sync beast2 issue 554

BEAST2-Dev · Mar 12, 2018 · fb4ff4f · fb4ff4f
1 parent acc1a52
commit fb4ff4f
Show file tree

Hide file tree

Showing 10 changed files with 11 additions and 14 deletions.
diff --git a/src/snap/AncestralTreeHeightLogger.java b/src/snap/AncestralTreeHeightLogger.java
@@ -32,7 +32,7 @@ public void init(PrintStream out) {
 	}
 
 	@Override
-	public void log(int nSample, PrintStream out) {
+	public void log(long nSample, PrintStream out) {
 		for (Node node : tree.getNodesAsArray()) {
 			out.append(node.getHeight() + "\t");
 		}

diff --git a/src/snap/CoalescentUnitTreeLogger.java b/src/snap/CoalescentUnitTreeLogger.java
@@ -34,7 +34,7 @@ public void init(PrintStream out) {
 	}
 
 	@Override
-	public void log(int nSample, PrintStream out) {
+	public void log(long nSample, PrintStream out) {
 		// make sure we get the current version of the inputs
        	coalescenceRate = (RealParameter) ((StateNode) coalescenceRate).getCurrent();
         // write out the log tree with meta data

diff --git a/src/snap/Data.java b/src/snap/Data.java
@@ -32,18 +32,15 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import beast.app.beauti.Beauti;
 import beast.core.Description;
 import beast.core.Input;
 import beast.core.Input.Validate;
-import beast.core.util.Log;
 import beast.evolution.alignment.Sequence;
 import beast.evolution.alignment.Taxon;
 import beast.evolution.alignment.TaxonSet;
 import beast.evolution.datatype.Binary;
 import beast.evolution.datatype.DataType;
 import beast.evolution.datatype.IntegerData;
-import beast.evolution.datatype.IntegerData2;
 import beast.evolution.datatype.Nucleotide;
 import beast.evolution.datatype.StandardData;
 

diff --git a/src/snap/MCMC.java b/src/snap/MCMC.java
@@ -66,7 +66,7 @@ public void run() throws SAXException, IOException, ParserConfigurationException
         operatorSchedule.setStateFileName(stateFileName);
 
         int nBurnIn = burnInInput.get();
-		int nChainLength = chainLengthInput.get();
+		long nChainLength = chainLengthInput.get();
 		int nStateBurnin = m_oStateBurnIn.get();
         if (restoreFromFile) {
         	state.restoreFromFile();
@@ -161,7 +161,7 @@ public void run() throws SAXException, IOException, ParserConfigurationException
 
 
 		boolean bStayAlive = true;
-		for (int iSample = -nBurnIn; iSample <= nChainLength && bStayAlive; iSample++) {
+		for (long iSample = -nBurnIn; iSample <= nChainLength && bStayAlive; iSample++) {
 
 			//State proposedState = state.copy();
         	state.store(iSample);

diff --git a/src/snap/ML.java b/src/snap/ML.java
@@ -66,7 +66,7 @@ public void run() throws IOException {
 		state.setEverythingDirty(true);
 
 		int nBurnIn = burnInInput.get();
-		int nChainLength = chainLengthInput.get();
+		long nChainLength = chainLengthInput.get();
 		//int nStateBurnin = m_oStateBurnIn.get();
 
 		System.err.println("Start state:");
@@ -121,7 +121,7 @@ public void run() throws IOException {
 		state.setEverythingDirty(true);
 		double fOldLogLikelihood = calc();
 		System.err.println("Start likelihood: = " + fOldLogLikelihood);
-		for (int iSample = -nBurnIn; iSample <= nChainLength; iSample++) {
+		for (long iSample = -nBurnIn; iSample <= nChainLength; iSample++) {
 
 			//State proposedState = state.copy();
         	state.store(iSample);

diff --git a/src/snap/ThetaLogger.java b/src/snap/ThetaLogger.java
@@ -36,7 +36,7 @@ public void init(PrintStream out) {
 	}
 
 	@Override
-	public void log(int nSample, PrintStream out) {
+	public void log(long nSample, PrintStream out) {
         RealParameter var = (RealParameter) m_coalescenceRate.get();
         int nValues = var.getDimension();
         for (int iValue = 0; iValue < nValues; iValue++) {

diff --git a/src/snap/TreeLengthLogger.java b/src/snap/TreeLengthLogger.java
@@ -29,7 +29,7 @@ public void init(PrintStream out) {
 	}
 
 	@Override
-	public void log(int nSample, PrintStream out) {
+	public void log(long nSample, PrintStream out) {
         Tree tree = (Tree) m_tree.get();
         double heightsum = tree.getRoot().getHeight();
         heightsum += heightSum(tree.getRoot());

diff --git a/src/snap/TreeNodeLogger.java b/src/snap/TreeNodeLogger.java
@@ -38,7 +38,7 @@ void initLog(PrintStream out, Node node) {
 	}
 
 	@Override
-	public void log(int nSample, PrintStream out) {
+	public void log(long nSample, PrintStream out) {
 		final Tree tree = m_tree.get();
 		logTree(out, tree.getRoot());
 	}

diff --git a/src/snap/likelihood/NormalisedDistributionLogger.java b/src/snap/likelihood/NormalisedDistributionLogger.java
@@ -29,7 +29,7 @@ public void init(PrintStream out) {
     }
 
     @Override
-    public void log(final int nSample, final PrintStream out) {
+    public void log(final long nSample, final PrintStream out) {
         out.print(distribution.getCurrentLogP() - treeLikelihood.getAscSitesLogP() + "\t");
     }
 

diff --git a/src/snap/likelihood/SnAPTreeLikelihood.java b/src/snap/likelihood/SnAPTreeLikelihood.java
@@ -381,7 +381,7 @@ public void init(PrintStream out) {
 	}
 
 	@Override
-	public void log(int nSample, PrintStream out) {
+	public void log(long nSample, PrintStream out) {
 		super.log(nSample, out);
 		if (!m_bUsenNonPolymorphic) {
 			out.append(m_fP0 + "\t");