JavaFX FXML doesn't see my controller methods correctly "Controller is not defined on root component" when using fxml as component within fxml

Question 1

It works quite well with:

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.stage.Stage;

public class LoadOwnFXML extends Application {

    @Override
    public void start(Stage primaryStage) {


            Scene scene = new Scene(new ProfilPane());
            primaryStage.setTitle("Hello World!");
            primaryStage.setScene(scene);
            primaryStage.show();
    }

    public static void main(String[] args) {
        launch(args);
    }

}

And the ProfilePane class

import java.io.IOException;
import java.util.logging.Level;
import java.util.logging.Logger;
import javafx.fxml.FXML;
import javafx.fxml.FXMLLoader;
import javafx.scene.layout.AnchorPane;

public class ProfilPane extends AnchorPane {

    public ProfilPane() {
        try {
            FXMLLoader loader = new FXMLLoader(getClass().getResource("my.fxml"));
            loader.setRoot(this);
            loader.setController(this);
            loader.load();
        } catch (IOException ex) {
            Logger.getLogger(ProfilPane.class.getName()).log(Level.SEVERE, null, ex);
        }
    }

    @FXML
    public void select() {
        System.out.println("selected");
    }

    @FXML
    public void hoverOver() {
        System.out.println("hovered");
    }

    @FXML
    public void hoverOut() {
        System.out.println("hovered out");
    }
}

The FXML File

<?xml version="1.0" encoding="UTF-8"?>

<?import java.lang.*?>
<?import java.util.*?>
<?import javafx.scene.control.*?>
<?import javafx.scene.effect.*?>
<?import javafx.scene.image.*?>
<?import javafx.scene.layout.*?>
<?import javafx.scene.paint.*?>
<?import javafx.scene.text.*?>
<?import javafx.geometry.*?>
<fx:root fx:id="profilePane" onMouseClicked="#select" onMouseEntered="#hoverOver" onMouseExited="#hoverOut" type="javafx.scene.layout.Pane" xmlns="http://javafx.com/javafx/8" xmlns:fx="http://javafx.com/fxml/1">
<children><AnchorPane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="384.0" prefWidth="270.0" style="-fx-border-color: #40464A;">
<children>
<StackPane prefHeight="430.0" prefWidth="270.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
<children>
<Pane prefWidth="270.0">
<children><ImageView fitHeight="288.0" fitWidth="270.0" layoutY="49.0" pickOnBounds="true" preserveRatio="true">
<image>
<Image url="@../resources/images/category/TechnologyTemp.png" />
</image>
<StackPane.margin>
<Insets top="45.0" />
</StackPane.margin>
<viewport>
<Rectangle2D />
</viewport></ImageView>
</children>
</Pane><BorderPane layoutX="79.0" layoutY="100.0" prefHeight="258.0" prefWidth="270.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
<top>
<Pane prefHeight="49.0" prefWidth="268.0" style="-fx-background-color: white;">
<children><VBox prefHeight="143.0" prefWidth="270.0" BorderPane.alignment="CENTER">
<children><Label text="Adobe">
<font>
<Font name="System Bold" size="15.0" />
</font>
<padding>
<Insets left="10.0" top="5.0" />
</padding>
</Label><Label text="Adobe Systems,inc">
<font>
<Font name="System Bold" size="14.0" />
</font>
<padding>
<Insets bottom="3.0" left="10.0" />
</padding>
</Label>
<Pane layoutX="-1.0" opacity="0.82" prefHeight="82.0" prefWidth="220.0">
<children><TextArea cache="true" editable="false" focusTraversable="false" mouseTransparent="true" pickOnBounds="false" prefHeight="82.0" prefWidth="268.0" style="-fx-background-radius: 0;" text="Oracle continually applies good corporate governance principles. The composition and activities of the company's Board of Directors, the approach to public disclosure" wrapText="true">
<VBox.margin>
<Insets top="53.0" />
</VBox.margin></TextArea>
</children>
</Pane>
</children></VBox>
</children>
</Pane>
</top>
<bottom>
<Pane prefHeight="45.0" prefWidth="270.0" style="-fx-background-color: white;">
<children><VBox prefHeight="55.0" prefWidth="270.0" BorderPane.alignment="CENTER">
<children><Label text="Technology">
<font>
<Font name="System Bold" size="14.0" />
</font>
<padding>
<Insets left="10.0" top="4.0" />
</padding>
</Label><Label text="Software services &amp; provider">
<padding>
<Insets left="10.0" />
</padding>
<font>
<Font size="13.0" />
</font></Label>
</children></VBox>
</children>
</Pane>
</bottom></BorderPane>
</children>
</StackPane><Pane prefHeight="382.0" prefWidth="270.0">
<children><ToggleButton fx:id="toggleButton" layoutX="1.0" layoutY="191.0" mnemonicParsing="false" prefHeight="30.0" prefWidth="268.0" style="-fx-background-radius: 0; -fx-background-color: #57A1DE;" text="Select profile" textFill="WHITE">
<font>
<Font name="System Bold" size="14.0" />
</font></ToggleButton>
</children></Pane>
</children></AnchorPane>
</children>
</fx:root>

Question 2

Try removing the fx:id attribute from the <fx:root ...> element, and the corresponding profilePane field from the Java code. These are redundant, since in the Java code the root element is simply this. I suspect that's just confusing your IDE.

Not relevant to your question, but you need to initialize your FadeTransition in the initialize() method, since the toggleButton won't have been initialized until that is called. And there is no need for the Platform.runLater(...) calls; the event handlers will be invoked on the FX Application Thread anyway.

Question 3

What worked for me (NetBeans 8.1 with jdk8u74) was adding a fx:controller attribute to the root element of my .fxml file. For example, with root element of GridPane and controller class FXMLTableViewController in the fxmltableview package:

<GridPane xmlns="http://javafx.com/javafx/8.0.111" xmlns:fx="http://javafx.com/fxml/1" fx:controller="fxmltableview.FXMLTableViewController">

Question 4

Add fx:controller="packagename.FXMLDocumentController" class to the upper most parent in fxml document. For example, in my case I added into top VBox and have all components in child of VBox, that's why everything is working fine with me now.