From e4c1a236e0b77f699227bc6300ac1fde6c04c666 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 21 Dec 2024 21:42:53 +0100 Subject: [PATCH 1/2] fix: various minor bugs (#575) * fix: closeModel comps-related fields * fix: generateNewIds default quantity * fix: readYAMLmodel if multiple annotations * chore: updateDocumentation * fix: read- and writeYAMLmodel empty fields * fix: generateNewIds if prefix used without numbers --- core/generateNewIds.m | 8 +- doc/core/generateNewIds.html | 52 +- doc/io/closeModel.html | 30 +- doc/io/readYAMLmodel.html | 1218 +++++++++++++++++----------------- doc/io/writeYAMLmodel.html | 181 ++--- io/closeModel.m | 30 +- io/readYAMLmodel.m | 18 +- io/writeYAMLmodel.m | 3 + 8 files changed, 779 insertions(+), 761 deletions(-) diff --git a/core/generateNewIds.m b/core/generateNewIds.m index d8b535c8..f66c6aa5 100755 --- a/core/generateNewIds.m +++ b/core/generateNewIds.m @@ -26,6 +26,9 @@ else error('type should be either ''rxns'' or ''mets''.') end +if nargin<4 + quantity=1; +end if nargin<5 numLength=4; end @@ -44,7 +47,10 @@ fprintf(['No ' type ' ids with prefix "' prefix ... '" currently exist in the model. The first new id will be "' ... [prefix,num2str(1,['%0' num2str(numLength) 'd'])] '"\n'],'%s') - lastId=0; +end + +if isnan(lastId) + lastId = 0; end newIds=cell(quantity,1); diff --git a/doc/core/generateNewIds.html b/doc/core/generateNewIds.html index 9bd3b1ea..557c9603 100644 --- a/doc/core/generateNewIds.html +++ b/doc/core/generateNewIds.html @@ -85,33 +85,39 @@

SOURCE CODE ^else 0027 error('type should be either ''rxns'' or ''mets''.') 0028 end -0029 if nargin<5 -0030 numLength=4; +0029 if nargin<4 +0030 quantity=1; 0031 end -0032 -0033 % Subset only existingIds that have the prefix -0034 existingIds=existingIds(~cellfun(@isempty,regexp(existingIds,['^' prefix]))); +0032 if nargin<5 +0033 numLength=4; +0034 end 0035 -0036 if ~isempty(existingIds) -0037 existingIds=regexprep(existingIds,['^' prefix],''); -0038 existingIds=sort(existingIds); -0039 lastId=existingIds{end}; -0040 numLength=length(lastId); -0041 lastId=str2double(lastId); -0042 else -0043 lastId=0; -0044 fprintf(['No ' type ' ids with prefix "' prefix ... -0045 '" currently exist in the model. The first new id will be "' ... -0046 [prefix,num2str(1,['%0' num2str(numLength) 'd'])] '"\n'],'%s') -0047 lastId=0; -0048 end -0049 -0050 newIds=cell(quantity,1); +0036 % Subset only existingIds that have the prefix +0037 existingIds=existingIds(~cellfun(@isempty,regexp(existingIds,['^' prefix]))); +0038 +0039 if ~isempty(existingIds) +0040 existingIds=regexprep(existingIds,['^' prefix],''); +0041 existingIds=sort(existingIds); +0042 lastId=existingIds{end}; +0043 numLength=length(lastId); +0044 lastId=str2double(lastId); +0045 else +0046 lastId=0; +0047 fprintf(['No ' type ' ids with prefix "' prefix ... +0048 '" currently exist in the model. The first new id will be "' ... +0049 [prefix,num2str(1,['%0' num2str(numLength) 'd'])] '"\n'],'%s') +0050 end 0051 -0052 for k=1:quantity -0053 newIds{k}=[prefix,num2str(k+lastId,['%0' num2str(numLength) 'd'])]; +0052 if isnan(lastId) +0053 lastId = 0; 0054 end -0055 end +0055 +0056 newIds=cell(quantity,1); +0057 +0058 for k=1:quantity +0059 newIds{k}=[prefix,num2str(k+lastId,['%0' num2str(numLength) 'd'])]; +0060 end +0061 end
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\ No newline at end of file diff --git a/doc/io/closeModel.html b/doc/io/closeModel.html index aeb88f3d..a8db94c9 100644 --- a/doc/io/closeModel.html +++ b/doc/io/closeModel.html @@ -63,11 +63,11 @@

SOURCE CODE ^'b'; -0015 closedModel.compNames{numel(closedModel.compNames)+1}='boundary'; +0014 closedModel.comps{numel(closedModel.comps)+1,1}='b'; +0015 closedModel.compNames{numel(closedModel.compNames)+1,1}='boundary'; 0016 if isfield(closedModel,'compMiriams') -0017 closedModel.compMiriams{numel(closedModel.compMiriams)+1}=[]; -0018 end; +0017 closedModel.compMiriams{numel(closedModel.compMiriams)+1,1}=[]; +0018 end 0019 closedModel.unconstrained=zeros(numel(closedModel.mets),1); 0020 0021 for i=1:numel(closedModel.rxns) @@ -75,29 +75,29 @@

SOURCE CODE ^'_b'); 0024 if isfield(closedModel,'metNames') 0025 closedModel.metNames{numel(closedModel.metNames)+1}=closedModel.metNames{find(closedModel.S(:,i))}; -0026 end; +0026 end 0027 closedModel.metComps(numel(closedModel.metComps)+1)=numel(closedModel.comps); 0028 if isfield(closedModel,'inchis') 0029 closedModel.inchis{numel(closedModel.inchis)+1}=closedModel.inchis{find(closedModel.S(:,i))}; -0030 end; +0030 end 0031 if isfield(closedModel,'metSmiles') 0032 closedModel.metSmiles{numel(closedModel.metSmiles)+1}=closedModel.metSmiles{find(closedModel.S(:,i))}; -0033 end; +0033 end 0034 if isfield(closedModel,'metFormulas') 0035 closedModel.metFormulas{numel(closedModel.metFormulas)+1}=closedModel.metFormulas{find(closedModel.S(:,i))}; -0036 end; +0036 end 0037 if isfield(closedModel,'metMiriams') 0038 closedModel.metMiriams{numel(closedModel.metMiriams)+1}=closedModel.metMiriams{find(closedModel.S(:,i))}; -0039 end; +0039 end 0040 if isfield(closedModel,'metFrom') 0041 closedModel.metFrom{numel(closedModel.metFrom)+1}=''; -0042 end; +0042 end 0043 if isfield(closedModel,'metCharges') 0044 closedModel.metCharges(numel(closedModel.metCharges)+1)=closedModel.metCharges(find(closedModel.S(:,i))); -0045 end; +0045 end 0046 if isfield(closedModel,'metDeltaG') 0047 closedModel.metDeltaG(numel(closedModel.metDeltaG)+1)=closedModel.metDeltaG(find(closedModel.S(:,i))); -0048 end; +0048 end 0049 closedModel.unconstrained(numel(closedModel.unconstrained)+1)=1; 0050 closedModel.b(numel(closedModel.b)+1)=0; 0051 closedModel.S=[closedModel.S;sparse(1,size(closedModel.S,2))]; @@ -105,9 +105,9 @@

SOURCE CODE ^else 0055 closedModel.S(numel(closedModel.mets),i)=1; -0056 end; -0057 end; -0058 end; +0056 end +0057 end +0058 end 0059 0060 end
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diff --git a/doc/io/readYAMLmodel.html b/doc/io/readYAMLmodel.html index 348b94b7..3a96f8c3 100644 --- a/doc/io/readYAMLmodel.html +++ b/doc/io/readYAMLmodel.html @@ -52,7 +52,7 @@

CROSS-REFERENCE INFORMATION ^ <h2><a name=SUBFUNCTIONS ^

+
  • function model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)
  • function model = readFieldValue(model, fieldName, value, pos)
  • function [miriams,miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber)

    • SOURCE CODE ^

    0001 function model=readYAMLmodel(fileName, verbose)
@@ -109,631 +109,631 @@ 
    SOURCE CODE ^end
 0053 line_raw(brokenLine)=[];
 0054 
-0055 line_key = regexprep(line_raw,'^ *-? ([^:]+)(:).*','$1');
+0055 line_key = regexprep(line_raw,'^ *-? ([^:]+)(:)($| .*)','$1');
 0056 line_key = regexprep(line_key,'(.*!!omap)|(---)|( {4,}.*)','');
 0057 
 0058 line_value = regexprep(line_raw, '.*:$','');
 0059 line_value = regexprep(line_value, '[^":]+: "?(.+)"?$','$1');
 0060 line_value = regexprep(line_value, '(")|(^ {4,}- )','');
 0061 
-0062 modelFields =   {'id',char();...
-0063                'name',char();...
-0064         'description',char();...
-0065             'version',char();...
-0066                'date',char();...
-0067          'annotation',struct();...
-0068                'rxns',{};...
-0069            'rxnNames',{};...
-0070                'mets',{};...
-0071            'metNames',{};...
-0072                   'S',sparse([]);...
-0073                  'lb',{};... %Changed to double in the end.
-0074                  'ub',{};... %Changed to double in the end.
-0075                 'rev',{};... %Changed to double in the end.
-0076                   'c',[];...
-0077                   'b',cell(0,0);... %Changed to double in the end.
-0078               'genes',cell(0,0);...
-0079             'grRules',cell(0,0);...
-0080          'rxnGeneMat',sparse([]);...
-0081            'rxnComps',cell(0,0);... %Changed to double in the end.
-0082          'subSystems',cell(0,0);...
-0083             'eccodes',cell(0,0);...
-0084          'rxnMiriams',cell(0,0);...
-0085           'rxnDeltaG',{};... %Changed to double in the end.
-0086            'rxnNotes',cell(0,0);...
-0087       'rxnReferences',cell(0,0);...
-0088 'rxnConfidenceScores',cell(0,0);...
-0089            'metComps',cell(0,0);... %Changed to double in the end.
-0090              'inchis',cell(0,0);...
-0091           'metSmiles',cell(0,0);...
-0092         'metFormulas',cell(0,0);...
-0093          'metMiriams',cell(0,0);...
-0094           'metDeltaG',{};... %Changed to double in the end.
-0095          'metCharges',cell(0,0);... %Changed to double in the end.
-0096            'metNotes',cell(0,0);...
-0097               'comps',cell(0,0);...
-0098           'compNames',cell(0,0);...
-0099         'compOutside',cell(0,0);...
-0100           'geneComps',cell(0,0);... %Changed to double in the end.
-0101         'geneMiriams',cell(0,0);...
-0102      'geneShortNames',cell(0,0);...
-0103        'proteins',cell(0,0);...
-0104       'unconstrained',cell(0,0);... %Changed to double in the end.
-0105             'metFrom',cell(0,0);...
-0106             'rxnFrom',cell(0,0)};
-0107 for i=1:size(modelFields,1)
-0108     model.(modelFields{i,1})=modelFields{i,2};
-0109 end
-0110 
-0111 % If GECKO model
-0112 if any(contains(line_key,'geckoLight'))
-0113     isGECKO=true;
-0114     ecFields = {'geckoLight', false;...
-0115                       'rxns', {};...
-0116                       'kcat', {};...
-0117                     'source', cell(0,0);...
-0118                      'notes', cell(0,0);...
-0119                    'eccodes', cell(0,0);...
-0120                      'genes', cell(0,0);...
-0121                    'enzymes', cell(0,0);...
-0122                         'mw', cell(0,0);...
-0123                   'sequence', cell(0,0);...
-0124                      'concs', cell(0,0);...
-0125                  'rxnEnzMat', []};
-0126     for i=1:size(ecFields,1)
-0127         model.ec.(ecFields{i,1})=ecFields{i,2};
-0128     end
-0129     ecGecko=cell(25000,2);      ecGeckoNo=1;
-0130     enzStoich=cell(100000,3);   enzStoichNo=1;
-0131 else
-0132     isGECKO=false;
-0133 end
-0134 
-0135 section = 0;
-0136 metMiriams=cell(100000,3);   metMirNo=1;
-0137 rxnMiriams=cell(100000,3);   rxnMirNo=1;
-0138 geneMiriams=cell(100000,3);  genMirNo=1;
-0139 subSystems=cell(100000,2);   subSysNo=1;
-0140 eccodes=cell(100000,2);      ecCodeNo=1;
-0141 equations=cell(100000,3);   equatiNo=1;
-0142 
-0143 for i=1:numel(line_key)
-0144     tline_raw = line_raw{i};
-0145     tline_key = line_key{i};
-0146     tline_value = line_value{i};
-0147     % import different sections
-0148     switch tline_raw
-0149         case '- metaData:'
-0150             section = 1;
-0151             if verbose
-0152                 fprintf('\t%d\n', section);
-0153             end
-0154             continue % Go to next line
-0155         case '- metabolites:'
-0156             section = 2;
-0157             if verbose
-0158                 fprintf('\t%d\n', section);
-0159             end
-0160             pos=0;
-0161             continue
-0162         case '- reactions:'
-0163             section = 3;
-0164             if verbose
-0165                 fprintf('\t%d\n', section);
-0166             end
-0167             pos=0;
-0168             continue
-0169         case '- genes:'
-0170             section = 4;
-0171             if verbose
-0172                 fprintf('\t%d\n', section);
-0173             end
-0174             pos=0;
-0175             continue
-0176         case '- compartments: !!omap'
-0177             section = 5;
-0178             if verbose
-0179                 fprintf('\t%d\n', section);
-0180             end
-0181             pos=0;
-0182             continue
-0183         case '- ec-rxns:'
-0184             section = 6;
-0185             if verbose
-0186                 fprintf('\t%d\n', section);
-0187             end
-0188             pos=0;
-0189             continue
-0190         case '- ec-enzymes:'
-0191             section = 7;
-0192             if verbose
-0193                 fprintf('\t%d\n', section);
-0194             end
-0195             pos=0;
-0196             continue
-0197     end
-0198 
-0199     % skip over empty keys
-0200     if isempty(tline_raw) || (isempty(tline_key) && contains(tline_raw,'!!omap'))
-0201         continue;
-0202     end
-0203     
-0204     % import metaData
-0205     if section == 1
-0206         switch tline_key
-0207             case {'short_name','id'} %short_name used by human-GEM
-0208                 model.id = tline_value;
-0209             case 'name'
-0210                 model.name = tline_value;                
-0211             case 'full_name' %used by human-GEM
-0212                 model.description = tline_value;
-0213             case 'version'
-0214                 model.version = tline_value;
-0215             case 'date'
-0216                 model.date = tline_value;                
-0217             case 'taxonomy'
-0218                 model.annotation.taxonomy = tline_value;
-0219             case {'description','note'} %description used by human-GEM
-0220                 model.annotation.note = tline_value;
-0221             case 'github'
-0222                 model.annotation.sourceUrl = tline_value;
-0223             case 'givenName'
-0224                 model.annotation.givenName = tline_value;
-0225             case 'familyName'
-0226                 model.annotation.familyName = tline_value;
-0227             case 'authors'
-0228                 model.annotation.authorList = tline_value;
-0229             case 'email'
-0230                 model.annotation.email = tline_value;
-0231             case 'organization'
-0232                 model.annotation.organization = tline_value;
-0233             case 'geckoLight'
-0234                 if strcmp(tline_value,'true')
-0235                     model.ec.geckoLight = true;
-0236                 end
-0237         end; continue
-0238     end
-0239 
-0240     % import metabolites:
-0241     if section == 2
-0242         switch tline_key
-0243             case 'id'
-0244                 pos = pos + 1;
-0245                 model = readFieldValue(model, 'mets', tline_value,pos);
-0246                 readList=''; miriamKey='';
-0247             case 'name'
-0248                 model = readFieldValue(model, 'metNames', tline_value, pos);
-0249                 readList=''; miriamKey='';
-0250             case 'compartment'
-0251                 model = readFieldValue(model, 'metComps', tline_value, pos);
-0252                 readList=''; miriamKey='';
-0253             case 'formula'
-0254                 model = readFieldValue(model, 'metFormulas', tline_value, pos);
-0255                 readList=''; miriamKey='';
-0256             case 'charge'
-0257                 model = readFieldValue(model, 'metCharges', tline_value, pos);
-0258                 readList=''; miriamKey='';
-0259             case 'notes'
-0260                 model = readFieldValue(model, 'metNotes', tline_value, pos);
-0261                 readList=''; miriamKey='';
-0262             case 'inchis'
-0263                 model = readFieldValue(model, 'inchis', tline_value, pos);
-0264                 readList=''; miriamKey='';
-0265             case 'smiles'
-0266                 model = readFieldValue(model, 'metSmiles', tline_value, pos);
-0267                 readList=''; miriamKey='';    
-0268             case 'deltaG'
-0269                 model = readFieldValue(model, 'metDeltaG', tline_value, pos);
-0270                 readList=''; miriamKey='';                                
-0271             case 'metFrom'
-0272                 model = readFieldValue(model, 'metFrom', tline_value, pos);
-0273                 readList=''; miriamKey='';
-0274             case 'annotation'
-0275                 readList = 'annotation';
-0276             otherwise
-0277                 switch readList
-0278                     case 'annotation'
-0279                         [metMiriams, miriamKey] = gatherAnnotation(pos,metMiriams,tline_key,tline_value,miriamKey,metMirNo);
-0280                         metMirNo = metMirNo + 1;
-0281                     otherwise
-0282                         error(['Unknown entry in yaml file: ' tline_raw])
-0283                 end
-0284         end; continue
-0285     end
-0286 
-0287     % import reactions:
-0288     if section == 3
-0289         switch tline_key
-0290             case 'id'
-0291                 pos = pos + 1;
-0292                 model = readFieldValue(model, 'rxns', tline_value,pos);
-0293                 readList=''; miriamKey='';
-0294             case 'name'
-0295                 model = readFieldValue(model, 'rxnNames', tline_value, pos);
+0062 line_value(strcmp(line_value,line_raw)) = {''};
+0063 
+0064 modelFields =   {'id',char();...
+0065                'name',char();...
+0066         'description',char();...
+0067             'version',char();...
+0068                'date',char();...
+0069          'annotation',struct();...
+0070                'rxns',{};...
+0071            'rxnNames',{};...
+0072                'mets',{};...
+0073            'metNames',{};...
+0074                   'S',sparse([]);...
+0075                  'lb',{};... %Changed to double in the end.
+0076                  'ub',{};... %Changed to double in the end.
+0077                 'rev',{};... %Changed to double in the end.
+0078                   'c',[];...
+0079                   'b',cell(0,0);... %Changed to double in the end.
+0080               'genes',cell(0,0);...
+0081             'grRules',cell(0,0);...
+0082          'rxnGeneMat',sparse([]);...
+0083            'rxnComps',cell(0,0);... %Changed to double in the end.
+0084          'subSystems',cell(0,0);...
+0085             'eccodes',cell(0,0);...
+0086          'rxnMiriams',cell(0,0);...
+0087           'rxnDeltaG',{};... %Changed to double in the end.
+0088            'rxnNotes',cell(0,0);...
+0089       'rxnReferences',cell(0,0);...
+0090 'rxnConfidenceScores',cell(0,0);...
+0091            'metComps',cell(0,0);... %Changed to double in the end.
+0092              'inchis',cell(0,0);...
+0093           'metSmiles',cell(0,0);...
+0094         'metFormulas',cell(0,0);...
+0095          'metMiriams',cell(0,0);...
+0096           'metDeltaG',{};... %Changed to double in the end.
+0097          'metCharges',cell(0,0);... %Changed to double in the end.
+0098            'metNotes',cell(0,0);...
+0099               'comps',cell(0,0);...
+0100           'compNames',cell(0,0);...
+0101         'compOutside',cell(0,0);...
+0102           'geneComps',cell(0,0);... %Changed to double in the end.
+0103         'geneMiriams',cell(0,0);...
+0104      'geneShortNames',cell(0,0);...
+0105        'proteins',cell(0,0);...
+0106       'unconstrained',cell(0,0);... %Changed to double in the end.
+0107             'metFrom',cell(0,0);...
+0108             'rxnFrom',cell(0,0)};
+0109 for i=1:size(modelFields,1)
+0110     model.(modelFields{i,1})=modelFields{i,2};
+0111 end
+0112 
+0113 % If GECKO model
+0114 if any(contains(line_key,'geckoLight'))
+0115     isGECKO=true;
+0116     ecFields = {'geckoLight', false;...
+0117                       'rxns', {};...
+0118                       'kcat', {};...
+0119                     'source', cell(0,0);...
+0120                      'notes', cell(0,0);...
+0121                    'eccodes', cell(0,0);...
+0122                      'genes', cell(0,0);...
+0123                    'enzymes', cell(0,0);...
+0124                         'mw', cell(0,0);...
+0125                   'sequence', cell(0,0);...
+0126                      'concs', cell(0,0);...
+0127                  'rxnEnzMat', []};
+0128     for i=1:size(ecFields,1)
+0129         model.ec.(ecFields{i,1})=ecFields{i,2};
+0130     end
+0131     ecGecko=cell(25000,2);      ecGeckoNo=1;
+0132     enzStoich=cell(100000,3);   enzStoichNo=1;
+0133 else
+0134     isGECKO=false;
+0135 end
+0136 
+0137 section = 0;
+0138 metMiriams=cell(100000,3);   metMirNo=1;
+0139 rxnMiriams=cell(100000,3);   rxnMirNo=1;
+0140 geneMiriams=cell(100000,3);  genMirNo=1;
+0141 subSystems=cell(100000,2);   subSysNo=1;
+0142 eccodes=cell(100000,2);      ecCodeNo=1;
+0143 equations=cell(100000,3);   equatiNo=1;
+0144 
+0145 for i=1:numel(line_key)
+0146     tline_raw = line_raw{i};
+0147     tline_key = line_key{i};
+0148     tline_value = line_value{i};
+0149     % import different sections
+0150     switch tline_raw
+0151         case '- metaData:'
+0152             section = 1;
+0153             if verbose
+0154                 fprintf('\t%d\n', section);
+0155             end
+0156             continue % Go to next line
+0157         case '- metabolites:'
+0158             section = 2;
+0159             if verbose
+0160                 fprintf('\t%d\n', section);
+0161             end
+0162             pos=0;
+0163             continue
+0164         case '- reactions:'
+0165             section = 3;
+0166             if verbose
+0167                 fprintf('\t%d\n', section);
+0168             end
+0169             pos=0;
+0170             continue
+0171         case '- genes:'
+0172             section = 4;
+0173             if verbose
+0174                 fprintf('\t%d\n', section);
+0175             end
+0176             pos=0;
+0177             continue
+0178         case '- compartments: !!omap'
+0179             section = 5;
+0180             if verbose
+0181                 fprintf('\t%d\n', section);
+0182             end
+0183             pos=0;
+0184             continue
+0185         case '- ec-rxns:'
+0186             section = 6;
+0187             if verbose
+0188                 fprintf('\t%d\n', section);
+0189             end
+0190             pos=0;
+0191             continue
+0192         case '- ec-enzymes:'
+0193             section = 7;
+0194             if verbose
+0195                 fprintf('\t%d\n', section);
+0196             end
+0197             pos=0;
+0198             continue
+0199     end
+0200 
+0201     % skip over empty keys
+0202     if isempty(tline_raw) || (isempty(tline_key) && contains(tline_raw,'!!omap'))
+0203         continue;
+0204     end
+0205     
+0206     % import metaData
+0207     if section == 1
+0208         switch tline_key
+0209             case {'short_name','id'} %short_name used by human-GEM
+0210                 model.id = tline_value;
+0211             case 'name'
+0212                 model.name = tline_value;                
+0213             case 'full_name' %used by human-GEM
+0214                 model.description = tline_value;
+0215             case 'version'
+0216                 model.version = tline_value;
+0217             case 'date'
+0218                 model.date = tline_value;                
+0219             case 'taxonomy'
+0220                 model.annotation.taxonomy = tline_value;
+0221             case {'description','note'} %description used by human-GEM
+0222                 model.annotation.note = tline_value;
+0223             case 'github'
+0224                 model.annotation.sourceUrl = tline_value;
+0225             case 'sourceUrl'
+0226                 model.annotation.sourceUrl = tline_value;                
+0227             case 'givenName'
+0228                 model.annotation.givenName = tline_value;
+0229             case 'familyName'
+0230                 model.annotation.familyName = tline_value;
+0231             case 'authors'
+0232                 model.annotation.authorList = tline_value;
+0233             case 'email'
+0234                 model.annotation.email = tline_value;
+0235             case 'organization'
+0236                 model.annotation.organization = tline_value;
+0237             case 'geckoLight'
+0238                 if strcmp(tline_value,'true')
+0239                     model.ec.geckoLight = true;
+0240                 end
+0241         end; continue
+0242     end
+0243 
+0244     % import metabolites:
+0245     if section == 2
+0246         switch tline_key
+0247             case 'id'
+0248                 pos = pos + 1;
+0249                 model = readFieldValue(model, 'mets', tline_value,pos);
+0250                 readList=''; miriamKey='';
+0251             case 'name'
+0252                 model = readFieldValue(model, 'metNames', tline_value, pos);
+0253                 readList=''; miriamKey='';
+0254             case 'compartment'
+0255                 model = readFieldValue(model, 'metComps', tline_value, pos);
+0256                 readList=''; miriamKey='';
+0257             case 'formula'
+0258                 model = readFieldValue(model, 'metFormulas', tline_value, pos);
+0259                 readList=''; miriamKey='';
+0260             case 'charge'
+0261                 model = readFieldValue(model, 'metCharges', tline_value, pos);
+0262                 readList=''; miriamKey='';
+0263             case 'notes'
+0264                 model = readFieldValue(model, 'metNotes', tline_value, pos);
+0265                 readList=''; miriamKey='';
+0266             case 'inchis'
+0267                 model = readFieldValue(model, 'inchis', tline_value, pos);
+0268                 readList=''; miriamKey='';
+0269             case 'smiles'
+0270                 model = readFieldValue(model, 'metSmiles', tline_value, pos);
+0271                 readList=''; miriamKey='';    
+0272             case 'deltaG'
+0273                 model = readFieldValue(model, 'metDeltaG', tline_value, pos);
+0274                 readList=''; miriamKey='';                                
+0275             case 'metFrom'
+0276                 model = readFieldValue(model, 'metFrom', tline_value, pos);
+0277                 readList=''; miriamKey='';
+0278             case 'annotation'
+0279                 readList = 'annotation';
+0280             otherwise
+0281                 switch readList
+0282                     case 'annotation'
+0283                         [metMiriams, miriamKey, metMirNo] = gatherAnnotation(pos,metMiriams,tline_key,tline_value,miriamKey,metMirNo);
+0284                     otherwise
+0285                         error(['Unknown entry in yaml file: ' tline_raw])
+0286                 end
+0287         end; continue
+0288     end
+0289 
+0290     % import reactions:
+0291     if section == 3
+0292         switch tline_key
+0293             case 'id'
+0294                 pos = pos + 1;
+0295                 model = readFieldValue(model, 'rxns', tline_value,pos);
 0296                 readList=''; miriamKey='';
-0297             case 'lower_bound'
-0298                 model.lb(pos,1) = {tline_value};
+0297             case 'name'
+0298                 model = readFieldValue(model, 'rxnNames', tline_value, pos);
 0299                 readList=''; miriamKey='';
-0300             case 'upper_bound'
-0301                 model.ub(pos,1) = {tline_value};
+0300             case 'lower_bound'
+0301                 model.lb(pos,1) = {tline_value};
 0302                 readList=''; miriamKey='';
-0303             case 'rev'
-0304                 model.rev(pos,1) = {tline_value};
+0303             case 'upper_bound'
+0304                 model.ub(pos,1) = {tline_value};
 0305                 readList=''; miriamKey='';
-0306             case 'gene_reaction_rule'
-0307                 model = readFieldValue(model, 'grRules', tline_value, pos);
+0306             case 'rev'
+0307                 model.rev(pos,1) = {tline_value};
 0308                 readList=''; miriamKey='';
-0309             case 'rxnNotes'
-0310                 model = readFieldValue(model, 'rxnNotes', tline_value, pos);
+0309             case 'gene_reaction_rule'
+0310                 model = readFieldValue(model, 'grRules', tline_value, pos);
 0311                 readList=''; miriamKey='';
-0312             case 'rxnFrom'
-0313                 model = readFieldValue(model, 'rxnFrom', tline_value, pos);
+0312             case 'rxnNotes'
+0313                 model = readFieldValue(model, 'rxnNotes', tline_value, pos);
 0314                 readList=''; miriamKey='';
-0315             case 'deltaG'
-0316                 model = readFieldValue(model, 'rxnDeltaG', tline_value, pos);
-0317                 readList=''; miriamKey='';                
-0318             case 'objective_coefficient'
-0319                 model.c(pos,1) = 1;
-0320                 readList=''; miriamKey='';
-0321             case 'references'
-0322                 model = readFieldValue(model, 'rxnReferences', tline_value, pos);
+0315             case 'rxnFrom'
+0316                 model = readFieldValue(model, 'rxnFrom', tline_value, pos);
+0317                 readList=''; miriamKey='';
+0318             case 'deltaG'
+0319                 model = readFieldValue(model, 'rxnDeltaG', tline_value, pos);
+0320                 readList=''; miriamKey='';                
+0321             case 'objective_coefficient'
+0322                 model.c(pos,1) = 1;
 0323                 readList=''; miriamKey='';
-0324             case 'confidence_score'
-0325                 model = readFieldValue(model, 'rxnConfidenceScores', tline_value, pos);
+0324             case 'references'
+0325                 model = readFieldValue(model, 'rxnReferences', tline_value, pos);
 0326                 readList=''; miriamKey='';
-0327             case 'eccodes'
-0328                 if isempty(tline_value)
-0329                     readList = 'eccodes';
-0330                 else
-0331                     eccodes(ecCodeNo,1:2)={pos,tline_value};
-0332                     ecCodeNo=ecCodeNo+1;
-0333                 end
-0334             case 'subsystem'
-0335                 if isempty(tline_value)
-0336                     readList = 'subsystem';
-0337                 else
-0338                     subSystems(subSysNo,1:2)={pos,tline_value};
-0339                     subSysNo=subSysNo+1;
-0340                 end
-0341             case 'metabolites'
-0342                 readList = 'equation';
-0343             case 'annotation'
-0344                 readList = 'annotation';
-0345                 
-0346             otherwise
-0347                 switch readList
-0348                     case 'eccodes'
-0349                         eccodes(ecCodeNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
-0350                         ecCodeNo=ecCodeNo+1;
-0351                     case 'subsystem'
-0352                         subSystems(subSysNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
-0353                         subSysNo=subSysNo+1;
-0354                     case 'annotation'
-0355                         [rxnMiriams, miriamKey,rxnMirNo] = gatherAnnotation(pos,rxnMiriams,tline_key,tline_value,miriamKey,rxnMirNo);
-0356                         rxnMirNo=rxnMirNo+1;
-0357                     case 'equation'
-0358                         coeff = sscanf(tline_value,'%f');
-0359                         equations(equatiNo,1:3)={pos,tline_key,coeff};
-0360                         equatiNo=equatiNo+1;
-0361                     otherwise
-0362                         error(['Unknown entry in yaml file: ' tline_raw])
-0363                 end                
-0364         end; continue
-0365     end
-0366 
-0367     % import genes:
-0368     if section == 4
-0369         switch tline_key
-0370             case 'id'
-0371                 pos = pos + 1;
-0372                 model = readFieldValue(model, 'genes', tline_value, pos);
-0373                 readList = '';
-0374                 miriamKey = '';
-0375             case 'name'
-0376                 model = readFieldValue(model, 'geneShortNames', tline_value, pos);
-0377             case 'protein'
-0378                 model = readFieldValue(model, 'proteins', tline_value, pos);
-0379             case 'annotation'
-0380                 readList = 'annotation';
-0381             otherwise
-0382                 switch readList
-0383                     case 'annotation'
-0384                         [geneMiriams, miriamKey] = gatherAnnotation(pos,geneMiriams,tline_key,tline_value,miriamKey,genMirNo);
-0385                         genMirNo = genMirNo + 1;
-0386                     otherwise
-0387                         error(['Unknown entry in yaml file: ' tline_raw])
-0388                 end
-0389         end; continue
-0390     end
-0391 
-0392     % import compartments:
-0393     if section == 5
-0394         model.comps(end+1,1) = {tline_key};
-0395         model.compNames(end+1,1) = {tline_value};
-0396     end
-0397 
-0398     % import ec reaction info
-0399     if section == 6
-0400         switch tline_key
-0401             case 'id'
-0402                 pos = pos + 1;
-0403                 model.ec = readFieldValue(model.ec, 'rxns', tline_value, pos);
-0404                 readList='';
-0405             case 'kcat'
-0406                 model.ec = readFieldValue(model.ec, 'kcat', tline_value, pos);
-0407                 readList='';
-0408             case 'source'
-0409                 model.ec = readFieldValue(model.ec, 'source', tline_value, pos);
-0410                 readList='';
-0411             case 'notes'
-0412                 model.ec = readFieldValue(model.ec, 'notes', tline_value, pos);
-0413                 readList='';
-0414             case 'eccodes'
-0415                 if isempty(tline_value)
-0416                     readList = 'eccodes';
-0417                 else
-0418                     ecGecko(ecGeckoNo,1:2)={pos,tline_value};
-0419                     ecGeckoNo=ecGeckoNo+1;
-0420                 end
-0421             case 'enzymes'
-0422                 readList = 'enzStoich';
-0423             otherwise
-0424                 switch readList
-0425                     case 'eccodes'
-0426                         ecGecko(ecGeckoNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
-0427                         ecGeckoNo=ecGeckoNo+1;
-0428                     case 'enzStoich'
-0429                         coeff = sscanf(tline_value,'%f');
-0430                         enzStoich(enzStoichNo,1:3)={pos,tline_key,coeff};
-0431                         enzStoichNo=enzStoichNo+1;
-0432                     otherwise
-0433                         error(['Unknown entry in yaml file: ' tline_raw])
-0434                 end
-0435         end; continue
-0436     end
-0437 
-0438     % import ec enzyme info
-0439     if section == 7
-0440         switch tline_key
-0441             case 'genes'
-0442                 pos = pos + 1;
-0443                 model.ec = readFieldValue(model.ec, 'genes', tline_value, pos);
-0444             case 'enzymes'
-0445                 model.ec = readFieldValue(model.ec, 'enzymes', tline_value, pos);
-0446             case 'mw'
-0447                 model.ec = readFieldValue(model.ec, 'mw', tline_value, pos);
-0448             case 'sequence'
-0449                 model.ec = readFieldValue(model.ec, 'sequence', tline_value, pos);
-0450             case 'concs'
-0451                 model.ec = readFieldValue(model.ec, 'concs', tline_value, pos);
-0452             otherwise
-0453                 error(['Unknown entry in yaml file: ' tline_raw])
-0454         end; continue
-0455     end
-0456 end
-0457 
-0458 %Parse annotations
-0459 if ~isempty(metMiriams)
-0460     locs = cell2mat(metMiriams(:,1));
-0461     for i=unique(locs)'
-0462         model.metMiriams{i,1}.name=metMiriams(locs==i,2);
-0463         model.metMiriams{i,1}.value=metMiriams(locs==i,3);
-0464     end
-0465 end
-0466 if ~isempty(rxnMiriams)
-0467     locs = cell2mat(rxnMiriams(:,1));
-0468     for i=unique(locs)'
-0469         model.rxnMiriams{i,1}.name=rxnMiriams(locs==i,2);
-0470         model.rxnMiriams{i,1}.value=rxnMiriams(locs==i,3);
-0471     end
-0472 end
-0473 if ~isempty(geneMiriams)
-0474     locs = cell2mat(geneMiriams(:,1));
-0475     for i=unique(locs)'
-0476         model.geneMiriams{i,1}.name=geneMiriams(locs==i,2);
-0477         model.geneMiriams{i,1}.value=geneMiriams(locs==i,3);
-0478     end
-0479 end
-0480 
-0481 %Parse subSystems
-0482 if ~isempty(subSystems)
-0483     locs = cell2mat(subSystems(:,1));
-0484     for i=unique(locs)'
-0485         model.subSystems{i,1}=subSystems(locs==i,2);
-0486     end
-0487 end
-0488 
-0489 %Parse ec-codes
-0490 if ~isempty(eccodes)
-0491     locs = cell2mat(eccodes(:,1));
-0492     for i=unique(locs)'
-0493         eccodesCat=strjoin(eccodes(locs==i,2),';');
-0494         model.eccodes{i,1}=eccodesCat;
-0495     end
-0496     emptyEc=cellfun('isempty',model.eccodes);
-0497     model.eccodes(emptyEc)={''};
-0498 end
-0499 
-0500 % follow-up data processing
-0501 if verbose
-0502     fprintf('\nimporting completed\nfollow-up processing...');
-0503 end
-0504 [~, model.metComps] = ismember(model.metComps, model.comps);
-0505 [~, model.geneComps] = ismember(model.geneComps, model.comps);
-0506 [~, model.rxnComps] = ismember(model.rxnComps, model.comps);
-0507 
-0508 % Fill S-matrix
-0509 rxnIdx = cellfun('isempty', equations(:,1));
-0510 equations(rxnIdx,:) = '';
-0511 rxnIdx = cell2mat(equations(:,1));
-0512 [~,metIdx] = ismember(equations(:,2),model.mets);
-0513 coeffs = cell2mat(equations(:,3));
-0514 model.S=sparse(max(metIdx),max(rxnIdx));
-0515 linearIndices = sub2ind([max(metIdx), max(rxnIdx)],metIdx,rxnIdx);
-0516 model.S(linearIndices) = coeffs;
-0517 
-0518 % Convert strings to numeric
-0519 model.metCharges = str2double(model.metCharges);
-0520 model.lb = str2double(model.lb);
-0521 model.ub = str2double(model.ub);
-0522 model.rxnConfidenceScores = str2double(model.rxnConfidenceScores);
-0523 model.b = zeros(length(model.mets),1);
-0524 model.metDeltaG = str2double(model.metDeltaG);
-0525 model.rxnDeltaG = str2double(model.rxnDeltaG);
-0526 
-0527 % Fill some other fields
-0528 model.annotation.defaultLB = min(model.lb);
-0529 model.annotation.defaultUB = max(model.ub);
-0530 if numel(model.lb)<numel(model.rxns) %No LB reported = min
-0531     model.lb(end+1:numel(model.rxns)-numel(model.lb),1) = double(model.annotation.defaultLB);
-0532 end
-0533 if numel(model.ub)<numel(model.rxns) %No UB reported = max
-0534     model.ub(end+1:numel(model.rxns)-numel(model.ub),1) = double(model.annotation.defaultUB);
-0535 end
-0536 if ~all(cellfun('isempty',model.rev))
-0537     model.rev = str2double(model.rev);
-0538 else
-0539     model.rev = [];
-0540 end
-0541 if numel(model.rev)<numel(model.rxns) %No rev reported, assume from LB and UB
-0542     model.rev(end+1:numel(model.rxns)-numel(model.rev),1) = double(model.lb<0 & model.ub>0);
-0543 end
-0544 
-0545 % Remove empty fields, otherwise fill to correct length
-0546 % Reactions
-0547 for i={'rxnNames','grRules','eccodes','rxnNotes','rxnReferences',...
-0548        'rxnFrom','subSystems','rxnMiriams'} % Empty strings
-0549    model = emptyOrFill(model,i{1},{''},'rxns');
-0550 end
-0551 for i={'c'} % Zeros
-0552    model = emptyOrFill(model,i{1},0,'rxns',true);
-0553 end
-0554 for i={'rxnConfidenceScores','rxnDeltaG'} % NaNs
-0555    model = emptyOrFill(model,i{1},NaN,'rxns');
-0556 end
-0557 for i={'rxnComps'} % Ones, assume first compartment
-0558    model = emptyOrFill(model,i{1},1,'rxns');
-0559 end
-0560 % Metabolites
-0561 for i={'metNames','inchis','metFormulas','metMiriams','metFrom','metSmiles','metNotes'} % Empty strings
-0562    model = emptyOrFill(model,i{1},{''},'mets');
-0563 end
-0564 for i={'metCharges','unconstrained'} % Zeros
-0565    model = emptyOrFill(model,i{1},0,'mets');
-0566 end
-0567 for i={'metDeltaG'} % % NaNs
-0568     model = emptyOrFill(model,i{1},NaN,'mets');
-0569  end
-0570 for i={'metComps'} % Ones, assume first compartment
-0571    model = emptyOrFill(model,i{1},1,'mets');
-0572 end
-0573 % Genes
-0574 for i={'geneMiriams','geneShortNames','proteins'} % Empty strings
-0575    model = emptyOrFill(model,i{1},{''},'genes');
-0576 end
-0577 for i={'geneComps'} % Ones, assume first compartment
-0578    model = emptyOrFill(model,i{1},1,'genes');
-0579 end
-0580 % Comps
-0581 for i={'compNames'} % Empty strings
-0582    model = emptyOrFill(model,i{1},{''},'comps');
-0583 end
-0584 for i={'compOutside'} % First comp
-0585    model = emptyOrFill(model,i{1},model.comps{1},'comps');
-0586 end
-0587 % Single fields are kept, even if empty
-0588 % for i={'description','name','version','date','annotation'}
-0589 %     if isempty(model.(i{1}))
-0590 %         model = rmfield(model,i{1});
-0591 %     end
-0592 % end
-0593 
-0594 % Make rxnGeneMat fields and map to the existing model.genes field
-0595 [genes, rxnGeneMat] = getGenesFromGrRules(model.grRules);
-0596 model.rxnGeneMat = sparse(numel(model.rxns),numel(model.genes));
-0597 [~,geneOrder] = ismember(genes,model.genes);
-0598 if any(geneOrder == 0)
-0599     error(['The grRules includes the following gene(s), that are not in '...
-0600            'the list of model genes: ', genes{~geneOrder}])
-0601 end
-0602 model.rxnGeneMat(:,geneOrder) = rxnGeneMat;
-0603 
-0604 % Finalize GECKO model
-0605 if isGECKO
-0606     % Fill in empty fields and empty entries
-0607     for i={'kcat','source','notes','eccodes'} % Even keep empty
-0608         model.ec = emptyOrFill(model.ec,i{1},{''},'rxns',true);
-0609     end
-0610     for i={'enzymes','mw','sequence'}
-0611         model.ec = emptyOrFill(model.ec,i{1},{''},'genes',true);
-0612     end
-0613     model.ec = emptyOrFill(model.ec,'concs',{'NaN'},'genes',true);
-0614     model.ec = emptyOrFill(model.ec,'kcat',{'0'},'genes',true);
-0615     % Change string to double
-0616     for i={'kcat','mw','concs'}
-0617         if isfield(model.ec,i{1})
-0618             model.ec.(i{1}) = str2double(model.ec.(i{1}));
-0619         end
-0620     end
-0621     % Fill rxnEnzMat
-0622     rxnIdx              = cellfun('isempty', enzStoich(:,1));
-0623     enzStoich(rxnIdx,:) = '';
-0624     rxnIdx              = cell2mat(enzStoich(:,1));
-0625     [~,enzIdx]          = ismember(enzStoich(:,2),model.ec.enzymes);
-0626     coeffs              = cell2mat(enzStoich(:,3));
-0627     model.ec.rxnEnzMat  = zeros(numel(model.ec.rxns), numel(model.ec.genes));
-0628     linearIndices       = sub2ind([numel(model.ec.rxns), numel(model.ec.genes)], rxnIdx, enzIdx);
-0629     model.ec.rxnEnzMat(linearIndices) = coeffs;
-0630     %Parse ec-codes
-0631     if ~isempty(ecGecko)
-0632         locs = cell2mat(ecGecko(:,1));
-0633         for i=unique(locs)'
-0634             ecGeckoCat=strjoin(ecGecko(locs==i,2),';');
-0635             model.ec.eccodes{i,1}=ecGeckoCat;
-0636         end
-0637         emptyEc=cellfun('isempty',model.ec.eccodes);
-0638         model.ec.eccodes(emptyEc)={''};
-0639     end
-0640 end
-0641 
-0642 if verbose
-0643     fprintf(' Done!\n');
-0644 end
+0327             case 'confidence_score'
+0328                 model = readFieldValue(model, 'rxnConfidenceScores', tline_value, pos);
+0329                 readList=''; miriamKey='';
+0330             case 'eccodes'
+0331                 if isempty(tline_value)
+0332                     readList = 'eccodes';
+0333                 else
+0334                     eccodes(ecCodeNo,1:2)={pos,tline_value};
+0335                     ecCodeNo=ecCodeNo+1;
+0336                 end
+0337             case 'subsystem'
+0338                 if isempty(tline_value)
+0339                     readList = 'subsystem';
+0340                 else
+0341                     subSystems(subSysNo,1:2)={pos,tline_value};
+0342                     subSysNo=subSysNo+1;
+0343                 end
+0344             case 'metabolites'
+0345                 readList = 'equation';
+0346             case 'annotation'
+0347                 readList = 'annotation';
+0348                 
+0349             otherwise
+0350                 switch readList
+0351                     case 'eccodes'
+0352                         eccodes(ecCodeNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
+0353                         ecCodeNo=ecCodeNo+1;
+0354                     case 'subsystem'
+0355                         subSystems(subSysNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
+0356                         subSysNo=subSysNo+1;
+0357                     case 'annotation'
+0358                         [rxnMiriams, miriamKey,rxnMirNo] = gatherAnnotation(pos,rxnMiriams,tline_key,tline_value,miriamKey,rxnMirNo);
+0359                     case 'equation'
+0360                         coeff = sscanf(tline_value,'%f');
+0361                         equations(equatiNo,1:3)={pos,tline_key,coeff};
+0362                         equatiNo=equatiNo+1;
+0363                     otherwise
+0364                         error(['Unknown entry in yaml file: ' tline_raw])
+0365                 end                
+0366         end; continue
+0367     end
+0368 
+0369     % import genes:
+0370     if section == 4
+0371         switch tline_key
+0372             case 'id'
+0373                 pos = pos + 1;
+0374                 model = readFieldValue(model, 'genes', tline_value, pos);
+0375                 readList = '';
+0376                 miriamKey = '';
+0377             case 'name'
+0378                 model = readFieldValue(model, 'geneShortNames', tline_value, pos);
+0379             case 'protein'
+0380                 model = readFieldValue(model, 'proteins', tline_value, pos);
+0381             case 'annotation'
+0382                 readList = 'annotation';
+0383             otherwise
+0384                 switch readList
+0385                     case 'annotation'
+0386                         [geneMiriams, miriamKey,genMirNo] = gatherAnnotation(pos,geneMiriams,tline_key,tline_value,miriamKey,genMirNo);
+0387                     otherwise
+0388                         error(['Unknown entry in yaml file: ' tline_raw])
+0389                 end
+0390         end; continue
+0391     end
+0392 
+0393     % import compartments:
+0394     if section == 5
+0395         model.comps(end+1,1) = {tline_key};
+0396         model.compNames(end+1,1) = {tline_value};
+0397     end
+0398 
+0399     % import ec reaction info
+0400     if section == 6
+0401         switch tline_key
+0402             case 'id'
+0403                 pos = pos + 1;
+0404                 model.ec = readFieldValue(model.ec, 'rxns', tline_value, pos);
+0405                 readList='';
+0406             case 'kcat'
+0407                 model.ec = readFieldValue(model.ec, 'kcat', tline_value, pos);
+0408                 readList='';
+0409             case 'source'
+0410                 model.ec = readFieldValue(model.ec, 'source', tline_value, pos);
+0411                 readList='';
+0412             case 'notes'
+0413                 model.ec = readFieldValue(model.ec, 'notes', tline_value, pos);
+0414                 readList='';
+0415             case 'eccodes'
+0416                 if isempty(tline_value)
+0417                     readList = 'eccodes';
+0418                 else
+0419                     ecGecko(ecGeckoNo,1:2)={pos,tline_value};
+0420                     ecGeckoNo=ecGeckoNo+1;
+0421                 end
+0422             case 'enzymes'
+0423                 readList = 'enzStoich';
+0424             otherwise
+0425                 switch readList
+0426                     case 'eccodes'
+0427                         ecGecko(ecGeckoNo,1:2)={pos,regexprep(tline_value,'^ +- "?(.*)"?$','$1')};
+0428                         ecGeckoNo=ecGeckoNo+1;
+0429                     case 'enzStoich'
+0430                         coeff = sscanf(tline_value,'%f');
+0431                         enzStoich(enzStoichNo,1:3)={pos,tline_key,coeff};
+0432                         enzStoichNo=enzStoichNo+1;
+0433                     otherwise
+0434                         error(['Unknown entry in yaml file: ' tline_raw])
+0435                 end
+0436         end; continue
+0437     end
+0438 
+0439     % import ec enzyme info
+0440     if section == 7
+0441         switch tline_key
+0442             case 'genes'
+0443                 pos = pos + 1;
+0444                 model.ec = readFieldValue(model.ec, 'genes', tline_value, pos);
+0445             case 'enzymes'
+0446                 model.ec = readFieldValue(model.ec, 'enzymes', tline_value, pos);
+0447             case 'mw'
+0448                 model.ec = readFieldValue(model.ec, 'mw', tline_value, pos);
+0449             case 'sequence'
+0450                 model.ec = readFieldValue(model.ec, 'sequence', tline_value, pos);
+0451             case 'concs'
+0452                 model.ec = readFieldValue(model.ec, 'concs', tline_value, pos);
+0453             otherwise
+0454                 error(['Unknown entry in yaml file: ' tline_raw])
+0455         end; continue
+0456     end
+0457 end
+0458 
+0459 %Parse annotations
+0460 if ~isempty(metMiriams)
+0461     locs = cell2mat(metMiriams(:,1));
+0462     for i=unique(locs)'
+0463         model.metMiriams{i,1}.name=metMiriams(locs==i,2);
+0464         model.metMiriams{i,1}.value=metMiriams(locs==i,3);
+0465     end
+0466 end
+0467 if ~isempty(rxnMiriams)
+0468     locs = cell2mat(rxnMiriams(:,1));
+0469     for i=unique(locs)'
+0470         model.rxnMiriams{i,1}.name=rxnMiriams(locs==i,2);
+0471         model.rxnMiriams{i,1}.value=rxnMiriams(locs==i,3);
+0472     end
+0473 end
+0474 if ~isempty(geneMiriams)
+0475     locs = cell2mat(geneMiriams(:,1));
+0476     for i=unique(locs)'
+0477         model.geneMiriams{i,1}.name=geneMiriams(locs==i,2);
+0478         model.geneMiriams{i,1}.value=geneMiriams(locs==i,3);
+0479     end
+0480 end
+0481 
+0482 %Parse subSystems
+0483 if ~isempty(subSystems)
+0484     locs = cell2mat(subSystems(:,1));
+0485     for i=unique(locs)'
+0486         model.subSystems{i,1}=subSystems(locs==i,2);
+0487     end
+0488 end
+0489 
+0490 %Parse ec-codes
+0491 if ~isempty(eccodes)
+0492     locs = cell2mat(eccodes(:,1));
+0493     for i=unique(locs)'
+0494         eccodesCat=strjoin(eccodes(locs==i,2),';');
+0495         model.eccodes{i,1}=eccodesCat;
+0496     end
+0497     emptyEc=cellfun('isempty',model.eccodes);
+0498     model.eccodes(emptyEc)={''};
+0499 end
+0500 
+0501 % follow-up data processing
+0502 if verbose
+0503     fprintf('\nimporting completed\nfollow-up processing...');
+0504 end
+0505 [~, model.metComps] = ismember(model.metComps, model.comps);
+0506 [~, model.geneComps] = ismember(model.geneComps, model.comps);
+0507 [~, model.rxnComps] = ismember(model.rxnComps, model.comps);
+0508 
+0509 % Fill S-matrix
+0510 rxnIdx = cellfun('isempty', equations(:,1));
+0511 equations(rxnIdx,:) = '';
+0512 rxnIdx = cell2mat(equations(:,1));
+0513 [~,metIdx] = ismember(equations(:,2),model.mets);
+0514 coeffs = cell2mat(equations(:,3));
+0515 model.S=sparse(max(metIdx),max(rxnIdx));
+0516 linearIndices = sub2ind([max(metIdx), max(rxnIdx)],metIdx,rxnIdx);
+0517 model.S(linearIndices) = coeffs;
+0518 
+0519 % Convert strings to numeric
+0520 model.metCharges = str2double(model.metCharges);
+0521 model.lb = str2double(model.lb);
+0522 model.ub = str2double(model.ub);
+0523 model.rxnConfidenceScores = str2double(model.rxnConfidenceScores);
+0524 model.b = zeros(length(model.mets),1);
+0525 model.metDeltaG = str2double(model.metDeltaG);
+0526 model.rxnDeltaG = str2double(model.rxnDeltaG);
+0527 
+0528 % Fill some other fields
+0529 model.annotation.defaultLB = min(model.lb);
+0530 model.annotation.defaultUB = max(model.ub);
+0531 if numel(model.lb)<numel(model.rxns) %No LB reported = min
+0532     model.lb(end+1:numel(model.rxns)-numel(model.lb),1) = double(model.annotation.defaultLB);
+0533 end
+0534 if numel(model.ub)<numel(model.rxns) %No UB reported = max
+0535     model.ub(end+1:numel(model.rxns)-numel(model.ub),1) = double(model.annotation.defaultUB);
+0536 end
+0537 if ~all(cellfun('isempty',model.rev))
+0538     model.rev = str2double(model.rev);
+0539 else
+0540     model.rev = [];
+0541 end
+0542 if numel(model.rev)<numel(model.rxns) %No rev reported, assume from LB and UB
+0543     model.rev(end+1:numel(model.rxns)-numel(model.rev),1) = double(model.lb<0 & model.ub>0);
+0544 end
+0545 
+0546 % Remove empty fields, otherwise fill to correct length
+0547 % Reactions
+0548 for i={'rxnNames','grRules','eccodes','rxnNotes','rxnReferences',...
+0549        'rxnFrom','subSystems','rxnMiriams'} % Empty strings
+0550    model = emptyOrFill(model,i{1},{''},'rxns');
+0551 end
+0552 for i={'c'} % Zeros
+0553    model = emptyOrFill(model,i{1},0,'rxns',true);
+0554 end
+0555 for i={'rxnConfidenceScores','rxnDeltaG'} % NaNs
+0556    model = emptyOrFill(model,i{1},NaN,'rxns');
+0557 end
+0558 for i={'rxnComps'} % Ones, assume first compartment
+0559    model = emptyOrFill(model,i{1},1,'rxns');
+0560 end
+0561 % Metabolites
+0562 for i={'metNames','inchis','metFormulas','metMiriams','metFrom','metSmiles','metNotes'} % Empty strings
+0563    model = emptyOrFill(model,i{1},{''},'mets');
+0564 end
+0565 for i={'metCharges','unconstrained'} % Zeros
+0566    model = emptyOrFill(model,i{1},0,'mets');
+0567 end
+0568 for i={'metDeltaG'} % % NaNs
+0569     model = emptyOrFill(model,i{1},NaN,'mets');
+0570  end
+0571 for i={'metComps'} % Ones, assume first compartment
+0572    model = emptyOrFill(model,i{1},1,'mets');
+0573 end
+0574 % Genes
+0575 for i={'geneMiriams','geneShortNames','proteins'} % Empty strings
+0576    model = emptyOrFill(model,i{1},{''},'genes');
+0577 end
+0578 for i={'geneComps'} % Ones, assume first compartment
+0579    model = emptyOrFill(model,i{1},1,'genes');
+0580 end
+0581 % Comps
+0582 for i={'compNames'} % Empty strings
+0583    model = emptyOrFill(model,i{1},{''},'comps');
+0584 end
+0585 for i={'compOutside'} % First comp
+0586    model = emptyOrFill(model,i{1},model.comps{1},'comps');
+0587 end
+0588 % Single fields are kept, even if empty
+0589 % for i={'description','name','version','date','annotation'}
+0590 %     if isempty(model.(i{1}))
+0591 %         model = rmfield(model,i{1});
+0592 %     end
+0593 % end
+0594 
+0595 % Make rxnGeneMat fields and map to the existing model.genes field
+0596 [genes, rxnGeneMat] = getGenesFromGrRules(model.grRules);
+0597 model.rxnGeneMat = sparse(numel(model.rxns),numel(model.genes));
+0598 [~,geneOrder] = ismember(genes,model.genes);
+0599 if any(geneOrder == 0)
+0600     error(['The grRules includes the following gene(s), that are not in '...
+0601            'the list of model genes: ', genes{~geneOrder}])
+0602 end
+0603 model.rxnGeneMat(:,geneOrder) = rxnGeneMat;
+0604 
+0605 % Finalize GECKO model
+0606 if isGECKO
+0607     % Fill in empty fields and empty entries
+0608     for i={'kcat','source','notes','eccodes'} % Even keep empty
+0609         model.ec = emptyOrFill(model.ec,i{1},{''},'rxns',true);
+0610     end
+0611     for i={'enzymes','mw','sequence'}
+0612         model.ec = emptyOrFill(model.ec,i{1},{''},'genes',true);
+0613     end
+0614     model.ec = emptyOrFill(model.ec,'concs',{'NaN'},'genes',true);
+0615     model.ec = emptyOrFill(model.ec,'kcat',{'0'},'genes',true);
+0616     % Change string to double
+0617     for i={'kcat','mw','concs'}
+0618         if isfield(model.ec,i{1})
+0619             model.ec.(i{1}) = str2double(model.ec.(i{1}));
+0620         end
+0621     end
+0622     % Fill rxnEnzMat
+0623     rxnIdx              = cellfun('isempty', enzStoich(:,1));
+0624     enzStoich(rxnIdx,:) = '';
+0625     rxnIdx              = cell2mat(enzStoich(:,1));
+0626     [~,enzIdx]          = ismember(enzStoich(:,2),model.ec.enzymes);
+0627     coeffs              = cell2mat(enzStoich(:,3));
+0628     model.ec.rxnEnzMat  = zeros(numel(model.ec.rxns), numel(model.ec.genes));
+0629     linearIndices       = sub2ind([numel(model.ec.rxns), numel(model.ec.genes)], rxnIdx, enzIdx);
+0630     model.ec.rxnEnzMat(linearIndices) = coeffs;
+0631     %Parse ec-codes
+0632     if ~isempty(ecGecko)
+0633         locs = cell2mat(ecGecko(:,1));
+0634         for i=unique(locs)'
+0635             ecGeckoCat=strjoin(ecGecko(locs==i,2),';');
+0636             model.ec.eccodes{i,1}=ecGeckoCat;
+0637         end
+0638         emptyEc=cellfun('isempty',model.ec.eccodes);
+0639         model.ec.eccodes(emptyEc)={''};
+0640     end
+0641 end
+0642 
+0643 if verbose
+0644     fprintf(' Done!\n');
 0645 end
-0646 
-0647 function model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)
-0648 if nargin<5
-0649     keepEmpty=false;
-0650 end
-0651 if isnumeric(emptyEntry)
-0652     emptyCells=isempty(model.(field));
-0653 else
-0654     emptyCells=cellfun('isempty',model.(field));
-0655 end
-0656 if all(emptyCells) && ~keepEmpty
-0657     model = rmfield(model, field);
-0658 elseif numel(model.(field))<numel(model.(type))
-0659     model.(field)(end+1:numel(model.(type)),1)=emptyEntry;
-0660 end
+0646 end
+0647 
+0648 function model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)
+0649 if nargin<5
+0650     keepEmpty=false;
+0651 end
+0652 if isnumeric(emptyEntry)
+0653     emptyCells=isempty(model.(field));
+0654 else
+0655     emptyCells=cellfun('isempty',model.(field));
+0656 end
+0657 if all(emptyCells) && ~keepEmpty
+0658     model = rmfield(model, field);
+0659 elseif numel(model.(field))<numel(model.(type))
+0660     model.(field)(end+1:numel(model.(type)),1)=emptyEntry;
 0661 end
-0662 
-0663 function model = readFieldValue(model, fieldName, value, pos)
-0664 if numel(model.(fieldName))<pos-1
-0665     model.(fieldName)(end+1:pos,1) = {''};
-0666 end
-0667 model.(fieldName)(pos,1) = {value};
-0668 end
-0669 
-0670 function [miriams, miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber)
-0671 if isempty(key)
-0672     key=miriamKey;
-0673 else
-0674     miriamKey=key;
-0675 end
-0676 if ~isempty(value)
-0677     miriams(entryNumber,1:3) = {pos, key, strip(value)};
-0678 else
-0679     entryNumber = entryNumber - 1;
+0662 end
+0663 
+0664 function model = readFieldValue(model, fieldName, value, pos)
+0665 if numel(model.(fieldName))<pos-1
+0666     model.(fieldName)(end+1:pos,1) = {''};
+0667 end
+0668 model.(fieldName)(pos,1) = {value};
+0669 end
+0670 
+0671 function [miriams,miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber)
+0672 if isempty(key)
+0673     key=miriamKey;
+0674 else
+0675     miriamKey=key;
+0676 end
+0677 if ~isempty(value)
+0678     miriams(entryNumber,1:3) = {pos, key, strip(value)};
+0679     entryNumber = entryNumber + 1;
 0680 end
 0681 end
    Generated by m2html © 2005
    diff --git a/doc/io/writeYAMLmodel.html b/doc/io/writeYAMLmodel.html index 8aafb9ee..d2f385a9 100644 --- a/doc/io/writeYAMLmodel.html +++ b/doc/io/writeYAMLmodel.html @@ -335,106 +335,109 @@

    SOURCE CODE ^if preserveQuotes 0277 list = ['"' list{1} '"']; 0278 end -0279 fprintf(fid,' %s: %s\n',name,list); -0280 elseif ischar(list) && strcmp(fieldName,'subSystems') -0281 if preserveQuotes -0282 list = ['"' list '"']; -0283 end -0284 fprintf(fid,' %s: %s\n',name,list); -0285 elseif length(list) > 1 || strcmp(fieldName,'subSystems') -0286 if preserveQuotes -0287 for j=1:numel(list) -0288 list{j} = ['"' list{j} '"']; -0289 end -0290 end -0291 fprintf(fid,' %s:\n',name); -0292 for i = 1:length(list) -0293 fprintf(fid,'%s - %s\n',regexprep(name,'(^\s*).*','$1'),list{i}); -0294 end -0295 end -0296 -0297 elseif sum(pos) > 0 -0298 %All other fields: -0299 if strcmp(type,'txt') -0300 value = field{pos}; -0301 if preserveQuotes && ~isempty(value) -0302 value = ['"',value,'"']; -0303 end -0304 elseif strcmp(type,'num') -0305 if isnan(field(pos)) -0306 value = []; -0307 else -0308 value = sprintf('%.15g',full(field(pos))); -0309 end -0310 end -0311 if ~isempty(value) -0312 fprintf(fid,' %s: %s\n',name,value); +0279 if iscell(list) +0280 list=list{1}; +0281 end +0282 fprintf(fid,' %s: %s\n',name,list); +0283 elseif ischar(list) && strcmp(fieldName,'subSystems') +0284 if preserveQuotes +0285 list = ['"' list '"']; +0286 end +0287 fprintf(fid,' %s: %s\n',name,list); +0288 elseif length(list) > 1 || strcmp(fieldName,'subSystems') +0289 if preserveQuotes +0290 for j=1:numel(list) +0291 list{j} = ['"' list{j} '"']; +0292 end +0293 end +0294 fprintf(fid,' %s:\n',name); +0295 for i = 1:length(list) +0296 fprintf(fid,'%s - %s\n',regexprep(name,'(^\s*).*','$1'),list{i}); +0297 end +0298 end +0299 +0300 elseif sum(pos) > 0 +0301 %All other fields: +0302 if strcmp(type,'txt') +0303 value = field{pos}; +0304 if preserveQuotes && ~isempty(value) +0305 value = ['"',value,'"']; +0306 end +0307 elseif strcmp(type,'num') +0308 if isnan(field(pos)) +0309 value = []; +0310 else +0311 value = sprintf('%.15g',full(field(pos))); +0312 end 0313 end -0314 end -0315 end -0316 end -0317 -0318 function writeMetadata(model,fid) -0319 % Writes model metadata to the yaml file. This information will eventually -0320 % be extracted entirely from the model, but for now, many of the entries -0321 % are hard-coded defaults for HumanGEM. -0322 -0323 fprintf(fid, '- metaData:\n'); -0324 if isfield(model,'id') -0325 fprintf(fid, ' id: "%s"\n', model.id); -0326 else -0327 fprintf(fid, ' id: "blankID"\n'); -0328 end -0329 if isfield(model,'name') -0330 fprintf(fid, ' name: "%s"\n',model.name); -0331 else -0332 fprintf(fid, ' name: "blankName"\n'); -0333 end -0334 if isfield(model,'version') -0335 fprintf(fid, ' version: "%s"\n',model.version); +0314 if ~isempty(value) +0315 fprintf(fid,' %s: %s\n',name,value); +0316 end +0317 end +0318 end +0319 end +0320 +0321 function writeMetadata(model,fid) +0322 % Writes model metadata to the yaml file. This information will eventually +0323 % be extracted entirely from the model, but for now, many of the entries +0324 % are hard-coded defaults for HumanGEM. +0325 +0326 fprintf(fid, '- metaData:\n'); +0327 if isfield(model,'id') +0328 fprintf(fid, ' id: "%s"\n', model.id); +0329 else +0330 fprintf(fid, ' id: "blankID"\n'); +0331 end +0332 if isfield(model,'name') +0333 fprintf(fid, ' name: "%s"\n',model.name); +0334 else +0335 fprintf(fid, ' name: "blankName"\n'); 0336 end -0337 fprintf(fid, ' date: "%s"\n',datestr(now,29)); % 29=YYYY-MM-DD -0338 if isfield(model,'annotation') -0339 if isfield(model.annotation,'defaultLB') -0340 fprintf(fid, ' defaultLB: "%g"\n', model.annotation.defaultLB); -0341 end -0342 if isfield(model.annotation,'defaultUB') -0343 fprintf(fid, ' defaultUB: "%g"\n', model.annotation.defaultUB); +0337 if isfield(model,'version') +0338 fprintf(fid, ' version: "%s"\n',model.version); +0339 end +0340 fprintf(fid, ' date: "%s"\n',datestr(now,29)); % 29=YYYY-MM-DD +0341 if isfield(model,'annotation') +0342 if isfield(model.annotation,'defaultLB') +0343 fprintf(fid, ' defaultLB: "%g"\n', model.annotation.defaultLB); 0344 end -0345 if isfield(model.annotation,'givenName') -0346 fprintf(fid, ' givenName: "%s"\n', model.annotation.givenName); +0345 if isfield(model.annotation,'defaultUB') +0346 fprintf(fid, ' defaultUB: "%g"\n', model.annotation.defaultUB); 0347 end -0348 if isfield(model.annotation,'familyName') -0349 fprintf(fid, ' familyName: "%s"\n', model.annotation.familyName); +0348 if isfield(model.annotation,'givenName') +0349 fprintf(fid, ' givenName: "%s"\n', model.annotation.givenName); 0350 end -0351 if isfield(model.annotation,'authors') -0352 fprintf(fid, ' authors: "%s"\n', model.annotation.authors); +0351 if isfield(model.annotation,'familyName') +0352 fprintf(fid, ' familyName: "%s"\n', model.annotation.familyName); 0353 end -0354 if isfield(model.annotation,'email') -0355 fprintf(fid, ' email: "%s"\n', model.annotation.email); +0354 if isfield(model.annotation,'authors') +0355 fprintf(fid, ' authors: "%s"\n', model.annotation.authors); 0356 end -0357 if isfield(model.annotation,'organization') -0358 fprintf(fid, ' organization: "%s"\n',model.annotation.organization); +0357 if isfield(model.annotation,'email') +0358 fprintf(fid, ' email: "%s"\n', model.annotation.email); 0359 end -0360 if isfield(model.annotation,'taxonomy') -0361 fprintf(fid, ' taxonomy: "%s"\n', model.annotation.taxonomy); +0360 if isfield(model.annotation,'organization') +0361 fprintf(fid, ' organization: "%s"\n',model.annotation.organization); 0362 end -0363 if isfield(model.annotation,'note') -0364 fprintf(fid, ' note: "%s"\n', model.annotation.note); +0363 if isfield(model.annotation,'taxonomy') +0364 fprintf(fid, ' taxonomy: "%s"\n', model.annotation.taxonomy); 0365 end -0366 if isfield(model.annotation,'sourceUrl') -0367 fprintf(fid, ' sourceUrl: "%s"\n', model.annotation.sourceUrl); +0366 if isfield(model.annotation,'note') +0367 fprintf(fid, ' note: "%s"\n', model.annotation.note); 0368 end -0369 end -0370 if isfield(model,'ec') -0371 if model.ec.geckoLight -0372 geckoLight = 'true'; -0373 else -0374 geckoLight = 'false'; -0375 end -0376 fprintf(fid,' geckoLight: "%s"\n',geckoLight); -0377 end -0378 end +0369 if isfield(model.annotation,'sourceUrl') +0370 fprintf(fid, ' sourceUrl: "%s"\n', model.annotation.sourceUrl); +0371 end +0372 end +0373 if isfield(model,'ec') +0374 if model.ec.geckoLight +0375 geckoLight = 'true'; +0376 else +0377 geckoLight = 'false'; +0378 end +0379 fprintf(fid,' geckoLight: "%s"\n',geckoLight); +0380 end +0381 end
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    \ No newline at end of file diff --git a/io/closeModel.m b/io/closeModel.m index fbee581f..b91d69f0 100755 --- a/io/closeModel.m +++ b/io/closeModel.m @@ -11,11 +11,11 @@ closedModel=model; -closedModel.comps{numel(closedModel.comps)+1}='b'; -closedModel.compNames{numel(closedModel.compNames)+1}='boundary'; +closedModel.comps{numel(closedModel.comps)+1,1}='b'; +closedModel.compNames{numel(closedModel.compNames)+1,1}='boundary'; if isfield(closedModel,'compMiriams') - closedModel.compMiriams{numel(closedModel.compMiriams)+1}=[]; -end; + closedModel.compMiriams{numel(closedModel.compMiriams)+1,1}=[]; +end closedModel.unconstrained=zeros(numel(closedModel.mets),1); for i=1:numel(closedModel.rxns) @@ -23,29 +23,29 @@ closedModel.mets{numel(closedModel.mets)+1}=strcat(closedModel.mets{find(closedModel.S(:,i))},'_b'); if isfield(closedModel,'metNames') closedModel.metNames{numel(closedModel.metNames)+1}=closedModel.metNames{find(closedModel.S(:,i))}; - end; + end closedModel.metComps(numel(closedModel.metComps)+1)=numel(closedModel.comps); if isfield(closedModel,'inchis') closedModel.inchis{numel(closedModel.inchis)+1}=closedModel.inchis{find(closedModel.S(:,i))}; - end; + end if isfield(closedModel,'metSmiles') closedModel.metSmiles{numel(closedModel.metSmiles)+1}=closedModel.metSmiles{find(closedModel.S(:,i))}; - end; + end if isfield(closedModel,'metFormulas') closedModel.metFormulas{numel(closedModel.metFormulas)+1}=closedModel.metFormulas{find(closedModel.S(:,i))}; - end; + end if isfield(closedModel,'metMiriams') closedModel.metMiriams{numel(closedModel.metMiriams)+1}=closedModel.metMiriams{find(closedModel.S(:,i))}; - end; + end if isfield(closedModel,'metFrom') closedModel.metFrom{numel(closedModel.metFrom)+1}=''; - end; + end if isfield(closedModel,'metCharges') closedModel.metCharges(numel(closedModel.metCharges)+1)=closedModel.metCharges(find(closedModel.S(:,i))); - end; + end if isfield(closedModel,'metDeltaG') closedModel.metDeltaG(numel(closedModel.metDeltaG)+1)=closedModel.metDeltaG(find(closedModel.S(:,i))); - end; + end closedModel.unconstrained(numel(closedModel.unconstrained)+1)=1; closedModel.b(numel(closedModel.b)+1)=0; closedModel.S=[closedModel.S;sparse(1,size(closedModel.S,2))]; @@ -53,8 +53,8 @@ closedModel.S(numel(closedModel.mets),i)=-1; else closedModel.S(numel(closedModel.mets),i)=1; - end; - end; -end; + end + end +end end diff --git a/io/readYAMLmodel.m b/io/readYAMLmodel.m index dd5e692f..ac3f256a 100755 --- a/io/readYAMLmodel.m +++ b/io/readYAMLmodel.m @@ -52,13 +52,15 @@ end line_raw(brokenLine)=[]; -line_key = regexprep(line_raw,'^ *-? ([^:]+)(:).*','$1'); +line_key = regexprep(line_raw,'^ *-? ([^:]+)(:)($| .*)','$1'); line_key = regexprep(line_key,'(.*!!omap)|(---)|( {4,}.*)',''); line_value = regexprep(line_raw, '.*:$',''); line_value = regexprep(line_value, '[^":]+: "?(.+)"?$','$1'); line_value = regexprep(line_value, '(")|(^ {4,}- )',''); +line_value(strcmp(line_value,line_raw)) = {''}; + modelFields = {'id',char();... 'name',char();... 'description',char();... @@ -220,6 +222,8 @@ model.annotation.note = tline_value; case 'github' model.annotation.sourceUrl = tline_value; + case 'sourceUrl' + model.annotation.sourceUrl = tline_value; case 'givenName' model.annotation.givenName = tline_value; case 'familyName' @@ -276,8 +280,7 @@ otherwise switch readList case 'annotation' - [metMiriams, miriamKey] = gatherAnnotation(pos,metMiriams,tline_key,tline_value,miriamKey,metMirNo); - metMirNo = metMirNo + 1; + [metMiriams, miriamKey, metMirNo] = gatherAnnotation(pos,metMiriams,tline_key,tline_value,miriamKey,metMirNo); otherwise error(['Unknown entry in yaml file: ' tline_raw]) end @@ -353,7 +356,6 @@ subSysNo=subSysNo+1; case 'annotation' [rxnMiriams, miriamKey,rxnMirNo] = gatherAnnotation(pos,rxnMiriams,tline_key,tline_value,miriamKey,rxnMirNo); - rxnMirNo=rxnMirNo+1; case 'equation' coeff = sscanf(tline_value,'%f'); equations(equatiNo,1:3)={pos,tline_key,coeff}; @@ -381,8 +383,7 @@ otherwise switch readList case 'annotation' - [geneMiriams, miriamKey] = gatherAnnotation(pos,geneMiriams,tline_key,tline_value,miriamKey,genMirNo); - genMirNo = genMirNo + 1; + [geneMiriams, miriamKey,genMirNo] = gatherAnnotation(pos,geneMiriams,tline_key,tline_value,miriamKey,genMirNo); otherwise error(['Unknown entry in yaml file: ' tline_raw]) end @@ -667,7 +668,7 @@ model.(fieldName)(pos,1) = {value}; end -function [miriams, miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber) +function [miriams,miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber) if isempty(key) key=miriamKey; else @@ -675,7 +676,6 @@ end if ~isempty(value) miriams(entryNumber,1:3) = {pos, key, strip(value)}; -else - entryNumber = entryNumber - 1; + entryNumber = entryNumber + 1; end end diff --git a/io/writeYAMLmodel.m b/io/writeYAMLmodel.m index b40bf18e..2b2bd612 100755 --- a/io/writeYAMLmodel.m +++ b/io/writeYAMLmodel.m @@ -276,6 +276,9 @@ function writeField(model,fid,fieldName,type,pos,name,preserveQuotes) if preserveQuotes list = ['"' list{1} '"']; end + if iscell(list) + list=list{1}; + end fprintf(fid,' %s: %s\n',name,list); elseif ischar(list) && strcmp(fieldName,'subSystems') if preserveQuotes From 8bfb82b777cba36ebff64ece251f1b513b220afb Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 21 Dec 2024 22:19:18 +0100 Subject: [PATCH 2/2] doc: updated PR template, refer to Wiki on how to make new release --- .github/pull_request_template.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 547498d1..35742302 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,14 +1,14 @@ ### Main improvements in this PR: +- documentation: + - updated all documentation +- features: + - introduced option to do function Y (solves #12345) --> #### Instructions on merging this PR: - [ ] This PR has `develop` as target branch, and will be resolved with a *squash-merge*. -- [ ] This PR has `main` as target branch, and will be resolved with a *merge commit*. +- [ ] This PR has `main` as target branch, and will be resolved as descriped [here](https://github.com/SysBioChalmers/RAVEN/wiki/Development-policy#make-a-new-release).