issue #4 add button to BEAUti for pre-calc mu rates

BEAST2-Dev · May 4, 2015 · e9decd8 · e9decd8
1 parent cc059e6
commit e9decd8
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Showing 2 changed files with 33 additions and 7 deletions.
diff --git a/src/beast/app/draw/SNAPPTreeLikelihoodEditor.java b/src/beast/app/draw/SNAPPTreeLikelihoodEditor.java
@@ -3,14 +3,17 @@
 import java.util.List;
 
 import javax.swing.Box;
+import javax.swing.JButton;
 
 import beast.app.beauti.BeautiDoc;
 import beast.app.draw.InputEditor;
 import beast.app.draw.ListInputEditor;
 import beast.app.draw.ParameterInputEditor;
 import beast.core.BEASTInterface;
 import beast.core.Input;
+import beast.core.parameter.RealParameter;
 import beast.evolution.sitemodel.SiteModel;
+import snap.Data;
 import snap.likelihood.SnAPTreeLikelihood;
 import snap.likelihood.SnapSubstitutionModel;
 
@@ -26,6 +29,8 @@ public Class<?> baseType() {
     }
 
     SnapSubstitutionModel substModel;
+    Data data;
+    JButton muButton;
 
     @Override
     public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption bExpand, boolean bAddButtons) {
@@ -40,17 +45,37 @@ public void init(Input<?> input, BEASTInterface plugin, int itemNr, ExpandOption
         for (Object o : (List<?>) input.get()) {
             if (o instanceof SnAPTreeLikelihood) {
             	SnAPTreeLikelihood plugin2 = (SnAPTreeLikelihood) o;
+            	if (plugin2.dataInput.get() instanceof Data) {
+            		data = (Data) plugin2.dataInput.get();
+            	}
             	substModel = (SnapSubstitutionModel) ((SiteModel.Base) plugin2.siteModelInput.get()).substModelInput.get();
             	doc.getInputEditorFactory().addInputs(m_listBox, substModel, this, null, doc);
             	doc.getInputEditorFactory().addInputs(m_listBox, plugin2, this, null, doc);
+            	muButton = new JButton("Calc mutation rates");
+            	muButton.setToolTipText("Calcaulate mutation rates based on data in the alignment");
+            	muButton.addActionListener(e -> setUpMutationRates());
+            	add(muButton);
             }
         }
 		add(m_listBox);
         updateState();
     }
 
 
-    public InputEditor createMutationRateVEditor() throws Exception {
+    private Object setUpMutationRates() {
+    	double proportionZeros = data.getProportionZeros();
+    	double muU = 1 / (2.0 * proportionZeros);
+    	double muV = 1 / (2.0 * (1.0- proportionZeros));
+    	RealParameter pU = substModel.m_pU.get();
+    	pU.valuesInput.setValue(muU + "", pU);
+    	RealParameter pV = substModel.m_pV.get();
+    	pV.valuesInput.setValue(muV + "", pV);
+    	refreshPanel();
+		return null;
+	}
+
+
+	public InputEditor createMutationRateVEditor() throws Exception {
     	ParameterInputEditor editor = (ParameterInputEditor) doc.getInputEditorFactory().createInputEditor(substModel.m_pV, substModel, doc);
     	editor.m_isEstimatedBox.setVisible(false);
     	return editor;

diff --git a/templates/SNAPP.xml b/templates/SNAPP.xml
@@ -64,6 +64,7 @@
             snap.likelihood.SnAPTreeLikelihood.useAmbiguities,
             snap.likelihood.SnAPTreeLikelihood.tree,
             snap.likelihood.SnAPTreeLikelihood.dominant,
+            snap.likelihood.SnAPTreeLikelihood.ascSiteCount,
             snap.likelihood.SnAPPrior.coalescenceRate
 '
         buttonLabelMap='beast.app.beauti.BeautiInitDlg.&gt;&gt; details=Edit parameters,
@@ -138,12 +139,12 @@
 		      </tree>
 		      <parameter name='coalescenceRate' id='coalescenceRate' value='10'/>
         </distribution>
-        <distribution id='alphaPrior.$(n)' spec='Prior' x='@alpha'><distr spec='OneOnX'/></distribution>
-        <distribution id='betaPrior.$(n)' spec='Prior' x='@beta'><distr spec='OneOnX'/></distribution>
-        <distribution id='lambdaPrior.$(n)' spec='Prior' x='@lambda'><distr spec='OneOnX'/></distribution>
-        <distribution id='kappaPrior.$(n)' spec='Prior' x='@kappa'><distr spec='OneOnX'/></distribution>
-        <distribution id='uPrior.$(n)' spec='Prior' x='@u'><distr spec='OneOnX'/></distribution>
-        <distribution id='vPrior.$(n)' spec='Prior' x='@v'><distr spec='OneOnX'/></distribution>
+        <distribution id='alphaPrior.$(n)' spec='beast.math.distributions.Prior' x='@alpha'><distr spec='OneOnX'/></distribution>
+        <distribution id='betaPrior.$(n)' spec='beast.math.distributions.Prior' x='@beta'><distr spec='OneOnX'/></distribution>
+        <distribution id='lambdaPrior.$(n)' spec='beast.math.distributions.Prior' x='@lambda'><distr spec='OneOnX'/></distribution>
+        <distribution id='kappaPrior.$(n)' spec='beast.math.distributions.Prior' x='@kappa'><distr spec='OneOnX'/></distribution>
+        <distribution id='uPrior.$(n)' spec='beast.math.distributions.Prior' x='@u'><distr spec='OneOnX'/></distribution>
+        <distribution id='vPrior.$(n)' spec='beast.math.distributions.Prior' x='@v'><distr spec='OneOnX'/></distribution>
 
 
          <snaptreelikelihood spec='snap.likelihood.SnAPTreeLikelihood' name='distribution' id='treeLikelihood.$(n)' initFromTree='false' pattern='coalescenceRate' non-polymorphic='true'>