don't run chain if cl = 0 and using truenet

NakhlehLab · Jun 16, 2021 · df82bb1 · df82bb1
1 parent 3129d89
commit df82bb1
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/src/edu/rice/cs/bioinfo/programs/phylonet/commands/MCMC_BiMarkers.java b/src/edu/rice/cs/bioinfo/programs/phylonet/commands/MCMC_BiMarkers.java
@@ -778,7 +778,7 @@ else if (newseq.charAt(i) == '1')
             Network cloneNetwork = edu.rice.cs.bioinfo.programs.phylonet.structs.network.util.Networks.readNetwork(_trueNetwork.substring(_trueNetwork.indexOf(']') + 1));
             cloneNetwork.getRoot().setRootPopSize(trueRootPopSize);
             if(!SNAPPLikelihood.usePseudoLikelihood && !SNAPPLikelihood.useApproximateBayesian){
-                //System.out.println("True Likelihood = " + SNAPPLikelihood.computeSNAPPLikelihoodST(cloneNetwork, alnwarp.get(0)._RPatterns, BAGTRModel));
+                System.out.println("True Likelihood = " + SNAPPLikelihood.computeSNAPPLikelihoodST(cloneNetwork, alnwarp.get(0)._RPatterns, BAGTRModel));
             }
 
             if(SNAPPLikelihood.usePseudoLikelihood) {
@@ -788,6 +788,10 @@ else if (newseq.charAt(i) == '1')
             if(SNAPPLikelihood.useApproximateBayesian) {
                 System.out.println("True Approximate Bayesian = " + SNAPPLikelihood.computeApproximateBayesian(cloneNetwork, allele2species, alnwarp, BAGTRModel, new HashMap<>()));
             }
+
+            if (_chainlen == 0) {
+                return "";
+            }
         }
 
         if(!_mle) {