src/jalview/gui/FeatureSettings.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.api.FeatureColourI;
  24 import jalview.api.FeatureSettingsControllerI;
  25 import jalview.bin.Cache;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.gui.Help.HelpId;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.schemabinding.version2.JalviewUserColours;
  32 import jalview.schemes.FeatureColour;
  33 import jalview.util.Format;
  34 import jalview.util.MessageManager;
  35 import jalview.util.Platform;
  36 import jalview.util.QuickSort;
  37 import jalview.viewmodel.AlignmentViewport;
  38 import jalview.ws.dbsources.das.api.jalviewSourceI;
  39
  40 import java.awt.BorderLayout;
  41 import java.awt.Color;
  42 import java.awt.Component;
  43 import java.awt.Dimension;
  44 import java.awt.Font;
  45 import java.awt.Graphics;
  46 import java.awt.GridLayout;
  47 import java.awt.Rectangle;
  48 import java.awt.event.ActionEvent;
  49 import java.awt.event.ActionListener;
  50 import java.awt.event.ItemEvent;
  51 import java.awt.event.ItemListener;
  52 import java.awt.event.MouseAdapter;
  53 import java.awt.event.MouseEvent;
  54 import java.awt.event.MouseMotionAdapter;
  55 import java.beans.PropertyChangeEvent;
  56 import java.beans.PropertyChangeListener;
  57 import java.io.File;
  58 import java.io.FileInputStream;
  59 import java.io.FileOutputStream;
  60 import java.io.InputStreamReader;
  61 import java.io.OutputStreamWriter;
  62 import java.io.PrintWriter;
  63 import java.util.Arrays;
  64 import java.util.HashSet;
  65 import java.util.Hashtable;
  66 import java.util.Iterator;
  67 import java.util.List;
  68 import java.util.Map;
  69 import java.util.Set;
  70 import java.util.Vector;
  71
  72 import javax.help.HelpSetException;
  73 import javax.swing.AbstractCellEditor;
  74 import javax.swing.BorderFactory;
  75 import javax.swing.Icon;
  76 import javax.swing.JButton;
  77 import javax.swing.JCheckBox;
  78 import javax.swing.JCheckBoxMenuItem;
  79 import javax.swing.JColorChooser;
  80 import javax.swing.JDialog;
  81 import javax.swing.JInternalFrame;
  82 import javax.swing.JLabel;
  83 import javax.swing.JLayeredPane;
  84 import javax.swing.JMenuItem;
  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
 101         implements 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   private static final int MIN_WIDTH = 400;
 132
 133   private static final int MIN_HEIGHT = 400;
 134
 135   /**
 136    * Constructor
 137    *
 138    * @param af
 139    */
 140   public FeatureSettings(AlignFrame af)
 141   {
 142     this.af = af;
 143     fr = af.getFeatureRenderer();
 144     // allow transparency to be recovered
 145     transparency.setMaximum(100
 146             - (int) ((originalTransparency = fr.getTransparency()) * 100));
 147
 148     try
 149     {
 150       jbInit();
 151     } catch (Exception ex)
 152     {
 153       ex.printStackTrace();
 154     }
 155
 156     table = new JTable()
 157     {
 158       @Override
 159       public String getToolTipText(MouseEvent e)
 160       {
 161         if (table.columnAtPoint(e.getPoint()) == 0)
 162         {
 163           /*
 164            * Tooltip for feature name only
 165            */
 166           return JvSwingUtils.wrapTooltip(true, MessageManager
 167                   .getString("label.feature_settings_click_drag"));
 168         }
 169         return null;
 170       }
 171     };
 172     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
 173     table.setFont(new Font("Verdana", Font.PLAIN, 12));
 174     table.setDefaultRenderer(Color.class, new ColorRenderer());
 175
 176     table.setDefaultEditor(Color.class, new ColorEditor(this));
 177
 178     table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
 179     table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
 180     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 181
 182     table.addMouseListener(new MouseAdapter()
 183     {
 184       @Override
 185       public void mousePressed(MouseEvent evt)
 186       {
 187         selectedRow = table.rowAtPoint(evt.getPoint());
 188         if (evt.isPopupTrigger())
 189         {
 190           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
 191                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
 192                   evt.getX(), evt.getY());
 193         }
 194         else if (evt.getClickCount() == 2)
 195         {
 196           boolean invertSelection = evt.isAltDown();
 197           boolean toggleSelection = Platform.isControlDown(evt);
 198           boolean extendSelection = evt.isShiftDown();
 199           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
 200                   invertSelection, extendSelection, toggleSelection,
 201                   (String) table.getValueAt(selectedRow, 0));
 202         }
 203       }
 204
 205       // isPopupTrigger fires on mouseReleased on Windows
 206       @Override
 207       public void mouseReleased(MouseEvent evt)
 208       {
 209         selectedRow = table.rowAtPoint(evt.getPoint());
 210         if (evt.isPopupTrigger())
 211         {
 212           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
 213                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
 214                   evt.getX(), evt.getY());
 215         }
 216       }
 217     });
 218
 219     table.addMouseMotionListener(new MouseMotionAdapter()
 220     {
 221       @Override
 222       public void mouseDragged(MouseEvent evt)
 223       {
 224         int newRow = table.rowAtPoint(evt.getPoint());
 225         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
 226         {
 227           /*
 228            * reposition 'selectedRow' to 'newRow' (the dragged to location)
 229            * this could be more than one row away for a very fast drag action
 230            * so just swap it with adjacent rows until we get it there
 231            */
 232           Object[][] data = ((FeatureTableModel) table.getModel())
 233                   .getData();
 234           int direction = newRow < selectedRow ? -1 : 1;
 235           for (int i = selectedRow; i != newRow; i += direction)
 236           {
 237             Object[] temp = data[i];
 238             data[i] = data[i + direction];
 239             data[i + direction] = temp;
 240           }
 241           updateFeatureRenderer(data);
 242           table.repaint();
 243           selectedRow = newRow;
 244         }
 245       }
 246     });
 247     // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
 248     // MessageManager.getString("label.feature_settings_click_drag")));
 249     scrollPane.setViewportView(table);
 250
 251     dassourceBrowser = new DasSourceBrowser(this);
 252     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 253
 254     if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
 255     {
 256       fr.findAllFeatures(true); // display everything!
 257     }
 258
 259     discoverAllFeatureData();
 260     final PropertyChangeListener change;
 261     final FeatureSettings fs = this;
 262     fr.addPropertyChangeListener(change = new PropertyChangeListener()
 263     {
 264       @Override
 265       public void propertyChange(PropertyChangeEvent evt)
 266       {
 267         if (!fs.resettingTable && !fs.handlingUpdate)
 268         {
 269           fs.handlingUpdate = true;
 270           fs.resetTable(null); // new groups may be added with new seuqence
 271           // feature types only
 272           fs.handlingUpdate = false;
 273         }
 274       }
 275
 276     });
 277
 278     frame = new JInternalFrame();
 279     frame.setContentPane(this);
 280     if (Platform.isAMac())
 281     {
 282       Desktop.addInternalFrame(frame,
 283               MessageManager.getString("label.sequence_feature_settings"),
 284               475, 480);
 285     }
 286     else
 287     {
 288       Desktop.addInternalFrame(frame,
 289               MessageManager.getString("label.sequence_feature_settings"),
 290               400, 450);
 291     }
 292     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 293
 294     frame.addInternalFrameListener(
 295             new javax.swing.event.InternalFrameAdapter()
 296             {
 297               @Override
 298               public void internalFrameClosed(
 299                       javax.swing.event.InternalFrameEvent evt)
 300               {
 301                 fr.removePropertyChangeListener(change);
 302                 dassourceBrowser.fs = null;
 303               };
 304             });
 305     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 306   }
 307
 308   protected void popupSort(final int selectedRow, final String type,
 309           final Object typeCol, final Map<String, float[][]> minmax, int x,
 310           int y)
 311   {
 312     final FeatureColourI featureColour = (FeatureColourI) typeCol;
 313
 314     JPopupMenu men = new JPopupMenu(MessageManager
 315             .formatMessage("label.settings_for_param", new String[]
 316             { type }));
 317     JMenuItem scr = new JMenuItem(
 318             MessageManager.getString("label.sort_by_score"));
 319     men.add(scr);
 320     final FeatureSettings me = this;
 321     scr.addActionListener(new ActionListener()
 322     {
 323
 324       @Override
 325       public void actionPerformed(ActionEvent e)
 326       {
 327         me.af.avc
 328                 .sortAlignmentByFeatureScore(Arrays.asList(new String[]
 329                 { type }));
 330       }
 331
 332     });
 333     JMenuItem dens = new JMenuItem(
 334             MessageManager.getString("label.sort_by_density"));
 335     dens.addActionListener(new ActionListener()
 336     {
 337
 338       @Override
 339       public void actionPerformed(ActionEvent e)
 340       {
 341         me.af.avc
 342                 .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
 343                 { type }));
 344       }
 345
 346     });
 347     men.add(dens);
 348     if (minmax != null)
 349     {
 350       final float[][] typeMinMax = minmax.get(type);
 351       /*
 352        * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
 353        * this is broken at the moment and isn't that useful anyway!
 354        * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new
 355        * ActionListener() {
 356        *
 357        * public void actionPerformed(ActionEvent e) {
 358        * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
 359        * null); } else { minmax.put(type, typeMinMax); } }
 360        *
 361        * });
 362        *
 363        * men.add(chb);
 364        */
 365       if (typeMinMax != null && typeMinMax[0] != null)
 366       {
 367         // if (table.getValueAt(row, column));
 368         // graduated colourschemes for those where minmax exists for the
 369         // positional features
 370         final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
 371                 "Graduated Colour");
 372         mxcol.setSelected(!featureColour.isSimpleColour());
 373         men.add(mxcol);
 374         mxcol.addActionListener(new ActionListener()
 375         {
 376           JColorChooser colorChooser;
 377
 378           @Override
 379           public void actionPerformed(ActionEvent e)
 380           {
 381             if (e.getSource() == mxcol)
 382             {
 383               if (featureColour.isSimpleColour())
 384               {
 385                 FeatureColourChooser fc = new FeatureColourChooser(me.fr,
 386                         type);
 387                 fc.addActionListener(this);
 388               }
 389               else
 390               {
 391                 // bring up simple color chooser
 392                 colorChooser = new JColorChooser();
 393                 JDialog dialog = JColorChooser.createDialog(me,
 394                         "Select new Colour", true, // modal
 395                         colorChooser, this, // OK button handler
 396                         null); // no CANCEL button handler
 397                 colorChooser.setColor(featureColour.getMaxColour());
 398                 dialog.setVisible(true);
 399               }
 400             }
 401             else
 402             {
 403               if (e.getSource() instanceof FeatureColourChooser)
 404               {
 405                 FeatureColourChooser fc = (FeatureColourChooser) e
 406                         .getSource();
 407                 table.setValueAt(fc.getLastColour(), selectedRow, 1);
 408                 table.validate();
 409               }
 410               else
 411               {
 412                 // probably the color chooser!
 413                 table.setValueAt(new FeatureColour(colorChooser.getColor()),
 414                         selectedRow, 1);
 415                 table.validate();
 416                 me.updateFeatureRenderer(
 417                         ((FeatureTableModel) table.getModel()).getData(),
 418                         false);
 419               }
 420             }
 421           }
 422
 423         });
 424       }
 425     }
 426     JMenuItem selCols = new JMenuItem(
 427             MessageManager.getString("label.select_columns_containing"));
 428     selCols.addActionListener(new ActionListener()
 429     {
 430       @Override
 431       public void actionPerformed(ActionEvent arg0)
 432       {
 433         fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
 434                 false, type);
 435       }
 436     });
 437     JMenuItem clearCols = new JMenuItem(MessageManager
 438             .getString("label.select_columns_not_containing"));
 439     clearCols.addActionListener(new ActionListener()
 440     {
 441       @Override
 442       public void actionPerformed(ActionEvent arg0)
 443       {
 444         fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
 445                 false, type);
 446       }
 447     });
 448     JMenuItem hideCols = new JMenuItem(
 449             MessageManager.getString("label.hide_columns_containing"));
 450     hideCols.addActionListener(new ActionListener()
 451     {
 452       @Override
 453       public void actionPerformed(ActionEvent arg0)
 454       {
 455         fr.ap.alignFrame.hideFeatureColumns(type, true);
 456       }
 457     });
 458     JMenuItem hideOtherCols = new JMenuItem(
 459             MessageManager.getString("label.hide_columns_not_containing"));
 460     hideOtherCols.addActionListener(new ActionListener()
 461     {
 462       @Override
 463       public void actionPerformed(ActionEvent arg0)
 464       {
 465         fr.ap.alignFrame.hideFeatureColumns(type, false);
 466       }
 467     });
 468     men.add(selCols);
 469     men.add(clearCols);
 470     men.add(hideCols);
 471     men.add(hideOtherCols);
 472     men.show(table, x, y);
 473   }
 474
 475   /**
 476    * true when Feature Settings are updating from feature renderer
 477    */
 478   private boolean handlingUpdate = false;
 479
 480   /**
 481    * contains a float[3] for each feature type string. created by setTableData
 482    */
 483   Map<String, float[]> typeWidth = null;
 484
 485   @Override
 486   synchronized public void discoverAllFeatureData()
 487   {
 488     Vector<String> allFeatures = new Vector<String>();
 489     Vector<String> allGroups = new Vector<String>();
 490     SequenceFeature[] tmpfeatures;
 491     String group;
 492     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 493     {
 494       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 495               .getSequenceFeatures();
 496       if (tmpfeatures == null)
 497       {
 498         continue;
 499       }
 500
 501       int index = 0;
 502       while (index < tmpfeatures.length)
 503       {
 504         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 505         {
 506           index++;
 507           continue;
 508         }
 509
 510         if (tmpfeatures[index].getFeatureGroup() != null)
 511         {
 512           group = tmpfeatures[index].featureGroup;
 513           if (!allGroups.contains(group))
 514           {
 515             allGroups.addElement(group);
 516             checkGroupState(group);
 517           }
 518         }
 519
 520         if (!allFeatures.contains(tmpfeatures[index].getType()))
 521         {
 522           allFeatures.addElement(tmpfeatures[index].getType());
 523         }
 524         index++;
 525       }
 526     }
 527
 528     resetTable(null);
 529
 530     validate();
 531   }
 532
 533   /**
 534    * Synchronise gui group list and check visibility of group
 535    *
 536    * @param group
 537    * @return true if group is visible
 538    */
 539   private boolean checkGroupState(String group)
 540   {
 541     boolean visible = fr.checkGroupVisibility(group, true);
 542
 543     for (int g = 0; g < groupPanel.getComponentCount(); g++)
 544     {
 545       if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
 546       {
 547         ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
 548         return visible;
 549       }
 550     }
 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     Set<String> foundGroups = new HashSet<String>();
 591
 592     // Find out which features should be visible depending on which groups
 593     // are selected / deselected
 594     // and recompute average width ordering
 595     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 596     {
 597
 598       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 599               .getSequenceFeatures();
 600       if (tmpfeatures == null)
 601       {
 602         continue;
 603       }
 604
 605       int index = 0;
 606       while (index < tmpfeatures.length)
 607       {
 608         group = tmpfeatures[index].featureGroup;
 609         foundGroups.add(group);
 610
 611         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 612         {
 613           index++;
 614           continue;
 615         }
 616
 617         if (group == null || checkGroupState(group))
 618         {
 619           type = tmpfeatures[index].getType();
 620           if (!visibleChecks.contains(type))
 621           {
 622             visibleChecks.addElement(type);
 623           }
 624         }
 625         if (!typeWidth.containsKey(tmpfeatures[index].getType()))
 626         {
 627           typeWidth.put(tmpfeatures[index].getType(),
 628                   avWidth = new float[3]);
 629         }
 630         else
 631         {
 632           avWidth = typeWidth.get(tmpfeatures[index].getType());
 633         }
 634         avWidth[0]++;
 635         if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
 636         {
 637           avWidth[1] += 1 + tmpfeatures[index].getBegin()
 638                   - tmpfeatures[index].getEnd();
 639         }
 640         else
 641         {
 642           avWidth[1] += 1 + tmpfeatures[index].getEnd()
 643                   - tmpfeatures[index].getBegin();
 644         }
 645         index++;
 646       }
 647     }
 648
 649     int fSize = visibleChecks.size();
 650     Object[][] data = new Object[fSize][3];
 651     int dataIndex = 0;
 652
 653     if (fr.hasRenderOrder())
 654     {
 655       if (!handlingUpdate)
 656       {
 657         fr.findAllFeatures(groupChanged != null); // prod to update
 658         // colourschemes. but don't
 659         // affect display
 660         // First add the checks in the previous render order,
 661         // in case the window has been closed and reopened
 662       }
 663       List<String> frl = fr.getRenderOrder();
 664       for (int ro = frl.size() - 1; ro > -1; ro--)
 665       {
 666         type = frl.get(ro);
 667
 668         if (!visibleChecks.contains(type))
 669         {
 670           continue;
 671         }
 672
 673         data[dataIndex][0] = type;
 674         data[dataIndex][1] = fr.getFeatureStyle(type);
 675         data[dataIndex][2] = new Boolean(
 676                 af.getViewport().getFeaturesDisplayed().isVisible(type));
 677         dataIndex++;
 678         visibleChecks.removeElement(type);
 679       }
 680     }
 681
 682     fSize = visibleChecks.size();
 683     for (int i = 0; i < fSize; i++)
 684     {
 685       // These must be extra features belonging to the group
 686       // which was just selected
 687       type = visibleChecks.elementAt(i).toString();
 688       data[dataIndex][0] = type;
 689
 690       data[dataIndex][1] = fr.getFeatureStyle(type);
 691       if (data[dataIndex][1] == null)
 692       {
 693         // "Colour has been updated in another view!!"
 694         fr.clearRenderOrder();
 695         return;
 696       }
 697
 698       data[dataIndex][2] = new Boolean(true);
 699       dataIndex++;
 700     }
 701
 702     if (originalData == null)
 703     {
 704       originalData = new Object[data.length][3];
 705       for (int i = 0; i < data.length; i++)
 706       {
 707         System.arraycopy(data[i], 0, originalData[i], 0, 3);
 708       }
 709     }
 710     else
 711     {
 712       updateOriginalData(data);
 713     }
 714
 715     table.setModel(new FeatureTableModel(data));
 716     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 717
 718     groupPanel.setLayout(
 719             new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4));
 720     pruneGroups(foundGroups);
 721     groupPanel.validate();
 722
 723     updateFeatureRenderer(data, groupChanged != null);
 724     resettingTable = false;
 725   }
 726
 727   /**
 728    * Updates 'originalData' (used for restore on Cancel) if we detect that
 729    * changes have been made outwith this dialog
 730    * <ul>
 731    * <li>a new feature type added (and made visible)</li>
 732    * <li>a feature colour changed (in the Amend Features dialog)</li>
 733    * </ul>
 734    *
 735    * @param foundData
 736    */
 737   protected void updateOriginalData(Object[][] foundData)
 738   {
 739     // todo LinkedHashMap instead of Object[][] would be nice
 740
 741     Object[][] currentData = ((FeatureTableModel) table.getModel())
 742             .getData();
 743     for (Object[] row : foundData)
 744     {
 745       String type = (String) row[0];
 746       boolean found = false;
 747       for (Object[] current : currentData)
 748       {
 749         if (type.equals(current[0]))
 750         {
 751           found = true;
 752           /*
 753            * currently dependent on object equality here;
 754            * really need an equals method on FeatureColour
 755            */
 756           if (!row[1].equals(current[1]))
 757           {
 758             /*
 759              * feature colour has changed externally - update originalData
 760              */
 761             for (Object[] original : originalData)
 762             {
 763               if (type.equals(original[0]))
 764               {
 765                 original[1] = row[1];
 766                 break;
 767               }
 768             }
 769           }
 770           break;
 771         }
 772       }
 773       if (!found)
 774       {
 775         /*
 776          * new feature detected - add to original data (on top)
 777          */
 778         Object[][] newData = new Object[originalData.length + 1][3];
 779         for (int i = 0; i < originalData.length; i++)
 780         {
 781           System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3);
 782         }
 783         newData[0] = row;
 784         originalData = newData;
 785       }
 786     }
 787   }
 788
 789   /**
 790    * Remove from the groups panel any checkboxes for groups that are not in the
 791    * foundGroups set. This enables removing a group from the display when the
 792    * last feature in that group is deleted.
 793    *
 794    * @param foundGroups
 795    */
 796   protected void pruneGroups(Set<String> foundGroups)
 797   {
 798     for (int g = 0; g < groupPanel.getComponentCount(); g++)
 799     {
 800       JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g);
 801       if (!foundGroups.contains(checkbox.getText()))
 802       {
 803         groupPanel.remove(checkbox);
 804       }
 805     }
 806   }
 807
 808   /**
 809    * reorder data based on the featureRenderers global priority list.
 810    *
 811    * @param data
 812    */
 813   private void ensureOrder(Object[][] data)
 814   {
 815     boolean sort = false;
 816     float[] order = new float[data.length];
 817     for (int i = 0; i < order.length; i++)
 818     {
 819       order[i] = fr.getOrder(data[i][0].toString());
 820       if (order[i] < 0)
 821       {
 822         order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
 823       }
 824       if (i > 1)
 825       {
 826         sort = sort || order[i - 1] > order[i];
 827       }
 828     }
 829     if (sort)
 830     {
 831       jalview.util.QuickSort.sort(order, data);
 832     }
 833   }
 834
 835   void load()
 836   {
 837     JalviewFileChooser chooser = new JalviewFileChooser("fc",
 838             "Sequence Feature Colours");
 839     chooser.setFileView(new JalviewFileView());
 840     chooser.setDialogTitle(
 841             MessageManager.getString("label.load_feature_colours"));
 842     chooser.setToolTipText(MessageManager.getString("action.load"));
 843
 844     int value = chooser.showOpenDialog(this);
 845
 846     if (value == JalviewFileChooser.APPROVE_OPTION)
 847     {
 848       File file = chooser.getSelectedFile();
 849
 850       try
 851       {
 852         InputStreamReader in = new InputStreamReader(
 853                 new FileInputStream(file), "UTF-8");
 854
 855         JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 856
 857         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
 858         {
 859           String name;
 860           jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
 861           if (newcol.hasMax())
 862           {
 863             Color mincol = null, maxcol = null;
 864             try
 865             {
 866               mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
 867               maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
 868
 869             } catch (Exception e)
 870             {
 871               Cache.log.warn("Couldn't parse out graduated feature color.",
 872                       e);
 873             }
 874             FeatureColourI gcol = new FeatureColour(mincol, maxcol,
 875                     newcol.getMin(), newcol.getMax());
 876             if (newcol.hasAutoScale())
 877             {
 878               gcol.setAutoScaled(newcol.getAutoScale());
 879             }
 880             if (newcol.hasColourByLabel())
 881             {
 882               gcol.setColourByLabel(newcol.getColourByLabel());
 883             }
 884             if (newcol.hasThreshold())
 885             {
 886               gcol.setThreshold(newcol.getThreshold());
 887             }
 888             if (newcol.getThreshType().length() > 0)
 889             {
 890               String ttyp = newcol.getThreshType();
 891               if (ttyp.equalsIgnoreCase("ABOVE"))
 892               {
 893                 gcol.setAboveThreshold(true);
 894               }
 895               if (ttyp.equalsIgnoreCase("BELOW"))
 896               {
 897                 gcol.setBelowThreshold(true);
 898               }
 899             }
 900             fr.setColour(name = newcol.getName(), gcol);
 901           }
 902           else
 903           {
 904             Color color = new Color(
 905                     Integer.parseInt(jucs.getColour(i).getRGB(), 16));
 906             fr.setColour(name = jucs.getColour(i).getName(),
 907                     new FeatureColour(color));
 908           }
 909           fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
 910         }
 911         if (table != null)
 912         {
 913           resetTable(null);
 914           Object[][] data = ((FeatureTableModel) table.getModel())
 915                   .getData();
 916           ensureOrder(data);
 917           updateFeatureRenderer(data, false);
 918           table.repaint();
 919         }
 920       } catch (Exception ex)
 921       {
 922         System.out.println("Error loading User Colour File\n" + ex);
 923       }
 924     }
 925   }
 926
 927   void save()
 928   {
 929     JalviewFileChooser chooser = new JalviewFileChooser("fc",
 930             "Sequence Feature Colours");
 931     chooser.setFileView(new JalviewFileView());
 932     chooser.setDialogTitle(
 933             MessageManager.getString("label.save_feature_colours"));
 934     chooser.setToolTipText(MessageManager.getString("action.save"));
 935
 936     int value = chooser.showSaveDialog(this);
 937
 938     if (value == JalviewFileChooser.APPROVE_OPTION)
 939     {
 940       String choice = chooser.getSelectedFile().getPath();
 941       jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 942       ucs.setSchemeName("Sequence Features");
 943       try
 944       {
 945         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 946                 new FileOutputStream(choice), "UTF-8"));
 947
 948         Set<String> fr_colours = fr.getAllFeatureColours();
 949         Iterator<String> e = fr_colours.iterator();
 950         float[] sortOrder = new float[fr_colours.size()];
 951         String[] sortTypes = new String[fr_colours.size()];
 952         int i = 0;
 953         while (e.hasNext())
 954         {
 955           sortTypes[i] = e.next();
 956           sortOrder[i] = fr.getOrder(sortTypes[i]);
 957           i++;
 958         }
 959         QuickSort.sort(sortOrder, sortTypes);
 960         sortOrder = null;
 961         for (i = 0; i < sortTypes.length; i++)
 962         {
 963           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 964           col.setName(sortTypes[i]);
 965           FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
 966           if (fcol.isSimpleColour())
 967           {
 968             col.setRGB(Format.getHexString(fcol.getColour()));
 969           }
 970           else
 971           {
 972             col.setRGB(Format.getHexString(fcol.getMaxColour()));
 973             col.setMin(fcol.getMin());
 974             col.setMax(fcol.getMax());
 975             col.setMinRGB(
 976                     jalview.util.Format.getHexString(fcol.getMinColour()));
 977             col.setAutoScale(fcol.isAutoScaled());
 978             col.setThreshold(fcol.getThreshold());
 979             col.setColourByLabel(fcol.isColourByLabel());
 980             col.setThreshType(fcol.isAboveThreshold() ? "ABOVE"
 981                     : (fcol.isBelowThreshold() ? "BELOW" : "NONE"));
 982           }
 983           ucs.addColour(col);
 984         }
 985         ucs.marshal(out);
 986         out.close();
 987       } catch (Exception ex)
 988       {
 989         ex.printStackTrace();
 990       }
 991     }
 992   }
 993
 994   public void invertSelection()
 995   {
 996     for (int i = 0; i < table.getRowCount(); i++)
 997     {
 998       Boolean value = (Boolean) table.getValueAt(i, 2);
 999
1000       table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
1001     }
1002   }
1003
1004   public void orderByAvWidth()
1005   {
1006     if (table == null || table.getModel() == null)
1007     {
1008       return;
1009     }
1010     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
1011     float[] width = new float[data.length];
1012     float[] awidth;
1013     float max = 0;
1014     int num = 0;
1015     for (int i = 0; i < data.length; i++)
1016     {
1017       awidth = typeWidth.get(data[i][0]);
1018       if (awidth[0] > 0)
1019       {
1020         width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
1021         // weight - but have to make per
1022         // sequence, too (awidth[2])
1023         // if (width[i]==1) // hack to distinguish single width sequences.
1024         num++;
1025       }
1026       else
1027       {
1028         width[i] = 0;
1029       }
1030       if (max < width[i])
1031       {
1032         max = width[i];
1033       }
1034     }
1035     boolean sort = false;
1036     for (int i = 0; i < width.length; i++)
1037     {
1038       // awidth = (float[]) typeWidth.get(data[i][0]);
1039       if (width[i] == 0)
1040       {
1041         width[i] = fr.getOrder(data[i][0].toString());
1042         if (width[i] < 0)
1043         {
1044           width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
1045         }
1046       }
1047       else
1048       {
1049         width[i] /= max; // normalize
1050         fr.setOrder(data[i][0].toString(), width[i]); // store for later
1051       }
1052       if (i > 0)
1053       {
1054         sort = sort || width[i - 1] > width[i];
1055       }
1056     }
1057     if (sort)
1058     {
1059       jalview.util.QuickSort.sort(width, data);
1060       // update global priority order
1061     }
1062
1063     updateFeatureRenderer(data, false);
1064     table.repaint();
1065   }
1066
1067   public void close()
1068   {
1069     try
1070     {
1071       frame.setClosed(true);
1072     } catch (Exception exe)
1073     {
1074     }
1075
1076   }
1077
1078   public void updateFeatureRenderer(Object[][] data)
1079   {
1080     updateFeatureRenderer(data, true);
1081   }
1082
1083   /**
1084    * Update the priority order of features; only repaint if this changed the
1085    * order of visible features
1086    *
1087    * @param data
1088    * @param visibleNew
1089    */
1090   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
1091   {
1092     if (fr.setFeaturePriority(data, visibleNew))
1093     {
1094       af.alignPanel.paintAlignment(true);
1095     }
1096   }
1097
1098   int selectedRow = -1;
1099
1100   JTabbedPane tabbedPane = new JTabbedPane();
1101
1102   BorderLayout borderLayout1 = new BorderLayout();
1103
1104   BorderLayout borderLayout2 = new BorderLayout();
1105
1106   BorderLayout borderLayout3 = new BorderLayout();
1107
1108   JPanel bigPanel = new JPanel();
1109
1110   BorderLayout borderLayout4 = new BorderLayout();
1111
1112   JButton invert = new JButton();
1113
1114   JPanel buttonPanel = new JPanel();
1115
1116   JButton cancel = new JButton();
1117
1118   JButton ok = new JButton();
1119
1120   JButton loadColours = new JButton();
1121
1122   JButton saveColours = new JButton();
1123
1124   JPanel dasButtonPanel = new JPanel();
1125
1126   JButton fetchDAS = new JButton();
1127
1128   JButton saveDAS = new JButton();
1129
1130   JButton cancelDAS = new JButton();
1131
1132   JButton optimizeOrder = new JButton();
1133
1134   JButton sortByScore = new JButton();
1135
1136   JButton sortByDens = new JButton();
1137
1138   JButton help = new JButton();
1139
1140   JPanel transbuttons = new JPanel(new GridLayout(5, 1));
1141
1142   private void jbInit() throws Exception
1143   {
1144     this.setLayout(borderLayout1);
1145     settingsPane.setLayout(borderLayout2);
1146     dasSettingsPane.setLayout(borderLayout3);
1147     bigPanel.setLayout(borderLayout4);
1148
1149     groupPanel = new JPanel();
1150     bigPanel.add(groupPanel, BorderLayout.NORTH);
1151
1152     invert.setFont(JvSwingUtils.getLabelFont());
1153     invert.setText(MessageManager.getString("label.invert_selection"));
1154     invert.addActionListener(new ActionListener()
1155     {
1156       @Override
1157       public void actionPerformed(ActionEvent e)
1158       {
1159         invertSelection();
1160       }
1161     });
1162     optimizeOrder.setFont(JvSwingUtils.getLabelFont());
1163     optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
1164     optimizeOrder.addActionListener(new ActionListener()
1165     {
1166       @Override
1167       public void actionPerformed(ActionEvent e)
1168       {
1169         orderByAvWidth();
1170       }
1171     });
1172     sortByScore.setFont(JvSwingUtils.getLabelFont());
1173     sortByScore
1174             .setText(MessageManager.getString("label.seq_sort_by_score"));
1175     sortByScore.addActionListener(new ActionListener()
1176     {
1177       @Override
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         af.avc.sortAlignmentByFeatureScore(null);
1181       }
1182     });
1183     sortByDens.setFont(JvSwingUtils.getLabelFont());
1184     sortByDens.setText(
1185             MessageManager.getString("label.sequence_sort_by_density"));
1186     sortByDens.addActionListener(new ActionListener()
1187     {
1188       @Override
1189       public void actionPerformed(ActionEvent e)
1190       {
1191         af.avc.sortAlignmentByFeatureDensity(null);
1192       }
1193     });
1194     help.setFont(JvSwingUtils.getLabelFont());
1195     help.setText(MessageManager.getString("action.help"));
1196     help.addActionListener(new ActionListener()
1197     {
1198       @Override
1199       public void actionPerformed(ActionEvent e)
1200       {
1201         try
1202         {
1203           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1204         } catch (HelpSetException e1)
1205         {
1206           e1.printStackTrace();
1207         }
1208       }
1209     });
1210     help.setFont(JvSwingUtils.getLabelFont());
1211     help.setText(MessageManager.getString("action.help"));
1212     help.addActionListener(new ActionListener()
1213     {
1214       @Override
1215       public void actionPerformed(ActionEvent e)
1216       {
1217         try
1218         {
1219           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1220         } catch (HelpSetException e1)
1221         {
1222           e1.printStackTrace();
1223         }
1224       }
1225     });
1226     cancel.setFont(JvSwingUtils.getLabelFont());
1227     cancel.setText(MessageManager.getString("action.cancel"));
1228     cancel.addActionListener(new ActionListener()
1229     {
1230       @Override
1231       public void actionPerformed(ActionEvent e)
1232       {
1233         fr.setTransparency(originalTransparency);
1234         updateFeatureRenderer(originalData);
1235         close();
1236       }
1237     });
1238     ok.setFont(JvSwingUtils.getLabelFont());
1239     ok.setText(MessageManager.getString("action.ok"));
1240     ok.addActionListener(new ActionListener()
1241     {
1242       @Override
1243       public void actionPerformed(ActionEvent e)
1244       {
1245         close();
1246       }
1247     });
1248     loadColours.setFont(JvSwingUtils.getLabelFont());
1249     loadColours.setText(MessageManager.getString("label.load_colours"));
1250     loadColours.addActionListener(new ActionListener()
1251     {
1252       @Override
1253       public void actionPerformed(ActionEvent e)
1254       {
1255         load();
1256       }
1257     });
1258     saveColours.setFont(JvSwingUtils.getLabelFont());
1259     saveColours.setText(MessageManager.getString("label.save_colours"));
1260     saveColours.addActionListener(new ActionListener()
1261     {
1262       @Override
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         save();
1266       }
1267     });
1268     transparency.addChangeListener(new ChangeListener()
1269     {
1270       @Override
1271       public void stateChanged(ChangeEvent evt)
1272       {
1273         fr.setTransparency((100 - transparency.getValue()) / 100f);
1274         af.alignPanel.paintAlignment(true);
1275       }
1276     });
1277
1278     transparency.setMaximum(70);
1279     transparency.setToolTipText(
1280             MessageManager.getString("label.transparency_tip"));
1281     fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
1282     fetchDAS.addActionListener(new ActionListener()
1283     {
1284       @Override
1285       public void actionPerformed(ActionEvent e)
1286       {
1287         fetchDAS_actionPerformed(e);
1288       }
1289     });
1290     saveDAS.setText(MessageManager.getString("action.save_as_default"));
1291     saveDAS.addActionListener(new ActionListener()
1292     {
1293       @Override
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         saveDAS_actionPerformed(e);
1297       }
1298     });
1299     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
1300     dasSettingsPane.setBorder(null);
1301     cancelDAS.setEnabled(false);
1302     cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
1303     cancelDAS.addActionListener(new ActionListener()
1304     {
1305       @Override
1306       public void actionPerformed(ActionEvent e)
1307       {
1308         cancelDAS_actionPerformed(e);
1309       }
1310     });
1311     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
1312     tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
1313             settingsPane);
1314     tabbedPane.addTab(MessageManager.getString("label.das_settings"),
1315             dasSettingsPane);
1316     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
1317     transbuttons.add(optimizeOrder);
1318     transbuttons.add(invert);
1319     transbuttons.add(sortByScore);
1320     transbuttons.add(sortByDens);
1321     transbuttons.add(help);
1322     JPanel sliderPanel = new JPanel();
1323     sliderPanel.add(transparency);
1324     transPanel.add(transparency);
1325     transPanel.add(transbuttons);
1326     buttonPanel.add(ok);
1327     buttonPanel.add(cancel);
1328     buttonPanel.add(loadColours);
1329     buttonPanel.add(saveColours);
1330     bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
1331     dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
1332     dasButtonPanel.add(fetchDAS);
1333     dasButtonPanel.add(cancelDAS);
1334     dasButtonPanel.add(saveDAS);
1335     settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
1336     settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
1337   }
1338
1339   public void fetchDAS_actionPerformed(ActionEvent e)
1340   {
1341     fetchDAS.setEnabled(false);
1342     cancelDAS.setEnabled(true);
1343     dassourceBrowser.setGuiEnabled(false);
1344     Vector<jalviewSourceI> selectedSources = dassourceBrowser
1345             .getSelectedSources();
1346     doDasFeatureFetch(selectedSources, true, true);
1347   }
1348
1349   /**
1350    * get the features from selectedSources for all or the current selection
1351    *
1352    * @param selectedSources
1353    * @param checkDbRefs
1354    * @param promptFetchDbRefs
1355    */
1356   private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
1357           boolean checkDbRefs, boolean promptFetchDbRefs)
1358   {
1359     SequenceI[] dataset, seqs;
1360     int iSize;
1361     AlignmentViewport vp = af.getViewport();
1362     if (vp.getSelectionGroup() != null
1363             && vp.getSelectionGroup().getSize() > 0)
1364     {
1365       iSize = vp.getSelectionGroup().getSize();
1366       dataset = new SequenceI[iSize];
1367       seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
1368     }
1369     else
1370     {
1371       iSize = vp.getAlignment().getHeight();
1372       seqs = vp.getAlignment().getSequencesArray();
1373     }
1374
1375     dataset = new SequenceI[iSize];
1376     for (int i = 0; i < iSize; i++)
1377     {
1378       dataset[i] = seqs[i].getDatasetSequence();
1379     }
1380
1381     cancelDAS.setEnabled(true);
1382     dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
1383             this, selectedSources, checkDbRefs, promptFetchDbRefs);
1384     af.getViewport().setShowSequenceFeatures(true);
1385     af.showSeqFeatures.setSelected(true);
1386   }
1387
1388   /**
1389    * blocking call to initialise the das source browser
1390    */
1391   public void initDasSources()
1392   {
1393     dassourceBrowser.initDasSources();
1394   }
1395
1396   /**
1397    * examine the current list of das sources and return any matching the given
1398    * nicknames in sources
1399    *
1400    * @param sources
1401    *          Vector of Strings to resolve to DAS source nicknames.
1402    * @return sources that are present in source list.
1403    */
1404   public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
1405   {
1406     return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
1407   }
1408
1409   /**
1410    * get currently selected das sources. ensure you have called initDasSources
1411    * before calling this.
1412    *
1413    * @return vector of selected das source nicknames
1414    */
1415   public Vector<jalviewSourceI> getSelectedSources()
1416   {
1417     return dassourceBrowser.getSelectedSources();
1418   }
1419
1420   /**
1421    * properly initialise DAS fetcher and then initiate a new thread to fetch
1422    * features from the named sources (rather than any turned on by default)
1423    *
1424    * @param sources
1425    * @param block
1426    *          if true then runs in same thread, otherwise passes to the Swing
1427    *          executor
1428    */
1429   public void fetchDasFeatures(Vector<String> sources, boolean block)
1430   {
1431     initDasSources();
1432     List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
1433             .resolveSourceNicknames(sources);
1434     if (resolved.size() == 0)
1435     {
1436       resolved = dassourceBrowser.getSelectedSources();
1437     }
1438     if (resolved.size() > 0)
1439     {
1440       final List<jalviewSourceI> dassources = resolved;
1441       fetchDAS.setEnabled(false);
1442       // cancelDAS.setEnabled(true); doDasFetch does this.
1443       Runnable fetcher = new Runnable()
1444       {
1445
1446         @Override
1447         public void run()
1448         {
1449           doDasFeatureFetch(dassources, true, false);
1450
1451         }
1452       };
1453       if (block)
1454       {
1455         fetcher.run();
1456       }
1457       else
1458       {
1459         SwingUtilities.invokeLater(fetcher);
1460       }
1461     }
1462   }
1463
1464   public void saveDAS_actionPerformed(ActionEvent e)
1465   {
1466     dassourceBrowser
1467             .saveProperties(jalview.bin.Cache.applicationProperties);
1468   }
1469
1470   public void complete()
1471   {
1472     fetchDAS.setEnabled(true);
1473     cancelDAS.setEnabled(false);
1474     dassourceBrowser.setGuiEnabled(true);
1475
1476   }
1477
1478   public void cancelDAS_actionPerformed(ActionEvent e)
1479   {
1480     if (dasFeatureFetcher != null)
1481     {
1482       dasFeatureFetcher.cancel();
1483     }
1484     complete();
1485   }
1486
1487   public void noDasSourceActive()
1488   {
1489     complete();
1490     JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
1491             MessageManager.getString("label.no_das_sources_selected_warn"),
1492             MessageManager.getString("label.no_das_sources_selected_title"),
1493             JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
1494   }
1495
1496   // ///////////////////////////////////////////////////////////////////////
1497   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
1498   // ///////////////////////////////////////////////////////////////////////
1499   class FeatureTableModel extends AbstractTableModel
1500   {
1501     FeatureTableModel(Object[][] data)
1502     {
1503       this.data = data;
1504     }
1505
1506     private String[] columnNames = {
1507         MessageManager.getString("label.feature_type"),
1508         MessageManager.getString("action.colour"),
1509         MessageManager.getString("label.display") };
1510
1511     private Object[][] data;
1512
1513     public Object[][] getData()
1514     {
1515       return data;
1516     }
1517
1518     public void setData(Object[][] data)
1519     {
1520       this.data = data;
1521     }
1522
1523     @Override
1524     public int getColumnCount()
1525     {
1526       return columnNames.length;
1527     }
1528
1529     public Object[] getRow(int row)
1530     {
1531       return data[row];
1532     }
1533
1534     @Override
1535     public int getRowCount()
1536     {
1537       return data.length;
1538     }
1539
1540     @Override
1541     public String getColumnName(int col)
1542     {
1543       return columnNames[col];
1544     }
1545
1546     @Override
1547     public Object getValueAt(int row, int col)
1548     {
1549       return data[row][col];
1550     }
1551
1552     @Override
1553     public Class getColumnClass(int c)
1554     {
1555       return getValueAt(0, c).getClass();
1556     }
1557
1558     @Override
1559     public boolean isCellEditable(int row, int col)
1560     {
1561       return col == 0 ? false : true;
1562     }
1563
1564     @Override
1565     public void setValueAt(Object value, int row, int col)
1566     {
1567       data[row][col] = value;
1568       fireTableCellUpdated(row, col);
1569       updateFeatureRenderer(data);
1570     }
1571
1572   }
1573
1574   class ColorRenderer extends JLabel implements TableCellRenderer
1575   {
1576     javax.swing.border.Border unselectedBorder = null;
1577
1578     javax.swing.border.Border selectedBorder = null;
1579
1580     final String baseTT = "Click to edit, right/apple click for menu.";
1581
1582     public ColorRenderer()
1583     {
1584       setOpaque(true); // MUST do this for background to show up.
1585       setHorizontalTextPosition(SwingConstants.CENTER);
1586       setVerticalTextPosition(SwingConstants.CENTER);
1587     }
1588
1589     @Override
1590     public Component getTableCellRendererComponent(JTable tbl, Object color,
1591             boolean isSelected, boolean hasFocus, int row, int column)
1592     {
1593       FeatureColourI cellColour = (FeatureColourI) color;
1594       // JLabel comp = new JLabel();
1595       // comp.
1596       setOpaque(true);
1597       // comp.
1598       // setBounds(getBounds());
1599       Color newColor;
1600       setToolTipText(baseTT);
1601       setBackground(tbl.getBackground());
1602       if (!cellColour.isSimpleColour())
1603       {
1604         Rectangle cr = tbl.getCellRect(row, column, false);
1605         FeatureSettings.renderGraduatedColor(this, cellColour,
1606                 (int) cr.getWidth(), (int) cr.getHeight());
1607
1608       }
1609       else
1610       {
1611         this.setText("");
1612         this.setIcon(null);
1613         newColor = cellColour.getColour();
1614         setBackground(newColor);
1615       }
1616       if (isSelected)
1617       {
1618         if (selectedBorder == null)
1619         {
1620           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1621                   tbl.getSelectionBackground());
1622         }
1623         setBorder(selectedBorder);
1624       }
1625       else
1626       {
1627         if (unselectedBorder == null)
1628         {
1629           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1630                   tbl.getBackground());
1631         }
1632         setBorder(unselectedBorder);
1633       }
1634
1635       return this;
1636     }
1637   }
1638
1639   /**
1640    * update comp using rendering settings from gcol
1641    *
1642    * @param comp
1643    * @param gcol
1644    */
1645   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
1646   {
1647     int w = comp.getWidth(), h = comp.getHeight();
1648     if (w < 20)
1649     {
1650       w = (int) comp.getPreferredSize().getWidth();
1651       h = (int) comp.getPreferredSize().getHeight();
1652       if (w < 20)
1653       {
1654         w = 80;
1655         h = 12;
1656       }
1657     }
1658     renderGraduatedColor(comp, gcol, w, h);
1659   }
1660
1661   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
1662           int w, int h)
1663   {
1664     boolean thr = false;
1665     String tt = "";
1666     String tx = "";
1667     if (gcol.isAboveThreshold())
1668     {
1669       thr = true;
1670       tx += ">";
1671       tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
1672     }
1673     if (gcol.isBelowThreshold())
1674     {
1675       thr = true;
1676       tx += "<";
1677       tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
1678     }
1679     if (gcol.isColourByLabel())
1680     {
1681       tt = "Coloured by label text. " + tt;
1682       if (thr)
1683       {
1684         tx += " ";
1685       }
1686       tx += "Label";
1687       comp.setIcon(null);
1688     }
1689     else
1690     {
1691       Color newColor = gcol.getMaxColour();
1692       comp.setBackground(newColor);
1693       // System.err.println("Width is " + w / 2);
1694       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
1695       comp.setIcon(ficon);
1696       // tt+="RGB value: Max (" + newColor.getRed() + ", "
1697       // + newColor.getGreen() + ", " + newColor.getBlue()
1698       // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
1699       // + ", " + minCol.getBlue() + ")");
1700     }
1701     comp.setHorizontalAlignment(SwingConstants.CENTER);
1702     comp.setText(tx);
1703     if (tt.length() > 0)
1704     {
1705       if (comp.getToolTipText() == null)
1706       {
1707         comp.setToolTipText(tt);
1708       }
1709       else
1710       {
1711         comp.setToolTipText(tt + " " + comp.getToolTipText());
1712       }
1713     }
1714   }
1715 }
1716
1717 class FeatureIcon implements Icon
1718 {
1719   FeatureColourI gcol;
1720
1721   Color backg;
1722
1723   boolean midspace = false;
1724
1725   int width = 50, height = 20;
1726
1727   int s1, e1; // start and end of midpoint band for thresholded symbol
1728
1729   Color mpcolour = Color.white;
1730
1731   FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
1732   {
1733     gcol = gfc;
1734     backg = bg;
1735     width = w;
1736     height = h;
1737     midspace = mspace;
1738     if (midspace)
1739     {
1740       s1 = width / 3;
1741       e1 = s1 * 2;
1742     }
1743     else
1744     {
1745       s1 = width / 2;
1746       e1 = s1;
1747     }
1748   }
1749
1750   @Override
1751   public int getIconWidth()
1752   {
1753     return width;
1754   }
1755
1756   @Override
1757   public int getIconHeight()
1758   {
1759     return height;
1760   }
1761
1762   @Override
1763   public void paintIcon(Component c, Graphics g, int x, int y)
1764   {
1765
1766     if (gcol.isColourByLabel())
1767     {
1768       g.setColor(backg);
1769       g.fillRect(0, 0, width, height);
1770       // need an icon here.
1771       g.setColor(gcol.getMaxColour());
1772
1773       g.setFont(new Font("Verdana", Font.PLAIN, 9));
1774
1775       // g.setFont(g.getFont().deriveFont(
1776       // AffineTransform.getScaleInstance(
1777       // width/g.getFontMetrics().stringWidth("Label"),
1778       // height/g.getFontMetrics().getHeight())));
1779
1780       g.drawString(MessageManager.getString("label.label"), 0, 0);
1781
1782     }
1783     else
1784     {
1785       Color minCol = gcol.getMinColour();
1786       g.setColor(minCol);
1787       g.fillRect(0, 0, s1, height);
1788       if (midspace)
1789       {
1790         g.setColor(Color.white);
1791         g.fillRect(s1, 0, e1 - s1, height);
1792       }
1793       g.setColor(gcol.getMaxColour());
1794       g.fillRect(0, e1, width - e1, height);
1795     }
1796   }
1797 }
1798
1799 class ColorEditor extends AbstractCellEditor
1800         implements TableCellEditor, ActionListener
1801 {
1802   FeatureSettings me;
1803
1804   FeatureColourI currentColor;
1805
1806   FeatureColourChooser chooser;
1807
1808   String type;
1809
1810   JButton button;
1811
1812   JColorChooser colorChooser;
1813
1814   JDialog dialog;
1815
1816   protected static final String EDIT = "edit";
1817
1818   int selectedRow = 0;
1819
1820   public ColorEditor(FeatureSettings me)
1821   {
1822     this.me = me;
1823     // Set up the editor (from the table's point of view),
1824     // which is a button.
1825     // This button brings up the color chooser dialog,
1826     // which is the editor from the user's point of view.
1827     button = new JButton();
1828     button.setActionCommand(EDIT);
1829     button.addActionListener(this);
1830     button.setBorderPainted(false);
1831     // Set up the dialog that the button brings up.
1832     colorChooser = new JColorChooser();
1833     dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal
1834             colorChooser, this, // OK button handler
1835             null); // no CANCEL button handler
1836   }
1837
1838   /**
1839    * Handles events from the editor button and from the dialog's OK button.
1840    */
1841   @Override
1842   public void actionPerformed(ActionEvent e)
1843   {
1844
1845     if (EDIT.equals(e.getActionCommand()))
1846     {
1847       // The user has clicked the cell, so
1848       // bring up the dialog.
1849       if (currentColor.isSimpleColour())
1850       {
1851         // bring up simple color chooser
1852         button.setBackground(currentColor.getColour());
1853         colorChooser.setColor(currentColor.getColour());
1854         dialog.setVisible(true);
1855       }
1856       else
1857       {
1858         // bring up graduated chooser.
1859         chooser = new FeatureColourChooser(me.fr, type);
1860         chooser.setRequestFocusEnabled(true);
1861         chooser.requestFocus();
1862         chooser.addActionListener(this);
1863       }
1864       // Make the renderer reappear.
1865       fireEditingStopped();
1866
1867     }
1868     else
1869     { // User pressed dialog's "OK" button.
1870       if (currentColor.isSimpleColour())
1871       {
1872         currentColor = new FeatureColour(colorChooser.getColor());
1873       }
1874       else
1875       {
1876         currentColor = chooser.getLastColour();
1877       }
1878       me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
1879       fireEditingStopped();
1880       me.table.validate();
1881     }
1882   }
1883
1884   // Implement the one CellEditor method that AbstractCellEditor doesn't.
1885   @Override
1886   public Object getCellEditorValue()
1887   {
1888     return currentColor;
1889   }
1890
1891   // Implement the one method defined by TableCellEditor.
1892   @Override
1893   public Component getTableCellEditorComponent(JTable table, Object value,
1894           boolean isSelected, int row, int column)
1895   {
1896     currentColor = (FeatureColourI) value;
1897     this.selectedRow = row;
1898     type = me.table.getValueAt(row, 0).toString();
1899     button.setOpaque(true);
1900     button.setBackground(me.getBackground());
1901     if (!currentColor.isSimpleColour())
1902     {
1903       JLabel btn = new JLabel();
1904       btn.setSize(button.getSize());
1905       FeatureSettings.renderGraduatedColor(btn, currentColor);
1906       button.setBackground(btn.getBackground());
1907       button.setIcon(btn.getIcon());
1908       button.setText(btn.getText());
1909     }
1910     else
1911     {
1912       button.setText("");
1913       button.setIcon(null);
1914       button.setBackground(currentColor.getColour());
1915     }
1916     return button;
1917   }
1918 }