Examples with MenuItem javafx.scene.control.MenuItem used on opensource projects

Example 41 with MenuItem

use of javafx.scene.control.MenuItem in project MiscellaneousStudy by mikoto2000.

the class ContextMenuSampleController method showContextMenu.

@FXML
public void showContextMenu(MouseEvent event) {
    ContextMenu cm = new ContextMenu();
    List<MenuItem> items = cm.getItems();
    MenuItem item1 = new MenuItem("Context Menu Item 1(instant)");
    item1.setOnAction((ActionEvent e) -> System.out.println("Clicked Context Menu Item 1"));
    items.add(item1);
    MenuItem item2 = new MenuItem("Context Menu Item 2(instant)");
    item2.setOnAction((ActionEvent e) -> System.out.println("Clicked Context Menu Item 2"));
    items.add(item2);
    MenuItem item3 = new MenuItem("Context Menu Item 3(instant)");
    item3.setOnAction((ActionEvent e) -> System.out.println("Clicked Context Menu Item 3"));
    items.add(item3);
    if (currentCm != null) {
        currentCm.hide();
    }
    currentCm = cm;
    cm.show(hbox, event.getScreenX(), event.getScreenY());
}

Example 42 with MenuItem

use of javafx.scene.control.MenuItem in project jvarkit by lindenb.

the class IgvReview method start.

@Override
public void start(final Stage stage) throws Exception {
    stage.setTitle(getClass().getSimpleName());
    Predicate<VariantContext> ctxFilter;
    Map<String, String> params = super.getParameters().getNamed();
    if (params.containsKey("--filter")) {
        ctxFilter = JexlVariantPredicate.create(params.get("--filter"));
    } else {
        ctxFilter = V -> true;
    }
    final List<String> args = super.getParameters().getUnnamed();
    final File configFile;
    if (args.isEmpty()) {
        final FileChooser fc = new FileChooser();
        final String lastDirStr = preferences.get(LAST_USED_DIR_KEY, null);
        if (lastDirStr != null && !lastDirStr.isEmpty()) {
            fc.setInitialDirectory(new File(lastDirStr));
        }
        fc.getExtensionFilters().addAll(Collections.singletonList(new FileChooser.ExtensionFilter("Config file", "*.config", "*.cfg", "*.list")));
        configFile = fc.showOpenDialog(stage);
    } else if (args.size() == 1) {
        configFile = new File(args.get(0));
    } else {
        configFile = null;
    }
    if (configFile == null || !configFile.exists()) {
        JfxUtils.dialog().cause("Illegal number of arguments or file doesn't exists.").show(stage);
        Platform.exit();
        return;
    }
    if (configFile.isFile() && configFile.getParentFile() != null) {
        this.preferences.put(LAST_USED_DIR_KEY, configFile.getParentFile().getPath());
    }
    final List<String> configLines = Files.readAllLines(configFile.toPath());
    final Predicate<String> ignoreComment = (S) -> !S.startsWith("#");
    final Predicate<String> predVcf = S -> S.endsWith(".vcf") || S.endsWith(".vcf.gz");
    if (configLines.stream().filter(ignoreComment).filter(predVcf).count() != 1) {
        JfxUtils.dialog().cause("Found more than one vcf file in " + configFile).show(stage);
        Platform.exit();
        return;
    }
    final File vcfFile = configLines.stream().filter(ignoreComment).filter(predVcf).map(S -> new File(S)).findFirst().get();
    LOG.info("Opening vcf file and loading in memory");
    VCFFileReader vfr = null;
    CloseableIterator<VariantContext> iter = null;
    final Set<String> sampleNames;
    try {
        this.variants.clear();
        vfr = new VCFFileReader(vcfFile, false);
        this.vcfHeader = vfr.getFileHeader();
        sampleNames = new HashSet<>(this.vcfHeader.getSampleNamesInOrder());
        if (sampleNames.isEmpty()) {
            JfxUtils.dialog().cause("No Genotypes in " + vcfFile).show(stage);
            Platform.exit();
            return;
        }
        iter = vfr.iterator();
        this.variants.addAll(iter.stream().filter(ctxFilter).filter(CTX -> CTX.isVariant()).collect(Collectors.toList()));
    } catch (final Exception err) {
        JfxUtils.dialog().cause(err).show(stage);
        Platform.exit();
        return;
    } finally {
        CloserUtil.close(iter);
        CloserUtil.close(vfr);
    }
    if (this.variants.isEmpty()) {
        JfxUtils.dialog().cause("No Variants").show(stage);
        Platform.exit();
        return;
    }
    final SAMSequenceDictionary dict = this.vcfHeader.getSequenceDictionary();
    if (dict == null || dict.isEmpty()) {
        JfxUtils.dialog().cause(JvarkitException.VcfDictionaryMissing.getMessage(vcfFile.getPath())).show(stage);
        Platform.exit();
        return;
    }
    final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
    configLines.stream().filter(ignoreComment).filter(S -> S.endsWith(".bam")).map(S -> new File(S)).forEach(F -> {
        final SamReader samIn = srf.open(F);
        final SAMFileHeader header = samIn.getFileHeader();
        CloserUtil.close(samIn);
        String sample = null;
        for (final SAMReadGroupRecord rg : header.getReadGroups()) {
            String s = rg.getSample();
            if (s == null)
                continue;
            if (sample == null) {
                sample = s;
            } else if (!sample.equals(s)) {
                JfxUtils.dialog().cause("Two samples in " + F).show(stage);
                Platform.exit();
                return;
            }
        }
        if (sample == null) {
            JfxUtils.dialog().cause("No sample in " + F + ". Ignoring").show(stage);
            return;
        }
        if (!sampleNames.contains(sample)) {
            JfxUtils.dialog().cause("Not in VCF header " + sample + " / " + F + ". Ignoring").show(stage);
            return;
        }
        this.sample2bamFile.put(sample, F);
    });
    if (this.sample2bamFile.isEmpty()) {
        JfxUtils.dialog().cause("No valid bam file in " + configFile).show(stage);
        return;
    }
    sampleNames.retainAll(this.sample2bamFile.keySet());
    if (sampleNames.isEmpty()) {
        JfxUtils.dialog().cause("No Sample associated to bam").show(stage);
        return;
    }
    ObservableList<VariantAndGenotype> genotypes = FXCollections.observableArrayList(this.variants.stream().flatMap(CTX -> CTX.getGenotypes().stream().filter(G -> sampleNames.contains(G.getSampleName())).map(G -> new VariantAndGenotype(CTX, G))).collect(Collectors.toList()));
    if (genotypes.isEmpty()) {
        JfxUtils.dialog().cause("No Genotype to show").show(stage);
        return;
    }
    Menu menu = new Menu("File");
    MenuItem menuItem = new MenuItem("Save as...");
    menuItem.setOnAction(AE -> {
        saveVariantsAs(stage);
    });
    menu.getItems().add(menuItem);
    menuItem = new MenuItem("Save");
    menuItem.setOnAction(AE -> {
        if (this.saveAsFile != null) {
            saveVariants(stage, this.saveAsFile);
        } else {
            saveVariantsAs(stage);
        }
    });
    menu.getItems().add(menuItem);
    menu.getItems().add(new SeparatorMenuItem());
    menuItem = new MenuItem("Quit");
    menuItem.setOnAction(AE -> {
        Platform.exit();
    });
    menu.getItems().add(menuItem);
    MenuBar bar = new MenuBar(menu);
    this.genotypeTable = new TableView<>(genotypes);
    this.genotypeTable.getColumns().add(makeColumn("CHROM", G -> G.ctx.getContig()));
    this.genotypeTable.getColumns().add(makeColumn("POS", G -> G.ctx.getStart()));
    this.genotypeTable.getColumns().add(makeColumn("ID", G -> G.ctx.getID()));
    this.genotypeTable.getColumns().add(makeColumn("REF", G -> G.ctx.getReference().getDisplayString()));
    this.genotypeTable.getColumns().add(makeColumn("ALT", G -> G.ctx.getAlternateAlleles().stream().map(A -> A.getDisplayString()).collect(Collectors.joining(","))));
    this.genotypeTable.getColumns().add(makeColumn("Sample", G -> G.g.getSampleName()));
    this.genotypeTable.getColumns().add(makeColumn("Type", G -> G.g.getType().name()));
    this.genotypeTable.getColumns().add(makeColumn("Alleles", G -> G.g.getAlleles().stream().map(A -> A.getDisplayString()).collect(Collectors.joining(","))));
    TableColumn<VariantAndGenotype, String> reviewCol = new TableColumn<>("Review");
    reviewCol.setCellValueFactory(C -> C.getValue().getReviewProperty());
    reviewCol.setCellFactory(TextFieldTableCell.forTableColumn());
    reviewCol.setOnEditCommit((E) -> {
        int y = E.getTablePosition().getRow();
        this.genotypeTable.getItems().get(y).setReview(E.getNewValue());
    });
    reviewCol.setEditable(true);
    this.genotypeTable.getColumns().add(reviewCol);
    this.genotypeTable.getSelectionModel().cellSelectionEnabledProperty().set(true);
    this.genotypeTable.setEditable(true);
    final ContextMenu cm = new ContextMenu();
    MenuItem mi1 = new MenuItem("Menu 1");
    cm.getItems().add(mi1);
    MenuItem mi2 = new MenuItem("Menu 2");
    cm.getItems().add(mi2);
    this.genotypeTable.setOnMousePressed(event -> {
        if (event.isPrimaryButtonDown() && (event.getClickCount() == 3 || event.isShiftDown())) {
            moveIgvTo(stage, genotypeTable.getSelectionModel().getSelectedItem());
        } else if (event.isSecondaryButtonDown()) {
            cm.show(genotypeTable, event.getScreenX(), event.getScreenY());
        }
    });
    final BorderPane pane2 = new BorderPane(this.genotypeTable);
    pane2.setPadding(new Insets(10, 10, 10, 10));
    VBox vbox1 = new VBox(bar, pane2);
    final Scene scene = new Scene(vbox1, 500, 300);
    stage.setScene(scene);
    stage.show();
}

Example 43 with MenuItem

use of javafx.scene.control.MenuItem in project jvarkit by lindenb.

the class JfxNgs method createCommonMenuItems.

List<MenuItem> createCommonMenuItems(final Stage stage) {
    final List<MenuItem> L = new ArrayList<>();
    L.add(createMenuItem("About...", () -> doMenuAbout(stage)));
    L.add(createMenuItem("Preferences...", () -> showPreferencesDialog(stage)));
    L.add(createMenuItem("Open in Microsoft Excel...", () -> doMenuOpenInExcel(stage)));
    L.add(new SeparatorMenuItem());
    L.add(createMenuItem("Open VCF/BAM File...", () -> openNgsFile(stage)));
    L.add(createMenuItem("Open Remote BAM...", () -> openBamUrl(stage)));
    L.add(createMenuItem("Open Remote VCF...", () -> openVcfUrl(stage)));
    L.add(new SeparatorMenuItem());
    L.add(createMenuItem("Tool: index BAM file...", () -> doMenuIndexBam(stage)));
    L.add(createMenuItem("Tool: index VCF file...", () -> doMenuIndexVcf(stage)));
    L.add(new SeparatorMenuItem());
    L.add(createMenuItem("Close", () -> stage.hide()));
    return L;
}

Example 44 with MenuItem

use of javafx.scene.control.MenuItem in project jvarkit by lindenb.

the class JfxNgs method start.

/*
    private void showPreferenceDialoge(Window parentStage)
	    {
	    Stage dialog = new Stage();


	     dialog.setTitle("Preferences");
		 dialog.initOwner(parentStage);
		 dialog.initModality(Modality.APPLICATION_MODAL);
		 dialog.showAndWait();
	    }*/
@Override
public void start(final Stage primaryStage) throws Exception {
    final Parameters params = this.getParameters();
    primaryStage.setTitle(getClass().getSimpleName());
    Menu menu = new Menu("File");
    menu.getItems().addAll(createCommonMenuItems(primaryStage));
    menu.getItems().add(new SeparatorMenuItem());
    MenuItem menuItem = new MenuItem("Quit...");
    menuItem.setOnAction(AE -> doMenuQuit());
    menu.getItems().add(menuItem);
    MenuBar bar = new MenuBar(menu);
    FlowPane flow = new FlowPane(5, 5);
    flow.setPadding(new Insets(10));
    flow.getChildren().add(new Label("Set Location of all frames to:"));
    final TextField textField = new TextField();
    textField.setPrefColumnCount(25);
    textField.setPromptText("Location. e:g '2:1234-5678'");
    flow.getChildren().add(textField);
    Button button = new Button("Go");
    flow.getChildren().add(button);
    textField.setTooltip(new Tooltip("set genomic location can be: empty, 'contig', 'contig:pos', 'contig:start-end' and (\"unmapped\" for bam)"));
    final EventHandler<ActionEvent> handler = new EventHandler<ActionEvent>() {

        @Override
        public void handle(final ActionEvent event) {
            final String loc = textField.getText().trim();
            LOG.info("moveTo all to " + loc);
            for (final NgsStage<?, ?> sc : all_opened_stages) {
                LOG.info("moveTo " + sc.getTitle() + " to " + loc);
                sc.moveTo(loc);
            }
        }
    };
    button.setOnAction(handler);
    button.setTooltip(new Tooltip("Go the specified genomic location."));
    textField.setOnAction(handler);
    BorderPane pane = new BorderPane();
    pane.setPadding(new Insets(5));
    pane.setBottom(new Label("Author: Pierre Lindenbaum PhD."));
    VBox vbox1 = new VBox(bar, flow, pane);
    final Scene scene = new Scene(vbox1, 500, 300);
    primaryStage.setScene(scene);
    Exception lastException = null;
    primaryStage.addEventHandler(WindowEvent.WINDOW_SHOWING, new EventHandler<WindowEvent>() {

        @Override
        public void handle(final WindowEvent event) {
            final List<String> unnamedParams = new ArrayList<>(params.getUnnamed());
            String startPos = "";
            int optind = 0;
            while (optind + 1 < unnamedParams.size()) {
                if (unnamedParams.get(optind).equals("-h") || unnamedParams.get(optind).equals("--help")) {
                    unnamedParams.remove(optind);
                    System.out.println("JfxNgs : Pierre Lindenbaum PhD 2017");
                    System.out.println("Options:");
                    System.out.println(" -h|--help this screen.");
                    System.out.println(" -p|--position (string) the starting position");
                    Platform.exit();
                } else if (unnamedParams.get(optind).equals("-p") || unnamedParams.get(optind).equals("--position")) {
                    startPos = unnamedParams.get(optind + 1);
                    unnamedParams.remove(optind + 1);
                    unnamedParams.remove(optind);
                } else {
                    optind++;
                }
            }
            for (final String arg : unnamedParams) {
                VcfFile vcfin = null;
                BamFile bamin = null;
                try {
                    if (IOUtil.isUrl(arg)) {
                        if (arg.endsWith(".bam")) {
                            bamin = BamFile.newInstance(arg);
                        } else if (arg.endsWith(".vcf.gz")) {
                            vcfin = VcfFile.newInstance(arg);
                        }
                    } else {
                        final File f = new File(arg);
                        if (fileMatchExtensionFilter(f.getName(), BamStage.EXTENSION_FILTERS)) {
                            bamin = BamFile.newInstance(f);
                        } else if (fileMatchExtensionFilter(f.getName(), VcfStage.EXTENSION_FILTERS)) {
                            vcfin = VcfFile.newInstance(f);
                        } else {
                            JfxNgs.showExceptionDialog(primaryStage, "Cannot open " + f);
                        }
                    }
                    if (vcfin != null) {
                        new VcfStage(JfxNgs.this, vcfin).setLocationOnOpen(startPos).show();
                    } else if (bamin != null) {
                        new BamStage(JfxNgs.this, bamin).show();
                    }
                } catch (Exception e) {
                    CloserUtil.close(vcfin);
                    CloserUtil.close(bamin);
                    showExceptionDialog(primaryStage, e);
                }
            }
        }
    });
    primaryStage.show();
}

Example 45 with MenuItem

use of javafx.scene.control.MenuItem in project jvarkit by lindenb.

the class NgsStage method createJavascriptSnippetMenu.

/**
 * generate the javascript Menu, containing the snippets.
 * the snippet are stored as a xml file in the jar file
 * @return
 */
protected Menu createJavascriptSnippetMenu() {
    final Menu menu = new Menu("Snippets");
    loadSnippets().stream().filter(C -> C.isFilterScope()).forEach(C -> {
        final MenuItem item = new MenuItem(C.label + (C.function ? "[Function]" : ""));
        item.setOnAction(new EventHandler<ActionEvent>() {

            @Override
            public void handle(ActionEvent event) {
                if (!C.function) {
                    NgsStage.this.javascriptArea.setText(C.code);
                } else {
                    final int caret = NgsStage.this.javascriptArea.getCaretPosition();
                    NgsStage.this.javascriptArea.insertText(caret, C.code);
                }
            }
        });
        menu.getItems().add(item);
    });
    return menu;
}