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chore: updateDocumentation
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edkerk committed Nov 4, 2021
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230 changes: 121 additions & 109 deletions doc/core/checkModelStruct.html
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Original file line number Diff line number Diff line change
Expand Up @@ -305,116 +305,128 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0246 EM=<span class="string">'The following reactions have bounds contradicting their reversibility:'</span>;
0247 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,throwErrors,model.rxns(model.lb&lt;0 &amp; model.rev==0),trimWarnings);
0248
0249 <span class="comment">%Mapping of compartments</span>
0250 <span class="keyword">if</span> isfield(model,<span class="string">'compOutside'</span>)
0251 EM=<span class="string">'The following compartments are in &quot;compOutside&quot; but not in &quot;comps&quot;:'</span>;
0252 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,throwErrors,setdiff(model.compOutside,[{<span class="string">''</span>};model.comps]),trimWarnings);
0253 <span class="keyword">end</span>
0254
0255 <span class="comment">%Met names which start with number</span>
0256 I=false(numel(model.metNames),1);
0257 <span class="keyword">for</span> i=1:numel(model.metNames)
0258 index=strfind(model.metNames{i},<span class="string">' '</span>);
0259 <span class="keyword">if</span> any(index)
0260 <span class="keyword">if</span> any(str2double(model.metNames{i}(1:index(1)-1)))
0261 I(i)=true;
0262 <span class="keyword">end</span>
0263 <span class="keyword">end</span>
0264 <span class="keyword">end</span>
0265 EM=<span class="string">'The following metabolite names begin with a number directly followed by space:'</span>;
0266 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,throwErrors,model.mets(I),trimWarnings);
0267
0268 <span class="comment">%Non-parseable composition</span>
0269 <span class="keyword">if</span> isfield(model,<span class="string">'metFormulas'</span>)
0270 [~, ~, exitFlag]=<a href="parseFormulas.html" class="code" title="function [elements, useMat, exitFlag, MW]=parseFormulas(formulas, noPolymers,isInchi,ignoreRX)">parseFormulas</a>(model.metFormulas,true,false);
0271 EM=<span class="string">'The composition for the following metabolites could not be parsed:'</span>;
0272 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,model.mets(exitFlag==-1),trimWarnings);
0273 <span class="keyword">end</span>
0274
0275 <span class="comment">%Check if there are metabolites with different names but the same MIRIAM</span>
0276 <span class="comment">%codes</span>
0277 <span class="keyword">if</span> isfield(model,<span class="string">'metMiriams'</span>)
0278 miriams=containers.Map();
0279 <span class="keyword">for</span> i=1:numel(model.mets)
0280 <span class="keyword">if</span> ~isempty(model.metMiriams{i})
0281 <span class="comment">%Loop through and add for each miriam</span>
0282 <span class="keyword">for</span> j=1:numel(model.metMiriams{i}.name)
0283 <span class="comment">%Get existing metabolite indexes</span>
0284 current=strcat(model.metMiriams{i}.name{j},<span class="string">'/'</span>,model.metMiriams{i}.value{j});
0285 <span class="keyword">if</span> isKey(miriams,current)
0286 existing=miriams(current);
0287 <span class="keyword">else</span>
0288 existing=[];
0289 <span class="keyword">end</span>
0290 miriams(current)=[existing;i];
0291 <span class="keyword">end</span>
0292 <span class="keyword">end</span>
0293 <span class="keyword">end</span>
0294
0295 <span class="comment">%Get all keys</span>
0296 allMiriams=keys(miriams);
0297
0298 hasMultiple=false(numel(allMiriams),1);
0299 <span class="keyword">for</span> i=1:numel(allMiriams)
0300 <span class="keyword">if</span> numel(miriams(allMiriams{i}))&gt;1
0301 <span class="comment">%Check if they all have the same name</span>
0302 <span class="keyword">if</span> numel(unique(model.metNames(miriams(allMiriams{i}))))&gt;1
0303 <span class="keyword">if</span> ~regexp(allMiriams{i},<span class="string">'^sbo\/SBO:'</span>) <span class="comment">% SBO terms are expected to be multiple</span>
0304 hasMultiple(i)=true;
0305 <span class="keyword">end</span>
0306 <span class="keyword">end</span>
0307 <span class="keyword">end</span>
0308 <span class="keyword">end</span>
0249 <span class="comment">%Multiple or no objective functions not allowed in SBML L3V1 FBCv2</span>
0250 <span class="keyword">if</span> find(model.c)&gt;1 |
0251 EM=<span class="string">'The model has multiple objective functions, which might be intended, but will not allow export to SBML'</span>;
0252 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false);
0253 <span class="keyword">else</span> ~any(model.c)
0254 EM=<span class="string">'The model no objective functions, which might be intended, but will not allow export to SBML'</span>;
0255 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false);
0256 <span class="keyword">end</span>
0257
0258 EM=<span class="string">'The following reactions have contradicting bounds:'</span>;
0259 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,throwErrors,model.rxns(model.lb&gt;model.ub),trimWarnings);
0260
0261 <span class="comment">%Mapping of compartments</span>
0262 <span class="keyword">if</span> isfield(model,<span class="string">'compOutside'</span>)
0263 EM=<span class="string">'The following compartments are in &quot;compOutside&quot; but not in &quot;comps&quot;:'</span>;
0264 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,throwErrors,setdiff(model.compOutside,[{<span class="string">''</span>};model.comps]),trimWarnings);
0265 <span class="keyword">end</span>
0266
0267 <span class="comment">%Met names which start with number</span>
0268 I=false(numel(model.metNames),1);
0269 <span class="keyword">for</span> i=1:numel(model.metNames)
0270 index=strfind(model.metNames{i},<span class="string">' '</span>);
0271 <span class="keyword">if</span> any(index)
0272 <span class="keyword">if</span> any(str2double(model.metNames{i}(1:index(1)-1)))
0273 I(i)=true;
0274 <span class="keyword">end</span>
0275 <span class="keyword">end</span>
0276 <span class="keyword">end</span>
0277 EM=<span class="string">'The following metabolite names begin with a number directly followed by space:'</span>;
0278 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,throwErrors,model.mets(I),trimWarnings);
0279
0280 <span class="comment">%Non-parseable composition</span>
0281 <span class="keyword">if</span> isfield(model,<span class="string">'metFormulas'</span>)
0282 [~, ~, exitFlag]=<a href="parseFormulas.html" class="code" title="function [elements, useMat, exitFlag, MW]=parseFormulas(formulas, noPolymers,isInchi,ignoreRX)">parseFormulas</a>(model.metFormulas,true,false);
0283 EM=<span class="string">'The composition for the following metabolites could not be parsed:'</span>;
0284 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,model.mets(exitFlag==-1),trimWarnings);
0285 <span class="keyword">end</span>
0286
0287 <span class="comment">%Check if there are metabolites with different names but the same MIRIAM</span>
0288 <span class="comment">%codes</span>
0289 <span class="keyword">if</span> isfield(model,<span class="string">'metMiriams'</span>)
0290 miriams=containers.Map();
0291 <span class="keyword">for</span> i=1:numel(model.mets)
0292 <span class="keyword">if</span> ~isempty(model.metMiriams{i})
0293 <span class="comment">%Loop through and add for each miriam</span>
0294 <span class="keyword">for</span> j=1:numel(model.metMiriams{i}.name)
0295 <span class="comment">%Get existing metabolite indexes</span>
0296 current=strcat(model.metMiriams{i}.name{j},<span class="string">'/'</span>,model.metMiriams{i}.value{j});
0297 <span class="keyword">if</span> isKey(miriams,current)
0298 existing=miriams(current);
0299 <span class="keyword">else</span>
0300 existing=[];
0301 <span class="keyword">end</span>
0302 miriams(current)=[existing;i];
0303 <span class="keyword">end</span>
0304 <span class="keyword">end</span>
0305 <span class="keyword">end</span>
0306
0307 <span class="comment">%Get all keys</span>
0308 allMiriams=keys(miriams);
0309
0310 <span class="comment">%Print output</span>
0311 EM=<span class="string">'The following MIRIAM strings are associated to more than one unique metabolite name:'</span>;
0312 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,allMiriams(hasMultiple),trimWarnings);
0313 <span class="keyword">end</span>
0314
0315 <span class="comment">%Check if there are metabolites with different names but the same InChI</span>
0316 <span class="comment">%codes</span>
0317 <span class="keyword">if</span> isfield(model,<span class="string">'inchis'</span>)
0318 inchis=containers.Map();
0319 <span class="keyword">for</span> i=1:numel(model.mets)
0320 <span class="keyword">if</span> ~isempty(model.inchis{i})
0321 <span class="comment">%Get existing metabolite indexes</span>
0322 <span class="keyword">if</span> isKey(inchis,model.inchis{i})
0323 existing=inchis(model.inchis{i});
0324 <span class="keyword">else</span>
0325 existing=[];
0326 <span class="keyword">end</span>
0327 inchis(model.inchis{i})=[existing;i];
0328 <span class="keyword">end</span>
0329 <span class="keyword">end</span>
0330
0331 <span class="comment">%Get all keys</span>
0332 allInchis=keys(inchis);
0333
0334 hasMultiple=false(numel(allInchis),1);
0335 <span class="keyword">for</span> i=1:numel(allInchis)
0336 <span class="keyword">if</span> numel(inchis(allInchis{i}))&gt;1
0337 <span class="comment">%Check if they all have the same name</span>
0338 <span class="keyword">if</span> numel(unique(model.metNames(inchis(allInchis{i}))))&gt;1
0339 hasMultiple(i)=true;
0340 <span class="keyword">end</span>
0341 <span class="keyword">end</span>
0342 <span class="keyword">end</span>
0343
0344 <span class="comment">%Print output</span>
0345 EM=<span class="string">'The following InChI strings are associated to more than one unique metabolite name:'</span>;
0346 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,allInchis(hasMultiple),trimWarnings);
0347 <span class="keyword">end</span>
0348 <span class="keyword">end</span>
0349
0350 <a name="_sub1" href="#_subfunctions" class="code">function I=duplicates(strings)</a>
0351 I=false(numel(strings),1);
0352 [J, K]=unique(strings);
0353 <span class="keyword">if</span> numel(J)~=numel(strings)
0354 L=1:numel(strings);
0355 L(K)=[];
0356 I(L)=true;
0357 <span class="keyword">end</span>
0358 <span class="keyword">end</span></pre></div>
0310 hasMultiple=false(numel(allMiriams),1);
0311 <span class="keyword">for</span> i=1:numel(allMiriams)
0312 <span class="keyword">if</span> numel(miriams(allMiriams{i}))&gt;1
0313 <span class="comment">%Check if they all have the same name</span>
0314 <span class="keyword">if</span> numel(unique(model.metNames(miriams(allMiriams{i}))))&gt;1
0315 <span class="keyword">if</span> ~regexp(allMiriams{i},<span class="string">'^sbo\/SBO:'</span>) <span class="comment">% SBO terms are expected to be multiple</span>
0316 hasMultiple(i)=true;
0317 <span class="keyword">end</span>
0318 <span class="keyword">end</span>
0319 <span class="keyword">end</span>
0320 <span class="keyword">end</span>
0321
0322 <span class="comment">%Print output</span>
0323 EM=<span class="string">'The following MIRIAM strings are associated to more than one unique metabolite name:'</span>;
0324 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,allMiriams(hasMultiple),trimWarnings);
0325 <span class="keyword">end</span>
0326
0327 <span class="comment">%Check if there are metabolites with different names but the same InChI</span>
0328 <span class="comment">%codes</span>
0329 <span class="keyword">if</span> isfield(model,<span class="string">'inchis'</span>)
0330 inchis=containers.Map();
0331 <span class="keyword">for</span> i=1:numel(model.mets)
0332 <span class="keyword">if</span> ~isempty(model.inchis{i})
0333 <span class="comment">%Get existing metabolite indexes</span>
0334 <span class="keyword">if</span> isKey(inchis,model.inchis{i})
0335 existing=inchis(model.inchis{i});
0336 <span class="keyword">else</span>
0337 existing=[];
0338 <span class="keyword">end</span>
0339 inchis(model.inchis{i})=[existing;i];
0340 <span class="keyword">end</span>
0341 <span class="keyword">end</span>
0342
0343 <span class="comment">%Get all keys</span>
0344 allInchis=keys(inchis);
0345
0346 hasMultiple=false(numel(allInchis),1);
0347 <span class="keyword">for</span> i=1:numel(allInchis)
0348 <span class="keyword">if</span> numel(inchis(allInchis{i}))&gt;1
0349 <span class="comment">%Check if they all have the same name</span>
0350 <span class="keyword">if</span> numel(unique(model.metNames(inchis(allInchis{i}))))&gt;1
0351 hasMultiple(i)=true;
0352 <span class="keyword">end</span>
0353 <span class="keyword">end</span>
0354 <span class="keyword">end</span>
0355
0356 <span class="comment">%Print output</span>
0357 EM=<span class="string">'The following InChI strings are associated to more than one unique metabolite name:'</span>;
0358 <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM,false,allInchis(hasMultiple),trimWarnings);
0359 <span class="keyword">end</span>
0360 <span class="keyword">end</span>
0361
0362 <a name="_sub1" href="#_subfunctions" class="code">function I=duplicates(strings)</a>
0363 I=false(numel(strings),1);
0364 [J, K]=unique(strings);
0365 <span class="keyword">if</span> numel(J)~=numel(strings)
0366 L=1:numel(strings);
0367 L(K)=[];
0368 I(L)=true;
0369 <span class="keyword">end</span>
0370 <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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2 changes: 1 addition & 1 deletion doc/external/kegg/getKEGGModelForOrganism.html
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Original file line number Diff line number Diff line change
Expand Up @@ -1249,7 +1249,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0933 <span class="keyword">end</span>
0934 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'</span>);
0935 <span class="keyword">else</span>
0936 fprintf([<span class="string">'Querying &lt;strong&gt;'</span> fastaFile <span class="string">'&lt;/strong&gt; against the KEGG Orthology specific HMMs... COMPLETE\n'</span>]);
0936 fprintf([<span class="string">'Querying &lt;strong&gt;'</span> strrep(fastaFile,<span class="string">'\'</span>,<span class="string">'/'</span>) <span class="string">'&lt;/strong&gt; against the KEGG Orthology specific HMMs... COMPLETE\n'</span>]);
0937 <span class="keyword">end</span>
0938
0939
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