testing parameter distance reproducibility

CovertLab · Aug 27, 2013 · e0c3866 · e0c3866
1 parent 4834466
commit e0c3866
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diff --git a/src/+edu/+stanford/+covert/+cell/+sim/+util/DreamScoring.m b/src/+edu/+stanford/+covert/+cell/+sim/+util/DreamScoring.m
@@ -204,7 +204,7 @@
     end
 
     %helper methods
-    methods (Static = true, Access = protected)       
+    methods (Static = true)       
         %Get struct of parameter values
         function parameterVals = loadParameterVals(parameterVals, parameterValsPath)
             import edu.stanford.covert.cell.sim.util.CachedSimulationObjectUtil;

diff --git a/src_test/+edu/+stanford/+covert/+cell/+sim/DreamCompetitionTest.m b/src_test/+edu/+stanford/+covert/+cell/+sim/DreamCompetitionTest.m
@@ -390,6 +390,32 @@ function test_averageHighthroughputExperimentsAndCalcErrors(~)
             assertEqual(0, dists.prediction);
         end
 
+        function test_calcAvgSumSquaredLogRatioReproducible(~)
+            import edu.stanford.covert.cell.sim.util.CachedSimulationObjectUtil;
+            import edu.stanford.covert.cell.sim.util.DreamScoring;
+
+            sim = CachedSimulationObjectUtil.load();
+            refParameterVals = sim.getAllParameters();
+
+            met = sim.process('Metabolism');
+            rxnId = met.reactionWholeCellModelIDs{1};
+            kinetics.(rxnId).for = 1;
+            sim.applyMetabolicReactionKinetics(kinetics);
+            sim.applyRnaHalfLives(struct('TU_001', 1));
+            sim.applyRnaPolTuBindingProbs(struct('TU_290', 1e-3));
+            paramVals = sim.getAllParameters();
+
+            distsA = DreamScoring.calcAvgSumSquaredLogRatio(...
+                DreamScoring.getParameterVector(paramVals), ...
+                DreamScoring.getParameterVector(refParameterVals));
+
+            distsB = DreamScoring.calcAvgSumSquaredLogRatio(...
+                DreamScoring.getParameterVector(paramVals), ...
+                DreamScoring.getParameterVector(refParameterVals));
+
+            assertEqual(distsA, distsB)
+        end
+
         function test_calcParameterAndPredictionScoring(~)
             refParameterValsPath = 'output/1_1.parameters.mat';
             refAvgValsPath = 'output/1_1.predictions.mat';