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