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@edkerk
edkerk committed May 13, 2022
2 parents 32d3421 + 6679990 commit 5ba11a6
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2 changes: 1 addition & 1 deletion doc/io/exportModel.html
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Expand Up @@ -200,7 +200,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0139 <span class="comment">%Generate an empty SBML structure</span>
0140 modelSBML=<a href="#_sub1" class="code" title="subfunction modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)">getSBMLStructure</a>(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
0141 modelSBML.metaid=model.id;
0142 modelSBML.id=model.id;
0142 modelSBML.id=regexprep(model.id,<span class="string">'([^0-9_a-zA-Z])'</span>,<span class="string">'__${num2str($1+0)}__'</span>);
0143 modelSBML.name=model.name;
0144
0145 <span class="keyword">if</span> isfield(model,<span class="string">'annotation'</span>)
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35 changes: 32 additions & 3 deletions doc/struct_conversion/standardizeModelFieldOrder.html
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Expand Up @@ -51,7 +51,9 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
<li><a href="ravenCobraWrapper.html" class="code" title="function newModel=ravenCobraWrapper(model)">ravenCobraWrapper</a> ravenCobraWrapper</li></ul>
<!-- crossreference -->


<h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<ul style="list-style-image:url(../matlabicon.gif)">
<li><a href="#_sub1" class="code">function vecT = columnVector(vec)</a></li></ul>

<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function orderedModel=standardizeModelFieldOrder(model)</a>
Expand Down Expand Up @@ -86,9 +88,36 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0030 modelfields = fieldnames(model);
0031 order = fields(ismember(fields(:,1),modelfields));
0032 remainingOrder = sort(setdiff(modelfields,order));
0033 overallOrder = [columnVector(order);columnVector(remainingOrder)];
0033 overallOrder = [<a href="#_sub1" class="code" title="subfunction vecT = columnVector(vec)">columnVector</a>(order);<a href="#_sub1" class="code" title="subfunction vecT = columnVector(vec)">columnVector</a>(remainingOrder)];
0034 orderedModel = orderfields(model,overallOrder);
0035 <span class="keyword">end</span></pre></div>
0035 <span class="keyword">end</span>
0036
0037 <a name="_sub1" href="#_subfunctions" class="code">function vecT = columnVector(vec)</a>
0038 <span class="comment">% Converts a vector to a column vector</span>
0039 <span class="comment">%</span>
0040 <span class="comment">% USAGE:</span>
0041 <span class="comment">%</span>
0042 <span class="comment">% vecT = columnVector(vec)</span>
0043 <span class="comment">%</span>
0044 <span class="comment">% INPUT:</span>
0045 <span class="comment">% vec: a vector</span>
0046 <span class="comment">%</span>
0047 <span class="comment">% OUTPUT:</span>
0048 <span class="comment">% vecT: a column vector</span>
0049 <span class="comment">%</span>
0050 <span class="comment">% .. Authors:</span>
0051 <span class="comment">% - Original file: Markus Herrgard</span>
0052 <span class="comment">% - Minor changes: Laurent Heirendt January 2017</span>
0053 <span class="comment">% - Copied from COBRA Toolbox May 2022</span>
0054
0055 [n, m] = size(vec);
0056
0057 <span class="keyword">if</span> (m ~= 1 &amp;&amp; n &lt; m) || n == 1
0058 vecT = vec';
0059 <span class="keyword">else</span>
0060 vecT = vec;
0061 <span class="keyword">end</span>
0062 <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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65 changes: 32 additions & 33 deletions doc/testing/unit_tests/mafftTests.html
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Expand Up @@ -80,39 +80,38 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0033 sourceDir = fileparts(which(mfilename));
0034 copyfile(fullfile(sourceDir,<span class="string">'test_data'</span>,<span class="string">'yeast_galactosidases.fa'</span>),tmpDIR);
0035
0036 <span class="comment">% Define WSL paths</span>
0037 wslPath.fastaFile=getWSLpath([tmpDIR filesep <span class="string">'yeast_galactosidases.fa'</span>]);
0038 wslPath.outFile=getWSLpath(outFile);
0039 wslPath.mafft=getWSLpath(fullfile(ravenPath,<span class="string">'software'</span>,<span class="string">'mafft'</span>,<span class="string">'mafft-linux64'</span>,<span class="string">'mafft.bat'</span>));
0040
0041 <span class="comment">%%</span>
0042 <span class="comment">%Run protein multi-sequence alignment with MAFFT</span>
0043 <span class="keyword">if</span> ismac
0044 [~, ~]=system([<span class="string">'&quot;'</span> fullfile(ravenPath,<span class="string">'software'</span>,<span class="string">'mafft'</span>,<span class="string">'mafft-mac'</span>,<span class="string">'mafft.bat'</span>) <span class="string">'&quot; --auto --anysymbol --thread &quot;'</span> num2str(cores) <span class="string">'&quot; &quot;'</span> fullfile(tmpDIR, <span class="string">'yeast_galactosidases.fa'</span>) <span class="string">'&quot; &gt; &quot;'</span> outFile <span class="string">'&quot;'</span>]);
0045 <span class="keyword">elseif</span> isunix
0046 [~, ~]=system([<span class="string">'&quot;'</span> fullfile(ravenPath,<span class="string">'software'</span>,<span class="string">'mafft'</span>,<span class="string">'mafft-linux64'</span>,<span class="string">'mafft.bat'</span>) <span class="string">'&quot; --auto --anysymbol --thread &quot;'</span> num2str(cores) <span class="string">'&quot; &quot;'</span> fullfile(tmpDIR, <span class="string">'yeast_galactosidases.fa'</span>) <span class="string">'&quot; &gt; &quot;'</span> outFile <span class="string">'&quot;'</span>]);
0047 <span class="keyword">elseif</span> ispc
0048 [~, ~]=system([<span class="string">'wsl &quot;'</span> wslPath.mafft <span class="string">'&quot; --auto --anysymbol --quiet --thread &quot;'</span> num2str(cores) <span class="string">'&quot; --out &quot;'</span> wslPath.outFile <span class="string">'&quot; &quot;'</span> wslPath.fastaFile <span class="string">'&quot;'</span>]);
0049 <span class="keyword">end</span>
0050
0051 <span class="comment">%%</span>
0052 <span class="comment">%Open actual MAFFT results file</span>
0053 actMafftOutput=importdata(fullfile(outFile));
0054
0055 <span class="comment">%Remove the old tempfiles</span>
0056 delete([outFile <span class="string">'*'</span>]);
0057
0058 <span class="comment">%Remove temporary folder, since testing is finished</span>
0059 [~, ~]=system([<span class="string">'rm &quot;'</span> tmpDIR <span class="string">'&quot; -r'</span>]);
0060
0061 <span class="comment">%%</span>
0062 <span class="comment">%Check 1a: Check if files for MAFFT results are the same</span>
0063 verifyEqual(testCase,actMafftOutput,expCdhitMafftOutput);
0064
0065 <span class="comment">%Check 1b: Change actual MAFFT results file and check if test fails</span>
0066 actMafftOutput=<span class="string">'abc'</span>;
0067 verifyNotEqual(testCase,actMafftOutput,expCdhitMafftOutput);
0068 <span class="keyword">end</span></pre></div>
0036 <span class="comment">%%</span>
0037 <span class="comment">%Run protein multi-sequence alignment with MAFFT</span>
0038 <span class="keyword">if</span> ismac
0039 [~, ~]=system([<span class="string">'&quot;'</span> fullfile(ravenPath,<span class="string">'software'</span>,<span class="string">'mafft'</span>,<span class="string">'mafft-mac'</span>,<span class="string">'mafft.bat'</span>) <span class="string">'&quot; --auto --anysymbol --thread &quot;'</span> num2str(cores) <span class="string">'&quot; &quot;'</span> fullfile(tmpDIR, <span class="string">'yeast_galactosidases.fa'</span>) <span class="string">'&quot; &gt; &quot;'</span> outFile <span class="string">'&quot;'</span>]);
0040 <span class="keyword">elseif</span> isunix
0041 [~, ~]=system([<span class="string">'&quot;'</span> fullfile(ravenPath,<span class="string">'software'</span>,<span class="string">'mafft'</span>,<span class="string">'mafft-linux64'</span>,<span class="string">'mafft.bat'</span>) <span class="string">'&quot; --auto --anysymbol --thread &quot;'</span> num2str(cores) <span class="string">'&quot; &quot;'</span> fullfile(tmpDIR, <span class="string">'yeast_galactosidases.fa'</span>) <span class="string">'&quot; &gt; &quot;'</span> outFile <span class="string">'&quot;'</span>]);
0042 <span class="keyword">elseif</span> ispc
0043 <span class="comment">% Define WSL paths</span>
0044 wslPath.fastaFile=getWSLpath([tmpDIR filesep <span class="string">'yeast_galactosidases.fa'</span>]);
0045 wslPath.outFile=getWSLpath(outFile);
0046 wslPath.mafft=getWSLpath(fullfile(ravenPath,<span class="string">'software'</span>,<span class="string">'mafft'</span>,<span class="string">'mafft-linux64'</span>,<span class="string">'mafft.bat'</span>));
0047 [~, ~]=system([<span class="string">'wsl &quot;'</span> wslPath.mafft <span class="string">'&quot; --auto --anysymbol --quiet --thread &quot;'</span> num2str(cores) <span class="string">'&quot; --out &quot;'</span> wslPath.outFile <span class="string">'&quot; &quot;'</span> wslPath.fastaFile <span class="string">'&quot;'</span>]);
0048 <span class="keyword">end</span>
0049
0050 <span class="comment">%%</span>
0051 <span class="comment">%Open actual MAFFT results file</span>
0052 actMafftOutput=importdata(fullfile(outFile));
0053
0054 <span class="comment">%Remove the old tempfiles</span>
0055 delete([outFile <span class="string">'*'</span>]);
0056
0057 <span class="comment">%Remove temporary folder, since testing is finished</span>
0058 [~, ~]=system([<span class="string">'rm &quot;'</span> tmpDIR <span class="string">'&quot; -r'</span>]);
0059
0060 <span class="comment">%%</span>
0061 <span class="comment">%Check 1a: Check if files for MAFFT results are the same</span>
0062 verifyEqual(testCase,actMafftOutput,expCdhitMafftOutput);
0063
0064 <span class="comment">%Check 1b: Change actual MAFFT results file and check if test fails</span>
0065 actMafftOutput=<span class="string">'abc'</span>;
0066 verifyNotEqual(testCase,actMafftOutput,expCdhitMafftOutput);
0067 <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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</html>
2 changes: 1 addition & 1 deletion io/exportModel.m
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Expand Up @@ -139,7 +139,7 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
%Generate an empty SBML structure
modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
modelSBML.metaid=model.id;
modelSBML.id=model.id;
modelSBML.id=regexprep(model.id,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
modelSBML.name=model.name;

if isfield(model,'annotation')
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