private void initSelectionModel() {
this.selectionModel =
new NucleotideSelectionModel(
rnaSequence3D
.getNucleotides()
.toArray(new Nucleotide[rnaSequence3D.getNucleotides().size()]));
}
/** Method that loads all necessary information and initiates the views, the keyhandlers etc. */
public void loadProgramDataFromPdb() {
// Extract nucleotide information
rnaSequence3D = new RNASequence(getModel().getPdbfile());
// Extract base-sequence and compute watson-crick bonds
getModel().setSequence(rnaSequence3D.extractString());
getModel().setBonds(rnaSequence3D.computeWCBonds());
// Init selection Model
initSelectionModel();
// Init the Views
initPrimaryView();
initSecondaryView();
initTertiaryView();
// init focus selection listener
initSelectionListener();
selectionFocusBinding();
// init keyhandler
if (keyPressedEventHandler != null)
scene.removeEventFilter(KeyEvent.KEY_PRESSED, keyPressedEventHandler);
initKeyEventHandler();
scene.addEventFilter(KeyEvent.KEY_PRESSED, keyPressedEventHandler);
}
private void loadOneModel(int model) {
switch (model) {
case 0:
rnaSequence3D.addModel(new StickModel());
break;
case 1:
rnaSequence3D.addModel(new MeshModel());
break;
case 2:
rnaSequence3D.addModel(new BallModel());
break;
}
tertiaryRoom.getObject().getChildren().addAll(rnaSequence3D.getModels().get(0));
}
private void activateRightSideButtons() {
colorPyrpur.setOnAction(
(me) -> {
((MeshModel) rnaSequence3D.getModels().get(1)).colorPyrPur();
});
colorAugc.setOnAction(
(me) -> {
((MeshModel) rnaSequence3D.getModels().get(1)).colorBases();
});
centerObject.setOnAction(
(me) -> {
tertiaryRoom.setCameraCenter(rnaSequence3D.computeCenter());
});
}
private void initSelectionListener() {
selectionFocusListener =
c -> {
if (selectionModel.getSelectedItems().isEmpty())
tertiaryRoom.setCameraCenter(rnaSequence3D.computeCenter());
if (selectionModel.getSelectedIndices().size() > 0) selectFocus();
};
}
private void clearModels() {
structureStick.selectedProperty().unbind();
structureBall.selectedProperty().unbind();
structureMesh.selectedProperty().unbind();
structureBall.setOnAction(event -> {});
rnaSequence3D.getModels().clear();
}
/** 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();
}
private void loadAllmodels() {
rnaSequence3D.addModel(new StickModel());
rnaSequence3D.addModel(new MeshModel());
rnaSequence3D.addModel(new BallModel());
structureStick.selectedProperty().unbind();
structureMesh.selectedProperty().unbind();
structureBall.selectedProperty().unbind();
rnaSequence3D.getModels().get(0).visibleProperty().bind(structureStick.selectedProperty());
rnaSequence3D.getModels().get(1).visibleProperty().bind(structureMesh.selectedProperty());
rnaSequence3D.getModels().get(2).visibleProperty().bind(structureBall.selectedProperty());
tertiaryRoom.getObject().getChildren().addAll(rnaSequence3D.getModels().get(0));
tertiaryRoom.getObject().getChildren().addAll(rnaSequence3D.getModels().get(1));
tertiaryRoom.getObject().getChildren().addAll(rnaSequence3D.getModels().get(2));
}