From 6aad9c73ae7680f7c61eb0c237a1b211cdfa6cf8 Mon Sep 17 00:00:00 2001
From: Remco Bouckaert <higgs.ml@gmail.com>
Date: Mon, 5 Sep 2022 08:05:49 +1200
Subject: [PATCH] towards fixing #5

---
 build.xml                                      |  2 +-
 src/beastfx/app/inputeditor/FastaImporter.java | 14 ++++++--------
 src/beastfx/app/util/Alert.java                | 10 +++++++++-
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/build.xml b/build.xml
index 69b0a4c..97c55aa 100644
--- a/build.xml
+++ b/build.xml
@@ -28,7 +28,7 @@
 
     <property name="openjreMac" value="../../Downloads/zulu17.34.19-ca-fx-jre17.0.3-macosx_x64"/>
     <property name="openjreWin" value="../../Downloads/zulu17.34.19-ca-fx-jre17.0.3-win_x64/"/>
-    <property name="openjreWin" value="../../Downloads/zulu17.34.19-ca-fx-jre17.0.3-linux_x64/"/>
+    <property name="openjreLnx" value="../../Downloads/zulu17.34.19-ca-fx-jre17.0.3-linux_x64/"/>
 
 	<path id="classpath">
 		<fileset dir="${libFX}" includes="jam.jar"/>
diff --git a/src/beastfx/app/inputeditor/FastaImporter.java b/src/beastfx/app/inputeditor/FastaImporter.java
index ddb6c22..8fcf0a6 100644
--- a/src/beastfx/app/inputeditor/FastaImporter.java
+++ b/src/beastfx/app/inputeditor/FastaImporter.java
@@ -134,14 +134,12 @@ public List<BEASTInterface> loadFile(File file) {
 									i++;
 								}
 							}
-				        	ComboBox<String> jcb = new ComboBox<>();
-				        	for (String s : new String[]{"aminoacid", "nucleotide", "all are aminoacid", "all are nucleotide"}) {
-				        		jcb.getItems().add(s);
-				        	}
-				        	jcb.setEditable(true);
-				        	jcb.setValue(datatype);
-				        	Alert.showMessageDialog(null, jcb, "Choose the datatype of alignment " + alignment.getID(), Alert.QUESTION_MESSAGE);
-				        	String selectedType = (String) jcb.getValue();
+				        	String [] providers = new String[]{"aminoacid", "nucleotide", "all are aminoacid", "all are nucleotide"};
+				        	String selectedType = (String) Alert.showInputDialog(null, "Choose the datatype of alignment " + alignment.getID(),
+				                    "Add partition",
+				                    Alert.QUESTION_MESSAGE, null, providers,
+				                    providers[0]);
+				        	
 				        	switch (selectedType) {
 					        	case "aminoacid": datatype = "aminoacid"; totalCount = 20; break;
 					        	case "nucleotide": datatype = "nucleotide"; totalCount = 4; break;
diff --git a/src/beastfx/app/util/Alert.java b/src/beastfx/app/util/Alert.java
index ce5b11d..1ea1cef 100644
--- a/src/beastfx/app/util/Alert.java
+++ b/src/beastfx/app/util/Alert.java
@@ -9,6 +9,7 @@
 import javax.swing.ImageIcon;
 
 import beast.base.core.BEASTInterface;
+import beastfx.app.beauti.ThemeProvider;
 import javafx.embed.swing.SwingFXUtils;
 import javafx.geometry.Insets;
 import javafx.scene.Node;
@@ -85,6 +86,7 @@ public static void showMessageDialog(Parent parent, String message) {
 			alert.setX(node.getX() + node.getWidth()/2);
 			alert.setY(node.getY() + node.getHeight()/2);
 		}
+//    	ThemeProvider.loadStyleSheet(alert.getDialogPane().getScene());
 		alert.showAndWait();
 	}
 
@@ -98,6 +100,7 @@ public static ButtonType showConfirmDialog(Parent parent, String message, String
 			alert.setX(node.getX() + node.getWidth()/2);
 			alert.setY(node.getY() + node.getHeight()/2);
 		}
+//    	ThemeProvider.loadStyleSheet(alert.getDialogPane().getScene());
 		Optional<ButtonType> option = alert.showAndWait();
 		return option.get();
 	}
@@ -117,6 +120,7 @@ public static void showMessageDialog(Parent parent, String message, String heade
 			alert.setX(node.getX() + node.getWidth()/2);
 			alert.setY(node.getY() + node.getHeight()/2);
 		}
+//    	ThemeProvider.loadStyleSheet(alert.getDialogPane().getScene());
 		alert.showAndWait();
 	}
 
@@ -169,6 +173,7 @@ public static void showMessageDialog(Parent parent, Node message, String header,
 		pane.setPrefHeight(600);
 		pane.setPrefWidth(600);
 		alert.setResizable(true);
+//		ThemeProvider.loadStyleSheet(alert.getDialogPane().getScene());
 		alert.showAndWait();
 	}
 
@@ -181,7 +186,9 @@ public static Object showInputDialog(Parent parent,
     	}
     	ChoiceDialog<?> dlg = new ChoiceDialog<>(valueOf(initialSelectionValue), 
     			values);
-    	dlg.setHeaderText(title);
+    	dlg.setTitle(title);
+    	dlg.setHeaderText(message.toString());
+//    	ThemeProvider.loadStyleSheet(dlg.getDialogPane().getScene());
     	Optional<?> option = dlg.showAndWait();
 		if (parent != null) {
 			Scene node = parent.getScene();
@@ -207,6 +214,7 @@ public static Object showInputDialog(Parent parent,
             Object message, String title, AlertType messageType, String initialSelectionValue) {    	
     	TextInputDialog dlg = new TextInputDialog(initialSelectionValue);
     	dlg.setHeaderText(title);
+//    	ThemeProvider.loadStyleSheet(dlg.getDialogPane().getScene());
     	Optional<?> option = dlg.showAndWait();
 		if (parent != null) {
 			Scene node = parent.getScene();