further stochastic mapping utilities

Author: jordandouglas

build.xml

@@ -36,6 +36,7 @@
 		<!-- <fileset dir="${beast2path}/lib" includes="fest.jar"/> -->
 		<!-- <fileset dir="${beast2path}/lib" includes="colt.jar"/> -->
 	<pathelement path="../codonsubstmodels/build"/>
+	<pathelement path="../BeastFX/build"/>
 	</path>
 
 
@@ -199,6 +200,7 @@
 		<mkdir dir="${Add_on_dir}/doc" />
 		<mkdir dir="${Add_on_dir}/fxtemplates" />
 		<mkdir dir="${Add_on_dir}/examples" />
+		<mkdir dir="${Add_on_dir}/icons" />
 
 		<copy todir="${Add_on_dir}">
 			<fileset file="version.xml"/>
@@ -209,6 +211,9 @@
 		<copy todir="${Add_on_dir}/fxtemplates">
 			<fileset dir="fxtemplates" />
 		</copy>
+		<copy todir="${Add_on_dir}/icons">
+			<fileset dir="icons" />
+		</copy>
 		<!--
 		<copy todir="${Add_on_dir}/doc">
 			<fileset dir="doc" includes="beastmap.pdf"/>

src/beastmap/evolution/AncestralSequenceTreeLikelihood.java

@@ -23,10 +23,8 @@
 
 
 /**
- * Adapted from AncestralStateTreeLikelihood in beast classic
+ * Adapted from AncestralStateTreeLikelihood in beast classic, which came from BEAST X
  */
-
-
 @Description("Ancestral State Tree Likelihood")
 public class AncestralSequenceTreeLikelihood extends TreeLikelihood  {
     public static final String STATES_KEY = "states";
@@ -239,7 +237,7 @@ protected boolean requiresRecalculation() {
     }
 
 
-    public DataType getDataType() {
+    public DataType getDataTypeOfMapper() {
         return dataType;
     }
 
@@ -377,7 +375,6 @@ public void traverseSample(TreeInterface tree, Node node, int[] parentState) {
                         state[j] = drawChoice(conditionalProbabilities);
                     } catch (Error e) {
                         System.err.println(e.toString());
-                        System.err.println("Please report error to Marc");
                         state[j] = 0;
                     }
                     reconstructedStates[nodeNum][j] = state[j];

src/beastmap/evolution/BranchMutationSampler.java

@@ -6,7 +6,10 @@
 import beast.base.core.Description;
 import beast.base.core.Input;
 import beast.base.core.Log;
+import beast.base.core.Input.Validate;
 import beast.base.evolution.alignment.Alignment;
+import beast.base.evolution.alignment.Sequence;
+import beast.base.evolution.branchratemodel.BranchRateModel;
 import beast.base.evolution.datatype.DataType;
 import beast.base.evolution.sitemodel.SiteModel;
 import beast.base.evolution.substitutionmodel.SubstitutionModel;
@@ -32,12 +35,18 @@ public class BranchMutationSampler extends AncestralSequenceTreeLikelihood imple
 	SiteModel.Base siteModel;
 	SubstitutionModel substitutionModel; 
 
+	
 	double[][] qmatrixBase;
 
 	final int MAX_N_LOOPS = 1000000;
 	final int MAX_MUT_BRANCH = 10000; // Any more than this and we risk running out of memory
 	int gapChar;
 
+	
+	int n1 = 0;
+	int n2 = 0;
+	
+	SimulatedAlignmentWithMutations unconditionalData; // Data simulated unconditional on the observed data
 	SimpleIndelCodingAlignment indelData;
 
 	@Override
@@ -76,18 +85,38 @@ public void initAndValidate() {
 			this.mutationsAlongEachBranch.add(new ArrayList<>());
 		}
 
-    	
-    	
 
+//		Log.warning("datatype " + getDataTypeOfMapper().getClass());		
+//		// Build a mock alignment
+//		List<Sequence> seqs = new ArrayList<>();
+//		for (int i = 0; i < tree.getLeafNodeCount(); i++) {
+//			Sequence s = new Sequence(tree.getNode(i).getID(), getDataTypeOfMapper().encodingToString(new int[] { 0 })); // Dummy sequence
+//			seqs.add(s);
+//		}
+//		Alignment mockData = new Alignment(seqs, getDataTypeOfMapper().getTypeDescription());
+//		
+//		unconditionalData = new SimulatedAlignmentWithMutations();
+//	    int nsites = dataInput.get().getPatternCount();
+//	    unconditionalData.initByName("data", mockData, "tree", tree, "siteModel", this.siteModel, "branchRateModel", this.branchRateModel, "sequencelength", nsites);
+//		
 	}
 
 
+	@Override
+	public StochasticMapper getUnconditionalData() {
+		return unconditionalData;
+	}
+	
+
 
 
 
 	@Override
 	 public void sampleMutations(long sample) {
 
+		
+		//Log.warning(this.getID() + " sampling regular mutations ");
+		
 		// Only do this once per logged state
     	if (sample == this.lastSample) return;
 
@@ -200,8 +229,29 @@ public void sampleMutations(long sample) {
     	}
 
 
+    	// Sample unconditional
+    	if (unconditionalData != null) {
+    		unconditionalData.simulate();
+    	}
+    	
+    	
     	// Update sample number
 		sample = this.lastSample;
+		
+		
+		
+//		for (int nodeNr = 0; nodeNr < nbranches; nodeNr ++) {
+//			n1 += this.getMutationsOnBranch(nodeNr).size();
+//			n2 += unconditionalData.getMutationsOnBranch(nodeNr).size();
+//		}
+//		
+//		if (n1 > n2) {
+//			Log.warning("UNCOND " + n1 + " / " + n2);
+//		}else {
+//			Log.warning("COND " + n1 + " / " + n2);
+//		}
+//		
+		
 
 
     }
@@ -469,7 +519,7 @@ public int[] getStatesForNode(Tree tree, Node node) {
 
 
 	@Override
-	public DataType getDataType() {
+	public DataType getDataTypeOfMapper() {
 		return dataInput.get().getDataType();
 	}