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