Creating an Alert Box that Always Appears over the Primary Stage.

DeleteAlertDemo.java

package deletealertdemo;

import javafx.application.Application;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.Alert;
import javafx.scene.control.Button;
import javafx.scene.control.ButtonType;
import javafx.scene.control.ListView;
import javafx.scene.layout.BorderPane;
import javafx.stage.Modality;
import javafx.stage.Stage;
import javafx.stage.Window;

/**
 * From an answer given on
 * http://stackoverflow.com/questions/33838293/how-to-set-alert-box-position-over-current-primarystage-javafx/33846225#33846225
 * @author david
 */
public class DeleteAlertDemo extends Application {

    ObservableList<String> observablePlantList;
    ListView<String> plantList;

    protected void handleDeleteButtonClick(ActionEvent event) {
        String item = plantList.getSelectionModel().getSelectedItem();
        Alert alertBox = new Alert(Alert.AlertType.CONFIRMATION, "Confirm Delete", 
                ButtonType.OK, ButtonType.CANCEL);
        alertBox.setContentText("Are you sure you want to delete this " 
                + item.toLowerCase() + "?");
        Window owner = ((Node)event.getTarget()).getScene().getWindow();
        alertBox.initModality(Modality.APPLICATION_MODAL);
        alertBox.initOwner(owner);
        alertBox.showAndWait();
        if (alertBox.getResult() == ButtonType.OK) {
            int selectedPlant = plantList.getSelectionModel().getSelectedIndex();
            observablePlantList.remove(selectedPlant);
        } else {
            alertBox.close();
        }
    }

    @Override
    public void start(Stage primaryStage) {
        Button deleteBtn = new Button();
        deleteBtn.setText("Delete");
        deleteBtn.setOnAction(this::handleDeleteButtonClick);

        observablePlantList = FXCollections.observableArrayList("Begonia", 
                "Peony", "Rose", "Lilly", "Chrysanthemum", "Hosta");
        plantList = new ListView<>(observablePlantList);
        plantList.getSelectionModel().select(0);
        BorderPane root = new BorderPane();
        root.setCenter(plantList);
        root.setRight(deleteBtn);

        Scene scene = new Scene(root, 300, 250);

        primaryStage.setTitle("Delete Alert Demo");
        primaryStage.setScene(scene);
        primaryStage.show();
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        launch(args);
    }

}