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