/** initialize secondary structure view items */
private void initSecondaryView() {
// clear the secondary structure pane on initialization
pane2D.getChildren().clear();
if (view2DController.getGraph2d() != null) {
pane2D.widthProperty().removeListener(view2DController.getWidthChangeListener());
pane2D.heightProperty().removeListener(view2DController.getHeightChangeListener());
}
view2DController.initGraph2d(
rnaSequence3D.extractString(),
rnaSequence3D.getNucleotides().size(),
rnaSequence3D.computeWCBonds(),
(int) pane2D.getWidth(),
(int) pane2D.getHeight());
listenOnPane2dResize();
view2DController.setScaleBinding(pane2D.widthProperty(), pane2D.heightProperty());
view2DController.getGraph2d().setSelectionModel(selectionModel);
pane2D.getChildren().add(view2DController.getGraph2d());
}
/** initialize tertiary structure view */
private void initTertiaryView() {
Group models3D = new Group();
rnaSequence3D = new RNASequence(model.getPdbfile());
if (tertiaryRoom == null) {
tertiaryRoom = new Room(models3D, 50, 50);
tertiaryRoom.rotateCamera(tertiaryRoom);
tertiaryRoom.scaleCamera(scene);
tertiaryRoom.alignToParent(pane3D);
tertiaryRoom.setPickOnBounds(false);
pane3D.getChildren().add(tertiaryRoom);
} else {
tertiaryRoom.setObject(rnaSequence3D);
}
if (reloadItem.isSelected()) loadOneModel(0);
if (!reloadItem.isSelected()) loadAllmodels();
((MeshModel) rnaSequence3D.getModels().get(1)).colorPyrPur();
rnaSequence3D.setSelectionModel(selectionModel);
tertiaryRoom.setCameraCenter(rnaSequence3D.computeCenter());
activateRightSideButtons();
}