src/jalview/gui/FeatureSettings.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.api.FeatureSettingsControllerI;
  24 import jalview.bin.Cache;
  25 import jalview.datamodel.SequenceFeature;
  26 import jalview.datamodel.SequenceI;
  27 import jalview.gui.Help.HelpId;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.schemes.AnnotationColourGradient;
  30 import jalview.schemes.GraduatedColor;
  31 import jalview.util.MessageManager;
  32 import jalview.viewmodel.AlignmentViewport;
  33 import jalview.ws.dbsources.das.api.jalviewSourceI;
  34
  35 import java.awt.BorderLayout;
  36 import java.awt.Color;
  37 import java.awt.Component;
  38 import java.awt.Font;
  39 import java.awt.Graphics;
  40 import java.awt.GridLayout;
  41 import java.awt.Rectangle;
  42 import java.awt.event.ActionEvent;
  43 import java.awt.event.ActionListener;
  44 import java.awt.event.ItemEvent;
  45 import java.awt.event.ItemListener;
  46 import java.awt.event.MouseAdapter;
  47 import java.awt.event.MouseEvent;
  48 import java.awt.event.MouseMotionAdapter;
  49 import java.beans.PropertyChangeEvent;
  50 import java.beans.PropertyChangeListener;
  51 import java.io.File;
  52 import java.io.FileInputStream;
  53 import java.io.FileOutputStream;
  54 import java.io.InputStreamReader;
  55 import java.io.OutputStreamWriter;
  56 import java.io.PrintWriter;
  57 import java.util.Arrays;
  58 import java.util.Hashtable;
  59 import java.util.Iterator;
  60 import java.util.List;
  61 import java.util.Map;
  62 import java.util.Set;
  63 import java.util.Vector;
  64
  65 import javax.help.HelpSetException;
  66 import javax.swing.AbstractCellEditor;
  67 import javax.swing.BorderFactory;
  68 import javax.swing.Icon;
  69 import javax.swing.JButton;
  70 import javax.swing.JCheckBox;
  71 import javax.swing.JCheckBoxMenuItem;
  72 import javax.swing.JColorChooser;
  73 import javax.swing.JDialog;
  74 import javax.swing.JInternalFrame;
  75 import javax.swing.JLabel;
  76 import javax.swing.JLayeredPane;
  77 import javax.swing.JMenuItem;
  78 import javax.swing.JOptionPane;
  79 import javax.swing.JPanel;
  80 import javax.swing.JPopupMenu;
  81 import javax.swing.JScrollPane;
  82 import javax.swing.JSlider;
  83 import javax.swing.JTabbedPane;
  84 import javax.swing.JTable;
  85 import javax.swing.ListSelectionModel;
  86 import javax.swing.SwingConstants;
  87 import javax.swing.SwingUtilities;
  88 import javax.swing.event.ChangeEvent;
  89 import javax.swing.event.ChangeListener;
  90 import javax.swing.table.AbstractTableModel;
  91 import javax.swing.table.TableCellEditor;
  92 import javax.swing.table.TableCellRenderer;
  93
  94 public class FeatureSettings extends JPanel implements
  95         FeatureSettingsControllerI
  96 {
  97   DasSourceBrowser dassourceBrowser;
  98
  99   jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
 100
 101   JPanel settingsPane = new JPanel();
 102
 103   JPanel dasSettingsPane = new JPanel();
 104
 105   final FeatureRenderer fr;
 106
 107   public final AlignFrame af;
 108
 109   Object[][] originalData;
 110
 111   private float originalTransparency;
 112
 113   final JInternalFrame frame;
 114
 115   JScrollPane scrollPane = new JScrollPane();
 116
 117   JTable table;
 118
 119   JPanel groupPanel;
 120
 121   JSlider transparency = new JSlider();
 122
 123   JPanel transPanel = new JPanel(new GridLayout(1, 2));
 124
 125   public FeatureSettings(AlignFrame af)
 126   {
 127     this.af = af;
 128     fr = af.getFeatureRenderer();
 129     // allow transparency to be recovered
 130     transparency.setMaximum(100 - (int) ((originalTransparency = fr
 131             .getTransparency()) * 100));
 132
 133     try
 134     {
 135       jbInit();
 136     } catch (Exception ex)
 137     {
 138       ex.printStackTrace();
 139     }
 140
 141     table = new JTable()
 142     {
 143       @Override
 144       public String getToolTipText(MouseEvent e)
 145       {
 146         if (table.columnAtPoint(e.getPoint()) == 0)
 147         {
 148           /*
 149            * Tooltip for feature name only
 150            */
 151           return JvSwingUtils.wrapTooltip(true, MessageManager
 152                   .getString("label.feature_settings_click_drag"));
 153         }
 154         return null;
 155       }
 156     };
 157     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
 158     table.setFont(new Font("Verdana", Font.PLAIN, 12));
 159     table.setDefaultRenderer(Color.class, new ColorRenderer());
 160
 161     table.setDefaultEditor(Color.class, new ColorEditor(this));
 162
 163     table.setDefaultEditor(GraduatedColor.class, new ColorEditor(this));
 164     table.setDefaultRenderer(GraduatedColor.class, new ColorRenderer());
 165     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 166
 167     table.addMouseListener(new MouseAdapter()
 168     {
 169       @Override
 170       public void mousePressed(MouseEvent evt)
 171       {
 172         selectedRow = table.rowAtPoint(evt.getPoint());
 173         if (evt.isPopupTrigger())
 174         {
 175           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
 176                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
 177                   evt.getX(), evt.getY());
 178         }
 179         else if (evt.getClickCount() == 2)
 180         {
 181           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
 182                   evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
 183                   evt.isMetaDown(),
 184                   (String) table.getValueAt(selectedRow, 0));
 185         }
 186       }
 187
 188       // isPopupTrigger fires on mouseReleased on Mac
 189       @Override
 190       public void mouseReleased(MouseEvent evt)
 191       {
 192         selectedRow = table.rowAtPoint(evt.getPoint());
 193         if (evt.isPopupTrigger())
 194         {
 195           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
 196                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
 197                   evt.getX(), evt.getY());
 198         }
 199       }
 200     });
 201
 202     table.addMouseMotionListener(new MouseMotionAdapter()
 203     {
 204       @Override
 205       public void mouseDragged(MouseEvent evt)
 206       {
 207         int newRow = table.rowAtPoint(evt.getPoint());
 208         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
 209         {
 210           Object[][] data = ((FeatureTableModel) table.getModel())
 211                   .getData();
 212           Object[] temp = data[selectedRow];
 213           data[selectedRow] = data[newRow];
 214           data[newRow] = temp;
 215           updateFeatureRenderer(data);
 216           table.repaint();
 217           selectedRow = newRow;
 218         }
 219       }
 220     });
 221     // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
 222     // MessageManager.getString("label.feature_settings_click_drag")));
 223     scrollPane.setViewportView(table);
 224
 225     dassourceBrowser = new DasSourceBrowser(this);
 226     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 227
 228     if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
 229     {
 230       fr.findAllFeatures(true); // display everything!
 231     }
 232
 233     discoverAllFeatureData();
 234     final PropertyChangeListener change;
 235     final FeatureSettings fs = this;
 236     fr.addPropertyChangeListener(change = new PropertyChangeListener()
 237     {
 238       @Override
 239       public void propertyChange(PropertyChangeEvent evt)
 240       {
 241         if (!fs.resettingTable && !fs.handlingUpdate)
 242         {
 243           fs.handlingUpdate = true;
 244           fs.resetTable(null); // new groups may be added with new seuqence
 245           // feature types only
 246           fs.handlingUpdate = false;
 247         }
 248       }
 249
 250     });
 251
 252     frame = new JInternalFrame();
 253     frame.setContentPane(this);
 254     if (new jalview.util.Platform().isAMac())
 255     {
 256       Desktop.addInternalFrame(frame,
 257               MessageManager.getString("label.sequence_feature_settings"),
 258               475, 480);
 259     }
 260     else
 261     {
 262       Desktop.addInternalFrame(frame,
 263               MessageManager.getString("label.sequence_feature_settings"),
 264               400, 450);
 265     }
 266
 267     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 268     {
 269       @Override
 270       public void internalFrameClosed(
 271               javax.swing.event.InternalFrameEvent evt)
 272       {
 273         fr.removePropertyChangeListener(change);
 274         dassourceBrowser.fs = null;
 275       };
 276     });
 277     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 278   }
 279
 280   protected void popupSort(final int selectedRow, final String type,
 281           final Object typeCol, final Map<String, float[][]> minmax, int x,
 282           int y)
 283   {
 284     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
 285             "label.settings_for_param", new String[] { type }));
 286     JMenuItem scr = new JMenuItem(
 287             MessageManager.getString("label.sort_by_score"));
 288     men.add(scr);
 289     final FeatureSettings me = this;
 290     scr.addActionListener(new ActionListener()
 291     {
 292
 293       @Override
 294       public void actionPerformed(ActionEvent e)
 295       {
 296         me.af.avc.sortAlignmentByFeatureScore(Arrays
 297                 .asList(new String[] { type }));
 298       }
 299
 300     });
 301     JMenuItem dens = new JMenuItem(
 302             MessageManager.getString("label.sort_by_density"));
 303     dens.addActionListener(new ActionListener()
 304     {
 305
 306       @Override
 307       public void actionPerformed(ActionEvent e)
 308       {
 309         me.af.avc.sortAlignmentByFeatureDensity(Arrays
 310                 .asList(new String[] { type }));
 311       }
 312
 313     });
 314     men.add(dens);
 315     if (minmax != null)
 316     {
 317       final float[][] typeMinMax = minmax.get(type);
 318       /*
 319        * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
 320        * this is broken at the moment and isn't that useful anyway!
 321        * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new
 322        * ActionListener() {
 323        *
 324        * public void actionPerformed(ActionEvent e) {
 325        * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
 326        * null); } else { minmax.put(type, typeMinMax); } }
 327        *
 328        * });
 329        *
 330        * men.add(chb);
 331        */
 332       if (typeMinMax != null && typeMinMax[0] != null)
 333       {
 334         // if (table.getValueAt(row, column));
 335         // graduated colourschemes for those where minmax exists for the
 336         // positional features
 337         final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
 338                 "Graduated Colour");
 339         mxcol.setSelected(!(typeCol instanceof Color));
 340         men.add(mxcol);
 341         mxcol.addActionListener(new ActionListener()
 342         {
 343           JColorChooser colorChooser;
 344
 345           @Override
 346           public void actionPerformed(ActionEvent e)
 347           {
 348             if (e.getSource() == mxcol)
 349             {
 350               if (typeCol instanceof Color)
 351               {
 352                 FeatureColourChooser fc = new FeatureColourChooser(me.fr,
 353                         type);
 354                 fc.addActionListener(this);
 355               }
 356               else
 357               {
 358                 // bring up simple color chooser
 359                 colorChooser = new JColorChooser();
 360                 JDialog dialog = JColorChooser.createDialog(me,
 361                         "Select new Colour", true, // modal
 362                         colorChooser, this, // OK button handler
 363                         null); // no CANCEL button handler
 364                 colorChooser.setColor(((GraduatedColor) typeCol)
 365                         .getMaxColor());
 366                 dialog.setVisible(true);
 367               }
 368             }
 369             else
 370             {
 371               if (e.getSource() instanceof FeatureColourChooser)
 372               {
 373                 FeatureColourChooser fc = (FeatureColourChooser) e
 374                         .getSource();
 375                 table.setValueAt(fc.getLastColour(), selectedRow, 1);
 376                 table.validate();
 377               }
 378               else
 379               {
 380                 // probably the color chooser!
 381                 table.setValueAt(colorChooser.getColor(), selectedRow, 1);
 382                 table.validate();
 383                 me.updateFeatureRenderer(
 384                         ((FeatureTableModel) table.getModel()).getData(),
 385                         false);
 386               }
 387             }
 388           }
 389
 390         });
 391       }
 392     }
 393     JMenuItem selCols = new JMenuItem(
 394             MessageManager.getString("label.select_columns_containing"));
 395     selCols.addActionListener(new ActionListener()
 396     {
 397       @Override
 398       public void actionPerformed(ActionEvent arg0)
 399       {
 400         fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
 401                 false, type);
 402       }
 403     });
 404     JMenuItem clearCols = new JMenuItem(
 405             MessageManager.getString("label.select_columns_not_containing"));
 406     clearCols.addActionListener(new ActionListener()
 407     {
 408       @Override
 409       public void actionPerformed(ActionEvent arg0)
 410       {
 411         fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
 412                 false, type);
 413       }
 414     });
 415     JMenuItem hideCols = new JMenuItem(
 416             MessageManager.getString("label.hide_columns_containing"));
 417     hideCols.addActionListener(new ActionListener()
 418     {
 419       @Override
 420       public void actionPerformed(ActionEvent arg0)
 421       {
 422         fr.ap.alignFrame.hideFeatureColumns(type, true);
 423       }
 424     });
 425     JMenuItem hideOtherCols = new JMenuItem(
 426             MessageManager.getString("label.hide_columns_not_containing"));
 427     hideOtherCols.addActionListener(new ActionListener()
 428     {
 429       @Override
 430       public void actionPerformed(ActionEvent arg0)
 431       {
 432         fr.ap.alignFrame.hideFeatureColumns(type, false);
 433       }
 434     });
 435     men.add(selCols);
 436     men.add(clearCols);
 437     men.add(hideCols);
 438     men.add(hideOtherCols);
 439     men.show(table, x, y);
 440   }
 441
 442   /**
 443    * true when Feature Settings are updating from feature renderer
 444    */
 445   private boolean handlingUpdate = false;
 446
 447   /**
 448    * contains a float[3] for each feature type string. created by setTableData
 449    */
 450   Hashtable typeWidth = null;
 451
 452   @Override
 453   synchronized public void discoverAllFeatureData()
 454   {
 455     Vector allFeatures = new Vector();
 456     Vector allGroups = new Vector();
 457     SequenceFeature[] tmpfeatures;
 458     String group;
 459     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 460     {
 461       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 462               .getSequenceFeatures();
 463       if (tmpfeatures == null)
 464       {
 465         continue;
 466       }
 467
 468       int index = 0;
 469       while (index < tmpfeatures.length)
 470       {
 471         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 472         {
 473           index++;
 474           continue;
 475         }
 476
 477         if (tmpfeatures[index].getFeatureGroup() != null)
 478         {
 479           group = tmpfeatures[index].featureGroup;
 480           if (!allGroups.contains(group))
 481           {
 482             allGroups.addElement(group);
 483             checkGroupState(group);
 484           }
 485         }
 486
 487         if (!allFeatures.contains(tmpfeatures[index].getType()))
 488         {
 489           allFeatures.addElement(tmpfeatures[index].getType());
 490         }
 491         index++;
 492       }
 493     }
 494
 495     resetTable(null);
 496
 497     validate();
 498   }
 499
 500   /**
 501    * Synchronise gui group list and check visibility of group
 502    *
 503    * @param group
 504    * @return true if group is visible
 505    */
 506   private boolean checkGroupState(String group)
 507   {
 508     boolean visible = fr.checkGroupVisibility(group, true);
 509
 510     if (groupPanel == null)
 511     {
 512       groupPanel = new JPanel();
 513     }
 514
 515     boolean alreadyAdded = false;
 516     for (int g = 0; g < groupPanel.getComponentCount(); g++)
 517     {
 518       if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
 519       {
 520         alreadyAdded = true;
 521         ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
 522         break;
 523       }
 524     }
 525
 526     if (alreadyAdded)
 527     {
 528
 529       return visible;
 530     }
 531     final String grp = group;
 532     final JCheckBox check = new JCheckBox(group, visible);
 533     check.setFont(new Font("Serif", Font.BOLD, 12));
 534     check.addItemListener(new ItemListener()
 535     {
 536       @Override
 537       public void itemStateChanged(ItemEvent evt)
 538       {
 539         fr.setGroupVisibility(check.getText(), check.isSelected());
 540         af.alignPanel.getSeqPanel().seqCanvas.repaint();
 541         if (af.alignPanel.overviewPanel != null)
 542         {
 543           af.alignPanel.overviewPanel.updateOverviewImage();
 544         }
 545
 546         resetTable(new String[] { grp });
 547       }
 548     });
 549     groupPanel.add(check);
 550     return visible;
 551   }
 552
 553   boolean resettingTable = false;
 554
 555   synchronized void resetTable(String[] groupChanged)
 556   {
 557     if (resettingTable == true)
 558     {
 559       return;
 560     }
 561     resettingTable = true;
 562     typeWidth = new Hashtable();
 563     // TODO: change avWidth calculation to 'per-sequence' average and use long
 564     // rather than float
 565     float[] avWidth = null;
 566     SequenceFeature[] tmpfeatures;
 567     String group = null, type;
 568     Vector visibleChecks = new Vector();
 569
 570     // Find out which features should be visible depending on which groups
 571     // are selected / deselected
 572     // and recompute average width ordering
 573     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 574     {
 575
 576       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 577               .getSequenceFeatures();
 578       if (tmpfeatures == null)
 579       {
 580         continue;
 581       }
 582
 583       int index = 0;
 584       while (index < tmpfeatures.length)
 585       {
 586         group = tmpfeatures[index].featureGroup;
 587
 588         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 589         {
 590           index++;
 591           continue;
 592         }
 593
 594         if (group == null || checkGroupState(group))
 595         {
 596           type = tmpfeatures[index].getType();
 597           if (!visibleChecks.contains(type))
 598           {
 599             visibleChecks.addElement(type);
 600           }
 601         }
 602         if (!typeWidth.containsKey(tmpfeatures[index].getType()))
 603         {
 604           typeWidth.put(tmpfeatures[index].getType(),
 605                   avWidth = new float[3]);
 606         }
 607         else
 608         {
 609           avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
 610         }
 611         avWidth[0]++;
 612         if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
 613         {
 614           avWidth[1] += 1 + tmpfeatures[index].getBegin()
 615                   - tmpfeatures[index].getEnd();
 616         }
 617         else
 618         {
 619           avWidth[1] += 1 + tmpfeatures[index].getEnd()
 620                   - tmpfeatures[index].getBegin();
 621         }
 622         index++;
 623       }
 624     }
 625
 626     int fSize = visibleChecks.size();
 627     Object[][] data = new Object[fSize][3];
 628     int dataIndex = 0;
 629
 630     if (fr.hasRenderOrder())
 631     {
 632       if (!handlingUpdate)
 633       {
 634         fr.findAllFeatures(groupChanged != null); // prod to update
 635         // colourschemes. but don't
 636         // affect display
 637         // First add the checks in the previous render order,
 638         // in case the window has been closed and reopened
 639       }
 640       List<String> frl = fr.getRenderOrder();
 641       for (int ro = frl.size() - 1; ro > -1; ro--)
 642       {
 643         type = frl.get(ro);
 644
 645         if (!visibleChecks.contains(type))
 646         {
 647           continue;
 648         }
 649
 650         data[dataIndex][0] = type;
 651         data[dataIndex][1] = fr.getFeatureStyle(type);
 652         data[dataIndex][2] = new Boolean(af.getViewport()
 653                 .getFeaturesDisplayed().isVisible(type));
 654         dataIndex++;
 655         visibleChecks.removeElement(type);
 656       }
 657     }
 658
 659     fSize = visibleChecks.size();
 660     for (int i = 0; i < fSize; i++)
 661     {
 662       // These must be extra features belonging to the group
 663       // which was just selected
 664       type = visibleChecks.elementAt(i).toString();
 665       data[dataIndex][0] = type;
 666
 667       data[dataIndex][1] = fr.getFeatureStyle(type);
 668       if (data[dataIndex][1] == null)
 669       {
 670         // "Colour has been updated in another view!!"
 671         fr.clearRenderOrder();
 672         return;
 673       }
 674
 675       data[dataIndex][2] = new Boolean(true);
 676       dataIndex++;
 677     }
 678
 679     if (originalData == null)
 680     {
 681       originalData = new Object[data.length][3];
 682       for (int i = 0; i < data.length; i++)
 683       {
 684         System.arraycopy(data[i], 0, originalData[i], 0, 3);
 685       }
 686     }
 687
 688     table.setModel(new FeatureTableModel(data));
 689     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 690
 691     if (groupPanel != null)
 692     {
 693       groupPanel.setLayout(new GridLayout(
 694               fr.getFeatureGroupsSize() / 4 + 1, 4));
 695
 696       groupPanel.validate();
 697       bigPanel.add(groupPanel, BorderLayout.NORTH);
 698     }
 699
 700     updateFeatureRenderer(data, groupChanged != null);
 701     resettingTable = false;
 702   }
 703
 704   /**
 705    * reorder data based on the featureRenderers global priority list.
 706    *
 707    * @param data
 708    */
 709   private void ensureOrder(Object[][] data)
 710   {
 711     boolean sort = false;
 712     float[] order = new float[data.length];
 713     for (int i = 0; i < order.length; i++)
 714     {
 715       order[i] = fr.getOrder(data[i][0].toString());
 716       if (order[i] < 0)
 717       {
 718         order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
 719       }
 720       if (i > 1)
 721       {
 722         sort = sort || order[i - 1] > order[i];
 723       }
 724     }
 725     if (sort)
 726     {
 727       jalview.util.QuickSort.sort(order, data);
 728     }
 729   }
 730
 731   void load()
 732   {
 733     JalviewFileChooser chooser = new JalviewFileChooser(
 734             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 735             new String[] { "fc" },
 736             new String[] { "Sequence Feature Colours" },
 737             "Sequence Feature Colours");
 738     chooser.setFileView(new jalview.io.JalviewFileView());
 739     chooser.setDialogTitle(MessageManager
 740             .getString("label.load_feature_colours"));
 741     chooser.setToolTipText(MessageManager.getString("action.load"));
 742
 743     int value = chooser.showOpenDialog(this);
 744
 745     if (value == JalviewFileChooser.APPROVE_OPTION)
 746     {
 747       File file = chooser.getSelectedFile();
 748
 749       try
 750       {
 751         InputStreamReader in = new InputStreamReader(new FileInputStream(
 752                 file), "UTF-8");
 753
 754         jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
 755         jucs = jucs.unmarshal(in);
 756
 757         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
 758         {
 759           String name;
 760           jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
 761           if (newcol.hasMax())
 762           {
 763             Color mincol = null, maxcol = null;
 764             try
 765             {
 766               mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
 767               maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
 768
 769             } catch (Exception e)
 770             {
 771               Cache.log.warn("Couldn't parse out graduated feature color.",
 772                       e);
 773             }
 774             GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
 775                     newcol.getMin(), newcol.getMax());
 776             if (newcol.hasAutoScale())
 777             {
 778               gcol.setAutoScaled(newcol.getAutoScale());
 779             }
 780             if (newcol.hasColourByLabel())
 781             {
 782               gcol.setColourByLabel(newcol.getColourByLabel());
 783             }
 784             if (newcol.hasThreshold())
 785             {
 786               gcol.setThresh(newcol.getThreshold());
 787               gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
 788             }
 789             if (newcol.getThreshType().length() > 0)
 790             {
 791               String ttyp = newcol.getThreshType();
 792               if (ttyp.equalsIgnoreCase("NONE"))
 793               {
 794                 gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
 795               }
 796               if (ttyp.equalsIgnoreCase("ABOVE"))
 797               {
 798                 gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
 799               }
 800               if (ttyp.equalsIgnoreCase("BELOW"))
 801               {
 802                 gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
 803               }
 804             }
 805             fr.setColour(name = newcol.getName(), gcol);
 806           }
 807           else
 808           {
 809             fr.setColour(name = jucs.getColour(i).getName(), new Color(
 810                     Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
 811           }
 812           fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
 813         }
 814         if (table != null)
 815         {
 816           resetTable(null);
 817           Object[][] data = ((FeatureTableModel) table.getModel())
 818                   .getData();
 819           ensureOrder(data);
 820           updateFeatureRenderer(data, false);
 821           table.repaint();
 822         }
 823       } catch (Exception ex)
 824       {
 825         System.out.println("Error loading User Colour File\n" + ex);
 826       }
 827     }
 828   }
 829
 830   void save()
 831   {
 832     JalviewFileChooser chooser = new JalviewFileChooser(
 833             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 834             new String[] { "fc" },
 835             new String[] { "Sequence Feature Colours" },
 836             "Sequence Feature Colours");
 837     chooser.setFileView(new jalview.io.JalviewFileView());
 838     chooser.setDialogTitle(MessageManager
 839             .getString("label.save_feature_colours"));
 840     chooser.setToolTipText(MessageManager.getString("action.save"));
 841
 842     int value = chooser.showSaveDialog(this);
 843
 844     if (value == JalviewFileChooser.APPROVE_OPTION)
 845     {
 846       String choice = chooser.getSelectedFile().getPath();
 847       jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 848       ucs.setSchemeName("Sequence Features");
 849       try
 850       {
 851         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 852                 new FileOutputStream(choice), "UTF-8"));
 853
 854         Set fr_colours = fr.getAllFeatureColours();
 855         Iterator e = fr_colours.iterator();
 856         float[] sortOrder = new float[fr_colours.size()];
 857         String[] sortTypes = new String[fr_colours.size()];
 858         int i = 0;
 859         while (e.hasNext())
 860         {
 861           sortTypes[i] = e.next().toString();
 862           sortOrder[i] = fr.getOrder(sortTypes[i]);
 863           i++;
 864         }
 865         jalview.util.QuickSort.sort(sortOrder, sortTypes);
 866         sortOrder = null;
 867         Object fcol;
 868         GraduatedColor gcol;
 869         for (i = 0; i < sortTypes.length; i++)
 870         {
 871           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 872           col.setName(sortTypes[i]);
 873           col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
 874                   .getName())));
 875           fcol = fr.getFeatureStyle(sortTypes[i]);
 876           if (fcol instanceof GraduatedColor)
 877           {
 878             gcol = (GraduatedColor) fcol;
 879             col.setMin(gcol.getMin());
 880             col.setMax(gcol.getMax());
 881             col.setMinRGB(jalview.util.Format.getHexString(gcol
 882                     .getMinColor()));
 883             col.setAutoScale(gcol.isAutoScale());
 884             col.setThreshold(gcol.getThresh());
 885             col.setColourByLabel(gcol.isColourByLabel());
 886             switch (gcol.getThreshType())
 887             {
 888             case AnnotationColourGradient.NO_THRESHOLD:
 889               col.setThreshType("NONE");
 890               break;
 891             case AnnotationColourGradient.ABOVE_THRESHOLD:
 892               col.setThreshType("ABOVE");
 893               break;
 894             case AnnotationColourGradient.BELOW_THRESHOLD:
 895               col.setThreshType("BELOW");
 896               break;
 897             }
 898           }
 899           ucs.addColour(col);
 900         }
 901         ucs.marshal(out);
 902         out.close();
 903       } catch (Exception ex)
 904       {
 905         ex.printStackTrace();
 906       }
 907     }
 908   }
 909
 910   public void invertSelection()
 911   {
 912     for (int i = 0; i < table.getRowCount(); i++)
 913     {
 914       Boolean value = (Boolean) table.getValueAt(i, 2);
 915
 916       table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
 917     }
 918   }
 919
 920   public void orderByAvWidth()
 921   {
 922     if (table == null || table.getModel() == null)
 923     {
 924       return;
 925     }
 926     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
 927     float[] width = new float[data.length];
 928     float[] awidth;
 929     float max = 0;
 930     int num = 0;
 931     for (int i = 0; i < data.length; i++)
 932     {
 933       awidth = (float[]) typeWidth.get(data[i][0]);
 934       if (awidth[0] > 0)
 935       {
 936         width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
 937         // weight - but have to make per
 938         // sequence, too (awidth[2])
 939         // if (width[i]==1) // hack to distinguish single width sequences.
 940         num++;
 941       }
 942       else
 943       {
 944         width[i] = 0;
 945       }
 946       if (max < width[i])
 947       {
 948         max = width[i];
 949       }
 950     }
 951     boolean sort = false;
 952     for (int i = 0; i < width.length; i++)
 953     {
 954       // awidth = (float[]) typeWidth.get(data[i][0]);
 955       if (width[i] == 0)
 956       {
 957         width[i] = fr.getOrder(data[i][0].toString());
 958         if (width[i] < 0)
 959         {
 960           width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
 961         }
 962       }
 963       else
 964       {
 965         width[i] /= max; // normalize
 966         fr.setOrder(data[i][0].toString(), width[i]); // store for later
 967       }
 968       if (i > 0)
 969       {
 970         sort = sort || width[i - 1] > width[i];
 971       }
 972     }
 973     if (sort)
 974     {
 975       jalview.util.QuickSort.sort(width, data);
 976       // update global priority order
 977     }
 978
 979     updateFeatureRenderer(data, false);
 980     table.repaint();
 981   }
 982
 983   public void close()
 984   {
 985     try
 986     {
 987       frame.setClosed(true);
 988     } catch (Exception exe)
 989     {
 990     }
 991
 992   }
 993
 994   public void updateFeatureRenderer(Object[][] data)
 995   {
 996     updateFeatureRenderer(data, true);
 997   }
 998
 999   /**
1000    * Update the priority order of features; only repaint if this changed the
1001    * order of visible features
1002    *
1003    * @param data
1004    * @param visibleNew
1005    */
1006   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
1007   {
1008     if (fr.setFeaturePriority(data, visibleNew))
1009     {
1010       af.alignPanel.paintAlignment(true);
1011     }
1012   }
1013
1014   int selectedRow = -1;
1015
1016   JTabbedPane tabbedPane = new JTabbedPane();
1017
1018   BorderLayout borderLayout1 = new BorderLayout();
1019
1020   BorderLayout borderLayout2 = new BorderLayout();
1021
1022   BorderLayout borderLayout3 = new BorderLayout();
1023
1024   JPanel bigPanel = new JPanel();
1025
1026   BorderLayout borderLayout4 = new BorderLayout();
1027
1028   JButton invert = new JButton();
1029
1030   JPanel buttonPanel = new JPanel();
1031
1032   JButton cancel = new JButton();
1033
1034   JButton ok = new JButton();
1035
1036   JButton loadColours = new JButton();
1037
1038   JButton saveColours = new JButton();
1039
1040   JPanel dasButtonPanel = new JPanel();
1041
1042   JButton fetchDAS = new JButton();
1043
1044   JButton saveDAS = new JButton();
1045
1046   JButton cancelDAS = new JButton();
1047
1048   JButton optimizeOrder = new JButton();
1049
1050   JButton sortByScore = new JButton();
1051
1052   JButton sortByDens = new JButton();
1053
1054   JButton help = new JButton();
1055
1056   JPanel transbuttons = new JPanel(new GridLayout(5, 1));
1057
1058   private void jbInit() throws Exception
1059   {
1060     this.setLayout(borderLayout1);
1061     settingsPane.setLayout(borderLayout2);
1062     dasSettingsPane.setLayout(borderLayout3);
1063     bigPanel.setLayout(borderLayout4);
1064     invert.setFont(JvSwingUtils.getLabelFont());
1065     invert.setText(MessageManager.getString("label.invert_selection"));
1066     invert.addActionListener(new ActionListener()
1067     {
1068       @Override
1069       public void actionPerformed(ActionEvent e)
1070       {
1071         invertSelection();
1072       }
1073     });
1074     optimizeOrder.setFont(JvSwingUtils.getLabelFont());
1075     optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
1076     optimizeOrder.addActionListener(new ActionListener()
1077     {
1078       @Override
1079       public void actionPerformed(ActionEvent e)
1080       {
1081         orderByAvWidth();
1082       }
1083     });
1084     sortByScore.setFont(JvSwingUtils.getLabelFont());
1085     sortByScore
1086             .setText(MessageManager.getString("label.seq_sort_by_score"));
1087     sortByScore.addActionListener(new ActionListener()
1088     {
1089       @Override
1090       public void actionPerformed(ActionEvent e)
1091       {
1092         af.avc.sortAlignmentByFeatureScore(null);
1093       }
1094     });
1095     sortByDens.setFont(JvSwingUtils.getLabelFont());
1096     sortByDens.setText(MessageManager
1097             .getString("label.sequence_sort_by_density"));
1098     sortByDens.addActionListener(new ActionListener()
1099     {
1100       @Override
1101       public void actionPerformed(ActionEvent e)
1102       {
1103         af.avc.sortAlignmentByFeatureDensity(null);
1104       }
1105     });
1106     help.setFont(JvSwingUtils.getLabelFont());
1107     help.setText(MessageManager.getString("action.help"));
1108     help.addActionListener(new ActionListener()
1109     {
1110       @Override
1111       public void actionPerformed(ActionEvent e)
1112       {
1113         try
1114         {
1115           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1116         } catch (HelpSetException e1)
1117         {
1118           e1.printStackTrace();
1119         }
1120       }
1121     });
1122     help.setFont(JvSwingUtils.getLabelFont());
1123     help.setText(MessageManager.getString("action.help"));
1124     help.addActionListener(new ActionListener()
1125     {
1126       @Override
1127       public void actionPerformed(ActionEvent e)
1128       {
1129         try
1130         {
1131           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1132         } catch (HelpSetException e1)
1133         {
1134           e1.printStackTrace();
1135         }
1136       }
1137     });
1138     cancel.setFont(JvSwingUtils.getLabelFont());
1139     cancel.setText(MessageManager.getString("action.cancel"));
1140     cancel.addActionListener(new ActionListener()
1141     {
1142       @Override
1143       public void actionPerformed(ActionEvent e)
1144       {
1145         fr.setTransparency(originalTransparency);
1146         updateFeatureRenderer(originalData);
1147         close();
1148       }
1149     });
1150     ok.setFont(JvSwingUtils.getLabelFont());
1151     ok.setText(MessageManager.getString("action.ok"));
1152     ok.addActionListener(new ActionListener()
1153     {
1154       @Override
1155       public void actionPerformed(ActionEvent e)
1156       {
1157         close();
1158       }
1159     });
1160     loadColours.setFont(JvSwingUtils.getLabelFont());
1161     loadColours.setText(MessageManager.getString("label.load_colours"));
1162     loadColours.addActionListener(new ActionListener()
1163     {
1164       @Override
1165       public void actionPerformed(ActionEvent e)
1166       {
1167         load();
1168       }
1169     });
1170     saveColours.setFont(JvSwingUtils.getLabelFont());
1171     saveColours.setText(MessageManager.getString("label.save_colours"));
1172     saveColours.addActionListener(new ActionListener()
1173     {
1174       @Override
1175       public void actionPerformed(ActionEvent e)
1176       {
1177         save();
1178       }
1179     });
1180     transparency.addChangeListener(new ChangeListener()
1181     {
1182       @Override
1183       public void stateChanged(ChangeEvent evt)
1184       {
1185         fr.setTransparency((100 - transparency.getValue()) / 100f);
1186         af.alignPanel.paintAlignment(true);
1187       }
1188     });
1189
1190     transparency.setMaximum(70);
1191     transparency.setToolTipText(MessageManager
1192             .getString("label.transparency_tip"));
1193     fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
1194     fetchDAS.addActionListener(new ActionListener()
1195     {
1196       @Override
1197       public void actionPerformed(ActionEvent e)
1198       {
1199         fetchDAS_actionPerformed(e);
1200       }
1201     });
1202     saveDAS.setText(MessageManager.getString("action.save_as_default"));
1203     saveDAS.addActionListener(new ActionListener()
1204     {
1205       @Override
1206       public void actionPerformed(ActionEvent e)
1207       {
1208         saveDAS_actionPerformed(e);
1209       }
1210     });
1211     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
1212     dasSettingsPane.setBorder(null);
1213     cancelDAS.setEnabled(false);
1214     cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
1215     cancelDAS.addActionListener(new ActionListener()
1216     {
1217       @Override
1218       public void actionPerformed(ActionEvent e)
1219       {
1220         cancelDAS_actionPerformed(e);
1221       }
1222     });
1223     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
1224     tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
1225             settingsPane);
1226     tabbedPane.addTab(MessageManager.getString("label.das_settings"),
1227             dasSettingsPane);
1228     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
1229     transbuttons.add(optimizeOrder);
1230     transbuttons.add(invert);
1231     transbuttons.add(sortByScore);
1232     transbuttons.add(sortByDens);
1233     transbuttons.add(help);
1234     JPanel sliderPanel = new JPanel();
1235     sliderPanel.add(transparency);
1236     transPanel.add(transparency);
1237     transPanel.add(transbuttons);
1238     buttonPanel.add(ok);
1239     buttonPanel.add(cancel);
1240     buttonPanel.add(loadColours);
1241     buttonPanel.add(saveColours);
1242     bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
1243     dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
1244     dasButtonPanel.add(fetchDAS);
1245     dasButtonPanel.add(cancelDAS);
1246     dasButtonPanel.add(saveDAS);
1247     settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
1248     settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
1249   }
1250
1251   public void fetchDAS_actionPerformed(ActionEvent e)
1252   {
1253     fetchDAS.setEnabled(false);
1254     cancelDAS.setEnabled(true);
1255     dassourceBrowser.setGuiEnabled(false);
1256     Vector selectedSources = dassourceBrowser.getSelectedSources();
1257     doDasFeatureFetch(selectedSources, true, true);
1258   }
1259
1260   /**
1261    * get the features from selectedSources for all or the current selection
1262    *
1263    * @param selectedSources
1264    * @param checkDbRefs
1265    * @param promptFetchDbRefs
1266    */
1267   private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
1268           boolean checkDbRefs, boolean promptFetchDbRefs)
1269   {
1270     SequenceI[] dataset, seqs;
1271     int iSize;
1272     AlignmentViewport vp = af.getViewport();
1273     if (vp.getSelectionGroup() != null
1274             && vp.getSelectionGroup().getSize() > 0)
1275     {
1276       iSize = vp.getSelectionGroup().getSize();
1277       dataset = new SequenceI[iSize];
1278       seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
1279     }
1280     else
1281     {
1282       iSize = vp.getAlignment().getHeight();
1283       seqs = vp.getAlignment().getSequencesArray();
1284     }
1285
1286     dataset = new SequenceI[iSize];
1287     for (int i = 0; i < iSize; i++)
1288     {
1289       dataset[i] = seqs[i].getDatasetSequence();
1290     }
1291
1292     cancelDAS.setEnabled(true);
1293     dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
1294             this, selectedSources, checkDbRefs, promptFetchDbRefs);
1295     af.getViewport().setShowSequenceFeatures(true);
1296     af.showSeqFeatures.setSelected(true);
1297   }
1298
1299   /**
1300    * blocking call to initialise the das source browser
1301    */
1302   public void initDasSources()
1303   {
1304     dassourceBrowser.initDasSources();
1305   }
1306
1307   /**
1308    * examine the current list of das sources and return any matching the given
1309    * nicknames in sources
1310    *
1311    * @param sources
1312    *          Vector of Strings to resolve to DAS source nicknames.
1313    * @return sources that are present in source list.
1314    */
1315   public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
1316   {
1317     return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
1318   }
1319
1320   /**
1321    * get currently selected das sources. ensure you have called initDasSources
1322    * before calling this.
1323    *
1324    * @return vector of selected das source nicknames
1325    */
1326   public Vector getSelectedSources()
1327   {
1328     return dassourceBrowser.getSelectedSources();
1329   }
1330
1331   /**
1332    * properly initialise DAS fetcher and then initiate a new thread to fetch
1333    * features from the named sources (rather than any turned on by default)
1334    *
1335    * @param sources
1336    * @param block
1337    *          if true then runs in same thread, otherwise passes to the Swing
1338    *          executor
1339    */
1340   public void fetchDasFeatures(Vector sources, boolean block)
1341   {
1342     initDasSources();
1343     List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
1344             .resolveSourceNicknames(sources);
1345     if (resolved.size() == 0)
1346     {
1347       resolved = dassourceBrowser.getSelectedSources();
1348     }
1349     if (resolved.size() > 0)
1350     {
1351       final List<jalviewSourceI> dassources = resolved;
1352       fetchDAS.setEnabled(false);
1353       // cancelDAS.setEnabled(true); doDasFetch does this.
1354       Runnable fetcher = new Runnable()
1355       {
1356
1357         @Override
1358         public void run()
1359         {
1360           doDasFeatureFetch(dassources, true, false);
1361
1362         }
1363       };
1364       if (block)
1365       {
1366         fetcher.run();
1367       }
1368       else
1369       {
1370         SwingUtilities.invokeLater(fetcher);
1371       }
1372     }
1373   }
1374
1375   public void saveDAS_actionPerformed(ActionEvent e)
1376   {
1377     dassourceBrowser
1378             .saveProperties(jalview.bin.Cache.applicationProperties);
1379   }
1380
1381   public void complete()
1382   {
1383     fetchDAS.setEnabled(true);
1384     cancelDAS.setEnabled(false);
1385     dassourceBrowser.setGuiEnabled(true);
1386
1387   }
1388
1389   public void cancelDAS_actionPerformed(ActionEvent e)
1390   {
1391     if (dasFeatureFetcher != null)
1392     {
1393       dasFeatureFetcher.cancel();
1394     }
1395     complete();
1396   }
1397
1398   public void noDasSourceActive()
1399   {
1400     complete();
1401     JOptionPane
1402             .showInternalConfirmDialog(
1403                     Desktop.desktop,
1404                     MessageManager
1405                             .getString("label.no_das_sources_selected_warn"),
1406                     MessageManager
1407                             .getString("label.no_das_sources_selected_title"),
1408                     JOptionPane.DEFAULT_OPTION,
1409                     JOptionPane.INFORMATION_MESSAGE);
1410   }
1411
1412   // ///////////////////////////////////////////////////////////////////////
1413   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
1414   // ///////////////////////////////////////////////////////////////////////
1415   class FeatureTableModel extends AbstractTableModel
1416   {
1417     FeatureTableModel(Object[][] data)
1418     {
1419       this.data = data;
1420     }
1421
1422     private String[] columnNames = {
1423         MessageManager.getString("label.feature_type"),
1424         MessageManager.getString("action.colour"),
1425         MessageManager.getString("label.display") };
1426
1427     private Object[][] data;
1428
1429     public Object[][] getData()
1430     {
1431       return data;
1432     }
1433
1434     public void setData(Object[][] data)
1435     {
1436       this.data = data;
1437     }
1438
1439     @Override
1440     public int getColumnCount()
1441     {
1442       return columnNames.length;
1443     }
1444
1445     public Object[] getRow(int row)
1446     {
1447       return data[row];
1448     }
1449
1450     @Override
1451     public int getRowCount()
1452     {
1453       return data.length;
1454     }
1455
1456     @Override
1457     public String getColumnName(int col)
1458     {
1459       return columnNames[col];
1460     }
1461
1462     @Override
1463     public Object getValueAt(int row, int col)
1464     {
1465       return data[row][col];
1466     }
1467
1468     @Override
1469     public Class getColumnClass(int c)
1470     {
1471       return getValueAt(0, c).getClass();
1472     }
1473
1474     @Override
1475     public boolean isCellEditable(int row, int col)
1476     {
1477       return col == 0 ? false : true;
1478     }
1479
1480     @Override
1481     public void setValueAt(Object value, int row, int col)
1482     {
1483       data[row][col] = value;
1484       fireTableCellUpdated(row, col);
1485       updateFeatureRenderer(data);
1486     }
1487
1488   }
1489
1490   class ColorRenderer extends JLabel implements TableCellRenderer
1491   {
1492     javax.swing.border.Border unselectedBorder = null;
1493
1494     javax.swing.border.Border selectedBorder = null;
1495
1496     final String baseTT = "Click to edit, right/apple click for menu.";
1497
1498     public ColorRenderer()
1499     {
1500       setOpaque(true); // MUST do this for background to show up.
1501       setHorizontalTextPosition(SwingConstants.CENTER);
1502       setVerticalTextPosition(SwingConstants.CENTER);
1503     }
1504
1505     @Override
1506     public Component getTableCellRendererComponent(JTable table,
1507             Object color, boolean isSelected, boolean hasFocus, int row,
1508             int column)
1509     {
1510       // JLabel comp = new JLabel();
1511       // comp.
1512       setOpaque(true);
1513       // comp.
1514       // setBounds(getBounds());
1515       Color newColor;
1516       setToolTipText(baseTT);
1517       setBackground(table.getBackground());
1518       if (color instanceof GraduatedColor)
1519       {
1520         Rectangle cr = table.getCellRect(row, column, false);
1521         FeatureSettings.renderGraduatedColor(this, (GraduatedColor) color,
1522                 (int) cr.getWidth(), (int) cr.getHeight());
1523
1524       }
1525       else
1526       {
1527         this.setText("");
1528         this.setIcon(null);
1529         newColor = (Color) color;
1530         // comp.
1531         setBackground(newColor);
1532         // comp.setToolTipText("RGB value: " + newColor.getRed() + ", "
1533         // + newColor.getGreen() + ", " + newColor.getBlue());
1534       }
1535       if (isSelected)
1536       {
1537         if (selectedBorder == null)
1538         {
1539           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1540                   table.getSelectionBackground());
1541         }
1542         // comp.
1543         setBorder(selectedBorder);
1544       }
1545       else
1546       {
1547         if (unselectedBorder == null)
1548         {
1549           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1550                   table.getBackground());
1551         }
1552         // comp.
1553         setBorder(unselectedBorder);
1554       }
1555
1556       return this;
1557     }
1558   }
1559
1560   /**
1561    * update comp using rendering settings from gcol
1562    *
1563    * @param comp
1564    * @param gcol
1565    */
1566   public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol)
1567   {
1568     int w = comp.getWidth(), h = comp.getHeight();
1569     if (w < 20)
1570     {
1571       w = (int) comp.getPreferredSize().getWidth();
1572       h = (int) comp.getPreferredSize().getHeight();
1573       if (w < 20)
1574       {
1575         w = 80;
1576         h = 12;
1577       }
1578     }
1579     renderGraduatedColor(comp, gcol, w, h);
1580   }
1581
1582   public static void renderGraduatedColor(JLabel comp, GraduatedColor gcol,
1583           int w, int h)
1584   {
1585     boolean thr = false;
1586     String tt = "";
1587     String tx = "";
1588     if (gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD)
1589     {
1590       thr = true;
1591       tx += ">";
1592       tt += "Thresholded (Above " + gcol.getThresh() + ") ";
1593     }
1594     if (gcol.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
1595     {
1596       thr = true;
1597       tx += "<";
1598       tt += "Thresholded (Below " + gcol.getThresh() + ") ";
1599     }
1600     if (gcol.isColourByLabel())
1601     {
1602       tt = "Coloured by label text. " + tt;
1603       if (thr)
1604       {
1605         tx += " ";
1606       }
1607       tx += "Label";
1608       comp.setIcon(null);
1609     }
1610     else
1611     {
1612       Color newColor = gcol.getMaxColor();
1613       comp.setBackground(newColor);
1614       // System.err.println("Width is " + w / 2);
1615       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
1616       comp.setIcon(ficon);
1617       // tt+="RGB value: Max (" + newColor.getRed() + ", "
1618       // + newColor.getGreen() + ", " + newColor.getBlue()
1619       // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
1620       // + ", " + minCol.getBlue() + ")");
1621     }
1622     comp.setHorizontalAlignment(SwingConstants.CENTER);
1623     comp.setText(tx);
1624     if (tt.length() > 0)
1625     {
1626       if (comp.getToolTipText() == null)
1627       {
1628         comp.setToolTipText(tt);
1629       }
1630       else
1631       {
1632         comp.setToolTipText(tt + " " + comp.getToolTipText());
1633       }
1634     }
1635   }
1636 }
1637
1638 class FeatureIcon implements Icon
1639 {
1640   GraduatedColor gcol;
1641
1642   Color backg;
1643
1644   boolean midspace = false;
1645
1646   int width = 50, height = 20;
1647
1648   int s1, e1; // start and end of midpoint band for thresholded symbol
1649
1650   Color mpcolour = Color.white;
1651
1652   FeatureIcon(GraduatedColor gfc, Color bg, int w, int h, boolean mspace)
1653   {
1654     gcol = gfc;
1655     backg = bg;
1656     width = w;
1657     height = h;
1658     midspace = mspace;
1659     if (midspace)
1660     {
1661       s1 = width / 3;
1662       e1 = s1 * 2;
1663     }
1664     else
1665     {
1666       s1 = width / 2;
1667       e1 = s1;
1668     }
1669   }
1670
1671   @Override
1672   public int getIconWidth()
1673   {
1674     return width;
1675   }
1676
1677   @Override
1678   public int getIconHeight()
1679   {
1680     return height;
1681   }
1682
1683   @Override
1684   public void paintIcon(Component c, Graphics g, int x, int y)
1685   {
1686
1687     if (gcol.isColourByLabel())
1688     {
1689       g.setColor(backg);
1690       g.fillRect(0, 0, width, height);
1691       // need an icon here.
1692       g.setColor(gcol.getMaxColor());
1693
1694       g.setFont(new Font("Verdana", Font.PLAIN, 9));
1695
1696       // g.setFont(g.getFont().deriveFont(
1697       // AffineTransform.getScaleInstance(
1698       // width/g.getFontMetrics().stringWidth("Label"),
1699       // height/g.getFontMetrics().getHeight())));
1700
1701       g.drawString(MessageManager.getString("label.label"), 0, 0);
1702
1703     }
1704     else
1705     {
1706       Color minCol = gcol.getMinColor();
1707       g.setColor(minCol);
1708       g.fillRect(0, 0, s1, height);
1709       if (midspace)
1710       {
1711         g.setColor(Color.white);
1712         g.fillRect(s1, 0, e1 - s1, height);
1713       }
1714       g.setColor(gcol.getMaxColor());
1715       g.fillRect(0, e1, width - e1, height);
1716     }
1717   }
1718 }
1719
1720 class ColorEditor extends AbstractCellEditor implements TableCellEditor,
1721         ActionListener
1722 {
1723   FeatureSettings me;
1724
1725   GraduatedColor currentGColor;
1726
1727   FeatureColourChooser chooser;
1728
1729   String type;
1730
1731   Color currentColor;
1732
1733   JButton button;
1734
1735   JColorChooser colorChooser;
1736
1737   JDialog dialog;
1738
1739   protected static final String EDIT = "edit";
1740
1741   int selectedRow = 0;
1742
1743   public ColorEditor(FeatureSettings me)
1744   {
1745     this.me = me;
1746     // Set up the editor (from the table's point of view),
1747     // which is a button.
1748     // This button brings up the color chooser dialog,
1749     // which is the editor from the user's point of view.
1750     button = new JButton();
1751     button.setActionCommand(EDIT);
1752     button.addActionListener(this);
1753     button.setBorderPainted(false);
1754     // Set up the dialog that the button brings up.
1755     colorChooser = new JColorChooser();
1756     dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal
1757             colorChooser, this, // OK button handler
1758             null); // no CANCEL button handler
1759   }
1760
1761   /**
1762    * Handles events from the editor button and from the dialog's OK button.
1763    */
1764   @Override
1765   public void actionPerformed(ActionEvent e)
1766   {
1767
1768     if (EDIT.equals(e.getActionCommand()))
1769     {
1770       // The user has clicked the cell, so
1771       // bring up the dialog.
1772       if (currentColor != null)
1773       {
1774         // bring up simple color chooser
1775         button.setBackground(currentColor);
1776         colorChooser.setColor(currentColor);
1777         dialog.setVisible(true);
1778       }
1779       else
1780       {
1781         // bring up graduated chooser.
1782         chooser = new FeatureColourChooser(me.fr, type);
1783         chooser.setRequestFocusEnabled(true);
1784         chooser.requestFocus();
1785         chooser.addActionListener(this);
1786       }
1787       // Make the renderer reappear.
1788       fireEditingStopped();
1789
1790     }
1791     else
1792     { // User pressed dialog's "OK" button.
1793       if (currentColor != null)
1794       {
1795         currentColor = colorChooser.getColor();
1796       }
1797       else
1798       {
1799         // class cast exceptions may be raised if the chooser created on a
1800         // non-graduated color
1801         currentGColor = (GraduatedColor) chooser.getLastColour();
1802       }
1803       me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
1804       fireEditingStopped();
1805       me.table.validate();
1806     }
1807   }
1808
1809   // Implement the one CellEditor method that AbstractCellEditor doesn't.
1810   @Override
1811   public Object getCellEditorValue()
1812   {
1813     if (currentColor == null)
1814     {
1815       return currentGColor;
1816     }
1817     return currentColor;
1818   }
1819
1820   // Implement the one method defined by TableCellEditor.
1821   @Override
1822   public Component getTableCellEditorComponent(JTable table, Object value,
1823           boolean isSelected, int row, int column)
1824   {
1825     currentGColor = null;
1826     currentColor = null;
1827     this.selectedRow = row;
1828     type = me.table.getValueAt(row, 0).toString();
1829     button.setOpaque(true);
1830     button.setBackground(me.getBackground());
1831     if (value instanceof GraduatedColor)
1832     {
1833       currentGColor = (GraduatedColor) value;
1834       JLabel btn = new JLabel();
1835       btn.setSize(button.getSize());
1836       FeatureSettings.renderGraduatedColor(btn, currentGColor);
1837       button.setBackground(btn.getBackground());
1838       button.setIcon(btn.getIcon());
1839       button.setText(btn.getText());
1840     }
1841     else
1842     {
1843       button.setText("");
1844       button.setIcon(null);
1845       currentColor = (Color) value;
1846       button.setBackground(currentColor);
1847     }
1848     return button;
1849   }
1850 }