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