sync

pom.xml

@@ -47,7 +47,6 @@
         <beast.main>beast.base.minimal.BeastMain</beast.main>
         <beast.args/>
         <beast.pkg.name>CCD</beast.pkg.name>
-        <beast.pkg.version>1.2.0</beast.pkg.version>
     </properties>
 
     <dependencies>
@@ -194,7 +193,7 @@
                     <descriptors>
                         <descriptor>src/assembly/beast-package.xml</descriptor>
                     </descriptors>
-                    <finalName>${beast.pkg.name}.v${beast.pkg.version}</finalName>
+                    <finalName>${beast.pkg.name}.v${project.version}</finalName>
                     <appendAssemblyId>false</appendAssemblyId>
                 </configuration>
                 <executions>

src/main/java/ccd/algorithms/NNICladeExpansion.java

@@ -120,6 +120,17 @@ private NovelClade(BitSet taxa) {
     private long candidatesAlreadyPresent = 0;
     private boolean computed = false;
 
+    /**
+     * Parent-probability gate: a parent clade whose marginal probability is at
+     * or above this threshold is not expanded, on the premise that a near-certain
+     * parent has no alternative resolution worth adding. The default
+     * {@link Double#POSITIVE_INFINITY} disables the gate (full expansion). Setting
+     * 1.0 skips only fully-supported parents; lower values prune more. Benchmark
+     * (Remco): 1.0 is strictly lossless yet ~halves the novel-clade count, and
+     * 0.99 prunes further for a ~0.02% loss in recovered probability mass.
+     */
+    private double parentProbabilityThreshold = Double.POSITIVE_INFINITY;
+
     /** Taxa-only bits of every clade in the CCD, for fast presence tests. */
     private Set<BitSet> existingTaxa;
 
@@ -132,12 +143,42 @@ public NNICladeExpansion(AbstractCCD ccd, PairingMode mode) {
         this.mode = mode;
     }
 
+    /**
+     * Sets the parent-probability gate: parent clades whose marginal probability
+     * is {@code >= threshold} are not expanded. Use
+     * {@link Double#POSITIVE_INFINITY} (the default) for full expansion. Must be
+     * called before {@link #compute()}.
+     *
+     * @param threshold parent-probability cutoff (skip a parent if its
+     *                  probability is at or above this value)
+     * @return this, for chaining
+     */
+    public NNICladeExpansion setParentProbabilityThreshold(double threshold) {
+        if (computed) {
+            throw new IllegalStateException(
+                    "setParentProbabilityThreshold must be called before compute()");
+        }
+        this.parentProbabilityThreshold = threshold;
+        return this;
+    }
+
+    /** @return the parent-probability gate (parents with prob &gt;= this are skipped). */
+    public double getParentProbabilityThreshold() {
+        return parentProbabilityThreshold;
+    }
+
     /** Runs the expansion if not already done; idempotent. */
     public NNICladeExpansion compute() {
         if (computed) {
             return this;
         }
 
+        // the parent-probability gate reads Clade#getProbability(), which is
+        // computed lazily and otherwise defaults to -1; populate it when gating
+        if (parentProbabilityThreshold < Double.POSITIVE_INFINITY) {
+            ccd.computeCladeProbabilitiesIfDirty();
+        }
+
         existingTaxa = new HashSet<>(ccd.getNumberOfClades() * 2);
         for (Clade clade : ccd.getClades()) {
             existingTaxa.add(clade.getCladeInBitsTaxaOnly());
@@ -160,6 +201,10 @@ private void expandGraphWide() {
             if (parent.size() < 3) {
                 continue;
             }
+            // skip near-certain parents: a stable parent yields no novel resolution
+            if (parent.getProbability() >= parentProbabilityThreshold) {
+                continue;
+            }
             for (CladePartition split : parent.getPartitions()) {
                 Clade childA = split.getChildClades()[0];
                 Clade childB = split.getChildClades()[1];
@@ -226,12 +271,15 @@ private void recombineTree(Node vertex, Map<Node, Clade> map) {
             Node left = children.get(0);
             Node right = children.get(1);
             Clade parent = map.get(vertex);
-            // edge above an internal child = NNI site; the other child is the sibling
-            if (!left.isLeaf()) {
-                recombineAt(parent, left, right, map);
-            }
-            if (!right.isLeaf()) {
-                recombineAt(parent, right, left, map);
+            // skip near-certain parents: a stable parent yields no novel resolution
+            if (parent.getProbability() < parentProbabilityThreshold) {
+                // edge above an internal child = NNI site; the other child is the sibling
+                if (!left.isLeaf()) {
+                    recombineAt(parent, left, right, map);
+                }
+                if (!right.isLeaf()) {
+                    recombineAt(parent, right, left, map);
+                }
             }
         }
         for (Node child : children) {

src/test/java/test/ccd/algorithms/KRegCCDParameterOptimiserTest.java → src/test/java/ccd/KRegCCDParameterOptimiserTest.java

@@ -1,4 +1,4 @@
-package test.ccd.algorithms;
+package ccd;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;

src/test/java/test/ccd/algorithms/NNICladeExpansionTest.java → src/test/java/ccd/NNICladeExpansionTest.java

@@ -1,4 +1,4 @@
-package test.ccd.algorithms;
+package ccd;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;

src/test/java/test/ccd/algorithms/NNIRegCCDOptimiserTest.java → src/test/java/ccd/NNIRegCCDOptimiserTest.java

@@ -1,4 +1,4 @@
-package test.ccd.algorithms;
+package ccd;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;

src/test/java/test/ccd/algorithms/TreeDistancesTest.java → src/test/java/ccd/TreeDistancesTest.java

@@ -1,4 +1,4 @@
-package test.ccd.algorithms;
+package ccd;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;

src/test/java/test/ccd/model/CCD0SJTest.java → src/test/java/ccd/model/CCD0SJTest.java

@@ -1,10 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
-import beast.base.evolution.tree.Node;
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import beastfx.app.inputeditor.BeautiPanelConfig;
-import ccd.model.*;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/CCD0Test.java → src/test/java/ccd/model/CCD0Test.java

@@ -1,9 +1,8 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
 import beastfx.app.treeannotator.TreeAnnotator;
-import ccd.model.*;
 import org.junit.jupiter.api.Test;
 
 import java.io.IOException;

src/test/java/test/ccd/model/CCD1CPTest.java → src/test/java/ccd/model/CCD1CPTest.java

@@ -1,10 +1,9 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
 import beastfx.app.treeannotator.TreeAnnotator;
 import ccd.algorithms.TreeDistances;
-import ccd.model.*;
 import org.junit.jupiter.api.Test;
 
 import java.io.IOException;

src/test/java/test/ccd/model/CCD1SJTest.java → src/test/java/ccd/model/CCD1SJTest.java

@@ -1,8 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.*;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/FiveTaxaTest.java → src/test/java/ccd/model/FiveTaxaTest.java

@@ -1,10 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.CCD0CP;
-import ccd.model.Clade;
-import ccd.model.CladePartition;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/FourTaxaRootSATest1.java → src/test/java/ccd/model/FourTaxaRootSATest1.java

@@ -1,10 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.CCD0CP;
-import ccd.model.Clade;
-import ccd.model.CladePartition;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/FourTaxaRootSATest2.java → src/test/java/ccd/model/FourTaxaRootSATest2.java

@@ -1,8 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.*;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/FourTaxaTest1.java → src/test/java/ccd/model/FourTaxaTest1.java

@@ -1,10 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.CCD0CP;
-import ccd.model.Clade;
-import ccd.model.CladePartition;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/FourTaxaTest2.java → src/test/java/ccd/model/FourTaxaTest2.java

@@ -1,11 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.CCD0CP;
-import ccd.model.CCD1CP;
-import ccd.model.Clade;
-import ccd.model.CladePartition;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/GRegCCDTest.java → src/test/java/ccd/model/GRegCCDTest.java

@@ -1,8 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.GRegCCD;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/GRegZApproxTest.java → src/test/java/ccd/model/GRegZApproxTest.java

@@ -1,9 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.GRegCCD;
-import ccd.model.GRegZApprox;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/KRegCCDEntropyTest.java → src/test/java/ccd/model/KRegCCDEntropyTest.java

@@ -1,8 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.KRegCCD;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/KRegCCDMapTreeTest.java → src/test/java/ccd/model/KRegCCDMapTreeTest.java

@@ -1,9 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.HeightSettingStrategy;
-import ccd.model.KRegCCD;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/KRegCCDSamplingTest.java → src/test/java/ccd/model/KRegCCDSamplingTest.java

@@ -1,11 +1,8 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Node;
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.AbstractCCD;
-import ccd.model.HeightSettingStrategy;
-import ccd.model.KRegCCD;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/KRegFourTaxaTest.java → src/test/java/ccd/model/KRegFourTaxaTest.java

@@ -1,11 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.Clade;
-import ccd.model.CladePartition;
-import ccd.model.KRegCCD;
-import ccd.model.RegCCD;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/MRegCCDTest.java → src/test/java/ccd/model/MRegCCDTest.java

@@ -1,11 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.CCD0;
-import ccd.model.Clade;
-import ccd.model.CladePartition;
-import ccd.model.MRegCCD;
 import ccd.model.bitsets.BitSet;
 import org.junit.jupiter.api.Test;
 

src/test/java/test/ccd/model/NNIRegCCDTest.java → src/test/java/ccd/model/NNIRegCCDTest.java

@@ -1,12 +1,8 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
 import ccd.algorithms.NNICladeExpansion.PairingMode;
-import ccd.model.Clade;
-import ccd.model.CladePartition;
-import ccd.model.NNIRegCCD;
-import ccd.model.RegCCD;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/ThreeTaxaRootSATest.java → src/test/java/ccd/model/ThreeTaxaRootSATest.java

@@ -1,8 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.*;
 import org.junit.jupiter.api.Test;
 
 import java.util.ArrayList;

src/test/java/test/ccd/model/UniformEscapeCCDTest.java → src/test/java/ccd/model/UniformEscapeCCDTest.java

@@ -1,8 +1,7 @@
-package test.ccd.model;
+package ccd.model;
 
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
-import ccd.model.UniformEscapeCCD;
 import org.junit.jupiter.api.Test;
 
 import java.math.BigInteger;