doc: adapterTemplate set reviewed to false

by default allow for more uniprot protein matches
SysBioChalmers · Jul 17, 2024 · bf8cfdc · bf8cfdc
1 parent d5db374
commit bf8cfdc
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diff --git a/doc/src/geckomat/model_adapter/adapterTemplate.html b/doc/src/geckomat/model_adapter/adapterTemplate.html
@@ -100,7 +100,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0054             <span class="comment">% Whether only reviewed data from UniProt should be considered.</span>
 0055             <span class="comment">% Reviewed data has highest confidence, but coverage might be (very)</span>
 0056             <span class="comment">% low for non-model organisms</span>
-0057             obj.params.uniprot.reviewed = true;
+0057             obj.params.uniprot.reviewed = false;
 0058 
 0059             <span class="comment">% Reaction ID for glucose exchange reaction (or other preferred carbon source)</span>
 0060             obj.params.c_source = <span class="string">'r_1714'</span>; 

diff --git a/src/geckomat/model_adapter/adapterTemplate.m b/src/geckomat/model_adapter/adapterTemplate.m
@@ -54,7 +54,7 @@
             % Whether only reviewed data from UniProt should be considered.
             % Reviewed data has highest confidence, but coverage might be (very)
             % low for non-model organisms
-            obj.params.uniprot.reviewed = true;
+            obj.params.uniprot.reviewed = false;
 
 			% Reaction ID for glucose exchange reaction (or other preferred carbon source)
 			obj.params.c_source = 'r_1714'; 

diff --git a/test/manual_tests/TestYeastGEMSimpleWorkflow.m b/test/manual_tests/TestYeastGEMSimpleWorkflow.m
@@ -2,8 +2,8 @@
 
 GECKORoot = findGECKOroot();
 
-yeastAdapter = ModelAdapterManager.getAdapter(fullfile(GECKORoot, 'tutorials', 'tutorial_yeast-GEM', 'YeastGEMAdapter.m'));
-yeastGEM = importModel(fullfile(yeastAdapter.getParameters().path,'models','yeast-GEM.yml'));
+yeastAdapter = ModelAdapterManager.getAdapter(fullfile(GECKORoot, 'tutorials', 'full_ecModel', 'YeastGEMAdapter.m'));
+yeastGEM = readYAMLmodel(fullfile(yeastAdapter.getParameters().path,'models','yeast-GEM.yml'));
 
 %Full model
 %%%%%%%%%%%%