Porting 'evaluateLate' interface method from 1.7 branch.

rambaut · rambaut · commit 7d48c50e23fa · 2012-08-07T22:19:28.000Z
diff --git a/src/dr/app/beagle/evomodel/substmodel/ComplexSubstitutionModel.java b/src/dr/app/beagle/evomodel/substmodel/ComplexSubstitutionModel.java
@@ -143,6 +143,14 @@ public double getLogLikelihood() {
         return Double.NEGATIVE_INFINITY;
     }
 
+    /**
+     * Needs to be evaluated before the corresponding data likelihood.
+     * @return
+     */
+    public boolean evaluateEarly() {
+        return true;
+    }
+
     public String prettyName() {
         return Abstract.getPrettyName(this);
     }
diff --git a/src/dr/app/beagle/evomodel/substmodel/SVSGeneralSubstitutionModel.java b/src/dr/app/beagle/evomodel/substmodel/SVSGeneralSubstitutionModel.java
@@ -69,6 +69,14 @@ public double getLogLikelihood() {
         return 0;
     }
 
+    /**
+     * Needs to be evaluated before the corresponding data likelihood.
+     * @return
+     */
+    public boolean evaluateEarly() {
+        return true;
+    }
+
     /**
      * Forces a complete recalculation of the likelihood next time getLikelihood is called
      */
diff --git a/src/dr/app/beast/BeastDialog.java b/src/dr/app/beast/BeastDialog.java
@@ -51,8 +51,8 @@ public class BeastDialog {
     private final JCheckBox overwriteCheckBox = new JCheckBox("Allow overwriting of log files");
     private final JCheckBox beagleCheckBox = new JCheckBox("Use BEAGLE library if available:");
     private final JCheckBox beagleInfoCheckBox = new JCheckBox("Show list of available BEAGLE resources and Quit");
-    private final JComboBox beagleResourceCombo = new JComboBox(new Object[]{"CPU", "CPU-SSE", "GPU"});
-    private final JCheckBox beagleSSECheckBox = new JCheckBox("Use CPU's SSE extensions");
+    private final JComboBox beagleResourceCombo = new JComboBox(new Object[]{"CPU", "GPU"});
+    private final JCheckBox beagleSSECheckBox = new JCheckBox("Use CPU's SSE extensions when possible");
     private final JComboBox beaglePrecisionCombo = new JComboBox(new Object[]{"Double", "Single"});
     private final JComboBox beagleScalingCombo = new JComboBox(new Object[]{"Default", "Dynamic", "Delayed", "Always", "Never"});
 
@@ -132,7 +132,7 @@ public void filesDropped(java.io.File[] files) {
         OptionsPanel optionPanel2 = new OptionsPanel(0, 12);
         optionPanel2.setBorder(BorderFactory.createEmptyBorder());
         final JLabel label1 = optionPanel2.addComponentWithLabel("Prefer use of: ", beagleResourceCombo);
-//        optionPanel2.addComponent(beagleSSECheckBox);
+        optionPanel2.addComponent(beagleSSECheckBox);
         beagleSSECheckBox.setSelected(true);
         final JLabel label2 = optionPanel2.addComponentWithLabel("Prefer precision: ", beaglePrecisionCombo);
         final JLabel label3 = optionPanel2.addComponentWithLabel("Rescaling scheme: ", beagleScalingCombo);
@@ -171,7 +171,7 @@ public void stateChanged(ChangeEvent e) {
         beagleResourceCombo.setSelectedItem("CPU");
     }
 
-    public boolean showDialog(String title, long seed) {
+    public boolean showDialog(String title) {
 
         JOptionPane optionPane = new JOptionPane(optionPanel,
                 JOptionPane.PLAIN_MESSAGE,
@@ -181,8 +181,6 @@ public boolean showDialog(String title, long seed) {
                 "Run");
         optionPane.setBorder(new EmptyBorder(12, 12, 12, 12));
 
-        seedText.setValue(seed);
-
         final JDialog dialog = optionPane.createDialog(frame, title);
         //dialog.setResizable(true);
         dialog.pack();
@@ -196,26 +194,45 @@ public long getSeed() {
         return seedText.getLongValue();
     }
 
+    public void setSeed(long seed) {
+        seedText.setValue(seed);
+    }
+
     public boolean allowOverwrite() {
         return overwriteCheckBox.isSelected();
     }
 
+    public void setAllowOverwrite(boolean allowOverwrite) {
+        overwriteCheckBox.setSelected(allowOverwrite);
+    }
+
     public boolean useBeagle() {
         return beagleCheckBox.isSelected();
     }
 
+    public void setUseBeagle(boolean useBeagle) {
+         beagleCheckBox.setSelected(useBeagle);
+    }
+
     public boolean preferBeagleGPU() {
         return beagleResourceCombo.getSelectedItem().equals("GPU");
     }
 
     public boolean preferBeagleCPU() {
-        return (beagleResourceCombo.getSelectedItem().equals("CPU")) ||
-                (beagleResourceCombo.getSelectedItem().equals("CPU-SSE"));
+        return (beagleResourceCombo.getSelectedItem().equals("CPU"));
     }
 
+    public void setPreferBeagleGPU() {
+        beagleResourceCombo.setSelectedItem("GPU");
+    }
+
+
     public boolean preferBeagleSSE() {
-        // SSE is currently causing a bug in some phylogeographic models, so setting as false until bug is fixed
-        return beagleResourceCombo.getSelectedItem().equals("CPU-SSE");
+        return beagleSSECheckBox.isSelected();
+    }
+
+    public void setPreferBeagleSSE(boolean preferBeagleSSE) {
+        beagleSSECheckBox.setSelected(preferBeagleSSE);
     }
 
     public boolean preferBeagleSingle() {
@@ -226,10 +243,18 @@ public boolean preferBeagleDouble() {
         return beaglePrecisionCombo.getSelectedItem().equals("Double");
     }
 
+    public void setPreferBeagleSingle() {
+         beaglePrecisionCombo.setSelectedItem("Single");
+    }
+
     public String scalingScheme() {
         return ((String) beagleScalingCombo.getSelectedItem()).toLowerCase();
     }
 
+    public void setScalingScheme(String scalingScheme) {
+        beagleScalingCombo.setSelectedItem(scalingScheme);
+    }
+
     public boolean showBeagleInfo() {
         return beagleInfoCheckBox.isSelected();
     }
diff --git a/src/dr/app/beast/BeastMain.java b/src/dr/app/beast/BeastMain.java
@@ -311,7 +311,7 @@ public static void main(String[] args) throws java.io.IOException {
         long seed = MathUtils.getSeed();
         boolean useJava = false;
 
-        int threadCount = -1;
+        int threadCount = 0;
 
         if (arguments.hasOption("java")) {
             useJava = true;
@@ -371,7 +371,6 @@ public static void main(String[] args) throws java.io.IOException {
         }
 
         if (arguments.hasOption("threads")) {
-            // threadCount defaults to -1 unless the user specifies an option
             threadCount = arguments.getIntegerOption("threads");
             if (threadCount < 0) {
                 printTitle();
@@ -429,7 +428,22 @@ public static void main(String[] args) throws java.io.IOException {
 
             BeastDialog dialog = new BeastDialog(new JFrame(), titleString, icon);
 
-            if (!dialog.showDialog(nameString, seed)) {
+            dialog.setAllowOverwrite(allowOverwrite);
+            dialog.setSeed(seed);
+
+            dialog.setUseBeagle(useBeagle);
+
+            if (BeagleFlag.PROCESSOR_GPU.isSet(beagleFlags)) {
+                dialog.setPreferBeagleGPU();
+            }
+
+            dialog.setPreferBeagleSSE(BeagleFlag.VECTOR_SSE.isSet(beagleFlags));
+
+            if (BeagleFlag.PRECISION_SINGLE.isSet(beagleFlags)) {
+                dialog.setPreferBeagleSingle();
+            }
+
+            if (!dialog.showDialog(nameString)) {
                 return;
             }
 
diff --git a/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentOptions.java b/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentOptions.java
@@ -94,9 +94,11 @@ public void selectParameters(final ModelOptions modelOptions, final List<Paramet
                 Set<String> states = partitionData.getPartitionSubstitutionModel().getDiscreteStateSet();
                 int K = states.size();
                 if (partitionData.getPartitionSubstitutionModel().getDiscreteSubstType() == DiscreteSubstModelType.SYM_SUBST) {
-                    nonZeroRates.offset = K - 1; // mean = 0.693 and offset = K-1
+                    nonZeroRates.mean = Math.log(2); // mean = 0.693 and offset = K-1
+                    nonZeroRates.offset = K - 1;
                 } else if (partitionData.getPartitionSubstitutionModel().getDiscreteSubstType() == DiscreteSubstModelType.ASYM_SUBST) {
                     nonZeroRates.mean = K - 1; // mean = K-1 and offset = 0
+                    nonZeroRates.offset = 0.0;
                 } else {
                     throw new IllegalArgumentException("unknown discrete substitution type");
                 }
diff --git a/src/dr/app/beauti/siteModelsPanel/SiteModelsPanel.java b/src/dr/app/beauti/siteModelsPanel/SiteModelsPanel.java
@@ -144,12 +144,6 @@ public void valueChanged(ListSelectionEvent evt) {
         splitPane.setBorder(BorderFactory.createEmptyBorder());
         splitPane.setOpaque(false);
 
-        // The bottom panel is now small enough that this is not necessary
-//        JScrollPane scrollPane2 = new JScrollPane(panel);
-//        scrollPane2.setOpaque(false);
-//        scrollPane2.setPreferredSize(new Dimension(400, 150));
-
-
         setOpaque(false);
         setBorder(new BorderUIResource.EmptyBorderUIResource(new Insets(12, 12, 12, 12)));
         setLayout(new BorderLayout(0, 0));
diff --git a/src/dr/app/pathogen/TemporalRooting.java b/src/dr/app/pathogen/TemporalRooting.java
@@ -123,8 +123,6 @@ public Regression getRootToTipRegression(Tree tree) {
             throw new IllegalArgumentException("Cannot do a root to tip regression on contemporaneous tips");
         }
 
-//        ((FlexibleTree)tree).setLengthsKnown(false);
-
         double[] dates = getTipDates(tree);
         double[] distances = getRootToTipDistances(tree);
 
diff --git a/src/dr/app/tracer/application/TracerApp.java b/src/dr/app/tracer/application/TracerApp.java
@@ -60,7 +60,7 @@ static public void main(String[] args) {
         }
 
         try {
-            java.net.URL url = TracerApp.class.getResource("images/Mapper.png");
+            java.net.URL url = TracerApp.class.getResource("images/Tracer.png");
             Icon icon = null;
 
             if (url != null) {
diff --git a/src/dr/evolution/util/Taxon.java b/src/dr/evolution/util/Taxon.java
@@ -25,7 +25,6 @@
 
 package dr.evolution.util;
 
-import dr.evolution.tree.NodeRef;
 import dr.util.Attributable;
 import dr.util.Identifiable;
 
@@ -77,7 +76,6 @@ public double getHeight() {
         return 0.0;
     }
 
-
     /**
      * Sets a location for this taxon.
      */
diff --git a/src/dr/evomodel/coalescent/GMRFDensityComponent.java b/src/dr/evomodel/coalescent/GMRFDensityComponent.java
@@ -42,6 +42,10 @@ public double getLogLikelihood() {
         return skyrideLogLikelihood;
     }
 
+    public boolean evaluateEarly() {
+        return false;
+    }
+
     public void makeDirty() {
         skyride.makeDirty();
     }
diff --git a/src/dr/evomodel/epidemiology/SIRModel.java b/src/dr/evomodel/epidemiology/SIRModel.java
@@ -160,6 +160,10 @@ protected boolean getLikelihoodKnown() {
         return likelihoodKnown;
     }
 
+    public boolean evaluateEarly() {
+        return false;
+    }
+
     public boolean isUsed() {
         return isUsed;
     }
diff --git a/src/dr/evomodel/substmodel/ComplexSubstitutionModel.java b/src/dr/evomodel/substmodel/ComplexSubstitutionModel.java
@@ -517,6 +517,14 @@ public double getLogLikelihood() {
         return Double.NEGATIVE_INFINITY;
     }
 
+    /**
+     * Needs to be evaluated before the corresponding data likelihood.
+     * @return
+     */
+    public boolean evaluateEarly() {
+        return true;
+    }
+
     public String prettyName() {
         return Abstract.getPrettyName(this);
     }
diff --git a/src/dr/evomodel/substmodel/MultivariateOUModel.java b/src/dr/evomodel/substmodel/MultivariateOUModel.java
@@ -360,7 +360,6 @@ public String getDimensionName(int dim) {
         return getId() + dim;
     }
 
-    @Override
     public void setDimensionNames(String[] names) {
         // do nothing
     }
diff --git a/src/dr/evomodel/substmodel/SVSGeneralSubstitutionModel.java b/src/dr/evomodel/substmodel/SVSGeneralSubstitutionModel.java
@@ -72,6 +72,14 @@ public double getLogLikelihood() {
         return 0;
     }
 
+    /**
+     * Needs to be evaluated before the corresponding data likelihood.
+     * @return
+     */
+    public boolean evaluateEarly() {
+        return true;
+    }
+
     /**
      * Forces a complete recalculation of the likelihood next time getLikelihood is called
      */
diff --git a/src/dr/inference/distribution/DistributionLikelihood.java b/src/dr/inference/distribution/DistributionLikelihood.java
@@ -44,23 +44,32 @@ public class DistributionLikelihood extends AbstractDistributionLikelihood {
 
     private int from = -1;
     private int to = Integer.MAX_VALUE;
+    private final boolean evaluateEarly;
 
     public DistributionLikelihood(Distribution distribution) {
-        super(null);
-        this.distribution = distribution;
-        this.offset = 0.0;
+        this(distribution, 0.0, false);
     }
 
     public DistributionLikelihood(Distribution distribution, double offset) {
+        this(distribution, offset, offset > 0.0);
+    }
+
+    public DistributionLikelihood(Distribution distribution, boolean evaluateEarly) {
+        this(distribution, 0.0, evaluateEarly);
+    }
+
+    public DistributionLikelihood(Distribution distribution, double offset, boolean evaluateEarly) {
         super(null);
         this.distribution = distribution;
         this.offset = offset;
+        this.evaluateEarly = evaluateEarly;
     }
 
     public DistributionLikelihood(ParametricDistributionModel distributionModel) {
         super(distributionModel);
         this.distribution = distributionModel;
         this.offset = 0.0;
+        this.evaluateEarly = false;
     }
 
     public Distribution getDistribution() {
@@ -110,6 +119,11 @@ public double calculateLogLikelihood() {
         return logL;
     }
 
+    @Override
+    public boolean evaluateEarly() {
+        return evaluateEarly;
+    }
+
     // **************************************************************
     // XMLElement IMPLEMENTATION
     // **************************************************************
diff --git a/src/dr/inference/model/AbstractModelLikelihood.java b/src/dr/inference/model/AbstractModelLikelihood.java
@@ -28,6 +28,10 @@ public void setUsed() {
         isUsed = true;
     }
 
+    public boolean evaluateEarly() {
+        return false;
+    }
+
     private boolean isUsed = false;
 
     // **************************************************************
diff --git a/src/dr/inference/model/BooleanLikelihood.java b/src/dr/inference/model/BooleanLikelihood.java
@@ -85,5 +85,14 @@ public boolean getBooleanState() {
         return false;
 	}
 
+    /**
+     * Boolean likelihoods would generally want to be evaluated early to allow for a quick
+     * termination of the evaluation in the case of a zero likelihood.
+     * @return
+     */
+    public boolean evaluateEarly() {
+        return true;
+    }
+
 }
 
diff --git a/src/dr/inference/model/CompoundLikelihood.java b/src/dr/inference/model/CompoundLikelihood.java
diff --git a/src/dr/inference/model/Likelihood.java b/src/dr/inference/model/Likelihood.java
diff --git a/src/dr/inference/model/PathLikelihood.java b/src/dr/inference/model/PathLikelihood.java
diff --git a/src/dr/inference/model/ThreadedCompoundLikelihood.java b/src/dr/inference/model/ThreadedCompoundLikelihood.java
diff --git a/src/dr/math/distributions/MultivariatePolyaDistributionLikelihood.java b/src/dr/math/distributions/MultivariatePolyaDistributionLikelihood.java

Original file line number	Diff line number	Diff line change
`@@ -143,6 +143,14 @@ public double getLogLikelihood() {`
`143`	`143`	`return Double.NEGATIVE_INFINITY;`
`144`	`144`	`}`
`145`	`145`
	`146`	`+ /**`
	`147`	`+ * Needs to be evaluated before the corresponding data likelihood.`
	`148`	`+ * @return`
	`149`	`+ */`
	`150`	`+ public boolean evaluateEarly() {`
	`151`	`+ return true;`
	`152`	`+ }`
	`153`	`+`
`146`	`154`	`public String prettyName() {`
`147`	`155`	`return Abstract.getPrettyName(this);`
`148`	`156`	`}`
Original file line number	Diff line number	Diff line change
`@@ -123,8 +123,6 @@ public Regression getRootToTipRegression(Tree tree) {`
`123`	`123`	`throw new IllegalArgumentException("Cannot do a root to tip regression on contemporaneous tips");`
`124`	`124`	`}`
`125`	`125`
`126`		`-// ((FlexibleTree)tree).setLengthsKnown(false);`
`127`		`-`
`128`	`126`	`double[] dates = getTipDates(tree);`
`129`	`127`	`double[] distances = getRootToTipDistances(tree);`
`130`	`128`
Original file line number	Diff line number	Diff line change
`@@ -60,7 +60,7 @@ static public void main(String[] args) {`
`60`	`60`	`}`
`61`	`61`
`62`	`62`	`try {`
`63`		`- java.net.URL url = TracerApp.class.getResource("images/Mapper.png");`
	`63`	`+ java.net.URL url = TracerApp.class.getResource("images/Tracer.png");`
`64`	`64`	`Icon icon = null;`
`65`	`65`
`66`	`66`	`if (url != null) {`
Original file line number	Diff line number	Diff line change
`@@ -42,6 +42,10 @@ public double getLogLikelihood() {`
`42`	`42`	`return skyrideLogLikelihood;`
`43`	`43`	`}`
`44`	`44`
	`45`	`+ public boolean evaluateEarly() {`
	`46`	`+ return false;`
	`47`	`+ }`
	`48`	`+`
`45`	`49`	`public void makeDirty() {`
`46`	`50`	`skyride.makeDirty();`
`47`	`51`	`}`