fix issues with TreeAnnotator. fixes CompEvol/beast2#1143

CompEvol · Mar 20, 2024 · 627864a · 627864a
1 parent f898660
commit 627864a
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Showing 3 changed files with 13 additions and 10 deletions.
diff --git a/src/beastfx/app/treeannotator/Controller.java b/src/beastfx/app/treeannotator/Controller.java
@@ -150,13 +150,14 @@ public double getPosteriorLimit() {
 		}
 	}
 
-	public Target getTargetOption() {
-		for (Target t : Target.values()) {
-			if (t.toString().equals(treeType.getValue())) {
-				return t;
-			}
-		}
-		return null;
+	public String getTargetOption() {
+		return treeType.getValue();
+//		for (Target t : Target.values()) {
+//			if (t.toString().equals(treeType.getValue())) {
+//				return t;
+//			}
+//		}
+//		return null;
 	}
 
 	public String getHeightsOption() {

diff --git a/src/beastfx/app/treeannotator/TAGui.java b/src/beastfx/app/treeannotator/TAGui.java
@@ -9,6 +9,7 @@
 import beast.pkgmgmt.BEASTVersion;
 import beastfx.app.beauti.ThemeProvider;
 import beastfx.app.treeannotator.TreeAnnotator.Target;
+import beastfx.app.treeannotator.services.UserTargetTreeTopologyService;
 import beastfx.app.util.Console;
 import javafx.fxml.FXMLLoader;
 import javafx.scene.control.ButtonType;
@@ -101,11 +102,11 @@ public void run() {
 	        }
 	        double posteriorLimit = controller.getPosteriorLimit();
 	        double hpd2D = 0.80;
-	        Target targetOption = controller.getTargetOption();
+	        String targetOption = controller.getTargetOption();
 	        String heightsOption = controller.getHeightsOption();
 
 	        String targetTreeFileName = controller.getTargetFileName();
-	        if (targetOption == Target.USER_TARGET_TREE && targetTreeFileName == null) {
+	        if (targetOption.equals(UserTargetTreeTopologyService.SERVICE_NAME) && targetTreeFileName == null) {
 	            Log.err.println("No target file specified");
 	            return;
 	        }
@@ -125,6 +126,7 @@ public void run() {
 
 	        try {
 	            TreeAnnotator ta = new TreeAnnotator();
+	            ta.topologyInput.setValue(targetOption, ta);
 	            ta.heightInput.setValue(heightsOption, ta);
 	            ta.run(burninPercentage,
 	            		lowMem,

diff --git a/src/beastfx/app/treeannotator/TreeAnnotator.java b/src/beastfx/app/treeannotator/TreeAnnotator.java
@@ -58,7 +58,7 @@
  */
 public class TreeAnnotator extends beast.base.inference.Runnable {
     final public Input<String> heightInput = new Input<> ("height", "name of the method for estimating node heights", "CA");
-    final public Input<Integer> burnInPercentageInput = new Input<>("burnin", "percentage of trees to used as burn-in (and will be ignored)", -1);
+    final public Input<Integer> burnInPercentageInput = new Input<>("burnin", "percentage of trees to used as burn-in (and will be ignored)", 10);
     final public Input<Double> limitInput = new Input<>("limit", "the minimum posterior probability for a node to be annotated", 0.0);
     final public Input<String> topologyInput = new Input<> ("topology", "name of the method for determining topology", "MCC");
     final public Input<String> targetInput = new Input<> ("target", "target_file_name, specifies a user target tree to be annotated");