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fix: various minor bugs (#575)
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* 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
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@edkerk
edkerk authored Dec 21, 2024
1 parent ca888bc commit e4c1a23
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Showing 8 changed files with 779 additions and 761 deletions.
8 changes: 7 additions & 1 deletion core/generateNewIds.m
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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);
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52 changes: 29 additions & 23 deletions doc/core/generateNewIds.html
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Expand Up @@ -85,33 +85,39 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0026 <span class="keyword">else</span>
0027 error(<span class="string">'type should be either ''rxns'' or ''mets''.'</span>)
0028 <span class="keyword">end</span>
0029 <span class="keyword">if</span> nargin&lt;5
0030 numLength=4;
0029 <span class="keyword">if</span> nargin&lt;4
0030 quantity=1;
0031 <span class="keyword">end</span>
0032
0033 <span class="comment">% Subset only existingIds that have the prefix</span>
0034 existingIds=existingIds(~cellfun(@isempty,regexp(existingIds,[<span class="string">'^'</span> prefix])));
0032 <span class="keyword">if</span> nargin&lt;5
0033 numLength=4;
0034 <span class="keyword">end</span>
0035
0036 <span class="keyword">if</span> ~isempty(existingIds)
0037 existingIds=regexprep(existingIds,[<span class="string">'^'</span> prefix],<span class="string">''</span>);
0038 existingIds=sort(existingIds);
0039 lastId=existingIds{end};
0040 numLength=length(lastId);
0041 lastId=str2double(lastId);
0042 <span class="keyword">else</span>
0043 lastId=0;
0044 fprintf([<span class="string">'No '</span> type <span class="string">' ids with prefix &quot;'</span> prefix <span class="keyword">...</span>
0045 <span class="string">'&quot; currently exist in the model. The first new id will be &quot;'</span> <span class="keyword">...</span>
0046 [prefix,num2str(1,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])] <span class="string">'&quot;\n'</span>],<span class="string">'%s'</span>)
0047 lastId=0;
0048 <span class="keyword">end</span>
0049
0050 newIds=cell(quantity,1);
0036 <span class="comment">% Subset only existingIds that have the prefix</span>
0037 existingIds=existingIds(~cellfun(@isempty,regexp(existingIds,[<span class="string">'^'</span> prefix])));
0038
0039 <span class="keyword">if</span> ~isempty(existingIds)
0040 existingIds=regexprep(existingIds,[<span class="string">'^'</span> prefix],<span class="string">''</span>);
0041 existingIds=sort(existingIds);
0042 lastId=existingIds{end};
0043 numLength=length(lastId);
0044 lastId=str2double(lastId);
0045 <span class="keyword">else</span>
0046 lastId=0;
0047 fprintf([<span class="string">'No '</span> type <span class="string">' ids with prefix &quot;'</span> prefix <span class="keyword">...</span>
0048 <span class="string">'&quot; currently exist in the model. The first new id will be &quot;'</span> <span class="keyword">...</span>
0049 [prefix,num2str(1,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])] <span class="string">'&quot;\n'</span>],<span class="string">'%s'</span>)
0050 <span class="keyword">end</span>
0051
0052 <span class="keyword">for</span> k=1:quantity
0053 newIds{k}=[prefix,num2str(k+lastId,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])];
0052 <span class="keyword">if</span> isnan(lastId)
0053 lastId = 0;
0054 <span class="keyword">end</span>
0055 <span class="keyword">end</span></pre></div>
0055
0056 newIds=cell(quantity,1);
0057
0058 <span class="keyword">for</span> k=1:quantity
0059 newIds{k}=[prefix,num2str(k+lastId,[<span class="string">'%0'</span> num2str(numLength) <span class="string">'d'</span>])];
0060 <span class="keyword">end</span>
0061 <span class="keyword">end</span></pre></div>
<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
</body>
</html>
30 changes: 15 additions & 15 deletions doc/io/closeModel.html
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Expand Up @@ -63,51 +63,51 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0011
0012 closedModel=model;
0013
0014 closedModel.comps{numel(closedModel.comps)+1}=<span class="string">'b'</span>;
0015 closedModel.compNames{numel(closedModel.compNames)+1}=<span class="string">'boundary'</span>;
0014 closedModel.comps{numel(closedModel.comps)+1,1}=<span class="string">'b'</span>;
0015 closedModel.compNames{numel(closedModel.compNames)+1,1}=<span class="string">'boundary'</span>;
0016 <span class="keyword">if</span> isfield(closedModel,<span class="string">'compMiriams'</span>)
0017 closedModel.compMiriams{numel(closedModel.compMiriams)+1}=[];
0018 <span class="keyword">end</span>;
0017 closedModel.compMiriams{numel(closedModel.compMiriams)+1,1}=[];
0018 <span class="keyword">end</span>
0019 closedModel.unconstrained=zeros(numel(closedModel.mets),1);
0020
0021 <span class="keyword">for</span> i=1:numel(closedModel.rxns)
0022 <span class="keyword">if</span> sum(abs(closedModel.S(:,i)))==1
0023 closedModel.mets{numel(closedModel.mets)+1}=strcat(closedModel.mets{find(closedModel.S(:,i))},<span class="string">'_b'</span>);
0024 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metNames'</span>)
0025 closedModel.metNames{numel(closedModel.metNames)+1}=closedModel.metNames{find(closedModel.S(:,i))};
0026 <span class="keyword">end</span>;
0026 <span class="keyword">end</span>
0027 closedModel.metComps(numel(closedModel.metComps)+1)=numel(closedModel.comps);
0028 <span class="keyword">if</span> isfield(closedModel,<span class="string">'inchis'</span>)
0029 closedModel.inchis{numel(closedModel.inchis)+1}=closedModel.inchis{find(closedModel.S(:,i))};
0030 <span class="keyword">end</span>;
0030 <span class="keyword">end</span>
0031 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metSmiles'</span>)
0032 closedModel.metSmiles{numel(closedModel.metSmiles)+1}=closedModel.metSmiles{find(closedModel.S(:,i))};
0033 <span class="keyword">end</span>;
0033 <span class="keyword">end</span>
0034 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metFormulas'</span>)
0035 closedModel.metFormulas{numel(closedModel.metFormulas)+1}=closedModel.metFormulas{find(closedModel.S(:,i))};
0036 <span class="keyword">end</span>;
0036 <span class="keyword">end</span>
0037 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metMiriams'</span>)
0038 closedModel.metMiriams{numel(closedModel.metMiriams)+1}=closedModel.metMiriams{find(closedModel.S(:,i))};
0039 <span class="keyword">end</span>;
0039 <span class="keyword">end</span>
0040 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metFrom'</span>)
0041 closedModel.metFrom{numel(closedModel.metFrom)+1}=<span class="string">''</span>;
0042 <span class="keyword">end</span>;
0042 <span class="keyword">end</span>
0043 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metCharges'</span>)
0044 closedModel.metCharges(numel(closedModel.metCharges)+1)=closedModel.metCharges(find(closedModel.S(:,i)));
0045 <span class="keyword">end</span>;
0045 <span class="keyword">end</span>
0046 <span class="keyword">if</span> isfield(closedModel,<span class="string">'metDeltaG'</span>)
0047 closedModel.metDeltaG(numel(closedModel.metDeltaG)+1)=closedModel.metDeltaG(find(closedModel.S(:,i)));
0048 <span class="keyword">end</span>;
0048 <span class="keyword">end</span>
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))];
0052 <span class="keyword">if</span> sum(closedModel.S(:,i))==1
0053 closedModel.S(numel(closedModel.mets),i)=-1;
0054 <span class="keyword">else</span>
0055 closedModel.S(numel(closedModel.mets),i)=1;
0056 <span class="keyword">end</span>;
0057 <span class="keyword">end</span>;
0058 <span class="keyword">end</span>;
0056 <span class="keyword">end</span>
0057 <span class="keyword">end</span>
0058 <span class="keyword">end</span>
0059
0060 <span class="keyword">end</span></pre></div>
<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
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