fix: change model field proteinNames to proteins (SysBioChalmers#564)

* fix: change model field proteinNames to proteins * fix: enforce column form for model.proteins * doc: importModel more informative warning * chore: update documentation --------- Co-authored-by: Eduard Kerkhoven <[email protected]>
ae-tafur · Oct 12, 2024 · e6f2837 · e6f2837
1 parent 38f8415
commit e6f2837
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Showing 32 changed files with 393 additions and 367 deletions.
diff --git a/INIT/getINITModel.m b/INIT/getINITModel.m
@@ -391,8 +391,8 @@
 if isfield(model,'geneShortNames')
     model.geneShortNames(I)=[];
 end
-if isfield(model,'proteinNames')
-    model.proteinNames(I)=[];
+if isfield(model,'proteins')
+    model.proteins(I)=[];
 end
 if isfield(model,'geneMiriams')
     model.geneMiriams(I)=[];

diff --git a/INIT/mergeLinear.m b/INIT/mergeLinear.m
@@ -29,8 +29,8 @@
 if isfield(reducedModel,'geneShortNames')
     reducedModel.geneShortNames={};
 end
-if isfield(reducedModel,'proteinNames')
-    reducedModel.proteinNames={};
+if isfield(reducedModel,'proteins')
+    reducedModel.proteins={};
 end
 if isfield(reducedModel,'geneMiriams')
     reducedModel.geneMiriams={};

diff --git a/INIT/removeLowScoreGenes.m b/INIT/removeLowScoreGenes.m
@@ -119,8 +119,8 @@
 if isfield(newModel,'geneShortNames')
     newModel.geneShortNames(remInd) = [];
 end
-if isfield(newModel,'proteinNames')
-    newModel.proteinNames(remInd) = [];
+if isfield(newModel,'proteins')
+    newModel.proteins(remInd) = [];
 end
 if isfield(newModel,'geneMiriams')
     newModel.geneMiriams(remInd) = [];

diff --git a/core/addGenesRaven.m b/core/addGenesRaven.m
@@ -14,7 +14,7 @@
 %                               default '')
 %                geneMiriams    cell array with MIRIAM structures (optional,
 %                               default [])
-%                proteinNames   cell array of protein names associated to
+%                proteins   cell array of protein names associated to
 %                               each gene (optional, default '')
 %
 %   newModel     an updated model structure
@@ -58,8 +58,8 @@
     if isfield(genesToAdd,'geneShortNames')
         genesToAdd.geneShortNames(I)=[];
     end
-    if isfield(genesToAdd,'proteinNames')
-        genesToAdd.proteinNames(I)=[];
+    if isfield(genesToAdd,'proteins')
+        genesToAdd.proteins(I)=[];
     end
     if isfield(genesToAdd,'geneMiriams')
         genesToAdd.geneMiriams(I)=[];
@@ -86,21 +86,21 @@
         newModel.geneShortNames=[newModel.geneShortNames;filler];
     end
 end
-if isfield(genesToAdd,'proteinNames')
-    genesToAdd.proteinNames=convertCharArray(genesToAdd.proteinNames);
-    if numel(genesToAdd.proteinNames)~=nGenes
-        EM='genesToAdd.proteinNames must have the same number of elements as genesToAdd.genes';
+if isfield(genesToAdd,'proteins')
+    genesToAdd.proteins=convertCharArray(genesToAdd.proteins);
+    if numel(genesToAdd.proteins)~=nGenes
+        EM='genesToAdd.proteins must have the same number of elements as genesToAdd.genes';
         dispEM(EM);
     end
     %Add empty field if it doesn't exist
-    if ~isfield(newModel,'proteinNames')
-        newModel.proteinNames=largeFiller;
+    if ~isfield(newModel,'proteins')
+        newModel.proteins=largeFiller;
     end
-    newModel.proteinNames=[newModel.proteinNames;genesToAdd.proteinNames(:)];
+    newModel.proteins=[newModel.proteins;genesToAdd.proteins(:)];
 else
     %Add empty strings if structure is in model
-    if isfield(newModel,'proteinNames')
-        newModel.proteinNames=[newModel.proteinNames;filler];
+    if isfield(newModel,'proteins')
+        newModel.proteins=[newModel.proteins;filler];
     end
 end
 

diff --git a/core/deleteUnusedGenes.m b/core/deleteUnusedGenes.m
@@ -37,8 +37,8 @@
     reducedModel.geneShortNames=reducedModel.geneShortNames(toKeep);
 end
 
-if isfield(reducedModel,'proteinNames')
-    reducedModel.proteinNames=reducedModel.proteinNames(toKeep);
+if isfield(reducedModel,'proteins')
+    reducedModel.proteins=reducedModel.proteins(toKeep);
 end
 
 if isfield(reducedModel,'geneMiriams')

diff --git a/core/getModelFromHomology.m b/core/getModelFromHomology.m
@@ -115,8 +115,8 @@
     if isfield(models{i},'geneMiriams')
         models{i}=rmfield(models{i},'geneMiriams');
     end
-    if isfield(models{i},'proteinNames')
-        models{i}=rmfield(models{i},'proteinNames');
+    if isfield(models{i},'proteins')
+        models{i}=rmfield(models{i},'proteins');
     end
     %The geneFrom field also loses meaning if the genes are replaced by
     %orthologs

diff --git a/core/mergeModels.m b/core/mergeModels.m
@@ -493,8 +493,8 @@
                 model.geneShortNames=models{i}.geneShortNames;
             end
 
-            if isfield(models{i},'proteinNames')
-                model.proteinNames=models{i}.proteinNames;
+            if isfield(models{i},'proteins')
+                model.proteins=models{i}.proteins;
             end
 
             if isfield(models{i},'geneMiriams')
@@ -535,19 +535,19 @@
                     end
                 end
 
-                if isfield(models{i},'proteinNames')
-                    if isfield(model,'proteinNames')
-                        model.proteinNames=[model.proteinNames;models{i}.proteinNames(genesToAdd)];
+                if isfield(models{i},'proteins')
+                    if isfield(model,'proteins')
+                        model.proteins=[model.proteins;models{i}.proteins(genesToAdd)];
                     else
                         emptyGeneSN=cell(numel(model.genes)-numel(genesToAdd),1);
                         emptyGeneSN(:)={''};
-                        model.proteinNames=[emptyGeneSN;models{i}.proteinNames(genesToAdd)];
+                        model.proteins=[emptyGeneSN;models{i}.proteins(genesToAdd)];
                     end
                 else
-                    if isfield(model,'proteinNames')
+                    if isfield(model,'proteins')
                         emptyGeneSN=cell(numel(genesToAdd),1);
                         emptyGeneSN(:)={''};
-                        model.proteinNames=[model.proteinNames;emptyGeneSN];
+                        model.proteins=[model.proteins;emptyGeneSN];
                     end
                 end
 

diff --git a/core/permuteModel.m b/core/permuteModel.m
@@ -132,8 +132,8 @@
         if isfield(newModel,'geneShortNames')
             newModel.geneShortNames=newModel.geneShortNames(indexes);
         end
-        if isfield(newModel,'proteinNames')
-            newModel.proteinNames=newModel.proteinNames(indexes);
+        if isfield(newModel,'proteins')
+            newModel.proteins=newModel.proteins(indexes);
         end
         if isfield(newModel,'rxnGeneMat')
             newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes);

diff --git a/core/predictLocalization.m b/core/predictLocalization.m
@@ -199,8 +199,8 @@
     if isfield(model,'geneMiriams')
         model.geneMiriams=[model.geneMiriams;{[]}];
     end
-    if isfield(model,'proteinNames')
-        model.proteinNames=[model.proteinNames;{[]}];
+    if isfield(model,'proteins')
+        model.proteins=[model.proteins;{[]}];
     end
     if isfield(model,'geneFrom')
         model.geneFrom=[model.geneFrom;{{'FAKE'}}];
@@ -261,8 +261,8 @@
     if isfield(model,'geneShortNames')
         model.geneShortNames=[model.geneShortNames;{''}];
     end
-    if isfield(model,'proteinNames')
-        model.proteinNames=[model.proteinNames;{''}];
+    if isfield(model,'proteins')
+        model.proteins=[model.proteins;{''}];
     end
     if isfield(model,'geneFrom')
         model.geneFrom=[model.geneFrom;{'COMPLEX'}];
@@ -765,8 +765,8 @@
 if isfield(outModel,'geneShortNames')
     outModel.geneShortNames(I)=[];
 end
-if isfield(outModel,'proteinNames')
-    outModel.proteinNames(I)=[];
+if isfield(outModel,'proteins')
+    outModel.proteins(I)=[];
 end
 outModel.rxnGeneMat(:,I)=[];
 

diff --git a/core/removeReactions.m b/core/removeReactions.m
@@ -130,8 +130,8 @@
             reducedModel.geneShortNames=reducedModel.geneShortNames(toKeep);
         end
 
-        if isfield(reducedModel,'proteinNames')
-            reducedModel.proteinNames=reducedModel.proteinNames(toKeep);
+        if isfield(reducedModel,'proteins')
+            reducedModel.proteins=reducedModel.proteins(toKeep);
         end
 
         if isfield(reducedModel,'geneMiriams')

diff --git a/core/simplifyModel.m b/core/simplifyModel.m
@@ -221,8 +221,8 @@
     if isfield(reducedModel,'geneShortNames')
         reducedModel.geneShortNames={};
     end
-    if isfield(reducedModel,'proteinNames')
-        reducedModel.proteinNames={};
+    if isfield(reducedModel,'proteins')
+        reducedModel.proteins={};
     end
     if isfield(reducedModel,'geneMiriams')
         reducedModel.geneMiriams={};

diff --git a/doc/INIT/getINITModel.html b/doc/INIT/getINITModel.html
@@ -544,8 +544,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0391 <span class="keyword">if</span> isfield(model,<span class="string">'geneShortNames'</span>)
 0392     model.geneShortNames(I)=[];
 0393 <span class="keyword">end</span>
-0394 <span class="keyword">if</span> isfield(model,<span class="string">'proteinNames'</span>)
-0395     model.proteinNames(I)=[];
+0394 <span class="keyword">if</span> isfield(model,<span class="string">'proteins'</span>)
+0395     model.proteins(I)=[];
 0396 <span class="keyword">end</span>
 0397 <span class="keyword">if</span> isfield(model,<span class="string">'geneMiriams'</span>)
 0398     model.geneMiriams(I)=[];

diff --git a/doc/INIT/mergeLinear.html b/doc/INIT/mergeLinear.html
@@ -92,8 +92,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0029 <span class="keyword">if</span> isfield(reducedModel,<span class="string">'geneShortNames'</span>)
 0030     reducedModel.geneShortNames={};
 0031 <span class="keyword">end</span>
-0032 <span class="keyword">if</span> isfield(reducedModel,<span class="string">'proteinNames'</span>)
-0033     reducedModel.proteinNames={};
+0032 <span class="keyword">if</span> isfield(reducedModel,<span class="string">'proteins'</span>)
+0033     reducedModel.proteins={};
 0034 <span class="keyword">end</span>
 0035 <span class="keyword">if</span> isfield(reducedModel,<span class="string">'geneMiriams'</span>)
 0036     reducedModel.geneMiriams={};

diff --git a/doc/INIT/removeLowScoreGenes.html b/doc/INIT/removeLowScoreGenes.html
@@ -223,8 +223,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0119 <span class="keyword">if</span> isfield(newModel,<span class="string">'geneShortNames'</span>)
 0120     newModel.geneShortNames(remInd) = [];
 0121 <span class="keyword">end</span>
-0122 <span class="keyword">if</span> isfield(newModel,<span class="string">'proteinNames'</span>)
-0123     newModel.proteinNames(remInd) = [];
+0122 <span class="keyword">if</span> isfield(newModel,<span class="string">'proteins'</span>)
+0123     newModel.proteins(remInd) = [];
 0124 <span class="keyword">end</span>
 0125 <span class="keyword">if</span> isfield(newModel,<span class="string">'geneMiriams'</span>)
 0126     newModel.geneMiriams(remInd) = [];

diff --git a/doc/core/addGenesRaven.html b/doc/core/addGenesRaven.html
@@ -42,7 +42,7 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
                                default '')
                 geneMiriams    cell array with MIRIAM structures (optional,
                                default [])
-                proteinNames   cell array of protein names associated to
+                proteins   cell array of protein names associated to
                                each gene (optional, default '')
 
    newModel     an updated model structure
@@ -81,7 +81,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0014 <span class="comment">%                               default '')</span>
 0015 <span class="comment">%                geneMiriams    cell array with MIRIAM structures (optional,</span>
 0016 <span class="comment">%                               default [])</span>
-0017 <span class="comment">%                proteinNames   cell array of protein names associated to</span>
+0017 <span class="comment">%                proteins   cell array of protein names associated to</span>
 0018 <span class="comment">%                               each gene (optional, default '')</span>
 0019 <span class="comment">%</span>
 0020 <span class="comment">%   newModel     an updated model structure</span>
@@ -125,8 +125,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0058     <span class="keyword">if</span> isfield(genesToAdd,<span class="string">'geneShortNames'</span>)
 0059         genesToAdd.geneShortNames(I)=[];
 0060     <span class="keyword">end</span>
-0061     <span class="keyword">if</span> isfield(genesToAdd,<span class="string">'proteinNames'</span>)
-0062         genesToAdd.proteinNames(I)=[];
+0061     <span class="keyword">if</span> isfield(genesToAdd,<span class="string">'proteins'</span>)
+0062         genesToAdd.proteins(I)=[];
 0063     <span class="keyword">end</span>
 0064     <span class="keyword">if</span> isfield(genesToAdd,<span class="string">'geneMiriams'</span>)
 0065         genesToAdd.geneMiriams(I)=[];
@@ -153,21 +153,21 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0086         newModel.geneShortNames=[newModel.geneShortNames;filler];
 0087     <span class="keyword">end</span>
 0088 <span class="keyword">end</span>
-0089 <span class="keyword">if</span> isfield(genesToAdd,<span class="string">'proteinNames'</span>)
-0090     genesToAdd.proteinNames=<a href="convertCharArray.html" class="code" title="function inputConverted = convertCharArray(funcInput)">convertCharArray</a>(genesToAdd.proteinNames);
-0091     <span class="keyword">if</span> numel(genesToAdd.proteinNames)~=nGenes
-0092         EM=<span class="string">'genesToAdd.proteinNames must have the same number of elements as genesToAdd.genes'</span>;
+0089 <span class="keyword">if</span> isfield(genesToAdd,<span class="string">'proteins'</span>)
+0090     genesToAdd.proteins=<a href="convertCharArray.html" class="code" title="function inputConverted = convertCharArray(funcInput)">convertCharArray</a>(genesToAdd.proteins);
+0091     <span class="keyword">if</span> numel(genesToAdd.proteins)~=nGenes
+0092         EM=<span class="string">'genesToAdd.proteins must have the same number of elements as genesToAdd.genes'</span>;
 0093         <a href="dispEM.html" class="code" title="function dispEM(string,throwErrors,toList,trimWarnings)">dispEM</a>(EM);
 0094     <span class="keyword">end</span>
 0095     <span class="comment">%Add empty field if it doesn't exist</span>
-0096     <span class="keyword">if</span> ~isfield(newModel,<span class="string">'proteinNames'</span>)
-0097         newModel.proteinNames=largeFiller;
+0096     <span class="keyword">if</span> ~isfield(newModel,<span class="string">'proteins'</span>)
+0097         newModel.proteins=largeFiller;
 0098     <span class="keyword">end</span>
-0099     newModel.proteinNames=[newModel.proteinNames;genesToAdd.proteinNames(:)];
+0099     newModel.proteins=[newModel.proteins;genesToAdd.proteins(:)];
 0100 <span class="keyword">else</span>
 0101     <span class="comment">%Add empty strings if structure is in model</span>
-0102     <span class="keyword">if</span> isfield(newModel,<span class="string">'proteinNames'</span>)
-0103         newModel.proteinNames=[newModel.proteinNames;filler];
+0102     <span class="keyword">if</span> isfield(newModel,<span class="string">'proteins'</span>)
+0103         newModel.proteins=[newModel.proteins;filler];
 0104     <span class="keyword">end</span>
 0105 <span class="keyword">end</span>
 0106 

diff --git a/doc/core/deleteUnusedGenes.html b/doc/core/deleteUnusedGenes.html
@@ -90,8 +90,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0037     reducedModel.geneShortNames=reducedModel.geneShortNames(toKeep);
 0038 <span class="keyword">end</span>
 0039 
-0040 <span class="keyword">if</span> isfield(reducedModel,<span class="string">'proteinNames'</span>)
-0041     reducedModel.proteinNames=reducedModel.proteinNames(toKeep);
+0040 <span class="keyword">if</span> isfield(reducedModel,<span class="string">'proteins'</span>)
+0041     reducedModel.proteins=reducedModel.proteins(toKeep);
 0042 <span class="keyword">end</span>
 0043 
 0044 <span class="keyword">if</span> isfield(reducedModel,<span class="string">'geneMiriams'</span>)

diff --git a/doc/core/getModelFromHomology.html b/doc/core/getModelFromHomology.html
@@ -222,8 +222,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0115     <span class="keyword">if</span> isfield(models{i},<span class="string">'geneMiriams'</span>)
 0116         models{i}=rmfield(models{i},<span class="string">'geneMiriams'</span>);
 0117     <span class="keyword">end</span>
-0118     <span class="keyword">if</span> isfield(models{i},<span class="string">'proteinNames'</span>)
-0119         models{i}=rmfield(models{i},<span class="string">'proteinNames'</span>);
+0118     <span class="keyword">if</span> isfield(models{i},<span class="string">'proteins'</span>)
+0119         models{i}=rmfield(models{i},<span class="string">'proteins'</span>);
 0120     <span class="keyword">end</span>
 0121     <span class="comment">%The geneFrom field also loses meaning if the genes are replaced by</span>
 0122     <span class="comment">%orthologs</span>

diff --git a/doc/core/mergeModels.html b/doc/core/mergeModels.html
@@ -554,8 +554,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0493                 model.geneShortNames=models{i}.geneShortNames;
 0494             <span class="keyword">end</span>
 0495 
-0496             <span class="keyword">if</span> isfield(models{i},<span class="string">'proteinNames'</span>)
-0497                 model.proteinNames=models{i}.proteinNames;
+0496             <span class="keyword">if</span> isfield(models{i},<span class="string">'proteins'</span>)
+0497                 model.proteins=models{i}.proteins;
 0498             <span class="keyword">end</span>
 0499 
 0500             <span class="keyword">if</span> isfield(models{i},<span class="string">'geneMiriams'</span>)
@@ -596,19 +596,19 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0535                     <span class="keyword">end</span>
 0536                 <span class="keyword">end</span>
 0537 
-0538                 <span class="keyword">if</span> isfield(models{i},<span class="string">'proteinNames'</span>)
-0539                     <span class="keyword">if</span> isfield(model,<span class="string">'proteinNames'</span>)
-0540                         model.proteinNames=[model.proteinNames;models{i}.proteinNames(genesToAdd)];
+0538                 <span class="keyword">if</span> isfield(models{i},<span class="string">'proteins'</span>)
+0539                     <span class="keyword">if</span> isfield(model,<span class="string">'proteins'</span>)
+0540                         model.proteins=[model.proteins;models{i}.proteins(genesToAdd)];
 0541                     <span class="keyword">else</span>
 0542                         emptyGeneSN=cell(numel(model.genes)-numel(genesToAdd),1);
 0543                         emptyGeneSN(:)={<span class="string">''</span>};
-0544                         model.proteinNames=[emptyGeneSN;models{i}.proteinNames(genesToAdd)];
+0544                         model.proteins=[emptyGeneSN;models{i}.proteins(genesToAdd)];
 0545                     <span class="keyword">end</span>
 0546                 <span class="keyword">else</span>
-0547                     <span class="keyword">if</span> isfield(model,<span class="string">'proteinNames'</span>)
+0547                     <span class="keyword">if</span> isfield(model,<span class="string">'proteins'</span>)
 0548                         emptyGeneSN=cell(numel(genesToAdd),1);
 0549                         emptyGeneSN(:)={<span class="string">''</span>};
-0550                         model.proteinNames=[model.proteinNames;emptyGeneSN];
+0550                         model.proteins=[model.proteins;emptyGeneSN];
 0551                     <span class="keyword">end</span>
 0552                 <span class="keyword">end</span>
 0553 

diff --git a/doc/core/permuteModel.html b/doc/core/permuteModel.html
@@ -189,8 +189,8 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0132         <span class="keyword">if</span> isfield(newModel,<span class="string">'geneShortNames'</span>)
 0133             newModel.geneShortNames=newModel.geneShortNames(indexes);
 0134         <span class="keyword">end</span>
-0135         <span class="keyword">if</span> isfield(newModel,<span class="string">'proteinNames'</span>)
-0136             newModel.proteinNames=newModel.proteinNames(indexes);
+0135         <span class="keyword">if</span> isfield(newModel,<span class="string">'proteins'</span>)
+0136             newModel.proteins=newModel.proteins(indexes);
 0137         <span class="keyword">end</span>
 0138         <span class="keyword">if</span> isfield(newModel,<span class="string">'rxnGeneMat'</span>)
 0139             newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes);