more responsive refresh + do not loose list view selection #16

src/beastfx/app/inputeditor/AVMNConnector.java

@@ -17,7 +17,7 @@
 public class AVMNConnector {
 
     public static boolean customConnector(BeautiDoc doc) {
-    	System.err.println("AVMNConnector::customConnector() called");
+    	// System.err.println("AVMNConnector::customConnector() called");
 
     	// count how many partitions have the a unique clock
     	List<BEASTInterface> partitions = doc.getPartitions("Partitions");

src/beastfx/app/inputeditor/AlignmentListInputEditor.java

@@ -16,6 +16,9 @@
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.event.EventHandler;
+import javafx.geometry.Bounds;
+import javafx.geometry.Point2D;
+import javafx.scene.Parent;
 import javafx.scene.control.Button;
 import javafx.scene.control.ButtonType;
 import javafx.scene.control.ComboBox;
@@ -169,7 +172,7 @@ public void handle(DragEvent event) {
         //scroller.setMinSize(doc.beauti.frame.getWidth(), doc.beauti.frame.getHeight()-155);
         BeautiPanel.resizeList.clear();
         BeautiPanel.resizeList.add(table);
-    	table.setMinWidth(1020);
+    	//table.setMinWidth(1020);
         getChildren().add(pane);
         updateStatus();
 	}
@@ -685,13 +688,23 @@ void initTableData() {
 		}
 
         try {
-        	if (!Double.isNaN(doc.beauti.frame.getWidth())) {
-        		table.setMinSize(doc.beauti.frame.getWidth() - 20, doc.beauti.frame.getHeight()-160);
-        	} else {
-            	table.setMinSize(1024 - 20, 768 - 138);
-        	}
+
+//        	Parent root = getScene().getRoot();
+//        	Bounds localRootBounds = root.getBoundsInLocal();
+//        	Point2D	 localRootTopLeft = new Point2D(localRootBounds.getMinX(), localRootBounds.getMinY());
+//        	Point2D screenRootTopLeft = root.localToScreen(localRootTopLeft);
+
+            table.setMinSize(doc.beauti.frame.getWidth() - 12, doc.beauti.frame.getHeight() - 160);
+        	// System.err.println("table.setMinSize(" + (doc.beauti.frame.getWidth()-12)+","+ (doc.beauti.frame.getHeight()-230) +")");
+
+//        	if (!Double.isNaN(doc.beauti.frame.getWidth())) {
+//        		table.setMinSize(doc.beauti.frame.getWidth() - 20, doc.beauti.frame.getHeight()-160);
+//        	} else {
+//            	table.setMinSize(1024 - 20, 768 - 138);
+//        	}
         } catch (NullPointerException e) {
         	// ignore
+        	// System.err.println("table.setMinSize(1024 - 20, 768 - 138)");
         	table.setMinSize(1024 - 20, 768 - 138);
         }
 

src/beastfx/app/inputeditor/BeautiPanel.java

@@ -213,8 +213,12 @@ private Node createList() {
     }
 
     public void updateList() {
+    	List<Integer> selected = null;
         if (listModel == null) {
             return;
+        } else {
+        	selected = new ArrayList<>();
+        	selected.addAll(listOfPartitions.getSelectionModel().getSelectedIndices());	
         }
         listModel.clear();
         if (listModel.size() > 0) {
@@ -237,8 +241,15 @@ public void updateList() {
             }
             listModel.add(partitionID);
         }
-        if (partitionIndex >= 0 && listModel.size() > 0)
-            listOfPartitions.getSelectionModel().select(partitionIndex);
+        if (partitionIndex >= 0 && listModel.size() > 0) {
+        	if (selected != null && selected.size() > 0) {
+        		for (int index : selected) {
+        			listOfPartitions.getSelectionModel().select(index);
+        		}
+        	} else {
+        		listOfPartitions.getSelectionModel().select(partitionIndex);
+        	}
+        }
     }
 
 

src/beastfx/app/inputeditor/InputEditor.java

@@ -458,7 +458,7 @@ protected void sync() {
             	BeautiPanel panel = beauti.getCurrentPanel();
                 BeautiPanelConfig cfgPanel = panel.config;
                 cfgPanel.sync(panel.partitionIndex);
-            	// Platform.runLater(() ->	beauti.refreshPanel());
+            	Platform.runLater(() ->	beauti.refreshPanel());
             }
         }
     }

src/beastfx/app/inputeditor/SiteModelInputEditor.java

@@ -318,7 +318,7 @@ public static boolean customConnector(BeautiDoc doc) {
     }
 
     public static boolean avmnConnector(BeautiDoc doc) {
-    	System.err.println("SiteModelInputEditor::avmnConnector() called");
+    	// System.err.println("SiteModelInputEditor::avmnConnector() called");
     	return AVMNConnector.customConnector(doc);
     }
 

src/test/beastfx/app/beauti/BeautiBase.java

@@ -611,13 +611,16 @@ protected FxRobot clickOnButtonWithText(FxRobot robot, String buttonText) {
 
 	protected FxRobot clickOnNodesWithID(FxRobot robot, String id) {
 		NodeQuery q = robot.lookup(target -> {
-			if (target.getId() != null) System.err.println(target.getId());
+			// if (target.getId() != null) System.err.println(target.getId());
 			return id.equals(target.getId()) && target.isVisible();
 		});
 		Set<Node> nodes = q.queryAll();
-		for (Node node : nodes) {
-			robot.clickOn(node);
+		if (nodes.size() > 0) {
+			robot.clickOn((Node)(nodes.toArray()[0]));
 		}
+//		for (Node node : nodes) {
+//			robot.clickOn(node);
+//		}
 		return robot;
 	}
 

src/test/beastfx/app/beauti/CloneTest.java

@@ -99,6 +99,9 @@ public void simpleSiteModelCloneTest(FxRobot robot) throws Exception {
         // set category count back to 1
         //beautiFrame.checkBox("shape.isEstimated").uncheck();
         clickOnNodesWithID(robot, "shape.isEstimated");
+        printBeautiState();
+        assertStateEquals("Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
+
         robot.doubleClickOn("#gammaCategoryCount").write("1");
         printBeautiState();
         assertStateEquals("Tree.t:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
@@ -149,10 +152,12 @@ public void simpleClockModelCloneTest(FxRobot robot) throws Exception {
         warning("1. Set the clock model of second partition to UCLD exponential");
         selectTab(robot, "Clock Model");
 //		final ListView<?> list = robot.lookup(".list-view").queryAs(ListView.class);
-		robot.clickOn("noncoding");
-		robot.clickOn(".combo-box");//.clickOn("coding");
-		robot.interact(()->robot.lookup(".combo-box").queryAs(ComboBox.class).getSelectionModel().select(1));
-		robot.clickOn("Relaxed Clock Exponential");
+		robot.clickOn(".list-view").clickOn("noncoding");
+
+//		robot.clickOn(".combo-box");//.clickOn("coding");
+//		robot.interact(()->robot.lookup(".combo-box").queryAs(ComboBox.class).getSelectionModel().select(1));
+		selectFromCombobox(robot, "indexComboBox", "Relaxed Clock Exponential");
+		robot.clickOn(".list-view").clickOn("noncoding");
 		//robot.clickOn("Relaxed Clock Log Normal");
 
 		// Platform.runLater(()->list.getSelectionModel().select(1));
@@ -188,7 +193,7 @@ public void simpleClockModelCloneTest(FxRobot robot) throws Exception {
         	list.getSelectionModel().clearAndSelect(2);
         });
 		// robot.clickOn(".combo-box").clickOn(".arrow-button").clickOn("Relaxed Clock Log Normal");
-        robot.interact(()->robot.lookup(".combo-box").queryAs(ComboBox.class).getSelectionModel().select(2));
+        robot.interact(()->robot.lookup(".combo-box").queryAs(ComboBox.class).getSelectionModel().select(3));
         printBeautiState();
         assertStateEquals("Tree.t:coding", "birthRate.t:coding", "clockRate.c:2ndpos", "ucedMean.c:noncoding", "expRateCategories.c:noncoding", "expRateCategories.c:coding", "ucedMean.c:3rdpos", "expRateCategories.c:3rdpos", "ucldMean.c:1stpos", "ucldStdev.c:1stpos", "rateCategories.c:1stpos");
         assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelBICEPSEpochTop.t:coding", "YuleModelBICEPSEpochAll.t:coding", "YuleModelBICEPSTreeFlex.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:2ndpos", "strictClockUpDownOperator.c:2ndpos", "ucedMeanScaler.c:noncoding", "ExpCategoriesRandomWalk.c:noncoding", "ExpCategoriesSwapOperator.c:noncoding", "ExpCategoriesUniform.c:noncoding", "relaxedUpDownOperatorExp.c:noncoding", "ExpCategoriesRandomWalk.c:coding", "ExpCategoriesSwapOperator.c:coding", "ExpCategoriesUniform.c:coding", "ucedMeanScaler.c:3rdpos", "ExpCategoriesRandomWalk.c:3rdpos", "ExpCategoriesSwapOperator.c:3rdpos", "ExpCategoriesUniform.c:3rdpos", "relaxedUpDownOperatorExp.c:3rdpos", "ucldMeanScaler.c:1stpos", "ucldStdevScaler.c:1stpos", "CategoriesRandomWalk.c:1stpos", "CategoriesSwapOperator.c:1stpos", "CategoriesUniform.c:1stpos", "relaxedUpDownOperator.c:1stpos");