fix: rename SBML binaries to ensure being used

doc/io/exportModel.html

@@ -728,16 +728,16 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0666 
 0667 <span class="keyword">if</span> sbmlPackageVersions(1) == 2
 0668     modelSBML.fbc_strict=1;
-0669 <span class="keyword">end</span>
-0670 
-0671 modelSBML.rule=[];
-0672 modelSBML.constraint=[];
-0673 
-0674 [ravenDir,prevDir]=findRAVENroot();
-0675 fileName=<a href="checkFileExistence.html" class="code" title="function files=checkFileExistence(files,fullOrTemp,allowSpace,checkExist)">checkFileExistence</a>(fileName,1,true,false);
-0676 cd(fullfile(ravenDir,<span class="string">'software'</span>,<span class="string">'libSBML'</span>));
-0677 OutputSBML(modelSBML,fileName,1,0,[1,0]);
-0678 cd(prevDir);
+0669     modelSBML.isSetfbc_strict = 1;
+0670 <span class="keyword">end</span>
+0671 
+0672 modelSBML.rule=[];
+0673 modelSBML.constraint=[];
+0674 
+0675 [ravenDir,prevDir]=findRAVENroot();
+0676 fileName=<a href="checkFileExistence.html" class="code" title="function files=checkFileExistence(files,fullOrTemp,allowSpace,checkExist)">checkFileExistence</a>(fileName,1,true,false);
+0677 
+0678 OutputSBML_RAVEN(modelSBML,fileName,1,0,[1,0]);
 0679 <span class="keyword">end</span>
 0680 
 0681 

doc/testing/unit_tests/fillGapsLargeTests.html

@@ -102,7 +102,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0055     rmpref(<span class="string">'RAVEN'</span>,<span class="string">'solver'</span>);
 0056 <span class="keyword">end</span>
 0057 <span class="comment">%Expect at least 5% of the original growth</span>
-0058 verifyTrue(testCase,-sol.f&gt;0);
+0058 verifyTrue(testCase,sol.f&gt;0);
 0059 <span class="keyword">end</span>
 0060 
 0061 <a name="_sub2" href="#_subfunctions" class="code">function testLargeSCIP(testCase)</a>
@@ -139,7 +139,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0092     rmpref(<span class="string">'RAVEN'</span>,<span class="string">'solver'</span>);
 0093 <span class="keyword">end</span>
 0094 <span class="comment">%Expect at least 5% of the original growth</span>
-0095 verifyTrue(testCase,-sol.f&gt;0);
+0095 verifyTrue(testCase,sol.f&gt;0);
 0096 <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>

doc/testing/unit_tests/fillGapsSmallTests.html

@@ -102,7 +102,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0055     rmpref(<span class="string">'RAVEN'</span>,<span class="string">'solver'</span>);
 0056 <span class="keyword">end</span>
 0057 <span class="comment">%Should give non-zero flux</span>
-0058 verifyTrue(testCase,-sol.f&gt;0);
+0058 verifyTrue(testCase,sol.f&gt;0);
 0059 <span class="keyword">end</span>
 0060 
 0061 <a name="_sub2" href="#_subfunctions" class="code">function testSmallGurobi(testCase)</a>
@@ -137,7 +137,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0090     rmpref(<span class="string">'RAVEN'</span>,<span class="string">'solver'</span>);
 0091 <span class="keyword">end</span>
 0092 <span class="comment">%Expect at least 5% of the original growth</span>
-0093 verifyTrue(testCase,-sol.f&gt;0);
+0093 verifyTrue(testCase,sol.f&gt;0);
 0094 <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>

io/exportModel.m

@@ -666,16 +666,16 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
 
 if sbmlPackageVersions(1) == 2
     modelSBML.fbc_strict=1;
+    modelSBML.isSetfbc_strict = 1;
 end
 
 modelSBML.rule=[];
 modelSBML.constraint=[];
 
 [ravenDir,prevDir]=findRAVENroot();
 fileName=checkFileExistence(fileName,1,true,false);
-cd(fullfile(ravenDir,'software','libSBML'));
-OutputSBML(modelSBML,fileName,1,0,[1,0]);
-cd(prevDir);
+
+OutputSBML_RAVEN(modelSBML,fileName,1,0,[1,0]);
 end
 
 

io/importModel.m

@@ -129,9 +129,7 @@
 %Load the model using libSBML
 [ravenDir,prevDir]=findRAVENroot();
 fileName=checkFileExistence(fileName,1);
-cd(fullfile(ravenDir,'software','libSBML'));
-modelSBML = TranslateSBML(fileName,0,0,[1 1]);
-cd(prevDir);
+modelSBML = TranslateSBML_RAVEN(fileName,0,0,[1 1]);
 
 if isempty(modelSBML)
     EM='There is a problem with the SBML file. Try using the SBML Validator at http://sbml.org/Facilities/Validator';
@@ -807,6 +805,9 @@
         model.annotation.note=modelSBML.notes(startString+7:endString-1);
         model.annotation.note=regexprep(model.annotation.note,'<p>|</p>','');
         model.annotation.note=strtrim(model.annotation.note);
+        if regexp(model.annotation.note,'This file was generated using the exportModel function in RAVEN Toolbox \d\.\d and OutputSBML in libSBML')
+            model.annotation=rmfield(model.annotation,'note'); % Default note added when running exportModel
+        end
     end
 end