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