src/jalview/gui/FeatureSettings.java

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