Advanced Java for Bioinformatics Winter 2017/18. Prof. Daniel Huson

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1 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, Introduction Advanced Java for Bioinformatics Winter 2017/18 Prof. Daniel Huson Office hours: Thursdays 17-18h (Sand 14, C310a) 1.1 Course details Lectures: Thursdays 18:15-10h Hörsaal 2, Sand 6/7 Tutorials: Weekly participation in the tutorials is mandatory: Day Time Place Mo 12-14h C311, Sand 14 Tue 12-14h C311, Sand 14 Wed 12-14h A301, Sand 14 Enrollment: Please use Ilias to enroll in this course. The course password is Java2017 A link to the Ilias webpage is provided on this website: Prerequisites: Participants must have already taken Grundlagen der Bioinformatik or Bioinformatics I, or an equivalent course. We will write a lot of code, so a keen interest in programming is essential. This is not an introduction to Java, you must already know Java to participate in this course. How to get credit for this course: Always participate in the weekly problem sessions and actively present your results. You must received at least 50% of possible points to take the exam. Assignments are set every Thursday and are due on at the beginning of the lecture on the following Thursday. Successfully implement the programming project requirements. Pass the final exam. Final Exam: The final exam will be a 30 minute oral exam or 90 minute written exam. The first half will cover concepts and constructs presented in the lectures and the second half will cover the structure and implementation of your software project. This course is worth 6 ETCS credit points and so expect to work about 180h in total for this course.

2 2 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, Topics We will cover the following topics: Java 8 and JavaFX 8 FXML and CSS Concurrent programming Java web services Design patterns, unit testing GitHub, intellij The introduction to JavaFX will be based on these books: Anton Epple, JavaFX 8, Grundlagen und fortgeschrittene Techniken, dpunkt.verlag 2015 Herbert Schildt, Introducing JavaFX 8 Programming, Oracle Press, 2015 Kishori Sharan, Learn JavaFX 8, APress, Setup We will use the following setup: Java SE Development Kit 8u144 Intellij IDE Language level 8 Later will use SceneBuilder to create FXML files Will edit CSS files Will use GitHub classroom as code repository We will use GitHub classroom as a code repository, sign up here:...

3 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, JavaFX Java 1.0 provided AWT for GUI development. In 1997, Swing was introduced to replace AWT. Swing GUIs now feel dull and static; they are hard to implement and impossible to customize. There is no support for 3D, for animation or for customization. Recently JavaFX was introduced to replace Swing as GUI Framework for Java. It is part of the offical Oracle SDK ( OpenJDK does not contain it by default.) Note that AWT and Swing remain part of Java releases. JavaFX can be integrated into existing Swing-based Java programs. Highlights are: Easy to use Stage and Scene paradigm. Easy to use 3D graphics Easy to use animation support Use of observables and bindings GUI specification in FXML using SceneBuilder Easy to use support for managing concurrent tasks and services Customization using CSS Only few lines of code necessary to write runnable GUI program JavaFX vs HTML5+JavaScript JavaFX competes with HTML+JavaScript. Here is a rough comparison: JavaFX HTML5+JavaScript + One framework Many frameworks with multiple parts requires Gluon to run on Android or + Runs everywhere ios + Strongly typed, nice language JavaScript messy language + Perfect for large projects + Perfect for small projects Future?? Oracle, open source High turnover of frameworks Basic concepts JavaFX consists of about 30 packages, such as: javafx.application javafx.stage javafx.scene javafx.scene.layout... JavaFX is built around the metaphor of a Stage that is a space in which stuff happens, that is, in which a Scene is presented.

4 4 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, 2017 Window on laptop is Stage Content shown in window is Scene A JavaFX Stage is a top level container such as a window. A Scene contains items that make up the scene, such as layout items, controls, text and graphical objects. To create a scene, add elements of the class Scene. Then, set the scene on a stage by adding the Scene object to an instance of Stage. Any JavaFX application has at least one stage and one scene Nodes and the scene graph Elements of a scene are called nodes, and extend the Node class. For example, a Button is a node. Some nodes can have one or more children. A node that can have childern extends Parent. The scene is represented by a tree of nodes, called the scene graph. There is one special node in the scene graph called the root, which has no parent. All other nodes in the scene graph have exactly one parent, which is contained in the scene graph. Any given node can occur at most once in any scene graph. As mentioned, Node is the base class for all nodes, e.g. Button extends Node. Other examples of extensions of Node are Parent, Group, Region or Control, and many more Layout nodes Simple controls such as buttons, checkboxes etc usually cannot be parents of other nodes and thus appear as leaves of the scene graph. There are a number of types of nodes that used to manage the placement of elements in a scene and these usually appear as internal nodes of the scene graph. Examples: FlowPane: a flow layout GridPane: grid-based layouty BorderPane: four borders and a center. All are extensions of Node and are contained in javafx.scene.layout.

5 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, Application class and life-cycle methods A JavaFX application extends the class Application, e.g. public class HelloWorld extends Application {... There are three methods in Application that you can overwrite: void init() abstract void start (Stage primarystage) void stop() init() is called at start up so that you can initialize stuff, but it is called outside of JavaFX, so can t be used to init the scene or stage. start() is called after init() and from within JavaFX. This is where you setup the scene and place it onto the stage. This method is abstract and so you must overwrite it. The stop() method is called from within JavaFX when the application is terminating and you can clean up here. When running a JavaFX application in a IDE, then no additional methods are required. However, for the sake of explicitness, you can add the following: public static void main (String[] args) { Application.launch(args); 2.2 JavaFX Hello World Here is a complete JavaFX program: public class HelloWorld extends A p p l i c a t i o n { public void s t a r t ( Stage primarystage ) throws Exception { FlowPane root = new FlowPane ( ) ; scene = new Scene ( root, 300, ) ; root. getchildren ( ). add (new Text ( Hello World ) ) ; primarystage. s e t S c e n e ( scene ) ; primarystage. show ( ) ; Here we have added a bye button that exits the program: public class HelloWorld extends A p p l i c a t i o n { public void s t a r t ( Stage primarystage ) throws Exception { FlowPane root = new FlowPane ( ) ; scene = new Scene ( root, 300, ) ; root. getchildren ( ). add (new Text ( H ello World ) ) ; Button button = new Button ( Bye ) ; button. setonaction ( e > Platform. e x i t ( ) ) ; root. getchildren ( ). add ( button ) ; primarystage. s e t S c e n e ( scene ) ; primarystage. show ( ) ;

6 6 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, JavaFX Application Thread You can t init the scene or stage in init() because this method is called in the Java Launcher Thread. The start() and stop() methods are called in the JavaFX Application Thread. Changes to the scene graph are only allowed from the Application Thread. You can call the following method to determine whether you are currently in the Application Thread: Platform.isFxApplicationThread(); 2.4 Defining the scene graph To define the scene graph, you first setup a root node root, which is usually a Layout object, and then supply this node to the Scene. The method root.getchildren() returns the list of children of the node. The return type is ObservableList<Node>, which is an extension of the Java class List<>. An ObservableList notifies registered listeners about changes to the list. Once you have a root node, you add children to the root node as follows: root.getchildren().add(helloworldlabel); root.getchildren().add(byebutton); where helloworldlabel and byebutton are instances of a Label and Button node, say. To remove a node (and all its descendants, if it has any) from a scene, remove it from its parent s list of children, e.g.: root.getchildren().remove(helloworldlabel);

7 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, Events and Controls Events are used to notify your application of actions taken by the user so that the application can respond to the event. JavaFX uses the delegation event model. Pressing a button, say, generates an event and this is delegated to an event handler. For example, here we a setup a handler for a button pressed event: Button button=new new Button("Bye"); button.setonaction((e)->platform.exit()); Use setonaction() to setup a handler for button pressed events. You will usually add event handlers to many of the nodes in your scene graph. Many nodes will be given multiple handlers for different types of events, such as mouse pressed, or mouse moved or swipped left. 3.1 The event dispatch chain When an event is generated, e.g. the user clicks the mouse on the window displaying the scene, then JavaFX has to determine the node whose event handler must handle the event. There may be more than one such node. JavaFX determines an event dispatch chain that is a path from the scene, through the root node to the target node of the even, e.g. a button: Click! scene flow pane Bye button 3.2 the event dispatch chain event handling has two phases: 1. Event capture: the event is passed down the event dispatch chain until the deepest node is found that wants to handle the event. The event is then handled. 2. Event bubbling: the event is passed back up the chain to give parent nodes the chance to handle it. An event handler can consume an event by calling event.consume(), in which case bubbling ceases. As an example of the use of event bubbling, imagine that you want to count all clicks that occur anywhere in a scene (but not on a button, as buttons consume mouse pressed events).

8 8 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, Handling events Above we saw an example of using setonaction() to setup a handler for a button-pressed event. There are many other such methods such as setonswipeleft(), setonmousepressed(), setoncontextmenurequested() etc. Use an instance of EventHandler<T extends Event> to handle events, in a number of ways, e.g.: as an anonymous for each handler, as a lambda expression for each handler, or as a single instancxe of a class that is used for multiple handlers. 3.4 Controls As discussed above, a simple push button control is given by the Button class. This extends or implements ButtonBase, Labeled, Region, Control, Parent and Node. Simplest way to use this: Button button=new Button("Bye"); button.setonaction((e)->...); Check box As another example, CheckBox extends ButtonBase and is a button that can be not selected, selected, or indeterminate. Selection: isselected() and setselected(boolean value) To allow an indeterminate state, use setallowindeterminate(boolean value) and use these methods to get and set: isindeterminate() and setindeterminate(boolean value) Key and mouse events The classes Node and Scene provide a number of methods for defining handlers for key and mouse events, such as: setonkeypressed(...) setonkeyreleased(...) setonkeytyped(...)... setonmouseentered(...) setonmouseclicked(...) setonmousemoved(...)... When called, a handler is given an instance of an Event that contains details of the event. For example, a MouseEvent has methods such as getbutton(), getclickcount(), getscenex(), getsceney(),... The following code could be used to monitor mouse clicks and entry events in the scene:

9 Advanced Java for Bioinformatics, WS 17/18, D. Huson, November 8, scene. setonmouseclicked ( ( e ) > { MouseButton mousebutton = e. getbutton ( ) ; System. e r r. p r i n t l n ( Clicked, Button : + mousebutton ) ; int c l i c k s = e. getclickcount ( ) ; System. e r r. p r i n t l n ( C l i c k s : + c l i c k s ) ; ) ; scene. setonmouseentered ( ( e ) > { MouseButton mousebutton = e. getbutton ( ) ; System. e r r. p r i n t l n ( Entered, Button : + mousebutton ) ; int c l i c k s = e. getclickcount ( ) ; System. e r r. p r i n t l n ( C l i c k s : + c l i c k s ) ; ) ;