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

Example 51 with TableColumn

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

the class BamStage method reloadData.

@Override
void reloadData() {
    updateStatusBar(AlertType.NONE, "");
    final int max_items = super.maxItemsLimitSpinner.getValue();
    final List<SAMRecord> L = new ArrayList<SAMRecord>(max_items);
    final String location = this.gotoField.getText().trim();
    final CloseableIterator<SAMRecord> iter;
    final java.util.function.Predicate<SAMRecord> recFilter = makeFlagPredicate();
    Long canvasFirstRecordGenomicIndex = null;
    Long canvasLastRecordGenomicIndex = null;
    try {
        if (location.isEmpty()) {
            iter = this.getBamFile().iterator();
        } else if (location.equalsIgnoreCase("unmapped")) {
            iter = this.getBamFile().queryUnmapped();
        } else {
            final Interval interval = parseInterval(location);
            if (interval == null) {
                iter = null;
            } else {
                iter = this.getBamFile().iterator(interval.getContig(), interval.getStart(), interval.getEnd());
            }
        }
    } catch (final IOException err) {
        err.printStackTrace();
        JfxNgs.showExceptionDialog(this, err);
        return;
    }
    Optional<BamJavascripFilter> bamjsfilter = Optional.empty();
    if (this.owner.javascriptCompiler.isPresent() && !this.javascriptArea.getText().trim().isEmpty()) {
        try {
            bamjsfilter = Optional.of(new BamJavascripFilter(this.getBamFile().getHeader(), Optional.of(this.owner.javascriptCompiler.get().compile(this.javascriptArea.getText()))));
        } catch (final Exception err) {
            LOG.warning(err.getMessage());
            updateStatusBar(AlertType.ERROR, err);
            bamjsfilter = Optional.empty();
        }
    }
    final Map<ContigPos, Pileup> pos2pileup = new TreeMap<>();
    final Function<ContigPos, Pileup> getpileup = new Function<ContigPos, Pileup>() {

        @Override
        public Pileup apply(ContigPos t) {
            Pileup p = pos2pileup.get(t);
            if (p == null) {
                p = new Pileup(t.contig, t.position);
                pos2pileup.put(t, p);
            }
            return p;
        }
    };
    int count_items = 0;
    while (iter != null && iter.hasNext() && count_items < max_items) {
        final SAMRecord rec = iter.next();
        ++count_items;
        if (bamjsfilter.isPresent()) {
            if (bamjsfilter.get().eval(rec) == null)
                continue;
        }
        if (!recFilter.test(rec))
            continue;
        L.add(rec);
        /* get bounds for canvas genmic browser */
        if (!rec.getReadUnmappedFlag() && rec.getCigar() != null) {
            final long endIndex = convertContigPosToGenomicIndex(rec.getContig(), rec.getUnclippedEnd());
            if (canvasFirstRecordGenomicIndex == null) {
                canvasFirstRecordGenomicIndex = convertContigPosToGenomicIndex(rec.getContig(), rec.getUnclippedStart());
                canvasLastRecordGenomicIndex = endIndex;
            } else if (canvasLastRecordGenomicIndex < endIndex) {
                canvasLastRecordGenomicIndex = endIndex;
            }
        }
        /* FILL pileup */
        if (!rec.getReadUnmappedFlag() && rec.getCigar() != null) {
            int refpos = rec.getUnclippedStart();
            int readpos = 0;
            final byte[] bases = rec.getReadBases();
            final byte[] quals = rec.getOriginalBaseQualities();
            /**
             * function getting the ith base
             */
            final Function<Integer, Character> getBaseAt = new Function<Integer, Character>() {

                @Override
                public Character apply(Integer readPos) {
                    char c;
                    if (bases == null || bases.length <= readPos) {
                        return '?';
                    } else {
                        c = (char) bases[readPos];
                    }
                    c = (rec.getReadNegativeStrandFlag() ? Character.toLowerCase(c) : Character.toUpperCase(c));
                    return c;
                }
            };
            /**
             * function getting the ith base quality
             */
            final Function<Integer, Character> getQualAt = new Function<Integer, Character>() {

                @Override
                public Character apply(Integer readPos) {
                    char c;
                    if (quals == null || quals.length <= readPos) {
                        return '#';
                    } else {
                        c = (char) quals[readPos];
                    }
                    return c;
                }
            };
            for (final CigarElement ce : rec.getCigar()) {
                switch(ce.getOperator()) {
                    case P:
                        break;
                    case N:
                    case D:
                        {
                            refpos += ce.getLength();
                            break;
                        }
                    case H:
                        {
                            for (int i = 0; i < ce.getLength(); ++i) {
                                final Pileup p = getpileup.apply(new ContigPos(rec.getContig(), refpos));
                                p.watch('-', '#', ce.getOperator());
                                ++refpos;
                            }
                            break;
                        }
                    case I:
                        {
                            for (int i = 0; i < ce.getLength(); ++i) {
                                final Pileup p = getpileup.apply(new ContigPos(rec.getContig(), refpos));
                                p.watch('<', getQualAt.apply(readpos), ce.getOperator());
                                readpos++;
                            }
                            break;
                        }
                    case S:
                        for (int i = 0; i < ce.getLength(); ++i) {
                            final Pileup p = getpileup.apply(new ContigPos(rec.getContig(), refpos));
                            p.watch('-', getQualAt.apply(readpos), ce.getOperator());
                            ++readpos;
                            ++refpos;
                        }
                        break;
                    case EQ:
                    case X:
                    case M:
                        for (int i = 0; i < ce.getLength(); ++i) {
                            final Pileup p = getpileup.apply(new ContigPos(rec.getContig(), refpos));
                            p.watch(getBaseAt.apply(readpos), getQualAt.apply(readpos), ce.getOperator());
                            ++readpos;
                            ++refpos;
                        }
                        break;
                }
            }
        }
    }
    if (iter != null)
        iter.close();
    this.canvasScrolVInCoverage.setMin(0);
    final int max_depth = pos2pileup.values().stream().map(P -> P.depth()).max((A, B) -> (A.compareTo(B))).orElse(0);
    this.canvasScrolVInCoverage.setMax(max_depth + 1);
    this.canvasScrolVInCoverage.setValue(0);
    this.recordTable.getItems().setAll(L);
    this.pileupTable.getItems().setAll(pos2pileup.values());
    if (canvasFirstRecordGenomicIndex != null && canvasLastRecordGenomicIndex != null && canvasFirstRecordGenomicIndex.longValue() < canvasLastRecordGenomicIndex.longValue()) {
        this.canvasScrollHGenomicLoc.setMin(canvasFirstRecordGenomicIndex);
        this.canvasScrollHGenomicLoc.setMax(canvasLastRecordGenomicIndex);
        // this.canvasScrollHGenomicLoc.setUnitIncrement(1);
        // this.canvasScrollHGenomicLoc.setBlockIncrement(Math.max(1.0,Math.min( canvasLastRecordGenomicIndex-canvasFirstRecordGenomicIndex, this.canvas.getWidth())));
        this.canvasScrollHGenomicLoc.setValue(canvasFirstRecordGenomicIndex);
    } else {
        this.canvasScrollHGenomicLoc.setMin(0);
        this.canvasScrollHGenomicLoc.setMax(0);
        this.canvasScrollHGenomicLoc.setValue(0);
        this.canvasScrollHGenomicLoc.setBlockIncrement(0);
        this.canvasScrollHGenomicLoc.setUnitIncrement(1);
    }
    if (!this.recordTable.getItems().isEmpty()) {
        final int last_index = this.recordTable.getItems().size() - 1;
        if (!this.recordTable.getItems().get(0).getReadUnmappedFlag() && !this.recordTable.getItems().get(last_index).getReadUnmappedFlag()) {
            super.seqDictionaryCanvas.setItemsInterval(new ContigPos(this.recordTable.getItems().get(0).getContig(), this.recordTable.getItems().get(0).getStart()), new ContigPos(this.recordTable.getItems().get(last_index).getContig(), this.recordTable.getItems().get(last_index).getEnd()));
            if (this.recordTable.getItems().get(0).getContig().equals(this.recordTable.getItems().get(last_index).getContig())) {
                this.gotoField.setText(this.recordTable.getItems().get(0).getContig() + ":" + this.recordTable.getItems().get(0).getStart() + "-" + this.recordTable.getItems().get(last_index).getEnd());
            }
        } else {
            super.seqDictionaryCanvas.setItemsInterval(null, null);
        }
    } else {
        super.seqDictionaryCanvas.setItemsInterval(null, null);
    }
    /* show hide columns for paired end data if no paired data found */
    {
        final boolean contains_paired = this.recordTable.getItems().stream().anyMatch(S -> S.getReadPairedFlag());
        for (final TableColumn<SAMRecord, ?> tc : this.pairedEndColumns) tc.setVisible(contains_paired);
    }
    repaintCanvas();
}

Example 52 with TableColumn

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

the class VcfStage method buildSampleTab.

/**
 * build table of Sample
 */
private Tab buildSampleTab() {
    final boolean editable = this.name2sampledef.size() > 1;
    final BorderPane pane = new BorderPane(this.sampleTable);
    pane.setPadding(new Insets(10));
    this.sampleTable.setEditable(editable);
    if (!getVcfFile().getPedigree().isEmpty()) {
        this.sampleTable.getColumns().add(makeColumn("Family", R -> {
            if (R.getPedSample().isPresent()) {
                return R.getPedSample().get().getFamily();
            }
            return null;
        }));
    }
    this.sampleTable.getColumns().add(makeColumn("Name", R -> R.getName()));
    final TableColumn<SampleDef, Boolean> selectCol = new TableColumn<>("Display");
    selectCol.setCellValueFactory(new PropertyValueFactory<>("displayed"));
    selectCol.setCellFactory(col -> {
        CheckBoxTableCell<SampleDef, Boolean> cell = new CheckBoxTableCell<>(index -> {
            return sampleTable.getItems().get(index).displayedProperty();
        });
        return cell;
    });
    selectCol.setEditable(editable);
    this.sampleTable.getColumns().add(selectCol);
    this.sampleTable.getColumns().add(makeColumn("Description", R -> R.getDescription()));
    this.sampleTable.setPlaceholder(new Label("No Sample."));
    this.sampleTable.getItems().addAll(this.name2sampledef.values());
    if (!getVcfFile().getPedigree().isEmpty()) {
        this.sampleTable.getColumns().add(makeColumn("Father", R -> {
            if (R.getPedSample().isPresent()) {
                final PedFile.Sample parent = R.getPedSample().get().getFather();
                return parent == null ? null : parent.getName();
            }
            return (String) null;
        }));
        this.sampleTable.getColumns().add(makeColumn("Mother", R -> {
            if (R.getPedSample().isPresent()) {
                final PedFile.Sample parent = R.getPedSample().get().getMother();
                return parent == null ? null : parent.getName();
            }
            return (String) null;
        }));
        this.sampleTable.getColumns().add(makeColumn("Sex", R -> {
            if (R.getPedSample().isPresent()) {
                return R.getPedSample().get().getSex().name();
            }
            return (String) null;
        }));
        this.sampleTable.getColumns().add(makeColumn("Status", R -> {
            if (R.getPedSample().isPresent()) {
                return R.getPedSample().get().getStatus().name();
            }
            return (String) null;
        }));
    }
    final HBox top = new HBox();
    top.setPadding(new Insets(10));
    Button but = new Button("Select all");
    but.setOnAction(AE -> {
        for (final SampleDef def : name2sampledef.values()) {
            def.setDisplayed(true);
        }
        if (getCurrentSelectedItem().isPresent()) {
            refreshGenotypeTable(getCurrentSelectedItem().get());
        }
    });
    top.getChildren().add(but);
    but = new Button("Unselect all");
    but.setOnAction(AE -> {
        for (final SampleDef def : name2sampledef.values()) {
            def.setDisplayed(false);
        }
        if (getCurrentSelectedItem().isPresent()) {
            refreshGenotypeTable(getCurrentSelectedItem().get());
        }
    });
    top.getChildren().add(but);
    pane.setTop(top);
    final Tab tab = new Tab("Samples", pane);
    tab.setClosable(false);
    return tab;
}

Example 53 with TableColumn

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

the class JvarkitCentral method start.

@Override
public void start(Stage primaryStage) throws Exception {
    primaryStage.setTitle("Jvarkit-Central");
    StackPane root = new StackPane();
    root.setPadding(new Insets(2));
    final TableView<Class<?>> tableView = new TableView<>();
    final TableColumn<Class<?>, String> nameCol = new TableColumn<>("Name");
    nameCol.setCellValueFactory(CB -> {
        final String value;
        Class<?> clazz = CB.getValue();
        final Program program = clazz.getAnnotation(Program.class);
        if (!Launcher.class.isAssignableFrom(clazz) || program == null) {
            value = null;
        } else {
            value = program.name();
        }
        return new SimpleStringProperty(value);
    });
    final TableColumn<Class<?>, String> descCol = new TableColumn<>("Description");
    descCol.setCellValueFactory(CB -> {
        final String value;
        Class<?> clazz = CB.getValue();
        final Program program = clazz.getAnnotation(Program.class);
        if (!Launcher.class.isAssignableFrom(clazz) || program == null) {
            value = null;
        } else {
            value = program.description();
        }
        return new SimpleStringProperty(value);
    });
    tableView.getColumns().addAll(nameCol, descCol);
    final BorderPane borderPane1 = new BorderPane(tableView);
    borderPane1.setPadding(new Insets(10));
    final Button but = new Button("New Instance...");
    but.setOnAction(AE -> {
        final Class<?> clazz = tableView.getSelectionModel().getSelectedItem();
        if (clazz == null)
            return;
        final Program program = clazz.getAnnotation(Program.class);
        if (!Launcher.class.isAssignableFrom(clazz) || program == null)
            return;
        createNewInstanceOf(clazz);
    });
    FlowPane bottom = new FlowPane(but);
    borderPane1.setBottom(bottom);
    tableView.getItems().addAll(String.class, Integer.class, VCFFilterJS.class, BioAlcidae.class);
    root.getChildren().add(borderPane1);
    // root.getChildren().add(btn);
    primaryStage.setScene(new Scene(root, 300, 250));
    primaryStage.show();
}

Example 54 with TableColumn

use of javafx.scene.control.TableColumn in project latexdraw by arnobl.

the class BadaboomController method initialize.

@SuppressWarnings("unchecked")
@Override
public void initialize(final URL location, final ResourceBundle resources) {
    final ObservableList<TableColumn<Throwable, ?>> cols = table.getColumns();
    ((TableColumn<Throwable, String>) cols.get(0)).setCellValueFactory(cell -> new ReadOnlyStringWrapper(cell.getValue().toString()));
    ((TableColumn<Throwable, String>) cols.get(1)).setCellValueFactory(cell -> new ReadOnlyStringWrapper(cell.getValue().getMessage()));
    ((TableColumn<Throwable, String>) cols.get(2)).setCellValueFactory(cell -> {
        final StackTraceElement[] stackTrace = cell.getValue().getStackTrace();
        final String msg = stackTrace != null && stackTrace.length > 0 ? stackTrace[0].toString() : "";
        return new ReadOnlyStringWrapper(msg);
    });
    cols.forEach(col -> col.prefWidthProperty().bind(table.widthProperty().divide(3)));
    table.setItems(FXCollections.observableArrayList(BadaboomCollector.INSTANCE));
    table.getSelectionModel().setSelectionMode(SelectionMode.SINGLE);
    final Callable<String> converter = () -> {
        final Throwable ex = table.getSelectionModel().getSelectedItem();
        if (ex == null)
            return "";
        // NON-NLS
        return Arrays.stream(ex.getStackTrace()).map(Object::toString).collect(Collectors.joining("\n\tat ", ex.toString() + "\n\tat ", ""));
    };
    stack.textProperty().bind(Bindings.createStringBinding(converter, table.getSelectionModel().selectedItemProperty()));
}

Example 55 with TableColumn

use of javafx.scene.control.TableColumn in project CST-135 by psradke.

the class FinalSale method start.

@Override
public void start(Stage primaryStage) throws Exception {
    // Background image
    BackgroundImage backImg = new BackgroundImage(new Image("file:src/DispenserDesign/Background&ButtonImages/FinalSalePage/FinalSaleBackground.png", 810, 720, false, true), BackgroundRepeat.NO_REPEAT, BackgroundRepeat.NO_REPEAT, BackgroundPosition.DEFAULT, BackgroundSize.DEFAULT);
    // PANE CREATION
    // Home and Back Buttons Pane
    GridPane buttons = new GridPane();
    buttons.setHgap(10);
    buttons.setVgap(10);
    buttons.setPadding(new Insets(0, 10, 0, 10));
    // TableView Cart Pane
    GridPane cartView = new GridPane();
    cartView.setHgap(9);
    cartView.setVgap(9);
    cartView.setOpacity(0.9);
    cartView.setPadding(new Insets(0, 10, 0, 10));
    // Delete and Purchase Buttons Pane
    GridPane buttons2 = new GridPane();
    buttons2.setHgap(10);
    buttons2.setVgap(10);
    buttons2.setPadding(new Insets(0, 10, 0, 10));
    // Main Pane for arrangement
    VBox vBox = new VBox();
    vBox.setPadding(new Insets(10, 10, 10, 10));
    vBox.getChildren().addAll(buttons, cartView, buttons2);
    // Background Pane
    StackPane root = new StackPane();
    root.setMaxSize(800, 610);
    root.setMinSize(800, 610);
    root.setBackground(new Background(backImg));
    root.setPadding(new Insets(0, 10, 0, 10));
    root.getChildren().add(vBox);
    // BUTTON CREATION
    // Home Button
    Button home = new Button("", new ImageView(new Image("file:src/DispenserDesign/Background&ButtonImages/NavigationButtons/HomeButton.png")));
    home.setBackground(Background.EMPTY);
    home.setMaxSize(5, 10);
    home.setMinSize(5, 10);
    buttons.add(home, 9, 2);
    // home.setOnAction(e -> {
    // homePage.setScene(scene);
    // });
    // Back Button
    Button back = new Button("", new ImageView(new Image("file:src/DispenserDesign/Background&ButtonImages/NavigationButtons/BackButton.png")));
    back.setBackground(Background.EMPTY);
    back.setMaxSize(5, 10);
    back.setMinSize(5, 10);
    buttons.add(back, 64, 2);
    back.setOnAction(new EventHandler<ActionEvent>() {

        @Override
        public void handle(ActionEvent event) {
            System.out.println("Back");
        }
    });
    // Purchase Button
    Button purchase = new Button("", new ImageView(new Image("file:src/DispenserDesign/Background&ButtonImages/FinalSalePage/Purchase.png")));
    purchase.setBackground(Background.EMPTY);
    purchase.setMaxSize(5, 10);
    purchase.setMinSize(5, 10);
    buttons2.add(purchase, 36, 11);
    purchase.setOnAction(new EventHandler<ActionEvent>() {

        @Override
        public void handle(ActionEvent event) {
            System.out.println("Purcahse");
        }
    });
    // Delete Button
    // Button delete = new Button("Delete Product");
    // delete.setOnAction(e -> deleteClicked());
    // CREATE TABLE FOR DISPLAYING CART
    TableView<Product> table;
    // Name column
    TableColumn<Product, String> nameCol = new TableColumn<>("Name");
    nameCol.setMinWidth(150);
    nameCol.setCellValueFactory(new PropertyValueFactory<>("name"));
    // Price column
    TableColumn<Product, Double> priceCol = new TableColumn<>("Price");
    priceCol.setMinWidth(20);
    priceCol.setCellValueFactory(new PropertyValueFactory<>("price"));
    // Weight column
    TableColumn<Product, Double> weightCol = new TableColumn<>("Weight");
    weightCol.setMinWidth(50);
    weightCol.setCellValueFactory(new PropertyValueFactory<>("weight"));
    // Quantity column
    TableColumn<Product, Double> quantityCol = new TableColumn<>("Quantity");
    quantityCol.setMinWidth(20);
    quantityCol.setCellValueFactory(new PropertyValueFactory<>("quantity"));
    table = new TableView<>();
    table.setItems(getProduct());
    table.setBackground(Background.EMPTY);
    table.setMaxSize(620, 313);
    table.setMinSize(620, 313);
    table.getColumns().addAll(nameCol, priceCol, weightCol, quantityCol);
    cartView.add(table, 7, 18);
    Scene scene = new Scene(root, 800, 710);
    primaryStage.setTitle("Checkout");
    primaryStage.setScene(scene);
    primaryStage.setResizable(false);
    primaryStage.show();
}