fix bug in weighted/probQR NNI moves

tkchafin · Apr 20, 2024 · 58a46bf · 58a46bf
1 parent a902d94
commit 58a46bf
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/src/moves_snaq.jl b/src/moves_snaq.jl
@@ -1218,8 +1218,8 @@ function chooseEdgeNNI(net::Network,N::Integer, probQR::Float64, d::DataCF)
     i = 0
     while((index1 == 0 || index1 > size(net.edge,1) || net.edge[index1].hybrid || hasNeighborHybrid(net.edge[index1]) || !isInternalEdge(net.edge[index1])) && i < N)
         if(probQR>0.0 && rand() < probQR)
-            println("NNI sampleEdgeQuartetWeighted")
             index1 = sampleEdgeQuartetWeighted(net.edge, d);
+            i += 1
         else
             index1 = round(Integer,rand()*size(net.edge,1));
             i += 1
@@ -1424,7 +1424,7 @@ function NNIRepeat!(net::HybridNetwork,N::Integer)
 end
 function NNIRepeat!(net::HybridNetwork,N::Integer, probQR::Float64, d::DataCF)
     N > 0 || error("N must be positive: $(N)")
-    flag,edge = chooseEdgeNNI(net,N)
+    flag,edge = chooseEdgeNNI(net,N, probQR, d)
     flag || return false
     i = 0
     success = false

diff --git a/src/snaq_optimization.jl b/src/snaq_optimization.jl
@@ -1122,13 +1122,13 @@ function proposedTop!(move::Integer, newT::HybridNetwork,random::Bool, count::In
         success = addHybridizationUpdateSmart!(newT, N, probQR, d)
     elseif(move == 2)
         node = chooseHybrid(newT)
-        #success = moveOriginUpdateRepeat!(newT,node,random, probQR, d)
-        success = moveOriginUpdateRepeat!(newT,node,random)
+        success = moveOriginUpdateRepeat!(newT,node,random, probQR, d)
+        #success = moveOriginUpdateRepeat!(newT,node,random)
         CHECKNET && isBadTriangle(node) && success && error("success is $(success) in proposedTop, but node $(node.number) is very bad triangle")
     elseif(move == 3)
         node = chooseHybrid(newT)
-        #success = moveTargetUpdateRepeat!(newT,node,random, probQR, d)
-        success = moveTargetUpdateRepeat!(newT,node,random)
+        success = moveTargetUpdateRepeat!(newT,node,random, probQR, d)
+        #success = moveTargetUpdateRepeat!(newT,node,random)
         CHECKNET && isBadTriangle(node) && success && error("success is $(success) in proposedTop, but node $(node.number) is very bad triangle")
     elseif(move == 4)
         node = chooseHybrid(newT)
@@ -1139,8 +1139,8 @@ function proposedTop!(move::Integer, newT::HybridNetwork,random::Bool, count::In
         deleteHybridizationUpdate!(newT,node)
         success = true
     elseif(move == 6)
-        #success = NNIRepeat!(newT,N,probQR, d)
-        success = NNIRepeat!(newT,N)
+        success = NNIRepeat!(newT,N,probQR, d)
+        #success = NNIRepeat!(newT,N)
     end
     if(multall)
         success2 = checkTop4multAllele(newT)