List of usage examples for javafx.scene.control Menu getItems
public final ObservableList<MenuItem> getItems()
From source file:com.ggvaidya.scinames.dataset.DatasetSceneController.java
private void setupTableWithChanges(TableView<Change> tv, Dataset tp) { tv.setEditable(true);// w w w . jav a2 s. c o m tv.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); tv.getColumns().clear(); TableColumn<Change, ChangeType> colChangeType = new TableColumn<>("Type"); colChangeType.setCellFactory(ComboBoxTableCell.forTableColumn(new ChangeTypeStringConverter(), ChangeType.ADDITION, ChangeType.DELETION, ChangeType.RENAME, ChangeType.LUMP, ChangeType.SPLIT, ChangeType.COMPLEX, ChangeType.ERROR)); colChangeType.setCellValueFactory(new PropertyValueFactory<>("type")); colChangeType.setPrefWidth(100.0); colChangeType.setEditable(true); tv.getColumns().add(colChangeType); TableColumn<Change, ObservableSet<Name>> colChangeFrom = new TableColumn<>("From"); colChangeFrom.setCellFactory(TextFieldTableCell.forTableColumn(new NameSetStringConverter())); colChangeFrom.setCellValueFactory(new PropertyValueFactory<>("from")); colChangeFrom.setPrefWidth(200.0); colChangeFrom.setEditable(true); tv.getColumns().add(colChangeFrom); TableColumn<Change, ObservableSet<Name>> colChangeTo = new TableColumn<>("To"); colChangeTo.setCellFactory(TextFieldTableCell.forTableColumn(new NameSetStringConverter())); colChangeTo.setCellValueFactory(new PropertyValueFactory<>("to")); colChangeTo.setPrefWidth(200.0); colChangeTo.setEditable(true); tv.getColumns().add(colChangeTo); TableColumn<Change, String> colExplicit = new TableColumn<>("Explicit or implicit?"); colExplicit.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( features.getValue().getDataset().isChangeImplicit(features.getValue()) ? "Implicit" : "Explicit")); tv.getColumns().add(colExplicit); ChangeFilter cf = datasetView.getProjectView().getProject().getChangeFilter(); TableColumn<Change, String> colFiltered = new TableColumn<>("Eliminated by filter?"); colFiltered.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( cf.test(features.getValue()) ? "Allowed" : "Eliminated")); tv.getColumns().add(colFiltered); TableColumn<Change, String> colNote = new TableColumn<>("Note"); colNote.setCellFactory(TextFieldTableCell.forTableColumn()); colNote.setCellValueFactory(new PropertyValueFactory<>("note")); colNote.setPrefWidth(100.0); colNote.setEditable(true); tv.getColumns().add(colNote); TableColumn<Change, String> colCitations = new TableColumn<>("Citations"); colCitations.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( features.getValue().getCitationStream().map(citation -> citation.getCitation()).sorted() .collect(Collectors.joining("; ")))); tv.getColumns().add(colCitations); TableColumn<Change, String> colGenera = new TableColumn<>("Genera"); colGenera.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( String.join(", ", features.getValue().getAllNames().stream().map(n -> n.getGenus()) .distinct().sorted().collect(Collectors.toList())))); tv.getColumns().add(colGenera); TableColumn<Change, String> colSpecificEpithet = new TableColumn<>("Specific epithets"); colSpecificEpithet.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper(String .join(", ", features.getValue().getAllNames().stream().map(n -> n.getSpecificEpithet()) .filter(s -> s != null).distinct().sorted().collect(Collectors.toList())))); tv.getColumns().add(colSpecificEpithet); // The infraspecific string. TableColumn<Change, String> colInfraspecificEpithet = new TableColumn<>("Infraspecific epithets"); colInfraspecificEpithet.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( String.join(", ", features.getValue().getAllNames().stream() .map(n -> n.getInfraspecificEpithetsAsString()).filter(s -> s != null) .distinct().sorted().collect(Collectors.toList())))); tv.getColumns().add(colInfraspecificEpithet); // The very last epithet of all TableColumn<Change, String> colTerminalEpithet = new TableColumn<>("Terminal epithet"); colTerminalEpithet.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( String.join(", ", features.getValue().getAllNames().stream().map(n -> { List<Name.InfraspecificEpithet> infraspecificEpithets = n.getInfraspecificEpithets(); if (!infraspecificEpithets.isEmpty()) { return infraspecificEpithets.get(infraspecificEpithets.size() - 1).getValue(); } else { return n.getSpecificEpithet(); } }).filter(s -> s != null).distinct().sorted().collect(Collectors.toList())))); tv.getColumns().add(colTerminalEpithet); // Properties TableColumn<Change, String> colProperties = new TableColumn<>("Properties"); colProperties.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( features.getValue().getProperties().entrySet().stream() .map(entry -> entry.getKey() + ": " + entry.getValue()).sorted() .collect(Collectors.joining("; ")))); tv.getColumns().add(colProperties); fillTableWithChanges(tv, tp); // When someone selects a cell in the Table, try to select the appropriate data in the // additional data view. tv.getSelectionModel().getSelectedItems().addListener((ListChangeListener<Change>) lcl -> { AdditionalData aData = additionalDataCombobox.getSelectionModel().getSelectedItem(); if (aData != null) { aData.onSelectChange(tv.getSelectionModel().getSelectedItems()); } }); // Create a right-click menu for table rows. changesTableView.setRowFactory(table -> { TableRow<Change> row = new TableRow<>(); row.setOnContextMenuRequested(event -> { if (row.isEmpty()) return; // We don't currently use the clicked change, since currently all options // change *all* the selected changes, but this may change in the future. Change change = row.getItem(); ContextMenu changeMenu = new ContextMenu(); Menu searchForName = new Menu("Search for name"); searchForName.getItems().addAll( change.getAllNames().stream().sorted().map(n -> createMenuItem(n.getFullName(), action -> { datasetView.getProjectView().openDetailedView(n); })).collect(Collectors.toList())); changeMenu.getItems().add(searchForName); changeMenu.getItems().add(new SeparatorMenuItem()); changeMenu.getItems().add(createMenuItem("Edit note", action -> { List<Change> changes = new ArrayList<>(changesTableView.getSelectionModel().getSelectedItems()); String combinedNotes = changes.stream().map(ch -> ch.getNote().orElse("").trim()).distinct() .collect(Collectors.joining("\n")).trim(); Optional<String> result = askUserForTextArea( "Modify the note for these " + changes.size() + " changes:", combinedNotes); if (result.isPresent()) { String note = result.get().trim(); LOGGER.info("Using 'Edit note' to set note to '" + note + "' on changes " + changes); changes.forEach(ch -> ch.noteProperty().set(note)); } })); changeMenu.getItems().add(new SeparatorMenuItem()); // Create a submenu for tags and urls. String note = change.noteProperty().get(); Menu removeTags = new Menu("Tags"); removeTags.getItems().addAll(change.getTags().stream().sorted() .map(tag -> new MenuItem(tag.getName())).collect(Collectors.toList())); Menu lookupURLs = new Menu("Lookup URL"); change.getURIs().stream().sorted().map(uri -> { return createMenuItem(uri.toString(), evt -> { try { Desktop.getDesktop().browse(uri); } catch (IOException ex) { LOGGER.warning("Could not open URL '" + uri + "': " + ex); } }); }).forEach(mi -> lookupURLs.getItems().add(mi)); changeMenu.getItems().add(lookupURLs); changeMenu.getItems().add(new SeparatorMenuItem()); changeMenu.getItems().add(createMenuItem("Prepend text to all notes", action -> { List<Change> changes = new ArrayList<>(changesTableView.getSelectionModel().getSelectedItems()); Optional<String> result = askUserForTextField( "Enter tags to prepend to notes in " + changes.size() + " changes:"); if (result.isPresent()) { String tags = result.get().trim(); changes.forEach(ch -> { String prevValue = change.getNote().orElse("").trim(); LOGGER.info("Prepending tags '" + tags + "' to previous value '" + prevValue + "' for change " + ch); ch.noteProperty().set((tags + " " + prevValue).trim()); }); } })); changeMenu.getItems().add(createMenuItem("Append text to all notes", action -> { List<Change> changes = new ArrayList<>(changesTableView.getSelectionModel().getSelectedItems()); Optional<String> result = askUserForTextField( "Enter tags to append to notes in " + changes.size() + " changes:"); if (result.isPresent()) { String tags = result.get().trim(); changes.forEach(ch -> { String prevValue = ch.getNote().orElse("").trim(); LOGGER.info("Appending tags '" + tags + "' to previous value '" + prevValue + "' for change " + ch); ch.noteProperty().setValue((prevValue + " " + tags).trim()); }); } })); changeMenu.show(datasetView.getScene().getWindow(), event.getScreenX(), event.getScreenY()); }); return row; }); LOGGER.info("setupTableWithChanges() completed"); }
From source file:be.makercafe.apps.makerbench.Main.java
/** * Creates the menubar//from ww w . j a va 2 s. co m * * @return */ private MenuBar createMenuBar() { MenuBar bar = new MenuBar(); Menu projectMenu = new Menu("Project"); MenuItem openProject = new MenuItem("Open..."); openProject.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent event) { directoryChooser.setTitle("Please choose a project folder"); File file = directoryChooser.showDialog(stage); viewer.setRoot(setRootFolder(file)); } }); Menu newProject = new Menu("New"); MenuItem newFolder = new MenuItem("Folder..."); newFolder.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent event) { TextInputDialog dialog = new TextInputDialog("my_project_folder"); dialog.setTitle("New folder"); dialog.setHeaderText("Create a new folder"); dialog.setContentText("Folder name:"); Optional<String> result = dialog.showAndWait(); if (result.isPresent()) { String homeDir = System.getProperty("user.home"); System.out.println("Folder name: " + result.get()); System.out.println("User home: " + homeDir); } } }); newProject.getItems().add(newFolder); MenuItem importProject = new MenuItem("Import"); importProject.setAccelerator(new KeyCodeCombination(KeyCode.I, KeyCombination.CONTROL_DOWN)); importProject.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent event) { System.out.println("Import"); } }); MenuItem deleteProject = new MenuItem("Delete"); deleteProject.setAccelerator(new KeyCodeCombination(KeyCode.D, KeyCombination.CONTROL_DOWN)); deleteProject.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent event) { System.out.println("Delete"); } }); projectMenu.getItems().addAll(openProject, newProject, importProject, deleteProject); Menu helpMenu = new Menu("Help"); MenuItem aboutItem = new MenuItem("About"); aboutItem.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent event) { Alert alert = new Alert(AlertType.INFORMATION); alert.setTitle("Information Dialog"); alert.setHeaderText("About makerbench"); alert.setContentText( "Makerbench is an open source IDE for designing and manufacturing objects and code.\nWritten by Luc De pauw\n\nUses opensource libraries from the next projects:\n-RichtextFX by Tomas Mikula\n-JCSG by Michael Hoffer\n-ControlsFX by FXexperience.com"); alert.showAndWait(); } }); helpMenu.getItems().add(aboutItem); bar.getMenus().addAll(projectMenu, helpMenu); return bar; }
From source file:com.cdd.bao.editor.EditSchema.java
private MenuItem addMenu(Menu parent, String title, KeyCombination accel) { MenuItem item = new MenuItem(title); parent.getItems().add(item); if (accel != null) item.setAccelerator(accel);/*ww w. j a va 2 s .c o m*/ return item; }
From source file:com.cdd.bao.editor.EditSchema.java
private CheckMenuItem addCheckMenu(Menu parent, String title, KeyCombination accel) { CheckMenuItem item = new CheckMenuItem(title); parent.getItems().add(item); if (accel != null) item.setAccelerator(accel);// w w w . j a v a2 s . c o m return item; }
From source file:org.nmrfx.processor.gui.MainApp.java
MenuBar makeMenuBar(String appName) {
MenuToolkit tk = null;//from w w w .j ava 2s .co m
if (isMac()) {
tk = MenuToolkit.toolkit();
}
MenuBar menuBar = new MenuBar();
// Application Menu
// TBD: services menu
Menu appMenu = new Menu(appName); // Name for appMenu can't be set at
// Runtime
MenuItem aboutItem = null;
Stage aboutStage = makeAbout(appName);
if (tk != null) {
aboutItem = tk.createAboutMenuItem(appName, aboutStage);
} else {
aboutItem = new MenuItem("About...");
aboutItem.setOnAction(e -> aboutStage.show());
}
MenuItem prefsItem = new MenuItem("Preferences...");
MenuItem quitItem;
prefsItem.setOnAction(e -> showPreferences(e));
if (tk != null) {
quitItem = tk.createQuitMenuItem(appName);
appMenu.getItems().addAll(aboutItem, new SeparatorMenuItem(), prefsItem, new SeparatorMenuItem(),
tk.createHideMenuItem(appName), tk.createHideOthersMenuItem(), tk.createUnhideAllMenuItem(),
new SeparatorMenuItem(), quitItem);
// createQuitMeneItem doesn't result in stop or quit being called
// therefore we can't check for waiting till a commit is done before leaving
// so explicitly set action to quit
quitItem.setOnAction(e -> quit());
} else {
quitItem = new MenuItem("Quit");
quitItem.setOnAction(e -> quit());
}
// File Menu (items TBD)
Menu fileMenu = new Menu("File");
MenuItem openMenuItem = new MenuItem("Open and Draw...");
openMenuItem.setOnAction(e -> FXMLController.getActiveController().openAction(e));
MenuItem addMenuItem = new MenuItem("Open...");
addMenuItem.setOnAction(e -> FXMLController.getActiveController().addNoDrawAction(e));
MenuItem newMenuItem = new MenuItem("New Window...");
newMenuItem.setOnAction(e -> newGraphics(e));
Menu recentMenuItem = new Menu("Open and Draw Recent");
List<Path> recentDatasets = PreferencesController.getRecentDatasets();
for (Path path : recentDatasets) {
int count = path.getNameCount();
int first = count - 3;
first = first >= 0 ? first : 0;
Path subPath = path.subpath(first, count);
MenuItem datasetMenuItem = new MenuItem(subPath.toString());
datasetMenuItem
.setOnAction(e -> FXMLController.getActiveController().openFile(path.toString(), false, false));
recentMenuItem.getItems().add(datasetMenuItem);
}
MenuItem pdfMenuItem = new MenuItem("Export PDF...");
pdfMenuItem.setOnAction(e -> FXMLController.getActiveController().exportPDFAction(e));
MenuItem svgMenuItem = new MenuItem("Export SVG...");
svgMenuItem.setOnAction(e -> FXMLController.getActiveController().exportSVGAction(e));
MenuItem loadPeakListMenuItem = new MenuItem("Load PeakLists");
loadPeakListMenuItem.setOnAction(e -> loadPeakLists());
Menu projectMenu = new Menu("Projects");
MenuItem projectOpenMenuItem = new MenuItem("Open...");
projectOpenMenuItem.setOnAction(e -> loadProject());
MenuItem projectSaveAsMenuItem = new MenuItem("Save As...");
projectSaveAsMenuItem.setOnAction(e -> saveProjectAs());
MenuItem projectSaveMenuItem = new MenuItem("Save");
projectSaveMenuItem.setOnAction(e -> saveProject());
Menu recentProjectMenuItem = new Menu("Open Recent");
List<Path> recentProjects = PreferencesController.getRecentProjects();
for (Path path : recentProjects) {
int count = path.getNameCount();
int first = count - 3;
first = first >= 0 ? first : 0;
Path subPath = path.subpath(first, count);
MenuItem projectMenuItem = new MenuItem(subPath.toString());
projectMenuItem.setOnAction(e -> loadProject(path));
recentProjectMenuItem.getItems().add(projectMenuItem);
}
projectMenu.getItems().addAll(projectOpenMenuItem, recentProjectMenuItem, projectSaveMenuItem,
projectSaveAsMenuItem);
fileMenu.getItems().addAll(openMenuItem, addMenuItem, newMenuItem, recentMenuItem, new SeparatorMenuItem(),
pdfMenuItem, svgMenuItem, loadPeakListMenuItem);
Menu spectraMenu = new Menu("Spectra");
MenuItem deleteItem = new MenuItem("Delete Spectrum");
deleteItem.setOnAction(e -> FXMLController.getActiveController().removeChart());
MenuItem syncMenuItem = new MenuItem("Sync Axes");
syncMenuItem.setOnAction(e -> PolyChart.activeChart.syncSceneMates());
Menu arrangeMenu = new Menu("Arrange");
MenuItem horizItem = new MenuItem("Horizontal");
horizItem.setOnAction(
e -> FXMLController.getActiveController().arrange(FractionPane.ORIENTATION.HORIZONTAL));
MenuItem vertItem = new MenuItem("Vertical");
vertItem.setOnAction(e -> FXMLController.getActiveController().arrange(FractionPane.ORIENTATION.VERTICAL));
MenuItem gridItem = new MenuItem("Grid");
gridItem.setOnAction(e -> FXMLController.getActiveController().arrange(FractionPane.ORIENTATION.GRID));
MenuItem overlayItem = new MenuItem("Overlay");
overlayItem.setOnAction(e -> FXMLController.getActiveController().overlay());
MenuItem minimizeItem = new MenuItem("Minimize Borders");
minimizeItem.setOnAction(e -> FXMLController.getActiveController().setBorderState(true));
MenuItem normalizeItem = new MenuItem("Normal Borders");
normalizeItem.setOnAction(e -> FXMLController.getActiveController().setBorderState(false));
arrangeMenu.getItems().addAll(horizItem, vertItem, gridItem, overlayItem, minimizeItem, normalizeItem);
MenuItem alignMenuItem = new MenuItem("Align Spectra");
alignMenuItem.setOnAction(e -> FXMLController.getActiveController().alignCenters());
MenuItem analyzeMenuItem = new MenuItem("Analyzer...");
analyzeMenuItem.setOnAction(e -> showAnalyzer(e));
spectraMenu.getItems().addAll(deleteItem, arrangeMenu, syncMenuItem, alignMenuItem, analyzeMenuItem);
// Format (items TBD)
// Menu formatMenu = new Menu("Format");
// formatMenu.getItems().addAll(new MenuItem("TBD"));
// View Menu (items TBD)
Menu viewMenu = new Menu("View");
MenuItem dataMenuItem = new MenuItem("Show Datasets");
dataMenuItem.setOnAction(e -> showDatasetsTable(e));
MenuItem consoleMenuItem = new MenuItem("Show Console");
consoleMenuItem.setOnAction(e -> showConsole(e));
MenuItem attrMenuItem = new MenuItem("Show Attributes");
attrMenuItem.setOnAction(e -> FXMLController.getActiveController().showSpecAttrAction(e));
MenuItem procMenuItem = new MenuItem("Show Processor");
procMenuItem.setOnAction(e -> FXMLController.getActiveController().showProcessorAction(e));
MenuItem scannerMenuItem = new MenuItem("Show Scanner");
scannerMenuItem.setOnAction(e -> FXMLController.getActiveController().showScannerAction(e));
viewMenu.getItems().addAll(consoleMenuItem, dataMenuItem, attrMenuItem, procMenuItem, scannerMenuItem);
Menu peakMenu = new Menu("Peaks");
MenuItem peakAttrMenuItem = new MenuItem("Show Peak Tool");
peakAttrMenuItem.setOnAction(e -> FXMLController.getActiveController().showPeakAttrAction(e));
MenuItem peakNavigatorMenuItem = new MenuItem("Show Peak Navigator");
peakNavigatorMenuItem.setOnAction(e -> FXMLController.getActiveController().showPeakNavigator());
MenuItem linkPeakDimsMenuItem = new MenuItem("Link by Labels");
linkPeakDimsMenuItem.setOnAction(e -> FXMLController.getActiveController().linkPeakDims());
MenuItem peakSliderMenuItem = new MenuItem("Show Peak Slider");
peakSliderMenuItem.setOnAction(e -> FXMLController.getActiveController().showPeakSlider());
peakMenu.getItems().addAll(peakAttrMenuItem, peakNavigatorMenuItem, linkPeakDimsMenuItem,
peakSliderMenuItem);
// Window Menu
// TBD standard window menu items
// Help Menu (items TBD)
Menu helpMenu = new Menu("Help");
MenuItem webSiteMenuItem = new MenuItem("NMRFx Web Site");
webSiteMenuItem.setOnAction(e -> showWebSiteAction(e));
MenuItem docsMenuItem = new MenuItem("Online Documentation");
docsMenuItem.setOnAction(e -> showDocAction(e));
MenuItem versionMenuItem = new MenuItem("Check Version");
versionMenuItem.setOnAction(e -> showVersionAction(e));
MenuItem mailingListItem = new MenuItem("Mailing List Site");
mailingListItem.setOnAction(e -> showMailingListAction(e));
MenuItem refMenuItem = new MenuItem("NMRFx Publication");
refMenuItem.setOnAction(e -> {
MainApp.hostServices.showDocument("http://link.springer.com/article/10.1007/s10858-016-0049-6");
});
// home
// mailing list
//
helpMenu.getItems().addAll(docsMenuItem, webSiteMenuItem, mailingListItem, versionMenuItem, refMenuItem);
if (tk != null) {
Menu windowMenu = new Menu("Window");
windowMenu.getItems().addAll(tk.createMinimizeMenuItem(), tk.createZoomMenuItem(),
tk.createCycleWindowsItem(), new SeparatorMenuItem(), tk.createBringAllToFrontItem());
menuBar.getMenus().addAll(appMenu, fileMenu, projectMenu, spectraMenu, viewMenu, peakMenu, windowMenu,
helpMenu);
tk.autoAddWindowMenuItems(windowMenu);
tk.setGlobalMenuBar(menuBar);
} else {
fileMenu.getItems().add(prefsItem);
fileMenu.getItems().add(quitItem);
menuBar.getMenus().addAll(fileMenu, projectMenu, spectraMenu, viewMenu, peakMenu, helpMenu);
helpMenu.getItems().add(0, aboutItem);
}
return menuBar;
}
From source file:com.ggvaidya.scinames.dataset.BinomialChangesSceneController.java
private void setupTableWithBinomialChanges() { changesTableView.setEditable(false); changesTableView.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); changesTableView.setItems(potentialChanges); changesTableView.getColumns().clear(); TableColumn<PotentialChange, ChangeType> colChangeType = new TableColumn<>("Type"); colChangeType.setCellFactory(ComboBoxTableCell.forTableColumn(new ChangeTypeStringConverter(), ChangeType.ADDITION, ChangeType.DELETION, ChangeType.RENAME, ChangeType.LUMP, ChangeType.SPLIT, ChangeType.COMPLEX, ChangeType.ERROR)); colChangeType.setCellValueFactory(new PropertyValueFactory<>("type")); colChangeType.setPrefWidth(100.0);// w w w . ja v a2 s.co m colChangeType.setEditable(true); changesTableView.getColumns().add(colChangeType); TableColumn<PotentialChange, ObservableSet<Name>> colChangeFrom = new TableColumn<>("From"); colChangeFrom.setCellFactory(TextFieldTableCell.forTableColumn(new NameSetStringConverter())); colChangeFrom.setCellValueFactory(new PropertyValueFactory<>("from")); colChangeFrom.setPrefWidth(200.0); colChangeFrom.setEditable(true); changesTableView.getColumns().add(colChangeFrom); TableColumn<PotentialChange, ObservableSet<Name>> colChangeTo = new TableColumn<>("To"); colChangeTo.setCellFactory(TextFieldTableCell.forTableColumn(new NameSetStringConverter())); colChangeTo.setCellValueFactory(new PropertyValueFactory<>("to")); colChangeTo.setPrefWidth(200.0); colChangeTo.setEditable(true); changesTableView.getColumns().add(colChangeTo); TableColumn<PotentialChange, String> colDataset = new TableColumn<>("Dataset"); colDataset.setCellValueFactory(cvf -> { return new ReadOnlyStringWrapper(cvf.getValue().getDataset().toString()); }); colDataset.setPrefWidth(150.0); changesTableView.getColumns().add(colDataset); TableColumn<PotentialChange, SimplifiedDate> dateCol = new TableColumn<>("Date"); dateCol.setCellFactory( TextFieldTableCell.forTableColumn(new SimplifiedDate.SimplifiedDateStringConverter())); dateCol.setCellValueFactory(cvf -> new ReadOnlyObjectWrapper<>(cvf.getValue().getDataset().getDate())); dateCol.setPrefWidth(150); dateCol.setSortable(true); dateCol.setSortType(SortType.ASCENDING); changesTableView.getColumns().add(dateCol); changesTableView.getSortOrder().add(dateCol); TableColumn<PotentialChange, String> colChangeSummary = new TableColumn<>("Changes summary"); colChangeSummary.setCellValueFactory(cvf -> { Set<Change> changes = changesByPotentialChange.get(cvf.getValue()); return new ReadOnlyStringWrapper(changes.size() + ": " + changes.stream().map(ch -> ch.toString()).collect(Collectors.joining("; "))); }); colChangeSummary.setPrefWidth(200.0); changesTableView.getColumns().add(colChangeSummary); /* TableColumn<PotentialChange, String> colExplicit = new TableColumn<>("Explicit or implicit?"); colExplicit.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( features.getValue().getDataset().isChangeImplicit(features.getValue()) ? "Implicit" : "Explicit" ) ); tv.getColumns().add(colExplicit); ChangeFilter cf = binomialChangesView.getProjectView().getProject().getChangeFilter(); TableColumn<Change, String> colFiltered = new TableColumn<>("Eliminated by filter?"); colFiltered.setCellValueFactory( (TableColumn.CellDataFeatures<Change, String> features) -> new ReadOnlyStringWrapper( cf.test(features.getValue()) ? "Allowed" : "Eliminated" ) ); tv.getColumns().add(colFiltered); */ TableColumn<PotentialChange, String> colNote = new TableColumn<>("Note"); colNote.setCellFactory(TextFieldTableCell.forTableColumn()); colNote.setCellValueFactory(new PropertyValueFactory<>("note")); colNote.setPrefWidth(100.0); changesTableView.getColumns().add(colNote); TableColumn<PotentialChange, String> colReason = new TableColumn<>("Reason"); colReason.setCellValueFactory(cvf -> new ReadOnlyStringWrapper(calculateReason(cvf.getValue()))); colReason.setPrefWidth(100.0); changesTableView.getColumns().add(colReason); TableColumn<PotentialChange, String> colReasonDate = new TableColumn<>("ReasonDate"); colReasonDate.setCellValueFactory(cvf -> { String result; Set<SimplifiedDate> dates = calculateReasonDate(cvf.getValue()); if (dates.size() > 1) { result = "(" + dates.size() + ") " + dates.stream().distinct().sorted() .map(sd -> sd.asYYYYmmDD("-")).collect(Collectors.joining("|")); } else if (dates.size() == 1) { result = dates.iterator().next().asYYYYmmDD("-"); } else { result = "NA"; } return new ReadOnlyStringWrapper(result); }); colReasonDate.setPrefWidth(100.0); changesTableView.getColumns().add(colReasonDate); TableColumn<PotentialChange, String> colCitations = new TableColumn<>("Citations"); colCitations.setCellValueFactory( (TableColumn.CellDataFeatures<PotentialChange, String> features) -> new ReadOnlyStringWrapper( features.getValue().getCitationStream().map(citation -> citation.getCitation()).sorted() .collect(Collectors.joining("; ")))); changesTableView.getColumns().add(colCitations); TableColumn<PotentialChange, String> colGenera = new TableColumn<>("Genera"); colGenera.setCellValueFactory( (TableColumn.CellDataFeatures<PotentialChange, String> features) -> new ReadOnlyStringWrapper( String.join(", ", features.getValue().getAllNames().stream().map(n -> n.getGenus()) .distinct().sorted().collect(Collectors.toList())))); changesTableView.getColumns().add(colGenera); TableColumn<PotentialChange, String> colSpecificEpithet = new TableColumn<>("Specific epithets"); colSpecificEpithet.setCellValueFactory( (TableColumn.CellDataFeatures<PotentialChange, String> features) -> new ReadOnlyStringWrapper(String .join(", ", features.getValue().getAllNames().stream().map(n -> n.getSpecificEpithet()) .filter(s -> s != null).distinct().sorted().collect(Collectors.toList())))); changesTableView.getColumns().add(colSpecificEpithet); // The infraspecific string. TableColumn<PotentialChange, String> colInfraspecificEpithet = new TableColumn<>("Infraspecific epithets"); colInfraspecificEpithet.setCellValueFactory( (TableColumn.CellDataFeatures<PotentialChange, String> features) -> new ReadOnlyStringWrapper( String.join(", ", features.getValue().getAllNames().stream() .map(n -> n.getInfraspecificEpithetsAsString()).filter(s -> s != null) .distinct().sorted().collect(Collectors.toList())))); changesTableView.getColumns().add(colInfraspecificEpithet); // The very last epithet of all TableColumn<PotentialChange, String> colTerminalEpithet = new TableColumn<>("Terminal epithet"); colTerminalEpithet.setCellValueFactory( (TableColumn.CellDataFeatures<PotentialChange, String> features) -> new ReadOnlyStringWrapper( String.join(", ", features.getValue().getAllNames().stream().map(n -> { List<Name.InfraspecificEpithet> infraspecificEpithets = n.getInfraspecificEpithets(); if (!infraspecificEpithets.isEmpty()) { return infraspecificEpithets.get(infraspecificEpithets.size() - 1).getValue(); } else { return n.getSpecificEpithet(); } }).filter(s -> s != null).distinct().sorted().collect(Collectors.toList())))); changesTableView.getColumns().add(colTerminalEpithet); TableColumn<PotentialChange, String> dateForRCol = new TableColumn<>("DateYMD"); dateForRCol.setCellValueFactory( cvf -> new ReadOnlyObjectWrapper<>(cvf.getValue().getDataset().getDate().asYYYYmmDD("-"))); changesTableView.getColumns().add(dateForRCol); // Properties TableColumn<PotentialChange, String> colProperties = new TableColumn<>("Properties"); colProperties.setCellValueFactory( (TableColumn.CellDataFeatures<PotentialChange, String> features) -> new ReadOnlyStringWrapper( features.getValue().getProperties().entrySet().stream() .map(entry -> entry.getKey() + ": " + entry.getValue()).sorted() .collect(Collectors.joining("; ")))); changesTableView.getColumns().add(colProperties); fillTableWithBinomialChanges(); // When someone selects a cell in the Table, try to select the appropriate data in the // additional data view. changesTableView.getSelectionModel().getSelectedItems() .addListener((ListChangeListener<PotentialChange>) lcl -> { AdditionalData aData = additionalDataCombobox.getSelectionModel().getSelectedItem(); if (aData != null) { aData.onSelectChange(changesTableView.getSelectionModel().getSelectedItems()); } }); // Create a right-click menu for table rows. changesTableView.setRowFactory(table -> { TableRow<PotentialChange> row = new TableRow<>(); row.setOnContextMenuRequested(event -> { if (row.isEmpty()) return; // We don't currently use the clicked change, since currently all options // change *all* the selected changes, but this may change in the future. PotentialChange change = row.getItem(); ContextMenu changeMenu = new ContextMenu(); Menu lookupChange = new Menu("Look up change"); lookupChange.getItems().addAll(changesByPotentialChange.getOrDefault(change, new HashSet<>()) .stream() .map(ch -> createMenuItem(ch.toString() + " in " + ch.getDataset().toString(), action -> { binomialChangesView.getProjectView().openDetailedView(ch); })).collect(Collectors.toList())); changeMenu.getItems().add(lookupChange); changeMenu.getItems().add(new SeparatorMenuItem()); Menu searchForName = new Menu("Search for name"); searchForName.getItems().addAll( change.getAllNames().stream().sorted().map(n -> createMenuItem(n.getFullName(), action -> { binomialChangesView.getProjectView().openDetailedView(n); })).collect(Collectors.toList())); changeMenu.getItems().add(searchForName); changeMenu.getItems().add(new SeparatorMenuItem()); // Create a submenu for tags and urls. String note = change.noteProperty().get(); Menu removeTags = new Menu("Tags"); removeTags.getItems().addAll(change.getTags().stream().sorted() .map(tag -> new MenuItem(tag.getName())).collect(Collectors.toList())); Menu lookupURLs = new Menu("Lookup URL"); change.getURIs().stream().sorted().map(uri -> { return createMenuItem(uri.toString(), evt -> { try { Desktop.getDesktop().browse(uri); } catch (IOException ex) { LOGGER.warning("Could not open URL '" + uri + "': " + ex); } }); }).forEach(mi -> lookupURLs.getItems().add(mi)); changeMenu.getItems().add(lookupURLs); changeMenu.show(binomialChangesView.getScene().getWindow(), event.getScreenX(), event.getScreenY()); }); return row; }); LOGGER.info("setupTableWithChanges() completed"); }
From source file:qupath.lib.gui.panels.survival.KaplanMeierDisplay.java
@SuppressWarnings("unchecked") private void generatePlot() { KaplanMeierDisplay.ScoreData newScoreData = scoreData; // If we have a hierarchy, update the scores with the most recent data if (hierarchy != null) { List<TMACoreObject> cores = PathObjectTools.getTMACoreObjects(hierarchy, false); double[] survival = new double[cores.size()]; boolean[] censored = new boolean[cores.size()]; double[] scores = new double[cores.size()]; // // Optionally sort by scores... helps a bit when debugging e.g. p-values, Hazard ratios etc. // cores.sort((c1, c2) -> Double.compare(c1.getMeasurementList().getMeasurementValue(scoreColumn), c2.getMeasurementList().getMeasurementValue(scoreColumn))); // scoreColumn = "Positive %"; // scoreColumn = "RoughScore"; for (int i = 0; i < cores.size(); i++) { TMACoreObject core = cores.get(i); MeasurementList ml = core.getMeasurementList(); survival[i] = core.getMeasurementList().getMeasurementValue(survivalColumn); double censoredValue = core.getMeasurementList().getMeasurementValue(censoredColumn); boolean hasCensoredValue = !Double.isNaN(censoredValue) && (censoredValue == 0 || censoredValue == 1); censored[i] = censoredValue != 0; if (!hasCensoredValue) { // If we don't have a censored value, ensure we mask out everything else scores[i] = Double.NaN; survival[i] = Double.NaN; } else if (ml.containsNamedMeasurement(scoreColumn)) // Get the score if we can scores[i] = ml.getMeasurementValue(scoreColumn); else { // // Try to compute score if we need to // Map<String, Number> map = ROIMeaningfulMeasurements.getPathClassSummaryMeasurements(core.getChildObjects(), true); // Number value = map.get(scoreColumn); // if (value == null) scores[i] = Double.NaN; // else // scores[i] = value.doubleValue(); }//from www .j ava 2s . co m } // Mask out any scores that don't have associated survival data for (int i = 0; i < survival.length; i++) { if (Double.isNaN(survival[i])) scores[i] = Double.NaN; } newScoreData = new ScoreData(scores, survival, censored); } if (newScoreData == null || newScoreData.scores.length == 0) return; // KaplanMeier kmHigh = new KaplanMeier("Above threshold"); // KaplanMeier kmLow = new KaplanMeier("Below threshold"); double[] quartiles = StatisticsHelper.getQuartiles(newScoreData.scores); double q1 = quartiles[0]; double median = quartiles[1]; double q3 = quartiles[2]; double[] thresholds; if (params != null) { Object thresholdMethod = params.getChoiceParameterValue("scoreThresholdMethod"); if (thresholdMethod.equals("Median")) { // panelParams.setNumericParameterValue("scoreThreshold", median); // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG! thresholds = new double[] { median }; } else if (thresholdMethod.equals("Tertiles")) { // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG! thresholds = StatisticsHelper.getTertiles(newScoreData.scores); } else if (thresholdMethod.equals("Quartiles")) { // ((DoubleParameter)params.getParameters().get("scoreThreshold")).setValue(median); // TODO: UPDATE DIALOG! thresholds = new double[] { q1, median, q3 }; } else if (thresholdMethod.equals("Manual (1)")) { thresholds = new double[] { params.getDoubleParameterValue("threshold1") }; } else if (thresholdMethod.equals("Manual (2)")) { thresholds = new double[] { params.getDoubleParameterValue("threshold1"), params.getDoubleParameterValue("threshold2") }; } else //if (thresholdMethod.equals("Manual (3)")) { thresholds = new double[] { params.getDoubleParameterValue("threshold1"), params.getDoubleParameterValue("threshold2"), params.getDoubleParameterValue("threshold3") }; } else thresholds = new double[] { median }; double minVal = Double.POSITIVE_INFINITY; double maxVal = Double.NEGATIVE_INFINITY; int numNonNaN = 0; for (double d : newScoreData.scores) { if (Double.isNaN(d)) continue; if (d < minVal) minVal = d; if (d > maxVal) maxVal = d; numNonNaN++; } boolean scoresValid = maxVal > minVal; // If not this, we don't have valid scores that we can work with double maxTimePoint = 0; for (double d : newScoreData.survival) { if (Double.isNaN(d)) continue; if (d > maxTimePoint) maxTimePoint = d; } if (panelParams != null && maxTimePoint > ((IntParameter) params.getParameters().get("censorTimePoints")).getUpperBound()) { panelParams.setNumericParameterValueRange("censorTimePoints", 0, Math.ceil(maxTimePoint)); } // Optionally censor at specified time double censorThreshold = params == null ? maxTimePoint : params.getIntParameterValue("censorTimePoints"); // Compute log-rank p-values for *all* possible thresholds // Simultaneously determine the threshold that yields the lowest p-value, // resolving ties in favour of a more even split between high/low numbers of events boolean pValuesChanged = false; if (calculateAllPValues) { if (!(pValues != null && pValueThresholds != null && newScoreData.equals(scoreData) && censorThreshold == lastPValueCensorThreshold)) { Map<Double, Double> mapLogRank = new TreeMap<>(); Set<Double> setObserved = new HashSet<>(); for (int i = 0; i < newScoreData.scores.length; i++) { Double d = newScoreData.scores[i]; boolean observed = !newScoreData.censored[i] && newScoreData.survival[i] < censorThreshold; if (observed) setObserved.add(d); if (mapLogRank.containsKey(d)) continue; List<KaplanMeierData> kmsTemp = splitByThresholds(newScoreData, new double[] { d }, censorThreshold, false); // if (kmsTemp.get(1).nObserved() == 0 || kmsTemp.get(1).nObserved() == 0) // continue; LogRankResult test = LogRankTest.computeLogRankTest(kmsTemp.get(0), kmsTemp.get(1)); double pValue = test.getPValue(); // double pValue = test.hazardRatio < 1 ? test.hazardRatio : 1.0/test.hazardRatio; // Checking usefulness of Hazard ratios... if (!Double.isFinite(pValue)) continue; // if (!Double.isFinite(test.getHazardRatio())) { //// continue; // pValue = Double.NaN; // } mapLogRank.put(d, pValue); } pValueThresholds = new double[mapLogRank.size()]; pValues = new double[mapLogRank.size()]; pValueThresholdsObserved = new boolean[mapLogRank.size()]; int count = 0; for (Entry<Double, Double> entry : mapLogRank.entrySet()) { pValueThresholds[count] = entry.getKey(); pValues[count] = entry.getValue(); if (setObserved.contains(entry.getKey())) pValueThresholdsObserved[count] = true; count++; } // Find the longest 'significant' stretch int maxSigCount = 0; int maxSigInd = -1; int sigCurrent = 0; int[] sigCount = new int[pValues.length]; for (int i = 0; i < pValues.length; i++) { if (pValues[i] < 0.05) { sigCurrent++; sigCount[i] = sigCurrent; if (sigCurrent > maxSigCount) { maxSigCount = sigCurrent; maxSigInd = i; } } else sigCurrent = 0; } if (maxSigCount == 0) { logger.info("No p-values < 0.05"); } else { double minThresh = maxSigInd - maxSigCount < 0 ? pValueThresholds[0] - 0.0000001 : pValueThresholds[maxSigInd - maxSigCount]; double maxThresh = pValueThresholds[maxSigInd]; int nBetween = 0; int nBetweenObserved = 0; for (int i = 0; i < newScoreData.scores.length; i++) { if (newScoreData.scores[i] > minThresh && newScoreData.scores[i] <= maxThresh) { nBetween++; if (newScoreData.survival[i] < censorThreshold && !newScoreData.censored[i]) nBetweenObserved++; } } logger.info("Longest stretch of p-values < 0.05: {} - {} ({} entries, {} observed)", minThresh, maxThresh, nBetween, nBetweenObserved); } pValuesSmoothed = new double[pValues.length]; Arrays.fill(pValuesSmoothed, Double.NaN); int n = (pValues.length / 20) * 2 + 1; logger.info("Smoothing log-rank test p-values by " + n); for (int i = n / 2; i < pValues.length - n / 2; i++) { double sum = 0; for (int k = i - n / 2; k < i - n / 2 + n; k++) { sum += pValues[k]; } pValuesSmoothed[i] = sum / n; } // for (int i = 0; i < pValues.length; i++) { // double sum = 0; // for (int k = Math.max(0, i-n/2); k < Math.min(pValues.length, i-n/2+n); k++) { // sum += pValues[k]; // } // pValuesSmoothed[i] = sum/n; // } // pValues = pValuesSmoothed; lastPValueCensorThreshold = censorThreshold; pValuesChanged = true; } } else { lastPValueCensorThreshold = Double.NaN; pValueThresholds = null; pValues = null; } // if (params != null && !Double.isNaN(bestThreshold) && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"))) if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"))) { int bestIdx = -1; double bestPValue = Double.POSITIVE_INFINITY; for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) { if (pValues[i] < bestPValue) { bestIdx = i; bestPValue = pValues[i]; } } thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0]; } else if (params != null && (params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest smoothed p-value"))) { int bestIdx = -1; double bestPValue = Double.POSITIVE_INFINITY; for (int i = pValueThresholds.length / 10; i < pValueThresholds.length * 9 / 10; i++) { if (pValuesSmoothed[i] < bestPValue) { bestIdx = i; bestPValue = pValuesSmoothed[i]; } } thresholds = bestIdx >= 0 ? new double[] { pValueThresholds[bestIdx] } : new double[0]; } // Split into different curves using the provided thresholds List<KaplanMeierData> kms = splitByThresholds(newScoreData, thresholds, censorThreshold, params != null && "Quartiles".equals(params.getChoiceParameterValue("scoreThresholdMethod"))); // for (KaplanMeier km : kms) // km.censorAtTime(censorThreshold); //// kmHigh.censorAtTime(censorThreshold); //// kmLow.censorAtTime(censorThreshold); // logger.info("High: " + kmHigh.toString()); // logger.info("Low: " + kmLow.toString()); // logger.info("Log rank comparison: {}", LogRankTest.computeLogRankTest(kmLow, kmHigh)); if (plotter == null) { plotter = new KaplanMeierChartWrapper(survivalColumn + " time"); // plotter.setBorder(BorderFactory.createTitledBorder("Survival plot")); // plotter.getCanvas().setWidth(300); // plotter.getCanvas().setHeight(300); } KaplanMeierData[] kmArray = new KaplanMeierData[kms.size()]; plotter.setKaplanMeierCurves(survivalColumn + " time", kms.toArray(kmArray)); tableModel.setSurvivalCurves(thresholds, params != null && params.getChoiceParameterValue("scoreThresholdMethod").equals("Lowest p-value"), kmArray); // Bar width determined using 'Freedman and Diaconis' rule' (but overridden if this gives < 16 bins...) double barWidth = (2 * q3 - q1) * Math.pow(numNonNaN, -1.0 / 3.0); int nBins = 100; if (!Double.isNaN(barWidth)) barWidth = (int) Math.max(16, Math.ceil((maxVal - minVal) / barWidth)); Histogram histogram = scoresValid ? new Histogram(newScoreData.scores, nBins) : null; if (histogramPanel == null) { GridPane paneHistogram = new GridPane(); histogramPanel = new HistogramPanelFX(); histogramPanel.getChart().setAnimated(false); histogramWrapper = new ThresholdedChartWrapper(histogramPanel.getChart()); for (ObservableNumberValue val : threshProperties) histogramWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128)); histogramWrapper.getPane().setPrefHeight(150); paneHistogram.add(histogramWrapper.getPane(), 0, 0); Tooltip.install(histogramPanel.getChart(), new Tooltip("Distribution of scores")); GridPane.setHgrow(histogramWrapper.getPane(), Priority.ALWAYS); GridPane.setVgrow(histogramWrapper.getPane(), Priority.ALWAYS); NumberAxis xAxis = new NumberAxis(); xAxis.setLabel("Score threshold"); NumberAxis yAxis = new NumberAxis(); yAxis.setLowerBound(0); yAxis.setUpperBound(1); yAxis.setTickUnit(0.1); yAxis.setAutoRanging(false); yAxis.setLabel("P-value"); chartPValues = new LineChart<>(xAxis, yAxis); chartPValues.setAnimated(false); chartPValues.setLegendVisible(false); // Make chart so it can be navigated ChartToolsFX.makeChartInteractive(chartPValues, xAxis, yAxis); pValuesChanged = true; Tooltip.install(chartPValues, new Tooltip( "Distribution of p-values (log-rank test) comparing low vs. high for all possible score thresholds")); // chartPValues.getYAxis().setAutoRanging(false); pValuesWrapper = new ThresholdedChartWrapper(chartPValues); for (ObservableNumberValue val : threshProperties) pValuesWrapper.addThreshold(val, ColorToolsFX.getCachedColor(240, 0, 0, 128)); pValuesWrapper.getPane().setPrefHeight(150); paneHistogram.add(pValuesWrapper.getPane(), 0, 1); GridPane.setHgrow(pValuesWrapper.getPane(), Priority.ALWAYS); GridPane.setVgrow(pValuesWrapper.getPane(), Priority.ALWAYS); ContextMenu popup = new ContextMenu(); ChartToolsFX.addChartExportMenu(chartPValues, popup); RadioMenuItem miZoomY1 = new RadioMenuItem("0-1"); miZoomY1.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(1); yAxis.setTickUnit(0.2); }); RadioMenuItem miZoomY05 = new RadioMenuItem("0-0.5"); miZoomY05.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.5); yAxis.setTickUnit(0.1); }); RadioMenuItem miZoomY02 = new RadioMenuItem("0-0.2"); miZoomY02.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.2); yAxis.setTickUnit(0.05); }); RadioMenuItem miZoomY01 = new RadioMenuItem("0-0.1"); miZoomY01.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.1); yAxis.setTickUnit(0.05); }); RadioMenuItem miZoomY005 = new RadioMenuItem("0-0.05"); miZoomY005.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.05); yAxis.setTickUnit(0.01); }); RadioMenuItem miZoomY001 = new RadioMenuItem("0-0.01"); miZoomY001.setOnAction(e -> { yAxis.setAutoRanging(false); yAxis.setUpperBound(0.01); yAxis.setTickUnit(0.005); }); ToggleGroup tgZoom = new ToggleGroup(); miZoomY1.setToggleGroup(tgZoom); miZoomY05.setToggleGroup(tgZoom); miZoomY02.setToggleGroup(tgZoom); miZoomY01.setToggleGroup(tgZoom); miZoomY005.setToggleGroup(tgZoom); miZoomY001.setToggleGroup(tgZoom); Menu menuZoomY = new Menu("Set y-axis range"); menuZoomY.getItems().addAll(miZoomY1, miZoomY05, miZoomY02, miZoomY01, miZoomY005, miZoomY001); MenuItem miCopyData = new MenuItem("Copy chart data"); miCopyData.setOnAction(e -> { String dataString = ChartToolsFX.getChartDataAsString(chartPValues); ClipboardContent content = new ClipboardContent(); content.putString(dataString); Clipboard.getSystemClipboard().setContent(content); }); popup.getItems().addAll(miCopyData, menuZoomY); chartPValues.setOnContextMenuRequested(e -> { popup.show(chartPValues, e.getScreenX(), e.getScreenY()); }); for (int col = 0; col < tableModel.getColumnCount(); col++) { TableColumn<Integer, String> column = new TableColumn<>(tableModel.getColumnName(col)); int colNumber = col; column.setCellValueFactory( new Callback<CellDataFeatures<Integer, String>, ObservableValue<String>>() { @Override public ObservableValue<String> call(CellDataFeatures<Integer, String> p) { return new SimpleStringProperty( (String) tableModel.getValueAt(p.getValue(), colNumber)); } }); column.setCellFactory(new Callback<TableColumn<Integer, String>, TableCell<Integer, String>>() { @Override public TableCell<Integer, String> call(TableColumn<Integer, String> param) { TableCell<Integer, String> cell = new TableCell<Integer, String>() { @Override protected void updateItem(String item, boolean empty) { super.updateItem(item, empty); setText(item); setTooltip(new Tooltip(item)); } }; return cell; } }); table.getColumns().add(column); } table.setPrefHeight(250); table.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY); table.maxHeightProperty().bind(table.prefHeightProperty()); params = new ParameterList(); // maxTimePoint = 0; // for (TMACoreObject core : hierarchy.getTMAGrid().getTMACoreList()) { // double os = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_OVERALL_SURVIVAL); // double rfs = core.getMeasurementList().getMeasurementValue(TMACoreObject.KEY_RECURRENCE_FREE_SURVIVAL); // if (os > maxTimePoint) // maxTimePoint = os; // if (rfs > maxTimePoint) // maxTimePoint = rfs; // } params.addIntParameter("censorTimePoints", "Max censored time", (int) (censorThreshold + 0.5), null, 0, (int) Math.ceil(maxTimePoint), "Latest time point beyond which data will be censored"); // params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Manual", Arrays.asList("Manual", "Median", "Log-rank test")); if (calculateAllPValues) // Don't include "Lowest smoothed p-value" - it's not an established method and open to misinterpretation... params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value")); // params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles", "Lowest p-value", "Lowest smoothed p-value")); else params.addChoiceParameter("scoreThresholdMethod", "Threshold method", "Median", Arrays.asList("Manual (1)", "Manual (2)", "Manual (3)", "Median", "Tertiles", "Quartiles")); params.addDoubleParameter("threshold1", "Threshold 1", thresholds.length > 0 ? thresholds[0] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups"); params.addDoubleParameter("threshold2", "Threshold 2", thresholds.length > 1 ? thresholds[1] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups"); params.addDoubleParameter("threshold3", "Threshold 3", thresholds.length > 2 ? thresholds[2] : (minVal + maxVal) / 2, null, "Threshold to distinguish between patient groups"); params.addBooleanParameter("showAtRisk", "Show at risk", plotter.getShowAtRisk(), "Show number of patients at risk below the plot"); params.addBooleanParameter("showTicks", "Show censored ticks", plotter.getShowCensoredTicks(), "Show ticks to indicate censored data"); params.addBooleanParameter("showKey", "Show key", plotter.getShowKey(), "Show key indicating display of each curve"); // params.addBooleanParameter("useColor", "Use color", plotter.getUseColor(), "Show each curve in a different color"); // params.addBooleanParameter("useStrokes", "Use strokes", plotter.getUseStrokes(), "Show each curve with a differed line stroke"); // Hide threshold parameters if threshold can't be used if (!scoresValid) { // params.setHiddenParameters(true, "scoreThresholdMethod", "scoreThreshold"); histogramPanel.getChart().setVisible(false); } panelParams = new ParameterPanelFX(params); panelParams.addParameterChangeListener(this); updateThresholdsEnabled(); for (int i = 0; i < threshProperties.length; i++) { String p = "threshold" + (i + 1); threshProperties[i].addListener((v, o, n) -> { if (interactiveThresholds()) { // Need to do a decent double check with tolerance to text field value changing while typing if (!GeneralTools.almostTheSame(params.getDoubleParameterValue(p), n.doubleValue(), 0.0001)) panelParams.setNumericParameterValue(p, n); } }); } BorderPane paneBottom = new BorderPane(); TitledPane paneOptions = new TitledPane("Options", panelParams.getPane()); // paneOptions.setCollapsible(false); Pane paneCanvas = new StackPane(); paneCanvas.getChildren().add(plotter.getCanvas()); GridPane paneLeft = new GridPane(); paneLeft.add(paneOptions, 0, 0); paneLeft.add(table, 0, 1); GridPane.setHgrow(paneOptions, Priority.ALWAYS); GridPane.setHgrow(table, Priority.ALWAYS); paneBottom.setLeft(paneLeft); paneBottom.setCenter(paneHistogram); paneMain.setCenter(paneCanvas); paneMain.setBottom(paneBottom); paneMain.setPadding(new Insets(10, 10, 10, 10)); } else if (thresholds.length > 0) { // Ensure the sliders/text fields are set sensibly if (!GeneralTools.almostTheSame(thresholds[0], params.getDoubleParameterValue("threshold1"), 0.0001)) { panelParams.setNumericParameterValue("threshold1", thresholds[0]); } if (thresholds.length > 1 && !GeneralTools.almostTheSame(thresholds[1], params.getDoubleParameterValue("threshold2"), 0.0001)) { panelParams.setNumericParameterValue("threshold2", thresholds[1]); } if (thresholds.length > 2 && !GeneralTools.almostTheSame(thresholds[2], params.getDoubleParameterValue("threshold3"), 0.0001)) { panelParams.setNumericParameterValue("threshold3", thresholds[2]); } } if (histogram != null) { histogramPanel.getHistogramData() .setAll(HistogramPanelFX.createHistogramData(histogram, false, (Color) null)); histogramPanel.getChart().getXAxis().setLabel(scoreColumn); histogramPanel.getChart().getYAxis().setLabel("Count"); ChartToolsFX.addChartExportMenu(histogramPanel.getChart(), null); // histogramWrapper.setVerticalLines(thresholds, ColorToolsFX.getCachedColor(240, 0, 0, 128)); // Deal with threshold adjustment // histogramWrapper.getThresholds().addListener((Observable o) -> generatePlot()); } if (pValues != null) { // TODO: Raise earlier where p-value calculation is if (pValuesChanged) { ObservableList<XYChart.Data<Number, Number>> data = FXCollections.observableArrayList(); for (int i = 0; i < pValueThresholds.length; i++) { double pValue = pValues[i]; if (Double.isNaN(pValue)) continue; data.add(new XYChart.Data<>(pValueThresholds[i], pValue, pValueThresholdsObserved[i])); } ObservableList<XYChart.Data<Number, Number>> dataSmoothed = null; if (pValuesSmoothed != null) { dataSmoothed = FXCollections.observableArrayList(); for (int i = 0; i < pValueThresholds.length; i++) { double pValueSmoothed = pValuesSmoothed[i]; if (Double.isNaN(pValueSmoothed)) continue; dataSmoothed.add(new XYChart.Data<>(pValueThresholds[i], pValueSmoothed)); } } // Don't bother showing the smoothed data... it tends to get in the way... // if (dataSmoothed != null) // chartPValues.getData().setAll(new XYChart.Series<>("P-values", data), new XYChart.Series<>("Smoothed P-values", dataSmoothed)); // else chartPValues.getData().setAll(new XYChart.Series<>("P-values", data)); // Add line to show 0.05 significance threshold if (pValueThresholds.length > 1) { Data<Number, Number> sigData1 = new Data<>(pValueThresholds[0], 0.05); Data<Number, Number> sigData2 = new Data<>(pValueThresholds[pValueThresholds.length - 1], 0.05); XYChart.Series<Number, Number> dataSignificant = new XYChart.Series<>("Signficance 0.05", FXCollections.observableArrayList(sigData1, sigData2)); chartPValues.getData().add(dataSignificant); sigData1.getNode().setVisible(false); sigData2.getNode().setVisible(false); } // chartPValues.getData().get(0).getNode().setVisible(true); // pValuesWrapper.clearThresholds(); for (XYChart.Data<Number, Number> dataPoint : data) { if (!Boolean.TRUE.equals(dataPoint.getExtraValue())) dataPoint.getNode().setVisible(false); } // if (dataSmoothed != null) { // for (XYChart.Data<Number, Number> dataPoint : dataSmoothed) { // dataPoint.getNode().setVisible(false); // } // chartPValues.getData().get(1).getNode().setOpacity(0.5); // } // int count = 0; // for (int i = 0; i < pValueThresholds.length; i++) { // double pValue = pValues[i]; // if (Double.isNaN(pValue)) // continue; // boolean observed = pValueThresholdsObserved[i]; //// if (observed) //// pValuesWrapper.addThreshold(new ReadOnlyDoubleWrapper(pValueThresholds[i]), Color.rgb(0, 0, 0, 0.05)); // // if (!observed) { //// StackPane pane = (StackPane)data.get(count).getNode(); //// pane.setEffect(new DropShadow()); // data.get(count).getNode().setVisible(false); // } // count++; // } } for (int i = 0; i < threshProperties.length; i++) { if (i < thresholds.length) threshProperties[i].set(thresholds[i]); else threshProperties[i].set(Double.NaN); } boolean isInteractive = interactiveThresholds(); histogramWrapper.setIsInteractive(isInteractive); pValuesWrapper.setIsInteractive(isInteractive); chartPValues.setVisible(true); } // else // chartPValues.setVisible(false); // Store values for next time scoreData = newScoreData; }
From source file:com.neuronrobotics.bowlerstudio.MainController.java
private void setToLoggedIn(final String name) { // new Exception().printStackTrace(); FxTimer.runLater(Duration.ofMillis(100), () -> { logoutGithub.disableProperty().set(false); logoutGithub.setText("Log out " + name); new Thread() { public void run() { GitHub github = ScriptingEngine.getGithub(); while (github == null) { github = ScriptingEngine.getGithub(); ThreadUtil.wait(20); }/*from ww w . ja v a2 s .c o m*/ try { GHMyself myself = github.getMyself(); PagedIterable<GHGist> gists = myself.listGists(); Platform.runLater(() -> { myGists.getItems().clear(); }); ThreadUtil.wait(20); for (GHGist gist : gists) { String desc = gist.getDescription(); if (desc == null || desc.length() == 0) { desc = gist.getFiles().keySet().toArray()[0].toString(); } Menu tmpGist = new Menu(desc); MenuItem loadWebGist = new MenuItem("Show Web Gist..."); loadWebGist.setOnAction(event -> { String webURL = gist.getHtmlUrl(); try { BowlerStudio.openUrlInNewTab(new URL(webURL)); } catch (MalformedURLException e) { // TODO Auto-generated catch block e.printStackTrace(); } }); MenuItem addFile = new MenuItem("Add file to Gist..."); addFile.setOnAction(event -> { new Thread() { public void run() { } }.start(); }); Platform.runLater(() -> { tmpGist.getItems().addAll(addFile, loadWebGist); }); EventHandler<Event> loadFiles = new EventHandler<Event>() { @Override public void handle(Event ev) { // for(ScriptingEngine.) new Thread() { public void run() { System.out.println("Loading files"); ArrayList<String> listofFiles = ScriptingEngine .filesInGit(gist.getGitPushUrl(), "master", null); for (String s : listofFiles) { MenuItem tmp = new MenuItem(s); tmp.setOnAction(event -> { new Thread() { public void run() { try { File fileSelected = ScriptingEngine .fileFromGit(gist.getGitPushUrl(), s); BowlerStudio.createFileTab(fileSelected); } catch (Exception e) { // TODO // Auto-generated // catch block e.printStackTrace(); } } }.start(); }); Platform.runLater(() -> { tmpGist.getItems().add(tmp); tmpGist.setOnShowing(null); }); } Platform.runLater(() -> { tmpGist.hide(); Platform.runLater(() -> { tmpGist.show(); }); }); } }.start(); } }; tmpGist.setOnShowing(loadFiles); Platform.runLater(() -> { myGists.getItems().add(tmpGist); }); } } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } }.start(); }); }
From source file:de.pixida.logtest.designer.MainWindow.java
private void createAndAppendHelpMenuItems(final Menu help) { final MenuItem visitDocumentation = new MenuItem("Visit Online Documentation"); visitDocumentation.setGraphic(Icons.getIconGraphics("help")); visitDocumentation.setOnAction(event -> { Exception ex = null;/*from w ww. j av a2 s. co m*/ final String url = "https://github.com/Pixida/logtest/wiki"; final Desktop desktop = java.awt.Desktop.getDesktop(); if (desktop.isSupported(java.awt.Desktop.Action.BROWSE)) { try { desktop.browse(new URI(url)); } catch (final Exception e) { ex = e; } } else { ex = new Exception("Browsing not supported."); } if (ex != null) { ExceptionDialog.showFatalException("Failed to open browser", "Visit us at " + url, ex); } }); final MenuItem about = new MenuItem("About " + APP_TITLE); about.setGraphic(Icons.getIconGraphics(APP_ICON)); about.setOnAction(event -> { final Alert alert = new Alert(Alert.AlertType.INFORMATION); alert.initStyle(StageStyle.UTILITY); alert.setTitle(about.getText()); alert.setHeaderText(APP_TITLE); alert.setContentText("Copyright (C) " + Calendar.getInstance().get(Calendar.YEAR) + " Pixida GmbH\n" + "\n" + "This application includes FAMFAMFAM icons (http://www.famfamfam.com)."); alert.showAndWait(); }); help.getItems().addAll(visitDocumentation, about); }
From source file:qupath.lib.gui.tma.TMASummaryViewer.java
private void initialize() { model = new TMATableModel(); groupByIDProperty.addListener((v, o, n) -> refreshTableData()); MenuBar menuBar = new MenuBar(); Menu menuFile = new Menu("File"); MenuItem miOpen = new MenuItem("Open..."); miOpen.setAccelerator(new KeyCodeCombination(KeyCode.O, KeyCombination.SHORTCUT_DOWN)); miOpen.setOnAction(e -> {/*from w w w .java 2 s .c o m*/ File file = QuPathGUI.getDialogHelper(stage).promptForFile(null, null, "TMA data files", new String[] { "qptma" }); if (file == null) return; setInputFile(file); }); MenuItem miSave = new MenuItem("Save As..."); miSave.setAccelerator( new KeyCodeCombination(KeyCode.S, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN)); miSave.setOnAction( e -> SummaryMeasurementTableCommand.saveTableModel(model, null, Collections.emptyList())); MenuItem miImportFromImage = new MenuItem("Import from current image..."); miImportFromImage.setAccelerator( new KeyCodeCombination(KeyCode.I, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN)); miImportFromImage.setOnAction(e -> setTMAEntriesFromOpenImage()); MenuItem miImportFromProject = new MenuItem("Import from current project... (experimental)"); miImportFromProject.setAccelerator( new KeyCodeCombination(KeyCode.P, KeyCombination.SHORTCUT_DOWN, KeyCombination.SHIFT_DOWN)); miImportFromProject.setOnAction(e -> setTMAEntriesFromOpenProject()); MenuItem miImportClipboard = new MenuItem("Import from clipboard..."); miImportClipboard.setOnAction(e -> { String text = Clipboard.getSystemClipboard().getString(); if (text == null) { DisplayHelpers.showErrorMessage("Import scores", "Clipboard is empty!"); return; } int n = importScores(text); if (n > 0) { setTMAEntries(new ArrayList<>(entriesBase)); } DisplayHelpers.showMessageDialog("Import scores", "Number of scores imported: " + n); }); Menu menuEdit = new Menu("Edit"); MenuItem miCopy = new MenuItem("Copy table to clipboard"); miCopy.setOnAction(e -> { SummaryMeasurementTableCommand.copyTableContentsToClipboard(model, Collections.emptyList()); }); combinedPredicate.addListener((v, o, n) -> { // We want any other changes triggered by this to have happened, // so that the data has already been updated Platform.runLater(() -> handleTableContentChange()); }); // Reset the scores for missing cores - this ensures they will be NaN and not influence subsequent results MenuItem miResetMissingScores = new MenuItem("Reset scores for missing cores"); miResetMissingScores.setOnAction(e -> { int changes = 0; for (TMAEntry entry : entriesBase) { if (!entry.isMissing()) continue; boolean changed = false; for (String m : entry.getMeasurementNames().toArray(new String[0])) { if (!TMASummaryEntry.isSurvivalColumn(m) && !Double.isNaN(entry.getMeasurementAsDouble(m))) { entry.putMeasurement(m, null); changed = true; } } if (changed) changes++; } if (changes == 0) { logger.info("No changes made when resetting scores for missing cores!"); return; } logger.info("{} change(s) made when resetting scores for missing cores!", changes); table.refresh(); updateSurvivalCurves(); if (scatterPane != null) scatterPane.updateChart(); if (histogramDisplay != null) histogramDisplay.refreshHistogram(); }); menuEdit.getItems().add(miResetMissingScores); QuPathGUI.addMenuItems(menuFile, miOpen, miSave, null, miImportClipboard, null, miImportFromImage, miImportFromProject); menuBar.getMenus().add(menuFile); menuEdit.getItems().add(miCopy); menuBar.getMenus().add(menuEdit); menuFile.setOnShowing(e -> { boolean imageDataAvailable = QuPathGUI.getInstance() != null && QuPathGUI.getInstance().getImageData() != null && QuPathGUI.getInstance().getImageData().getHierarchy().getTMAGrid() != null; miImportFromImage.setDisable(!imageDataAvailable); boolean projectAvailable = QuPathGUI.getInstance() != null && QuPathGUI.getInstance().getProject() != null && !QuPathGUI.getInstance().getProject().getImageList().isEmpty(); miImportFromProject.setDisable(!projectAvailable); }); // Double-clicking previously used for comments... but conflicts with tree table expansion // table.setOnMouseClicked(e -> { // if (!e.isPopupTrigger() && e.getClickCount() > 1) // promptForComment(); // }); table.setPlaceholder(new Text("Drag TMA data folder onto window, or choose File -> Open")); table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE); BorderPane pane = new BorderPane(); pane.setTop(menuBar); menuBar.setUseSystemMenuBar(true); // Create options ToolBar toolbar = new ToolBar(); Label labelMeasurementMethod = new Label("Combination method"); labelMeasurementMethod.setLabelFor(comboMeasurementMethod); labelMeasurementMethod .setTooltip(new Tooltip("Method whereby measurements for multiple cores with the same " + TMACoreObject.KEY_UNIQUE_ID + " will be combined")); CheckBox cbHidePane = new CheckBox("Hide pane"); cbHidePane.setSelected(hidePaneProperty.get()); cbHidePane.selectedProperty().bindBidirectional(hidePaneProperty); CheckBox cbGroupByID = new CheckBox("Group by ID"); entriesBase.addListener((Change<? extends TMAEntry> event) -> { if (!event.getList().stream().anyMatch(e -> e.getMetadataValue(TMACoreObject.KEY_UNIQUE_ID) != null)) { cbGroupByID.setSelected(false); cbGroupByID.setDisable(true); } else { cbGroupByID.setDisable(false); } }); cbGroupByID.setSelected(groupByIDProperty.get()); cbGroupByID.selectedProperty().bindBidirectional(groupByIDProperty); CheckBox cbUseSelected = new CheckBox("Use selection only"); cbUseSelected.selectedProperty().bindBidirectional(useSelectedProperty); CheckBox cbSkipMissing = new CheckBox("Hide missing cores"); cbSkipMissing.selectedProperty().bindBidirectional(skipMissingCoresProperty); skipMissingCoresProperty.addListener((v, o, n) -> { table.refresh(); updateSurvivalCurves(); if (histogramDisplay != null) histogramDisplay.refreshHistogram(); updateSurvivalCurves(); if (scatterPane != null) scatterPane.updateChart(); }); toolbar.getItems().addAll(labelMeasurementMethod, comboMeasurementMethod, new Separator(Orientation.VERTICAL), cbHidePane, new Separator(Orientation.VERTICAL), cbGroupByID, new Separator(Orientation.VERTICAL), cbUseSelected, new Separator(Orientation.VERTICAL), cbSkipMissing); comboMeasurementMethod.getItems().addAll(MeasurementCombinationMethod.values()); comboMeasurementMethod.getSelectionModel().select(MeasurementCombinationMethod.MEDIAN); selectedMeasurementCombinationProperty.addListener((v, o, n) -> table.refresh()); ContextMenu popup = new ContextMenu(); MenuItem miSetMissing = new MenuItem("Set missing"); miSetMissing.setOnAction(e -> setSelectedMissingStatus(true)); MenuItem miSetAvailable = new MenuItem("Set available"); miSetAvailable.setOnAction(e -> setSelectedMissingStatus(false)); MenuItem miExpand = new MenuItem("Expand all"); miExpand.setOnAction(e -> { if (table.getRoot() == null) return; for (TreeItem<?> item : table.getRoot().getChildren()) { item.setExpanded(true); } }); MenuItem miCollapse = new MenuItem("Collapse all"); miCollapse.setOnAction(e -> { if (table.getRoot() == null) return; for (TreeItem<?> item : table.getRoot().getChildren()) { item.setExpanded(false); } }); popup.getItems().addAll(miSetMissing, miSetAvailable, new SeparatorMenuItem(), miExpand, miCollapse); table.setContextMenu(popup); table.setRowFactory(e -> { TreeTableRow<TMAEntry> row = new TreeTableRow<>(); // // Make rows invisible if they don't pass the predicate // row.visibleProperty().bind(Bindings.createBooleanBinding(() -> { // TMAEntry entry = row.getItem(); // if (entry == null || (entry.isMissing() && skipMissingCoresProperty.get())) // return false; // return entries.getPredicate() == null || entries.getPredicate().test(entry); // }, // skipMissingCoresProperty, // entries.predicateProperty())); // Style rows according to what they contain row.styleProperty().bind(Bindings.createStringBinding(() -> { if (row.isSelected()) return ""; TMAEntry entry = row.getItem(); if (entry == null || entry instanceof TMASummaryEntry) return ""; else if (entry.isMissing()) return "-fx-background-color:rgb(225,225,232)"; else return "-fx-background-color:rgb(240,240,245)"; }, row.itemProperty(), row.selectedProperty())); // row.itemProperty().addListener((v, o, n) -> { // if (n == null || n instanceof TMASummaryEntry || row.isSelected()) // row.setStyle(""); // else if (n.isMissing()) // row.setStyle("-fx-background-color:rgb(225,225,232)"); // else // row.setStyle("-fx-background-color:rgb(240,240,245)"); // }); return row; }); BorderPane paneTable = new BorderPane(); paneTable.setTop(toolbar); paneTable.setCenter(table); MasterDetailPane mdTablePane = new MasterDetailPane(Side.RIGHT, paneTable, createSidePane(), true); mdTablePane.showDetailNodeProperty().bind(Bindings.createBooleanBinding( () -> !hidePaneProperty.get() && !entriesBase.isEmpty(), hidePaneProperty, entriesBase)); mdTablePane.setDividerPosition(2.0 / 3.0); pane.setCenter(mdTablePane); model.getEntries().addListener(new ListChangeListener<TMAEntry>() { @Override public void onChanged(ListChangeListener.Change<? extends TMAEntry> c) { if (histogramDisplay != null) histogramDisplay.refreshHistogram(); updateSurvivalCurves(); if (scatterPane != null) scatterPane.updateChart(); } }); Label labelPredicate = new Label(); labelPredicate.setPadding(new Insets(5, 5, 5, 5)); labelPredicate.setAlignment(Pos.CENTER); // labelPredicate.setStyle("-fx-background-color: rgba(20, 120, 20, 0.15);"); labelPredicate.setStyle("-fx-background-color: rgba(120, 20, 20, 0.15);"); labelPredicate.textProperty().addListener((v, o, n) -> { if (n.trim().length() > 0) pane.setBottom(labelPredicate); else pane.setBottom(null); }); labelPredicate.setMaxWidth(Double.MAX_VALUE); labelPredicate.setMaxHeight(labelPredicate.getPrefHeight()); labelPredicate.setTextAlignment(TextAlignment.CENTER); predicateMeasurements.addListener((v, o, n) -> { if (n == null) labelPredicate.setText(""); else if (n instanceof TablePredicate) { TablePredicate tp = (TablePredicate) n; if (tp.getOriginalCommand().trim().isEmpty()) labelPredicate.setText(""); else labelPredicate.setText("Predicate: " + tp.getOriginalCommand()); } else labelPredicate.setText("Predicate: " + n.toString()); }); // predicate.set(new TablePredicate("\"Tumor\" > 100")); scene = new Scene(pane); scene.addEventHandler(KeyEvent.KEY_PRESSED, e -> { KeyCode code = e.getCode(); if ((code == KeyCode.SPACE || code == KeyCode.ENTER) && entrySelected != null) { promptForComment(); return; } }); }