close fxml window by code, javafx

1. give your close button an fx:id, if you haven't yet: <Button fx:id="closeButton" onAction="#closeButtonAction">

2. In your controller class:

   @FXML private javafx.scene.control.Button closeButton;
   
   @FXML
   private void closeButtonAction(){
       // get a handle to the stage
       Stage stage = (Stage) closeButton.getScene().getWindow();
       // do what you have to do
       stage.close();
   }
   

If you don't want to overspread you your controller with fxml linked methods you can do something like this:

You have to give it a fx:id. "closeButton" for Example. Should look like this in your FXML file:

<Button fx:id="closeButton" layoutX="876.0" layoutY="74.0" mnemonicParsing="false" textAlignment="CENTER">

Then you can just code the button in your initialize method or wherever you want:

@FXML
Button closeButton

public initialize(){
    closeButton.setOnAction(new EventHandler<ActionEvent>(){
        @Override
        public void handle(ActionEvent e){
            ((Stage) closeButton.getScence().getWindow()).close();
        }
    });
}

If you have a window which extends javafx.application.Application; you can use the following method. (This will close the whole application, not just the window. I misinterpreted the OP, thanks to the commenters for pointing it out).

Platform.exit();

Example:

public class MainGUI extends Application {
.........

Button exitButton = new Button("Exit");
exitButton.setOnAction(new ExitButtonListener());
.........

public class ExitButtonListener implements EventHandler<ActionEvent> {

  @Override
  public void handle(ActionEvent arg0) {
    Platform.exit();
  }
}

Edit for the beauty of Java 8:

 public class MainGUI extends Application {
    .........

    Button exitButton = new Button("Exit");
    exitButton.setOnAction(actionEvent -> Platform.exit());
 }

I implemented this in the following way after receiving a NullPointerException from the accepted answer.

In my FXML:

<Button onMouseClicked="#onMouseClickedCancelBtn" text="Cancel">

In my Controller class:

@FXML public void onMouseClickedCancelBtn(InputEvent e) {
    final Node source = (Node) e.getSource();
    final Stage stage = (Stage) source.getScene().getWindow();
    stage.close();
}