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

Author: edkerk

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);

doc/core/generateNewIds.html

@@ -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>

doc/io/closeModel.html

@@ -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>