public void createNodes(Graph graph, double[][] coordinates) {
nodeArray = new ArrayList<>();
double radius = graph.getNumberOfNodes() < 25 ? 100 / graph.getNumberOfNodes() : 4;
for (int i = 0; i < coordinates.length; i++) {
Circle nodeI = new Circle(radius);
nodeI.setTranslateX(coordinates[i][0]);
nodeI.setTranslateY(coordinates[i][1]);
Tooltip tip =
new Tooltip("node number " + (i + 1) + ", \"" + root.sequence.getText().charAt(i) + "\"");
Tooltip.install(nodeI, tip);
nodeI.setId(root.sequence.getText().substring(i, i + 1));
Timeline timeline = new Timeline();
nodeI.setOnMouseDragged(
event -> {
nodeI.setTranslateX(event.getSceneX() - root.nodes.getLayoutX());
nodeI.setTranslateY(event.getSceneY() - root.nodes.getLayoutY());
});
final int finalI = i;
nodeI.setOnMouseReleased(
event -> {
double[][] newCoordinates =
SpringEmbedder.computeSpringEmbedding(
100, graph.getNumberOfNodes(), graph.getEdges(), null);
SpringEmbedder.centerCoordinates(
newCoordinates,
0,
(int) root.getWidth(),
20,
(int) (root.getHeight() - root.vbox.getHeight() * 1.5));
timeline
.getKeyFrames()
.add(
new KeyFrame(
Duration.millis(200),
new KeyValue(nodeI.translateXProperty(), coordinates[finalI][0])));
timeline
.getKeyFrames()
.add(
new KeyFrame(
Duration.millis(200),
new KeyValue(nodeI.translateYProperty(), coordinates[finalI][1])));
timeline.play();
});
nodeI.disableProperty().bind(Bindings.not(root.animate.selectedProperty()));
root.nodes.getChildren().add(nodeI);
nodeArray.add(nodeI);
}
}
@Override
public void start(Stage primaryStage) throws Exception {
// UI fields
VBox mainBox = new VBox();
sequenceField = new TextField(myLabels.TEXTAREA_SEQUENCE);
bracketField = new TextField(myLabels.TEXTAREA_BRACKET);
HBox buttonBox = new HBox();
Button computeButton = new Button(myLabels.BUTTON_COMPUTE);
Button drawButton = new Button(myLabels.BUTTON_DRAW);
CheckBox animateChecker = new CheckBox(myLabels.CHECKBOX_ANIMATE);
drawPane = new Pane();
buttonBox.getChildren().addAll(computeButton, drawButton, animateChecker);
mainBox.getChildren().addAll(sequenceField, bracketField, buttonBox, drawPane);
// Compute Button disable
sequenceField
.textProperty()
.addListener(
(observable, oldValue, newValue) -> {
if (newValue.length() == 0) {
computeButton.setDisable(true);
} else {
computeButton.setDisable(false);
}
});
// Animate Checkbox
animateChecker.setOnAction(
(value) -> {
if (animateChecker.isSelected() != isAnimated) {
isAnimated = animateChecker.isSelected();
// set Eventhandler für Drag & Drop
for (Circle currentCircle : circleList) {
currentCircle.setOnMousePressed(isAnimated ? circleOnMousePressedEventHandler : null);
currentCircle.setOnMouseDragged(isAnimated ? circleOnMouseDraggedEventHandler : null);
currentCircle.setOnMouseReleased(
isAnimated ? circleOnMouseReleasedEventHandler : null);
}
}
});
// computeButton
computeButton.setOnAction(
(value) -> {
bracketField.setText(new Nussinov(sequenceField.getText()).getBracketNotation());
});
// drawButton
drawButton.setOnAction(
(value) -> {
Graph myGraph = new Graph();
try {
myGraph.parseNotation(bracketField.getText());
} catch (IOException e) {
Alert alert = new Alert(Alert.AlertType.ERROR);
alert.setTitle(myLabels.ALERT_TITLE);
alert.setHeaderText(myLabels.ALTERT_MESSAGE);
alert.setContentText(bracketField.getText());
alert.showAndWait();
}
coordsRepresentation[0] =
SpringEmbedder.computeSpringEmbedding(
iterations, myGraph.getNumberOfNodes(), myGraph.getEdges(), null);
SpringEmbedder.centerCoordinates(coordsRepresentation[0], 50, 550, 50, 550);
drawShapes(
drawPane, coordsRepresentation[0], myGraph.getEdges(), myGraph.getNumberOfNodes());
});
// prepare scene
Scene scene = new Scene(mainBox, 600, 800);
primaryStage.setScene(scene);
primaryStage.setTitle(myLabels.CAPTION);
// show scene
primaryStage.show();
}
/**
* 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);
}
// 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));
}
}