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