fix: setParam and removeMets bugs (#544)

* fix: setParam correct error message * fix: removeMets metNotes field * doc: updateDocumentation
SysBioChalmers · May 27, 2024 · 0f53134 · 0f53134
1 parent 89296e7
commit 0f53134
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Showing 4 changed files with 36 additions and 30 deletions.
diff --git a/core/removeMets.m b/core/removeMets.m
@@ -95,6 +95,9 @@
     if isfield(reducedModel,'metDeltaG')
         reducedModel.metDeltaG(indexesToDelete)=[];
     end
+    if isfield(reducedModel,'metNotes')
+        reducedModel.metNotes(indexesToDelete)=[];
+    end    
 end
 
 %Remove unused reactions

diff --git a/core/setParam.m b/core/setParam.m
@@ -31,7 +31,7 @@
 
 paramType=convertCharArray(paramType);
 if ~any(strcmpi(paramType,{'lb','ub','eq','obj','rev','var','unc'}))
-    EM=['Incorrect parameter type: "' paramType '"'];
+    EM=['Incorrect parameter type: "' paramType{1} '"'];
     dispEM(EM);
 end
 if isnumeric(rxnList) || islogical(rxnList)

diff --git a/doc/core/removeMets.html b/doc/core/removeMets.html
@@ -161,35 +161,38 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0095     <span class="keyword">if</span> isfield(reducedModel,<span class="string">'metDeltaG'</span>)
 0096         reducedModel.metDeltaG(indexesToDelete)=[];
 0097     <span class="keyword">end</span>
-0098 <span class="keyword">end</span>
-0099 
-0100 <span class="comment">%Remove unused reactions</span>
-0101 <span class="keyword">if</span> removeUnusedRxns==true
-0102     <span class="comment">%Get unused reactions</span>
-0103     [~, a]=find(reducedModel.S);
-0104     rxnsToRemove=1:numel(reducedModel.rxns);
-0105     rxnsToRemove(a)=[];
-0106     reducedModel=<a href="removeReactions.html" class="code" title="function reducedModel=removeReactions(model,rxnsToRemove,removeUnusedMets,removeUnusedGenes,removeUnusedComps)">removeReactions</a>(reducedModel,rxnsToRemove,false,removeUnusedGenes);
-0107 <span class="keyword">end</span>
-0108 
-0109 <span class="comment">%Remove unused compartments</span>
-0110 <span class="keyword">if</span> removeUnusedComps==true
-0111     oldComps=reducedModel.comps;
-0112     I=ismember(1:numel(oldComps),reducedModel.metComps);
-0113     <span class="keyword">if</span> ~all(I)
-0114         reducedModel.comps(~I)=[];
-0115         reducedModel.compNames(~I)=[];
-0116         <span class="keyword">if</span> isfield(reducedModel,<span class="string">'compOutside'</span>)
-0117             reducedModel.compOutside(~I)=[];
-0118         <span class="keyword">end</span>
-0119         <span class="keyword">if</span> isfield(reducedModel,<span class="string">'compMiriams'</span>)
-0120             reducedModel.compMiriams(~I)=[];
+0098     <span class="keyword">if</span> isfield(reducedModel,<span class="string">'metNotes'</span>)
+0099         reducedModel.metNotes(indexesToDelete)=[];
+0100     <span class="keyword">end</span>    
+0101 <span class="keyword">end</span>
+0102 
+0103 <span class="comment">%Remove unused reactions</span>
+0104 <span class="keyword">if</span> removeUnusedRxns==true
+0105     <span class="comment">%Get unused reactions</span>
+0106     [~, a]=find(reducedModel.S);
+0107     rxnsToRemove=1:numel(reducedModel.rxns);
+0108     rxnsToRemove(a)=[];
+0109     reducedModel=<a href="removeReactions.html" class="code" title="function reducedModel=removeReactions(model,rxnsToRemove,removeUnusedMets,removeUnusedGenes,removeUnusedComps)">removeReactions</a>(reducedModel,rxnsToRemove,false,removeUnusedGenes);
+0110 <span class="keyword">end</span>
+0111 
+0112 <span class="comment">%Remove unused compartments</span>
+0113 <span class="keyword">if</span> removeUnusedComps==true
+0114     oldComps=reducedModel.comps;
+0115     I=ismember(1:numel(oldComps),reducedModel.metComps);
+0116     <span class="keyword">if</span> ~all(I)
+0117         reducedModel.comps(~I)=[];
+0118         reducedModel.compNames(~I)=[];
+0119         <span class="keyword">if</span> isfield(reducedModel,<span class="string">'compOutside'</span>)
+0120             reducedModel.compOutside(~I)=[];
 0121         <span class="keyword">end</span>
-0122         [~, J]=ismember(oldComps(reducedModel.metComps),reducedModel.comps);
-0123         reducedModel.metComps=J;
-0124     <span class="keyword">end</span>
-0125 <span class="keyword">end</span>
-0126 <span class="keyword">end</span></pre></div>
+0122         <span class="keyword">if</span> isfield(reducedModel,<span class="string">'compMiriams'</span>)
+0123             reducedModel.compMiriams(~I)=[];
+0124         <span class="keyword">end</span>
+0125         [~, J]=ismember(oldComps(reducedModel.metComps),reducedModel.comps);
+0126         reducedModel.metComps=J;
+0127     <span class="keyword">end</span>
+0128 <span class="keyword">end</span>
+0129 <span class="keyword">end</span></pre></div>
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diff --git a/doc/core/setParam.html b/doc/core/setParam.html
@@ -103,7 +103,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0031 
 0032 paramType=<a href="convertCharArray.html" class="code" title="function inputConverted = convertCharArray(funcInput)">convertCharArray</a>(paramType);
 0033 <span class="keyword">if</span> ~any(strcmpi(paramType,{<span class="string">'lb'</span>,<span class="string">'ub'</span>,<span class="string">'eq'</span>,<span class="string">'obj'</span>,<span class="string">'rev'</span>,<span class="string">'var'</span>,<span class="string">'unc'</span>}))
-0034     EM=[<span class="string">'Incorrect parameter type: &quot;'</span> paramType <span class="string">'&quot;'</span>];
+0034     EM=[<span class="string">'Incorrect parameter type: &quot;'</span> paramType{1} <span class="string">'&quot;'</span>];
 0035     <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM);
 0036 <span class="keyword">end</span>
 0037 <span class="keyword">if</span> isnumeric(rxnList) || islogical(rxnList)