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