// Explicit implementation of readObject, but called implicitly as a result of recursive calls to
// readObject() based on Serializable interface
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
name = new SimpleStringProperty((String) in.readObject());
strength = new SimpleDoubleProperty(in.readDouble());
health = new SimpleDoubleProperty(in.readDouble());
speed = new SimpleDoubleProperty(in.readDouble());
createAvatar();
getAvatar().setTranslateX(in.readDouble());
getAvatar().setTranslateY(in.readDouble());
tooltip = new Tooltip(toString());
Tooltip.install(getAvatar(), tooltip);
resetAvatarAttributes();
} // end readObject() to support serialization
public void addImageTab(Path imagePath) {
TabPane previewTabPane = controller.getPreviewTabPane();
ImageTab tab = new ImageTab();
tab.setPath(imagePath);
tab.setText(imagePath.getFileName().toString());
if (previewTabPane.getTabs().contains(tab)) {
previewTabPane.getSelectionModel().select(tab);
return;
}
Image image = new Image(IOHelper.pathToUrl(imagePath));
ImageView imageView = new ImageView(image);
imageView.setPreserveRatio(true);
imageView.setFitWidth(previewTabPane.getWidth());
previewTabPane
.widthProperty()
.addListener(
(observable, oldValue, newValue) -> {
imageView.setFitWidth(previewTabPane.getWidth());
});
Tooltip tip = new Tooltip(imagePath.toString());
Tooltip.install(tab.getGraphic(), tip);
ScrollPane scrollPane = new ScrollPane();
scrollPane.setVbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
scrollPane.setHbarPolicy(ScrollPane.ScrollBarPolicy.AS_NEEDED);
scrollPane.setContent(imageView);
scrollPane.addEventFilter(
ScrollEvent.SCROLL,
e -> {
if (e.isControlDown() && e.getDeltaY() > 0) {
// zoom in
imageView.setFitWidth(imageView.getFitWidth() + 16.0);
} else if (e.isControlDown() && e.getDeltaY() < 0) {
// zoom out
imageView.setFitWidth(imageView.getFitWidth() - 16.0);
}
});
tab.setContent(scrollPane);
TabPane tabPane = previewTabPane;
tabPane.getTabs().add(tab);
tabPane.getSelectionModel().select(tab);
}
/**
* <i>Actor</i> constructor is used when building <i>Actor</i> objects automatically:
* <i>strength</i>, <i>health</i>, <i>speed</i> fields are given randomly generated values within
* their range; <i>name</i> is given a sequentially numbered name: <i>Auto:<b>n</b></i> where
* <i><b>n</b></i> is the sequence number. The <i>name</i> can be edited to create an unique
* <i>Actor</i>.
*
* @param subclassCount used to support automatic naming (which includes a unique serial number).
* @param armyAllegiance used to support the <i>Army</i>-specific <i>DropShadow</i> glow around
* this Actor object.
*/
public Actor(int subclassCount, Army armyAllegiance) {
this.armyAllegiance = armyAllegiance;
++actorSerialNumber; // static class-oriented variable. There is one-and-only-one instance of
// this variable regardless of the number of Actor objects in existence
// (from none to infinity).
setName(
String.format(
"%d:%s:%d:",
actorSerialNumber,
getClass().getSimpleName(),
subclassCount)); // An alternate way to assemble a String to use as a name. Because of
// polymorphism "getClass().getName()" will return the subclass name
// when they exist.
setStrength(SingletonRandom.instance.getNormalDistribution(MIN_STRENGTH, MAX_STRENGTH, 2.0));
setHealth(SingletonRandom.instance.getNormalDistribution(MIN_HEALTH, MAX_HEALTH, 2.0));
setSpeed(SingletonRandom.instance.getNormalDistribution(MIN_SPEED, MAX_SPEED, 2.0));
createAvatar();
tooltip = new Tooltip(toString());
Tooltip.install(getAvatar(), tooltip);
tt = new TranslateTransition();
tt.setNode(getAvatar()); // reuse
} // end Actor constructor
/**
* Drawing function for Circles and Lines
*
* @param drawPane
* @param coords Circle Coordinates
* @param edges array of edges
* @param startIndex NumberOfNodes
*/
private void drawShapes(Pane drawPane, double[][] coords, int[][] edges, int startIndex) {
// clear previous pane
drawPane.getChildren().clear();
circleList = new ArrayList<>();
// generate Circles
for (int i = 0; i < coords.length; i++) {
Circle currentCircle = new Circle(coords[i][0], coords[i][1], nodeSize, Color.BLACK);
String toolTipText = "Node " + Integer.toString(i + 1);
// expand toolTip text with nucleotide and Circle color, if possible
if (sequenceField.getText().length() > i) {
toolTipText += ": " + sequenceField.getText().charAt(i);
currentCircle.setFill(getNodeColor(sequenceField.getText().charAt(i)));
}
Tooltip.install(currentCircle, new Tooltip(toolTipText));
if (isAnimated) {
currentCircle.setOnMousePressed(circleOnMousePressedEventHandler);
currentCircle.setOnMouseDragged(circleOnMouseDraggedEventHandler);
currentCircle.setOnMouseReleased(circleOnMouseReleasedEventHandler);
}
circleList.add(currentCircle);
}
// generate basic Lines
ArrayList<Line> lineList = new ArrayList<>();
for (int i = 0; i < circleList.size() - 1; i++) {
Line line = new Line();
line.setStroke(Color.BLACK);
line.setFill(Color.BLACK);
Circle circle1 = circleList.get(i);
Circle circle2 = circleList.get(i + 1);
// bind ends of line:
line.startXProperty().bind(circle1.centerXProperty().add(circle1.translateXProperty()));
line.startYProperty().bind(circle1.centerYProperty().add(circle1.translateYProperty()));
line.endXProperty().bind(circle2.centerXProperty().add(circle2.translateXProperty()));
line.endYProperty().bind(circle2.centerYProperty().add(circle2.translateYProperty()));
lineList.add(line);
}
// generate edges
for (int i = startIndex - 1; i < edges.length; i++) {
Line line = new Line();
line.setStroke(Color.ORANGE);
Circle circle1 = circleList.get(edges[i][0]);
Circle circle2 = circleList.get(edges[i][1]);
line.startXProperty().bind(circle1.centerXProperty().add(circle1.translateXProperty()));
line.startYProperty().bind(circle1.centerYProperty().add(circle1.translateYProperty()));
line.endXProperty().bind(circle2.centerXProperty().add(circle2.translateXProperty()));
line.endYProperty().bind(circle2.centerYProperty().add(circle2.translateYProperty()));
lineList.add(line);
}
drawPane.getChildren().addAll(lineList);
drawPane.getChildren().addAll(circleList);
}
public void addTab(Path path, Runnable... runnables) {
ObservableList<String> recentFiles = controller.getRecentFilesList();
if (Files.notExists(path)) {
recentFiles.remove(path.toString());
return;
}
ObservableList<Tab> tabs = controller.getTabPane().getTabs();
for (Tab tab : tabs) {
MyTab myTab = (MyTab) tab;
Path currentPath = myTab.getPath();
if (Objects.nonNull(currentPath))
if (currentPath.equals(path)) {
myTab.select(); // Select already added tab
return;
}
}
AnchorPane anchorPane = new AnchorPane();
EditorPane editorPane = webviewService.createWebView();
MyTab tab = createTab();
tab.setEditorPane(editorPane);
tab.setTabText(path.getFileName().toString());
editorPane.confirmHandler(
param -> {
if ("command:ready".equals(param)) {
JSObject window = editorPane.getWindow();
window.setMember("afx", controller);
window.call("updateOptions", new Object[] {});
Map<String, String> shortCuts = controller.getShortCuts();
Set<String> keySet = shortCuts.keySet();
for (String key : keySet) {
window.call("addNewCommand", new Object[] {key, shortCuts.get(key)});
}
if (Objects.isNull(path)) return true;
threadService.runTaskLater(
() -> {
String content = IOHelper.readFile(path);
threadService.runActionLater(
() -> {
window.call("changeEditorMode", path.toUri().toString());
window.call("setInitialized");
window.call("setEditorValue", new Object[] {content});
for (Runnable runnable : runnables) {
runnable.run();
}
});
});
}
return false;
});
threadService.runActionLater(
() -> {
TabPane tabPane = controller.getTabPane();
tabPane.getTabs().add(tab);
tab.select();
});
Node editorVBox = editorService.createEditorVBox(editorPane, tab);
controller.fitToParent(editorVBox);
anchorPane.getChildren().add(editorVBox);
tab.setContent(anchorPane);
tab.setPath(path);
Tooltip tip = new Tooltip(path.toString());
Tooltip.install(tab.getGraphic(), tip);
recentFiles.remove(path.toString());
recentFiles.add(0, path.toString());
editorPane.focus();
}
// drawing
public void drawGraph() {
Timeline timeline = new Timeline();
if (graph != null && finalCoordinates != null) {
// reset pane
drawing.getChildren().clear();
SpringEmbedder.centerCoordinates(finalCoordinates, 20, 380, 20, 380);
SpringEmbedder.centerCoordinates(startingCoordinates, 20, 380, 20, 380);
// draw nucleotides
circles = new Circle[finalCoordinates.length];
for (int i = 0; i < finalCoordinates.length; i++) {
// create nodes
Circle circle = new Circle(5);
circle.setCenterX(finalCoordinates[i][0]);
circle.setCenterY(finalCoordinates[i][1]);
switch (graph.getSequence().charAt(i)) {
case 'A':
circle.setFill(Color.YELLOW);
break;
case 'a':
circle.setFill(Color.YELLOW);
break;
case 'U':
circle.setFill(Color.GREEN);
break;
case 'u':
circle.setFill(Color.GREEN);
break;
case 'C':
circle.setFill(Color.BLUE);
break;
case 'c':
circle.setFill(Color.BLUE);
break;
case 'G':
circle.setFill(Color.RED);
break;
case 'g':
circle.setFill(Color.RED);
break;
}
circle.setStroke(Color.BLACK);
// add tooltip
Tooltip t =
new Tooltip("Nucleotide: " + graph.getSequence().charAt(i) + "\nPosition: " + i);
Tooltip.install(circle, t);
// add drag-and-drop behaviour
circle.setOnMousePressed(
event -> {
if (isAnimationActivated) {
dragStartX = circle.getCenterX();
dragStartY = circle.getCenterY();
}
});
circle.setOnMouseDragged(
event -> {
if (isAnimationActivated) {
circle.setCenterX(event.getX());
circle.setCenterY(event.getY());
}
});
circle.setOnMouseReleased(
event -> {
if (isAnimationActivated) {
Timeline dragTimeline = new Timeline();
KeyValue circlePositionXKey = new KeyValue(circle.centerXProperty(), dragStartX);
KeyValue circlePositionYKey = new KeyValue(circle.centerYProperty(), dragStartY);
dragTimeline
.getKeyFrames()
.add(new KeyFrame(Duration.millis(animationTime), circlePositionXKey));
dragTimeline
.getKeyFrames()
.add(new KeyFrame(Duration.millis(animationTime), circlePositionYKey));
dragTimeline.play();
}
});
// save circle locally
circles[i] = circle;
// animate circles
KeyValue startingXKey = new KeyValue(circle.centerXProperty(), startingCoordinates[i][0]);
KeyValue finalXKey = new KeyValue(circle.centerXProperty(), circle.getCenterX());
KeyValue startingYKey = new KeyValue(circle.centerYProperty(), startingCoordinates[i][1]);
KeyValue finalYKey = new KeyValue(circle.centerYProperty(), circle.getCenterY());
timeline.getKeyFrames().add(new KeyFrame(Duration.millis(0), startingXKey));
timeline.getKeyFrames().add(new KeyFrame(Duration.millis(0), startingYKey));
timeline.getKeyFrames().add(new KeyFrame(Duration.millis(animationTime), finalXKey));
timeline.getKeyFrames().add(new KeyFrame(Duration.millis(animationTime), finalYKey));
}
// create edges
int[][] edges = graph.getEdges();
for (int i = 0; i < edges.length; i++) {
// bind edges to nodes
Line line =
new Line(
finalCoordinates[edges[i][0]][0],
finalCoordinates[edges[i][0]][1],
finalCoordinates[edges[i][1]][0],
finalCoordinates[edges[i][1]][1]);
line.startYProperty().bind(circles[edges[i][0]].centerYProperty());
line.startXProperty().bind(circles[edges[i][0]].centerXProperty());
line.endYProperty().bind(circles[edges[i][1]].centerYProperty());
line.endXProperty().bind(circles[edges[i][1]].centerXProperty());
// draw edges
if (edges[i][1] - edges[i][0] != 1) {
line.setStroke(Color.CADETBLUE);
} else {
line.setFill(Color.DARKGRAY);
}
drawing.getChildren().add(line);
}
// draw all circles in order to overlap the edges
drawing.getChildren().addAll(circles);
if (isAnimationActivated) {
timeline.play();
}
} else {
throw new IllegalArgumentException(
"graph is null: "
+ graph.equals(null)
+ "\ncoordinates is null: "
+ finalCoordinates.equals(null));
}
}