Exemplo n.º 1
0
  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);
    }
  }
Exemplo n.º 2
0
  @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();
  }
Exemplo n.º 3
0
  /**
   * 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);
  }
Exemplo n.º 4
0
  // 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));
    }
  }