Example usage for javafx.scene.control TextField setPromptText

List of usage examples for javafx.scene.control TextField setPromptText

Introduction

In this page you can find the example usage for javafx.scene.control TextField setPromptText.

Prototype

public final void setPromptText(String value) 

Source Link

Usage

From source file:account.management.controller.inventory.InsertStockController.java

public void addRow() {

    ComboBox<Product> select_item = new ComboBox();
    select_item.setPromptText("Select Item");
    select_item.setPrefWidth(190);// w  w w .j a  v  a 2 s. c om
    select_item.setPrefHeight(25);

    new AutoCompleteComboBoxListener<>(select_item);
    select_item.setOnHiding((e) -> {
        Product a = select_item.getSelectionModel().getSelectedItem();
        select_item.setEditable(false);
        select_item.getSelectionModel().select(a);
    });
    select_item.setOnShowing((e) -> {
        select_item.setEditable(true);
    });

    TextField qty = new TextField();
    qty.setPromptText("Quantity");
    qty.setPrefWidth(97);
    qty.setPrefHeight(25);

    TextField rate = new TextField();
    rate.setPrefWidth(100);
    rate.setPrefHeight(25);

    if (this.voucher_type.getSelectionModel().getSelectedItem().equals("Purchase")) {
        rate.setPromptText("Purchase Rate");
    } else {
        rate.setPromptText("Sell Rate");
    }

    Button del = new Button("Delete");

    HBox row = new HBox();
    row.getChildren().addAll(select_item, qty, rate, del);
    row.setSpacing(10);
    row.setPadding(new Insets(0, 0, 0, 15));

    this.conatiner.getChildren().add(row);

    del.setOnAction((e) -> {
        this.conatiner.getChildren().remove(row);
        this.add_row.setDisable(false);
        calculateTotal();
    });

    select_item.getItems().addAll(this.products_list);

    select_item.setOnAction((e) -> {
        qty.setText("0");
        if (this.voucher_type.getSelectionModel().getSelectedItem().equals("Purchase")) {
            rate.setText(String.valueOf(select_item.getSelectionModel().getSelectedItem().getLast_p_rate()));
        } else {
            rate.setText(String.valueOf(select_item.getSelectionModel().getSelectedItem().getLast_s_rate()));
        }
        calculateTotal();
    });

    qty.setOnKeyReleased((e) -> {
        calculateTotal();
    });
    rate.setOnKeyReleased((e) -> {
        calculateTotal();
    });

    if (this.conatiner.getChildren().size() >= 8) {
        this.add_row.setDisable(true);
        return;
    }

}

From source file:account.management.controller.POVoucherController.java

public void addNewRow() {
    TextField sl = new TextField();
    sl.setPromptText("SL");
    sl.setPrefWidth(54);/*from   w w  w. java  2 s.  c  o m*/
    sl.setEditable(false);

    TextField desc = new TextField();
    desc.setPromptText("Description");
    desc.setPrefWidth(216);

    TextField qty = new TextField();
    qty.setPromptText("Quantity");
    qty.setPrefWidth(62);
    qty.setOnKeyReleased((e) -> {
        calculate();
    });

    TextField rate = new TextField();
    rate.setPromptText("Rate");
    rate.setPrefWidth(72);
    rate.setOnKeyReleased((e) -> {
        calculate();
    });

    TextField total = new TextField();
    total.setPromptText("Total");
    total.setPrefWidth(80);
    total.setEditable(false);

    TextField commision = new TextField();
    commision.setPromptText("Commision %");
    commision.setPrefWidth(90);
    commision.setOnKeyReleased((e) -> {
        calculate();
    });

    TextField total_commision = new TextField();
    total_commision.setPromptText("Total Commision");
    total_commision.setPrefWidth(132);
    total_commision.setEditable(false);

    TextField neat_total = new TextField();
    neat_total.setPromptText("Neat Amount");
    neat_total.setPrefWidth(115);
    neat_total.setEditable(false);

    Button delete = new Button("Delete");

    HBox row = new HBox();
    row.setSpacing(10);
    row.getChildren().addAll(sl, desc, qty, rate, total, commision, total_commision, neat_total, delete);

    delete.setOnAction((e) -> {
        this.container.getChildren().remove(row);
        calculate();
    });

    this.container.getChildren().add(row);
    calculate();

}

From source file:tachyon.view.ProjectProperties.java

public ProjectProperties(JavaProject project, Window w) {
    this.project = project;
    stage = new Stage();
    stage.initOwner(w);//from   w  w  w  .  ja va2s.c o  m
    stage.initModality(Modality.APPLICATION_MODAL);
    stage.setWidth(600);
    stage.setTitle("Project Properties - " + project.getProjectName());
    stage.getIcons().add(tachyon.Tachyon.icon);
    stage.setResizable(false);
    HBox mai, libs, one, two, thr, fou;
    ListView<String> compileList, runtimeList;
    Button compileAdd, compileRemove, preview, selectIm, runtimeAdd, runtimeRemove;
    TextField iconField;
    stage.setScene(new Scene(new VBox(5, pane = new TabPane(
            new Tab("Library Settings",
                    box1 = new VBox(15,
                            libs = new HBox(10, new Label("External Libraries"), libsView = new ListView<>(),
                                    new VBox(5, addJar = new Button("Add Jar"),
                                            removeJar = new Button("Remove Jar"))))),
            new Tab("Program Settings",
                    new ScrollPane(box2 = new VBox(15, one = new HBox(10, new Label("Main-Class"),
                            mainClass = new TextField(project.getMainClassName()),
                            select = new Button("Select")),
                            two = new HBox(10, new Label("Compile-Time Arguments"),
                                    compileList = new ListView<>(),
                                    new VBox(5, compileAdd = new Button("Add Argument"),
                                            compileRemove = new Button("Remove Argument")))))),
            new Tab("Deployment Settings",
                    box3 = new VBox(15, thr = new HBox(10, new Label("Icon File"),
                            iconField = new TextField(project.getFileIconPath()),
                            preview = new Button("Preview Image"), selectIm = new Button("Select Icon")),
                            fou = new HBox(10, new Label("Runtime Arguments"), runtimeList = new ListView<>(),
                                    new VBox(5, runtimeAdd = new Button("Add Argument"),
                                            runtimeRemove = new Button("Remove Argument")))))),
            new VBox(15, mai = new HBox(10, cancel = new Button("Cancel"), confirm = new Button("Confirm"))))));
    if (applyCss.get()) {
        stage.getScene().getStylesheets().add(css);
    }
    for (Tab b : pane.getTabs()) {
        b.setClosable(false);
    }
    mainClass.setPromptText("Main-Class");
    box1.setPadding(new Insets(5, 10, 5, 10));
    mai.setAlignment(Pos.CENTER_RIGHT);
    mai.setPadding(box1.getPadding());
    libs.setAlignment(Pos.CENTER);
    one.setAlignment(Pos.CENTER);
    two.setAlignment(Pos.CENTER);
    thr.setAlignment(Pos.CENTER);
    fou.setAlignment(Pos.CENTER);
    box1.setAlignment(Pos.CENTER);
    box2.setPadding(box1.getPadding());
    box2.setAlignment(Pos.CENTER);
    box3.setPadding(box1.getPadding());
    box3.setAlignment(Pos.CENTER);
    mainClass.setEditable(false);
    mainClass.setPrefWidth(200);
    for (JavaLibrary lib : project.getAllLibs()) {
        libsView.getItems().add(lib.getBinaryAbsolutePath());
    }
    for (String sa : project.getCompileTimeArguments().keySet()) {
        compileList.getItems().add(sa + ":" + project.getCompileTimeArguments().get(sa));
    }
    for (String sa : project.getRuntimeArguments()) {
        runtimeList.getItems().add(sa);
    }
    compileAdd.setOnAction((e) -> {
        Dialog<Pair<String, String>> dialog = new Dialog<>();
        dialog.setTitle("Compiler Argument");
        dialog.initOwner(stage);
        dialog.setHeaderText("Entry the argument");

        ButtonType loginButtonType = new ButtonType("Done", ButtonData.OK_DONE);
        dialog.getDialogPane().getButtonTypes().addAll(loginButtonType, ButtonType.CANCEL);

        GridPane grid = new GridPane();
        grid.setHgap(10);
        grid.setVgap(10);
        grid.setPadding(new Insets(20, 150, 10, 10));

        TextField username = new TextField();
        username.setPromptText("Key");
        TextField password = new TextField();
        password.setPromptText("Value");

        grid.add(new Label("Key:"), 0, 0);
        grid.add(username, 1, 0);
        grid.add(new Label("Value:"), 0, 1);
        grid.add(password, 1, 1);

        Node loginButton = dialog.getDialogPane().lookupButton(loginButtonType);
        loginButton.setDisable(true);

        username.textProperty().addListener((observable, oldValue, newValue) -> {
            loginButton.setDisable(newValue.trim().isEmpty());
        });

        dialog.getDialogPane().setContent(grid);

        Platform.runLater(() -> username.requestFocus());

        dialog.setResultConverter(dialogButton -> {
            if (dialogButton == loginButtonType) {
                return new Pair<>(username.getText(), password.getText());
            }
            return null;
        });

        Optional<Pair<String, String>> result = dialog.showAndWait();
        if (result.isPresent()) {
            compileList.getItems().add(result.get().getKey() + ":" + result.get().getValue());
        }
    });
    compileRemove.setOnAction((e) -> {
        if (compileList.getSelectionModel().getSelectedItem() != null) {
            compileList.getItems().remove(compileList.getSelectionModel().getSelectedItem());
        }
    });
    runtimeAdd.setOnAction((e) -> {
        TextInputDialog dia = new TextInputDialog();
        dia.setTitle("Add Runtime Argument");
        dia.setHeaderText("Enter an argument");
        dia.initOwner(stage);
        Optional<String> res = dia.showAndWait();
        if (res.isPresent()) {
            runtimeList.getItems().add(res.get());
        }
    });
    runtimeRemove.setOnAction((e) -> {
        if (runtimeList.getSelectionModel().getSelectedItem() != null) {
            runtimeList.getItems().remove(runtimeList.getSelectionModel().getSelectedItem());
        }
    });
    preview.setOnAction((e) -> {
        if (!iconField.getText().isEmpty()) {
            if (iconField.getText().endsWith(".ico")) {
                List<BufferedImage> read = new ArrayList<>();
                try {
                    read.addAll(ICODecoder.read(new File(iconField.getText())));
                } catch (IOException ex) {
                }
                if (read.size() >= 1) {
                    Image im = SwingFXUtils.toFXImage(read.get(0), null);
                    Stage st = new Stage();
                    st.initOwner(stage);
                    st.initModality(Modality.APPLICATION_MODAL);
                    st.setTitle("Icon Preview");
                    st.getIcons().add(Tachyon.icon);
                    st.setScene(new Scene(new BorderPane(new ImageView(im))));
                    if (applyCss.get()) {
                        st.getScene().getStylesheets().add(css);
                    }
                    st.showAndWait();
                }
            } else if (iconField.getText().endsWith(".icns")) {
                try {
                    BufferedImage ima = Imaging.getBufferedImage(new File(iconField.getText()));
                    if (ima != null) {
                        Image im = SwingFXUtils.toFXImage(ima, null);
                        Stage st = new Stage();
                        st.initOwner(stage);
                        st.initModality(Modality.APPLICATION_MODAL);
                        st.setTitle("Icon Preview");
                        st.getIcons().add(Tachyon.icon);
                        st.setScene(new Scene(new BorderPane(new ImageView(im))));
                        if (applyCss.get()) {
                            st.getScene().getStylesheets().add(css);
                        }
                        st.showAndWait();
                    }
                } catch (ImageReadException | IOException ex) {
                }
            } else {
                Image im = new Image(new File(iconField.getText()).toURI().toString());
                Stage st = new Stage();
                st.initOwner(stage);
                st.initModality(Modality.APPLICATION_MODAL);
                st.setTitle("Icon Preview");
                st.getIcons().add(Tachyon.icon);
                st.setScene(new Scene(new BorderPane(new ImageView(im))));
                if (applyCss.get()) {
                    st.getScene().getStylesheets().add(css);
                }
                st.showAndWait();
            }
        }
    });
    selectIm.setOnAction((e) -> {
        FileChooser fc = new FileChooser();
        fc.setTitle("Icon File");
        String OS = System.getProperty("os.name").toLowerCase();
        fc.getExtensionFilters().add(new ExtensionFilter("Icon File",
                OS.contains("win") ? getWindowsImageExtensions() : getMacImageExtensions()));
        fc.setSelectedExtensionFilter(fc.getExtensionFilters().get(0));
        File lf = fc.showOpenDialog(stage);
        if (lf != null) {
            iconField.setText(lf.getAbsolutePath());
        }
    });

    addJar.setOnAction((e) -> {
        FileChooser f = new FileChooser();
        f.setTitle("External Libraries");
        f.setSelectedExtensionFilter(new ExtensionFilter("Jar Files", "*.jar"));
        List<File> showOpenMultipleDialog = f.showOpenMultipleDialog(stage);
        if (showOpenMultipleDialog != null) {
            for (File fi : showOpenMultipleDialog) {
                if (!libsView.getItems().contains(fi.getAbsolutePath())) {
                    libsView.getItems().add(fi.getAbsolutePath());
                }
            }
        }
    });

    removeJar.setOnAction((e) -> {
        String selected = libsView.getSelectionModel().getSelectedItem();
        if (selected != null) {
            libsView.getItems().remove(selected);
        }
    });

    select.setOnAction((e) -> {
        List<String> all = getAll();
        ChoiceDialog<String> di = new ChoiceDialog<>(project.getMainClassName(), all);
        di.setTitle("Select Main Class");
        di.initOwner(stage);
        di.setHeaderText("Select A Main Class");
        Optional<String> show = di.showAndWait();
        if (show.isPresent()) {
            mainClass.setText(show.get());
        }
    });
    cancel.setOnAction((e) -> {
        stage.close();
    });
    confirm.setOnAction((e) -> {
        project.setMainClassName(mainClass.getText());
        project.setFileIconPath(iconField.getText());
        project.setRuntimeArguments(runtimeList.getItems());
        HashMap<String, String> al = new HashMap<>();
        for (String s : compileList.getItems()) {
            String[] spl = s.split(":");
            al.put(spl[0], spl[1]);
        }
        project.setCompileTimeArguments(al);
        project.setAllLibs(libsView.getItems());
        stage.close();
    });
}

From source file:account.management.controller.NewVoucherController.java

@FXML
private void onAddNewFieldButtonClick(ActionEvent event) {

    HBox row = new HBox();
    row.setId("field_row");
    ComboBox<Account> select_account = new ComboBox<>();
    if (this.select_type.getSelectionModel().isEmpty()) {
        select_account.getItems().addAll(this.account_list);
    } else {//ww  w. java2 s .c o  m
        select_account.getItems().addAll(this.filter_acc);
    }

    TextField dr = new TextField();
    TextField cr = new TextField();
    TextField remarks = new TextField();
    Button del_row = new Button("Delete");

    row.setSpacing(field_row.getSpacing());

    ComboBox<Account> combo = (ComboBox) field_row.getChildren().get(0);
    select_account.setPrefWidth(combo.getPrefWidth());
    select_account.setPromptText("Select account");

    TextField tf = (TextField) field_row.getChildren().get(1);
    dr.setPrefWidth(tf.getPrefWidth());
    dr.setPromptText("Dr");

    tf = (TextField) field_row.getChildren().get(2);
    cr.setPrefWidth(tf.getPrefWidth());
    cr.setPromptText("Cr");

    tf = (TextField) field_row.getChildren().get(3);
    remarks.setPrefWidth(tf.getPrefWidth());
    remarks.setPromptText("remarks");

    row.getChildren().addAll(select_account, dr, cr, remarks, del_row);
    field_container.getChildren().add(row);

    del_row.setOnMouseClicked((MouseEvent event1) -> {
        field_container.getChildren().removeAll(row);
        validateFields();
    });

    combo.setOnAction((e) -> {
        if (!combo.getSelectionModel().isEmpty() && combo.getSelectionModel().getSelectedItem().getId() == 21) {
            combo.setPromptText("Select Party");
            combo.getItems().clear();
            combo.getItems().addAll(this.filter_party_rec);
        }
        if (!combo.getSelectionModel().isEmpty() && combo.getSelectionModel().getSelectedItem().getId() == 34) {
            combo.getItems().clear();
            combo.getItems().addAll(this.filter_party_pay);
            combo.setPromptText("Select Party");
        }
    });

    new AutoCompleteComboBoxListener<>(select_account);
    select_account.setOnHiding((e) -> {
        Account a = select_account.getSelectionModel().getSelectedItem();
        select_account.setEditable(false);
        select_account.getSelectionModel().select(a);
    });
    select_account.setOnShowing((e) -> {
        select_account.setEditable(true);
    });

    validateFields();

}

From source file:snpviewer.SnpViewer.java

public void refreshView(String chrom, boolean forceRedraw) {
    //if forceRedraw is false look for existing png files for each snpFile
    if (chrom == null) {
        /*if null is passed then select/reselect chromosome from 
         * chromosomeSelector, return and let chromosomeSelector's 
         * listener refire this method/*from w w w  .ja  v a  2s.co  m*/
         */
        if (chromosomeSelector.getSelectionModel().isEmpty()) {
            chromosomeSelector.getSelectionModel().selectFirst();
        } else {
            int sel = chromosomeSelector.getSelectionModel().getSelectedIndex();
            chromosomeSelector.getSelectionModel().clearSelection();
            chromosomeSelector.getSelectionModel().select(sel);
        }
        return;
    }
    int totalFiles = affFiles.size() + unFiles.size();
    if (totalFiles < 1) {
        return;
    }
    ArrayList<Pane> panesToAdd = new ArrayList<>();
    ArrayList<ScrollPane> labelsToAdd = new ArrayList<>();
    clearSplitPanes();

    setProgressMode(true);
    nextChromMenu.setDisable(false);
    nextChromMenu.setDisable(false);
    for (final SnpFile f : affFiles) {
        Pane sPane = new Pane();
        sPane.setMinHeight(chromSplitPane.getHeight() / totalFiles);
        sPane.setMinWidth(chromSplitPane.getWidth());
        sPane.setVisible(true);
        panesToAdd.add(sPane);
        ScrollPane labelPane = new ScrollPane();
        Label fileLabel = new Label(f.inputFile.getName() + "\n(Affected)");
        fileLabel.setTextFill(Color.WHITE);
        labelPane.setMinHeight(labelSplitPane.getHeight() / totalFiles);
        labelPane.setPrefWidth(labelSplitPane.getWidth());
        labelPane.minHeightProperty().bind(labelSplitPane.heightProperty().divide(totalFiles));
        VBox vbox = new VBox();
        vbox.setSpacing(10);
        vbox.getChildren().add(fileLabel);
        final TextField textField = new TextField();
        textField.setStyle("-fx-text-fill: white; -fx-background-color: "
                + "rgba(90%,90%,90%,0.3); -fx-border-color:white");
        textField.setPromptText("Sample Name");
        if (f.getSampleName() != null) {
            textField.setText(f.getSampleName());
        }
        textField.setFocusTraversable(true);
        textField.setOnKeyPressed(new EventHandler<KeyEvent>() {
            @Override
            public void handle(KeyEvent ke) {
                if (ke.getCode().equals(KeyCode.ENTER)) {
                    if (!textField.getText().isEmpty()) {
                        String name = textField.getText().trim();
                        if (name.length() > 0) {
                            f.setSampleName(name);
                        }
                        textField.getParent().requestFocus();
                        saveProject();
                    }
                }
            }
        });
        textField.focusedProperty().addListener(new ChangeListener<Boolean>() {
            @Override
            public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue,
                    Boolean newValue) {
                if (!textField.isFocused()) {
                    if (!textField.getText().isEmpty()) {
                        String name = textField.getText().trim();
                        if (name.length() > 0) {
                            f.setSampleName(name);
                        }
                        saveProject();
                    }
                }
            }
        });
        vbox.getChildren().add(textField);
        Label noCalls = new Label();
        if (f.getPercentNoCall() != null) {
            noCalls.setText("No Calls: " + DecimalFormat.getInstance().format(f.getPercentNoCall()) + " %");
        } else {
            noCalls.setText("No Calls: none");
        }
        Label meanQual = new Label();
        if (f.getMeanQuality() != null) {
            meanQual.setText("Av. Call Conf: "
                    + DecimalFormat.getInstance().format(100 - (f.getMeanQuality() * 100)) + " %");
        } else {
            meanQual.setText("No Call Confidence Data");
        }
        vbox.getChildren().add(noCalls);
        vbox.getChildren().add(meanQual);
        labelPane.setContent(vbox);
        //            labelPane.getChildren().add(fileLabel);
        //            labelPane.getChildren().add(new TextField());
        labelsToAdd.add(labelPane);
    }
    for (final SnpFile f : unFiles) {
        Pane sPane = new Pane();
        sPane.setMinHeight(chromSplitPane.getHeight() / totalFiles);
        sPane.setMinWidth(chromSplitPane.getWidth());
        sPane.setVisible(true);
        panesToAdd.add(sPane);
        ScrollPane labelPane = new ScrollPane();
        Label fileLabel = new Label(f.inputFile.getName() + "\n(Unaffected)");
        fileLabel.setStyle("-fx-text-fill: black");
        labelPane.setMinHeight(labelSplitPane.getHeight() / totalFiles);
        labelPane.setPrefWidth(labelSplitPane.getWidth());
        labelPane.minHeightProperty().bind(labelSplitPane.heightProperty().divide(totalFiles));
        VBox vbox = new VBox();
        vbox.setSpacing(10);
        vbox.getChildren().add(fileLabel);
        final TextField textField = new TextField();
        textField.setStyle("-fx-text-fill: black; " + "-fx-background-color: rgba(90%,90%,90%,0.3);"
                + " -fx-border-color:white");
        textField.setPromptText("Sample Name");
        if (f.getSampleName() != null) {
            textField.setText(f.getSampleName());
        }
        textField.setFocusTraversable(true);
        textField.setOnKeyPressed(new EventHandler<KeyEvent>() {
            @Override
            public void handle(KeyEvent ke) {
                if (ke.getCode().equals(KeyCode.ENTER)) {
                    if (!textField.getText().isEmpty()) {
                        f.setSampleName(textField.getText());
                        textField.getParent().requestFocus();
                        saveProject();
                    }
                }
            }
        });
        textField.focusedProperty().addListener(new ChangeListener<Boolean>() {
            @Override
            public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue,
                    Boolean newValue) {
                if (!textField.isFocused()) {
                    if (!textField.getText().isEmpty()) {
                        f.setSampleName(textField.getText());
                        saveProject();
                    }
                }
            }
        });
        vbox.getChildren().add(textField);
        Label noCalls = new Label();
        if (f.getPercentNoCall() != null) {
            noCalls.setText("No Calls: " + DecimalFormat.getInstance().format(f.getPercentNoCall()) + " %");
        } else {
            noCalls.setText("No Calls: none");
        }
        Label meanQual = new Label();
        if (f.getMeanQuality() != null) {
            meanQual.setText("Av. Call Conf: "
                    + DecimalFormat.getInstance().format(100 - (f.getMeanQuality() * 100)) + " %");
        } else {
            meanQual.setText("No Call Confidence Data");
        }
        vbox.getChildren().add(noCalls);
        vbox.getChildren().add(meanQual);
        labelPane.setContent(vbox);
        //            labelPane.getChildren().add(fileLabel);
        labelsToAdd.add(labelPane);
    }
    if (panesToAdd.size() > 0) {
        chromSplitPane.getItems().addAll(panesToAdd);
        labelSplitPane.getItems().addAll(labelsToAdd);

        ArrayList<SnpFile> bothFiles = new ArrayList<>(affFiles);
        bothFiles.addAll(unFiles);
        final Iterator<SnpFile> fileIter = bothFiles.iterator();
        final Iterator<Pane> paneIter = panesToAdd.iterator();
        SnpFile firstFileToProcess = fileIter.next();
        Pane firstPaneToProcess = paneIter.next();
        String pngPath = null;
        if (qualityFilter != null) {
            Integer percent = new Integer(100 - (int) (qualityFilter * 100));
            pngPath = percent.toString();
        }
        drawWithIterator(firstFileToProcess, firstPaneToProcess, pngPath, fileIter, paneIter, 1, totalFiles,
                chrom, forceRedraw, chromSplitPane);
    } else {
        setProgressMode(false);
    }
}

From source file:org.simmi.GeneSetHead.java

License:asdf

private void showGeneTable(
        /*final Map<String, Gene> genemap, final List<Gene> genelist, 
        final List<Function> funclist, final List<Set<String>> iclusterlist, final List<Set<String>> uclusterlist,
        final Map<Set<String>, ShareNum> specset,*/ final Map<Set<String>, ClusterInfo> clustInfoMap,
        final Button jb, final TableView<Gene> genetable, final TableView<Function> upper,
        final TableView<GeneGroup> lower, final ToolBar toolbar, final ToolBar btoolbar, final Container comp,
        final JApplet applet, final ComboBox<String> selcomblocal) throws IOException {
    //JSplitPane splitpane = new JSplitPane();
    //splitpane.setOrientation(JSplitPane.VERTICAL_SPLIT);
    //splitpane.setDividerLocation(400);
    //JScrollPane scrollpane = new JScrollPane();

    /*table = new JTable() {
       public String getToolTipText(MouseEvent me) {
    Point p = me.getPoint();//  w  ww. j  a  va 2s .co m
    int r = rowAtPoint(p);
    int c = columnAtPoint(p);
    if (r >= 0 && r < super.getRowCount()) {
       Object ret = super.getValueAt(r, c);
       if (ret != null) {
          return ret.toString(); // super.getToolTipText( me );
       }
    }
    return "";
       }
    };*/

    //table.setDragEnabled(true);
    try {
        final DataFlavor df = new DataFlavor("text/plain;charset=utf-8");
        // System.err.println( df.getHumanPresentableName() + " " +
        // df.getPrimaryType() + " " + df.getSubType() + " " +
        // df.getMimeType() );
        // DataFlavor df1 = DataFlavor.getTextPlainUnicodeFlavor();
        // System.err.println( df.getHumanPresentableName() + " " +
        // df.getPrimaryType() + " " + df.getSubType() + " " +
        // df.getMimeType() );
        TransferHandler th = new TransferHandler() {
            /**
             * 
             */
            private static final long serialVersionUID = 1L;

            public int getSourceActions(JComponent c) {
                return TransferHandler.COPY_OR_MOVE;
            }

            public boolean canImport(TransferHandler.TransferSupport support) {
                return true;
            }

            protected Transferable createTransferable(JComponent c) {
                return new Transferable() {
                    @Override
                    public Object getTransferData(DataFlavor arg0)
                            throws UnsupportedFlavorException, IOException {
                        Map<String, List<Tegeval>> contigs = new HashMap<>();
                        StringBuilder ret = new StringBuilder();
                        for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                            Tegeval tv = gg.tegeval;
                            if (!contigs.containsKey(tv.getContshort())) {
                                List<Tegeval> ltv = new ArrayList<>();
                                ltv.add(tv);
                                contigs.put(tv.getContshort().getName(), ltv);
                            } else {
                                List<Tegeval> ltv = contigs.get(tv.getContshort());
                                ltv.add(tv);
                            }
                            /*
                             * ret.append( ">" + tv.cont + " " +
                             * tv.teg + " " + tv.eval + "\n" );
                             * if( tv.dna != null ) { for( int i
                             * = 0; i < tv.dna.length(); i+=70 )
                             * { ret.append(tv.dna.substring( i,
                             * Math.min(i+70,tv.dna.length())
                             * )+"\n"); } }
                             */
                        }
                        for (String cont : contigs.keySet()) {
                            List<Tegeval> tv = contigs.get(cont);
                            String dna = tv.get(0).getSequence();
                            ret.append(">" + cont + "\n"); // + " " + tv.teg
                            // + " " +
                            // tv.eval +
                            // "\n" );
                            if (dna != null) {
                                for (int i = 0; i < dna.length(); i += 70) {
                                    ret.append(dna.substring(i, Math.min(i + 70, dna.length())) + "\n");
                                }
                            }
                        }
                        for (String cont : contigs.keySet()) {
                            List<Tegeval> ltv = contigs.get(cont);
                            ret.append(">" + cont + "\n"); // + " " + tv.teg
                            // + " " +
                            // tv.eval +
                            // "\n" );
                            for (Tegeval tv : ltv) {
                                ret.append("erm\t#0000ff\t" + tv.start + "\t" + tv.stop + "\n");
                            }
                        }

                        return new ByteArrayInputStream(ret.toString().getBytes());
                    }

                    @Override
                    public DataFlavor[] getTransferDataFlavors() {
                        return new DataFlavor[] { df };
                    }

                    @Override
                    public boolean isDataFlavorSupported(DataFlavor arg0) {
                        if (arg0.equals(df)) {
                            return true;
                        }
                        return false;
                    }
                };
            }

            public boolean importData(TransferHandler.TransferSupport support) {
                Object obj = null;

                System.err.println(support.getDataFlavors().length);
                int b = Arrays.binarySearch(support.getDataFlavors(), DataFlavor.javaFileListFlavor,
                        (o1, o2) -> o1 == o2 ? 1 : 0);

                try {
                    obj = support.getTransferable().getTransferData(DataFlavor.imageFlavor);
                } catch (UnsupportedFlavorException e) {
                    e.printStackTrace();
                } catch (IOException e) {
                    e.printStackTrace();
                }

                try {
                    if (obj != null && obj instanceof File[]) {
                        // File[] ff = (File[])obj;
                        // wbStuff( ff[0].getCanonicalPath() );
                    } else if (obj instanceof Image) {

                    } else {
                        obj = support.getTransferable().getTransferData(DataFlavor.stringFlavor);
                        System.err.println(obj);
                        URL url = null;
                        try {
                            url = new URL((String) obj);
                            Image image = ImageIO.read(url);
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                } catch (UnsupportedFlavorException e) {
                    e.printStackTrace();
                } catch (IOException e) {
                    e.printStackTrace();
                }

                return true;
            }
        };
        //table.setTransferHandler(th);
    } catch (ClassNotFoundException e2) {
        e2.printStackTrace();
    }

    final Color darkgreen = new Color(0, 128, 0);
    final Color darkred = new Color(128, 0, 0);
    final Color darkblue = new Color(0, 0, 128);
    final Color darkmag = new Color(128, 0, 128);
    /*table.setDefaultRenderer(Teg.class, new DefaultTableCellRenderer() {
       @Override
       public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
    Component label = super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
    if( value == null ) {
       label.setBackground(Color.white);
    } else {
       cellRender();
    }
    return label;
       }
    });*/

    //table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
    //table.setAutoCreateRowSorter(true);
    //scrollpane.setViewportView(table);

    Set<String> current = null;
    Set<String> currentko = null;
    InputStream is = GeneSet.class.getResourceAsStream("/kegg_pathways");
    BufferedReader br = new BufferedReader(new InputStreamReader(is));
    String line = br.readLine();
    while (line != null) {
        if (line.startsWith(">")) {
            current = new HashSet<>();
            currentko = new HashSet<>();
            geneset.pathwaymap.put(line.substring(1), current);
            geneset.pathwaykomap.put(line.substring(1), currentko);
        } else if (!line.startsWith("K")) {
            if (current != null) {
                String str = line.split("[\t ]+")[0];
                current.add(str);
            }
        } else {
            if (currentko != null) {
                String str = line.split("[\t ]+")[0];
                currentko.add(str);
            }
        }
        line = br.readLine();
    }
    br.close();

    //FileReader fr = new FileReader("/vg454flx/ko2go.txt");
    /*is = GeneSet.class.getResourceAsStream("/ko2go.txt");
    InputStreamReader isr = new InputStreamReader( is );
    br = new BufferedReader( isr );
    line = br.readLine();
    while (line != null) {
       String[] split = line.split(" = ");
       String[] subsplit = split[1].split(" ");
       Set<String> gos = new HashSet<String>();
       for( String go : subsplit ) {
    gos.add( go );
       }
       ko2go.put( split[0], gos );
       line = br.readLine();
    }
    br.close();*/

    final TextField textfield = new TextField();
    //JComponent topcomp = new JComponent() {};
    //topcomp.setLayout(new BorderLayout());
    //topcomp.add(scrollpane);

    textfield.setPrefSize(350, 25);

    final RadioButton search = new RadioButton("Search");
    final RadioButton filter = new RadioButton("Filter");

    ToggleGroup bgsf = new ToggleGroup();
    search.setToggleGroup(bgsf);
    filter.setToggleGroup(bgsf);
    //ButtonGroup bgsf = new ButtonGroup();
    //bgsf.add( search );
    //bgsf.add( filter );

    filter.setSelected(true);

    //ToolBar topcombo = new ToolBar();
    // topcombo.
    // topcombo.setLayout( new FlowLayout() );

    specombo = new ComboBox<>();
    combo = new ComboBox<>();

    specombo.getItems().add("Select blast species");
    combo.getItems().add("Select pathway");
    btoolbar.getItems().add(combo);
    btoolbar.getItems().add(specombo);
    //topcomp.add(topcombo, BorderLayout.SOUTH);

    //JComponent ttopcom = new JComponent() {};
    //ttopcom.setLayout(new FlowLayout());

    /*            frame.setVisible( true );
             }
          };
          AbstractAction   sharenumaction = new AbstractAction("Update share numbers") {
             @Override
             public void actionPerformed(ActionEvent e) {
    Set<String> specs = getSelspec(GeneSetHead.this, specList, null);
    updateShareNum(specs);
             }
          };
          AbstractAction   importgenesymbolaction = new AbstractAction("Import gene symbols") {
             @Override
             public void actionPerformed(ActionEvent e) {
    JFileChooser fc = new JFileChooser();
    if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) {
       try {
          Map<String,String> env = new HashMap<String,String>();
          env.put("create", "true");
          Path path = zipfile.toPath();
          String uristr = "jar:" + path.toUri();
          geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")* );
          geneset.zipfilesystem = FileSystems.newFileSystem( geneset.zipuri, env );
                  
          Path nf = geneset.zipfilesystem.getPath("/smap_short.txt");
          BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE);
                  
          InputStream is = new GZIPInputStream( new FileInputStream( fc.getSelectedFile() ) );
          uni2symbol(new InputStreamReader(is), bw, unimap);
                  
          bw.close();
          //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING );
          geneset.zipfilesystem.close();
       } catch (IOException e1) {
          e1.printStackTrace();
       }
    }
             }
          };
                  
          AbstractAction   importidmappingaction = new AbstractAction("Id mapping") {
             @Override
             public void actionPerformed(ActionEvent e) {
    JFileChooser fc = new JFileChooser();
    if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) {
       try {
          Map<String,String> env = new HashMap<String,String>();
          env.put("create", "true");
          Path path = zipfile.toPath();
          String uristr = "jar:" + path.toUri();
          geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")/ );
          geneset.zipfilesystem = FileSystems.newFileSystem( geneset.zipuri, env );
                  
          Path nf = geneset.zipfilesystem.getPath("/idmapping_short.dat");
          BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE);
                  
          InputStream is = new GZIPInputStream( new FileInputStream( fc.getSelectedFile() ) );
          if( unimap != null ) unimap.clear();
          unimap = idMapping(new InputStreamReader(is), bw, 2, 0, refmap, genmap, gimap);
                  
          bw.close();
          //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING );
          geneset.zipfilesystem.close();
       } catch (IOException e1) {
          e1.printStackTrace();
       }
    }
             }
          };
                  
          final JCheckBoxMenuItem checkbox = new JCheckBoxMenuItem();
          checkbox.setAction(new AbstractAction("Sort by location") {
             @Override
             public void actionPerformed(ActionEvent e) {
    Tegeval.locsort = checkbox.isSelected();
             }
          });
          AbstractAction saveselAction = new AbstractAction("Save selection") {
             @Override
             public void actionPerformed(ActionEvent e) {
    int[] rr = table.getSelectedRows();
    if( rr.length > 0 ) {
       String val = Integer.toString( table.convertRowIndexToModel(rr[0]) );
       for( int i = 1; i < rr.length; i++ ) {
          val += ","+table.convertRowIndexToModel(rr[i]);
       }
       String selname = JOptionPane.showInputDialog("Selection name");
       if( comp instanceof Applet ) {
          try {
             ((GeneSet)comp).saveSel( selname, val);
          } catch (Exception e1) {
             e1.printStackTrace();
          }
       }
    }
             }
          };
                  
          JMenuBar   menubar = new JMenuBar();
          JMenu      menu = new JMenu("Functions");
          menu.add( importidmappingaction );
          menu.add( functionmappingaction );
          menu.add( importgenesymbolaction );
          menu.add( fetchaction );
          menu.add( blast2action );
          menu.add( sharenumaction );
          menu.addSeparator();
          menu.add( checkbox );
          menu.add( saveselAction );
          menu.addSeparator();
          menu.add( genomestataction );
          menu.add( selectsharingaction );
          menu.add( shuffletreeaction );
          menu.add( presabsaction );
          menu.add( freqdistaction );
          menu.add( gcpaction );
          menu.add( matrixaction );
          menu.add( pancoreaction );
          menu.add( blastaction );
          menu.add( koexportaction );
          menu.add( genomesizeaction );
          menu.add( gcaction );
          menu.add( gcskewaction );
          menu.add( mltreemapaction );
          menu.add( sevenaction );
          menu.add( cogaction );
          menu.add( genexyplotaction );
          menu.add( compareplotaction );
          menu.add( syntenygradientaction );
          menu.add( codregaction );
          menu.add( fetchcoreaction );
          menu.add( loadcontiggraphaction );
          menu.add( selectflankingaction );
          menu.add( showflankingaction );
          menu.add( showcontigsaction );
          menu.add( showunresolved );
          menu.add( genephyl );
                  
          menubar.add( menu );
          ttopcom.add( menubar );
                  
          JMenu      view = new JMenu("View");
          menubar.add( view );
                  
          gb = new JRadioButtonMenuItem( new AbstractAction("Genes") {
             @Override
             public void actionPerformed(ActionEvent e) {
    table.setModel( defaultModel );
             }
          });
          view.add( gb );
          ggb = new JRadioButtonMenuItem( new AbstractAction("Gene groups") {
             @Override
             public void actionPerformed(ActionEvent e) {
    table.setModel( groupModel );
             }
                     
          });
          ButtonGroup   bg = new ButtonGroup();
          bg.add( gb );
          bg.add( ggb );
                  
          ggb.setSelected( true );
                  
          view.add( ggb );*/

    //ttopcom.add( shuffletreebutton );
    //ttopcom.add( presabsbutton );
    //ttopcom.add(freqdistbutton);
    //ttopcom.add(matrixbutton);

    toolbar.getItems().add(textfield);
    toolbar.getItems().add(search);
    toolbar.getItems().add(filter);
    toolbar.getItems().add(label);

    selcomblocal.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
        String key = newValue;
        if (((GeneSetHead) comp).selectionMap.containsKey(key)) {
            Set<Integer> val = ((GeneSetHead) comp).selectionMap.get(key);
            if (val != null) {
                table.getSelectionModel().clearSelection();
                for (int i : val) {
                    //int r = table.convertRowIndexToView(i);
                    table.getSelectionModel().select(i);
                }
            } else {
                System.err.println("null " + key);
            }
        } else {
            System.err.println("no " + key);
        }
    });
    toolbar.getItems().add(selcomblocal);

    /*syncolorcomb.addItemListener( new ItemListener() {
       @Override
       public void itemStateChanged(ItemEvent e) {
    String spec = (String)syncolorcomb.getSelectedItem();
    //if( spec.length() > 0 )
       }
    });*/
    toolbar.getItems().add(searchcolcomb);
    toolbar.getItems().add(syncolorcomb);
    //topcomp.add(ttopcom, BorderLayout.NORTH);

    table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    table.getSelectionModel().selectedItemProperty().addListener(e -> {
        label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size());
    });

    gtable.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    gtable.getSelectionModel().selectedItemProperty().addListener(e -> {
        label.setText(gtable.getItems().size() + "/" + gtable.getSelectionModel().getSelectedItems().size());
    });

    /*JButton but = new JButton(new AbstractAction("Gene sorter") {
       @Override
       public void actionPerformed(ActionEvent e) {
    try {
       GeneSorter.mynd(genelist, table, "t.scotoductusSA01", contigs);
    } catch (IOException e1) {
       e1.printStackTrace();
    }
       }
    });*/

    final TextField ftextfield = new TextField();
    btoolbar.getItems().add(ftextfield);

    ComboBox<String> scombo = new ComboBox();
    scombo.getItems().add("5S/8S");
    scombo.getItems().add("16S/18S");
    scombo.getItems().add("23S/28S");
    scombo.getSelectionModel().selectedItemProperty().addListener(e -> {
        String name = e.toString().split("/")[0];
        InputStream iss = GeneSet.class.getResourceAsStream("/all" + name + ".fsa");
        InputStreamReader isr = new InputStreamReader(iss);
        BufferedReader brr = new BufferedReader(isr);

        JTextArea textarea = new JTextArea();
        JScrollPane scrollpane = new JScrollPane(textarea);

        try {
            String ln = brr.readLine();
            while (ln != null) {
                textarea.append(ln + "\n");

                ln = brr.readLine();
            }
        } catch (IOException e1) {
            e1.printStackTrace();
        }

        JFrame frame = new JFrame();
        frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        frame.add(scrollpane);
        frame.setSize(400, 300);
        frame.setVisible(true);
    });
    btoolbar.getItems().add(scombo);

    Button swsearch = new Button("SW Search");
    swsearch.setOnAction(e -> {
        JComponent c = new JComponent() {
        };
        final JProgressBar pb = new JProgressBar();
        final JTextArea textarea = new JTextArea();
        JButton searchbut = new JButton(new AbstractAction("Blast") {
            @Override
            public void actionPerformed(ActionEvent e) {
                final String fasta = textarea.getText();
                final SmithWater sw = new SmithWater();
                final InputStream is = GeneSet.class.getResourceAsStream("/allthermus.aa");
                new Thread() {
                    public void run() {
                        try {
                            sw.fasta_align(new StringReader(fasta), new InputStreamReader(is), pb);
                            List<SmithWater.ALN> alns = sw.getAlignments();
                            SmithWater.ALN first = null;
                            int count = 0;
                            String result = "";
                            Set<String> regnames = new HashSet<String>();
                            for (SmithWater.ALN aln : alns) {
                                if (first == null) {
                                    first = aln;
                                } else if (aln.getScore() < 3.0f * (first.getScore() / 4.0f))
                                    break;
                                result += aln.toString();
                                regnames.add(aln.getShortDestName());

                                if (++count == 10)
                                    break;
                            }
                            textarea.setText(result);

                            for (Gene g : geneset.genelist) {
                                boolean found = false;
                                Tegeval tv = g.tegeval;
                                if (regnames.contains(tv.name)) {
                                    found = true;
                                    break;
                                }
                                if (found) {
                                    gtable.getSelectionModel().select(g);
                                    break;
                                }
                            }
                        } catch (IOException e) {
                            e.printStackTrace();
                        }
                    }
                }.start();
            }
        });
        c.setLayout(new BorderLayout());
        JScrollPane scrollpane = new JScrollPane(textarea);
        c.add(scrollpane);
        c.add(pb, BorderLayout.NORTH);
        c.add(searchbut, BorderLayout.SOUTH);

        JFrame frame = new JFrame();
        frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        frame.add(c);
        frame.setSize(400, 300);
        frame.setVisible(true);
    });
    btoolbar.getItems().add(swsearch);
    btoolbar.getItems().add(jb);

    TableColumn<GeneGroup, String> namedesccol = new TableColumn("Desc");
    namedesccol.setCellValueFactory(new PropertyValueFactory<>("name"));
    table.getColumns().add(namedesccol);
    TableColumn<GeneGroup, String> origincol = new TableColumn("Origin");
    origincol.setCellValueFactory(new PropertyValueFactory<>("origin"));
    table.getColumns().add(origincol);
    TableColumn<GeneGroup, String> geneidcol = new TableColumn("Genid");
    geneidcol.setCellValueFactory(new PropertyValueFactory<>("genid"));
    table.getColumns().add(geneidcol);
    TableColumn<GeneGroup, String> refidcol = new TableColumn("Refid");
    refidcol.setCellValueFactory(new PropertyValueFactory<>("refid"));
    table.getColumns().add(refidcol);
    TableColumn<GeneGroup, String> unidcol = new TableColumn("Unid");
    unidcol.setCellValueFactory(new PropertyValueFactory<>("unid"));
    table.getColumns().add(unidcol);
    TableColumn<GeneGroup, String> keggidcol = new TableColumn("Keggid");
    keggidcol.setCellValueFactory(new PropertyValueFactory<>("keggid"));
    table.getColumns().add(keggidcol);
    TableColumn<GeneGroup, String> keggpathcol = new TableColumn("Kegg pathway");
    keggpathcol.setCellValueFactory(new PropertyValueFactory<>("keggPathway"));
    table.getColumns().add(keggpathcol);
    TableColumn<GeneGroup, String> kocol = new TableColumn("KO");
    kocol.setCellValueFactory(new PropertyValueFactory<>("ko"));
    table.getColumns().add(kocol);
    TableColumn<GeneGroup, String> ksymbcol = new TableColumn("Ksymbol");
    ksymbcol.setCellValueFactory(new PropertyValueFactory<>("ksymbol"));
    table.getColumns().add(ksymbcol);
    TableColumn<GeneGroup, String> symbcol = new TableColumn("Symbol");
    symbcol.setCellValueFactory(new PropertyValueFactory<>("symbol"));
    table.getColumns().add(symbcol);
    TableColumn<GeneGroup, String> konamecol = new TableColumn("KO name");
    konamecol.setCellValueFactory(new PropertyValueFactory<>("koname"));
    table.getColumns().add(konamecol);
    TableColumn<GeneGroup, String> pbidcol = new TableColumn("Pbid");
    pbidcol.setCellValueFactory(new PropertyValueFactory<>("pbid"));
    table.getColumns().add(pbidcol);
    TableColumn<GeneGroup, String> eccol = new TableColumn("Ec");
    eccol.setCellValueFactory(new PropertyValueFactory<>("ec"));
    table.getColumns().add(eccol);
    TableColumn<GeneGroup, String> cognamecol = new TableColumn("Cog name");
    cognamecol.setCellValueFactory(new PropertyValueFactory<>("cogname"));
    table.getColumns().add(cognamecol);
    TableColumn<GeneGroup, String> cogcol = new TableColumn("Cog");
    cogcol.setCellValueFactory(new PropertyValueFactory<>("cog"));
    table.getColumns().add(cogcol);
    TableColumn<GeneGroup, String> cogannocol = new TableColumn("Cog annotation");
    cogannocol.setCellValueFactory(new PropertyValueFactory<>("coganno"));
    table.getColumns().add(cogannocol);
    TableColumn<GeneGroup, String> cogsymbcol = new TableColumn("Cog symbol");
    cogsymbcol.setCellValueFactory(new PropertyValueFactory<>("cogsymbol"));
    table.getColumns().add(cogsymbcol);
    TableColumn<GeneGroup, String> cazycol = new TableColumn("Cazy");
    cazycol.setCellValueFactory(new PropertyValueFactory<>("cazy"));
    table.getColumns().add(cazycol);
    TableColumn<GeneGroup, String> prescol = new TableColumn("Present in");
    prescol.setCellValueFactory(new PropertyValueFactory<>("presentin"));
    table.getColumns().add(prescol);

    TableColumn<GeneGroup, Integer> groupindcol = new TableColumn("Group index");
    groupindcol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupIndex"));
    table.getColumns().add(groupindcol);
    TableColumn<GeneGroup, Integer> groupcovcol = new TableColumn("Group coverage");
    groupcovcol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupCoverage"));
    table.getColumns().add(groupcovcol);
    TableColumn<GeneGroup, Integer> groupsizecol = new TableColumn("Group size");
    groupsizecol.setCellValueFactory(new PropertyValueFactory<GeneGroup, Integer>("groupGeneCount"));
    table.getColumns().add(groupsizecol);

    TableColumn<GeneGroup, String> locprefcol = new TableColumn("Loc pref");
    locprefcol.setCellValueFactory(new PropertyValueFactory<>("locpref"));
    table.getColumns().add(locprefcol);
    TableColumn<GeneGroup, String> avgcpcol = new TableColumn("Avg GC%");
    avgcpcol.setCellValueFactory(new PropertyValueFactory<>("avggcp"));
    table.getColumns().add(avgcpcol);
    TableColumn<GeneGroup, String> numloccol = new TableColumn("#Loc");
    numloccol.setCellValueFactory(new PropertyValueFactory<>("numloc"));
    table.getColumns().add(numloccol);
    TableColumn<GeneGroup, String> numlocgroupcol = new TableColumn("#Loc group");
    numlocgroupcol.setCellValueFactory(new PropertyValueFactory<>("numlocgroup"));
    table.getColumns().add(numlocgroupcol);

    TableColumn<GeneGroup, ShareNum> sharenumcol = new TableColumn("Sharing number");
    sharenumcol.setCellValueFactory(new PropertyValueFactory<>("sharingNumber"));
    table.getColumns().add(sharenumcol);
    TableColumn<GeneGroup, String> maxcyccol = new TableColumn("Max cyc");
    maxcyccol.setCellValueFactory(new PropertyValueFactory<>("maxCyc"));
    table.getColumns().add(maxcyccol);

    TableColumn<Gene, String> gnamedesccol = new TableColumn("Desc");
    gnamedesccol.setCellValueFactory(new PropertyValueFactory<>("name"));
    gtable.getColumns().add(gnamedesccol);
    TableColumn<Gene, String> gorigincol = new TableColumn("Origin");
    gorigincol.setCellValueFactory(new PropertyValueFactory<>("origin"));
    gtable.getColumns().add(gorigincol);
    TableColumn<Gene, String> ggeneidcol = new TableColumn("Genid");
    ggeneidcol.setCellValueFactory(new PropertyValueFactory<>("genid"));
    gtable.getColumns().add(ggeneidcol);
    TableColumn<Gene, String> grefidcol = new TableColumn("Refid");
    grefidcol.setCellValueFactory(new PropertyValueFactory<>("refid"));
    gtable.getColumns().add(grefidcol);
    TableColumn<Gene, String> gunidcol = new TableColumn("Unid");
    gunidcol.setCellValueFactory(new PropertyValueFactory<>("unid"));
    gtable.getColumns().add(gunidcol);
    TableColumn<Gene, String> gkeggidcol = new TableColumn("Keggid");
    gkeggidcol.setCellValueFactory(new PropertyValueFactory<>("keggid"));
    gtable.getColumns().add(gkeggidcol);
    TableColumn<Gene, String> gkeggpathcol = new TableColumn("Kegg pathway");
    gkeggpathcol.setCellValueFactory(new PropertyValueFactory<>("keggPathway"));
    gtable.getColumns().add(gkeggpathcol);
    TableColumn<Gene, String> gkocol = new TableColumn("KO");
    gkocol.setCellValueFactory(new PropertyValueFactory<>("ko"));
    gtable.getColumns().add(gkocol);
    TableColumn<Gene, String> gksymbcol = new TableColumn("Ksymbol");
    gksymbcol.setCellValueFactory(new PropertyValueFactory<>("ksymbol"));
    gtable.getColumns().add(gksymbcol);
    TableColumn<Gene, String> gsymbcol = new TableColumn("Symbol");
    gsymbcol.setCellValueFactory(new PropertyValueFactory<>("symbol"));
    gtable.getColumns().add(gsymbcol);
    TableColumn<Gene, String> gkonamecol = new TableColumn("KO name");
    gkonamecol.setCellValueFactory(new PropertyValueFactory<>("koname"));
    gtable.getColumns().add(gkonamecol);
    TableColumn<Gene, String> gpbidcol = new TableColumn("Pbid");
    gpbidcol.setCellValueFactory(new PropertyValueFactory<>("pbid"));
    gtable.getColumns().add(gpbidcol);
    TableColumn<Gene, String> geccol = new TableColumn("Ec");
    geccol.setCellValueFactory(new PropertyValueFactory<>("ec"));
    gtable.getColumns().add(geccol);
    TableColumn<Gene, String> gcognamecol = new TableColumn("Cog name");
    gcognamecol.setCellValueFactory(new PropertyValueFactory<>("cogname"));
    gtable.getColumns().add(gcognamecol);
    TableColumn<Gene, String> gcogcol = new TableColumn("Cog");
    gcogcol.setCellValueFactory(new PropertyValueFactory<>("cog"));
    gtable.getColumns().add(gcogcol);
    TableColumn<Gene, String> gcogannocol = new TableColumn("Cog annotation");
    gcogannocol.setCellValueFactory(new PropertyValueFactory<>("coganno"));
    gtable.getColumns().add(gcogannocol);
    TableColumn<Gene, String> gcogsymbcol = new TableColumn("Cog symbol");
    gcogsymbcol.setCellValueFactory(new PropertyValueFactory<>("cogsymbol"));
    gtable.getColumns().add(gcogsymbcol);
    TableColumn<Gene, String> gcazycol = new TableColumn("Cazy");
    gcazycol.setCellValueFactory(new PropertyValueFactory<>("cazy"));
    gtable.getColumns().add(gcazycol);
    TableColumn<Gene, String> gprescol = new TableColumn("Present in");
    gprescol.setCellValueFactory(new PropertyValueFactory<>("presentin"));
    gtable.getColumns().add(gprescol);

    TableColumn<Gene, Integer> ggroupindcol = new TableColumn("Group index");
    ggroupindcol.setCellValueFactory(new PropertyValueFactory<>("groupIndex"));
    gtable.getColumns().add(ggroupindcol);
    TableColumn<Gene, Integer> ggroupcovcol = new TableColumn("Group coverage");
    ggroupcovcol.setCellValueFactory(new PropertyValueFactory<>("groupCoverage"));
    gtable.getColumns().add(ggroupcovcol);
    TableColumn<Gene, Integer> ggroupsizecol = new TableColumn("Group size");
    ggroupsizecol.setCellValueFactory(new PropertyValueFactory<>("groupGeneCount"));
    gtable.getColumns().add(ggroupsizecol);

    TableColumn<Gene, String> glocprefcol = new TableColumn("Loc pref");
    glocprefcol.setCellValueFactory(new PropertyValueFactory<>("locpref"));
    gtable.getColumns().add(glocprefcol);
    TableColumn<Gene, String> gavgcpcol = new TableColumn("Avg GC%");
    gavgcpcol.setCellValueFactory(new PropertyValueFactory<>("avggcp"));
    gtable.getColumns().add(gavgcpcol);
    TableColumn<Gene, String> gnumloccol = new TableColumn("#Loc");
    gnumloccol.setCellValueFactory(new PropertyValueFactory<>("numloc"));
    gtable.getColumns().add(gnumloccol);
    TableColumn<Gene, String> gnumlocgroupcol = new TableColumn("#Loc group");
    gnumlocgroupcol.setCellValueFactory(new PropertyValueFactory<>("numlocgroup"));
    gtable.getColumns().add(gnumlocgroupcol);

    TableColumn<Gene, ShareNum> gsharenumcol = new TableColumn("Sharing number");
    gsharenumcol.setCellValueFactory(new PropertyValueFactory<>("sharingNumber"));
    gtable.getColumns().add(gsharenumcol);
    TableColumn<Gene, String> gmaxcyccol = new TableColumn("Max cyc");
    gmaxcyccol.setCellValueFactory(new PropertyValueFactory<>("maxCyc"));
    gtable.getColumns().add(gmaxcyccol);

    /*if( upper != null ) {
       SwingUtilities.invokeLater( new Runnable() {
    public void run() {
       //upper.setContent( botcomp );
       lower.setContent( topcomp );
    }
       });
    } else {
       splitpane.setBottomComponent(botcomp);
       splitpane.setTopComponent(topcomp);
    }
            
    groupModel = new TableModel() {
       @Override
       public int getRowCount() {
    return geneset.allgenegroups == null ? 0 : geneset.allgenegroups.size();
       }
            
       @Override
       public int getColumnCount() {
    return 32+geneset.specList.size();
       }
            
       @Override
       public String getColumnName(int columnIndex) {
    if (columnIndex == 0) {
       return "Desc";
    } else if (columnIndex == 1) {
       return "Origin";
    } else if (columnIndex == 2) {
       return "Genid";
    } else if (columnIndex == 3) {
       return "Refid";
    } else if (columnIndex == 4) {
       return "Unid";
    } else if (columnIndex == 5) {
       return "Keggid";
    } else if (columnIndex == 6) {
       return "Kegg pathway";
    } else if (columnIndex == 7) {
       return "KO";
    } else if (columnIndex == 8) {
       return "KSymbol";
    } else if (columnIndex == 9) {
       return "Symbol";
    } else if (columnIndex == 10) {
       return "KO name";
    } else if (columnIndex == 11) {
       return "Pdbid";
    } else if (columnIndex == 12) {
       return "EC";
    } else if (columnIndex == 13) {
       return "Cog name";
    } else if (columnIndex == 14) {
       return "Cog";
    } else if (columnIndex == 15) {
       return "Cog annotation";
    } else if (columnIndex == 16) {
       return "Cog symbol";
    } else if (columnIndex == 17) {
       return "Cazy";
    } else if (columnIndex == 18) {
       return "Present in";
    } else if (columnIndex == 19) {
       return "Group index";
    } else if (columnIndex == 20) {
       return "Group coverage";
    } else if (columnIndex == 21) {
       return "Group size";
    } else if (columnIndex == 22) {
       return "Locprev";
    } else if (columnIndex == 23) {
       return "Avg GC%";
    } else if (columnIndex == 24) {
       return "# of locus";
    } else if (columnIndex == 25) {
       return "# of loc in group";
    } else if (columnIndex == 26) {
       return "max length";
    } else if (columnIndex == 27) {
       return "sharing number";
    } else if (columnIndex == 28) {
       return "# Cyc";
    } else if (columnIndex == 29) {
       return "16S Corr";
    } else if (columnIndex == 30) {
       return "SingalP";
    } else if (columnIndex == 31) {
       return "TransM";
    } else {
       String spec = geneset.specList.get( columnIndex - 32 );
       if( spec != null ) {
          if( spec.toLowerCase().contains("thermus") ) {
             int i = spec.indexOf('_');
             return spec.substring(i+1, spec.length());
          } else return spec;
       }
       return "";
    }
    /* else if (columnIndex == 19) {
       return "T.tSG0";
    } else if (columnIndex == 20) {
       return "T.tJL18";
    } else if (columnIndex == 21) {
       return "T.tHB8";
    } else if (columnIndex == 22) {
       return "T.tHB27";
    } else if (columnIndex == 23) {
       return "T.scotoSA01";
    } else if (columnIndex == 24) {
       return "T.aqua";
    } else if (columnIndex == 25) {
       return "T.eggert";
    } else if (columnIndex == 26) {
       return "T.island";
    } else if (columnIndex == 27) {
       return "T.antan";
    } else if (columnIndex == 28) {
       return "T.scoto346";
    } else if (columnIndex == 29) {
       return "T.scoto1572";
    } else if (columnIndex == 30) {
       return "T.scoto252";
    } else if (columnIndex == 31) {
       return "T.scoto2101";
    } else if (columnIndex == 32) {
       return "T.scoto2127";
    } else if (columnIndex == 33) {
       return "T.scoto4063";
    } else if (columnIndex == 34) {
       return "T.oshimai";
    } else if (columnIndex == 35) {
       return "T.brockianus";
    } else if (columnIndex == 36) {
       return "T.filiformis";
    } else if (columnIndex == 37) {
       return "T.igniterrae";
    } else if (columnIndex == 38) {
       return "T.kawarayensis";
    } else if (columnIndex == 39) {
       return "T.arciformis";
    } else if (columnIndex == 40) {
       return "T.spCCB";
    } else if (columnIndex == 41) {
       return "T.spRLM";
    } else if (columnIndex == 42) {
       return "T.oshimaiJL2";
    } else if (columnIndex == 43) {
       return "MT.silvianus";
    } else if (columnIndex == 44) {
       return "MT.ruber";
    } else if (columnIndex == 45) {
       return "M.hydro";
    } else if (columnIndex == 46) {
       return "O.profu";
    }*
            
    //return "";
       }
            
       @Override
       public Class<?> getColumnClass(int columnIndex) {
    if( columnIndex == 19 || columnIndex == 20 || columnIndex == 28 )
       return Double.class;
    else if(columnIndex == 10 || (columnIndex >= 17 && columnIndex <= 28) )
       return Integer.class;
    else if (columnIndex >= 32)
       return Teg.class;
    return String.class;
       }
            
       @Override
       public boolean isCellEditable(int rowIndex, int columnIndex) {
    return false;
       }
            
       @Override
       public Object getValueAt(int rowIndex, int columnIndex) {
    GeneGroup gg = geneset.allgenegroups.get(rowIndex);
    if (columnIndex == 0) {
       return gg.getCommonName();
    } else if (columnIndex == 1) {
       return gg.getCommonOrigin();
    } else if (columnIndex == 2) {
       return null;//gene.genid;
    } else if (columnIndex == 3) {
       return gg.getCommonRefId();
    } else if (columnIndex == 4) {
       return gg.getCommonUnId();
    } else if (columnIndex == 5) {
       return gg.getKeggid();
    } else if (columnIndex == 6) {
       return gg.getKeggPathway();
    } else if (columnIndex == 7) {
       return gg.getCommonKO();
    } else if (columnIndex == 8) {
       return gg.getCommonKSymbol();
    } else if (columnIndex == 9) {
       return gg.getCommonSymbol(); //ko2name != null ? ko2name.get( gg.getCommonKO() ) : null;
    } else if (columnIndex == 10) {
       String ret = geneset.ko2name != null ? geneset.ko2name.get( gg.getCommonKO() ) : null;
       if( ret == null ) {
          String symbol = gg.getCommonSymbol();
          if( symbol != null ) {
             if( symbol.length() <= 5 ) ret = symbol;
          }
       }
       return ret;
    } else if (columnIndex == 11) {
       return null;//gene.pdbid;
    } else if (columnIndex == 12) {
       return gg.getCommonEc();
    } else if (columnIndex == 13) {
       Cog cog = gg.getCommonCog( geneset.cogmap );
       if( cog != null ) {
          if( cog.name == null ) cog.name = geneset.cogidmap.get( cog.id );
          return cog.name;
       }
       return null;
    } else if (columnIndex == 14) {
       Cog cog = gg.getCommonCog( geneset.cogmap );
       return cog != null ? cog.id : null;
    } else if (columnIndex == 15) {
       Cog cog = gg.getCommonCog( geneset.cogmap );
       return cog != null ? cog.annotation : null;
    } else if (columnIndex == 16) {
       Cog cog = gg.getCommonCog( geneset.cogmap );
       return cog != null ? cog.genesymbol : null;
    } else if (columnIndex == 17) {
       return gg.getCommonCazy( geneset.cazymap );
    } else if (columnIndex == 18) {
       return gg.getSpecies().size();
    } else if (columnIndex == 19) {
       return gg.groupIndex;
    } else if (columnIndex == 20) {
       return gg.getGroupCoverage();
    } else if (columnIndex == 21) {
       return gg.getGroupGeneCount();
    } else if (columnIndex == 22) {
       return null;//gene.proximityGroupPreservation;
    } else if (columnIndex == 23) {
       return gg.getAvgGCPerc();
    } else if (columnIndex == 24) {
       return gg.genes.size();
    } else if (columnIndex == 25) {
       return gg.getGroupCount();
    } else if (columnIndex == 26) {
       return gg.getMaxLength();
    } else if (columnIndex == 27) {
       return geneset.specset.get( gg.getSpecies() );
    } else if (columnIndex == 28) {
       return gg.getMaxCyc();
    } else if (columnIndex == 29) {
       return gg.getGroupCoverage() == 39 && gg.getGroupCount() == 39 ? 0 : -1;
    } else if (columnIndex == 30) {
       return gg.getCommonSignalP();
    } else if (columnIndex == 31) {
       return gg.getCommonTransM();
    } else {
       String spec = geneset.specList.get( columnIndex - 32 );
       Teginfo ret = geneset.getGroupTes( gg, spec );
       return ret;
       //return null;
    }
    //return columnIndex >= 11 ? null : "";
       }
            
       @Override
       public void setValueAt(Object aValue, int rowIndex, int columnIndex) {}
            
       @Override
       public void addTableModelListener(TableModelListener l) {}
            
       @Override
       public void removeTableModelListener(TableModelListener l) {}
    };
    defaultModel = new TableModel() {
       @Override
       public int getRowCount() {
    int gs = geneset.genelist.size();
    return gs;
       }
            
       @Override
       public int getColumnCount() {
    return 26+geneset.specList.size();
       }
            
       @Override
       public String getColumnName(int columnIndex) {
    if (columnIndex == 0) {
       return "Desc";
    } else if (columnIndex == 1) {
       return "Origin";
    } else if (columnIndex == 2) {
       return "Genid";
    } else if (columnIndex == 3) {
       return "Refid";
    } else if (columnIndex == 4) {
       return "Unid";
    } else if (columnIndex == 5) {
       return "Keggid";
    } else if (columnIndex == 6) {
       return "KOid";
    } else if (columnIndex == 7) {
       return "KSymbol";
    } else if (columnIndex == 8) {
       return "Symbol";
    } else if (columnIndex == 9) {
       return "KOname";
    } else if (columnIndex == 10) {
       return "Pdbid";
    } else if (columnIndex == 11) {
       return "ecid";
    } else if (columnIndex == 12) {
       return "COG";
    } else if (columnIndex == 13) {
       return "COG name";
    } else if (columnIndex == 14) {
       return "Present in";
    } else if (columnIndex == 15) {
       return "Group index";
    } else if (columnIndex == 16) {
       return "Group coverage";
    } else if (columnIndex == 17) {
       return "Group size";
    } else if (columnIndex == 18) {
       return "Locprev";
    } else if (columnIndex == 19) {
       return "Avg GC%";
    } else if (columnIndex == 20) {
       return "# of locus";
    } else if (columnIndex == 21) {
       return "# of loc in group";
    } else if (columnIndex == 22) {
       return "max length";
    } else if (columnIndex == 23) {
       return "sharing number";
    } else if (columnIndex == 24) {
       return "# Cyc";
    } else if (columnIndex == 25) {
       return "16S Corr";
    } else {
       return geneset.specList.get( columnIndex - 26 );
    } /*else if (columnIndex == 19) {
       return "T.tSG0";
    } else if (columnIndex == 20) {
       return "T.tJL18";
    } else if (columnIndex == 21) {
       return "T.tHB8";
    } else if (columnIndex == 22) {
       return "T.tHB27";
    } else if (columnIndex == 23) {
       return "T.scotoSA01";
    } else if (columnIndex == 24) {
       return "T.aqua";
    } else if (columnIndex == 25) {
       return "T.eggert";
    } else if (columnIndex == 26) {
       return "T.island";
    } else if (columnIndex == 27) {
       return "T.antan";
    } else if (columnIndex == 28) {
       return "T.scoto346";
    } else if (columnIndex == 29) {
       return "T.scoto1572";
    } else if (columnIndex == 30) {
       return "T.scoto252";
    } else if (columnIndex == 31) {
       return "T.scoto2101";
    } else if (columnIndex == 32) {
       return "T.scoto2127";
    } else if (columnIndex == 33) {
       return "T.scoto4063";
    } else if (columnIndex == 34) {
       return "T.oshimai";
    } else if (columnIndex == 35) {
       return "T.brockianus";
    } else if (columnIndex == 36) {
       return "T.filiformis";
    } else if (columnIndex == 37) {
       return "T.igniterrae";
    } else if (columnIndex == 38) {
       return "T.kawarayensis";
    } else if (columnIndex == 39) {
       return "T.arciformis";
    } else if (columnIndex == 40) {
       return "T.spCCB";
    } else if (columnIndex == 41) {
       return "T.spRLM";
    } else if (columnIndex == 42) {
       return "T.oshimaiJL2";
    } else if (columnIndex == 43) {
       return "MT.silvianus";
    } else if (columnIndex == 44) {
       return "MT.ruber";
    } else if (columnIndex == 45) {
       return "M.hydro";
    } else if (columnIndex == 46) {
       return "O.profu";
    }*
       }
            
       @Override
       public Class<?> getColumnClass(int columnIndex) {
    if( columnIndex == 16 || columnIndex == 19 || columnIndex == 25 )
       return Double.class;
    else if(columnIndex >= 13 && columnIndex <= 24)
       return Integer.class;
    else if (columnIndex >= 26)
       return Teg.class;
    return String.class;
       }
            
       @Override
       public boolean isCellEditable(int rowIndex, int columnIndex) {
    return false;
       }
            
       @Override
       public Object getValueAt(int rowIndex, int columnIndex) {
    Gene gene = geneset.genelist.get(rowIndex);
    if (columnIndex == 0) {
       GeneGroup gg = gene.getGeneGroup();
       return gg != null ? gene.getGeneGroup().getCommonName() : null;
    } else if (columnIndex == 1) {
       return gene.getSpecies();
    } else if (columnIndex == 2) {
       return gene.genid;
    } else if (columnIndex == 3) {
       return gene.refid;
    } else if (columnIndex == 4) {
       return gene.uniid;
    } else if (columnIndex == 5) {
       return gene.keggid;
    } else if (columnIndex == 6) {
       GeneGroup gg = gene.getGeneGroup();
       return gg != null ? gg.getCommonKO() : null;
    } else if (columnIndex == 7) {
       GeneGroup gg = gene.getGeneGroup();
       return gg != null ? gg.getCommonKSymbol() : null;
    } else if (columnIndex == 8) {
       GeneGroup gg = gene.getGeneGroup();
       return gg != null ? gg.getCommonSymbol() : null; //gene.symbol
    } else if (columnIndex == 9) {
       GeneGroup gg = gene.getGeneGroup();
       return gg != null ? gg.getCommonKOName( geneset.ko2name ) : null;
    } else if (columnIndex == 10) {
       return gene.pdbid;
    } else if (columnIndex == 11) {
       return gene.ecid;
    } else if (columnIndex == 12) {
       Cog cog = gene.getGeneGroup() != null ? gene.getGeneGroup().getCommonCog( geneset.cogmap ) : null;
       if( cog != null ) return cog.id;
       return null;
    } else if (columnIndex == 13) {
       Cog cog = gene.getGeneGroup() != null ? gene.getGeneGroup().getCommonCog( geneset.cogmap ) : null;
       if( cog != null ) return cog.name;
       return null;
    } else if (columnIndex == 14) {
       return gene.getGeneGroup().getSpecies().size();
    } else if (columnIndex == 15) {
       return gene.getGroupIndex();
    } else if (columnIndex == 16) {
       return gene.getGroupCoverage();
    } else if (columnIndex == 17) {
       return gene.getGroupGenCount();
    } else if (columnIndex == 18) {
       return gene.proximityGroupPreservation;
    } else if (columnIndex == 19) {
       return gene.getGCPerc();
    } else if (columnIndex == 20) {
       /*int val = 0;
       for (String str : gene.species.keySet()) {
          val += gene.species.get(str).tset.size();
       }*
       return 1;
    } else if (columnIndex == 21) {
       return gene.getGroupCount();
    } else if (columnIndex == 22) {
       return gene.getMaxLength();
    } else if (columnIndex == 23) {
       GeneGroup gg = gene.getGeneGroup();
       if( gg != null && gg.getSpecies() != null ) {
          return geneset.specset.get( gg.getSpecies() );
       }
       return null;
    } else if (columnIndex == 24) {
       gene.getMaxCyc();
    } else if (columnIndex == 25) {
       return gene.getGroupCoverage() == 35 && gene.getGroupCount() == 35 ? gene.corr16s : -1;
    } else {
       /*String spec = specList.get( columnIndex-26 );
       /*if( spec.contains("timidus") ) {
          System.err.println();
       }*
       //Teginfo set = gene.species.equals(spec) ? gene.teginfo : null;
       if( gene.getSpecies().equals( spec ) ) {
          return gene.tegeval;
       } else {
          return gene.getGeneGroup().species.get( spec );
       }*
               
       return null;
    }
    return columnIndex >= 17 ? null : "";
       }
            
       @Override
       public void setValueAt(Object aValue, int rowIndex, int columnIndex) {}
            
       @Override
       public void addTableModelListener(TableModelListener l) {}
            
       @Override
       public void removeTableModelListener(TableModelListener l) {}
    };
    table.setModel( groupModel );*/
    //table.setModel( defaultModel );

    /*
     * Comparator<Tegeval> wrapMe = new Comparator<Tegeval>() { public int
     * compare(Tegeval o1, Tegeval o2) { return o1.compareTo(o2); } };
     * DefaultRowSorter<TableModel, Integer> rowsorter =
     * (DefaultRowSorter<TableModel,Integer>)table.getRowSorter(); for( int
     * i = 10; i < 23; i++ ) { rowsorter.setComparator(i,
     * NullComparators.atEnd(wrapMe)); }
     */

    /*table.getRowSorter().addRowSorterListener( new RowSorterListener() {
       @Override
       public void sorterChanged(RowSorterEvent e) {
    for (String cstr : geneset.contigmap.keySet()) {
       Sequence c = geneset.contigmap.get(cstr);
       //c.count = 0;
       c.loc = 0.0;
    }
            
    if( table.getModel() == defaultModel ) {
       for (Gene g : geneset.genelist) {
          Tegeval tv = g.tegeval;
             // int first = tv.cont.indexOf('_');
             // int sec = tv.cont.indexOf('_',first+1);
          Sequence cont = tv.getContshort(); // tv.cont.substring(0,sec);
          if( cont != null && geneset.contigmap.containsKey(cont.getName()) ) {
             Sequence c = geneset.contigmap.get(cont.getName());
             //c.count++;
             int val = table.convertRowIndexToView(g.index);
             c.loc += (double) val;
          }
       }
    }
    for( JSplitPane gsplitpane : splitpaneList ) {
       gsplitpane.repaint();
    }
       }
    });*/

    ftable = upper;
    ftable.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
    /*ftable = new JTable() {
       public String getToolTipText(MouseEvent me) {
    Point p = me.getPoint();
    int r = rowAtPoint(p);
    int c = columnAtPoint(p);
    if (r >= 0 && r < super.getRowCount()) {
       Object ret = super.getValueAt(r, c);
       if (ret != null) {
          return ret.toString(); // super.getToolTipText( me );
       }
    }
    return "";
       }
    };*/

    ContextMenu fpopup = new ContextMenu();
    MenuItem amigo = new MenuItem("Amigo lookup");
    amigo.setOnAction(e -> {
        String go = ftable.getSelectionModel().getSelectedItem().getGo();
        try {
            // GeneSetHead.this.getAppletContext().
            Desktop.getDesktop()
                    .browse(new URI("http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=" + go));
        } catch (IOException e1) {
            e1.printStackTrace();
        } catch (URISyntaxException e1) {
            e1.printStackTrace();
        }
    });
    fpopup.getItems().add(amigo);
    MenuItem keggl = new MenuItem("KEGG lookup");
    keggl.setOnAction(e -> {
        String kegg = ftable.getSelectionModel().getSelectedItem().getKegg();
        try {
            Desktop.getDesktop().browse(new URI("http://www.genome.jp/dbget-bin/www_bget?rn:" + kegg));
        } catch (IOException e1) {
            e1.printStackTrace();
        } catch (URISyntaxException e1) {
            e1.printStackTrace();
        }
    });
    fpopup.getItems().add(keggl);
    MenuItem ecl = new MenuItem("EC lookup");
    ecl.setOnAction(e -> {
        String ec = ftable.getSelectionModel().getSelectedItem().getEc();
        try {
            Desktop.getDesktop().browse(new URI("http://enzyme.expasy.org/EC/" + ec));
        } catch (IOException e1) {
            e1.printStackTrace();
        } catch (URISyntaxException e1) {
            e1.printStackTrace();
        }
    });
    fpopup.getItems().add(ecl);
    fpopup.getItems().add(new SeparatorMenuItem());

    MenuItem excelreport = new MenuItem("Excel report");
    excelreport.setOnAction(e -> {
        Workbook workbook = new XSSFWorkbook();
        Sheet sheet = workbook.createSheet("enzyme");
        int k = 0;
        for (Function f : ftable.getSelectionModel().getSelectedItems()) {
            //String ec = (String)ftable.getValueAt(r, 1);
            //String go = (String)ftable.getValueAt(r, 0);

            //int i = ftable.getSelectionModel().convertRowIndexToModel(r);
            //Function f = geneset.funclist.get(i);
            for (GeneGroup gg : f.getGeneGroups()) {
                for (String spec : gg.getSpecies()) {
                    Teginfo ti = gg.getGenes(spec);

                    Row row = sheet.createRow(k++);
                    Cell ecell = row.createCell(0);
                    ecell.setCellValue("EC:" + f.getEc());
                    Cell ncell = row.createCell(1);
                    ncell.setCellValue(f.getName());
                    Cell spell = row.createCell(2);
                    spell.setCellValue(spec);
                    Cell seqcell = row.createCell(3);
                    seqcell.setCellValue(ti.tset.size());
                }
                /*for( Gene g :gg.genes ) {
                   Row    row = sheet.createRow(k++);
                   Cell    ecell = row.createCell(0);
                   ecell.setCellValue( "EC:"+f.ec );
                   Cell    ncell = row.createCell(1);
                   ncell.setCellValue( f.name );
                   Cell    spell = row.createCell(2);
                   spell.setCellValue( g.getSpecies() );
                   Cell    seqcell = row.createCell(3);
                   seqcell.setCellValue( g.tegeval.getAlignedSequence().toString() );
                }*/
            }
            sheet.createRow(k++);
        }

        try {
            Path tempfile = Files.createTempFile("enzyme", ".xlsx");
            OutputStream os = Files.newOutputStream(tempfile);
            workbook.write(os);
            os.close();

            Desktop.getDesktop().open(tempfile.toFile());
        } catch (FileNotFoundException e1) {
            e1.printStackTrace();
        } catch (IOException e1) {
            e1.printStackTrace();
        }
    });
    fpopup.getItems().add(excelreport);
    ftable.setContextMenu(fpopup);

    ContextMenu popup = new ContextMenu();
    MenuItem splitaction = new MenuItem("Split");
    splitaction.setOnAction(e -> {
        Dialog<Set<GeneGroup>> dialog = new Dialog<>();
        dialog.setResizable(true);

        GridPane grid = new GridPane();
        grid.setHgap(10);
        grid.setVgap(10);
        grid.setPadding(new Insets(20, 20, 10, 10));

        TextField len = new TextField();
        len.setPromptText("0.5");
        TextField id = new TextField();
        id.setPromptText("0.5");

        grid.add(new Label("%Length:"), 0, 0);
        grid.add(len, 1, 0);
        grid.add(new Label("%Identity:"), 0, 1);
        grid.add(id, 1, 1);

        final ListView<GeneGroup> list = new ListView<>();
        list.setPrefWidth(400);
        grid.add(list, 0, 2, 2, 1);

        final GeneGroup gg = table.getSelectionModel().getSelectedItem();
        list.setItems(FXCollections.singletonObservableList(gg));

        Label groupsize = new Label("" + gg.genes.size());
        grid.add(groupsize, 0, 3, 2, 1);

        len.textProperty().addListener((observable, oldValue, newValue) -> {
            if (!newValue.equals(oldValue)) {
                double d = 0;
                try {
                    d = Double.parseDouble(newValue);
                } catch (Exception ex) {
                }

                if (d > 0) {
                    Set<GeneGroup> ggmap = new HashSet<>();
                    Map<String, Integer> blosumMap = JavaFasta.getBlosumMap(false);
                    for (Gene gene : gg.genes) {
                        if (ggmap.stream().flatMap(f -> f.genes.stream()).noneMatch(p -> gene == p)) {
                            Set<Gene> ggset = new HashSet<>();
                            Sequence seq1 = gene.tegeval.getAlignedSequence();
                            for (Gene cgene : gg.genes) {
                                Sequence seq2 = cgene.tegeval.getAlignedSequence();
                                int[] tscore = GeneCompare.blosumValue(seq1, seq1, seq2, blosumMap);
                                int sscore = GeneCompare.blosumValue(seq1, seq2, blosumMap);

                                double dval = (double) (sscore - tscore[1]) / (double) (tscore[0] - tscore[1]);
                                if (dval > d) {
                                    ggset.add(cgene);
                                }
                            }
                            System.err.println(ggset.size());

                            Set<GeneGroup> osubgg = ggmap.stream().filter(f -> {
                                Set<Gene> gs = new HashSet<>(ggset);
                                gs.retainAll(f.genes);
                                return gs.size() > 0;
                            }).collect(Collectors.toSet());
                            GeneGroup subgg;
                            if (osubgg.size() > 0) {
                                Iterator<GeneGroup> git = osubgg.iterator();
                                subgg = git.next();
                                while (git.hasNext()) {
                                    GeneGroup remgg = git.next();
                                    subgg.addGenes(remgg.genes);
                                    ggmap.remove(remgg);
                                }
                            } else {
                                subgg = new GeneGroup();
                                subgg.setCogMap(gg.getCogMap());
                                subgg.setKonameMap(gg.getKonameMap());
                                subgg.setSpecSet(gg.getSpecSet());
                                ggmap.add(subgg);
                            }
                            subgg.addGenes(ggset);
                        }
                    }
                    Set<GeneGroup> sgg = ggmap.stream().collect(Collectors.toSet());

                    List<GeneGroup> lgg = new ArrayList(sgg);
                    list.setItems(FXCollections.observableList(lgg));
                    dialog.setResultConverter(param -> sgg);
                }
            }
        });

        dialog.getDialogPane().setContent(grid);
        dialog.getDialogPane().getButtonTypes().add(ButtonType.OK);
        dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL);
        Optional<Set<GeneGroup>> ogg = dialog.showAndWait();

        ogg.ifPresent(c -> {
            geneset.allgenegroups.remove(gg);
            geneset.allgenegroups.addAll(c);

            Map<String, String> env = new HashMap<>();
            env.put("create", "true");
            try {
                geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                    Files.walk(root).filter(f -> f.toString().startsWith("/aligned"))
                            .filter(f -> f.toString().endsWith(".aa")).filter(f -> {
                                String filename = f.getFileName().toString();
                                return gg.genes.stream().anyMatch(g -> {
                                    String fnid = filename.substring(0, filename.length() - 3);
                                    return g.name.equals(fnid);
                                });
                            }).forEach(p -> {
                                try {
                                    Files.deleteIfExists(p);
                                } catch (IOException e1) {
                                    e1.printStackTrace();
                                }
                            });
                    /*for( Gene g : gg.genes ) {
                       if( g.keggpathway != null ) {
                          String sub = g.keggpathway.substring(0,3);
                          Path subf = root.resolve(sub);
                          if( Files.exists(subf) ) {
                             String[] split = g.keggpathway.split(" ");
                             for( String s : split ) {
                      Path pimg = subf.resolve(s+".png");
                      if( Files.exists(pimg) ) {
                         showKeggPathway( sub, pimg );
                      }
                             }
                          }
                       }
                    }*/
                    final Path p = root.resolve("/aligned");
                    c.stream().forEach(fgg -> {
                        Path np = p.resolve(fgg.genes.iterator().next().getName());
                        try {
                            Writer w = Files.newBufferedWriter(np);
                            fgg.getFasta(w, false);
                            w.close();
                        } catch (IOException e1) {
                            e1.printStackTrace();
                        }
                    });
                    break;
                }
                geneset.zipfilesystem.close();
            } catch (Exception ex) {
                ex.printStackTrace();
            }
        });
    });
    popup.getItems().add(splitaction);
    MenuItem joinaction = new MenuItem("Join");

    popup.getItems().add(joinaction);
    popup.getItems().add(new SeparatorMenuItem());
    MenuItem showkegg = new MenuItem("Show KEGG pathway");
    showkegg.setOnAction(e -> {
        GeneGroup gg = table.getSelectionModel().getSelectedItem();

        Map<String, String> env = new HashMap<>();
        env.put("create", "true");

        /*String uristr = "jar:" + geneset.zippath.toUri();
        URI zipuri = URI.create( uristr /*.replace("file://", "file:")* );
        final List<Path>   lbi = new ArrayList<>();*/
        boolean shown = false;
        try {
            geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
            for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                for (Gene g : gg.genes) {
                    if (g.keggpathway != null) {
                        String sub = g.keggpathway.substring(0, 3);
                        Path subf = root.resolve(sub);
                        if (Files.exists(subf)) {
                            String[] split = g.keggpathway.split(" ");
                            for (String s : split) {
                                Path pimg = subf.resolve(s + ".png");
                                if (Files.exists(pimg)) {
                                    showKeggPathway(sub, pimg);
                                    shown = true;
                                    break;
                                }
                            }
                        }
                    }
                }
                break;
            }
            geneset.zipfilesystem.close();
        } catch (Exception ex) {
            ex.printStackTrace();
        }

        if (!shown) {
            for (Gene g : gg.genes) {
                if (g.keggpathway != null) {
                    String[] keggsplit = g.keggpathway.split(";");
                    Arrays.stream(keggsplit).map(s -> s.split(":")[0]).findFirst().ifPresent(c -> {
                        try {
                            Desktop.getDesktop().browse(
                                    URI.create("http://www.genome.jp/dbget-bin/www_bget?map" + c.substring(2)));
                        } catch (IOException e1) {
                            e1.printStackTrace();
                        }
                    });
                }
            }
        }
    });
    popup.getItems().add(showkegg);
    MenuItem plasmid = new MenuItem("Plasmid");
    plasmid.setOnAction(e -> {
        Gene g = gtable.getSelectionModel().getSelectedItem();
        Sequence contig = g.tegeval.getContshort();
        String contigstr = contig.toString();
        contig.plasmid = !geneset.plasmids.contains(contigstr);
        if (contig.plasmid)
            geneset.plasmids.add(contigstr);
        else
            geneset.plasmids.remove(contigstr);

        try {
            Map<String, String> env = new HashMap<>();
            env.put("create", "true");
            //Path path = zipfile.toPath();
            String uristr = "jar:" + geneset.zippath.toUri();
            geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );
            geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);

            //fs = FileSystems.newFileSystem( uri, env );
            //FileSystem fs = FileSystems.newFileSystem(uri, env);

            ByteArrayOutputStream baos = new ByteArrayOutputStream();
            for (String contigname : geneset.plasmids) {
                baos.write((contigname + "\n").getBytes());
            }

            Path nf = geneset.zipfilesystem.getPath("/plasmids.txt");
            long bl = Files.copy(new ByteArrayInputStream(baos.toByteArray()), nf,
                    StandardCopyOption.REPLACE_EXISTING);
            //System.err.println( "eeerm " + bl );
            geneset.zipfilesystem.close();

            /*Writer writer = Files.newBufferedWriter(nf, StandardCharsets.UTF_8, StandardOpenOption.CREATE);
            for( String phage : phageset ) {
               writer.write( phage + "\n" );
            }
            writer.close();*/

            //writer.write("hello");
        } catch (IOException e1) {
            e1.printStackTrace();
        }
    });
    popup.getItems().add(plasmid);
    MenuItem designate = new MenuItem("Designate");
    designate.setOnAction(e -> {
        SwingUtilities.invokeLater(() -> {
            JComboBox<String> descombo = new JComboBox<>(
                    geneset.deset.toArray(new String[geneset.deset.size()]));
            descombo.setEditable(true);
            JOptionPane.showMessageDialog(GeneSetHead.this, descombo);
            String val = descombo.getSelectedItem().toString();
            geneset.deset.add(val);
            for (Gene g : gtable.getSelectionModel().getSelectedItems()) {
                g.tegeval.designation = val;
                if (g.id != null) {
                    geneset.designations.put(g.id, val);
                } else {
                    System.err.println(g.refid);
                }
                //ta.append( g.tegeval.id + "\n" );
            }

            try {
                Map<String, String> env = new HashMap<String, String>();
                env.put("create", "true");
                //Path path = zipfile.toPath();
                String uristr = "jar:" + geneset.zippath.toUri();
                geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );
                geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);

                //fs = FileSystems.newFileSystem( uri, env );
                //FileSystem fs = FileSystems.newFileSystem(uri, env);

                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                for (String geneid : geneset.designations.keySet()) {
                    String design = geneset.designations.get(geneid);
                    baos.write((geneid + "\t" + design + "\n").getBytes());
                }

                Path nf = geneset.zipfilesystem.getPath("/designations.txt");
                long bl = Files.copy(new ByteArrayInputStream(baos.toByteArray()), nf,
                        StandardCopyOption.REPLACE_EXISTING);
                //System.err.println( "eeerm " + bl );
                geneset.zipfilesystem.close();

                /*Writer writer = Files.newBufferedWriter(nf, StandardCharsets.UTF_8, StandardOpenOption.CREATE);
                for( String phage : phageset ) {
                    writer.write( phage + "\n" );
                }
                writer.close();*/

                //writer.write("hello");
            } catch (IOException e1) {
                e1.printStackTrace();
            }

            /*JFrame frame = new JFrame("Ids");
            frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE );
            frame.setSize(800, 600);
            JTextArea   ta = new JTextArea();
            JScrollPane sp = new JScrollPane( ta );
            frame.add( sp );
                    
            frame.setVisible( true );*/
        });
    });
    popup.getItems().add(designate);
    MenuItem koname = new MenuItem("KO to name");
    koname.setOnAction(e -> {
        Set<String> koids = new HashSet<>();
        for (Gene g : geneset.genelist) {
            if (g.koid != null && g.koid.length() > 0
                    && !(geneset.ko2name != null && geneset.ko2name.containsKey(g.koid)))
                koids.add(g.koid);
        }

        try {
            Map<String, String> ko2name = new HashMap<>();
            int cnt = 0;
            for (String koid : koids) {
                URL url = new URL("http://www.kegg.jp/dbget-bin/www_bget?ko:" + koid);
                InputStream is0 = url.openStream();
                StringBuilder sb = new StringBuilder();
                BufferedReader br0 = new BufferedReader(new InputStreamReader(is0));
                String line0 = br0.readLine();
                while (line0 != null) {
                    sb.append(line0);
                    line0 = br0.readLine();
                }
                br0.close();

                int i = sb.indexOf("<nobr>Name</nobr>");
                if (i != -1) {
                    int k = sb.indexOf(":hidden\">");
                    if (k != -1) {
                        k = sb.indexOf(":hidden\">", k + 9);
                        if (k != -1) {
                            String koname0 = sb.substring(k + 9, sb.indexOf("<br>", k));
                            ko2name.put(koid, koname0);

                            System.err.println(koid + "\t" + koname0);
                        }
                    }
                }

                System.err.println(ko2name.size() + " " + koids.size());
                //if( cnt++ > 20 ) break;
            }

            FileWriter fw = new FileWriter("~ko2name.txt");
            for (String koid : ko2name.keySet()) {
                fw.write(koid + "\t" + ko2name.get(koid) + "\n");
            }
            fw.close();
        } catch (IOException e1) {
            e1.printStackTrace();
        }
    });
    popup.getItems().add(koname);
    popup.getItems().add(new SeparatorMenuItem());
    MenuItem genegainloss = new MenuItem("Gene gain/loss");
    genegainloss.setOnAction(e -> {
        Map<Node, List<GeneGroup>> nodeGainMap = new HashMap<>();
        Map<Node, List<GeneGroup>> nodeLossMap = new HashMap<>();

        /*String treestr = "";
        JFileChooser fc = new JFileChooser();
        if( fc.showOpenDialog( applet ) == JFileChooser.APPROVE_OPTION ) {
           File file = fc.getSelectedFile();
           try {
              byte[] bb = Files.readAllBytes( Paths.get(file.toURI()) );
              treestr = new String( bb );
           } catch (IOException e1) {
              e1.printStackTrace();
           }
        }*/

        Serifier serifier = getConcatenatedSequences(false, true);
        String tree = serifier.getFastTree(serifier.lseq, geneset.user, false);

        TreeUtil tu = new TreeUtil();
        Node n = tu.parseTreeRecursive(tree, false);

        TableModel model = new TableModel() {
            @Override
            public int getRowCount() {
                return geneset.getSpecies().size();
            }

            @Override
            public int getColumnCount() {
                return 1;
            }

            @Override
            public String getColumnName(int columnIndex) {
                return null;
            }

            @Override
            public Class<?> getColumnClass(int columnIndex) {
                return String.class;
            }

            @Override
            public boolean isCellEditable(int rowIndex, int columnIndex) {
                return false;
            }

            @Override
            public Object getValueAt(int rowIndex, int columnIndex) {
                return geneset.getSpecies().get(rowIndex);
            }

            @Override
            public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
            }

            @Override
            public void addTableModelListener(TableModelListener l) {
            }

            @Override
            public void removeTableModelListener(TableModelListener l) {
            }
        };
        JTable table = new JTable(model);
        table.getSelectionModel().setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
        JScrollPane scroll = new JScrollPane(table);
        FlowLayout flowlayout = new FlowLayout();
        JComponent c = new JComponent() {
        };
        c.setLayout(flowlayout);
        c.add(scroll);
        JOptionPane.showMessageDialog(comp, c);

        List<String> rootgroup = new ArrayList<>();
        int[] rr = table.getSelectedRows();
        for (int r : rr) {
            rootgroup.add((String) table.getValueAt(r, 0));
        }

        //String[] sobj = {"mt.ruber", "mt.silvanus", "o.profundus", "m.hydrothermalis"};
        Node newnode = tu.getParent(n, new HashSet<>(rootgroup));
        tu.rerootRecur(n, newnode);

        File f = new File("/home/sigmar/gain_list.txt");
        try {
            PrintStream ps = new PrintStream(f);
            geneset.assignGain(newnode, nodeGainMap, ps);
            ps.close();
        } catch (FileNotFoundException e1) {
            e1.printStackTrace();
        }

        f = new File("/home/sigmar/loss_list.txt");
        try {
            PrintStream ps = new PrintStream(f);
            geneset.assignLoss(newnode, nodeLossMap, ps);
            ps.close();
        } catch (FileNotFoundException e1) {
            e1.printStackTrace();
        }
    });
    popup.getItems().add(genegainloss);
    MenuItem concattree = new MenuItem("Concatenate tree");
    concattree.setOnAction(e -> {
        Serifier serifier = getConcatenatedSequences(false, true);

        boolean succ = true;
        if (comp instanceof Applet) {
            try {
                JSObject win = JSObject.getWindow((Applet) comp);
                StringWriter sw = new StringWriter();
                serifier.writeFasta(serifier.lseq, sw, null);
                sw.close();
                win.call("fasttree", new Object[] { sw.toString() });
            } catch (NoSuchMethodError | Exception e1) {
                e1.printStackTrace();
                succ = false;
            }
        }

        /*if( !succ ) {
           String             tree = serifier.getFastTree();
           if( cs.connections().size() > 0 ) {
        cs.sendToAll( tree );
            } else if( Desktop.isDesktopSupported() ) {
        cs.message = tree;
        //String uristr = "http://webconnectron.appspot.com/Treedraw.html?tree="+URLEncoder.encode( tree, "UTF-8" );
        String uristr = "http://webconnectron.appspot.com/Treedraw.html?ws=127.0.0.1:8887";
              try {
          Desktop.getDesktop().browse( new URI(uristr) );
              } catch (IOException | URISyntaxException e1) {
          e1.printStackTrace();
              }
            }
           System.err.println( tree );
        }*/
        showAlignedSequences(comp, serifier);
    });
    popup.getItems().add(concattree);
    MenuItem majocons = new MenuItem("Majority rule consensus");
    majocons.setOnAction(e -> {
        Serifier serifier = new Serifier();

        Set<GeneGroup> genegroups = new HashSet<GeneGroup>();
        if (!isGeneview()) {
            genegroups.addAll(table.getSelectionModel().getSelectedItems());
        } else {
            for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                genegroups.add(gg.getGeneGroup());
            }
        }

        TreeUtil treeutil = new TreeUtil();
        Map<Set<String>, NodeSet> nmap = new HashMap<Set<String>, NodeSet>();
        for (GeneGroup ggroup : genegroups) {
            //List<Sequence>   seqlist = new ArrayList<Sequence>();

            for (Tegeval tv : ggroup.getTegevals()) {
                String spec = tv.getContshort().getSpec();
                Sequence seq = tv.getAlignedSequence();

                //Sequence seq = new Sequence( spec, null );
                //if( seqstr != null && seqstr.length() > 0 ) seq.append( seqstr );
                serifier.addSequence(seq);
            }

            String tree = serifier.getFastTree(serifier.lseq, geneset.user, false);
            Node n = treeutil.parseTreeRecursive(tree, false);
            treeutil.setLoc(0);
            n.nodeCalcMap(nmap);
        }

        Node guidetree = null;

        /*********************************** Serifier serifier = getConcatenatedSequences();
        String tree = serifier.getFastTree();
        guidetree = treeutil.parseTreeRecursive( tree, false );*/

        Node root = DataTable.majoRuleConsensus(treeutil, nmap, guidetree, false);
        String tree = root.toString();

        if (geneset.cs.connections().size() > 0) {
            geneset.cs.sendToAll(tree);
        } else if (Desktop.isDesktopSupported()) {
            geneset.cs.message = tree;
            //String uristr = "http://webconnectron.appspot.com/Treedraw.html?tree="+URLEncoder.encode( tree, "UTF-8" );
            String uristr = "http://webconnectron.appspot.com/Treedraw.html?ws=127.0.0.1:8887";
            try {
                Desktop.getDesktop().browse(new URI(uristr));
            } catch (IOException | URISyntaxException e1) {
                e1.printStackTrace();
            }
        }
    });
    popup.getItems().add(majocons);
    MenuItem addsim = new MenuItem("Add similar");
    addsim.setOnAction(e -> {
        /*int r = table.getSelectedRow();
        int c = table.getSelectedColumn();
                
        Object o = table.getValueAt(r, c);
                
        if (c >= 18) {
           for (int i = 0; i < table.getRowCount(); i++) {
              Object no = table.getValueAt(i, c);
              if (no != null && !table.isRowSelected(i))
          table.addRowSelectionInterval(i, i);
           }
        } else {
           for (int i = 0; i < table.getRowCount(); i++) {
              Object no = table.getValueAt(i, c);
              if (o.equals(no) && !table.isRowSelected(i))
          table.addRowSelectionInterval(i, i);
           }
        }*/
    });
    popup.getItems().add(addsim);
    MenuItem selsim = new MenuItem("Select similar");
    selsim.setOnAction(e -> {
        /*int r = table.getSelectedRow();
        int c = table.getSelectedColumn();
                
        Object o = table.getValueAt(r, c);
                
        table.removeRowSelectionInterval(0, table.getRowCount() - 1);
        if (c >= 18) {
           for (int i = 0; i < table.getRowCount(); i++) {
              Object no = table.getValueAt(i, c);
              if (no != null)
          table.addRowSelectionInterval(i, i);
           }
        } else {
           for (int i = 0; i < table.getRowCount(); i++) {
              Object no = table.getValueAt(i, c);
              if (o.equals(no))
          table.addRowSelectionInterval(i, i);
           }
        }*/
    });
    popup.getItems().add(selsim);
    MenuItem tabtxt = new MenuItem("Table text");
    tabtxt.setOnAction(e -> {
        /*JTextArea ta = new JTextArea();
        ta.setDragEnabled(true);
        JScrollPane scrollpane = new JScrollPane(ta);
                
        StringBuilder sb = new StringBuilder();
        int[] rr = table.getSelectedRows();
        for (int r : rr) {
           for (int c = 0; c < table.getColumnCount() - 1; c++) {
              Object o = table.getValueAt(r, c);
              if (c > 18) {
          if (o != null) {
             String val = o.toString();
             int k = val.indexOf(' ');
             sb.append(val.substring(0, k));
             sb.append("\t" + val.substring(k + 1));
          } else
             sb.append("\t");
              } else {
          if (o != null) {
             sb.append(o.toString());
          }
              }
              sb.append("\t");
           }
           Object o = table.getValueAt(r, table.getColumnCount() - 1);
           if (o != null) {
              String val = o.toString();
              int k = val.indexOf(' ');
              sb.append(val.substring(0, k));
              sb.append("\t" + val.substring(k + 1));
           } else
              sb.append("\t");
           sb.append("\n");
        }
                
        ta.setText(sb.toString());
        JFrame frame = new JFrame();
        frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        frame.add(scrollpane);
        frame.setSize(400, 300);
        frame.setVisible(true);*/
    });
    popup.getItems().add(tabtxt);
    popup.getItems().add(new SeparatorMenuItem());
    MenuItem ncbil = new MenuItem("NCBI lookup");
    ncbil.setOnAction(e -> {
        /*int r = table.getSelectedRow();
        if (r >= 0) {
           String ref = (String) table.getValueAt(r, 2);
           try {
              Desktop.getDesktop().browse(new URI("http://www.ncbi.nlm.nih.gov/gene?term=" + ref));
           } catch (IOException e1) {
              e1.printStackTrace();
           } catch (URISyntaxException e1) {
              e1.printStackTrace();
           }
        }*/
    });
    popup.getItems().add(ncbil);
    table.setContextMenu(popup);
    gtable.setContextMenu(popup);

    TableColumn<Function, String> gocol = new TableColumn("GO");
    gocol.setCellValueFactory(new PropertyValueFactory<>("go"));
    ftable.getColumns().add(gocol);
    TableColumn<Function, String> ecfcol = new TableColumn("EC");
    ecfcol.setCellValueFactory(new PropertyValueFactory<>("ec"));
    ftable.getColumns().add(ecfcol);
    TableColumn<Function, String> metacyccol = new TableColumn("MetaCyc");
    metacyccol.setCellValueFactory(new PropertyValueFactory<>("metacyc"));
    ftable.getColumns().add(metacyccol);
    TableColumn<Function, String> keggcol = new TableColumn("KEGG");
    keggcol.setCellValueFactory(new PropertyValueFactory<>("kegg"));
    ftable.getColumns().add(keggcol);
    TableColumn<Function, String> funcovcol = new TableColumn("Funciton coverage");
    funcovcol.setCellValueFactory(new PropertyValueFactory<>("speciesCount"));
    ftable.getColumns().add(funcovcol);
    TableColumn<Function, String> numprotcol = new TableColumn("Number of proteins");
    numprotcol.setCellValueFactory(new PropertyValueFactory<>("groupCount"));
    ftable.getColumns().add(numprotcol);

    TableColumn<Function, String> namecol = new TableColumn("Name");
    namecol.setCellValueFactory(new PropertyValueFactory<>("name"));
    ftable.getColumns().add(namecol);
    TableColumn<Function, String> namespacecol = new TableColumn("Namespace");
    namespacecol.setCellValueFactory(new PropertyValueFactory<>("namespace"));
    ftable.getColumns().add(namespacecol);
    TableColumn<Function, String> desccol = new TableColumn("Desc");
    desccol.setCellValueFactory(new PropertyValueFactory<>("desc"));
    ftable.getColumns().add(desccol);

    ftable.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);

    //ftable.setAutoCreateRowSorter(true);
    /*ftablemodel = new TableModel() {
       @Override
       public int getRowCount() {
    return geneset.funclist.size();
       }
            
       @Override
       public int getColumnCount() {
    return 9;
       }
            
       @Override
       public String getColumnName(int columnIndex) {
    if (columnIndex == 0)
       return "GO";
    else if (columnIndex == 1)
       return "EC";
    else if (columnIndex == 2)
       return "MetaCyc";
    else if (columnIndex == 3)
       return "KEGG";
    else if (columnIndex == 4)
       return "Function coverage";
    else if (columnIndex == 5)
       return "Number of proteins";
    else if (columnIndex == 6)
       return "Name";
    else if (columnIndex == 7)
       return "Namespace";
    else if (columnIndex == 8)
       return "Def";
    return "";
       }
            
       @Override
       public Class<?> getColumnClass(int columnIndex) {
    if( columnIndex == 4 || columnIndex == 5 )
       return Integer.class;
    return String.class;
       }
            
       @Override
       public boolean isCellEditable(int rowIndex, int columnIndex) {
    return false;
       }
            
       @Override
       public Object getValueAt(int rowIndex, int columnIndex) {
    Function func = geneset.funclist.get(rowIndex);
    if( columnIndex == 0 )
       return func.go;
    else if( columnIndex == 1 )
       return func.ec;
    else if( columnIndex == 2 )
       return func.metacyc;
    else if( columnIndex == 3 )
       return func.kegg;
    else if( columnIndex == 4 )
       return func.getSpeciesCount();
    else if( columnIndex == 5 )
       return table.getModel() == groupModel ? func.getGroupSize() : func.getGeneCount();
    else if( columnIndex == 6 )
       return func.name;
    else if( columnIndex == 7 )
       return func.namespace;
    else if( columnIndex == 8 )
       return func.desc;
    return null;
       }
            
       @Override
       public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
       }
            
       @Override
       public void addTableModelListener(TableModelListener l) {
       }
            
       @Override
       public void removeTableModelListener(TableModelListener l) {
       }
    };
    ftable.setModel( ftablemodel );
    fscrollpane.setViewportView(ftable);*/

    updateFilter(ftable, null);
    updateFilter(table, label);

    combo.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
        String sel = newValue;
        filterset.clear();
        if (geneset.pathwaymap.containsKey(sel)) {
            Set<String> enz = geneset.pathwaymap.get(sel);
            for (Function f : geneset.funclist) {
                if (f.getEc() != null && enz.contains(f.getEc())) {
                    filterset.add(f.index);
                }
            }
        }
        updateFilter(ftable, null);
    });

    specombo.getSelectionModel().selectedItemProperty().addListener((observable, oldValue, newValue) -> {
        String sel = newValue;
        genefilterset.clear();
        for (Gene g : geneset.genelist) {
            Tegeval tv = g.tegeval;
            if (sel.equals(tv.teg)) {
                //System.out.println(g.name + " " + sp + " " + sel + "  " + tv.eval);
                genefilterset.add(g.index);
            }
        }
        updateFilter(table, label);
    });

    MenuItem findcon = new MenuItem("Find conserved terms");
    findcon.setOnAction(e -> {
        Set<Integer> res = new HashSet<>();
        for (Function f : geneset.funclist) {
            if (f.getGeneGroups() != null) {
                Set<String> check = new HashSet<>();
                for (GeneGroup g : f.getGeneGroups()) {
                    //Gene g = genemap.get(str);
                    if (g.species != null) {
                        if (check.isEmpty())
                            check.addAll(g.species.keySet());
                        else if (!(check.size() == g.species.size() && check.containsAll(g.species.keySet()))) {
                            check.clear();
                            break;
                        }
                    }
                }
                if (!check.isEmpty())
                    res.add(f.index);
            }
        }
        filterset.clear();
        for (int i : res) {
            filterset.add(i);
        }
        updateFilter(ftable, null);
    });
    fpopup.getItems().add(findcon);
    fpopup.getItems().add(new SeparatorMenuItem());

    MenuItem showgen = new MenuItem("Show genes");
    showgen.setOnAction(e -> {
        genefilterset.clear();
        Set<GeneGroup> sset = new HashSet<>();
        for (Function f : (ObservableList<Function>) ftable.getSelectionModel().getSelectedItems()) {
            if (!isGeneview()) {
                sset.addAll(f.getGeneGroups());
                /*if( sset != null ) for (GeneGroup gg : sset) {
                   //Gene g = genemap.get(s);
                   genefilterset.add(gg.index);
                }*/
            } else {
                /*Set<Gene> sset = f.getGeneentries();
                for (Gene g : sset) {
                   //Gene g = genemap.get(s);
                   genefilterset.add(g.index);
                }*/
            }
        }

        //int[] rows = sset.stream().mapToInt( gg -> sortedData.indexOf(gg) ).toArray();
        //table.getSelectionModel().selectIndices(rows[0], rows);

        filteredData.setPredicate(genegroup -> {
            return sset.contains(genegroup);
        });
        if (label != null)
            label.setText(
                    table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size());
    });
    fpopup.getItems().add(showgen);

    table.getSelectionModel().selectedItemProperty().addListener(e -> {
        // table.clearSelection();
        tableisselecting = true;
        if (!ftableisselecting && filterset.isEmpty()) {
            //ftable.removeRowSelectionInterval(0, ftable.getRowCount() - 1);
            if (!isGeneview()) {
                for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                    for (Function f : gg.getFunctions()) {
                        try {
                            ftable.getSelectionModel().select(f);
                            //int rf = ftable.convertRowIndexToView(f.index);
                            //if( rf >= 0 && rf < ftable.getRowCount() ) ftable.addRowSelectionInterval(rf, rf);
                        } catch (Exception ex) {
                            ex.printStackTrace();
                        }
                    }
                }
            } else {
                for (Gene g : gtable.getSelectionModel().getSelectedItems()) {
                    if (g.funcentries != null) {
                        for (Function f : g.funcentries) {
                            //Function f = funcmap.get(go);
                            try {
                                ftable.getSelectionModel().select(f);
                                //int rf = ftable.convertRowIndexToView(f.index);
                                //if( rf >= 0 && rf < ftable.getRowCount() ) ftable.addRowSelectionInterval(rf, rf);
                            } catch (Exception ex) {
                                ex.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
        tableisselecting = false;
    });

    ftable.setOnKeyPressed(ke -> {
        if (ke.getCode() == KeyCode.ESCAPE) {
            ffilteredData.setPredicate(null);
        }
    });

    table.setOnKeyPressed(ke -> {
        if (ke.getCode() == KeyCode.ESCAPE) {
            GeneGroup selgg = table.getSelectionModel().getSelectedItem();

            List<GeneGroup> sel = new ArrayList<>(filteredData);
            filteredData.setPredicate(null);
            int[] rows = sel.stream().mapToInt(gg -> sortedData.indexOf(gg)).toArray();
            if (rows.length > 0)
                table.getSelectionModel().selectIndices(rows[0], rows);
            if (label != null)
                label.setText(
                        table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size());

            table.scrollTo(selgg);
            //genefilterset.clear();
            //updateFilter(table, genefilter, label);
            //geneset.scrollToSelection( table );
        }
    });

    table.setOnMousePressed(e -> {
        tableisselecting = true;
        if (!ftableisselecting && e.getClickCount() == 2) {
            /*
             * int[] rr = ftable.getSelectedRows(); int minr =
             * ftable.getRowCount(); int maxr = 0; for( int r : rr ) {
             * if( r < minr ) minr = r; if( r > maxr ) maxr = r; }
             * ftable.removeRowSelectionInterval(minr, maxr);
             */
            // ftable.removeRowSelectionInterval(0, filterset.isEmpty()
            // ? ftable.getRowCount()-1 : filterset.size()-1 );

            Set<Function> fset = new HashSet<>();
            filterset.clear();
            if (!isGeneview()) {
                for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                    fset.addAll(gg.getFunctions());
                }
            } else {
                for (Gene g : gtable.getSelectionModel().getSelectedItems()) {
                    if (g.funcentries != null) {
                        for (Function f : g.funcentries) {
                            //Function f = funcmap.get(go);
                            // ftable.getRowSorter().convertRowIndexToView(index)
                            // int rf = ftable.convertRowIndexToView(
                            // f.index );
                            filterset.add(f.index);
                            // ftable.addRowSelectionInterval(rf, rf);
                        }
                    }
                }
            }
            ffilteredData.setPredicate(p -> fset.contains(p));
        }
        tableisselecting = false;
    });

    ftable.setOnMousePressed(e -> {
        ftableisselecting = true;
        Set<GeneGroup> ggset = new HashSet<>();
        if (!tableisselecting && e.getClickCount() == 2) {
            genefilterset.clear();
            for (Function f : (ObservableList<Function>) ftable.getSelectionModel().getSelectedItems()) {
                if (f.getGeneentries() != null) {
                    if (!isGeneview()) {
                        ggset.addAll(f.getGeneGroups());
                    } else {
                        for (Gene g : f.getGeneentries()) {
                            //Gene g = genemap.get(ref);
                            // int rf = table.convertRowIndexToView( g.index
                            // );
                            // table.addRowSelectionInterval(rf, rf);
                            genefilterset.add(g.index);
                        }
                    }
                }
            }
            filteredData.setPredicate(p -> ggset.contains(p));
        }
        ftableisselecting = false;
    });

    ftable.getSelectionModel().selectedItemProperty().addListener(e -> {
        ftableisselecting = true;
        if (!tableisselecting && genefilterset.isEmpty()) {
            table.getSelectionModel().clearSelection();
            //table.removeRowSelectionInterval(0, table.getRowCount() - 1);
            for (Function f : ftable.getSelectionModel().getSelectedItems()) {
                if (f.getGeneentries() != null) {
                    for (Gene g : f.getGeneentries()) {
                        table.getSelectionModel().select(g.getGeneGroup());

                        //Gene g = genemap.get(ref);
                        /*int i = g.getGroupIndex();
                        if( i >= 0 && i <= table.getItems().size() ) {
                           int rf = table.convertRowIndexToView(i);
                           table.addRowSelectionInterval(rf, rf);
                        }*/
                    }
                }
            }
        }
        ftableisselecting = false;
    });

    textfield.setOnKeyPressed(e -> {
        String text = textfield.getText().toLowerCase();
        if (e.getCode() == KeyCode.ENTER) {
            searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol")
                    ? searchTable(table, text, searchi, e.isAltDown(), 8, 9, 10, 16)
                    : searchTable(table, text, searchi, e.isAltDown(), 0);
        }
    });

    textfield.textProperty().addListener((observable, oldValue, newValue) -> {
        //String text = textfield.getText().toLowerCase();
        String lowerCaseFilter = newValue.toLowerCase();
        Predicate<GeneGroup> p = genegroup -> {
            if (newValue == null || newValue.isEmpty()) {
                return true;
            }

            if (searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol")) {
                if ((genegroup.getCogsymbol() != null
                        && genegroup.getCogsymbol().toLowerCase().contains(lowerCaseFilter))
                        || (genegroup.getSymbol() != null
                                && genegroup.getSymbol().toLowerCase().contains(lowerCaseFilter))
                        || (genegroup.getKoname() != null
                                && genegroup.getKoname().toLowerCase().contains(lowerCaseFilter))) {
                    return true; // Filter matches first name.
                }
            } else {
                if (genegroup.getName().toLowerCase().contains(lowerCaseFilter) || genegroup.genes.stream()
                        .anyMatch(gg -> gg.getName().toLowerCase().contains(lowerCaseFilter))) {
                    return true; // Filter matches first name.
                } /* else if (genegroup.getLastName().toLowerCase().contains(lowerCaseFilter)) {
                    return true; // Filter matches last name.
                  }*/
            }
            return false; // Does not match.
        };
        if (filter.isSelected()) {
            filteredData.setPredicate(p);
            if (label != null)
                label.setText(
                        table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size());
            //if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(0, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 );
            //else updateFilter(0, text, table, genefilter, genefilterset, label, 0 );
        } else {
            Optional<GeneGroup> ogg = filteredData.stream().filter(p).findFirst();
            if (ogg.isPresent()) {
                GeneGroup gg = ogg.get();
                table.getSelectionModel().select(gg);
                table.scrollTo(gg);
            }
            //searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 );
        }
    });
    /*textfield.getDocument().addDocumentListener(new DocumentListener() {
       public void changedUpdate(DocumentEvent e) {
    String text = textfield.getText().toLowerCase();
    if( filter.isSelected() ) {
       if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(0, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 );
       else updateFilter(0, text, table, genefilter, genefilterset, label, 0 );
    } else {
       searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 );
    }
       }
            
       public void insertUpdate(DocumentEvent e) {
    String text = textfield.getText().toLowerCase();
    if( filter.isSelected() ) {
       if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(1, text, table, genefilter, genefilterset, label, 8, 9, 10, 16);
       else updateFilter(1, text, table, genefilter, genefilterset, label, 0);
    } else {
       searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 );
    }
       }
            
       public void removeUpdate(DocumentEvent e) {
    String text = textfield.getText().toLowerCase();
    if( filter.isSelected() ) {
       if( searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ) updateFilter(2, text, table, genefilter, genefilterset, label, 8, 9, 10, 16 );
       else updateFilter(2, text, table, genefilter, genefilterset, label, 0);
    } else {
       searchi = searchTable( table, text, 0, false, searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? 7 : 0 );
    }
       }
    });*/

    ftextfield.textProperty().addListener(new javafx.beans.value.ChangeListener<String>() {
        public void changed(ObservableValue<? extends String> observable, String oldValue, String newValue) {
            //String text = textfield.getText().toLowerCase();
            if (filter.isSelected()) {
                ffilteredData.setPredicate(function -> {
                    // If filter text is empty, display all persons.
                    if (newValue == null || newValue.isEmpty()) {
                        return true;
                    }

                    // Compare first name and last name of every person with filter text.
                    String lowerCaseFilter = newValue.toLowerCase();

                    boolean desc = function.getDesc() != null
                            && function.getDesc().toLowerCase().contains(lowerCaseFilter);
                    boolean name = function.getName() != null
                            && function.getName().toLowerCase().contains(lowerCaseFilter);
                    boolean go = function.getGo() != null
                            && function.getGo().toLowerCase().contains(lowerCaseFilter);
                    boolean ec = function.getEc() != null
                            && function.getEc().toLowerCase().contains(lowerCaseFilter);

                    if (desc || name || go || ec) {
                        return true; // Filter matches first name.
                    } /* else if (genegroup.getLastName().toLowerCase().contains(lowerCaseFilter)) {
                         return true; // Filter matches last name.
                      }*/
                    return false; // Does not match.
                });
            } else {
                //searchi = searchcolcomb.getSelectionModel().getSelectedItem().equals("Symbol") ? searchTable( table, text, 0, false, 8, 9, 10, 16 ) : searchTable( table, text, 0, false, 0 );
            }
        }
    });
    /*ftextfield.getDocument().addDocumentListener(new DocumentListener() {
       public void changedUpdate(DocumentEvent e) {
    updateFilter(0, ftextfield.getText(), ftable, rowfilter, filterset, null, 6);
       }
            
       public void insertUpdate(DocumentEvent e) {
    updateFilter(1, ftextfield.getText(), ftable, rowfilter, filterset, null, 6);
       }
            
       public void removeUpdate(DocumentEvent e) {
    updateFilter(2, ftextfield.getText(), ftable, rowfilter, filterset, null, 6);
       }
    });*/
    MenuItem kegggl = new MenuItem("KEGG gene lookup");
    kegggl.setOnAction(e -> {
        Gene g = gtable.getSelectionModel().getSelectedItem();
        try {
            Desktop.getDesktop().browse(new URI("http://www.genome.jp/dbget-bin/www_bget?" + g.keggid));
        } catch (IOException e1) {
            e1.printStackTrace();
        } catch (URISyntaxException e1) {
            e1.printStackTrace();
        }
    });
    popup.getItems().add(kegggl);
    MenuItem showgenes = new MenuItem("Show genes with same sharing");
    showgenes.setOnAction(e -> {
        genefilterset.clear();
        GeneGroup gg = table.getSelectionModel().getSelectedItem();
        for (GeneGroup g : geneset.allgenegroups) {
            if (gg.species != null && g.species != null) {
                Set<String> ggset = gg.species.keySet();
                Set<String> gset = g.species.keySet();

                if (gset.size() == ggset.size() && gset.containsAll(ggset)) {
                    genefilterset.add(g.index);
                }
            }
        }
        updateFilter(table, label);
    });
    popup.getItems().add(showgenes);
    MenuItem showshared = new MenuItem("Show shared function");
    showshared.setOnAction(e -> {
        filterset.clear();
        Set<Function> startfunc = new HashSet<Function>();
        if (isGeneview()) {
            for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                if (gg.funcentries != null) {
                    if (startfunc.isEmpty()) {
                        startfunc.addAll(gg.funcentries);
                    } else {
                        startfunc.retainAll(gg.funcentries);
                    }
                }
                /*if (startfunc == null)
                startfunc = new HashSet<Function>(gg.funcentries);
                else {
                startfunc.retainAll(gg.funcentries);
                }*/
            }
        } else {
            for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                Set<Function> fset = gg.getFunctions();
                if (startfunc.isEmpty()) {
                    startfunc.addAll(fset);
                } else {
                    startfunc.retainAll(fset);
                }
            }
        }
        for (Function f : geneset.funclist) {
            filterset.add(f.index);
        }
        updateFilter(ftable, null);
    });
    popup.getItems().add(showshared);
    MenuItem showall = new MenuItem("Show all functions");
    showall.setOnAction(e -> {
        filterset.clear();
        Set<Function> startfunc = null;
        if (isGeneview()) {
            for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                if (gg.funcentries != null) {
                    for (Function f : gg.funcentries) {
                        filterset.add(f.index);
                    }
                }
            }
        } else {
            for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                Set<Function> fset = gg.getFunctions();
                for (Function f : fset) {
                    filterset.add(f.index);
                }
            }
        }
        updateFilter(ftable, null);
    });
    popup.getItems().add(showall);
    popup.getItems().add(new SeparatorMenuItem());
    MenuItem showgenegroups = new MenuItem("Show gene groups in proximity");
    showgenegroups.setOnAction(e -> {
        proxi(filteredData, false);
        updateFilter(table, label);
    });
    popup.getItems().add(showgenegroups);
    MenuItem selgenegroups = new MenuItem("Select gene groups in proximity");
    selgenegroups.setOnAction(e -> {
        genefilterset.clear();
        proxi(filteredData, false);
        for (int i : genefilterset) {
            table.getSelectionModel().select(i);
        }
        //table.tableChanged( new TableModelEvent( table.getModel() ) );
        if (label != null)
            label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size());
        //updateFilter(table, genefilter, label);
    });
    popup.getItems().add(selgenegroups);
    MenuItem selgenes = new MenuItem("Select genes in proximity");
    selgenes.setOnAction(e -> {
        genefilterset.clear();
        proxi(filteredData, true);
        for (int i : genefilterset) {
            table.getSelectionModel().select(i);
        }
        //table.tableChanged( new TableModelEvent( table.getModel() ) );
        if (label != null)
            label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedItems().size());
        //updateFilter(table, genefilter, label);
    });
    popup.getItems().add(selgenes);
    MenuItem addgene = new MenuItem("Add gene groups in proximity");
    addgene.setOnAction(e -> {
        proxi(filteredData, false);
        updateFilter(table, label);
    });
    popup.getItems().add(addgene);
    MenuItem remgene = new MenuItem("Remove gene groups in proximity");
    remgene.setOnAction(e -> {
        ObservableList<Integer> rr = table.getSelectionModel().getSelectedIndices();
        if (genefilterset.isEmpty()) {
            Set<Integer> ii = new HashSet<>();
            for (int r : rr)
                ii.add(r);
            for (int i = 0; i < geneset.genelist.size(); i++) {
                if (!ii.contains(i))
                    genefilterset.add(i);
            }
        }
        proxi(filteredData, false);
        updateFilter(table, label);
    });
    popup.getItems().add(remgene);
    popup.getItems().add(new SeparatorMenuItem());
    MenuItem showrel = new MenuItem("Show related genes");
    showrel.setOnAction(e -> {
        genefilterset.clear();
        relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, false);
        updateFilter(gtable, label);
    });
    popup.getItems().add(showrel);
    MenuItem addrel = new MenuItem("Add related genes");
    addrel.setOnAction(e -> {
        relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, false);
        updateFilter(gtable, label);
    });
    popup.getItems().add(addrel);
    MenuItem remrel = new MenuItem("Remove related genes");
    remrel.setOnAction(e -> {
        ObservableList<Integer> rr = gtable.getSelectionModel().getSelectedIndices();
        if (genefilterset.isEmpty()) {
            Set<Integer> ii = new HashSet<>();
            for (int r : rr)
                ii.add(r);
            for (int i = 0; i < geneset.genelist.size(); i++) {
                if (!ii.contains(i))
                    genefilterset.add(i);
            }
        }
        relati(gtable, geneset.genelist, genefilterset, geneset.uclusterlist, true);
        updateFilter(table, label);
    });
    popup.getItems().add(remrel);
    popup.getItems().add(new SeparatorMenuItem());
    MenuItem showcloserel = new MenuItem("Show closely related genes");
    showcloserel.setOnAction(e -> {
        genefilterset.clear();
        Set<String> ct = new HashSet<>();
        for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
            // genefilterset.add( gg.index );
            Tegeval tv = gg.tegeval;
            for (Set<String> uset : geneset.iclusterlist) {
                if (uset.contains(tv.name)) {
                    ct.addAll(uset);
                    break;
                }
            }
        }

        for (Gene g : geneset.genelist) {
            Tegeval tv = g.tegeval;
            if (ct.contains(tv.name)) {
                genefilterset.add(g.index);
                break;
            }
        }

        updateFilter(table, label);
    });
    popup.getItems().add(showcloserel);
    MenuItem showdist = new MenuItem("Show distance matrix");
    showdist.setOnAction(e -> {
        JTextArea textarea = new JTextArea();

        try {
            if (clipboardService == null)
                clipboardService = (ClipboardService) ServiceManager.lookup("javax.jnlp.ClipboardService");
            Action action = new CopyAction("Copy", null, "Copy data",
                    new Integer(KeyEvent.VK_CONTROL + KeyEvent.VK_C));
            textarea.getActionMap().put("copy", action);
            grabFocus = true;
        } catch (Exception ee) {
            ee.printStackTrace();
            System.err.println("Copy services not available.  Copy using 'Ctrl-c'.");
        }
        textarea.setDragEnabled(true);

        JScrollPane scrollpane = new JScrollPane(textarea);
        Gene gg = gtable.getSelectionModel().getSelectedItem();
        if (gg.getSpecies() != null) {
            for (String s : geneset.corrInd) {
                if (s.equals(geneset.corrInd.get(0)))
                    textarea.append(s);
                else
                    textarea.append("\t" + s);
            }

            int i = 0;
            int j = 0;

            int len = 16;
            double[] min = new double[len];
            double[] max = new double[len];

            for (i = 0; i < len; i++) {
                min[i] = Double.MAX_VALUE;
                max[i] = 0.0;
            }

            double[] corrarr = gg.corrarr;
            boolean symmetrize = true;
            if (symmetrize) {
                for (i = 0; i < len; i++) {
                    for (int k = i + 1; k < len; k++) {
                        corrarr[i * len + k] = (corrarr[k * len + i] + corrarr[i * len + k]) / 2.0;
                        corrarr[k * len + i] = corrarr[i * len + k];
                    }
                }
            }

            for (i = 0; i < len; i++) {
                for (int k = 0; k < len; k++) {
                    if (corrarr[i * len + k] < min[i])
                        min[i] = corrarr[i * len + k];
                    if (corrarr[i * len + k] > max[i])
                        max[i] = corrarr[i * len + k];
                }

                /*for (int k = 0; k < len; k++) {
                   corrarr[i * 16 + k] = corrarr[i * 16 + k] - min;
                }*/
            }

            i = 0;
            for (double d : corrarr) {
                double dval = d;
                if (i % len == 0)
                    textarea.append("\n" + dval);
                else
                    textarea.append("\t" + dval);

                i++;
            }
            textarea.append("\n");

            i = 0;
            for (double d : corrarr) {
                double dval = Math.exp((d - min[i / len]) / 20.0 + 1.0) / 100.0; // 0.0 ?
                // 0.0 :
                // 100.0/d;
                if (i % len == 0)
                    textarea.append("\n" + dval);
                else
                    textarea.append("\t" + dval);

                i++;
            }
            double[] newcorr = Arrays.copyOf(corrarr, corrarr.length);
            textarea.append("\nD matrix\n");
            i = 0;
            for (double d : corrarr) {
                double dval = max[i / len] - d;
                newcorr[i] = dval;
                if (i % len == 0)
                    textarea.append("\n" + dval);
                else
                    textarea.append("\t" + dval);

                i++;
            }

            TreeUtil treeutil = new TreeUtil();
            treeutil.neighborJoin(newcorr, geneset.corrInd, null, true, true);
        }

        /*
         * int[] rr = table.getSelectedRows(); for( int r : rr ) { int
         * cr = table.convertRowIndexToModel(r); Gene gg =
         * genelist.get(cr); if( gg.species != null ) { textarea.append(
         * gg.name + ":\n" ); for( String sp : gg.species.keySet() ) {
         * Teginfo stv = gg.species.get( sp ); for( Tegeval tv :
         * stv.tset ) { textarea.append( ">" + tv.cont + " " + tv.teg +
         * " " + tv.eval + "\n" ); for( int i = 0; i < tv.seq.length();
         * i+=70 ) { int end = Math.min(i+70,tv.seq.length());
         * textarea.append( tv.seq.substring(i, end)+"\n" ); //new
         * String( tv.seq, i, Math.min(i+70,tv.seq.length()) )+"\n"); }
         * //textarea.append( ">" + tv.cont + " " + tv.teg + " " +
         * tv.eval + "\n" + tv.seq + "\n" ); } } } }
         */
        JFrame frame = new JFrame();
        frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
        frame.add(scrollpane);
        frame.setSize(400, 300);
        frame.setVisible(true);
    });

    /*
     * final List<String> reglist = new ArrayList<String>(); final
     * Map<String,Gene> regidx = new TreeMap<String,Gene>();
     * 
     * for( Gene g : geneset.genelist ) { if( g.species != null ) { for( String key
     * : g.species.keySet() ) { Set<Tegeval> stv = g.species.get(key); for(
     * Tegeval tv : stv ) { regidx.put(tv.cont, g); } } } }
     * 
     * for( String key : regidx.keySet() ) { reglist.add(key); }
     * 
     * final JTable contigtable = new JTable();
     * contigtable.setAutoCreateRowSorter( true ); contigtable.setModel( new
     * TableModel() {
     * 
     * @Override public int getRowCount() { return reglist.size(); }
     * 
     * @Override public int getColumnCount() { return 1; }
     * 
     * @Override public String getColumnName(int columnIndex) { return
     * "Region"; }
     * 
     * @Override public Class<?> getColumnClass(int columnIndex) { return
     * String.class; }
     * 
     * @Override public boolean isCellEditable(int rowIndex, int
     * columnIndex) { return false; }
     * 
     * @Override public Object getValueAt(int rowIndex, int columnIndex) {
     * return reglist.get(rowIndex); }
     * 
     * @Override public void setValueAt(Object aValue, int rowIndex, int
     * columnIndex) { // TODO Auto-generated method stub
     * 
     * }
     * 
     * @Override public void addTableModelListener(TableModelListener l) {
     * // TODO Auto-generated method stub
     * 
     * }
     * 
     * @Override public void removeTableModelListener(TableModelListener l)
     * { // TODO Auto-generated method stub
     * 
     * } });
     * 
     * contigtable.getSelectionModel().addListSelectionListener( new
     * ListSelectionListener() {
     * 
     * @Override public void valueChanged(ListSelectionEvent e) {
     * genefilterset.clear(); int[] rr = contigtable.getSelectedRows(); for(
     * int r : rr ) { String s = (String)contigtable.getValueAt(r, 0); Gene
     * g = regidx.get( s );
     * 
     * genefilterset.add( g.index ); updateFilter(table, genefilter, label);
     * //int k = table.convertRowIndexToView(g.index); //if( k != -1
     * )table.addRowSelectionInterval(k, k); } } }); JScrollPane
     * contigscroll = new JScrollPane( contigtable );
     * 
     * JSplitPane mainsplit = new JSplitPane( JSplitPane.HORIZONTAL_SPLIT );
     * mainsplit.setLeftComponent( contigscroll );
     * mainsplit.setRightComponent( splitpane );
     */
}