFormat. % The naming of the resulting text files is to preserve backward @@ -14,11 +16,17 @@ function exportToTabDelimited(model,path) % NOTE: No checks are made regarding the correctness of the model. Use % checkModelStruct to identify problems in the model structure % -% Usage: exportToTabDelimited(model,path) +% Usage: exportToTabDelimited(model,path,sortIds) if nargin<2 path='./'; end +if nargin<3 + sortIds=false; +end +if sortIds==true + model=sortIdentifiers(model); +end %If the folder doesn't exist then create it if ~exist(path,'dir') diff --git a/io/sortIdentifiers.m b/io/sortIdentifiers.m new file mode 100644 index 00000000..2974a9eb --- /dev/null +++ b/io/sortIdentifiers.m @@ -0,0 +1,25 @@ +function newModel = sortIdentifiers(model) +% exportModel +% Sort reactions, metabolites, genes and compartments alphabetically by +% their identifier. +% +% Input: +% model a model structure +% +% Output: +% newModel an updated model structure with alphabetically sorted +% identifiers +% +% Usage: newModel=sortIdentifiers(model) + +[~,I]=sort(model.rxns); +newModel=permuteModel(model,I,'rxns'); +[~,I]=sort(newModel.mets); +newModel=permuteModel(newModel,I,'mets'); +if isfield(newModel,'genes') + [~,I]=sort(newModel.genes); + newModel=permuteModel(newModel,I,'genes'); +end +[~,I]=sort(newModel.comps); +newModel=permuteModel(newModel,I,'comps'); +end \ No newline at end of file diff --git a/io/writeYaml.m b/io/writeYaml.m index 1a29ccdd..0f5199d6 100755 --- a/io/writeYaml.m +++ b/io/writeYaml.m @@ -19,7 +19,6 @@ function writeYaml(model,name,preserveQuotes,sortIds) if nargin < 4 sortIds = false; end - if ~endsWith(name,{'.yml','.yaml'}) name = strcat(name,'.yml'); end @@ -29,6 +28,11 @@ function writeYaml(model,name,preserveQuotes,sortIds) model = ravenCobraWrapper(model); end +%Sort identifiers alphabetically +if sortIds == true + model = sortIdentifiers(model); +end + %Simplify Miriam fields: if isfield(model,'metMiriams') [model.newMetMiriams,model.newMetMiriamNames] = extractMiriam(model.metMiriams); @@ -56,11 +60,6 @@ function writeYaml(model,name,preserveQuotes,sortIds) %Metabolites: fprintf(fid,'- metabolites:\n'); -if sortIds==true - [~,pos] = sort(model.mets); -else - pos = 1:numel(model.mets); -end for i = 1:length(model.mets) fprintf(fid,' - !!omap\n'); writeField(model, fid, 'mets', 'txt', pos(i), ' - id', preserveQuotes) @@ -75,11 +74,6 @@ function writeYaml(model,name,preserveQuotes,sortIds) %Reactions: fprintf(fid,'- reactions:\n'); -if sortIds==true - [~,pos] = sort(model.rxns); -else - pos = 1:numel(model.rxns); -end for i = 1:length(model.rxns) fprintf(fid,' - !!omap\n'); writeField(model, fid, 'rxns', 'txt', pos(i), ' - id', preserveQuotes) @@ -101,11 +95,6 @@ function writeYaml(model,name,preserveQuotes,sortIds) %Genes: fprintf(fid,'- genes:\n'); -if sortIds==true - [~,pos] = sort(model.genes); -else - pos = 1:numel(model.genes); -end for i = 1:length(model.genes) fprintf(fid,' - !!omap\n'); writeField(model, fid, 'genes', 'txt', pos(i), ' - id', preserveQuotes) @@ -115,11 +104,6 @@ function writeYaml(model,name,preserveQuotes,sortIds) %Compartments: fprintf(fid,'- compartments: !!omap\n'); -if sortIds==true - [~,pos] = sort(model.comps); -else - pos = 1:numel(model.comps); -end for i = 1:length(model.comps) writeField(model, fid, 'compNames', 'txt', pos(i), ['- ' model.comps{pos(i)}], preserveQuotes) writeField(model, fid, 'compMiriams', 'txt', pos(i), '- annotation', preserveQuotes) diff --git a/testing/unit_tests/sortIdentifiers_and_permuteModelTests.m b/testing/unit_tests/sortIdentifiers_and_permuteModelTests.m new file mode 100644 index 00000000..26cb61a4 --- /dev/null +++ b/testing/unit_tests/sortIdentifiers_and_permuteModelTests.m @@ -0,0 +1,54 @@ +%run this test case with the command +%results = runtests('sortIdentifiers_and_permuteModelTests.m') +function tests = sortIdentifiers_and_permuteModelTests +tests = functiontests(localfunctions); +end + +function sortRandomizedModelTest(testCase) + +%Load the expected (i.e. sorted) model +sourceDir = fileparts(which(mfilename)); +load([sourceDir,'/test_data/ecoli_textbook.mat'], 'model'); +expModel = model; + +%Create the actual model that will be permuted and sorted +actModel = expModel; + +%Randomly permutate model, do not use RAVEN functions +rndIdx = randperm(numel(actModel.rxns)); +fieldsToChange = {'rxns','lb','ub','rev','c','rxnNames','grRules','eccodes'}; +for i=1:numel(fieldsToChange) + actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx); +end +actModel.S = actModel.S(:,rndIdx); +actModel.rxnGeneMat = actModel.rxnGeneMat(rndIdx,:); + +rndIdx = randperm(numel(actModel.mets)); +fieldsToChange = {'mets','metNames','metComps','metFormulas'}; +for i=1:numel(fieldsToChange) + actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx); +end +actModel.S = actModel.S(rndIdx,:); + +rndIdx = randperm(numel(actModel.genes)); +fieldsToChange = {'genes','geneShortNames'}; +for i=1:numel(fieldsToChange) + actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx); +end +actModel.rxnGeneMat = actModel.rxnGeneMat(:,rndIdx); + +rndIdx = randperm(numel(actModel.comps)); +fieldsToChange = {'comps','compNames'}; +for i=1:numel(fieldsToChange) + actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx); +end +[~,J]=sort(rndIdx); +[toreplace, bywhat] = ismember(actModel.metComps,1:length(J)); +actModel.metComps(toreplace) = J(bywhat(toreplace)); + +%Sort randomly permutated model +actModel = sortIdentifiers(actModel); + +%Check that the actual model is the same as the expected model +verifyEqual(testCase,actModel,expModel) +end diff --git a/testing/unit_tests/test_data/ecoli_textbook.mat b/testing/unit_tests/test_data/ecoli_textbook.mat new file mode 100644 index 00000000..546abbae Binary files /dev/null and b/testing/unit_tests/test_data/ecoli_textbook.mat differ