src/jalview/gui/FeatureSettings.java

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