org.simmi.GeneSetHead.java Source code

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Here is the source code for org.simmi.GeneSetHead.java

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/*
 * Copyright (c) 2015 deCODE Genetics Inc.
 * All Rights Reserved.
 *
 * This software is the confidential and proprietary information of
 * deCODE Genetics Inc. ("Confidential Information"). You shall not
 * disclose such Confidential Information and shall use it only in
 * accordance with the terms of the license agreement you entered into
 * with deCODE.
 */

package org.simmi;

import java.applet.Applet;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Container;
import java.awt.Desktop;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GraphicsDevice;
import java.awt.GraphicsEnvironment;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Image;
import java.awt.Point;
import java.awt.Window;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
import java.awt.datatransfer.UnsupportedFlavorException;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.image.BufferedImage;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintStream;
import java.io.StringReader;
import java.io.StringWriter;
import java.io.Writer;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.UnknownHostException;
import java.nio.file.FileSystems;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.StandardCopyOption;
import java.nio.file.StandardOpenOption;
import java.nio.file.attribute.BasicFileAttributes;
import java.nio.file.attribute.PosixFilePermission;
import java.util.*;
import java.util.function.Consumer;
import java.util.function.Predicate;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import java.util.zip.GZIPInputStream;

import javax.imageio.ImageIO;
import javax.jnlp.ClipboardService;
import javax.jnlp.FileContents;
import javax.jnlp.FileSaveService;
import javax.jnlp.ServiceManager;
import javax.jnlp.UnavailableServiceException;
import javax.swing.AbstractAction;
import javax.swing.Action;
import javax.swing.DefaultRowSorter;
import javax.swing.ImageIcon;
import javax.swing.JApplet;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDialog;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
import javax.swing.JScrollPane;
import javax.swing.JSpinner;
import javax.swing.JSplitPane;
import javax.swing.JTable;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
import javax.swing.RowFilter;
import javax.swing.SwingUtilities;
import javax.swing.TransferHandler;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import javax.swing.event.TableModelEvent;
import javax.swing.event.TableModelListener;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableModel;
import javax.swing.table.TableRowSorter;

import javafx.geometry.Insets;
import javafx.scene.control.*;
import javafx.scene.layout.GridPane;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.simmi.GeneSet.ClusterInfo;
import org.simmi.GeneSet.RunnableResult;
import org.simmi.shared.*;
import org.simmi.shared.TreeUtil.Node;
import org.simmi.shared.TreeUtil.NodeSet;
import org.simmi.unsigned.FlxReader;
import org.simmi.unsigned.JavaFasta;
import org.simmi.unsigned.NativeRun;
import org.simmi.unsigned.SmithWater;

import javafx.application.Platform;
import javafx.beans.property.ReadOnlyObjectWrapper;
import javafx.beans.property.SimpleStringProperty;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.collections.transformation.FilteredList;
import javafx.collections.transformation.SortedList;
import javafx.embed.swing.JFXPanel;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.cell.PropertyValueFactory;
import javafx.scene.input.KeyCode;
import javafx.scene.layout.HBox;
import javafx.scene.layout.VBox;
import javafx.stage.FileChooser;
import javafx.stage.FileChooser.ExtensionFilter;
import javafx.stage.Stage;
import javafx.stage.WindowEvent;
import netscape.javascript.JSObject;

/**
 *
 * @version $Id:  $
 */
public class GeneSetHead extends JApplet {
    GeneSet geneset;
    DistannFX app;
    List<JSplitPane> splitpaneList = new ArrayList<JSplitPane>();
    JFrame frame = new JFrame();

    public GeneSetHead(DistannFX app, GeneSet geneset) {
        super();
        this.geneset = geneset;
        this.app = app;
    }

    final Set<Integer> filterset = new HashSet<>();
    final Set<Integer> genefilterset = new HashSet<>();

    final Label label = new Label();

    final RowFilter rowfilter = new RowFilter() {
        @Override
        public boolean include(Entry entry) {
            return filterset.isEmpty() || filterset.contains(entry.getIdentifier());
        }
    };
    final RowFilter genefilter = new RowFilter() {
        @Override
        public boolean include(Entry entry) {
            return genefilterset.isEmpty() || genefilterset.contains(entry.getIdentifier());
        }
    };

    public void repaintGCSkew(List<Sequence> selclist, Graphics2D g2, int size, GeneGroup gg, String selspec) {
        g2.setColor(Color.white);
        g2.fillRect(0, 0, 1024, 1024);
        g2.setFont(g2.getFont().deriveFont(10.0f));
        int total = 0;
        int g = 0;
        int c = 0;
        double gcstotal = 0.0;
        for (Sequence ctg : selclist) {
            //Sequence ctg = clist.get( u );
            if (gg != null) {
                for (Tegeval tv : gg.getTegevals()) {
                    if (tv.getContshort() == ctg) {
                        int i = tv.start;

                        int x1 = (int) (512.0 + (384.0 - 100.0) * Math.cos((i + total) * 2.0 * Math.PI / size));
                        int y1 = (int) (512.0 + (384.0 - 100.0) * Math.sin((i + total) * 2.0 * Math.PI / size));
                        int x2 = (int) (512.0 + (384.0 + 100.0) * Math.cos((i + total) * 2.0 * Math.PI / size));
                        int y2 = (int) (512.0 + (384.0 + 100.0) * Math.sin((i + total) * 2.0 * Math.PI / size));

                        g2.setColor(Color.green);
                        g2.drawLine(x1, y1, x2, y2);
                    }
                }
            }

            double horn = total * 2.0 * Math.PI / size;
            double horn2 = (total + ctg.length()) * 2.0 * Math.PI / size;

            int x1 = (int) (512.0 + (384.0 - 100.0) * Math.cos(horn));
            int y1 = (int) (512.0 + (384.0 - 100.0) * Math.sin(horn));
            int x2 = (int) (512.0 + (384.0 + 100.0) * Math.cos(horn));
            int y2 = (int) (512.0 + (384.0 + 100.0) * Math.sin(horn));
            g2.setColor(Color.black);
            g2.drawLine(x1, y1, x2, y2);

            int xoff = (int) (512.0 + (384.0 + 100.0) * Math.cos(horn2));
            int yoff = (int) (512.0 + (384.0 + 100.0) * Math.sin(horn2));
            if (horn < Math.PI) {
                g2.translate(x2, y2);
                g2.rotate(horn + Math.PI / 2.0);
                g2.drawString(ctg.getName(), 0, 0);
                g2.rotate(-horn - Math.PI / 2.0);
                g2.translate(-x2, -y2);
            } else {
                g2.translate(xoff, yoff);
                g2.rotate(horn2 + Math.PI / 2.0);
                g2.drawString(ctg.getName(), -g2.getFontMetrics().stringWidth(ctg.getName()), 0);
                g2.rotate(-horn2 - Math.PI / 2.0);
                g2.translate(-xoff, -yoff);
            }

            for (int i = 0; i < ctg.length(); i += 500) {
                for (int k = i; k < Math.min(ctg.length(), i + 500); k++) {
                    char chr = ctg.charAt(k);
                    if (chr == 'g' || chr == 'G') {
                        g++;
                    } else if (chr == 'c' || chr == 'C') {
                        c++;
                    }
                }

                int gcount = 0;
                int ccount = 0;
                int acount = 0;
                int tcount = 0;
                for (int k = i; k < Math.min(ctg.length(), i + 10000); k++) {
                    char chr = k - 5000 < 0 ? ctg.charAt(ctg.length() + (k - 5000)) : ctg.charAt(k - 5000);
                    if (chr == 'g' || chr == 'G') {
                        gcount++;
                    } else if (chr == 'c' || chr == 'C') {
                        ccount++;
                    } else if (chr == 'a' || chr == 'A')
                        acount++;
                    else if (chr == 't' || chr == 'T')
                        tcount++;
                }

                if (gcount > 0 || ccount > 0) {
                    double gcskew = (gcount - ccount) / (double) (gcount + ccount);

                    gcstotal += gcskew;

                    x1 = (int) (512.0 + (384.0) * Math.cos((i + total) * 2.0 * Math.PI / size));
                    y1 = (int) (512.0 + (384.0) * Math.sin((i + total) * 2.0 * Math.PI / size));
                    x2 = (int) (512.0 + (384.0 + gcskew * 100.0) * Math.cos((i + total) * 2.0 * Math.PI / size));
                    y2 = (int) (512.0 + (384.0 + gcskew * 100.0) * Math.sin((i + total) * 2.0 * Math.PI / size));

                    if (gcskew >= 0)
                        g2.setColor(Color.blue);
                    else
                        g2.setColor(Color.red);
                    g2.drawLine(x1, y1, x2, y2);
                }

                if (acount > 0 || tcount > 0) {
                    double atskew = (acount - tcount) / (double) (acount + tcount);

                    x1 = (int) (512.0 + (300.0) * Math.cos((i + total) * 2.0 * Math.PI / size));
                    y1 = (int) (512.0 + (300.0) * Math.sin((i + total) * 2.0 * Math.PI / size));
                    x2 = (int) (512.0 + (300.0 + atskew * 100.0) * Math.cos((i + total) * 2.0 * Math.PI / size));
                    y2 = (int) (512.0 + (300.0 + atskew * 100.0) * Math.sin((i + total) * 2.0 * Math.PI / size));

                    if (atskew >= 0)
                        g2.setColor(Color.blue);
                    else
                        g2.setColor(Color.red);
                    g2.drawLine(x1, y1, x2, y2);
                }
            }
            total += ctg.length();
        }

        g2.setColor(Color.black);
        g2.setFont(g2.getFont().deriveFont(java.awt.Font.ITALIC).deriveFont(32.0f));
        String[] specsplit; // = selspec.split("_");

        if (selspec.contains("hermus"))
            specsplit = selspec.split("_");
        else {
            Matcher m = Pattern.compile("\\d").matcher(selspec);
            int firstDigitLocation = m.find() ? m.start() : 0;
            if (firstDigitLocation == 0)
                specsplit = new String[] { "Thermus", selspec };
            else
                specsplit = new String[] { "Thermus", selspec.substring(0, firstDigitLocation),
                        selspec.substring(firstDigitLocation) };
        }

        int k = 0;
        for (String spec : specsplit) {
            int strw = g2.getFontMetrics().stringWidth(spec);
            g2.drawString(spec, (1024 - strw) / 2, 1024 / 2 - specsplit.length * 32 / 2 + 32 + k * 32);
            k++;
        }

        /*double gcs = gcstotal/total; //(g-c)/(g+c);
        String gcstr = Double.toString( Math.round( gcs*1000000.0 ) );
        g2.drawString( gcstr+"ppm", 768, 512 );*/
    }

    static ClipboardService clipboardService;
    static boolean grabFocus;

    public static void copyData(Component source) {
        JTextArea textarea = (JTextArea) source;
        String s = textarea.getText();

        if (s == null || s.trim().length() == 0) {
            JOptionPane.showMessageDialog(source, "There is no data selected!");
        } else {
            StringSelection selection = new StringSelection(s);
            clipboardService.setContents(selection);
        }

        if (grabFocus) {
            source.requestFocus();
        }
    }

    static class CopyAction extends AbstractAction {
        public CopyAction(String text, ImageIcon icon, String desc, Integer mnemonic) {
            super(text, icon);
            putValue(SHORT_DESCRIPTION, desc);
            putValue(MNEMONIC_KEY, mnemonic);
        }

        public void actionPerformed(ActionEvent e) {
            copyData((Component) e.getSource());
        }
    }

    Map<String, Set<Integer>> selectionMap = new HashMap<>();

    public void fillSelectionSave(String json) throws JSONException {
        selectionMap.clear();
        selcomb.getItems().clear();

        System.err.println(json.toString());
        JSONObject jsono = new JSONObject(json);
        Iterator<String> keys = jsono.keys();
        while (keys.hasNext()) {
            String key = keys.next();
            System.err.println("key: " + key);
            selcomb.getItems().add(key);
            JSONArray jo = jsono.getJSONArray(key);
            System.err.println("array: " + jo.toString());
            Set<Integer> selset = new HashSet<>();
            for (int i = 0; i < jo.length(); i++) {
                selset.add(jo.getInt(i));
            }
            selectionMap.put(key, selset);
        }
    }

    boolean ftableisselecting = false;
    boolean tableisselecting = false;

    static TableModel nullmodel = new AbstractTableModel() {
        @Override
        public Object getValueAt(int rowIndex, int columnIndex) {
            return null;
        }

        @Override
        public int getRowCount() {
            return 0;
        }

        @Override
        public int getColumnCount() {
            return 0;
        }
    };

    FilteredList<GeneGroup> filteredData;
    SortedList<GeneGroup> sortedData;
    FilteredList<Function> ffilteredData;
    SortedList<Function> fsortedData;

    private void importStuff() throws IOException, UnavailableServiceException {
        boolean fail = true;
        /*try {
           FileOpenService fos = (FileOpenService)ServiceManager.lookup("javax.jnlp.FileOpenService");
           FileContents fc = fos.openFileDialog(null, null);
           is = fc.getInputStream();
        } catch( Exception e ) {
           fail = true;
        }*/

        Path zipp = null;
        if (fail && zipp == null) {
            FileChooser fc = new FileChooser();
            File f = fc.showOpenDialog(app.getOwner());
            if (f != null)
                zipp = f.toPath();
        }

        //if( is != null ) {
        /*ByteArrayOutputStream baos = new ByteArrayOutputStream();
        byte[] bab = new byte[1024];
        int rd = is.read( bab );
        while( rd > 0 ) {
           baos.write(bab, 0, rd);
           rd = is.read( bab );
        }
        baos.close();
        zipf = baos.toByteArray();*/

        /*ZipInputStream zipm = new ZipInputStream( new ByteArrayInputStream( zipf ) );
        ZipEntry ze = zipm.getNextEntry();
        while( ze != null ) {
           String zname = ze.getName();
           if( zname.equals("unresolved.blastout") ) {
        unresolvedmap = loadunresolvedmap( new InputStreamReader( zipm ) );
           } else if( zname.equals("namemap.txt") ) {
        namemap = loadnamemap( new InputStreamReader( zipm ) );
           } else if( ze.getName().equals("designations.txt") ) {
        designations = loadDesignations( new InputStreamReader(zipm), deset );
           } else if( ze.getName().equals("plasmids.txt") ) {
        plasmids = loadPlasmids( new InputStreamReader(zipm) );
           }
           ze = zipm.getNextEntry();
        }
        if( designations == null ) designations = new TreeMap<String,String>();
        //List<Set<String>> uclusterlist = null;*/

        if (zipp != null) {
            geneset.loadStuff(zipp);

            //syncolorcomb = new JComboBox();
            syncolorcomb.getItems().clear();
            syncolorcomb.getItems().add("");
            for (String spec : geneset.speccontigMap.keySet()) {
                syncolorcomb.getItems().add(spec);
            }
            syncolorcomb.getItems().add("All");

            /*
             * is = GeneSet.class.getResourceAsStream(""); Map<String,String> komap
             * = koMapping( new FileReader("/home/sigmar/asgard-bio/data/ko"),
             * funclist, genelist ); for( Function f : funclist ) { if(
             * komap.containsKey( f.ec ) ) { for( String gn : f.geneentries ) { Gene
             * g = refmap.get(gn); if( g.keggid == null ) g.keggid =
             * komap.get(f.ec); } } }
             */

            geneset.updateShareNum(geneset.specList);

            Set<String> allecs = new HashSet<>();
            for (Function f : geneset.funclist) {
                if (f.getEc() != null)
                    allecs.add(f.getEc());
            }

            for (String val : geneset.pathwaymap.keySet()) {
                Set<String> set = geneset.pathwaymap.get(val);
                for (String s : set) {
                    if (allecs.contains(s)) {
                        combo.getItems().add(val);
                        break;
                    }
                }
            }

            Set<String> set = new TreeSet<>();
            for (Gene g : geneset.genelist) {
                Tegeval tv = g.tegeval;
                if (tv.eval <= 0.00001 && tv.teg != null && tv.teg.startsWith("[") && tv.teg.endsWith("]"))
                    set.add(tv.teg);
            }

            for (String sp : set) {
                specombo.getItems().add(sp);
            }

            if (geneset.uclusterlist != null)
                geneset.clusterMap = Serifier.initClusterNew(geneset.uclusterlist, null, null);
            //table.tableChanged( new TableModelEvent( table.getModel() ) );
            //ftable.tableChanged( new TableModelEvent( ftable.getModel() ) );
            //table.setModel( nullmodel );
            //ftable.setModel( nullmodel );
            //table.setModel( groupModel );
            //ftable.setModel( ftablemodel );
            //ftable.setItems( geneset.f);

            for (String spec : geneset.specList) {
                TableColumn<GeneGroup, Teginfo> speccol = new TableColumn(spec);
                //speccol.getStyleClass().add("tabstyle");
                speccol.setCellFactory(cell -> {
                    final TableCell<GeneGroup, Teginfo> tc = new TableCell<GeneGroup, Teginfo>() {
                        @Override
                        protected void updateItem(Teginfo item, boolean empty) {
                            super.updateItem(item, empty);

                            if (item == null || item.toString().length() == 0 || empty) {
                                setText(null);
                                setStyle("");
                                //getStyleClass().remove("tabcellstyle");
                            } else {
                                setText(item.toString());
                                cellRender(this, item, 0);
                                //getStyleClass().add("tabcellstyle");
                                /*if( (this.getTableRow() != null && getTableRow().isSelected()) || isSelected() ) {
                                   //setTextFill( javafx.scene.paint.Color.WHITE );
                                   setStyle("-fx-background-color: darkgreen");
                                } else {
                                   //setTextFill( javafx.scene.paint.Color.BLACK );
                                   setStyle("-fx-background-color: green");
                                }*/
                            }
                        }
                    };
                    return tc;
                });
                speccol.setCellValueFactory(cellValue -> {
                    GeneGroup gg = cellValue.getValue();
                    Teginfo tes = gg.getTes(spec);
                    return new ReadOnlyObjectWrapper(tes);
                    //return new SimpleStringProperty( tes != null ? tes.toString() : "" );
                    //Teginfo ret = geneset.getGroupTes( cellValue.getValue(), spec );
                    //return new ObservableValue<String>( ret.toString() );
                    //return ret;
                });
                table.getColumns().add(speccol);

                TableColumn<Gene, Teg> gspeccol = new TableColumn(spec);
                gspeccol.setComparator((o1, o2) -> {
                    if (o1 == null) {
                        if (o2 == null) {
                            return 0;
                        } else
                            return -1;
                    } else if (o1 instanceof Tegeval) {
                        if (o2 == null || o2 instanceof Teginfo) {
                            return 1;
                        }
                    } else {
                        if (o2 == null) {
                            return 1;
                        } else if (o2 instanceof Tegeval) {
                            return -1;
                        }
                    }
                    return o1.compareTo(o2);
                });
                gspeccol.setCellFactory(cell -> {
                    final TableCell<Gene, Teg> tc = new TableCell<Gene, Teg>() {
                        @Override
                        protected void updateItem(Teg item, boolean empty) {
                            super.updateItem(item, empty);

                            if (item == null || item.toString().length() == 0 || empty) {
                                setText("");
                                setStyle("");
                            } else {
                                boolean render = cellRenderGene(this, item);
                                setText(item.toString());
                                if (!render)
                                    setStyle("");
                                //getStyleClass().add("tabcellstyle");
                                /*if( (this.getTableRow() != null && getTableRow().isSelected()) || isSelected() ) {
                                   //setTextFill( javafx.scene.paint.Color.WHITE );
                                   setStyle("-fx-background-color: white");
                                } else {
                                   //setTextFill( javafx.scene.paint.Color.BLACK );
                                   setStyle("-fx-background-color: black");
                                }*/
                            }
                        }
                    };
                    return tc;
                });
                gspeccol.setCellValueFactory(cellValue -> {
                    Gene g = cellValue.getValue();

                    //Teginfo tes = g.tegeval;//getTes( spec );
                    if (spec.equals(g.getSpecies())) {
                        return new ReadOnlyObjectWrapper(g.tegeval);
                    } else {
                        GeneGroup gg = g.getGeneGroup();
                        Set<String> specset = gg.getSpecies();
                        if (specset.contains(spec)) {
                            Teginfo ti = gg.getGenes(spec);
                            return new ReadOnlyObjectWrapper(ti);
                        }
                    }
                    //return new SimpleStringProperty( tes != null ? tes.toString() : "" );
                    //Teginfo ret = geneset.getGroupTes( cellValue.getValue(), spec );
                    //return new ObservableValue<String>( ret.toString() );
                    //return ret;
                    return null;
                });

                /*gspeccol.setCellValueFactory( cellValue -> {
                   return new SimpleStringProperty( cellValue.getValue().toString() );
                   //Teginfo ret = geneset.getGroupTes( cellValue.getValue(), spec );
                   //return new ObservableValue<String>( ret.toString() );
                   //return ret;
                });*/
                gtable.getColumns().add(gspeccol);
            }

            ObservableList<Function> ofunc = FXCollections.observableList(geneset.funclist);
            ffilteredData = new FilteredList<>(ofunc, p -> true);
            fsortedData = new SortedList<>(ffilteredData);
            fsortedData.comparatorProperty().bind(ftable.comparatorProperty());
            ftable.setItems(fsortedData);

            ObservableList<GeneGroup> ogenegroup = FXCollections.observableList(geneset.allgenegroups);
            filteredData = new FilteredList<>(ogenegroup, p -> true);
            sortedData = new SortedList<>(filteredData);
            sortedData.comparatorProperty().bind(table.comparatorProperty());
            table.setItems(sortedData);

            ObservableList<Gene> ogene = FXCollections.observableList(geneset.genelist);
            gtable.setItems(ogene);

            int me = 0;
            int mu = 0;
            for (Gene g : geneset.genelist) {
                if (g.getGeneGroup() != null)
                    me++;
                else
                    mu++;
            }
            System.err.println(me + "  " + mu);
        }

        String userhome = System.getProperty("user.home");
        File f = new File(userhome);
        File idf = new File(f, "idspec.txt");
        BufferedWriter bw = new BufferedWriter(new FileWriter(idf)); //Files.newBufferedWriter(idf.toPath(), OpenOption.);
        for (String id : geneset.refmap.keySet()) {
            Gene g = geneset.refmap.get(id);
            bw.write(id + "\t" + g.getSpecies() + "\n");
        }
        bw.close();
    }

    public Serifier getConcatenatedSequencesMaxLength() {
        Map<String, Sequence> smap = new HashMap<String, Sequence>();
        Set<String> specset = new HashSet<String>();
        Map<GeneGroup, Integer> genegroups = new HashMap<GeneGroup, Integer>();
        //int[] rr = table.getSelectedRows();
        if (!isGeneview()) {
            for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                //int cr = table.convertRowIndexToModel(r);
                int max = 0;
                //GeneGroup gg = geneset.allgenegroups.get(cr);
                specset.addAll(gg.getSpecies());

                for (Tegeval tv : gg.getTegevals()) {
                    int l = tv.getAlignedSequence().length();
                    if (l > max)
                        max = l;
                }
                genegroups.put(gg, max);
            }
        } else {
            for (Gene g : gtable.getSelectionModel().getSelectedItems()) {
                //int cr = table.convertRowIndexToModel(r);
                //Gene g = geneset.genelist.get(cr);
                int max = 0;
                GeneGroup gg = g.getGeneGroup();
                specset.addAll(gg.getSpecies());
                for (Tegeval tv : gg.getTegevals()) {
                    int l = tv.getAlignedSequence().length();
                    if (l > max)
                        max = l;
                }
                genegroups.put(gg, max);
            }
        }

        //List<Sequence>   seqs = new ArrayList<Sequence>();
        /*Map<String>   specset = new HashMap<String,Integer>();
        for( GeneGroup ggroup : genegroups ) {
           int max = 0;
           for( Tegeval tv : ggroup.getTegevals() ) {
        int len = tv.getAlignedSequence().length();
        if( len > max ) {
           max = len;
           specset.put( tv.getContshort().getSpec(), max );
        }
           }
        }*/

        for (GeneGroup ggroup : genegroups.keySet()) {
            int len = genegroups.get(ggroup);
            for (String selspec : specset) {
                List<Tegeval> ltv = ggroup.getTegevals(selspec);

                String spec;
                if (selspec.contains("hermus"))
                    spec = selspec;
                else {
                    Matcher m = Pattern.compile("\\d").matcher(selspec);
                    int firstDigitLocation = m.find() ? m.start() : 0;
                    if (firstDigitLocation == 0)
                        spec = "Thermus_" + selspec;
                    else
                        spec = "Thermus_" + selspec.substring(0, firstDigitLocation) + "_"
                                + selspec.substring(firstDigitLocation);
                }

                Sequence seq;
                if (smap.containsKey(spec)) {
                    seq = smap.get(spec);
                } else {
                    seq = new Sequence(spec, null);
                    smap.put(spec, seq);
                }

                int max = 0;
                StringBuilder seqstr = null;
                for (Tegeval tv : ltv) {
                    int seqlen = tv.getLength();
                    if (seqlen > max) {
                        seqstr = tv.getAlignedSequence().getStringBuilder();
                        max = seqlen;
                    }

                    /*if( seqstr != null && seqstr.length() > 0 ) {
                       break;
                    }*/
                }

                if (seqstr != null && seqstr.length() > 0) {
                    seq.append(seqstr);
                } else {
                    for (int i = 0; i < len; i++)
                        seq.append("-");
                }
            }
        }

        Serifier serifier = new Serifier();
        for (String spec : smap.keySet()) {
            Sequence seq = smap.get(spec);
            serifier.addSequence(seq);
        }
        return serifier;
    }

    public Serifier getConcatenatedSequences(boolean proximityJoin, boolean namefix) {
        Set<String> specset = new HashSet<String>();
        Map<GeneGroup, Integer> genegroups = new HashMap<GeneGroup, Integer>();
        //int[] rr = table.getSelectedRows();
        if (!isGeneview()) {
            for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                //int cr = table.convertRowIndexToModel(r);
                int max = 0;
                //GeneGroup gg = geneset.allgenegroups.get(cr);
                specset.addAll(gg.getSpecies());

                for (Tegeval tv : gg.getTegevals()) {
                    Sequence seq = tv.getAlignedSequence();
                    int l = seq != null ? seq.length() : 0;
                    if (l > max)
                        max = l;
                }
                genegroups.put(gg, max);
            }
        } else {
            for (Gene g : gtable.getSelectionModel().getSelectedItems()) {
                //int cr = table.convertRowIndexToModel(r);
                //Gene g = geneset.genelist.get(cr);
                int max = 0;
                GeneGroup gg = g.getGeneGroup();
                specset.addAll(gg.getSpecies());
                for (Tegeval tv : gg.getTegevals()) {
                    int l = tv.getAlignedSequence().length();
                    if (l > max)
                        max = l;
                }
                genegroups.put(gg, max);
            }
        }
        return geneset.getConcatenatedSequences(proximityJoin, genegroups, specset, namefix);
    }

    public void blastn(boolean show) {
        String dbname = null;

        final JTextArea ta = new JTextArea();
        JScrollPane sp = new JScrollPane(ta);
        Dimension dim = new Dimension(400, 300);
        sp.setSize(dim);
        sp.setPreferredSize(dim);
        JTextField tf = new JTextField();
        tf.setText("0.00001");
        Object[] objs = new Object[] { sp, tf };
        JOptionPane.showMessageDialog(GeneSetHead.this, objs);

        doBlastn(ta.getText(), tf.getText(), false, null, show);
    }

    private void proxi(FilteredList genefilterset, boolean onlygenes) {
        if (!isGeneview()) {
            genefilterset.setPredicate(p -> {
                GeneGroup thegg = (GeneGroup) p;
                for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                    if (thegg.index == gg.index)
                        return true;
                    for (Gene g : gg.genes) {
                        Annotation next = g.tegeval.getNext();
                        if (next != null) {
                            GeneGroup ngg = next.getGene().getGeneGroup();
                            if (ngg != null)
                                if (thegg.index == ngg.index)
                                    return true;
                        }
                        Annotation prev = g.tegeval.getPrevious();
                        if (prev != null) {
                            GeneGroup pgg = prev.getGene().getGeneGroup();
                            if (pgg != null)
                                if (thegg.index == pgg.index)
                                    return true;
                        }
                    }
                }
                return false;
            });
        } else {
            genefilterset.setPredicate(p -> {
                Gene thegene = (Gene) p;
                for (Gene gene : gtable.getSelectionModel().getSelectedItems()) {
                    GeneGroup gg = gene.getGeneGroup();

                    if (onlygenes) {
                        if (thegene.index == gene.index)
                            return true;
                        Annotation next = gene.tegeval.getNext();
                        if (next != null) {
                            Gene ng = next.getGene();
                            if (ng != null)
                                if (thegene.index == ng.index)
                                    return true;
                        }
                        Annotation prev = gene.tegeval.getPrevious();
                        if (prev != null) {
                            Gene pg = prev.getGene();
                            if (pg != null)
                                if (thegene.index == pg.index)
                                    return true;
                        }
                    } else {
                        genefilterset.add(gg.index);
                        for (Gene g : gg.genes) {
                            Annotation next = g.tegeval.getNext();
                            if (next != null) {
                                GeneGroup ngg = next.getGene().getGeneGroup();
                                if (ngg != null)
                                    if (thegene.index == ngg.index)
                                        return true;
                            }
                            Annotation prev = g.tegeval.getPrevious();
                            if (prev != null) {
                                GeneGroup pgg = prev.getGene().getGeneGroup();
                                if (pgg != null)
                                    if (thegene.index == pgg.index)
                                        return true;
                            }
                        }
                    }
                }
                return false;
            });
        }
    }

    public void blast(boolean x) {
        //String dbname = null;

        /*try {
           Map<String,String> env = new HashMap<String,String>();
           Path path = zipfile.toPath();
           String uristr = "jar:" + path.toUri();
           geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")* );
           geneset.zipfilesystem = FileSystems.newFileSystem( geneset.zipuri, env );
               
           final PathMatcher pm = geneset.zipfilesystem.getPathMatcher("*.p??");
           for( Path p : zipfilesystem.getRootDirectories() ) {
        Files.walkFileTree( p, new SimpleFileVisitor<Path>() {
           @Override
           public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
              if( pm.matches( file ) ) {
                 ByteArrayOutputStream baos = new ByteArrayOutputStream();
                 byte[] bb = new byte[1024];
                 int r = zipm.read( bb );
                 while( r > 0 ) {
                    baos.write(bb, 0, r);
                    r = zipm.read( bb );
                 }
                 Files.write( new File("c:/"+file.getFileName().).toPath(), baos.toByteArray(), StandardOpenOption.CREATE);
                 //unresolvedmap = loadunresolvedmap( new InputStreamReader( zipm ) );
                     
                 dbname = zname.substring(0, zname.length()-4);
              }
              return null;*
           }
        });
           }*/
        //Path nf = zipfilesystem.getPath("/unresolved.blastout");
        //unresolvedmap = loadunresolvedmap( new InputStreamReader( Files.newInputStream(nf, StandardOpenOption.READ) ) );

        /*ZipInputStream zipm = new ZipInputStream( new ByteArrayInputStream( zipf ) );
        ZipEntry ze = zipm.getNextEntry();
        while( ze != null ) {
        String zname = ze.getName();
        if( zname.endsWith(".phr") || zname.endsWith(".pin") || zname.endsWith(".psq") ) {
           ByteArrayOutputStream baos = new ByteArrayOutputStream();
           byte[] bb = new byte[1024];
           int r = zipm.read( bb );
           while( r > 0 ) {
              baos.write(bb, 0, r);
              r = zipm.read( bb );
           }
           Files.write( new File("c:/"+zname).toPath(), baos.toByteArray(), StandardOpenOption.CREATE);
           //unresolvedmap = loadunresolvedmap( new InputStreamReader( zipm ) );
               
           dbname = zname.substring(0, zname.length()-4);
        }
        ze = zipm.getNextEntry();
        }*
        } catch (IOException e1) {
        e1.printStackTrace();
        }*/

        final JTextArea ta = new JTextArea();
        JScrollPane sp = new JScrollPane(ta);
        Dimension dim = new Dimension(400, 300);
        sp.setSize(dim);
        sp.setPreferredSize(dim);
        JTextField tf = new JTextField();
        tf.setText("0.00001");
        Object[] objs = new Object[] { sp, tf };
        JOptionPane.showMessageDialog(GeneSetHead.this, objs);

        doBlast(ta.getText(), tf.getText(), true, null, x);
    }

    public Set<String> getSelspec(Component comp, final List<String> specs, final JCheckBox... contigs) {
        final JTable table = new JTable();
        table.setDragEnabled(true);
        JScrollPane scroll = new JScrollPane(table);
        table.setAutoCreateRowSorter(true);

        final List<Sequence> ctgs = new ArrayList<Sequence>(geneset.contigmap.values());
        final TableModel contigmodel = new TableModel() {
            @Override
            public int getRowCount() {
                return ctgs.size();
            }

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

            @Override
            public String getColumnName(int columnIndex) {
                return "Contigs/Scaffolds";
            }

            @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 ctgs.get(rowIndex).toString();
            }

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

            @Override
            public void addTableModelListener(TableModelListener l) {
            }

            @Override
            public void removeTableModelListener(TableModelListener l) {
            }
        };
        final TableModel specmodel = new TableModel() {
            @Override
            public int getRowCount() {
                return specs.size();
            }

            @Override
            public int getColumnCount() {
                return 2;
            }

            @Override
            public String getColumnName(int columnIndex) {
                return columnIndex == 0 ? "Id" : "Spec";
            }

            @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) {
                if (columnIndex == 1)
                    return Sequence.nameFix(specs.get(rowIndex), true);
                else
                    return specs.get(rowIndex);
            }

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

            @Override
            public void addTableModelListener(TableModelListener l) {
            }

            @Override
            public void removeTableModelListener(TableModelListener l) {
            }
        };
        table.setModel(specmodel);

        TransferHandler th = dragRows(table, specs);
        table.setTransferHandler(th);

        if (contigs != null && contigs.length > 0 && !contigs[0].getText().equals("Plasmid"))
            contigs[0].addChangeListener(new ChangeListener() {
                @Override
                public void stateChanged(ChangeEvent e) {
                    if (contigs[0] != null && contigs[0].isSelected())
                        table.setModel(contigmodel);
                    else
                        table.setModel(specmodel);
                }
            });

        Object[] ctls = new Object[] { scroll, contigs };
        //Object[] ctls2 = new Object[] { scroll };

        //if( contigs != null ) 
        JOptionPane.showMessageDialog(comp, ctls);
        //else JOptionPane.showMessageDialog( comp, ctls2 );
        Set<String> selspec = new LinkedHashSet<>();
        for (int i = 0; i < table.getRowCount(); i++) {
            if (table.isRowSelected(i)) {
                String spec = (String) table.getValueAt(i, 0);
                System.err.println("test " + spec);
                selspec.add(spec);
            }
        }
        return selspec;
    }

    public TableView<GeneGroup> getGeneGroupTable() {
        return table;
    }

    public TableView<Gene> getGeneTable() {
        return gtable;
    }

    public TableView<Function> getFunctionTable() {
        return ftable;
    }

    int searchi = 0;

    public int searchTable(TableView table, String text, int i, boolean back, int... columns) {
        int v;
        if (back) {
            v = i - 1;
            if (v == -1)
                v = table.getItems().size();
        } else
            v = (i + 1) % table.getItems().size();
        if (isGeneview()) {
            while (v != i) {
                //int m = table.convertRowIndexToModel(v);
                //if( m != -1 ) {
                //Gene g = geneset.genelist.get(m);
                //String name = column == 7 || column[0] == 8 ? g.getGeneGroup().getCommonSymbol() + ", " + g.getGeneGroup().getCommonKOName( ko2name ) + ", " +  : g.getGeneGroup().getCommonName();

                ObservableList<TableColumn> cc = table.getColumns();
                String name = "";
                for (int k : columns) {
                    TableColumn tc = cc.get(k);
                    String val = tc.getCellObservableValue(v).toString();
                    name += val;//table.getValueAt(v, k);
                }

                if (name.toLowerCase().contains(text)) {
                    //int r = table.convertRowIndexToView(v);
                    table.scrollTo(v);
                    //Rectangle rect = table.getCellRect(v, 0, true);
                    //table.scrollRectToVisible( rect );
                    break;
                }
                if (back) {
                    v--;
                    if (v == -1)
                        v = table.getItems().size() - 1;
                } else
                    v = (v + 1) % table.getItems().size();

                //} else break;
            }
        } else {
            while (v != i) {
                //int m = table.convertRowIndexToModel(v);
                //if( m != -1 ) {

                //GeneGroup gg = allgenegroups.get(m);
                //String name = gg.getCommonName();
                ObservableList<TableColumn> cc = table.getColumns();
                String name = "";
                for (int k : columns) {
                    TableColumn tc = cc.get(k);
                    String val = tc.getCellObservableValue(v).toString();
                    name += val;
                    //name += table.getValueAt(v, k);
                }

                if (name.toLowerCase().contains(text)) {
                    //int r = table.convertRowIndexToView(i);
                    //Rectangle rect = table.getCellRect(v, 0, true);
                    //table.scrollRectToVisible( rect );
                    table.scrollTo(v);
                    break;
                }
                if (back) {
                    v--;
                    if (v == -1)
                        v = table.getItems().size() - 1;
                } else
                    v = (v + 1) % table.getItems().size();

                //} else break;
            }
        }
        return v;
    }

    public void doBlast(final String fasta, final String evaluestr, final boolean ids, final RunnableResult rr,
            boolean x) {
        /*File blastn;
        File blastp;
        File makeblastdb;
        File blastx = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\blastx.exe" );
        if( !blastx.exists() ) {
           blastx = new File( "/opt/ncbi-blast-2.2.29+/bin/blastx" );
           if( !blastx.exists() ) {
        blastx = new File( "/usr/local/ncbi/blast/bin/blastx" );
        blastn = new File( "/usr/local/ncbi/blast/bin/blastn" );
        blastp = new File( "/usr/local/ncbi/blast/bin/blastp" );
            
        makeblastdb = new File( "/usr/local/ncbi/blast/bin/makeblastdb" );
           } else {
        blastn = new File( "/opt/ncbi-blast-2.2.29+/bin/blastn" );
        blastp = new File( "/opt/ncbi-blast-2.2.29+/bin/blastp" );
            
        makeblastdb = new File( "/opt/ncbi-blast-2.2.29+/bin/makeblastdb" );
           }
        } else {
           blastn = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\blastn.exe" );
           blastp = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\blastp.exe" );
               
           makeblastdb = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\makeblastdb.exe" );
        }*/

        String OS = System.getProperty("os.name").toLowerCase();
        int procs = Runtime.getRuntime().availableProcessors();
        String[] mcmds = { OS.indexOf("mac") >= 0 ? "/usr/local/bin/makeblastdb" : "makeblastdb", "-dbtype", "prot",
                "-title", "tmp", "-out", "tmp" };
        List<String> lcmd = new ArrayList<String>(Arrays.asList(mcmds));

        final ProcessBuilder mpb = new ProcessBuilder(lcmd);
        mpb.redirectErrorStream(true);
        try {
            final Process mp = mpb.start();

            new Thread() {
                public void run() {
                    try {
                        OutputStream pos = mp.getOutputStream();
                        Writer ow = new OutputStreamWriter(pos);
                        for (Gene g : geneset.genelist) {
                            if (g.getTag() == null || g.getTag().length() == 0) {
                                GeneGroup gg = g.getGeneGroup();

                                if (gg != null) {
                                    String name;
                                    if (ids)
                                        name = g.id;
                                    else {
                                        String addstr = "";
                                        Cog cog = gg.getCog(geneset.cogmap);
                                        String cazy = gg.getCommonCazy(geneset.cazymap);
                                        if (cog != null)
                                            addstr += "_" + cog.id;
                                        if (cazy != null) {
                                            if (addstr.length() > 0)
                                                addstr += cazy;
                                            addstr += "_" + cazy;
                                        }
                                        if (addstr.length() > 0)
                                            addstr += "_";

                                        name = g.name + addstr + "[" + g.id + "]";
                                        //pos.write( (">" + g.name + addstr + "[" + g.id + "]\n").getBytes() );
                                    }
                                    Sequence sb = g.tegeval.getProteinSequence();
                                    sb.setName(name);
                                    sb.writeSequence(ow);
                                    /*for( int i = 0; i < sb.length(); i+=70 ) {
                                       pos.write( sb.substring(i, Math.min( sb.length(), i+70) ).getBytes() );
                                    }
                                    pos.write( '\n' );*/
                                }
                            }
                        }
                        ow.close();
                        pos.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }.start();

            new Thread() {
                public void run() {
                    try {
                        InputStream pin = mp.getInputStream();
                        InputStreamReader rdr = new InputStreamReader(pin);
                        //FileReader fr = new FileReader( new File("c:/dot.blastout") );
                        BufferedReader br = new BufferedReader(rdr);
                        String line = br.readLine();
                        while (line != null) {
                            System.out.println(line);
                            line = br.readLine();
                        }
                        pin.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }.run();

            //File blastFile = x ? blastx : blastp; //dbType.equals("prot") ? type.equals("prot") ? blastp : blastx : blastn;

            String[] cmds = { OS.indexOf("mac") >= 0 ? "/usr/local/bin/blastp" : "blastp", "-query", "-", "-db",
                    "tmp", "-evalue", evaluestr, "-num_threads", Integer.toString(procs) };
            lcmd = new ArrayList<String>(Arrays.asList(cmds));
            //String[] exts = extrapar.trim().split("[\t ]+");

            ProcessBuilder pb = new ProcessBuilder(lcmd);
            pb.redirectErrorStream(true);
            final Process p = pb.start();

            final Thread t = new Thread() {
                public void run() {
                    try {
                        OutputStream pos = p.getOutputStream();
                        pos.write(fasta.getBytes());
                        pos.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            };
            t.start();

            final Thread t2 = new Thread() {
                public void run() {
                    try {
                        System.err.println("WHY NOT");
                        InputStreamReader rdr = new InputStreamReader(p.getInputStream());
                        //FileReader fr = new FileReader( new File("c:/dot.blastout") );

                        String res = "";
                        BufferedReader br = new BufferedReader(rdr);
                        String line = br.readLine();
                        while (line != null) {
                            //System.err.println( line );
                            if (line.startsWith("> ")) {
                                int i = line.indexOf(' ', 2);
                                if (i == -1)
                                    i = line.length();
                                String id = line.substring(2, i);

                                Gene g = geneset.genemap.get(id);
                                if (g != null) {
                                    if (!isGeneview()) {
                                        /*i = geneset.allgenegroups.indexOf( g.getGeneGroup() );
                                        if( i != -1 && i < table.getRowCount() ) {
                                           int r = table.convertRowIndexToView( i );
                                           table.addRowSelectionInterval(r, r);
                                        }*/
                                        table.getSelectionModel().select(g.getGeneGroup());
                                    } else {
                                        /*i = geneset.genelist.indexOf( g );
                                        if( i != -1 && i < table.getRowCount() ) {
                                           int r = table.convertRowIndexToView( i );
                                           table.addRowSelectionInterval(r, r);
                                        }*/
                                        gtable.getSelectionModel().select(g);
                                    }
                                }

                                String stuff = line + "\n";
                                line = br.readLine();
                                while (line != null && !line.startsWith("Query=") && !line.startsWith("> ")) {
                                    stuff += line + "\n";
                                    line = br.readLine();
                                }
                                if (rr != null) {
                                    rr.run(stuff);
                                    //res += line+"\n";
                                }
                            } else
                                line = br.readLine();
                        }
                        br.close();
                        //System.err.println("wn done");
                        p.destroy();

                        if (rr != null)
                            rr.run("close");

                        /*if( rr != null ) {
                           rr.run( res );
                        }*/
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            };
            t2.start();
            //fr.close();
        } catch (IOException e2) {
            e2.printStackTrace();
        }
    }

    public void doBlastn(final String fasta, final String evaluestr, final boolean ids, final RunnableResult rr,
            boolean show) {
        /*File blastn;
        File blastp;
        File makeblastdb;
        File blastx = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\blastx.exe" );
        if( !blastx.exists() ) {
           blastx = new File( "/opt/ncbi-blast-2.2.29+/bin/blastx" );
           if( !blastx.exists() ) {
        blastx = new File( "/usr/local/ncbi/blast/bin/blastx" );
        blastn = new File( "/usr/local/ncbi/blast/bin/blastn" );
        blastp = new File( "/usr/local/ncbi/blast/bin/blastp" );
            
        makeblastdb = new File( "/usr/local/ncbi/blast/bin/makeblastdb" );
           } else {
        blastn = new File( "/opt/ncbi-blast-2.2.29+/bin/blastn" );
        blastp = new File( "/opt/ncbi-blast-2.2.29+/bin/blastp" );
            
        makeblastdb = new File( "/opt/ncbi-blast-2.2.29+/bin/makeblastdb" );
           }
        } else {
           blastn = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\blastn.exe" );
           blastp = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\blastp.exe" );
               
           makeblastdb = new File( "c:\\\\Program files\\NCBI\\blast-2.2.29+\\bin\\makeblastdb.exe" );
        }*/

        int procs = Runtime.getRuntime().availableProcessors();
        String[] mcmds = { "makeblastdb", "-dbtype", "nucl", "-title", "tmp", "-out", "tmp" };
        List<String> lcmd = new ArrayList<String>(Arrays.asList(mcmds));

        final ProcessBuilder mpb = new ProcessBuilder(lcmd);
        mpb.redirectErrorStream(true);
        try {
            final Process mp = mpb.start();

            new Thread() {
                public void run() {
                    try {
                        OutputStream pos = mp.getOutputStream();
                        for (String cname : geneset.contigmap.keySet()) {
                            Sequence c = geneset.contigmap.get(cname);
                            if (ids)
                                pos.write((">" + c.id + "\n").getBytes());
                            else {
                                pos.write((">" + c.getName() + "\n").getBytes());
                            }
                            StringBuilder sb = c.getStringBuilder();
                            for (int i = 0; i < sb.length(); i += 70) {
                                pos.write(sb.substring(i, Math.min(sb.length(), i + 70)).getBytes());
                            }
                            pos.write('\n');
                        }
                        pos.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }.start();

            new Thread() {
                public void run() {
                    try {
                        InputStream pin = mp.getInputStream();
                        InputStreamReader rdr = new InputStreamReader(pin);
                        //FileReader fr = new FileReader( new File("c:/dot.blastout") );
                        BufferedReader br = new BufferedReader(rdr);
                        String line = br.readLine();
                        while (line != null) {
                            System.out.println(line);
                            line = br.readLine();
                        }
                        pin.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }.run();

            //File blastFile = blastn; //dbType.equals("prot") ? type.equals("prot") ? blastp : blastx : blastn;

            String[] cmds1 = { "blastn", "-dust", "no", "-perc_identity", "99", "-word_size", "21", "-query", "-",
                    "-db", "tmp", "-evalue", evaluestr, "-num_threads", Integer.toString(procs) };
            String[] cmds2 = { "blastn", "-query", "-", "-db", "tmp", "-evalue", evaluestr, "-num_threads",
                    Integer.toString(procs) };
            String[] cmds = show ? cmds2 : cmds1;

            lcmd = new ArrayList<String>(Arrays.asList(cmds));
            //String[] exts = extrapar.trim().split("[\t ]+");

            ProcessBuilder pb = new ProcessBuilder(lcmd);
            pb.redirectErrorStream(true);
            final Process p = pb.start();

            final Thread t = new Thread() {
                public void run() {
                    try {
                        OutputStream pos = p.getOutputStream();
                        pos.write(fasta.getBytes());
                        pos.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            };
            t.start();

            Map<String, Set<String>> tph = new HashMap<String, Set<String>>();
            Map<String, Map<String, String>> tvp = new HashMap<String, Map<String, String>>();
            Map<String, Map<String, String>> tmr = new HashMap<String, Map<String, String>>();

            Map<String, Integer> specindex = new LinkedHashMap<String, Integer>();
            Map<String, Integer> phindex = new LinkedHashMap<String, Integer>();

            /*final Thread t2 = new Thread() {
               public void run() {*/
            try {
                System.err.println("WHY NOT");
                InputStreamReader rdr = new InputStreamReader(p.getInputStream());
                //FileReader fr = new FileReader( new File("c:/dot.blastout") );

                String qspec = null;
                String query = null;
                String ctype = null;
                Annotation at = new Annotation();
                int o = 0;
                StringBuilder res = new StringBuilder();
                BufferedReader br = new BufferedReader(rdr);
                String line = br.readLine();
                res.append(line + "\n");
                while (line != null) {
                    if (line.startsWith("Query= ")) {
                        query = line.substring(7, line.length());
                        int e = query.indexOf("CRISPR") - 1;
                        if (e > 0) {
                            qspec = query.substring(0, e);
                            qspec = Sequence.getSpec(qspec);
                            String rest = query.substring(e + 8);
                            int ri = rest.lastIndexOf('-');
                            if (ri != -1)
                                ctype = rest.substring(ri + 1);
                        } else {
                            System.err.println();
                        }

                        line = br.readLine();
                        res.append(line + "\n");
                        while (!line.startsWith("Length")) {
                            line = br.readLine();
                            res.append(line + "\n");
                        }
                        o = Integer.parseInt(line.substring(7));
                    } else if (line.startsWith("> ")) {
                        String contname = line.substring(1).trim();
                        //line = br.readLine();
                        //res.append( line+"\n" );
                        //int o = Integer.parseInt( line.substring(7) );

                        Sequence cont = geneset.contigmap.get(contname);

                        if (cont != null) {
                            int start = -1;
                            int stop = 0;
                            line = br.readLine();
                            res.append(line + "\n");
                            String lastmatch = null;
                            while (line != null && !line.startsWith(">")
                                    && !line.startsWith("Query=") /*&& !line.contains("Expect =")*/ ) {
                                if (line.startsWith("Sbjct")) {
                                    String[] split = line.split("[\t ]+");
                                    int k = Integer.parseInt(split[1]);
                                    int m = Integer.parseInt(split[3]);
                                    lastmatch = split[2];

                                    if (start == -1)
                                        start = k;
                                    stop = m;
                                }
                                line = br.readLine();
                                res.append(line + "\n");
                            }

                            if (start > stop) {
                                int tmp = start;
                                start = stop;
                                stop = tmp;
                            }

                            at.start = start;
                            at.stop = stop;

                            //if( stop - start < o*2 ) {
                            List<Annotation> lann = cont.getAnnotations();
                            if (lann != null) {
                                int k = Collections.binarySearch(lann, at);

                                //System.err.println( "kkk  " + k + "   " + lann.size() );

                                if (k < 0)
                                    k = -(k + 1) - 1;

                                Annotation ann = lann.get(Math.max(0, k));

                                boolean yes = true;
                                if (ann.type != null && ann.type.contains("ummer")) {
                                    yes = false;
                                }

                                int u = k - 1;
                                Annotation nann = null;
                                if (u >= 0 && u < lann.size())
                                    nann = lann.get(u);

                                u = k + 1;
                                Annotation rann = null;
                                if (u >= 0 && u < lann.size())
                                    rann = lann.get(u);

                                if (nann != null && nann.type != null && nann.type.contains("ummer")) {
                                    yes = false;
                                }

                                if (rann != null && rann.type != null && rann.type.contains("ummer")) {
                                    yes = false;
                                }

                                if (!yes) {
                                    //System.err.println();
                                }

                                Gene g = ann.getGene();
                                String desig = ann.designation;

                                if (yes && g != null) { //ann.stop > at.start && ann.start < at.stop ) {
                                    GeneGroup gg = g.getGeneGroup();
                                    if (desig != null && desig.contains("phage")) {
                                        if (!phindex.containsKey(desig))
                                            phindex.put(desig, phindex.size());

                                        Map<String, String> tvps;
                                        String specname = qspec;//Sequence.nameFix(qspec, true);
                                        if (!specindex.containsKey(specname))
                                            specindex.put(specname, specindex.size());

                                        if (tvp.containsKey(specname)) {
                                            tvps = tvp.get(specname);
                                        } else {
                                            tvps = new HashMap<String, String>();
                                            tvp.put(specname, tvps);
                                        }
                                        tvps.put(desig, ctype);

                                        String contspec = cont.getSpec();
                                        System.err.println(query + " asdf " + contspec + " " + lastmatch + "  "
                                                + at.start + " " + at.stop + "  " + ann.start + " " + ann.stop
                                                + " rann " + (rann != null ? rann.start + "  " + rann.stop : "")
                                                + " nann " + (nann != null ? nann.start + "  " + nann.stop : ""));
                                        if (qspec.equals(contspec)) {
                                            if (tmr.containsKey(specname)) {
                                                tvps = tmr.get(specname);
                                            } else {
                                                tvps = new HashMap<String, String>();
                                                tmr.put(specname, tvps);
                                            }
                                            tvps.put(desig, ctype);
                                        }

                                        /*if( specname.contains("brockianus_MAT_338") ) {
                                           System.err.println();
                                        }*/
                                    }

                                    Platform.runLater(() -> {
                                        if (!isGeneview()) {
                                            /*int ggindex = geneset.allgenegroups.indexOf( gg );
                                            int i = table.convertRowIndexToView( ggindex );
                                            if( i != -1 ) table.addRowSelectionInterval(i, i);*/

                                            table.getSelectionModel().select(gg);
                                        } else {
                                            /*int gindex = geneset.genelist.indexOf( g );
                                            int i = table.convertRowIndexToView( gindex );
                                            table.addRowSelectionInterval(i, i);*/

                                            gtable.getSelectionModel().select(g);
                                        }
                                    });
                                }

                                /*for( Annotation ann : lann ) {
                                   if( ann.stop > start && ann.start < stop ) {
                                Gene g = ann.getGene();
                                if( g != null ) {
                                   if( table.getModel() == groupModel ) {
                                      GeneGroup gg = g.getGeneGroup();
                                          
                                      int ggindex = allgenegroups.indexOf( gg );
                                      int i = table.convertRowIndexToView( ggindex );
                                      table.addRowSelectionInterval(i, i);
                                   } else if( table.getModel() == defaultModel ) {
                                      int gindex = geneset.genelist.indexOf( g );
                                      int i = table.convertRowIndexToView( gindex );
                                      table.addRowSelectionInterval(i, i);
                                   }
                                }
                                   }
                                }*/
                            }
                            //}
                            continue;
                        }
                    }

                    /*int i = line.indexOf(' ', 2);
                    if( i == -1 ) i = line.length();
                    String id = line.substring(2, i);
                        
                    Gene g = genemap.get( id );
                    if( g != null ) {
                       if( table.getModel() == groupModel ) {
                          i = allgenegroups.indexOf( g.getGeneGroup() );
                          if( i != -1 && i < table.getRowCount() ) {
                             int r = table.convertRowIndexToView( i );
                             table.addRowSelectionInterval(r, r);
                          }
                       } else {
                          i = geneset.genelist.indexOf( g );
                          if( i != -1 && i < table.getRowCount() ) {
                             int r = table.convertRowIndexToView( i );
                             table.addRowSelectionInterval(r, r);
                          }
                       }
                    }
                        
                    String stuff = line+"\n";
                    line = br.readLine();
                    while( line != null && !line.startsWith("Query=") && !line.startsWith("> ") ) {
                       stuff += line+"\n";
                       line = br.readLine();
                    }
                    if( rr != null ) {
                       rr.run( stuff );
                       //res += line+"\n";
                    }
                    } //else*/
                    line = br.readLine();
                    res.append(line + "\n");
                }
                br.close();
                p.destroy();

                for (String specname : geneset.speccontigMap.keySet()) {
                    List<Sequence> lseq = geneset.speccontigMap.get(specname);
                    for (Sequence seq : lseq) {
                        List<Annotation> lann = seq.getAnnotations();
                        if (lann != null) {
                            for (Annotation a : lann) {
                                String desig = a.designation;
                                if (desig != null && desig.contains("phage") && phindex.containsKey(desig)) {
                                    if (!specindex.containsKey(specname))
                                        specindex.put(specname, specindex.size());

                                    Set<String> tvps;
                                    if (tph.containsKey(specname)) {
                                        tvps = tph.get(specname);
                                    } else {
                                        tvps = new HashSet<String>();
                                        tph.put(specname, tvps);
                                    }
                                    tvps.add(desig);
                                }
                            }
                        }
                    }
                }

                int k = 0;
                int u = 0;
                Workbook wb = new XSSFWorkbook();
                Sheet sh = wb.createSheet("Phage");
                Row rw = sh.createRow(u++);
                //res = new StringBuilder();
                for (String ph : phindex.keySet()) {
                    res.append("\t" + ph);
                    rw.createCell(++k).setCellValue(ph);
                }
                res.append("\n");
                for (String rspec : specindex.keySet()) {
                    String spec = Sequence.nameFix(rspec, true);
                    rw = sh.createRow(u++);
                    k = 0;
                    rw.createCell(k++).setCellValue(spec);

                    Map<String, String> set = tvp.get(rspec);
                    res.append(spec);
                    if (set != null) {
                        for (String ph : phindex.keySet()) {
                            if (set.containsKey(ph)) {
                                String type = set.get(ph);
                                if (type == null || type.length() == 0)
                                    type = "yes";
                                res.append("\t" + type);
                                rw.createCell(k).setCellValue(type);
                            } else {
                                res.append("\t");
                            }

                            k++;
                        }
                    }
                    res.append("\n");
                }

                for (String ph : phindex.keySet()) {
                    res.append("\t" + ph);
                }
                res.append("\n");

                u++;
                for (String rspec : specindex.keySet()) {
                    String spec = Sequence.nameFix(rspec, true);

                    rw = sh.createRow(u++);
                    k = 0;
                    rw.createCell(k++).setCellValue(spec);

                    Map<String, String> set = tmr.get(rspec);
                    res.append(spec);
                    if (set != null) {
                        for (String ph : phindex.keySet()) {
                            if (set.containsKey(ph)) {
                                String type = set.get(ph);
                                if (type == null || type.length() == 0)
                                    type = "yes";
                                res.append("\t" + type);
                                rw.createCell(k).setCellValue(type);
                            } else
                                res.append("\t");

                            k++;
                        }
                    }
                    res.append("\n");
                }

                u++;
                for (String rspec : specindex.keySet()) {
                    String spec = Sequence.nameFix(rspec, true);

                    rw = sh.createRow(u++);
                    k = 0;
                    rw.createCell(k++).setCellValue(spec);

                    Set<String> set = tph.get(rspec);
                    Map<String, String> setvp = tvp.get(rspec);
                    res.append(spec);
                    if (set != null) {
                        for (String ph : phindex.keySet()) {
                            if (set.contains(ph)) {
                                if (setvp != null && setvp.containsKey(ph)) {
                                    res.append("\tyes wspacer");
                                    rw.createCell(k).setCellValue("yes wspacer");
                                } else {
                                    res.append("\tyes");
                                    rw.createCell(k).setCellValue("yes");
                                }
                            } else
                                res.append("\t");

                            k++;
                        }
                    }
                    res.append("\n");
                }

                File file = new File("/Users/sigmar/phage.xlsx");
                FileOutputStream fos = new FileOutputStream(file);
                wb.write(fos);
                fos.close();

                Desktop.getDesktop().open(file);

                //if( !show ) {
                JFrame frame = new JFrame();
                frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
                frame.setSize(800, 600);

                JTextArea ta = new JTextArea();
                ta.setFont(new Font("monospaced", Font.PLAIN, 12));
                ta.append(res.toString());
                JScrollPane sp = new JScrollPane(ta);
                frame.add(sp);

                frame.setVisible(true);

                FileWriter fw = new FileWriter("/Users/sigmar/file.txt");
                fw.write(res.toString());
                fw.close();

                if (rr != null)
                    rr.run("close");
                //}

                /*if( rr != null ) {
                 rr.run( res );
                }*/
            } catch (IOException e) {
                e.printStackTrace();
            }
            /*   }
            };
            t2.start();*/
            //fr.close();
        } catch (IOException e2) {
            e2.printStackTrace();
        }
    }

    public void cogCalc(String filename, Set<Character> includedCogs, Map<String, Map<Character, Integer>> map,
            Set<String> selspec, boolean contigs) throws IOException {
        if (!isGeneview()) {
            for (String spec : selspec) {
                Map<Character, Integer> submap = new HashMap<>();
                map.put(spec, submap);

                List<Sequence> sctg = geneset.speccontigMap.get(spec);
                for (Sequence c : sctg) {
                    if (c.getAnnotations() != null)
                        for (Annotation a : c.getAnnotations()) {
                            Cog cog = a.getGene().cog;
                            if (cog == null) {
                                cog = geneset.cogmap.get(a.getGene().id);
                            }
                            if (cog != null && cog.symbol != null) {
                                int val = 0;
                                if (submap.containsKey(cog.symbol))
                                    val = submap.get(cog.symbol);
                                submap.put(cog.symbol, val + 1);
                            } else if (cog != null) {
                                System.err.println("null symbol" + cog.id + "  " + cog.name + "   " + cog.genesymbol
                                        + "  " + cog.annotation);
                            }
                        }
                }
                System.err.println();
            }

            /*for( int r = 0; r < table.getRowCount(); r++ ) {
               //int i = table.convertRowIndexToModel(r);
               //if( i >= 0 && i < allgenegroups.size() ) {
            for( int i = 0; i < allgenegroups.size(); i++ ) {
                  GeneGroup gg = allgenegroups.get(i);
                  Cog cog = gg.getCommonCog(cogmap);
                  if( cog != null && includedCogs.contains(cog.symbol) ) {
              for( String spec : selspec ) {
                 if( gg.species.containsKey( spec ) ) {
                    Teginfo ti = gg.species.get( spec );
                    for( Tegeval tv : ti.tset ) {
                       Map<Character,Integer> submap;
                       if( contigs ) {
                          if( map.containsKey( tv.contloc ) ) {
                                 
                          }
                       } else {
                          int val = 0;
                          //if( map.containsKey( tv.getSpecies() ) ) {
                          submap = map.get( tv.getSpecies() );
                          if( submap.containsKey(cog.symbol) ) val = submap.get(cog.symbol);
                          /*} else {
                             submap = new HashMap<Character,Integer>();
                             map.put(spec, submap);
                          }*
                          submap.put( cog.symbol, val+1 );
                       }
                    }
                 }
              }
                  }
               //}
            }*/
        } else {

        }
        //cogCalc(filename, br, map, selspec, contigs);
    }

    public StringBuffer getSelectedASeqs(TableView table, List<Gene> genelist, JApplet applet,
            Collection<String> species) throws IOException {
        StringWriter sb = new StringWriter();

        Set<String> selectedSpecies = getSelspec(applet, new ArrayList<String>(species));
        for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
            //if (gg.species != null) {
            sb.append(gg.name + ":\n");
            //for (String sp : gg.species.keySet()) {
            //for( String sp : selectedSpecies ) {
            if (selectedSpecies.contains(species)) {
                Tegeval tv = gg.tegeval;
                //sb.append(">" + tv.name + " " + tv.teg + " " + tv.eval + "\n");
                Sequence protseq = tv.getProteinSequence();
                protseq.setName(tv.name + " " + tv.teg + " " + tv.eval);
                protseq.writeSequence(sb);
                /*for (int i = 0; i < tv.getProteinLength(); i += 70) {
                   int end = Math.min(i + 70, tv.getProteinLength());
                   sb.append( protseq.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" );
            }
        }
        return sb.getBuffer();
    }

    /*int[]      currentRowSelection;
    public TransferHandler dragRows( final JTable table, final List<String> specs ) {
       TransferHandler th = null;
       try {
     final DataFlavor ndf = new DataFlavor( DataFlavor.javaJVMLocalObjectMimeType );
     final DataFlavor df = DataFlavor.getTextPlainUnicodeFlavor();
     final String charset = df.getParameter("charset");
     final Transferable transferable = new Transferable() {
        @Override
        public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException {
           if( arg0.equals( ndf ) ) {
              int[] rr = currentRowSelection; //table.getSelectedRows();
              List<String>   selseq = new ArrayList<String>( rr.length );
              for( int r : rr ) {
                 int i = table.convertRowIndexToModel(r);
                 selseq.add( specs.get(i) );
              }
              return selseq;
           } else {
              String ret = "";//makeCopyString();
              for( int r = 0; r < table.getRowCount(); r++ ) {
                 Object o = table.getValueAt(r, 0);
                 if( o != null ) {
                    ret += o.toString();
                 } else {
                    ret += "";
                 }
                 for( int c = 1; c < table.getColumnCount(); c++ ) {
                    o = table.getValueAt(r, c);
                    if( o != null ) {
                       ret += "\t"+o.toString();
                    } else {
                       ret += "\t";
                    }
                 }
                 ret += "\n";
              }
              //return arg0.getReaderForText( this );
              return new ByteArrayInputStream( ret.getBytes( charset ) );
           }
           //return ret;
        }
        
        @Override
        public DataFlavor[] getTransferDataFlavors() {
           return new DataFlavor[] { df, ndf };
        }
        
        @Override
        public boolean isDataFlavorSupported(DataFlavor arg0) {
           if( arg0.equals(df) || arg0.equals(ndf) ) {
              return true;
           }
           return false;
        }
     };
        
     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) {
           currentRowSelection = table.getSelectedRows();
        
           return transferable;
        }
        
        public boolean importData(TransferHandler.TransferSupport support) {
           try {
              System.err.println( table.getSelectedRows().length );
        
              DataFlavor[] dfs = support.getDataFlavors();
              if( support.isDataFlavorSupported( ndf ) ) {
                 Object obj = support.getTransferable().getTransferData( ndf );
                 ArrayList<String>   seqs = (ArrayList<String>)obj;
                 Point p = support.getDropLocation().getDropPoint();
                 int k = table.rowAtPoint( p );
        
                 specs.removeAll( seqs );
                 for( String s : seqs ) {
                    specs.add(k++, s);
                 }
        
                 TableRowSorter<TableModel>   trs = (TableRowSorter<TableModel>)table.getRowSorter();
                 trs.setSortKeys( null );
        
                 table.tableChanged( new TableModelEvent(table.getModel()) );
        
                 return true;
              }
           } catch (UnsupportedFlavorException e) {
              e.printStackTrace();
           } catch (IOException e) {
              e.printStackTrace();
           }
           return false;
        }
     };
       } catch( Exception e ) {
     e.printStackTrace();
       }
       return th;
    }*/

    int[] currentRowSelection;

    public TransferHandler dragRows(final JTable table, final List<String> specs) {
        TransferHandler th = null;
        try {
            final DataFlavor ndf = new DataFlavor(DataFlavor.javaJVMLocalObjectMimeType);
            final DataFlavor df = DataFlavor.getTextPlainUnicodeFlavor();
            final String charset = df.getParameter("charset");
            final Transferable transferable = new Transferable() {
                @Override
                public Object getTransferData(DataFlavor arg0) throws UnsupportedFlavorException, IOException {
                    if (arg0.equals(ndf)) {
                        int[] rr = currentRowSelection; //table.getSelectedRows();
                        List<String> selseq = new ArrayList<String>(rr.length);
                        for (int r : rr) {
                            int i = table.convertRowIndexToModel(r);
                            selseq.add(specs.get(i));
                        }
                        return selseq;
                    } else {
                        String ret = "";//makeCopyString();
                        for (int r = 0; r < table.getRowCount(); r++) {
                            Object o = table.getValueAt(r, 0);
                            if (o != null) {
                                ret += o.toString();
                            } else {
                                ret += "";
                            }
                            for (int c = 1; c < table.getColumnCount(); c++) {
                                o = table.getValueAt(r, c);
                                if (o != null) {
                                    ret += "\t" + o.toString();
                                } else {
                                    ret += "\t";
                                }
                            }
                            ret += "\n";
                        }
                        //return arg0.getReaderForText( this );
                        return new ByteArrayInputStream(ret.getBytes(charset));
                    }
                    //return ret;
                }

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

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

            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) {
                    currentRowSelection = table.getSelectedRows();

                    return transferable;
                }

                public boolean importData(TransferHandler.TransferSupport support) {
                    try {
                        System.err.println(table.getSelectedRows().length);

                        DataFlavor[] dfs = support.getDataFlavors();
                        if (support.isDataFlavorSupported(ndf)) {
                            Object obj = support.getTransferable().getTransferData(ndf);
                            ArrayList<String> seqs = (ArrayList<String>) obj;

                            /*ArrayList<String> newlist = new ArrayList<String>( serifier.lgse.size() );
                            for( int r = 0; r < table.getRowCount(); r++ ) {
                               int i = table.convertRowIndexToModel(r);
                               newlist.add( specs.get(i) );
                            }
                            serifier.lgseq.clear();
                            serifier.lgseq = newlist;*/

                            Point p = support.getDropLocation().getDropPoint();
                            int k = table.rowAtPoint(p);

                            specs.removeAll(seqs);
                            for (String s : seqs) {
                                specs.add(k++, s);
                            }

                            TableRowSorter<TableModel> trs = (TableRowSorter<TableModel>) table.getRowSorter();
                            trs.setSortKeys(null);

                            table.tableChanged(new TableModelEvent(table.getModel()));

                            return true;
                        } /* else if( support.isDataFlavorSupported( df ) ) {                     
                            Object obj = support.getTransferable().getTransferData( df );
                            InputStream is = (InputStream)obj;
                                
                            System.err.println( charset );
                            importReader( new BufferedReader(new InputStreamReader(is, charset)) );
                                
                            updateView();
                                
                            return true;
                          }  else if( support.isDataFlavorSupported( DataFlavor.stringFlavor ) ) {                     
                            Object obj = support.getTransferable().getTransferData( DataFlavor.stringFlavor );
                            String str = (String)obj;
                            importReader( new BufferedReader( new StringReader(str) ) );
                                
                            updateView();
                                
                            return true;
                          }*/
                    } catch (UnsupportedFlavorException e) {
                        e.printStackTrace();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                    return false;
                }
            };
        } catch (Exception e) {
            e.printStackTrace();
        }
        return th;
    }

    RadioMenuItem gb;
    RadioMenuItem ggb;

    TableView<GeneGroup> table;
    TableView<Gene> gtable;
    TableView<Function> ftable;
    TableModel defaultModel;
    TableModel groupModel;

    public void updateFilter(TableView table, Label label) {
        if (label != null)
            label.setText(table.getItems().size() + "/" + table.getSelectionModel().getSelectedIndices().size());
    }

    public void updateFilter(JTable table, RowFilter filter, Label label) {
        DefaultRowSorter<TableModel, Integer> rowsorter = (DefaultRowSorter<TableModel, Integer>) table
                .getRowSorter();
        rowsorter.setRowFilter(filter);
        if (label != null)
            label.setText(table.getRowCount() + "/" + table.getSelectedRowCount());
    }

    public BufferedImage gatest(String spec1) {
        GeneCompare gc = new GeneCompare(); //comparePlot( GeneSetHead.this, comp, genelist, clusterMap );
        final BufferedImage bimg = new BufferedImage(1024, 1024, BufferedImage.TYPE_INT_RGB);
        final Graphics2D g2 = bimg.createGraphics();
        final Map<String, Integer> blosumap = JavaFasta.getBlosumMap();

        if (spec1 != null && spec1.length() > 0) {
            List<Sequence> clist = geneset.speccontigMap.get(spec1);
            int total = 0;
            int ptotal = 0;
            for (Sequence ctg : clist) {
                if (ctg.isPlasmid())
                    ptotal += ctg.getAnnotationCount();
                else
                    total += ctg.getAnnotationCount();
            }

            gc.draw(g2, spec1, GeneSetHead.this, 1024, 1024, clist, geneset.specList, blosumap, total, ptotal);
        } else {
            gc.draw(g2, null, GeneSetHead.this, 1024, 1024, null, geneset.specList, blosumap,
                    table.getItems().size(), 0);
        }
        g2.dispose();

        return bimg;
    }

    public void updateFilter(int val, String ustr, TableView table, RowFilter filter, Set<Integer> filterset,
            Label label, int... ind) {
        filterset.clear();
        /*TableModel model = table.getModel();
        for (int r = 0; r < model.getRowCount(); r++) {
           for( int i = 0; i < ind.length; i++ ) {
        String vstr = (String)model.getValueAt(r, ind[i]);
        String s = vstr != null ? vstr.toLowerCase() : null;
            
        if( (s != null && s.contains(ustr)) ) {
           filterset.add(r);
           break;
        }
           }
        }
            
        if( filterset.isEmpty() ) {
           int i = 0;
           if( table.getModel() == groupModel ) {
        for( GeneGroup gg : geneset.allgenegroups ) {
           for( Gene g : gg.genes ) {
              if( g.refid.toLowerCase().contains(ustr) ) {
                 filterset.add(i);
                 break;
              }
           }
           i++;
        }
           } else {
        for( Gene g : geneset.genelist ) {
           if( g.refid.toLowerCase().contains(ustr) ) {
              filterset.add(i);
           }
           i++;
        }
           }
        }*/

        updateFilter(table, label);
    }

    public void updateFilter(int val, String ustr, JTable table, RowFilter filter, Set<Integer> filterset,
            Label label, int... ind) {
        filterset.clear();
        TableModel model = table.getModel();
        for (int r = 0; r < model.getRowCount(); r++) {
            for (int i = 0; i < ind.length; i++) {
                String vstr = (String) model.getValueAt(r, ind[i]);
                String s = vstr != null ? vstr.toLowerCase() : null;

                if ((s != null && s.contains(ustr))) {
                    filterset.add(r);
                    break;
                }
            }
        }

        if (filterset.isEmpty()) {
            int i = 0;
            if (table.getModel() == groupModel) {
                for (GeneGroup gg : geneset.allgenegroups) {
                    for (Gene g : gg.genes) {
                        if (g.refid.toLowerCase().contains(ustr)) {
                            filterset.add(i);
                            break;
                        }
                    }
                    i++;
                }
            } else {
                for (Gene g : geneset.genelist) {
                    if (g.refid.toLowerCase().contains(ustr)) {
                        filterset.add(i);
                    }
                    i++;
                }
            }
        }

        updateFilter(table, filter, label);
    }

    public void showAlignedSequences(Component comp, Serifier serifier) {
        SwingUtilities.invokeLater(() -> {
            JFrame frame1 = new JFrame();
            frame1.setSize(800, 600);
            frame1.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame1);
            jf.updateView();

            frame1.setVisible(true);
        });
    }

    public void showSomeSequences(Component comp, Serifier serifier) {
        SwingUtilities.invokeLater(() -> {
            JFrame frame1 = new JFrame();
            frame1.setSize(800, 600);
            frame1.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame1);

            /*for( String contig : contset.keySet() ) {
            Sequence seq = contset.get(contig);
            serifier.addSequence(seq);
            if (seq.getAnnotations() != null)
                Collections.sort(seq.getAnnotations());
            }*/
            jf.getSerifier().checkMaxMin();
            jf.updateView();

            frame1.setVisible(true);
        });
    }

    public void showSelectedSequences(Component comp, Set<Annotation> tset, boolean dna, String names) {
        SwingUtilities.invokeLater(() -> {
            JFrame frame1 = new JFrame();
            frame1.setSize(800, 600);
            frame1.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            Serifier serifier = new Serifier();
            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame1);

            for (Annotation tv : tset) {
                Sequence cont = tv.getContig();
                if (cont != null) {
                    //String contig = cont.getSpec();//tv.getContig();
                    Sequence seq = dna ? tv.createSequence() : tv.getProteinSequence();
                    seq.setName(geneset.nameFix(tv.getSpecies()));
                    //Sequence seq = new Sequence( nameFix(tv.getSpecies())/*getGeneName(names, tv.getGene())*/, seqstr, serifier.mseq );
                    serifier.addSequence(seq);
                }
            }

            /*for( String contig : contset.keySet() ) {
            Sequence seq = contset.get(contig);
            serifier.addSequence(seq);
            if (seq.getAnnotations() != null)
                Collections.sort(seq.getAnnotations());
            }*/
            jf.updateView();

            frame1.setVisible(true);
        });
    }

    public void showSequences(Component comp, Set<GeneGroup> ggset, boolean dna, Set<String> specs) {
        showSequences(comp, ggset, dna, specs, false);
    }

    public void showSequences(Component comp, Set<GeneGroup> ggset, boolean dna, Set<String> specs,
            boolean genename) {
        SwingUtilities.invokeLater(() -> {
            JFrame frame1 = new JFrame();
            frame1.setSize(800, 600);
            frame1.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            Serifier serifier = new Serifier();
            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame1);

            for (GeneGroup ggroup : ggset) {
                //for( Gene gg : ggroup.genes ) {
                //if (gg.species != null) {
                //for (String sp : gg.species.keySet()) {
                //   Teginfo stv = gg.species.get(sp);
                for (Tegeval tv : ggroup.getTegevals()) {
                    Sequence cont = tv.getContshort();
                    if (cont != null) {
                        String selspec = cont.getSpec();//tv.getContig();
                        if (genename) {
                            Sequence seq = dna ? tv.createSequence() : tv.getProteinSequence();
                            seq.setName(tv.gene != null ? tv.gene.name : tv.name);
                            serifier.mseq.put(seq.getName(), seq);
                            //Sequence seq = new Sequence( tv.gene != null ? tv.gene.name : tv.name, seqstr, serifier.mseq );
                            serifier.addSequence(seq);
                        } else if (specs == null || specs.contains(selspec)) {
                            String spec = geneset.nameFix(selspec);

                            Sequence seq = dna ? tv.createSequence() : tv.getProteinSequence();
                            seq.setName(spec);
                            /*String name = tv.getGene().id;
                            String cazy = tv.getGene().getGeneGroup().getCommonCazy(cazymap);
                            String ec = tv.getGene().getGeneGroup().getCommonEc();
                            if( cazy != null ) name += " " + cazy;
                            if( ec != null ) name += " " + ec;*/
                            //Sequence seq = new Sequence( spec, seqstr, serifier.mseq );
                            serifier.addSequence(seq);
                        }
                    }
                    //contset.put( contig, seq );

                    /*String contig = tv.contshort;
                    if (contset.containsKey(contig)) {
                    seq = contset.get(contig);
                    } else {
                    if (GeneSet.contigs.containsKey(contig)) {
                        StringBuilder dna = GeneSet.contigs.get(contig);
                        seq = new Sequence(contig, dna, jf.mseq);
                    } else
                        seq = new Sequence(contig, jf.mseq);
                    contset.put(contig, seq);
                    }
                        
                    Annotation a = seq.new Annotation(seq, contig, Color.red, jf.mann);
                    a.setStart(tv.start);
                    a.setStop(tv.stop);
                    a.setOri(tv.ori);
                    a.setGroup(gg.name);
                    a.setType("gene");
                    jf.addAnnotation(a);*/
                    // seq.addAnnotation( new Annotation( seq, ) );
                }
            }

            /*for( String contig : contset.keySet() ) {
            Sequence seq = contset.get(contig);
            serifier.addSequence(seq);
            if (seq.getAnnotations() != null)
                Collections.sort(seq.getAnnotations());
            }*/
            jf.updateView();

            frame1.setVisible(true);
        });
    }

    KeyListener keylistener;

    public void initFSKeyListener(final Window window) {
        keylistener = new KeyListener() {
            @Override
            public void keyTyped(KeyEvent e) {

            }

            @Override
            public void keyReleased(KeyEvent e) {

            }

            @Override
            public void keyPressed(KeyEvent e) {
                GraphicsDevice gd = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice();
                if (e.getKeyCode() == KeyEvent.VK_F11 && gd.isFullScreenSupported()) {
                    Window w = gd.getFullScreenWindow();
                    if (w != null) {
                        gd.setFullScreenWindow(null);
                    } else {
                        gd.setFullScreenWindow(window);
                    }
                }
            }
        };
    }

    private static void setColors() {
        Sequence.colorCodes[0] = new Color(180, 255, 180);
        Sequence.colorCodes[1] = new Color(180, 245, 190);
        Sequence.colorCodes[2] = new Color(180, 235, 200);
        Sequence.colorCodes[3] = new Color(180, 225, 210);
        Sequence.colorCodes[4] = new Color(180, 215, 220);
        Sequence.colorCodes[5] = new Color(180, 205, 230);
        Sequence.colorCodes[6] = new Color(180, 195, 240);
        Sequence.colorCodes[7] = new Color(180, 185, 250);
        Sequence.colorCodes[8] = new Color(180, 180, 255);
    }

    public boolean isGeneview() {
        return splitpane.getItems().contains(gtable);
    }

    public int getSelectionSize() {
        return isGeneview() ? gtable.getSelectionModel().getSelectedIndices().size()
                : table.getSelectionModel().getSelectedIndices().size();
    }

    public void cogBlastDlg(Set<String> species) {
        Dialog<String> cogdlg = new Dialog();

        ToggleGroup group = new ToggleGroup();
        VBox vbox = new VBox();
        RadioButton docker = new RadioButton("docker");
        docker.setToggleGroup(group);
        RadioButton local = new RadioButton("local");
        local.setToggleGroup(group);
        docker.setSelected(true);
        TextField dbpath = new TextField("/cdd_delta");
        TextField host = new TextField("geneset");

        vbox.getChildren().add(docker);
        vbox.getChildren().add(local);
        vbox.getChildren().add(dbpath);
        vbox.getChildren().add(host);

        cogdlg.getDialogPane().setContent(vbox);

        /*String dbPath = "/data/Cog";
        JTextField tf = new JTextField( dbPath );
        JTextField host = new JTextField("localhost");
        JOptionPane.showMessageDialog( null, new Object[] {tf, host} );*/

        cogdlg.getDialogPane().getButtonTypes().add(ButtonType.OK);
        cogdlg.getDialogPane().getButtonTypes().add(ButtonType.CANCEL);
        cogdlg.setResultConverter(param -> {
            if (!param.getButtonData().isCancelButton()) {
                return dbpath.getText();
            }
            return "";
        });
        Optional<String> ostr = cogdlg.showAndWait();
        if (ostr.isPresent()) {
            String str = ostr.get();
            if (str.length() > 0)
                SwingUtilities.invokeLater(() -> {
                    geneset.cogBlast(species, dbpath.getText(), host.getText(), false, docker.isSelected());
                });
        }
    }

    TextField tb1 = null;
    TextField tb2 = null;
    TextField epar = null;
    final JFXPanel fxpanel = new JFXPanel();
    Scene fxs = null;

    BufferedImage bimg;

    ComboBox<String> selcomb;
    ComboBox<String> searchcolcomb;
    ComboBox<String> syncolorcomb;

    ComboBox<String> specombo;
    ComboBox<String> combo;

    SplitPane splitpane;
    Stage primaryStage;

    Component comp;

    public void init(final Stage primaryStage, final Container comp, final SplitPane splitpane,
            final TableView<Gene> genetable, final TableView<Function> upper, final TableView<GeneGroup> lower,
            final MenuBar menubar, final ToolBar toolbar, final ToolBar btoolbar) {
        geneset.user = System.getProperty("user.name");
        JavaFasta.user = geneset.user;
        this.splitpane = splitpane;
        this.primaryStage = primaryStage;

        table = lower;
        gtable = genetable;
        //SerifyApplet.user = user;

        /*try {
           UIManager.setLookAndFeel("com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel");
        } catch (ClassNotFoundException e) {
           e.printStackTrace();
        } catch (InstantiationException e) {
           e.printStackTrace();
        } catch (IllegalAccessException e) {
           e.printStackTrace();
        } catch (UnsupportedLookAndFeelException e) {
           e.printStackTrace();
        }*/

        String userhome = System.getProperty("user.home");
        boolean windows = false;
        try {
            InputStream isk = GeneSet.class.getClassLoader().getResourceAsStream("org/simmi/genesetkey");
            //Path gkey = Paths.get( url.toURI() );
            InputStream iskp = GeneSet.class.getClassLoader().getResourceAsStream("org/simmi/genesetkey.pub");
            //Path gkeypub = Paths.get( url.toURI() );

            Path gkeyssh = Paths.get(userhome);
            //Path gkeyssh = userpath.resolve(".ssh");
            if (!Files.exists(gkeyssh))
                Files.createDirectory(gkeyssh);
            Path gkeylocal = gkeyssh.resolve("org/simmi/genesetkey");
            Path gkeylocalpub = gkeyssh.resolve("org/simmi/genesetkey.pub");
            if (!Files.exists(gkeylocal) && isk != null) {
                Files.copy(isk, gkeylocal, StandardCopyOption.REPLACE_EXISTING);
            }
            if (!Files.exists(gkeylocalpub) && iskp != null) {
                Files.copy(iskp, gkeylocalpub);
            }

            Set<PosixFilePermission> poset = new HashSet<PosixFilePermission>();
            poset.add(PosixFilePermission.OWNER_READ);
            poset.add(PosixFilePermission.OWNER_WRITE);
            if (Files.exists(gkeylocal))
                Files.setPosixFilePermissions(gkeylocal, poset);
            if (Files.exists(gkeylocalpub))
                Files.setPosixFilePermissions(gkeylocalpub, poset);
        } catch (IOException e1) {
            e1.printStackTrace();
        } catch (UnsupportedOperationException e2) {
            windows = true;
            e2.printStackTrace();
        }

        if (windows) {
            File f = new File(userhome + "\\genesetkey");
            f.setExecutable(false, false);
            f.setWritable(false, false);
            f.setReadable(false, false);

            f.setWritable(true, true);
            f.setReadable(true, true);
        }

        this.comp = comp;
        selcomb = new ComboBox<>();
        searchcolcomb = new ComboBox<>();
        syncolorcomb = new ComboBox<>();

        searchcolcomb.getItems().add("Name");
        searchcolcomb.getItems().add("Symbol");
        searchcolcomb.getSelectionModel().select(0);

        setColors();

        JMenuBar jmenubar = new JMenuBar();
        Menu file = new Menu("File");

        MenuItem newitem = new MenuItem("New");
        newitem.setOnAction(actionEvent -> newFile());
        file.getItems().add(newitem);

        MenuItem openitem = new MenuItem("Open");
        openitem.setOnAction(actionEvent -> {
            try {
                importStuff();
            } catch (IOException e3) {
                e3.printStackTrace();
            } catch (UnavailableServiceException e3) {
                e3.printStackTrace();
            }
        });
        file.getItems().add(openitem);
        file.getItems().add(new SeparatorMenuItem());

        MenuItem importitem = new MenuItem("Import genomes");
        importitem.setOnAction(actionEvent -> fetchGenomes());
        file.getItems().add(importitem);

        MenuItem exportitem = new MenuItem("Export genomes");
        exportitem.setOnAction(actionEvent -> exportGenomes(geneset.speccontigMap));
        file.getItems().add(exportitem);

        file.getItems().add(new SeparatorMenuItem());

        MenuItem exportproteinitem = new MenuItem("Export protein sequences");
        exportproteinitem.setOnAction(actionEvent -> exportProteinSequences(geneset.genelist));
        file.getItems().add(exportproteinitem);

        MenuItem exportgeneitem = new MenuItem("Export gene clusters");
        exportgeneitem.setOnAction(actionEvent -> exportGeneClusters(geneset.allgenegroups));
        file.getItems().add(exportgeneitem);

        file.getItems().add(new SeparatorMenuItem());

        MenuItem quititem = new MenuItem("Quit");
        quititem.setOnAction(actionEvent -> System.exit(0));
        file.getItems().add(quititem);

        Menu edit = new Menu("Edit");
        MenuItem clustergenes = new MenuItem("Cluster genes");
        clustergenes.setOnAction(actionEvent -> {
            //fxpanel.setScene( null );
            /*Platform.runLater(new Runnable() {
                  @Override
                  public void run() {
              Label label1 = new Label("Id:");
                  tb1 = new TextField("0.5");
                  Label label2 = new Label("Len:");
                  tb2 = new TextField("0.5");
                      
                  VBox vbox = new VBox();
                  HBox hbox1 = new HBox();
                  hbox1.getChildren().addAll( label1, tb1 );
                  HBox hbox2 = new HBox();
                  hbox2.getChildren().addAll( label2, tb2 );
                      
                  epar = new TextField();
                  vbox.getChildren().add( epar );
                      
                  vbox.getChildren().addAll( hbox1, hbox2 );
                  if( fxs == null ) fxs = new Scene( vbox );
                  fxs.setRoot( vbox );
                      
                  fxpanel.setScene( fxs );
                  }
            });*/

            JPanel panel = new JPanel();
            GridBagLayout grid = new GridBagLayout();
            GridBagConstraints c = new GridBagConstraints();
            panel.setLayout(grid);

            /*JLabel label1 = new JLabel("Id:");
            JTextField tb1 = new JTextField("0.5");
            JLabel label2 = new JLabel("Len:");
            JTextField tb2 = new JTextField("0.5");
                
            Dimension d = new Dimension( 300, 30 );
            JTextField epar = new JTextField();
            epar.setSize( d );
            epar.setPreferredSize( d );
                
            c.fill = GridBagConstraints.HORIZONTAL;
            c.gridwidth = 1;
            c.gridheight = 1;
                
            c.gridx = 0;
            c.gridy = 0;
            panel.add( label1, c );
            c.gridx = 1;
            c.gridy = 0;
            panel.add( tb1, c );
            c.gridx = 0;
            c.gridy = 1;
            panel.add( label2, c );
            c.gridx = 1;
            c.gridy = 1;
            panel.add( tb2, c );
            c.gridx = 0;
            c.gridy = 2;
            c.gridwidth = 2;
            panel.add( epar, c );
                
            JOptionPane.showMessageDialog(comp, new Object[] {panel}, "Clustering parameters", JOptionPane.PLAIN_MESSAGE );*/

            /*if( tb1 != null ) {
               float id = Float.parseFloat( tb1.getText() );
               float len = Float.parseFloat( tb2.getText() );
               String expar = epar.getText();
                   
               tb1 = null;
               tb2 = null;
               epar = null;*/

            Set<String> species = getSelspec(null, geneset.getSpecies(), null);
            geneset.clusterGenes(species, false);
            //}
        });
        MenuItem alignclusters = new MenuItem("Align clusters");
        alignclusters.setOnAction(actionEvent -> {
            try {
                String OS = System.getProperty("os.name").toLowerCase();

                Map<String, String> env = new HashMap<String, String>();
                env.put("create", "true");
                String uristr = "jar:" + geneset.zippath.toUri();
                geneset.zipuri = URI.create(uristr);
                geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                //s.makeBlastCluster(zipfilesystem.getPath("/"), p, 1);
                Path aldir = geneset.zipfilesystem.getPath("aligned");
                final Path aligneddir = Files.exists(aldir) ? aldir : Files.createDirectory(aldir);

                Runnable run = new Runnable() {
                    @Override
                    public void run() {
                        try {
                            geneset.zipfilesystem.close();
                        } catch (IOException e) {
                            e.printStackTrace();
                        }
                    }
                };

                NativeRun nrun = new NativeRun(run);
                //ExecutorService es = Executors.newFixedThreadPool( Runtime.getRuntime().availableProcessors() );

                Object[] cont = new Object[3];

                Collection<GeneGroup> ggset;
                ObservableList<GeneGroup> ogg = table.getSelectionModel().getSelectedItems();
                ggset = new HashSet<GeneGroup>();
                if (ogg.size() == 0) {
                    for (GeneGroup gg : geneset.allgenegroups) {
                        //GeneGroup gg = allgenegroups.get(table.convertRowIndexToModel(r));
                        //gg.getCommonTag()
                        if (gg != null && gg.getCommonTag() == null && gg.size() > 1)
                            ggset.add(gg);
                    }
                } else {
                    for (GeneGroup gg : ogg) {
                        //GeneGroup gg = geneset.allgenegroups.get(table.convertRowIndexToModel(r));
                        //gg.getCommonTag()
                        if (gg != null && gg.getCommonTag() == null && gg.size() > 1)
                            ggset.add(gg);
                    }
                }

                //int i = 0;
                List commandsList = new ArrayList();
                for (GeneGroup gg : ggset) {
                    String fasta = gg.getFasta(true);
                    String[] cmds = new String[] {
                            OS.indexOf("mac") >= 0 ? "/usr/local/bin/mafft" : "/usr/bin/mafft", "-" };
                    Object[] paths = new Object[] { fasta.getBytes(), aligneddir.resolve(gg.getCommonId() + ".aa"),
                            null };
                    commandsList.add(paths);
                    commandsList.add(Arrays.asList(cmds));

                    //if( i++ > 5000 ) break;
                }
                nrun.runProcessBuilder("Running mafft", commandsList, cont, true, run, false);
            } catch (IOException e1) {
                if (geneset.zipfilesystem != null) {
                    try {
                        geneset.zipfilesystem.close();
                    } catch (IOException e2) {
                        e2.printStackTrace();
                    }
                }
                e1.printStackTrace();
            }
        });

        MenuItem sharenumaction = new MenuItem("Update share numbers");
        sharenumaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            Set<String> specs = getSelspec(GeneSetHead.this, geneset.specList, null);
            geneset.updateShareNum(specs);
        }));

        MenuItem importgeneclusteringaction = new MenuItem("Import gene clustering");
        importgeneclusteringaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            JPanel panel = new JPanel();
            GridBagLayout grid = new GridBagLayout();
            GridBagConstraints c = new GridBagConstraints();
            panel.setLayout(grid);

            JLabel label1 = new JLabel("Id:");
            JTextField tb11 = new JTextField("0.5");
            JLabel label2 = new JLabel("Len:");
            JTextField tb21 = new JTextField("0.5");

            Dimension d = new Dimension(300, 30);
            JTextField epar1 = new JTextField();
            epar1.setSize(d);
            epar1.setPreferredSize(d);

            c.fill = GridBagConstraints.HORIZONTAL;
            c.gridwidth = 1;
            c.gridheight = 1;

            c.gridx = 0;
            c.gridy = 0;
            panel.add(label1, c);
            c.gridx = 1;
            c.gridy = 0;
            panel.add(tb11, c);
            c.gridx = 0;
            c.gridy = 1;
            panel.add(label2, c);
            c.gridx = 1;
            c.gridy = 1;
            panel.add(tb21, c);
            c.gridx = 0;
            c.gridy = 2;
            c.gridwidth = 2;
            panel.add(epar1, c);

            JOptionPane.showMessageDialog(comp, new Object[] { panel }, "Clustering parameters",
                    JOptionPane.PLAIN_MESSAGE);

            float id = Float.parseFloat(tb11.getText());
            float len = Float.parseFloat(tb21.getText());

            //JFileChooser fc = new JFileChooser();
            //if( fc.showOpenDialog( GeneSetHead.this ) == JFileChooser.APPROVE_OPTION ) {
            Serifier s = new Serifier();
            //s.mseq = aas;
            for (String gk : geneset.refmap.keySet()) {
                Gene g = geneset.refmap.get(gk);
                if (g.tegeval.getAlignedSequence() != null)
                    System.err.println(g.tegeval.getAlignedSequence().getName());
                s.mseq.put(gk, g.tegeval.getAlignedSequence());
            }

            Map<String, String> idspec = new HashMap<String, String>();
            for (String idstr : geneset.refmap.keySet()) {
                if (idstr.contains(" ")) {
                    System.err.println("coooonnnnnni " + idstr);
                }

                Gene gene = geneset.refmap.get(idstr);
                idspec.put(idstr, gene.getSpecies());
            }
            //Sequences seqs = new Sequences(user, name, type, path, nseq)
            try {
                Map<String, String> env = new HashMap<String, String>();
                env.put("create", "true");
                String uristr = "jar:" + geneset.zippath.toUri();
                geneset.zipuri = URI.create(uristr);
                geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);

                Path root = geneset.zipfilesystem.getPath("/");
                Path p = geneset.zipfilesystem.getPath("cluster.blastout"); //root.resolve("culster.blastout");

                List<Set<String>> cluster = geneset.uclusterlist == null ? new ArrayList<>()
                        : new ArrayList<>(geneset.uclusterlist);
                s.makeBlastCluster(root, p, 1, id, len, idspec, cluster, geneset.refmap);

                System.err.println(cluster.get(0));
                if (geneset.uclusterlist != null)
                    System.err.println(geneset.uclusterlist.get(0));

                geneset.zipfilesystem.close();
            } catch (IOException e1) {
                if (geneset.zipfilesystem != null) {
                    try {
                        geneset.zipfilesystem.close();
                    } catch (IOException e2) {
                        e2.printStackTrace();
                    }
                }
                e1.printStackTrace();
            }
        }));
        MenuItem importgenesymbolaction = new MenuItem("Import gene symbols");
        importgenesymbolaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            JFileChooser fc = new JFileChooser();
            if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) {
                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);

                    Path nf = geneset.zipfilesystem.getPath("/smap_short.txt");
                    BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE);

                    File f = fc.getSelectedFile();
                    InputStream is = new FileInputStream(f);
                    if (f.getName().endsWith(".gz"))
                        is = new GZIPInputStream(is);
                    geneset.uni2symbol(new InputStreamReader(is), bw, geneset.unimap);

                    bw.close();
                    //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING );
                    geneset.zipfilesystem.close();
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            }
        }));

        MenuItem importcazyaction = new MenuItem("Import Cazy");
        importcazyaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            JFileChooser fc = new JFileChooser();
            if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) {
                try {
                    BufferedReader rd = Files.newBufferedReader(fc.getSelectedFile().toPath());
                    geneset.loadcazymap(geneset.cazymap, rd);
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            }
        }));

        MenuItem gene2refseqaction = new MenuItem("Gene 2 refseq");
        gene2refseqaction.setOnAction(actionEvent -> {
            try {
                TextField tf = new TextField();
                tf.setText("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz");
                Dialog<Path> dialog = new Dialog();
                dialog.getDialogPane().setContent(tf);
                dialog.getDialogPane().getButtonTypes().add(ButtonType.OK);
                dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL);
                dialog.setResultConverter(param -> param.getButtonData().isCancelButton() ? null
                        : Paths.get(URI.create(tf.getText())));
                Optional<Path> opath = dialog.showAndWait();

                if (opath.isPresent()) {
                    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);

                    Path path = opath.get();
                    InputStream is = path.toUri().toURL().openStream();
                    if (path.getFileName().toString().endsWith(".gz")) {
                        is = new GZIPInputStream(is);
                    }
                    Path nf = geneset.zipfilesystem.getPath("/org/simmi/gene2refseq_short.txt");
                    BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE,
                            StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE);
                    geneset.idMapping(new InputStreamReader(is), bw, 5, 1, geneset.refmap, null, geneset.gimap);
                    bw.close();
                }
            } catch (Exception e) {
                e.printStackTrace();
            } finally {
                try {
                    geneset.zipfilesystem.close();
                } catch (IOException e) {
                    e.printStackTrace();
                }
            }
        });

        MenuItem functionmappingaction = new MenuItem("Function mapping");
        functionmappingaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            final JTextField tf = new JTextField();
            JButton btn = new JButton("File");
            JComponent comp2 = new JComponent() {
            };
            comp2.setLayout(new BorderLayout());
            comp2.add(tf);
            comp2.add(btn, BorderLayout.EAST);
            tf.setText("http://130.208.252.239/data/sp2go.txt.gz");

            final File[] file2 = new File[1];
            btn.addActionListener(e -> {
                JFileChooser fc = new JFileChooser();
                if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) {
                    file2[0] = fc.getSelectedFile();
                    try {
                        tf.setText(fc.getSelectedFile().toURI().toURL().toString());
                    } catch (MalformedURLException e1) {
                        e1.printStackTrace();
                    }
                }
            });

            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);

                Path nf = geneset.zipfilesystem.getPath("/org/simmi/sp2go_short.txt");
                BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE,
                        StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE);

                JOptionPane.showMessageDialog(GeneSetHead.this, comp2);

                final JDialog dialog = new JDialog();
                dialog.setTitle("Function mapping");
                dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
                dialog.setSize(400, 300);

                comp2 = new JComponent() {
                };
                comp2.setLayout(new BorderLayout());

                final JTextArea ta = new JTextArea();
                /*final InputStream fis;
                if( file[0] != null ) fis = new FileInputStream( file[0] );
                else {
                JTextField host = new JTextField("localhost");
                JOptionPane.showMessageDialog(null, host);
                    
                String username = System.getProperty("user.name");
                String hostname = host.getText();
                    
                List<String> commandsList = Arrays.asList( new String[] {"ssh",username+"@"+hostname,"cat",tf.getText()} );
                ProcessBuilder pb = new ProcessBuilder( commandsList );
                Process p = pb.start();
                    
                for( Object commands : commandsList ) {
                    if( commands instanceof List ) {
                        for( Object cmd : (List)commands ) {
                            ta.append(cmd+" ");
                        }
                        ta.append("\n");
                    } else {
                        ta.append(commands+" ");
                    }
                }
                ta.append("\n");
                    
                fis = p.getInputStream();
                }*/

                final JProgressBar pbar = new JProgressBar();
                final Thread t = new Thread() {
                    public void run() {
                        try {
                            URL url = new URL(tf.getText());
                            InputStream fis = url.openStream();

                            BufferedReader br = new BufferedReader(new InputStreamReader(new GZIPInputStream(fis)));
                            //if( unimap != null ) unimap.clear();
                            //unimap = idMapping(new InputStreamReader(is), bw, 2, 0, refmap, genmap, gimap);
                            geneset.funcMappingUni(br, geneset.unimap, bw);

                            fis.close();
                            bw.close();

                            try {
                                geneset.zipfilesystem.close();
                            } catch (Exception e2) {
                                e2.printStackTrace();
                            }
                            ;

                            pbar.setIndeterminate(false);
                            pbar.setEnabled(false);
                        } catch (IOException e) {
                            e.printStackTrace();
                        }
                    }
                };

                ta.setEditable(false);
                final JScrollPane sp = new JScrollPane(ta);

                dialog.add(comp2);
                comp2.add(pbar, BorderLayout.NORTH);
                comp2.add(sp, BorderLayout.CENTER);
                pbar.setIndeterminate(true);

                t.start();
                /*okokdialog.addWindowListener( new WindowListener() {
                    
                @Override
                public void windowOpened(WindowEvent e) {}
                    
                @Override
                public void windowIconified(WindowEvent e) {}
                    
                @Override
                public void windowDeiconified(WindowEvent e) {}
                    
                @Override
                public void windowDeactivated(WindowEvent e) {}
                    
                @Override
                public void windowClosing(WindowEvent e) {}
                    
                @Override
                public void windowClosed(WindowEvent e) {
                    if( pbar.isEnabled() ) {
                        pbar.setIndeterminate( false );
                        pbar.setEnabled( false );
                    }
                }
                    
                @Override
                public void windowActivated(WindowEvent e) {}
                });*/
                dialog.setVisible(true);
                //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING );
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        }));
        MenuItem importidmappingaction = new MenuItem("Import idmapping");
        importidmappingaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            final JTextField tf = new JTextField();
            JButton btn = new JButton("File");
            JComponent comp2 = new JComponent() {
            };
            comp2.setLayout(new BorderLayout());
            comp2.add(tf);
            comp2.add(btn, BorderLayout.EAST);
            tf.setText(
                    "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz");

            final File[] file2 = new File[1];
            btn.addActionListener(new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                    JFileChooser fc = new JFileChooser();
                    if (fc.showOpenDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) {
                        file2[0] = fc.getSelectedFile();
                        try {
                            tf.setText(fc.getSelectedFile().toURI().toURL().toString());
                        } catch (MalformedURLException e1) {
                            e1.printStackTrace();
                        }
                    }
                }
            });

            JOptionPane.showMessageDialog(GeneSetHead.this, comp2);

            //Thread t = new Thread() {
            //   public void run() {
            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);

                Path nf = geneset.zipfilesystem.getPath("/org/simmi/idmapping_short.dat");
                final BufferedWriter bw = Files.newBufferedWriter(nf, StandardOpenOption.CREATE,
                        StandardOpenOption.WRITE, StandardOpenOption.TRUNCATE_EXISTING);

                final JDialog dialog = new JDialog();
                dialog.setTitle("Id mapping");
                dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
                dialog.setSize(400, 300);

                comp2 = new JComponent() {
                };
                comp2.setLayout(new BorderLayout());

                final JTextArea ta = new JTextArea();

                /*final InputStream fis;
                if( file[0] != null ) fis = new FileInputStream( file[0] );
                else {
                /*Object[] cont = new Object[3];
                Runnable run = new Runnable() {
                    public void run() {
                        try {
                            bw.close();
                            geneset.zipfilesystem.close();
                        } catch (IOException e) {
                            e.printStackTrace();
                        }
                    }
                };*
                    
                JTextField host = new JTextField("localhost");
                JOptionPane.showMessageDialog(null, host);
                    
                String username = System.getProperty("user.name");
                String hostname = host.getText();
                    
                List<String> commandsList = Arrays.asList( new String[] {"ssh",username+"@"+hostname,"cat",tf.getText()} );
                ProcessBuilder pb = new ProcessBuilder( commandsList );
                Process p = pb.start();
                    
                for( Object commands : commandsList ) {
                    if( commands instanceof List ) {
                        for( Object cmd : (List)commands ) {
                            ta.append(cmd+" ");
                        }
                        ta.append("\n");
                    } else {
                        ta.append(commands+" ");
                    }
                }
                ta.append("\n");
                    
                fis = p.getInputStream();
                }*/

                final JProgressBar pbar = new JProgressBar();
                final Thread t = new Thread() {
                    public void run() {
                        try {
                            URL url = new URL(tf.getText());
                            InputStream fis = url.openStream();
                            InputStream is = new GZIPInputStream(fis);
                            if (geneset.unimap != null)
                                geneset.unimap.clear();
                            geneset.unimap = geneset.idMapping(new InputStreamReader(is), bw, 2, 0, geneset.refmap,
                                    geneset.genmap, geneset.gimap);
                            is.close();
                            fis.close();
                            bw.close();

                            try {
                                geneset.zipfilesystem.close();
                            } catch (Exception ep) {
                                ep.printStackTrace();
                            }
                            ;

                            pbar.setIndeterminate(false);
                            pbar.setEnabled(false);
                        } catch (IOException e) {
                            e.printStackTrace();
                        }
                    }
                };

                ta.setEditable(false);
                final JScrollPane sp = new JScrollPane(ta);

                dialog.add(comp2);
                comp2.add(pbar, BorderLayout.NORTH);
                comp2.add(sp, BorderLayout.CENTER);
                pbar.setIndeterminate(true);

                t.start();

                /*System.err.println( "about to run" );
                for( Object commands : commandsList ) {
                    if( commands instanceof List ) {
                        for( Object c : (List)commands ) {
                            System.err.print( c+" " );
                        }
                        System.err.println();
                    } else {
                        System.err.print( commands+" " );
                    }
                }
                System.err.println();*/

                /*okokdialog.addWindowListener( new WindowListener() {
                    
                @Override
                public void windowOpened(WindowEvent e) {}
                    
                @Override
                public void windowIconified(WindowEvent e) {}
                    
                @Override
                public void windowDeiconified(WindowEvent e) {}
                    
                @Override
                public void windowDeactivated(WindowEvent e) {}
                    
                @Override
                public void windowClosing(WindowEvent e) {}
                    
                @Override
                public void windowClosed(WindowEvent e) {
                    if( pbar.isEnabled() ) {
                        /*String result = ta.getText().trim();
                        if( run != null ) {
                            cont[0] = null;
                            cont[1] = result;
                            cont[2] = new Date( System.currentTimeMillis() ).toString();
                            run.run();
                        }*
                    
                        pbar.setIndeterminate( false );
                        pbar.setEnabled( false );
                    }
                }
                    
                @Override
                public void windowActivated(WindowEvent e) {}
                });*/
                dialog.setVisible(true);

                /*NativeRun nrun = new NativeRun();
                nrun.runProcessBuilder("Idmapping", Arrays.asList( tf.getText().split(" ") ), run, cont, false);
                ProcessBuilder pb = new ProcessBuilder( tf.getText().split(" ") );
                Process p = pb.start();
                fis = p.getInputStream();
                }*/

                //long bl = Files.copy( new ByteArrayInputStream( baos.toByteArray() ), nf, StandardCopyOption.REPLACE_EXISTING );
            } catch (IOException e1) {
                e1.printStackTrace();
                try {
                    geneset.zipfilesystem.close();
                } catch (Exception e2) {
                    e2.printStackTrace();
                }
                ;
            }
            //   }
            //};
            //t.start();
            //}
        }));
        MenuItem cogblastaction = new MenuItem("Cog blast");
        cogblastaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            Set<String> species = getSelspec(null, geneset.getSpecies(), null);

            if (species != null && species.size() > 0)
                Platform.runLater(() -> cogBlastDlg(species));
        }));
        MenuItem unresolvedblastaction = new MenuItem("Unresolved blast");
        unresolvedblastaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            try {
                Set<String> species = getSelspec(null, geneset.getSpecies(), null);

                StringWriter sb = new StringWriter();
                Path dbPath = Paths.get("/data/nr");
                ObservableList<Gene> genes = gtable.getSelectionModel().getSelectedItems();
                if (genes.size() > 0) {
                    if (isGeneview()) {
                        for (Gene g : gtable.getSelectionModel().getSelectedItems()) {
                            //int i = table.convertRowIndexToModel(r);
                            //Gene g = geneset.genelist.get(i);
                            Sequence gs = g.tegeval.getProteinSequence();
                            gs.setName(g.id);
                            gs.writeSequence(sb);
                        }
                    } else {
                        for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                            //int i = table.convertRowIndexToModel(r);
                            //GeneGroup gg = geneset.allgenegroups.get(i);
                            Gene g = null;
                            for (Gene gene : gg.genes) {
                                g = gene;
                                break;
                            }
                            Sequence gs = g.tegeval.getProteinSequence();
                            gs.setName(g.id);
                            gs.writeSequence(sb);
                        }
                    }
                } else {
                    for (Gene g : geneset.genelist) {
                        if (g.getTag() == null || g.getTag().equalsIgnoreCase("gene")) {
                            if (species.contains(g.getSpecies())) {
                                Sequence gs = g.tegeval.getProteinSequence();
                                gs.setName(g.id);
                                gs.writeSequence(sb);

                                /*sb.append(">" + g.id + "\n");
                                for (int i = 0; i < gs.length(); i += 70) {
                                sb.append( gs.substring(i, Math.min( i + 70, gs.length() )) + "\n");
                                }*/
                            }
                        }
                    }
                }

                Map<String, String> env = new HashMap<>();
                env.put("create", "true");
                String uristr = "jar:" + geneset.zippath.toUri();
                geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );
                geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                Path resPath = geneset.zipfilesystem.getPath("/unresolved.blastout");

                NativeRun nrun = new NativeRun();
                SerifyApplet.blastpRun(nrun, sb.getBuffer(), dbPath, resPath, "-evalue 0.00001", null, true,
                        geneset.zipfilesystem, geneset.user, primaryStage);
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        }));

        MenuItem importbiosystemsaction = new MenuItem("Import biosystems");
        importbiosystemsaction.setOnAction(actionEvent -> {
            Dialog<Map<String, Set<String>>> dialog = new Dialog();

            TextField gene = new TextField();
            TextField biosys = new TextField();

            gene.setText("ftp://ftp.ncbi.nlm.nih.gov/pub/biosystems/biosystems.20160519/biosystems_gene_all.gz");
            biosys.setText("ftp://ftp.ncbi.nlm.nih.gov/pub/biosystems/biosystems.20160519/bsid2info.gz");

            VBox duo = new VBox();
            duo.getChildren().add(gene);
            duo.getChildren().add(biosys);

            dialog.getDialogPane().setContent(duo);
            dialog.getDialogPane().getButtonTypes().add(ButtonType.OK);
            dialog.getDialogPane().getButtonTypes().add(ButtonType.CANCEL);
            dialog.setResultConverter(param -> {
                if (!param.getButtonData().isCancelButton()) {
                    Map<String, Set<String>> result = null;
                    Set<String> geneidset = geneset.genelist.stream().map(g -> g.genid).collect(Collectors.toSet());
                    try {
                        InputStream p = new URI(gene.getText()).toURL().openStream();
                        InputStream b = new URI(biosys.getText()).toURL().openStream();

                        if (gene.getText().endsWith(".gz"))
                            p = new GZIPInputStream(p);
                        if (biosys.getText().endsWith(".gz"))
                            b = new GZIPInputStream(b);

                        Map<String, List<String[]>> group = new BufferedReader(new InputStreamReader(p)).lines()
                                .map(l -> l.split("\t")).filter(s -> geneidset.contains(s[1]))
                                .collect(Collectors.groupingBy(s -> s[1]));
                        Set<String> bsids = group.entrySet().stream().flatMap(e -> e.getValue().stream())
                                .map(s -> s[0]).collect(Collectors.toSet());
                        Map<String, String> bsid2name = new BufferedReader(new InputStreamReader(b)).lines()
                                .map(s -> s.split("\t")).filter(s -> bsids.contains(s[0]))
                                .collect(Collectors.toMap(s -> s[0], s -> s[2] + ":" + s[3]));
                        result = group.entrySet().stream()
                                .collect(Collectors.toMap(s -> s.getKey(), s -> s.getValue().stream()
                                        .map(sub -> bsid2name.get(sub[0])).collect(Collectors.toSet())));
                    } catch (IOException e) {
                        e.printStackTrace();
                    } catch (URISyntaxException e) {
                        e.printStackTrace();
                    }
                    //Path p = Paths.get(gene.getText());
                    //Path b = Paths.get(biosys.getText());
                    return result;
                }
                return null;
            });
            Optional<Map<String, Set<String>>> od = dialog.showAndWait();

            if (od.isPresent()) {
                geneset.biosystemsmap = od.get();
                Map<String, String> env = new HashMap<>();
                env.put("create", "true");
                String uristr = "jar:" + geneset.zippath.toUri();
                geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );
                try {
                    geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                    Path resPath = geneset.zipfilesystem.getPath("/biosystems.txt");
                    BufferedWriter bw = Files.newBufferedWriter(resPath, StandardOpenOption.TRUNCATE_EXISTING);
                    geneset.biosystemsmap.entrySet().stream().forEach(e -> {
                        try {
                            bw.write(e.getKey() + "\t" + e.getValue().stream().collect(Collectors.joining(";"))
                                    + "\n");
                        } catch (IOException e1) {
                            e1.printStackTrace();
                        }
                    });
                    bw.close();
                } catch (Exception e) {
                    e.printStackTrace();
                } finally {
                    try {
                        geneset.zipfilesystem.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
        });

        MenuItem importkeggpathwayaction = new MenuItem("Import kegg pathways");
        importkeggpathwayaction.setOnAction(actionEvent -> {
            Set<String> keggids = new HashSet<>();
            for (Gene g : geneset.genelist) {
                if (g.keggid != null) {
                    int i = g.keggid.indexOf(':');
                    if (i > 0) {
                        keggids.add(g.keggid.substring(0, i));
                    }
                }
            }
            System.err.println(keggids);

            JTextField tf = new JTextField("http://130.208.252.239/organisms/");
            JOptionPane.showMessageDialog(null, tf);

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

            Path rootp = null;
            try {
                geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
            } catch (Exception ee) {
                ee.printStackTrace();
            }

            for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                rootp = root;
                break;
            }

            for (String kegg : keggids) {
                try {
                    URL url = new URL(tf.getText() + kegg + ".tar.gz");
                    InputStream is = url.openStream();
                    GZIPInputStream gz = new GZIPInputStream(is);

                    TarArchiveInputStream tar = new TarArchiveInputStream(gz);
                    TarArchiveEntry tae = (TarArchiveEntry) tar.getNextEntry();
                    while (tae != null) {
                        geneset.traverseTar(tar, tae, rootp);

                        tae = (TarArchiveEntry) tar.getNextEntry();
                    }

                    is.close();
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            }

            try {
                geneset.zipfilesystem.close();
            } catch (Exception ee) {
                ee.printStackTrace();
            }
            ;
        });

        edit.getItems().add(clustergenes);
        edit.getItems().add(alignclusters);
        edit.getItems().add(new SeparatorMenuItem());
        edit.getItems().add(sharenumaction);
        edit.getItems().add(importgeneclusteringaction);
        edit.getItems().add(importgenesymbolaction);
        edit.getItems().add(importcazyaction);
        edit.getItems().add(functionmappingaction);
        edit.getItems().add(importidmappingaction);
        edit.getItems().add(gene2refseqaction);
        edit.getItems().add(importbiosystemsaction);
        edit.getItems().add(importkeggpathwayaction);
        edit.getItems().add(new SeparatorMenuItem());
        edit.getItems().add(cogblastaction);
        edit.getItems().add(unresolvedblastaction);

        Menu view = new Menu("View");
        gb = new RadioMenuItem("Genes");
        gb.setOnAction(actionEvent -> {
            splitpane.getItems().remove(table);
            splitpane.getItems().add(0, gtable);
            //table.setModel( defaultModel );
        });
        view.getItems().add(gb);
        ggb = new RadioMenuItem("Gene groups");
        ggb.setOnAction(actionEvent -> {
            splitpane.getItems().remove(gtable);
            splitpane.getItems().add(0, table);
            //table.setModel( groupModel );
        });

        ToggleGroup bg = new ToggleGroup();
        gb.setToggleGroup(bg);
        ggb.setToggleGroup(bg);
        //ButtonGroup   bg = new ButtonGroup();
        //bg.add( gb );
        //bg.add( ggb );

        ggb.setSelected(true);
        view.getItems().add(ggb);
        ActionCollection.addAll(view, geneset.clusterMap, GeneSetHead.this, geneset.speccontigMap, table, comp,
                geneset.cs);

        Menu help = new Menu("Help");
        MenuItem about = new MenuItem("About");
        about.setOnAction(actionEvent -> SwingUtilities
                .invokeLater(() -> JOptionPane.showMessageDialog(comp, "CompGen 1.0")));
        help.getItems().add(about);

        MenuItem test = new MenuItem("Test");
        test.setOnAction(actionEvent -> {
            /*for( Gene g : geneset.genelist ) {
               Sequence seq = g.tegeval.getContig();
               if( seq == null ) {
              System.err.println();
               }
            }*/

            for (String spec : geneset.speccontigMap.keySet()) {
                if (spec.contains("RAST")) {
                    List<Sequence> lseq = geneset.speccontigMap.get(spec);
                    for (Sequence seq : lseq) {
                        for (Annotation a : seq.getAnnotations()) {
                            System.err.println(a.getGene().getGeneGroup().species);
                            /*Sequence tseq = a.getContig();
                            if( tseq == null ) {
                               System.err.println();
                            }*/
                        }
                    }
                }
            }

            /*for( GeneGroup gg : allgenegroups ) {
               if( gg.species.size() > 1 ) {
              System.err.println( gg.species );
               }
            }*/
        });
        help.getItems().add(test);
        help.getItems().add(new SeparatorMenuItem());
        MenuItem runserver = new MenuItem("Run server");
        runserver.setOnAction(actionEvent -> {
            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    JSpinner spin = new JSpinner();
                    JOptionPane.showMessageDialog(GeneSetHead.this, spin, "Port", JOptionPane.QUESTION_MESSAGE);
                    try {
                        geneset.cs = WSServer.startServer(GeneSetHead.this, (Integer) spin.getValue());
                    } catch (UnknownHostException e1) {
                        e1.printStackTrace();
                    }
                }

            });
        });
        help.getItems().add(runserver);
        help.getItems().add(new SeparatorMenuItem());

        CheckMenuItem cbmi = new CheckMenuItem("Use geneset user");
        help.getItems().add(cbmi);

        cbmi.setOnAction(actionEvent -> {
            if (cbmi.isSelected()) {
                geneset.user = "geneset";
            } else
                geneset.user = System.getProperty("user.name");

            JavaFasta.user = geneset.user;
            if (geneset.currentSerify != null)
                geneset.currentSerify.user = geneset.user;
        });

        help.getItems().add(new SeparatorMenuItem());
        MenuItem helptut = new MenuItem("Help & Tutorial");
        helptut.setOnAction(actionEvent -> {
            try {
                Desktop.getDesktop().browse(new URI("http://thermusgenes.appspot.com/pancore.html"));
            } catch (IOException | URISyntaxException e1) {
                e1.printStackTrace();
            }
        });
        help.getItems().add(helptut);

        Menu sequencemenu = new Menu("Sequence");
        MenuItem showgroupseq = new MenuItem("Show group sequences");
        showgroupseq.setOnAction(actionEvent -> {
            //JTextArea textarea = new JTextArea();
            //JScrollPane scrollpane = new JScrollPane(textarea);

            /*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);*/

            JFrame frame = null;
            if (geneset.currentSerify == null) {
                frame = new JFrame();
                frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
                frame.setSize(400, 300);

                Map<String, String> env = new HashMap<String, String>();
                //Path path = zipfile.toPath();
                String uristr = "jar:" + geneset.zippath.toUri();
                geneset.zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );
                try {
                    geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                } catch (IOException e1) {
                    e1.printStackTrace();
                }

                SerifyApplet sa = new SerifyApplet(geneset.zipfilesystem);
                sa.init(frame, null, geneset.user);
                //frame.add( )
                geneset.currentSerify = sa;
            } /* else frame = (JFrame)currentSerify.cnt;*/

            String[] farr = new String[] { "o.profundus", "mt.silvanus", "mt.ruber", "m.hydrothermalis",
                    "t.thermophilus_SG0_5JP17_16", "t.thermophilusJL18", "t.thermophilusHB8", "t.thermophilusHB27",
                    "t.scotoductusSA01", "t.scotoductus4063", "t.scotoductus1572", "t.scotoductus2101",
                    "t.scotoductus2127", "t.scotoductus346", "t.scotoductus252", "t.antranikiani", "t.kawarayensis",
                    "t.brockianus", "t.igniterrae", "t.eggertsoni", "t.RLM", "t.oshimai_JL2", "t.oshimai",
                    "t.filiformis", "t.arciformis", "t.islandicus", "t.aquaticus", "t.spCCB" };

            Map<Integer, String> ups = new HashMap<Integer, String>();
            Set<Integer> stuck = new HashSet<Integer>();
            Map<Integer, List<Tegeval>> ups2 = new HashMap<Integer, List<Tegeval>>();
            //int[] rr = table.getSelectedRows();
            for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                //int cr = table.convertRowIndexToModel(r);
                //Gene gg = geneset.genelist.get(cr);
                if (gg.getSpecies() != null) {
                    if (gg.genid != null && gg.genid.length() > 0) {
                        ups.put(gg.getGroupIndex(), gg.name);
                        stuck.add(gg.getGroupIndex());
                    }
                    if (!stuck.contains(gg.getGroupIndex())) {
                        if (!ups.containsKey(gg.getGroupIndex())
                                || !(gg.name.contains("unnamed") || gg.name.contains("hypot")))
                            ups.put(gg.getGroupIndex(), gg.name);
                    }

                    List<Tegeval> tlist;
                    if (ups2.containsKey(gg.getGroupIndex()))
                        tlist = ups2.get(gg.getGroupIndex());
                    else {
                        tlist = new ArrayList<Tegeval>();
                        ups2.put(gg.getGroupIndex(), tlist);
                    }

                    //Set<String>    specs = new HashSet<String>();
                    //textarea.append(gg.name + ":\n");
                    //for (String sp : gg.species.keySet()) {
                    int count = 0;
                    for (String sp : farr) {
                        //Teginfo stv = gg.species.equals(sp) ? gg.teginfo : null;

                        if (gg.getSpecies().equals(sp))
                            tlist.add(gg.tegeval);
                        /*for( String key : gg.species.keySet() ) {
                           if( key.contains("JL2") ) {
                              System.err.println( " erm " + key );
                           }
                        }*/
                        /*if( stv == null && gg.species.size() == 28 ) {
                           System.err.println( gg.species );
                           System.err.println( sp );
                        }*/
                        //System.err.println( gg.species.keySet() );
                        /*if( stv == null ) {
                           //System.err.println( sp );
                        } else {
                           count++;
                           //specs.add( sp );
                           for (Tegeval tv : stv.tset) {
                              tlist.add( tv );
                              /*textarea.append(">" + tv.cont + " " + tv.teg + " " + tv.eval + "\n");
                              if (tv.dna != null) {
                          for (int i = 0; i < tv.dna.length(); i += 70) {
                             textarea.append(tv.dna.gg.speciessubstring(i, Math.min(i + 70, tv.dna.length())) + "\n");
                          }
                              }*
                           }
                        }*/
                    }
                    //if( count < gg.species.size() ) {
                    //   System.err.println( gg.species );
                    //   System.err.println();
                    //}
                    //if( specs.size() < 28 ) System.err.println("mu " + specs);
                }
            }

            try {
                StringWriter sb = new StringWriter();
                for (int gi : ups.keySet()) {
                    String name = ups.get(gi);
                    List<Tegeval> tlist = ups2.get(gi);

                    sb.append(name.replace('/', '-') + ":\n");
                    if (tlist.size() < 28) {
                        for (Tegeval tv : tlist) {
                            System.err.println(tv.name);
                        }
                        System.err.println();
                    }
                    for (Tegeval tv : tlist) {
                        Sequence ps = tv.getProteinSequence();
                        ps.setName(tv.name.substring(0, tv.name.indexOf('_')));
                        ps.writeSequence(sb);
                        /*sb.append(">" + tv.name.substring(0, tv.name.indexOf('_')) + "\n");
                        for (int i = 0; i < ps.length(); i += 70) {
                           sb.append( ps.substring(i, Math.min(i + 70, tv.getProteinLength() )) + "\n");
                        }*/
                    }
                }

                geneset.currentSerify.addSequences("uh", new StringReader(sb.toString()), Paths.get("/"), null);
            } catch (URISyntaxException | IOException e1) {
                e1.printStackTrace();
            }
            frame.setVisible(true);
        });
        sequencemenu.getItems().add(showgroupseq);

        MenuItem showgroupdnaseq = new MenuItem("Show group DNA sequences");
        showgroupdnaseq.setOnAction(actionEvent -> {
            final JTextArea textarea = new JTextArea();
            JScrollPane scrollpane = new JScrollPane(textarea);

            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);

            try {
                final DataFlavor df = new DataFlavor("text/plain;charset=utf-8");
                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 false;
                    }

                    protected Transferable createTransferable(JComponent c) {
                        return new Transferable() {
                            @Override
                            public Object getTransferData(DataFlavor arg0)
                                    throws UnsupportedFlavorException, IOException {
                                if (arg0.equals(df)) {
                                    return new ByteArrayInputStream(textarea.getText().getBytes());
                                } else {
                                    return textarea.getText();
                                }
                            }

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

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

                    public boolean importData(TransferHandler.TransferSupport support) {
                        return false;
                    }
                };
                textarea.setTransferHandler(th);
            } catch (ClassNotFoundException e1) {
                e1.printStackTrace();
            }

            Map<Integer, String> ups = new HashMap<Integer, String>();
            Set<Integer> stuck = new HashSet<Integer>();
            Map<Integer, List<Tegeval>> ups2 = new HashMap<Integer, List<Tegeval>>();
            //int[] rr = table.getSelectedRows();
            for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                //int cr = table.convertRowIndexToModel(r);
                //Gene gg = geneset.genelist.get(cr);
                if (gg.getSpecies() != null) {
                    if (gg.genid != null && gg.genid.length() > 0) {
                        ups.put(gg.getGroupIndex(), gg.name);
                        stuck.add(gg.getGroupIndex());
                    }
                    if (!stuck.contains(gg.getGroupIndex())) {
                        if (!ups.containsKey(gg.getGroupIndex())
                                || !(gg.name.contains("unnamed") || gg.name.contains("hypot")))
                            ups.put(gg.getGroupIndex(), gg.name);
                    }

                    List<Tegeval> tlist;
                    if (ups2.containsKey(gg.getGroupIndex()))
                        tlist = ups2.get(gg.getGroupIndex());
                    else {
                        tlist = new ArrayList<Tegeval>();
                        ups2.put(gg.getGroupIndex(), tlist);
                    }

                    //textarea.append(gg.name + ":\n");
                    tlist.add(gg.tegeval);
                    /*textarea.append(">" + tv.cont + " " + tv.teg + " " + tv.eval + "\n");
                    if (tv.dna != null) {
                       for (int i = 0; i < tv.dna.length(); i += 70) {
                          textarea.append(tv.dna.substring(i, Math.min(i + 70, tv.dna.length())) + "\n");
                       }
                    }*/
                }
            }

            for (int gi : ups.keySet()) {
                String name = ups.get(gi);
                List<Tegeval> tlist = ups2.get(gi);

                textarea.append(name.replace('/', '-') + ":\n");
                for (Tegeval tv : tlist) {
                    textarea.append(">" + tv.name.substring(0, tv.name.indexOf('_')) + "\n");
                    for (int i = 0; i < tv.getLength(); i += 70) {
                        textarea.append(tv.getSubstring(i, Math.min(i + 70, tv.getLength())) + "\n");
                    }
                }
            }

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

        MenuItem showallseq = new MenuItem("Show all sequences");
        showallseq.setOnAction(actionEvent -> {
            JFrame frame = new JFrame();
            frame.setSize(800, 600);
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            Serifier serifier = new Serifier();
            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame);

            Map<String, Sequence> contset = new HashMap<String, Sequence>();
            //int[] rr = table.getSelectedRows();
            for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                //int cr = table.convertRowIndexToModel(r);
                //Gene gg = geneset.genelist.get(cr);
                Tegeval tv = gg.tegeval;
                String contig = tv.getContshort().getName();
                Sequence seq = tv.getProteinSequence();
                seq.setName(contig);
                serifier.mseq.put(seq.getName(), seq);
                //Sequence seq = new Sequence( contig, aa, serifier.mseq );
                serifier.addSequence(seq);
            }
            jf.updateView();

            frame.setVisible(true);
        });
        sequencemenu.getItems().add(showallseq);

        MenuItem showseq = new MenuItem("Show sequences");
        showseq.setOnAction(actionEvent -> {
            Set<GeneGroup> genegroups = new HashSet<GeneGroup>();
            //int[] rr = table.getSelectedRows();
            if (!isGeneview()) {
                for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                    //int cr = table.convertRowIndexToModel(r);
                    //GeneGroup gg = geneset.allgenegroups.get(cr);
                    genegroups.add(gg);
                }
            } else {
                for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                    //int cr = table.convertRowIndexToModel(r);
                    //Gene gg = geneset.genelist.get(cr);
                    genegroups.add(gg.getGeneGroup());
                }
            }
            Platform.runLater(() -> {
                Set<String> specs = null;
                if (table.getItems().size() > 1)
                    specs = getSelspec(comp, geneset.specList, null);
                showSequences(comp, genegroups, false, specs);
            });
        });
        sequencemenu.getItems().add(showseq);

        MenuItem showseqwgenenames = new MenuItem("Show sequences w/genenames");
        showseqwgenenames.setOnAction(actionEvent -> {
            Set<GeneGroup> genegroups = new HashSet<GeneGroup>();
            //int[] rr = table.getSelectedRows();
            if (!isGeneview()) {
                for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                    //int cr = table.convertRowIndexToModel(r);
                    //GeneGroup gg = geneset.allgenegroups.get(cr);
                    genegroups.add(gg);
                }
            } else {
                for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                    //int cr = table.convertRowIndexToModel(r);
                    //Gene gg = geneset.genelist.get(cr);
                    genegroups.add(gg.getGeneGroup());
                }
            }
            //Set<String>   specs = null;
            //if( rr.length > 1 ) specs = getSelspec(comp, specList, null);
            showSequences(comp, genegroups, false, null, true);
        });
        sequencemenu.getItems().add(showseqwgenenames);

        MenuItem showalignseq = new MenuItem("Show aligned sequences");
        showalignseq.setOnAction(actionEvent -> {
            Set<GeneGroup> genegroups = new HashSet<GeneGroup>();
            //int[] rr = table.getSelectedRows();
            if (!isGeneview()) {
                for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                    genegroups.add(gg);
                }
            } else {
                for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                    genegroups.add(gg.getGeneGroup());
                }
            }

            Serifier serifier = new Serifier();
            for (GeneGroup ggroup : genegroups) {
                for (Tegeval tv : ggroup.getTegevals()) {
                    String selspec = tv.getContshort().getSpec();//tv.getContig();
                    String spec = geneset.nameFix(selspec);
                    /*if( selspec.contains("hermus") ) spec = selspec;
                    else {
                       Matcher m = Pattern.compile("\\d").matcher(selspec); 
                       int firstDigitLocation = m.find() ? m.start() : 0;
                       if( firstDigitLocation == 0 ) spec = "Thermus_" + selspec;
                       else spec = "Thermus_" + selspec.substring(0,firstDigitLocation) + "_" + selspec.substring(firstDigitLocation);
                    }*/

                    Sequence seq = tv.getAlignedSequence();
                    //System.err.println( "seqlen " + seq.length() );
                    if (seq != null) {
                        seq.setName(spec);
                        //Sequence seq = new Sequence( contig, seqstr, null );
                        serifier.addSequence(seq);
                    } else {
                        Sequence sb = tv.getProteinSequence();
                        sb.setName(spec);
                        //Sequence sseq = new Sequence( spec, sb, serifier.mseq );
                        serifier.addSequence(sb);
                    }
                }
            }
            showAlignedSequences(comp, serifier);
        });
        sequencemenu.getItems().add(showalignseq);

        MenuItem splitseq = new MenuItem("Split/Show sequences");
        splitseq.setOnAction(actionEvent -> {
            try {
                StringBuffer sb = getSelectedASeqs(table, geneset.genelist, GeneSetHead.this, geneset.specList);
                if (geneset.currentSerify == null) {
                    JFrame frame = new JFrame();
                    frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
                    frame.setSize(800, 600);

                    SerifyApplet sa = new SerifyApplet(geneset.zipfilesystem);
                    sa.init(frame, null, geneset.user);
                    geneset.currentSerify = sa;

                    frame.setVisible(true);
                }
                geneset.currentSerify.addSequences("uh", new StringReader(sb.toString()), Paths.get("/"), null);
            } catch (URISyntaxException | IOException e1) {
                e1.printStackTrace();
            }

            //JTextArea textarea = new JTextArea();
            //textarea.append( sb.toString() );

            /*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'.");
            }
                
            *
             * final DataFlavor df =
             * DataFlavor.getTextPlainUnicodeFlavor();//new
             * DataFlavor("text/plain;charset=utf-8"); final String charset
             * = df.getParameter("charset"); final Transferable transferable
             * = new Transferable() {
             * 
             * @Override public Object getTransferData(DataFlavor arg0)
             * throws UnsupportedFlavorException, IOException { String ret =
             * makeCopyString( detailTable ); return new
             * ByteArrayInputStream( ret.getBytes( charset ) ); }
             * 
             * @Override public DataFlavor[] getTransferDataFlavors() {
             * return new DataFlavor[] { df }; }
             * 
             * @Override public boolean isDataFlavorSupported(DataFlavor
             * arg0) { if( arg0.equals(df) ) { return true; } return false;
             * } };
             * 
             * 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 false; }
             * 
             * protected Transferable createTransferable(JComponent c) {
             * return transferable; }
             * 
             * public boolean importData(TransferHandler.TransferSupport
             * support) { /*try { Object obj =
             * support.getTransferable().getTransferData( df ); InputStream
             * is = (InputStream)obj;
             * 
             * byte[] bb = new byte[2048]; int r = is.read(bb);
             * 
             * //importFromText( new String(bb,0,r) ); } catch
             * (UnsupportedFlavorException e) { e.printStackTrace(); } catch
             * (IOException e) { e.printStackTrace(); }* return false; } };
             * textarea.setTransferHandler( th );
             *
            textarea.setDragEnabled(true);
                
            JScrollPane scrollpane = new JScrollPane(textarea);
                
            JFrame frame = new JFrame();
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
            frame.add(scrollpane);
            frame.setSize(400, 300);
            frame.setVisible(true);*/
        });
        sequencemenu.getItems().add(splitseq);

        MenuItem showdnaseq = new MenuItem("Show DNA sequences");
        showdnaseq.setOnAction(actionEvent -> {
            Set<GeneGroup> genegroups = new HashSet<GeneGroup>();
            int rr = 0;
            if (!isGeneview()) {
                ObservableList<GeneGroup> lgg = table.getSelectionModel().getSelectedItems();
                genegroups.addAll(lgg);
                rr = lgg.size();
            } else {
                for (Gene gg : gtable.getSelectionModel().getSelectedItems()) {
                    genegroups.add(gg.getGeneGroup());
                    rr++;
                }
            }
            Set<String> specs = null;
            if (rr > 1)
                specs = getSelspec(comp, geneset.specList, null);
            showSequences(comp, genegroups, true, specs);

            /*StringBuilder sb = getSelectedSeqs( table, genelist );
                
            if( currentSerify == null ) {
               JFrame frame = new JFrame();
               frame.setDefaultCloseOperation( JFrame.DO_NOTHING_ON_CLOSE );
               frame.setSize(800, 600);
                   
               SerifyApplet sa = new SerifyApplet();
               sa.init( frame );
                   
               try {
              sa.addSequences("uh", new StringReader( sb.toString() ), "/");
               } catch (URISyntaxException | IOException e1) {
              e1.printStackTrace();
               }
                   
               frame.setVisible( true );
            }
                
            JTextArea textarea = new JTextArea();
            JScrollPane scrollpane = new JScrollPane(textarea);
                
            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);
            textarea.append( sb.toString() );
                
            JFrame frame = new JFrame();
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
            frame.add(scrollpane);
            frame.setSize(400, 300);
            frame.setVisible(true);*/
        });
        sequencemenu.getItems().add(showdnaseq);

        MenuItem expalldna = new MenuItem("Export all DNA sequences");
        expalldna.setOnAction(actionEvent -> {
            JFileChooser jfc = new JFileChooser();
            jfc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);

            try {
                Map<Integer, FileWriter> lfw = new HashMap<Integer, FileWriter>();
                if (jfc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) {
                    File f = jfc.getSelectedFile();
                    for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) {
                        FileWriter fw = null;
                        if (lfw.containsKey(gg.getGroupIndex())) {
                            fw = lfw.get(gg.getGroupIndex());
                        } else {
                            fw = new FileWriter(new File(f, "group_" + gg.getGroupIndex() + ".fasta"));
                            lfw.put(gg.getGroupIndex(), fw);
                        }

                        Tegeval tv = gg.tegeval;
                        fw.append(">" + tv.name + " " + tv.teg + " " + tv.eval + "\n");
                        for (int i = 0; i < tv.getLength(); i += 70) {
                            fw.append(tv.getSubstring(i, Math.min(i + 70, tv.getLength())) + "\n");
                        }
                    }
                }
                for (int gi : lfw.keySet()) {
                    lfw.get(gi).close();
                }
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        });
        sequencemenu.getItems().add(expalldna);

        MenuItem exprelcont = new MenuItem("Export relevant contigs");
        exprelcont.setOnAction(actionEvent -> {
            JFileChooser jfc = new JFileChooser();

            try {
                Map<Integer, FileWriter> lfw = new HashMap<Integer, FileWriter>();
                if (jfc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) {
                    File f = jfc.getSelectedFile();

                    Set<Sequence> contset = new HashSet<Sequence>();
                    for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) {
                        Tegeval tv = gg.tegeval;
                        contset.add(tv.getContshort());
                    }

                    FileWriter fw = new FileWriter(f);
                    for (Sequence contig : contset) {
                        fw.append(">" + contig + "\n");
                        if (geneset.contigmap.containsKey(contig)) {
                            StringBuilder dna = geneset.contigmap.get(contig).getStringBuilder();
                            for (int i = 0; i < dna.length(); i += 70) {
                                fw.append(dna.substring(i, Math.min(i + 70, dna.length())) + "\n");
                            }
                        }
                    }
                    fw.close();
                }
                for (int gi : lfw.keySet()) {
                    lfw.get(gi).close();
                }
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        });
        sequencemenu.getItems().add(exprelcont);
        sequencemenu.getItems().add(new SeparatorMenuItem());

        MenuItem viewselrange = new MenuItem("View selected range");
        viewselrange.setOnAction(actionEvent -> {
            JFrame frame = new JFrame();
            frame.setSize(800, 600);
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            Serifier serifier = new Serifier();
            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame);

            Set<Sequence> contset = new HashSet<Sequence>();
            Set<Tegeval> tvset = new HashSet<>();
            if (isGeneview()) {
                for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) {
                    Tegeval tv = gg.tegeval;
                    tvset.add(tv);
                    //serifier.addAnnotation( tv );
                    contset.add(tv.getContshort());
                }
            } else {
                for (GeneGroup gg : getGeneGroupTable().getSelectionModel().getSelectedItems()) {
                    for (Tegeval tv : gg.getTegevals()) {
                        tv.color = Color.red;
                        tvset.add(tv);
                        Sequence contig = tv.getContshort();
                        contset.add(contig);
                        //serifier.addAnnotation( tv );
                    }
                }
            }
            /*Sequence seq;
            Sequence contig = tv.getContshort();
            /*if (contset.containsKey(contig)) {
              seq = contset.get(contig);
            } else {
              if( contigmap.containsKey(contig) ) {
                 StringBuilder dna = contigmap.get(contig).getStringBuilder();
                 seq = new Sequence(contig.getName(), dna, serifier.mseq);
              } else
                 seq = new Sequence(contig.getName(), serifier.mseq);
              contset.put(contig, seq);
            }
                
            Annotation a = new Annotation(contig, contig.getName(), Color.green, serifier.mann);
            a.setStart(tv.start);
            a.setStop(tv.stop);
            a.setOri(tv.ori);
            a.setGroup(gg.name);
            a.setType("gene");*/
            // seq.addAnnotation( new Annotation( seq, ) );

            for (Sequence contig : contset) {
                int start = Integer.MAX_VALUE;
                int stop = Integer.MIN_VALUE;
                for (Tegeval tv : tvset) {
                    if (contig == tv.seq) {
                        start = Math.min(start, tv.start);
                        stop = Math.max(stop, tv.stop);
                    }
                }

                int rstart = 0;
                int rstop = contig.length();
                if (contig.annset != null)
                    for (Annotation tv : contig.annset) {
                        if (contig == tv.seq) {
                            if (tv.stop < start && tv.stop > rstart) {
                                rstart = tv.stop;
                            }
                            if (tv.start > stop && tv.start < rstop) {
                                rstop = tv.start;
                            }
                        }
                    }

                start = rstart;
                stop = rstop;

                Sequence newseq = new Sequence(contig.getName(),
                        new StringBuilder(contig.getSubstring(start, stop, 1)), serifier.mseq);
                /*if( contig.isReverse() ) {
                   newseq.reverse();
                   newseq.complement();
                }*/

                serifier.addSequence(newseq);
                for (Tegeval tv : tvset) {
                    Annotation newann = new Annotation(newseq, tv.start - start, tv.stop - start, tv.ori, tv.name);
                    if (contig == tv.seq) {
                        newseq.addAnnotation(newann);
                    }
                    serifier.addAnnotation(newann);
                }
                /*for( Annotation ann : contig.getAnnotations() ) {
                   serifier.addAnnotation( ann );
                }*/
                /*if (seq.getAnnotations() != null)
                   Collections.sort(seq.getAnnotations());*/
            }
            jf.updateView();

            frame.setVisible(true);
        });
        sequencemenu.getItems().add(viewselrange);

        MenuItem viewwhole = new MenuItem("View whole contigs for selection");
        viewwhole.setOnAction(actionEvent -> {
            JFrame frame = new JFrame();
            frame.setSize(800, 600);
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            Serifier serifier = new Serifier();
            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame);

            //Map<Sequence, Sequence> contset = new HashMap<Sequence, Sequence>();
            /*int[] rr = table.getSelectedRows();
            for (int r : rr) {
               int cr = table.convertRowIndexToModel(r);
               Gene gg = geneset.genelist.get(cr);
               if (gg.species != null) {
              for (String sp : gg.species.keySet()) {
                 Teginfo stv = gg.species.get(sp);
                 for (Tegeval tv : stv.tset) {
                    Sequence seq;
                    Sequence contig = tv.getContshort();
                    if (contset.containsKey(contig)) {
                       seq = contset.get(contig);
                    } else {
                       if( GeneSet.contigmap.containsKey(contig) ) {
                          //StringBuilder dna = GeneSet.contigmap.get(contig).seq;
                          StringBuilder dna = contig.getSequence().getStringBuilder();
                          seq = new Sequence(contig.getName(), dna, serifier.mseq);
                       } else {
                          seq = new Sequence(contig.getName(), serifier.mseq);
                       }
                
                       contset.put(contig, seq);
                    }
                
                    /*
                     * Annotation a = jf.new Annotation( seq,
                     * contig, Color.red ); a.setStart( tv.start );
                     * a.setStop( tv.stop ); a.setOri( tv.ori );
                     * a.setGroup( gg.name ); a.setType( "gene" );
                     * jf.addAnnotation( a );
                     *
                    // seq.addAnnotation( new Annotation( seq, ) );
                 }
              }
               }
            }*/

            Set<Sequence> contigs = new HashSet<Sequence>();
            if (isGeneview()) {
                for (Gene gg : getGeneTable().getSelectionModel().getSelectedItems()) {
                    Tegeval tv = gg.tegeval;
                    tv.color = Color.red;
                    Sequence contig = tv.getContshort();
                    //contig.offset = -tv.start;
                    contigs.add(contig);
                }

                /*Annotation a = new Annotation(contig, contig.getName(), Color.red, serifier.mann);
                a.setStart(tv.start);
                a.setStop(tv.stop);
                a.setOri(tv.ori);
                a.setGroup(g.name);
                a.setType("gene");*/
                //serifier.addAnnotation( tv );
            } else {
                for (GeneGroup gg : getGeneGroupTable().getSelectionModel().getSelectedItems()) {
                    for (Tegeval tv : gg.getTegevals()) {
                        tv.color = Color.red;
                        Sequence contig = tv.getContshort();
                        //contig.offset = -tv.start;
                        contigs.add(contig);

                        /*Annotation a = new Annotation(contig, contig.getName(), Color.red, serifier.mann);
                        a.setStart(tv.start);
                        a.setStop(tv.stop);
                        a.setOri(tv.ori);
                        a.setGroup(gg.getCommonName());
                        a.setType("gene");*/
                        //serifier.addAnnotation( tv );
                    }
                }
            }
            //Gene gg = geneset.genelist.get(cr);
            //for (Gene g : geneset.genelist) {
            //if (g.species != null) {
            //for (String sp : g.species.keySet()) {

            for (Sequence contig : contigs) {
                for (Annotation ann : contig.getAnnotations()) {
                    serifier.addAnnotation(ann);
                }

                serifier.addSequence(contig);
                serifier.mseq.put(contig.getName(), contig);
                //if(contig.getAnnotations() != null)
                //   Collections.sort(contig.getAnnotations());
            }
            jf.updateView();

            frame.setVisible(true);
        });
        sequencemenu.getItems().add(viewwhole);
        sequencemenu.getItems().add(new SeparatorMenuItem());

        MenuItem viewspecseq = new MenuItem("View species sequence");
        viewspecseq.setOnAction(actionEvent -> {
            Set<String> selspec = getSelspec(GeneSetHead.this, geneset.specList);

            JFrame frame = new JFrame();
            frame.setSize(800, 600);
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            Serifier serifier = new Serifier();
            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame);

            for (String spec : selspec) {
                List<Sequence> contigs = geneset.speccontigMap.get(spec);

                for (Sequence contig : contigs) {
                    List<Annotation> lann = contig.getAnnotations();
                    if (lann != null)
                        for (Annotation ann : lann) {
                            serifier.addAnnotation(ann);
                        }

                    serifier.addSequence(contig);
                    serifier.mseq.put(contig.getName(), contig);
                }
            }

            jf.updateView();

            frame.setVisible(true);
        });
        sequencemenu.getItems().add(viewspecseq);

        Menu windowmenu = new Menu("Tools");
        MenuItem seqviewer = new MenuItem("Sequence viewer");
        seqviewer.setOnAction(actionEvent -> {
            JFrame frame = new JFrame();
            frame.setSize(800, 600);
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);

            Serifier serifier = new Serifier();
            JavaFasta jf = new JavaFasta((comp instanceof JApplet) ? (JApplet) comp : null, serifier, geneset.cs);
            jf.initGui(frame);
            jf.updateView();

            frame.setVisible(true);
        });
        windowmenu.getItems().add(seqviewer);
        windowmenu.getItems().add(new SeparatorMenuItem());
        MenuItem genesorter = new MenuItem("Gene sorter");
        genesorter.setOnAction(actionEvent -> {
            try {
                //if( gb.isSelected() ) new GeneSorter().mynd( GeneSetHead.this, genelist, table, null, contigmap );
                //else 
                new GeneSorter().groupMynd(GeneSetHead.this, geneset.allgenegroups, geneset.specList,
                        geneset.genelist, table, geneset.contigmap, geneset.specset);
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        });
        windowmenu.getItems().add(genesorter);
        MenuItem specorderaction = new MenuItem("Order species list");
        specorderaction.setOnAction(actionEvent -> {
            TreeUtil tu = new TreeUtil();
            /*corrInd.clear();
            for( String spec : specList ) {
               corrInd.add( nameFix( spec ) );
            }*/

            Serifier serifier = getConcatenatedSequences(false, false);

            Map<String, Integer> blosumap = JavaFasta.getBlosumMap();
            double[] dmat = new double[serifier.lseq.size() * serifier.lseq.size()];
            Sequence.distanceMatrixNumeric(serifier.lseq, dmat, null, false, false, null, blosumap);

            List<String> ret = new ArrayList<String>();
            for (Sequence seqname : serifier.lseq) {
                ret.add(seqname.getName()); //.replace(' ', '_') );
            }
            //List<String>   corrInd = currentjavafasta.getNames();

            //Sequence.distanceMatrixNumeric(serifier.lseq, dmat, idxs, bootstrap, cantor, ent, blosum);
            Node n = tu.neighborJoin(dmat, ret, null, false, false);

            Comparator<Node> comp2 = (o1, o2) -> {
                int c1 = o1.countLeaves();
                int c2 = o2.countLeaves();

                if (c1 > c2)
                    return 1;
                else if (c1 == c2)
                    return 0;

                return -1;
            };
            tu.arrange(n, comp2);
            //corrInd.clear();
            List<String> ordInd = n.traverse();

            for (String spec : ordInd) {
                System.err.println(spec);
            }

            for (String oldspec : geneset.specList) {
                if (!ordInd.contains(oldspec)) {
                    ordInd.add(oldspec);
                }
            }
            geneset.specList = ordInd;

            //TableModel model = table.getModel();
            //table.setModel( nullmodel );
            //table.setModel( model );

            //table.tableChanged( new TableModelEvent( table.getModel() ) );
            //table.getColumnModel().
            System.err.println(geneset.specList.size());
        });
        MenuItem matrixaction = new MenuItem("Relation matrix");
        matrixaction.setOnAction(actionEvent -> {
            SwingUtilities.invokeLater(() -> {
                JComboBox<String> descombo = new JComboBox<String>(
                        geneset.deset.toArray(new String[geneset.deset.size()]));
                JCheckBox anicheck = new JCheckBox("ANImatrix");
                JCheckBox plasmidcheck = new JCheckBox("Skip plasmids");
                descombo.insertItemAt("", 0);
                descombo.setSelectedIndex(0);
                JOptionPane.showMessageDialog(GeneSetHead.this, new Object[] { descombo, anicheck, plasmidcheck });
                String val = descombo.getSelectedItem().toString();

                Collection<GeneGroup> ss = new HashSet<>();
                /*int[] rr = table.getSelectedRows();
                for( int r : rr ) {
                   ss.add( geneset.allgenegroups.get( table.convertRowIndexToModel(r) ) );
                }*/
                ss.addAll(table.getSelectionModel().getSelectedItems());
                if (ss.isEmpty())
                    ss = geneset.allgenegroups;

                Set<String> species = getSelspec(GeneSetHead.this, geneset.specList);
                bimg = anicheck.isSelected()
                        ? geneset.animatrix(species, geneset.clusterMap, val, ss, plasmidcheck.isSelected())
                        : geneset.bmatrix(species, geneset.clusterMap, val);

                JFrame f = new JFrame("Relation matrix");
                f.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
                f.setSize(500, 500);

                /*
                 * { public void paintComponent( Graphics g ) {
                 * super.paintComponent(g); g.drawImage(bimg, 0, 0, this); } };
                 */

                try {
                    final DataFlavor df = new DataFlavor("text/plain;charset=utf-8");
                    final Transferable transferable = new Transferable() {
                        @Override
                        public Object getTransferData(DataFlavor arg0)
                                throws UnsupportedFlavorException, IOException {
                            StringBuilder ret = new StringBuilder();

                            int i = 0;
                            for (String spc : geneset.specList) {
                                if (++i == geneset.specList.size())
                                    ret.append(spc + "\n");
                                else
                                    ret.append(spc + "\t");
                            }

                            int where = 0;
                            for (String spc1 : geneset.specList) {
                                int wherex = 0;
                                for (String spc2 : geneset.specList) {
                                    int spc1tot = 0;
                                    int spc2tot = 0;
                                    int totot = 0;

                                    int spc1totwocore = 0;
                                    int spc2totwocore = 0;
                                    int tototwocore = 0;
                                    for (Set<String> set : geneset.clusterMap.keySet()) {
                                        Set<Map<String, Set<String>>> erm = geneset.clusterMap.get(set);
                                        if (set.contains(spc1)) {
                                            if (set.size() < geneset.specList.size()) {
                                                spc1totwocore += erm.size();
                                                for (Map<String, Set<String>> sm : erm) {
                                                    Set<String> hset = sm.get(spc1);
                                                    tototwocore += hset.size();
                                                }

                                                if (set.contains(spc2)) {
                                                    spc2totwocore += erm.size();
                                                }

                                                if (spc2totwocore > spc1totwocore)
                                                    System.err.println(
                                                            "okoko " + spc1totwocore + " " + spc2totwocore);
                                            }

                                            spc1tot += erm.size();
                                            for (Map<String, Set<String>> sm : erm) {
                                                Set<String> hset = sm.get(spc1);
                                                totot += hset.size();
                                            }

                                            if (set.contains(spc2)) {
                                                spc2tot += erm.size();
                                            }
                                        }
                                    }

                                    if (where == wherex) {
                                        if (where == geneset.specList.size() - 1)
                                            ret.append(0 + "\n");
                                        else
                                            ret.append(0 + "\t");
                                    } else {
                                        double hlut = (double) spc2totwocore / (double) spc1totwocore;
                                        double sval = hlut; // 1.0/( 1.1-hlut );
                                        double val = Math.pow(50.0, sval - 0.3) - 1.0;
                                        double dval = Math.round(100.0 * (val)) / 100.0;

                                        if (wherex == geneset.specList.size() - 1)
                                            ret.append(dval + "\n");
                                        else
                                            ret.append(dval + "\t");
                                    }
                                    wherex++;
                                }
                                where++;
                            }

                            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;
                        }
                    };
                    final TransferComponent comp2 = new TransferComponent(bimg, transferable);

                    TransferHandler th = new TransferHandler() {
                        private static final long serialVersionUID = 1L;

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

                        public boolean canImport(TransferSupport support) {
                            return false;
                        }

                        protected Transferable createTransferable(JComponent c) {
                            return transferable;
                        }

                        public boolean importData(TransferSupport support) {
                            return true;
                        }
                    };
                    comp2.setTransferHandler(th);

                    comp2.setEnabled(true);
                    JScrollPane fsc = new JScrollPane(comp2);
                    comp2.setPreferredSize(new Dimension(bimg.getWidth(), bimg.getHeight()));

                    JPopupMenu popup = new JPopupMenu();
                    popup.add(new AbstractAction("Save image") {
                        @Override
                        public void actionPerformed(ActionEvent e) {
                            FileSaveService fss = null;
                            FileContents fileContents = null;

                            try {
                                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                                OutputStreamWriter osw = new OutputStreamWriter(baos);
                                ImageIO.write(bimg, "png", baos);
                                baos.close();

                                try {
                                    fss = (FileSaveService) ServiceManager.lookup("javax.jnlp.FileSaveService");
                                } catch (UnavailableServiceException e1) {
                                    fss = null;
                                }

                                if (fss != null) {
                                    ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
                                    fileContents = fss.saveFileDialog(null, null, bais, "export.png");
                                    bais.close();
                                    OutputStream os = fileContents.getOutputStream(true);
                                    os.write(baos.toByteArray());
                                    os.close();
                                } else {
                                    JFileChooser jfc = new JFileChooser();
                                    if (jfc.showSaveDialog(GeneSetHead.this) == JFileChooser.APPROVE_OPTION) {
                                        File f = jfc.getSelectedFile();
                                        FileOutputStream fos = new FileOutputStream(f);
                                        fos.write(baos.toByteArray());
                                        fos.close();

                                        Desktop.getDesktop().browse(f.toURI());
                                    }
                                }
                            } catch (IOException e2) {
                                e2.printStackTrace();
                            }
                        }
                    });
                    comp2.setComponentPopupMenu(popup);

                    f.add(fsc);
                    f.setVisible(true);
                } catch (ClassNotFoundException e1) {
                    e1.printStackTrace();
                }
            });
        });
        MenuItem tniaction = new MenuItem("TNI/ANI");
        tniaction.setOnAction(actionEvent -> {
            SwingUtilities.invokeLater(() -> {
                Set<String> species = getSelspec(GeneSetHead.this, geneset.specList);
                String makeblastdb = "makeblastdb";
                String OS = System.getProperty("os.name").toLowerCase();
                if (OS.indexOf("mac") != -1)
                    makeblastdb = "/usr/local/bin/makeblastdb";
                for (String spec : species) {
                    List<Sequence> lseq = geneset.speccontigMap.get(spec);
                    ProcessBuilder pb = new ProcessBuilder(makeblastdb, "-dbtype", "nucl", "-title", spec, "-out",
                            spec);
                    File dir = new File(System.getProperty("user.home"));

                    /*try {
                        FileWriter w = new FileWriter( new File(dir, spec+".fna") );
                        for( Sequence seq : lseq ) {
                    seq.writeSequence(w);
                        }
                        w.close();
                    } catch (IOException e2) {
                        e2.printStackTrace();
                    }*/

                    pb.directory(dir);
                    try {
                        Process p = pb.start();
                        Writer fw = new OutputStreamWriter(p.getOutputStream());
                        for (Sequence seq : lseq) {
                            seq.writeSequence(fw);
                        }
                        fw.close();
                    } catch (IOException e1) {
                        e1.printStackTrace();
                    }
                }

                int y = 0;
                double[] matrix = new double[species.size() * species.size()];
                for (String dbspec : species) {
                    int x = 0;
                    for (String spec : species) {
                        //if( !spec.equals(dbspec) ) {
                        final List<Sequence> lseq = geneset.speccontigMap.get(spec);
                        String blastn = "blastn";
                        if (OS.indexOf("mac") != -1)
                            blastn = "/usr/local/bin/blastn";
                        ProcessBuilder pb = new ProcessBuilder(blastn, "-db", dbspec, "-num_threads",
                                Integer.toString(Runtime.getRuntime().availableProcessors()), "-num_alignments",
                                "1", "-num_descriptions", "1"); //,"-max_hsps","1");
                        File dir = new File(System.getProperty("user.home"));
                        pb.directory(dir);
                        try {
                            Process p = pb.start();
                            final BufferedWriter fw = new BufferedWriter(
                                    new OutputStreamWriter(p.getOutputStream()));
                            Thread t = new Thread() {
                                public void run() {
                                    try {
                                        for (Sequence seq : lseq) {
                                            seq.writeSplitSequence(fw);
                                            //seq.writeSequence(fw);
                                        }
                                        fw.close();
                                    } catch (IOException e1) {
                                        e1.printStackTrace();
                                    }
                                }
                            };
                            t.start();
                            //Path path = Paths.get("/Users/sigmar/"+spec+"_"+dbspec+".blastout");
                            //Files.copy(p.getInputStream(), path, StandardCopyOption.REPLACE_EXISTING);

                            int tnum = 0;
                            int tdenum = 0;
                            double avg = 0.0;
                            int count = 0;

                            BufferedReader br = new BufferedReader(new InputStreamReader(p.getInputStream()));
                            String line = br.readLine();
                            while (line != null) {
                                if (line.startsWith(" Identities")) {
                                    int i = line.indexOf('(');
                                    String sub = line.substring(14, i - 1);
                                    String[] split = sub.split("/");
                                    int num = Integer.parseInt(split[0]);
                                    int denum = Integer.parseInt(split[1]);

                                    avg += (double) num / (double) denum;

                                    tnum += num;
                                    tdenum += denum;
                                    count++;
                                }
                                line = br.readLine();
                            }
                            br.close();

                            if (count > 0)
                                avg /= count;
                            double val = (double) tnum / (double) tdenum;
                            matrix[y * species.size() + x] = avg;//val;
                            System.err.println(spec + " on " + dbspec + " " + val);
                        } catch (IOException e1) {
                            e1.printStackTrace();
                        }
                        //}
                        x++;
                    }
                    y++;
                }

                geneset.corrInd.clear();
                for (String spec : species) {
                    geneset.corrInd.add(geneset.nameFix(spec));
                }

                final BufferedImage bi = geneset.showRelation(geneset.corrInd, matrix, false);
                JFrame f = new JFrame("TNI matrix");
                f.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
                f.setSize(500, 500);

                JComponent comp2 = new JComponent() {
                    public void paintComponent(Graphics g) {
                        super.paintComponent(g);
                        g.drawImage(bi, 0, 0, bi.getWidth(), bi.getHeight(), 0, 0, bi.getWidth(), bi.getHeight(),
                                this);
                    }
                };
                Dimension dim = new Dimension(bi.getWidth(), bi.getHeight());
                comp2.setPreferredSize(dim);
                comp2.setSize(dim);
                JScrollPane scroll = new JScrollPane(comp2);
                f.add(scroll);

                f.setVisible(true);
            });
        });
        MenuItem anitreeaction = new MenuItem("ANI tree");
        anitreeaction.setOnAction(actionEvent -> {
            Set<String> species = getSelspec(GeneSetHead.this, geneset.specList);
            List<String> speclist = new ArrayList<String>(species);

            Collection<GeneGroup> allgg = new HashSet<GeneGroup>();
            allgg.addAll(table.getSelectionModel().getSelectedItems());
            if (allgg.isEmpty())
                allgg = geneset.allgenegroups;
            Map<String, Integer> blosumap = JavaFasta.getBlosumMap();

            double[] corrarr = new double[speclist.size() * speclist.size()];
            int where = 0;
            for (String spec1 : speclist) {
                int wherex = 0;

                String spc1 = geneset.nameFix(spec1);

                //String spc1 = nameFix( spec1 );
                for (String spec2 : speclist) {
                    if (where != wherex) {
                        int totalscore = 0;
                        int totaltscore = 1;
                        for (GeneGroup gg : allgg) {
                            if ( /*gg.getSpecies().size() > 40 &&*/ gg.getSpecies().contains(spec1)
                                    && gg.getSpecies().contains(spec2)) {
                                Teginfo ti1 = gg.species.get(spec1);
                                Teginfo ti2 = gg.species.get(spec2);
                                //if( ti1.tset.size() == 1 && ti2.tset.size() == 1 ) {
                                //double bval = 0.0;

                                int score = 0;
                                int tscore = 1;
                                for (Tegeval tv1 : ti1.tset) {
                                    for (Tegeval tv2 : ti2.tset) {
                                        Sequence seq1 = tv1.getAlignedSequence();
                                        Sequence seq2 = tv2.getAlignedSequence();
                                        if (seq1 != null && seq2 != null) {
                                            int mest = 0;
                                            int tmest = 0;

                                            int startcheck = 0;
                                            int start = -1;
                                            int stopcheck = 0;
                                            int stop = -1;
                                            for (int i = 0; i < seq1.length(); i++) {
                                                if (seq1.getCharAt(i) != '-') {
                                                    startcheck |= 1;
                                                }
                                                if (seq2.getCharAt(i) != '-') {
                                                    startcheck |= 2;
                                                }

                                                if (start == -1 && startcheck == 3) {
                                                    start = i;
                                                    break;
                                                }
                                            }

                                            for (int i = seq1.length() - 1; i >= 0; i--) {
                                                if (seq1.getCharAt(i) != '-') {
                                                    stopcheck |= 1;
                                                }
                                                if (seq2.getCharAt(i) != '-') {
                                                    stopcheck |= 2;
                                                }

                                                if (stop == -1 && stopcheck == 3) {
                                                    stop = i + 1;
                                                    break;
                                                }
                                            }
                                            //count += stop-start;

                                            for (int i = start; i < stop; i++) {
                                                char lc = seq1.getCharAt(i);
                                                char c = Character.toUpperCase(lc);
                                                //if( )
                                                String comb = c + "" + c;
                                                if (blosumap.containsKey(comb))
                                                    tmest += blosumap.get(comb);
                                            }

                                            for (int i = start; i < stop; i++) {
                                                char lc = seq1.getCharAt(i);
                                                char c = Character.toUpperCase(lc);
                                                char lc2 = seq2.getCharAt(i);
                                                char c2 = Character.toUpperCase(lc2);

                                                String comb = c + "" + c2;
                                                if (blosumap.containsKey(comb))
                                                    mest += blosumap.get(comb);
                                            }

                                            double tani = (double) mest / (double) tmest;
                                            if (tani > (double) score / (double) tscore) {
                                                score = mest;
                                                tscore = tmest;
                                            }
                                            //ret = (double)score/(double)tscore; //int cval = tscore == 0 ? 0 : Math.min( 192, 512-score*512/tscore );
                                            //return ret;
                                        }
                                        //if( where == 0 ) d1.add( gg.getCommonName() );
                                        //else d2.add( gg.getCommonName() );
                                    }
                                }
                                totalscore += score;
                                totaltscore += tscore;

                                /*if( bval > 0 ) {
                                   ani += bval;
                                   count++;
                                }*/
                                //}
                            }
                        }
                        double ani = (double) (totaltscore - totalscore) / (double) totaltscore;
                        corrarr[where * speclist.size() + wherex] = ani;
                    }
                    wherex++;
                }
                where++;
            }
            TreeUtil tu = new TreeUtil();
            geneset.corrInd.clear();
            for (String spec : speclist) {
                geneset.corrInd.add(geneset.nameFix(spec));
            }
            Node n = tu.neighborJoin(corrarr, geneset.corrInd, null, false, false);
            System.err.println(n);
        });
        windowmenu.getItems().add(specorderaction);
        windowmenu.getItems().add(matrixaction);
        windowmenu.getItems().add(tniaction);
        windowmenu.getItems().add(anitreeaction);

        MenuItem neighbourhood = new MenuItem("Neighbourhood");
        neighbourhood.setOnAction(actionEvent -> {
            try {
                Set<GeneGroup> genset = new HashSet<>();
                if (!isGeneview()) {
                    for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                        genset.add(gg);
                    }
                } else {
                    for (Gene gene : gtable.getSelectionModel().getSelectedItems()) {
                        genset.add(gene.getGeneGroup());
                    }
                }
                new Neighbour(genset).neighbourMynd(GeneSetHead.this, comp, geneset.genelist, geneset.contigmap);
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        });
        windowmenu.getItems().add(neighbourhood);

        MenuItem synteny = new MenuItem("Synteny");
        synteny.setOnAction(actionEvent -> {
            SwingUtilities.invokeLater(() -> {
                //Set<String> species = speciesFromCluster( clusterMap );
                new Synteni().syntenyMynd(GeneSetHead.this, comp, geneset.genelist);
            });
        });
        windowmenu.getItems().add(synteny);
        MenuItem compareplotaction = new MenuItem("Gene atlas");
        compareplotaction.setOnAction(actionEvent -> {
            SwingUtilities.invokeLater(() -> {
                try {
                    new GeneCompare().comparePlot(GeneSetHead.this, comp, geneset.genelist, geneset.clusterMap,
                            8192, 8192);
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            });

            /*gatest("MAT4726");
                
            final JFrame frame = new JFrame();
            frame.setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE );
            frame.setSize(800, 600);
                
            final JComponent c = new JComponent() {
               public void paintComponent( Graphics g ) {
              g.drawImage(bimg, 0, 0, frame);
               }
            };
            c.setPreferredSize( new Dimension(bimg.getWidth(), bimg.getHeight()) );
            JScrollPane   scrollpane = new JScrollPane( c );
            frame.add( scrollpane );
            frame.setVisible( true );*/
        });
        windowmenu.getItems().add(compareplotaction);

        MenuItem syntenygradientaction = new MenuItem("Synteny gradient");
        syntenygradientaction.setOnAction(actionEvent -> {
            SwingUtilities.invokeLater(() -> {
                Set<String> presel = new HashSet<>();
                if (isGeneview()) {
                    for (Gene g : gtable.getSelectionModel().getSelectedItems()) {
                        presel.addAll(g.getGeneGroup().getSpecies());
                    }
                } else {
                    for (GeneGroup gg : table.getSelectionModel().getSelectedItems()) {
                        presel.addAll(gg.getSpecies());
                    }
                }
                new SyntGrad().syntGrad(GeneSetHead.this, 4096, 4096, presel);
            });
        });
        windowmenu.getItems().add(syntenygradientaction);

        MenuItem genexyplotaction = new MenuItem("Gene XY plot");
        genexyplotaction.setOnAction(actionEvent -> SwingUtilities.invokeLater(
                () -> new XYPlot().xyPlot(GeneSetHead.this, comp, geneset.genelist, geneset.clusterMap)));
        windowmenu.getItems().add(genexyplotaction);

        MenuItem refalignaction = new MenuItem("Reference align");
        refalignaction.setOnAction(actionEvent -> {
            SwingUtilities.invokeLater(() -> {
                final TableView<Gene> table12 = getGeneTable();
                final Collection<String> specset = geneset.getSpecies(); //speciesFromCluster( clusterMap );
                final List<String> species = new ArrayList<>(specset);

                TableModel model = new TableModel() {
                    @Override
                    public int getRowCount() {
                        return species.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.nameFix(species.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 table1 = new JTable(model);
                JTable table2 = new JTable(model);

                table1.getSelectionModel().setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
                table2.getSelectionModel().setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);

                JScrollPane scroll1 = new JScrollPane(table1);
                JScrollPane scroll2 = new JScrollPane(table2);

                FlowLayout flowlayout = new FlowLayout();
                JComponent c = new JComponent() {
                };
                c.setLayout(flowlayout);

                c.add(scroll1);
                c.add(scroll2);

                JOptionPane.showMessageDialog(comp, c);

                int r = table1.getSelectedRow();
                int i = table1.convertRowIndexToModel(r);
                String spec = i == -1 ? null : species.get(i);
                List<Sequence> lcont = geneset.speccontigMap.get(spec);

                r = table2.getSelectedRow();
                i = table2.convertRowIndexToModel(r);
                String refspec = i == -1 ? null : species.get(i);
                List<Sequence> lrefcont = geneset.speccontigMap.get(spec);

                /*ByteArrayOutputStream baos = new ByteArrayOutputStream();
                Writer fw = new OutputStreamWriter( baos );
                try {
                List<Sequence> lcont = geneset.speccontigMap.get(spec);
                for( Sequence seq : lcont ) {
                    seq.writeSequence(fw);
                }
                fw.close();
                } catch (IOException e1) {
                e1.printStackTrace();
                }
                    
                String comp = spec;
                byte[] bb = baos.toByteArray();*/

                FlxReader flx = new FlxReader();

                Map<String, String> env = new HashMap<String, String>();
                env.put("create", "true");
                //String uristr = "jar:" + geneset.zippath.toUri();
                //URI geneset.zipuri = URI.create( uristr /*.replace("file://", "file:")*/ );

                try {
                    geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                    for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                        Path subf = root.resolve(spec + ".grp");
                        if (Files.exists(subf)) {
                            BufferedReader br = Files.newBufferedReader(subf);
                            Map<String, Map<String, String>> mm = flx.loadContigGraph(br);
                            br.close();

                            String home = System.getProperty("user.home") + "/";
                            StringBuilder sb = comp != null
                                    ? flx.referenceAssembly(home, spec, refspec, lrefcont, lcont)
                                    : null;
                            Sequence cseq = new Sequence(spec + "_chromosome", null);
                            if (sb != null && sb.length() > 0) {
                                br = new BufferedReader(new StringReader(sb.toString()));
                            } else {
                                Path sca = root.resolve(spec + ".csc");
                                if (!Files.exists(sca)) {
                                    sca = root.resolve(spec + ".sca");
                                }
                                br = Files.newBufferedReader(sca);
                            }
                            //br = new BufferedReader( fr );

                            flx.connectContigs(br, cseq, false, new FileWriter(home + spec + "_new.fna"), spec);
                            br.close();
                        }

                        break;
                    }
                } catch (Exception ex) {
                    ex.printStackTrace();
                } finally {
                    try {
                        geneset.zipfilesystem.close();
                    } catch (IOException ie) {
                        ie.printStackTrace();
                    }
                    ;
                }
            });

            //flx.start( f.getParentFile().getAbsolutePath()+"/", f.getName(), false, fw, comp, bb);
        });
        windowmenu.getItems().add(refalignaction);

        windowmenu.getItems().add(new SeparatorMenuItem());

        MenuItem runantismash = new MenuItem("Run antismash");
        runantismash.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() {
            public void run() {
                try {
                    Serifier ser = new Serifier();
                    Set<String> selspec = getSelspec(null, geneset.getSpecies(), null);

                    JTextField host = new JTextField("localhost");
                    JOptionPane.showMessageDialog(null, host);

                    String username = System.getProperty("user.name");
                    String hostname = host.getText();

                    /*Path[] pt = null;
                    JFileChooser fc = new JFileChooser();
                    fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY );
                    if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) {
                       pt = new Path[3];
                       pt[2] = fc.getSelectedFile().toPath();
                    }*/

                    List<Object> commands = new ArrayList<Object>();
                    //commands.add(genexyplotaction)

                    for (String spec : selspec) {
                        Path pp = Paths.get(userhome);
                        Path p = pp.resolve(spec + ".gbk");
                        //BufferedWriter fw = Files.newBufferedWriter( p );
                        List<Sequence> clist = geneset.speccontigMap.get(spec);

                        Map<String, List<Annotation>> mapan = new HashMap<String, List<Annotation>>();
                        Serifier serifier = new Serifier();
                        for (Sequence c : clist) {
                            serifier.addSequence(c);
                            serifier.mseq.put(c.getName(), c);

                            List<Annotation> lann = new ArrayList<Annotation>();
                            if (c.getAnnotations() != null)
                                for (Annotation ann : c.getAnnotations()) {
                                    Tegeval tv = (Tegeval) ann;

                                    Gene g = tv.getGene();
                                    GeneGroup gg = g.getGeneGroup();
                                    String name = g.getName();
                                    if (gg != null && name.contains(spec)) {
                                        name = gg.getName();
                                    }
                                    Annotation anno = new Annotation(c, tv.start, tv.stop, tv.ori, name);
                                    anno.id = tv.getGene().getId();
                                    anno.type = "CDS";

                                    String cazy = gg != null ? gg.getCommonCazy(geneset.cazymap) : null;
                                    if (cazy != null)
                                        anno.addDbRef("CAZY:" + cazy);
                                    lann.add(anno);
                                }
                            mapan.put(c.getName(), lann);
                        }
                        Sequences s = new Sequences(null, spec, "nucl", null, clist.size());
                        //serifier.addSequences(seqs);
                        serifier.writeGenebank(p, false, true, s, mapan);

                        //fw.close();

                        String apath = p.toAbsolutePath().toString();
                        if (hostname.equals("localhost")) {
                            String[] cmds = { "run_antismash", apath };
                            //commands.add( pt );
                            commands.add(Arrays.asList(cmds));
                        } else {
                            String aname = p.getFileName().toString();
                            String adir = aname.substring(0, aname.length() - 4);
                            String cyghome = NativeRun.cygPath(userhome);
                            String[] cmds = { "scp", apath, hostname + ":~", ";", "ssh", hostname, "run_antismash",
                                    aname, ";", "scp", "-r", hostname + ":~/" + adir, cyghome };//userhome+"~"};
                            //commands.add( pt );
                            commands.add(Arrays.asList(cmds));
                        }
                    }

                    Runnable run = new Runnable() {
                        @Override
                        public void run() {
                            for (String spec : selspec) {
                                Path p = Paths.get(userhome, spec);

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

                                String uristr = "jar:" + geneset.zippath.toUri();
                                URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );
                                final List<Path> lbi = new ArrayList<Path>();
                                try {
                                    geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                                    for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                                        Path specdir = root;
                                        Files.walkFileTree(p, new SimpleFileVisitor<Path>() {
                                            @Override
                                            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs)
                                                    throws IOException {
                                                final Path destFile = Paths.get(specdir.toString(),
                                                        file.toString());
                                                //System.out.printf("Extracting file %s to %s\n", file, destFile);
                                                Files.copy(file, destFile, StandardCopyOption.REPLACE_EXISTING);
                                                return FileVisitResult.CONTINUE;
                                            }

                                            @Override
                                            public FileVisitResult preVisitDirectory(Path dir,
                                                    BasicFileAttributes attrs) throws IOException {
                                                String specdirstr = specdir.toString();
                                                String dirstr = dir.toString();
                                                final Path dirToCreate = specdir
                                                        .resolve(dirstr.substring(userhome.length() + 1));
                                                if (Files.notExists(dirToCreate)) {
                                                    System.out.printf("Creating directory %s\n", dirToCreate);
                                                    Files.createDirectory(dirToCreate);
                                                }
                                                return FileVisitResult.CONTINUE;
                                            }
                                        });
                                        break;
                                    }

                                    URI uri = new URI("file://" + userhome + "/" + spec + "/index.html");
                                    Desktop.getDesktop().browse(uri);
                                } catch (Exception ex) {
                                    ex.printStackTrace();
                                } finally {
                                    try {
                                        geneset.zipfilesystem.close();
                                    } catch (Exception e) {
                                        e.printStackTrace();
                                    }
                                    ;
                                }
                            }
                        }
                    };

                    NativeRun nr = new NativeRun(run);
                    nr.runProcessBuilder("antismash", commands, new Object[3], false, run, false);
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            }
        }));
        windowmenu.getItems().add(runantismash);

        MenuItem runsignalp = new MenuItem("Run signalP");
        runsignalp.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() {
            public void run() {
                try {
                    Serifier ser = new Serifier();
                    Set<String> selspec = getSelspec(null, geneset.getSpecies(), null);

                    JTextField host = new JTextField("localhost");
                    JOptionPane.showMessageDialog(null, host);

                    String username = System.getProperty("user.name");
                    String hostname = host.getText();

                    /*Path[] pt = null;
                    JFileChooser fc = new JFileChooser();
                    fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY );
                    if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) {
                       pt = new Path[3];
                       pt[2] = fc.getSelectedFile().toPath();
                    }*/

                    List<Object> commands = new ArrayList<Object>();
                    //commands.add(genexyplotaction)

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

                        String uristr = "jar:" + geneset.zippath.toUri();
                        URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );

                        geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                        for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                            for (String spec : selspec) {
                                /*Path specdir = root.resolve(spec+".prodigal.fsa");
                                if( !Files.exists(specdir) ) {
                                   if( spec.startsWith("MAT") ) {
                                      specdir = root.resolve(spec+".gbk.aa");
                                   } else specdir = root.resolve("fn_"+spec+"_scaffolds.prodigal.fsa");
                                }*/
                                Stream<Gene> genestream = geneset.genelist.stream()
                                        .filter(gene -> spec.equals(gene.getSpecies())
                                                && (gene.tegeval.type == null || gene.tegeval.type.length() == 0));
                                Path sigout = root.resolve(spec + ".signalp");
                                Path[] pt = new Path[] { null, sigout, null };
                                if (hostname.equals("localhost")) {
                                    String[] cmds = { "signalp", "-t", "gram-", "-" };
                                    commands.add(pt);
                                    commands.add(Arrays.asList(cmds));
                                } else {
                                    Path p = Paths.get(spec + ".signalp");
                                    BufferedWriter bw = Files.newBufferedWriter(p, StandardOpenOption.CREATE,
                                            StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.WRITE);
                                    genestream.forEachOrdered(gene -> {
                                        try {
                                            gene.writeGeneIdFasta(bw);
                                        } catch (Exception e1) {
                                            e1.printStackTrace();
                                        }
                                    });
                                    bw.close();

                                    //Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING);

                                    String[] cmds = { "scp", spec + ".signalp", hostname + ":~", ";", "ssh",
                                            hostname, "signalp", "-t", "gram-", spec + ".signalp" };
                                    //String[] cmds = {"ssh",hostname,"signalp","-t","gram-","-"};
                                    commands.add(pt);
                                    commands.add(Arrays.asList(cmds));
                                }
                            }

                            break;
                        }
                    } catch (Exception ex) {
                        ex.printStackTrace();
                    }

                    Runnable run = new Runnable() {
                        @Override
                        public void run() {
                            try {
                                geneset.zipfilesystem.close();
                            } catch (Exception e) {
                                e.printStackTrace();
                            }
                            ;
                        }
                    };

                    NativeRun nr = new NativeRun(run);
                    nr.runProcessBuilder("signalp", commands, new Object[3], false, run, false);
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            }
        }));
        windowmenu.getItems().add(runsignalp);

        MenuItem runtransm = new MenuItem("Run TransM");
        runtransm.setOnAction(actionEvent -> SwingUtilities.invokeLater(new Runnable() {
            public void run() {
                try {
                    Serifier ser = new Serifier();
                    Set<String> selspec = getSelspec(null, geneset.getSpecies(), null);

                    JTextField host = new JTextField("localhost");
                    JOptionPane.showMessageDialog(null, host);

                    String username = System.getProperty("user.name");
                    String hostname = host.getText();

                    /*Path[] pt = null;
                    JFileChooser fc = new JFileChooser();
                    fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY );
                    if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) {
                       pt = new Path[3];
                       pt[2] = fc.getSelectedFile().toPath();
                    }*/

                    List<Object> commands = new ArrayList<>();
                    //commands.add(genexyplotaction)

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

                        String uristr = "jar:" + geneset.zippath.toUri();
                        URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );

                        geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                        for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                            for (String spec : selspec) {
                                /*Path specdir = root.resolve(spec+".prodigal.fsa");
                                if( !Files.exists(specdir) ) {
                                   if( spec.startsWith("MAT") ) {
                                      specdir = root.resolve(spec+".gbk.aa");
                                   } else specdir = root.resolve("fn_"+spec+"_scaffolds.prodigal.fsa");
                                }*/

                                Stream<Gene> genestream = geneset.genelist.stream()
                                        .filter(gene -> spec.equals(gene.getSpecies())
                                                && (gene.tegeval.type == null || gene.tegeval.type.length() == 0));
                                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                                BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(baos));
                                genestream.forEach(gene -> {
                                    try {
                                        gene.writeGeneIdFasta(bw);
                                    } catch (Exception e1) {
                                        e1.printStackTrace();
                                    }
                                });
                                bw.close();
                                baos.close();
                                String seqs = baos.toString();
                                seqs = seqs.replace('*', 'X');
                                byte[] bb = seqs.getBytes();
                                Path sigout = root.resolve(spec + ".tm");
                                Object[] pt = new Object[] { bb, sigout, null };
                                if (hostname.equals("localhost")) {
                                    String[] cmds = { "decodeanhmm", "-f", "/opt/tmhmm-2.0c/lib/TMHMM2.0.options",
                                            "-modelfile", "/opt/tmhmm-2.0c/lib/TMHMM2.0.model" };
                                    commands.add(pt);
                                    commands.add(Arrays.asList(cmds));
                                } else {
                                    //Path p = Paths.get(spec+".tm");
                                    //Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING);

                                    String[] cmds = { "ssh", hostname, "decodeanhmm", "-f",
                                            "/opt/tmhmm-2.0c/lib/TMHMM2.0.options", "-modelfile",
                                            "/opt/tmhmm-2.0c/lib/TMHMM2.0.model" };
                                    commands.add(pt);
                                    commands.add(Arrays.asList(cmds));
                                }
                            }

                            break;
                        }
                    } catch (Exception ex) {
                        ex.printStackTrace();
                    }

                    Runnable run = () -> {
                        try {
                            geneset.zipfilesystem.close();
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                        ;
                    };

                    NativeRun nr = new NativeRun(run);
                    nr.runProcessBuilder("transm", commands, new Object[3], false, run, false);
                } catch (IOException e1) {
                    e1.printStackTrace();
                }
            }
        }));
        windowmenu.getItems().add(runtransm);

        MenuItem runtrnascan = new MenuItem("tRNAscan");
        runtrnascan.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> {
            try {
                Serifier ser = new Serifier();
                Set<String> selspec = getSelspec(null, geneset.getSpecies(), null);

                JTextField host = new JTextField("localhost");
                JOptionPane.showMessageDialog(null, host);

                String username = System.getProperty("user.name");
                String hostname = host.getText();

                /*Path[] pt = null;
                JFileChooser fc = new JFileChooser();
                fc.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY );
                if( fc.showSaveDialog(null) == JFileChooser.APPROVE_OPTION ) {
                pt = new Path[3];
                pt[2] = fc.getSelectedFile().toPath();
                }*/

                List<Object> commands = new ArrayList<>();
                //commands.add(genexyplotaction)

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

                    String uristr = "jar:" + geneset.zippath.toUri();
                    URI zipuri = URI.create(uristr /*.replace("file://", "file:")*/ );

                    geneset.zipfilesystem = FileSystems.newFileSystem(geneset.zipuri, env);
                    for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                        for (String spec : selspec) {
                            Path specdir = root.resolve(spec + ".fna");
                            if (!Files.exists(specdir)) {
                                if (spec.startsWith("MAT")) {
                                    specdir = root.resolve(spec + ".gbk.fna");
                                } else
                                    specdir = root.resolve("fn_" + spec + "_scaffolds.fastg");
                            }

                            System.err.println(Files.exists(specdir));

                            Path sigout = root.resolve("trnas.txt");
                            if (hostname.equals("localhost1")) {
                                Path[] pt = new Path[] { specdir, sigout, null };
                                String[] cmds = { "/usr/local/bin/tRNAscan-SE", "-B", "-" };
                                commands.add(pt);
                                commands.add(Arrays.asList(cmds));
                            } else {
                                Path[] pt = new Path[] { null, sigout, null };
                                Path p = Paths.get(spec + ".trnascan");
                                Files.copy(specdir, p, StandardCopyOption.REPLACE_EXISTING);

                                List<String> lcmd;
                                if (hostname.equals("localhost")) {
                                    //String[] cmds = {"/usr/local/bin/trnascan-1.4", spec + ".trnascan"};
                                    String[] cmds = { "/usr/local/bin/tRNAscan-SE", "-B", spec + ".trnascan" };
                                    lcmd = Arrays.asList(cmds);
                                } else {
                                    String[] cmds = { "scp", spec + ".trnascan", hostname + ":~", ";", "ssh",
                                            hostname, "trnascan-1.4", spec + ".trnascan" };
                                    lcmd = Arrays.asList(cmds);
                                    //String[] cmds = {"ssh",hostname,"tRNAscan-SE","-B","-"};
                                }

                                commands.add(pt);
                                commands.add(lcmd);
                            }
                        }

                        break;
                    }
                } catch (Exception ex) {
                    ex.printStackTrace();
                }

                Runnable run = () -> {
                    try {
                        geneset.zipfilesystem.close();
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                    ;
                };

                NativeRun nr = new NativeRun(run);
                nr.runProcessBuilder("tRNAscan", commands, new Object[3], false, run, false);
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        }));
        windowmenu.getItems().add(runtrnascan);

        Menu select = new Menu("Select");
        MenuItem breakpointselAction = new MenuItem("Select breakpoints");
        breakpointselAction.setOnAction(actionEvent -> {
            String spec = syncolorcomb.getSelectionModel().getSelectedItem();

            int rr = 0;
            for (Gene g : geneset.genelist) {
                if (!spec.equals(g.getSpecies()) && g.getSpecies().contains("eggert")) {
                    Tegeval tv2 = g.tegeval;
                    Annotation n2 = tv2.getNext();
                    Annotation p2 = tv2.getPrevious();

                    GeneGroup gg = g.getGeneGroup();

                    if (gg.getName().contains("rhodane")) {
                        System.err.println();
                    }

                    Teginfo ti = gg.getGenes(spec);
                    int msimcount = 0;
                    if (ti != null) {
                        for (Tegeval tv1 : ti.tset) {
                            int simcount = 0;

                            Annotation n = tv1.getNext();
                            Annotation p = tv1.getPrevious();

                            GeneGroup ggg = tv1.getGene().getGeneGroup();
                            if (n2 != null) {
                                if (ggg == n2.getGene().getGeneGroup()) {
                                    simcount++;
                                }

                                Annotation nn2 = n2.getNext();
                                if (nn2 != null) {
                                    if (ggg == nn2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }
                                }
                            }

                            if (p2 != null) {
                                if (ggg == p2.getGene().getGeneGroup()) {
                                    simcount++;
                                }

                                Annotation pp2 = p2.getPrevious();
                                if (pp2 != null) {
                                    if (ggg == pp2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }
                                }
                            }

                            if (n != null) {
                                GeneGroup ngg = n.getGene().getGeneGroup();

                                if (ngg == tv2.getGene().getGeneGroup()) {
                                    simcount++;
                                }

                                if (n2 != null) {
                                    if (ngg == n2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }
                                }

                                if (p2 != null) {
                                    if (ngg == p2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }
                                }

                                Annotation nn = n.getNext();
                                if (nn != null) {
                                    ngg = nn.getGene().getGeneGroup();

                                    if (ngg == tv2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }

                                    if (n2 != null) {
                                        if (ngg == n2.getGene().getGeneGroup()) {
                                            simcount++;
                                        }
                                    }

                                    if (p2 != null) {
                                        if (ngg == p2.getGene().getGeneGroup()) {
                                            simcount++;
                                        }
                                    }
                                }
                            }

                            if (p != null) {
                                GeneGroup pgg = p.getGene().getGeneGroup();

                                if (pgg == tv2.getGene().getGeneGroup()) {
                                    simcount++;
                                }

                                if (n2 != null) {
                                    if (pgg == n2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }
                                }

                                if (p2 != null) {
                                    if (pgg == p2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }
                                }

                                Annotation pp = p.getPrevious();
                                if (pp != null) {
                                    pgg = pp.getGene().getGeneGroup();

                                    if (pgg == tv2.getGene().getGeneGroup()) {
                                        simcount++;
                                    }

                                    if (n2 != null) {
                                        if (pgg == n2.getGene().getGeneGroup()) {
                                            simcount++;
                                        }
                                    }

                                    if (p2 != null) {
                                        if (pgg == p2.getGene().getGeneGroup()) {
                                            simcount++;
                                        }
                                    }
                                }
                            }

                            //double rat = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv);
                            if (simcount >= msimcount) {
                                //tv = tv1;
                                msimcount = simcount;
                            }

                            //double ratio = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv);
                            //GeneCompare.gradientColor();
                        }

                        if (msimcount < 2) {
                            gtable.getSelectionModel().select(g);
                        }
                    }
                }
                rr++;
            }
            /*List<Sequence> contigs = geneset.speccontigMap.get( spec );
            for( Sequence c : contigs ) {
               for( Annotation ann : c.annset ) {
              Tegeval tv = (Tegeval)ann;
                  
               }
            }*/
        });
        MenuItem saveselAction = new MenuItem("Save selection");
        saveselAction.setOnAction(actionEvent -> {
            /*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 {
              ((GeneSetHead)comp).saveSel( selname, val);
                  } catch (Exception e1) {
              e1.printStackTrace();
                  }
               }
            }*/
        });
        select.getItems().add(breakpointselAction);
        select.getItems().add(saveselAction);
        select.getItems().add(new SeparatorMenuItem());

        MenuItem showall = new MenuItem("Show all");
        showall.setOnAction(actionEvent -> {
            genefilterset.clear();
            updateFilter(table, label);
        });
        select.getItems().add(showall);
        MenuItem croptosel = new MenuItem("Crop to selection");
        croptosel.setOnAction(actionEvent -> {
            Set<GeneGroup> selitems = new HashSet<>(table.getSelectionModel().getSelectedItems());
            filteredData.setPredicate(p -> selitems.contains(p));
        });
        select.getItems().add(croptosel);
        MenuItem croptoinvsel = new MenuItem("Crop to inverted selection");
        croptoinvsel.setOnAction(actionEvent -> {
            genefilterset.clear();
            for (int i = 0; i < table.getItems().size(); i++) {
                if (!table.getSelectionModel().isSelected(i)) {
                    genefilterset.add(i);
                }
            }
            updateFilter(table, label);
        });
        select.getItems().add(croptoinvsel);
        MenuItem removesel = new MenuItem("Remove selection");
        removesel.setOnAction(actionEvent -> {
            // genefilterset.clear();
            //int[] rr = table.getSelectedRows();
            if (genefilterset.isEmpty()) {
                Set<Integer> ii = new HashSet<Integer>();
                for (int r : table.getSelectionModel().getSelectedIndices())
                    ii.add(r);
                for (int i = 0; i < geneset.genelist.size(); i++) {
                    if (!ii.contains(i))
                        genefilterset.add(i);
                }
            } else {
                for (int r : table.getSelectionModel().getSelectedIndices()) {
                    //int mr = table.convertRowIndexToModel(r);
                    genefilterset.remove(r);
                }
            }
            updateFilter(table, label);
        });
        select.getItems().add(removesel);
        MenuItem invsel = new MenuItem("Invert selection");
        invsel.setOnAction(actionEvent -> {
            ObservableList<GeneGroup> selitems = table.getSelectionModel().getSelectedItems();
            List<GeneGroup> newsel = new ArrayList<>(filteredData);
            newsel.removeAll(selitems);

            table.getSelectionModel().clearSelection();
            newsel.stream().forEach(gg -> table.getSelectionModel().select(gg));

            // genefilterset.clear();
            //int[] rr = table.getSelectedRows();
            /*Set<Integer> iset = new HashSet<>();
            for( int r : table.getSelectionModel().getSelectedIndices() ) {
               iset.add( r );
            }
            table.getSelectionModel().clearSelection();
            for (int r = 0; r < table.getItems().size(); r++) {
               if( !iset.contains(r) ) table.getSelectionModel().select(r);
               /*if (table.isRowSelected(r))
              table.removeRowSelectionInterval(r, r);
               else
              table.addRowSelectionInterval(r, r);
            }*/
        });
        select.getItems().add(invsel);
        //select.addSeparator();
        select.getItems().add(new SeparatorMenuItem());
        MenuItem selsinglemult = new MenuItem("Select single copy genes found in multiple strains");
        selsinglemult.setOnAction(actionEvent -> {
            Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList);
            for (GeneGroup gg : geneset.allgenegroups) {
                Set<String> checkspec = new HashSet<String>(gg.species.keySet());
                checkspec.retainAll(specset);
                if (gg.getCommonTag() == null && checkspec.size() > 1
                        && gg.getTegevals().size() == gg.species.size()) {//gg.getTegevals(checkspec).size() == checkspec.size() ) {
                    table.getSelectionModel().select(gg);
                    //table.setro
                }
            }
        });
        select.getItems().add(selsinglemult);
        MenuItem selsinglemultstrain = new MenuItem(
                "Select single copy genes in accessory genome of multiple strains");
        selsinglemultstrain.setOnAction(actionEvent -> {
            Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList);
            for (GeneGroup gg : geneset.allgenegroups) {
                Set<String> checkspec = new HashSet<String>(gg.species.keySet());
                checkspec.retainAll(specset);
                if (gg.getCommonTag() == null && checkspec.size() > 1 && checkspec.size() < specset.size()
                        && gg.getTegevals().size() == gg.species.size()) {//gg.getTegevals(checkspec).size() == checkspec.size() ) {
                    table.getSelectionModel().select(gg);
                    //table.setro
                }
            }
        });
        select.getItems().add(selsinglemultstrain);

        MenuItem selsinglecopygenes = new MenuItem("Select single copy genes");
        selsinglecopygenes.setOnAction(actionEvent -> {
            Set<String> specset = getSelspec(GeneSetHead.this, geneset.specList);
            for (GeneGroup gg : geneset.allgenegroups) {
                if (gg.getTegevals().size() == gg.species.size()) {
                    table.getSelectionModel().select(gg);
                    //table.setro
                }
            }
        });
        select.getItems().add(selsinglecopygenes);
        MenuItem selduplgenes = new MenuItem("Select duplicated genes");
        selduplgenes.setOnAction(actionEvent -> {
            for (GeneGroup gg : geneset.allgenegroups) {
                int cnt = 0;
                for (String spec : gg.species.keySet()) {
                    Teginfo ti = gg.species.get(spec);
                    if (ti.tset.size() == 2) {
                        List<Tegeval> ta = new ArrayList<Tegeval>(ti.tset);
                        if (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1))
                            cnt++;
                    }
                }
                if ((float) cnt / (float) gg.species.size() > 0.7) {
                    table.getSelectionModel().select(gg);
                }
            }
        });
        select.getItems().add(selduplgenes);
        MenuItem seltriplgenes = new MenuItem("Select triplicated genes");
        seltriplgenes.setOnAction(actionEvent -> {
            for (GeneGroup gg : geneset.allgenegroups) {
                int cnt = 0;
                for (String spec : gg.species.keySet()) {
                    Teginfo ti = gg.species.get(spec);
                    if (ti.tset.size() == 3) {
                        List<Tegeval> ta = new ArrayList<Tegeval>(ti.tset);
                        if ((ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1))
                                && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2)))
                            cnt++;
                    }
                }
                if ((float) cnt / (float) gg.species.size() > 0.7) {
                    table.getSelectionModel().select(gg);
                }
            }
        });
        select.getItems().add(seltriplgenes);

        MenuItem selplasmidgenes = new MenuItem("Select plasmid genes");
        selplasmidgenes.setOnAction(actionEvent -> {
            for (GeneGroup gg : geneset.allgenegroups) {
                if (gg.isOnAnyPlasmid()) {
                    table.getSelectionModel().select(gg);
                }
                /*int cnt = 0;
                for( String spec : gg.species.keySet() ) {
                   Teginfo ti = gg.species.get( spec );
                   if( ti.tset.size() == 3 ) {
                 List<Tegeval> ta = new ArrayList<Tegeval>( ti.tset );
                 if( (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++;
                   }
                }
                if( (float)cnt / (float)gg.species.size() > 0.7 ) {
                   int r = table.convertRowIndexToView(gg.index);
                   table.addRowSelectionInterval(r, r);
                }*/
            }
        });
        select.getItems().add(selplasmidgenes);

        MenuItem selectphagegenes = new MenuItem("Select phage genes");
        selectphagegenes.setOnAction(actionEvent -> {
            for (GeneGroup gg : geneset.allgenegroups) {
                if (gg.isInAnyPhage()) {
                    table.getSelectionModel().select(gg);
                }
                /*int cnt = 0;
                for( String spec : gg.species.keySet() ) {
                   Teginfo ti = gg.species.get( spec );
                   if( ti.tset.size() == 3 ) {
                 List<Tegeval> ta = new ArrayList<Tegeval>( ti.tset );
                 if( (ta.get(0).getNext() == ta.get(1) || ta.get(0).getPrevious() == ta.get(1)) && (ta.get(1).getNext() == ta.get(2) || ta.get(1).getPrevious() == ta.get(2))) cnt++;
                   }
                }
                if( (float)cnt / (float)gg.species.size() > 0.7 ) {
                   int r = table.convertRowIndexToView(gg.index);
                   table.addRowSelectionInterval(r, r);
                }*/
            }
        });
        select.getItems().add(selectphagegenes);
        select.getItems().add(new SeparatorMenuItem());
        MenuItem selectsharingaction = new MenuItem("Select sharing");
        selectsharingaction.setOnAction(actionEvent -> {
            RadioButton panbtn = new RadioButton("Pan");
            RadioButton corebtn = new RadioButton("Core");
            RadioButton blehbtn = new RadioButton("Only in");
            ToggleGroup tg = new ToggleGroup();
            panbtn.setToggleGroup(tg);
            corebtn.setToggleGroup(tg);
            blehbtn.setToggleGroup(tg);

            HBox sp = new HBox();
            sp.getChildren().add(panbtn);
            sp.getChildren().add(corebtn);
            sp.getChildren().add(blehbtn);
            Scene scene = new Scene(sp);

            //FlowLayout flowlayout = new FlowLayout();
            final JFXPanel c = new JFXPanel();
            c.setScene(scene);

            /*Group  root  =  new  Group();
              Scene  scene  =  new  Scene(root, javafx.scene.paint.Color.ALICEBLUE);
              root.getChildren().add(panbtn);
              root.getChildren().add(corebtn);
              root.getChildren().add(blehbtn);
            JFXPanel fxpanel = new JFXPanel();
            fxpanel.setScene( scene );*/
            //bg.add( panbtn );
            //bg.add( corebtn );
            //bg.add( blehbtn );
            corebtn.setSelected(true);
            //Object[] objs = new Object[] { panbtn, corebtn };
            //JOptionPane.showMessageDialog( geneset, objs, "Select id types", JOptionPane.PLAIN_MESSAGE );

            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    final List<String> species = geneset.getSpecies();
                    TableModel model = new TableModel() {
                        @Override
                        public int getRowCount() {
                            return species.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 species.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);

                    Object[] objs = new Object[] { scroll, c };
                    JOptionPane.showMessageDialog(comp, objs);

                    final Set<String> specs = new HashSet<String>();
                    int[] rr = table.getSelectedRows();
                    for (int r : rr) {
                        String spec = (String) table.getValueAt(r, 0);
                        specs.add(spec);
                    }

                    Platform.runLater(new Runnable() {
                        public void run() {
                            for (GeneGroup gg : geneset.allgenegroups) {
                                if (blehbtn.isSelected()) {
                                    Set<String> ss = new HashSet<String>(gg.species.keySet());
                                    ss.removeAll(specs);
                                    if (ss.size() == 0) {
                                        GeneSetHead.this.table.getSelectionModel().select(gg);
                                    }
                                } else if (gg.species.keySet().containsAll(specs)
                                        && (panbtn.isSelected() || specs.size() == gg.species.size())) {
                                    GeneSetHead.this.table.getSelectionModel().select(gg);
                                }
                            }
                        }
                    });
                }
            });
        });
        select.getItems().add(selectsharingaction);
        MenuItem selectdirtyaction = new MenuItem("Select dirty");
        selectdirtyaction.setOnAction(actionEvent -> {
            if (!isGeneview()) {
                int i = 0;
                for (GeneGroup gg : geneset.allgenegroups) {
                    if (gg.containsDirty()) {
                        table.getSelectionModel().select(gg);
                    }
                    i++;
                }
            }
        });
        select.getItems().add(selectdirtyaction);
        MenuItem selectdesignationaction = new MenuItem("Select designation");
        selectdesignationaction.setOnAction(actionEvent -> {
            JComboBox<String> descombo = new JComboBox<String>(
                    geneset.deset.toArray(new String[geneset.deset.size()]));
            descombo.insertItemAt("", 0);
            descombo.setSelectedIndex(0);

            JOptionPane.showMessageDialog(GeneSetHead.this, descombo);
            String seldes = (String) descombo.getSelectedItem();
            if (!isGeneview()) {
                int i = 0;
                for (GeneGroup gg : geneset.allgenegroups) {
                    if (gg.genes != null)
                        for (Gene g : gg.genes) {
                            if (seldes.equals(g.tegeval.designation)) {
                                table.getSelectionModel().select(gg);
                            }
                        }
                    i++;
                }
            }
        });
        select.getItems().add(selectdesignationaction);

        MenuItem blastselect = new MenuItem("Blast select");
        blastselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blast(false)));
        select.getItems().add(blastselect);

        MenuItem blastxselect = new MenuItem("Blastx select");
        blastxselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blast(true)));
        select.getItems().add(blastxselect);

        MenuItem blastnselect = new MenuItem("Blastn select");
        blastnselect.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blastn(true)));
        select.getItems().add(blastnselect);

        MenuItem blastsearch = new MenuItem("Blastn search");
        blastsearch.setOnAction(actionEvent -> SwingUtilities.invokeLater(() -> blastn(false)));
        select.getItems().add(blastsearch);

        menubar.getMenus().add(file);
        menubar.getMenus().add(edit);
        menubar.getMenus().add(view);
        menubar.getMenus().add(sequencemenu);
        menubar.getMenus().add(windowmenu);
        menubar.getMenus().add(select);
        menubar.getMenus().add(help);

        if (comp != null) {
            final Window window = SwingUtilities.windowForComponent(comp);
            initFSKeyListener(window);
            if (comp instanceof JFrame || window instanceof JFrame) {
                JFrame frame = (JFrame) (window == null ? comp : window);
                if (!frame.isResizable())
                    frame.setResizable(true);

                frame.addKeyListener(keylistener);
                frame.setJMenuBar(jmenubar);
            }
        }

        final Button jb = new Button("Atlas");
        jb.setOnAction(event -> {
            try {
                URL url = new URL("file:///home/sigmar/workspace/distann/bin/circle.html");
                GeneSetHead.this.getAppletContext().showDocument(url, "_blank");
            } catch (MalformedURLException e1) {
                e1.printStackTrace();
            }
        });

        try {
            newSoft(jb, comp, genetable, upper, lower, toolbar, btoolbar, GeneSetHead.this, selcomb);
        } catch (IOException e) {
            e.printStackTrace();
        }
        if (comp != null) {
            if (comp instanceof Applet)
                try {
                    ((GeneSetHead) comp).saveSel(null, null);
                } catch (NoSuchMethodError | Exception e1) {
                    e1.printStackTrace();
                }
            //comp.add( cc );
        }
    }

    public void saveSel(String name, String val) throws Exception, NoSuchMethodError {
        JSObject jso = JSObject.getWindow(this);
        jso.call("saveSel", new Object[] { name, val });
    }

    public String colorToRGBString(Color c) {
        int r = c.getRed();
        int g = c.getGreen();
        int b = c.getBlue();

        return "rgba(" + r + "," + g + "," + b + ",0.0)";
    }

    public String colorToString(Color c) {
        int r = c.getRed();
        int g = c.getGreen();
        int b = c.getBlue();

        String red = r < 16 ? 0 + Integer.toString(r, 16) : Integer.toString(r, 16);
        String green = g < 16 ? 0 + Integer.toString(g, 16) : Integer.toString(g, 16);
        String blue = b < 16 ? 0 + Integer.toString(b, 16) : Integer.toString(b, 16);

        return "#" + red + green + blue;
    }

    public void cellRender(TableCell<GeneGroup, Teginfo> cell, Teginfo ti, int row) {
        cell.setStyle("-fx-background-color: white");
        String spec = syncolorcomb.getSelectionModel().getSelectedItem();
        if (spec != null && spec.length() > 0) {
            if (spec.equals("All")) {
                cell.setStyle("-fx-background-color: green");
                for (Tegeval tv : ti.tset) {
                    String tspec = tv.getGene().getSpecies();
                    List<Sequence> scontigs = geneset.speccontigMap.get(tspec);
                    GeneGroup gg = tv.getGene().getGeneGroup();
                    double ratio = GeneCompare.invertedGradientRatio(tspec, scontigs, -1.0, gg, tv);
                    if (ratio == -1) {
                        ratio = GeneCompare.invertedGradientPlasmidRatio(tspec, scontigs, -1.0, gg);
                        cell.setStyle("-fx-background-color: "
                                + colorToString(GeneCompare.gradientGrayscaleColor(ratio)));
                        //label.setForeground( Color.white );
                    } else {
                        cell.setStyle("-fx-background-color: " + colorToString(GeneCompare.gradientColor(ratio)));
                        //label.setForeground( Color.black );
                    }
                    break;
                    //GeneCompare.gradientColor();
                }
            } else {
                List<Sequence> contigs = geneset.speccontigMap.get(spec);
                cell.setStyle("-fx-background-color: green");

                //GeneGroup    gg = ti.best.getGene().getGeneGroup();
                //Teginfo      gene2s = gg.getGenes(spec);
                //double ratio = -1.0;
                int msimcount = 0;
                Tegeval tv2 = null;

                GeneGroup gg = table.getItems().get(row);
                if (gg != null) {
                    Teginfo gene2s = gg.getGenes(spec);
                    Tegeval tv = gene2s.best;
                    tv2 = gene2s.best;
                    if (gene2s != null && gene2s.tset != null)
                        for (Tegeval tv1 : gene2s.tset) {
                            int simcount = 0;

                            Annotation n = tv1.getNext();
                            Annotation p = tv1.getPrevious();
                            Annotation n2 = tv2.getNext();
                            Annotation p2 = tv2.getPrevious();

                            if (n != null) {
                                GeneGroup ngg = n.getGene().getGeneGroup();
                                if (n2 != null) {
                                    if (ngg == n2.getGene().getGeneGroup())
                                        simcount++;
                                }

                                if (p2 != null) {
                                    if (ngg == p2.getGene().getGeneGroup())
                                        simcount++;
                                }
                            }

                            if (p != null) {
                                GeneGroup pgg = p.getGene().getGeneGroup();
                                if (n2 != null) {
                                    if (pgg == n2.getGene().getGeneGroup())
                                        simcount++;
                                }

                                if (p2 != null) {
                                    if (pgg == p2.getGene().getGeneGroup())
                                        simcount++;
                                }
                            }

                            //double rat = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv);
                            if (simcount >= msimcount) {
                                tv = tv1;
                                msimcount = simcount;
                            }

                            //double ratio = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv);
                            //GeneCompare.gradientColor();
                        }

                    double ratio = GeneCompare.invertedGradientRatio(spec, contigs, tv);
                    if (ratio == -1) {
                        if (gg != null)
                            ratio = GeneCompare.invertedGradientPlasmidRatio(spec, contigs, -1.0, gg);
                        String color = colorToString(GeneCompare.gradientGrayscaleColor(ratio));
                        cell.setStyle("-fx-background-color: " + color);
                        //label.setForeground( Color.black );
                    } else {
                        String color = colorToString(GeneCompare.gradientColor(ratio));
                        cell.setStyle("-fx-background-color: " + color);
                        //label.setForeground( Color.black );
                    }
                }
            }
        } else {
            boolean plasmid = false;
            boolean phage = false;
            for (Tegeval tv : ti.tset) {
                phage = phage | tv.isPhage();

                Sequence seq = tv.getContshort();

                if (seq == null) {
                    //System.err.println();
                }

                plasmid = plasmid | (seq != null && seq.isPlasmid());
            }

            if (phage && plasmid) {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkmagenta");
                else
                    cell.setStyle("-fx-background-color: magenta");
            } else if (phage) {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkblue");
                else
                    cell.setStyle("-fx-background-color: blue");
            } else if (plasmid) {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkred");
                else
                    cell.setStyle("-fx-background-color: red");
            } else {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkgreen");
                else
                    cell.setStyle("-fx-background-color: green");
            }
        }
        // label.setText( value.toString() );
        /*if (colorCodes[0] == null)
           GeneSet.setColors();
        if (tv.best.eval == 0) {
           label.setBackground(colorCodes[0]);
        } else if (tv.best.eval < 1e-100)
           label.setBackground(colorCodes[0]);
        else if (tv.best.eval < 1e-50)
           label.setBackground(colorCodes[1]);
        else if (tv.best.eval < 1e-24)
           label.setBackground(colorCodes[2]);
        else if (tv.best.eval < 1e-10)
           label.setBackground(colorCodes[3]);
        else if (tv.best.eval < 1e-5)
           label.setBackground(colorCodes[4]);
        else if (tv.best.eval < 1e-2)
           label.setBackground(colorCodes[5]);
        else if (tv.best.eval < 1e-1)
           label.setBackground(colorCodes[6]);
        else if (tv.best.eval < 1e0)
           label.setBackground(colorCodes[7]);
        else if (tv.best.eval < 1e10)
           label.setBackground(colorCodes[8]);*/
    }

    public boolean cellRenderGene(TableCell<Gene, Teg> cell, Teg tev) {
        Tegeval tv;
        if (tev instanceof Tegeval) {
            tv = (Tegeval) tev;
        } else if (tev instanceof Teginfo) {
            tv = ((Teginfo) tev).best;
        } else {
            cell.setStyle("-fx-background-color: white");
            return false;
        }
        String spec = syncolorcomb.getSelectionModel().getSelectedItem();
        if (spec != null && spec.length() > 0) {
            if (spec.equals("All")) {
                String tspec = tv.getGene().getSpecies();
                List<Sequence> scontigs = geneset.speccontigMap.get(tspec);
                GeneGroup gg = tv.getGene().getGeneGroup();
                double ratio = GeneCompare.invertedGradientRatio(tspec, scontigs, -1.0, gg, tv);
                if (ratio == -1) {
                    ratio = GeneCompare.invertedGradientPlasmidRatio(tspec, scontigs, -1.0, gg);
                    cell.setStyle(
                            "-fx-background-color: " + colorToString(GeneCompare.gradientGrayscaleColor(ratio))
                                    + (cell.isSelected() ? ";-fx-text-fill: black;" : ";-fx-text-fill: white;"));
                    //label.setForeground( Color.white );
                } else {
                    cell.setStyle("-fx-background-color: " + colorToString(GeneCompare.gradientColor(ratio))
                            + (cell.isSelected() ? ";-fx-text-fill: white;" : ";-fx-text-fill: black;"));
                    //label.setForeground( Color.black );
                }
            } else {
                List<Sequence> contigs = geneset.speccontigMap.get(spec);
                Tegeval tv2 = null;
                GeneGroup gg = tv.getGene().getGeneGroup();
                int msimcount = 0;
                if (gg != null) {
                    Teginfo gene2s = gg.getGenes(spec);
                    if (gene2s != null && gene2s.tset != null)
                        for (Tegeval tv1 : gene2s.tset) {
                            int simcount = 0;

                            Annotation n = tv1.getNext();
                            Annotation p = tv1.getPrevious();
                            Annotation n2 = tv.getNext();
                            Annotation p2 = tv.getPrevious();

                            if (n != null) {
                                GeneGroup ngg = n.getGene().getGeneGroup();
                                if (n2 != null) {
                                    if (ngg == n2.getGene().getGeneGroup())
                                        simcount++;
                                }

                                if (p2 != null) {
                                    if (ngg == p2.getGene().getGeneGroup())
                                        simcount++;
                                }
                            }

                            if (p != null) {
                                GeneGroup pgg = p.getGene().getGeneGroup();
                                if (n2 != null) {
                                    if (pgg == n2.getGene().getGeneGroup())
                                        simcount++;
                                }

                                if (p2 != null) {
                                    if (pgg == p2.getGene().getGeneGroup())
                                        simcount++;
                                }
                            }

                            //double rat = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv);
                            if (simcount >= msimcount) {
                                tv2 = tv1;
                                msimcount = simcount;
                            }

                            //double ratio = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv);
                            //GeneCompare.gradientColor();
                        }
                }
                //double ratio = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, gg, tv);
                double ratio = GeneCompare.invertedGradientRatio(spec, contigs, tv2);
                if (ratio == -1) {
                    ratio = GeneCompare.invertedGradientPlasmidRatio(spec, contigs, -1.0, gg);
                    String color = colorToString(GeneCompare.gradientGrayscaleColor(ratio));
                    cell.setStyle("-fx-background-color: " + color
                            + (cell.isSelected() ? ";-fx-text-fill: white;" : ";-fx-text-fill: black;"));
                    //label.setForeground( Color.black );
                } else {
                    String color = colorToString(GeneCompare.gradientColor(ratio));
                    cell.setStyle("-fx-background-color: " + color
                            + (cell.isSelected() ? ";-fx-text-fill: white;" : ";-fx-text-fill: black;"));
                    //label.setForeground( Color.black );
                }
                /*double ratio = GeneCompare.invertedGradientRatio(spec, contigs, -1.0, tv.getGene().getGeneGroup());
                label.setBackground( GeneCompare.gradientColor( ratio ) );*/
            }
        } else {
            Gene g = tv.getGene();
            GeneGroup gg = g.getGeneGroup();
            Teginfo ti = gg.species.get(g.getSpecies());

            boolean phage = tv.isPhage();
            boolean plasmid = tv.getContshort().isPlasmid();
            if (phage && plasmid) {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkmagenta");
                else
                    cell.setStyle("-fx-background-color: magenta");
            } else if (phage) {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkblue");
                else
                    cell.setStyle("-fx-background-color: blue");
            } else if (plasmid) {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkred");
                else
                    cell.setStyle("-fx-background-color: red");
            } else {
                if (ti.tset.size() > 1)
                    cell.setStyle("-fx-background-color: darkgreen");
                else
                    cell.setStyle("-fx-background-color: green");
            }
        }
        // label.setText( value.toString() );
        /*if (colorCodes[0] == null)
           GeneSet.setColors();
        if (tv.best.eval == 0) {
           label.setBackground(colorCodes[0]);
        } else if (tv.best.eval < 1e-100)
           label.setBackground(colorCodes[0]);
        else if (tv.best.eval < 1e-50)
           label.setBackground(colorCodes[1]);
        else if (tv.best.eval < 1e-24)
           label.setBackground(colorCodes[2]);
        else if (tv.best.eval < 1e-10)
           label.setBackground(colorCodes[3]);
        else if (tv.best.eval < 1e-5)
           label.setBackground(colorCodes[4]);
        else if (tv.best.eval < 1e-2)
           label.setBackground(colorCodes[5]);
        else if (tv.best.eval < 1e-1)
           label.setBackground(colorCodes[6]);
        else if (tv.best.eval < 1e0)
           label.setBackground(colorCodes[7]);
        else if (tv.best.eval < 1e10)
           label.setBackground(colorCodes[8]);*/
        return true;
    }

    public void stop() {
        super.stop();
        try {
            if (geneset.zippath != null)
                geneset.saveContigOrder();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    public void newFile() {
        FileChooser fc = new FileChooser();
        fc.getExtensionFilters().add(new ExtensionFilter("Zip files", "*.zip"));
        File f = fc.showSaveDialog(null);
        geneset.zippath = f.toPath();
    }

    public void fetchGenomes() {
        if (geneset.zippath == null) {
            newFile();
        }

        VBox vbox = new VBox();

        Stage stage = new Stage();
        stage.setTitle("Fetch genomes");
        stage.setScene(new Scene(vbox));
        stage.initOwner(primaryStage);

        //frame.setSize(400, 600);

        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);

            final SerifyApplet sa = new SerifyApplet(geneset.zipfilesystem);
            sa.init(frame, vbox, geneset.user);

            for (Path root : geneset.zipfilesystem.getRootDirectories()) {
                Files.list(root).filter(t -> {
                    String fname = t.getFileName().toString();
                    return /*fname.endsWith(".gbk") || */fname.endsWith(".fna") || fname.endsWith("fastg")
                            || fname.endsWith(".fsa") || fname.endsWith(".fa") || fname.endsWith(".fasta")
                            || fname.endsWith(".aa") || fname.endsWith(".nn") || fname.endsWith(".trna")
                            || fname.endsWith(".rrna") || fname.endsWith(".ssu") || fname.endsWith(".lsu")
                            || fname.endsWith(".tsu");
                }).forEach(t -> {
                    try {
                        sa.addSequences(t.getFileName().toString(), t, null);
                    } catch (URISyntaxException | IOException e) {
                        e.printStackTrace();
                    }
                });
                ;
            }
        } catch (IOException e1) {
            try {
                geneset.zipfilesystem.close();
            } catch (IOException e2) {
                e2.printStackTrace();
            }
            e1.printStackTrace();
        }

        //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 );

        /*frame.addWindowListener( new WindowListener() {
               
           @Override
           public void windowOpened(WindowEvent e) {}
               
           @Override
           public void windowIconified(WindowEvent e) {}
               
           @Override
           public void windowDeiconified(WindowEvent e) {}
               
           @Override
           public void windowDeactivated(WindowEvent e) {}
               
           @Override
           public void windowClosing(WindowEvent e) {}
               
           @Override
           public void windowClosed(WindowEvent e) {
        try {
           geneset.zipfilesystem.close();
            
           geneset.cleanUp();
           importStuff();
        } catch (IOException | UnavailableServiceException e1) {
           e1.printStackTrace();
        }
           }
               
           @Override
           public void windowActivated(WindowEvent e) {}
        });
            
        frame.setVisible( true );*/

        stage.setOnCloseRequest(new EventHandler<WindowEvent>() {
            public void handle(WindowEvent event) {
                try {
                    geneset.zipfilesystem.close();

                    geneset.cleanUp();
                    importStuff();
                } catch (IOException | UnavailableServiceException e1) {
                    e1.printStackTrace();
                }
            }
        });
        stage.show();
    }

    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();
        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 );
         */
    }

    private static void relati(TableView<Gene> table, List<Gene> genelist, Set<Integer> genefilterset,
            List<Set<String>> uclusterlist, boolean remove) {
        Set<String> ct = new HashSet<String>();
        for (Gene gg : table.getSelectionModel().getSelectedItems()) {
            GeneGroup ggroup = gg.getGeneGroup();
            for (Gene g : ggroup.genes) {
                ct.add(g.refid);
            }
            // genefilterset.add( gg.index );
            /*Tegeval tv = gg.tegeval;
               //System.err.println( tv.cont );
               //int li = tv.cont.lastIndexOf('_');
               //String tvshort = tv.contshort+tv.cont.substring(li);
            for (Set<String> uset : uclusterlist) {
               if (uset.contains(tv.cont)) {
                  System.err.println( uset );
                  ct.addAll(uset);
                  break;
               }
            }*/
        }

        for (Gene g : genelist) {
            //Tegeval tv = g.tegeval;
            //System.err.println( tv.cont );
            //int li = tv.cont.lastIndexOf('_');
            //String tvshort = tv.contshort+tv.cont.substring(li);
            if (ct.contains(g.refid)) {
                if (remove)
                    genefilterset.remove(genelist.indexOf(g));
                else
                    genefilterset.add(genelist.indexOf(g));
                //break;
            }
        }
        System.err.println(genefilterset.size() + "  " + ct.size());
    }

    private void newSoft(Button jb, Container comp, TableView<Gene> genetable, TableView<Function> upper,
            TableView<GeneGroup> lower, ToolBar toolbar, ToolBar btoolbar, JApplet applet, ComboBox selcomblocal)
            throws IOException {
        /*InputStream nis2 = GeneSet.class.getResourceAsStream("/exp_short.blastout");
        BufferedReader br2 = new BufferedReader( new InputStreamReader(nis2) );
        String line2 = br2.readLine();
        br2.close();*/
        // aas.clear();

        // return new JComponent() {};
        showGeneTable(null, jb, genetable, upper, lower, toolbar, btoolbar, comp, applet, selcomblocal);// clustInfoMap// );
    }

    public void init() {
        init(primaryStage, this, null, null, null, null, null, null, null);
    }

    public void exportGenomes(Map<String, List<Sequence>> speccontigMap) {
        JCheckBox joincontigs = new JCheckBox("Join contigs");
        JCheckBox translations = new JCheckBox("Include translations");
        JComponent[] comps = new JComponent[] { joincontigs, translations };
        List scl = getSelspecContigs(Arrays.asList(comps), speccontigMap);

        if (scl.get(0) instanceof String) {
            List<String> lspec = (List<String>) scl;

            JFileChooser filechooser = new JFileChooser();
            filechooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
            if (filechooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) {
                for (String spec : lspec) {
                    Map<String, List<Annotation>> mapan = new HashMap<String, List<Annotation>>();
                    List<Sequence> contigs = geneset.speccontigMap.get(spec);
                    Serifier serifier = new Serifier();
                    for (Sequence c : contigs) {
                        serifier.addSequence(c);
                        serifier.mseq.put(c.getName(), c);

                        List<Annotation> lann = new ArrayList();
                        if (c.getAnnotations() != null)
                            for (Annotation ann : c.getAnnotations()) {
                                Tegeval tv = (Tegeval) ann;
                                GeneGroup gg = tv.getGene().getGeneGroup();

                                Annotation anno = new Annotation(c, tv.start, tv.stop, tv.ori,
                                        gg != null ? gg.getName() : tv.getGene().getName());
                                anno.type = "CDS";
                                anno.id = tv.getGene().id;

                                String cazy = gg != null ? gg.getCommonCazy(geneset.cazymap) : null;
                                if (cazy != null)
                                    anno.addDbRef("CAZY:" + cazy);
                                Cog cog = gg != null ? gg.getCog(geneset.cogmap) : null;
                                if (cog != null)
                                    anno.addDbRef("COG:" + cog.id);
                                String ec = gg != null ? gg.getEc() : null;
                                if (ec != null)
                                    anno.addDbRef("EC:" + ec);

                                lann.add(anno);
                            }
                        mapan.put(c.getName(), lann);
                    }
                    Sequences s = new Sequences(null, spec, "nucl", null, contigs.size());
                    try {
                        serifier.writeGenebank(filechooser.getSelectedFile().toPath().resolve(spec + ".gbk"),
                                !joincontigs.isSelected(), translations.isSelected(), s, mapan);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
        } else {
            Map<String, List<Annotation>> mapan = new HashMap<>();
            List<Sequence> contigs = (List<Sequence>) scl;
            Serifier serifier = new Serifier();
            for (Sequence c : contigs) {
                serifier.addSequence(c);
                serifier.mseq.put(c.getName(), c);

                List<Annotation> lann = new ArrayList<>();
                if (c.getAnnotations() != null)
                    for (Annotation ann : c.getAnnotations()) {
                        Tegeval tv = (Tegeval) ann;
                        GeneGroup gg = tv.getGene().getGeneGroup();

                        Annotation anno = new Annotation(c, tv.start, tv.stop, tv.ori,
                                gg != null ? gg.getName() : tv.getGene().getName());
                        anno.type = "CDS";
                        anno.id = tv.getGene().id;

                        String cazy = gg != null ? gg.getCommonCazy(geneset.cazymap) : null;
                        if (cazy != null)
                            anno.addDbRef("CAZY:" + cazy);
                        lann.add(anno);
                    }
                mapan.put(c.getName(), lann);
            }
            Sequences s = new Sequences(null, contigs.get(0).getSpec(), "nucl", null, contigs.size());

            JFileChooser filechooser = new JFileChooser();
            if (filechooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) {
                try {
                    serifier.writeGenebank(filechooser.getSelectedFile().toPath(), !joincontigs.isSelected(),
                            translations.isSelected(), s, mapan);
                } catch (IOException e) {
                    e.printStackTrace();
                }
            }
            //serifier.addSequences(seqs);
        }
    }

    public void exportProteinSequences(List<Gene> genelist) {
        JFileChooser filechooser = new JFileChooser();
        if (filechooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) {
            try {
                Path dbPath = filechooser.getSelectedFile().toPath();
                BufferedWriter bw = Files.newBufferedWriter(dbPath);
                for (Gene g : geneset.genelist) {
                    if (g.getTag() == null || g.getTag().equalsIgnoreCase("gene")) {
                        g.getFasta(bw, true);
                        /*StringBuilder sb = g.tegeval.getProteinSequence();
                        if( sb.toString().contains("0") ) {
                           System.err.println( g.id );
                        }
                        bw.append(">" + g.id + "\n");
                        for (int i = 0; i < sb.length(); i += 70) {
                           bw.append( sb.substring(i, Math.min(i + 70, sb.length())) + "\n");
                        }*/
                    }
                }
                bw.close();
                //serifier.writeGenebank( filechooser.getSelectedFile(), !joincontigs.isSelected(), translations.isSelected(), s, mapan);
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }

    public void exportGeneClusters(List<GeneGroup> allgenegroups) {
        JFileChooser filechooser = new JFileChooser();
        filechooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
        if (filechooser.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) {
            try {
                Path dbPath = filechooser.getSelectedFile().toPath();
                for (GeneGroup gg : allgenegroups) {
                    if (gg != null && gg.getCommonTag() == null) {
                        Path file = dbPath.resolve(gg.getCommonId() + ".aa");
                        BufferedWriter bw = Files.newBufferedWriter(file);
                        gg.getFasta(bw, true);
                        bw.close();
                        /*StringBuilder sb = g.tegeval.getProteinSequence();
                        if( sb.toString().contains("0") ) {
                           System.err.println( g.id );
                        }
                        bw.append(">" + g.id + "\n");
                        for (int i = 0; i < sb.length(); i += 70) {
                           bw.append( sb.substring(i, Math.min(i + 70, sb.length())) + "\n");
                        }*/
                    }
                }
                //serifier.writeGenebank( filechooser.getSelectedFile(), !joincontigs.isSelected(), translations.isSelected(), s, mapan);
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }

    public void showKeggPathway(String sub, Path p) throws IOException {
        final BufferedImage selimg = ImageIO.read(Files.newInputStream(p));
        if (selimg != null) {
            JFrame frame = new JFrame(sub);
            frame.setSize(800, 600);
            final JComponent c = new JComponent() {
                public void paintComponent(Graphics g) {
                    super.paintComponent(g);
                    g.drawImage(selimg, 0, 0, this);
                }
            };
            Dimension dim = new Dimension(selimg.getWidth(), selimg.getHeight());
            c.setSize(dim);
            c.setPreferredSize(dim);
            JScrollPane sc2 = new JScrollPane(c);
            frame.add(sc2);
            frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
            frame.setVisible(true);
        }
    }

    public List getSelspecContigs(List<JComponent> complist, final Map<String, List<Sequence>> speccontigMap,
            final String... selspec) {
        List<Sequence> contigs = null;
        final List<String> specs = new ArrayList<String>(speccontigMap.keySet());
        final JTable stable = new JTable();
        stable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
        final TableModel stablemodel = new TableModel() {
            @Override
            public int getRowCount() {
                return specs.size();
            }

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

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

            @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) {
                if (rowIndex >= 0 && rowIndex < specs.size())
                    return specs.get(rowIndex);
                return null;
            }

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

            @Override
            public void addTableModelListener(TableModelListener l) {
            }

            @Override
            public void removeTableModelListener(TableModelListener l) {
            }
        };
        stable.setModel(stablemodel);

        final JTable ctable = new JTable();
        ctable.setAutoCreateRowSorter(true);
        final TableModel ctablemodel = new TableModel() {
            @Override
            public int getRowCount() {
                int r = stable.getSelectedRow();
                String spec = selspec.length > 0 ? selspec[0] : (String) stable.getValueAt(r, 0);
                if (spec != null) {
                    List<Sequence> contigs = geneset.speccontigMap.get(spec);
                    return contigs.size();
                }
                return 0;
            }

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

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

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

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

            @Override
            public Object getValueAt(int rowIndex, int columnIndex) {
                int r = stable.getSelectedRow();
                String spec = selspec.length > 0 ? selspec[0] : (String) stable.getValueAt(r, 0);
                List<Sequence> contigs = geneset.speccontigMap.get(spec);
                return contigs.get(rowIndex);
            }

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

            @Override
            public void addTableModelListener(TableModelListener l) {
            }

            @Override
            public void removeTableModelListener(TableModelListener l) {
            }
        };
        ctable.setModel(ctablemodel);

        JScrollPane sscrollpane = new JScrollPane(stable);
        JScrollPane cscrollpane = new JScrollPane(ctable);

        FlowLayout flowlayout = new FlowLayout();
        JComponent c = new JComponent() {
        };
        c.setLayout(flowlayout);
        if (selspec.length == 0)
            c.add(sscrollpane);
        c.add(cscrollpane);

        if (complist != null) {
            for (JComponent comp : complist) {
                c.add(comp);
            }
        }

        stable.getSelectionModel().addListSelectionListener(new ListSelectionListener() {
            @Override
            public void valueChanged(ListSelectionEvent e) {
                ctable.tableChanged(new TableModelEvent(ctablemodel));
            }
        });
        JOptionPane.showMessageDialog(this, c);

        int[] rr = stable.getSelectedRows();
        if (rr.length > 1) {
            List slist = new ArrayList();
            for (int r : rr) {
                int i = stable.convertRowIndexToModel(r);
                slist.add(specs.get(i));
            }

            return slist;
        } else {
            int sr = stable.getSelectedRow();
            String spec = selspec.length > 0 ? selspec[0] : (String) stable.getValueAt(sr, 0);
            if (spec != null) {
                List<Sequence> ctgs = geneset.speccontigMap.get(spec);
                rr = ctable.getSelectedRows();
                contigs = new ArrayList<Sequence>();
                for (int r : rr) {
                    int i = ctable.convertRowIndexToModel(r);
                    contigs.add(ctgs.get(i));
                }
            }

            return contigs;
        }
    }
}