From df82bb1e4e479db958de4bcfbebc462865b81b8a Mon Sep 17 00:00:00 2001 From: genomescale Date: Tue, 15 Jun 2021 23:27:30 -0500 Subject: [PATCH] don't run chain if cl = 0 and using truenet --- .../bioinfo/programs/phylonet/commands/MCMC_BiMarkers.java | 6 +++++- 1 file changed, 5 insertions(+), 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 index b2d85bce..8fb0934b 100644 --- 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) {