src/jalview/gui/FeatureSettings.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.api.FeatureColourI;
  24 import jalview.api.FeatureSettingsControllerI;
  25 import jalview.bin.Cache;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.gui.Help.HelpId;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.schemabinding.version2.JalviewUserColours;
  32 import jalview.schemes.FeatureColour;
  33 import jalview.util.Format;
  34 import jalview.util.MessageManager;
  35 import jalview.util.Platform;
  36 import jalview.util.QuickSort;
  37 import jalview.viewmodel.AlignmentViewport;
  38 import jalview.ws.dbsources.das.api.jalviewSourceI;
  39
  40 import java.awt.BorderLayout;
  41 import java.awt.Color;
  42 import java.awt.Component;
  43 import java.awt.Font;
  44 import java.awt.Graphics;
  45 import java.awt.GridLayout;
  46 import java.awt.Rectangle;
  47 import java.awt.event.ActionEvent;
  48 import java.awt.event.ActionListener;
  49 import java.awt.event.ItemEvent;
  50 import java.awt.event.ItemListener;
  51 import java.awt.event.MouseAdapter;
  52 import java.awt.event.MouseEvent;
  53 import java.awt.event.MouseMotionAdapter;
  54 import java.beans.PropertyChangeEvent;
  55 import java.beans.PropertyChangeListener;
  56 import java.io.File;
  57 import java.io.FileInputStream;
  58 import java.io.FileOutputStream;
  59 import java.io.InputStreamReader;
  60 import java.io.OutputStreamWriter;
  61 import java.io.PrintWriter;
  62 import java.util.Arrays;
  63 import java.util.Hashtable;
  64 import java.util.Iterator;
  65 import java.util.List;
  66 import java.util.Map;
  67 import java.util.Set;
  68 import java.util.Vector;
  69
  70 import javax.help.HelpSetException;
  71 import javax.swing.AbstractCellEditor;
  72 import javax.swing.BorderFactory;
  73 import javax.swing.Icon;
  74 import javax.swing.JButton;
  75 import javax.swing.JCheckBox;
  76 import javax.swing.JCheckBoxMenuItem;
  77 import javax.swing.JColorChooser;
  78 import javax.swing.JDialog;
  79 import javax.swing.JInternalFrame;
  80 import javax.swing.JLabel;
  81 import javax.swing.JLayeredPane;
  82 import javax.swing.JMenuItem;
  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 (evt.isPopupTrigger())
 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 toggleSelection = Platform.isControlDown(evt);
 187           boolean extendSelection = evt.isShiftDown();
 188           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
 189                   invertSelection, extendSelection, toggleSelection,
 190                   (String) table.getValueAt(selectedRow, 0));
 191         }
 192       }
 193
 194       // isPopupTrigger fires on mouseReleased on Windows
 195       @Override
 196       public void mouseReleased(MouseEvent evt)
 197       {
 198         selectedRow = table.rowAtPoint(evt.getPoint());
 199         if (evt.isPopupTrigger())
 200         {
 201           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
 202                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
 203                   evt.getX(), evt.getY());
 204         }
 205       }
 206     });
 207
 208     table.addMouseMotionListener(new MouseMotionAdapter()
 209     {
 210       @Override
 211       public void mouseDragged(MouseEvent evt)
 212       {
 213         int newRow = table.rowAtPoint(evt.getPoint());
 214         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
 215         {
 216           /*
 217            * reposition 'selectedRow' to 'newRow' (the dragged to location)
 218            * this could be more than one row away for a very fast drag action
 219            * so just swap it with adjacent rows until we get it there
 220            */
 221           Object[][] data = ((FeatureTableModel) table.getModel())
 222                   .getData();
 223           int direction = newRow < selectedRow ? -1 : 1;
 224           for (int i = selectedRow; i != newRow; i += direction)
 225           {
 226             Object[] temp = data[i];
 227             data[i] = data[i + direction];
 228             data[i + direction] = temp;
 229           }
 230           updateFeatureRenderer(data);
 231           table.repaint();
 232           selectedRow = newRow;
 233         }
 234       }
 235     });
 236     // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
 237     // MessageManager.getString("label.feature_settings_click_drag")));
 238     scrollPane.setViewportView(table);
 239
 240     dassourceBrowser = new DasSourceBrowser(this);
 241     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 242
 243     if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
 244     {
 245       fr.findAllFeatures(true); // display everything!
 246     }
 247
 248     discoverAllFeatureData();
 249     final PropertyChangeListener change;
 250     final FeatureSettings fs = this;
 251     fr.addPropertyChangeListener(change = new PropertyChangeListener()
 252     {
 253       @Override
 254       public void propertyChange(PropertyChangeEvent evt)
 255       {
 256         if (!fs.resettingTable && !fs.handlingUpdate)
 257         {
 258           fs.handlingUpdate = true;
 259           fs.resetTable(null); // new groups may be added with new seuqence
 260           // feature types only
 261           fs.handlingUpdate = false;
 262         }
 263       }
 264
 265     });
 266
 267     frame = new JInternalFrame();
 268     frame.setContentPane(this);
 269     if (Platform.isAMac())
 270     {
 271       Desktop.addInternalFrame(frame,
 272               MessageManager.getString("label.sequence_feature_settings"),
 273               475, 480);
 274     }
 275     else
 276     {
 277       Desktop.addInternalFrame(frame,
 278               MessageManager.getString("label.sequence_feature_settings"),
 279               400, 450);
 280     }
 281
 282     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 283     {
 284       @Override
 285       public void internalFrameClosed(
 286               javax.swing.event.InternalFrameEvent evt)
 287       {
 288         fr.removePropertyChangeListener(change);
 289         dassourceBrowser.fs = null;
 290       };
 291     });
 292     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 293   }
 294
 295   protected void popupSort(final int selectedRow, final String type,
 296           final Object typeCol, final Map<String, float[][]> minmax, int x,
 297           int y)
 298   {
 299     final FeatureColourI featureColour = (FeatureColourI) typeCol;
 300
 301     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
 302             "label.settings_for_param", new String[] { type }));
 303     JMenuItem scr = new JMenuItem(
 304             MessageManager.getString("label.sort_by_score"));
 305     men.add(scr);
 306     final FeatureSettings me = this;
 307     scr.addActionListener(new ActionListener()
 308     {
 309
 310       @Override
 311       public void actionPerformed(ActionEvent e)
 312       {
 313         me.af.avc.sortAlignmentByFeatureScore(Arrays
 314                 .asList(new String[] { type }));
 315       }
 316
 317     });
 318     JMenuItem dens = new JMenuItem(
 319             MessageManager.getString("label.sort_by_density"));
 320     dens.addActionListener(new ActionListener()
 321     {
 322
 323       @Override
 324       public void actionPerformed(ActionEvent e)
 325       {
 326         me.af.avc.sortAlignmentByFeatureDensity(Arrays
 327                 .asList(new String[] { type }));
 328       }
 329
 330     });
 331     men.add(dens);
 332     if (minmax != null)
 333     {
 334       final float[][] typeMinMax = minmax.get(type);
 335       /*
 336        * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
 337        * this is broken at the moment and isn't that useful anyway!
 338        * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new
 339        * ActionListener() {
 340        *
 341        * public void actionPerformed(ActionEvent e) {
 342        * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
 343        * null); } else { minmax.put(type, typeMinMax); } }
 344        *
 345        * });
 346        *
 347        * men.add(chb);
 348        */
 349       if (typeMinMax != null && typeMinMax[0] != null)
 350       {
 351         // if (table.getValueAt(row, column));
 352         // graduated colourschemes for those where minmax exists for the
 353         // positional features
 354         final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
 355                 "Graduated Colour");
 356         mxcol.setSelected(!featureColour.isSimpleColour());
 357         men.add(mxcol);
 358         mxcol.addActionListener(new ActionListener()
 359         {
 360           JColorChooser colorChooser;
 361
 362           @Override
 363           public void actionPerformed(ActionEvent e)
 364           {
 365             if (e.getSource() == mxcol)
 366             {
 367               if (featureColour.isSimpleColour())
 368               {
 369                 FeatureColourChooser fc = new FeatureColourChooser(me.fr,
 370                         type);
 371                 fc.addActionListener(this);
 372               }
 373               else
 374               {
 375                 // bring up simple color chooser
 376                 colorChooser = new JColorChooser();
 377                 JDialog dialog = JColorChooser.createDialog(me,
 378                         "Select new Colour", true, // modal
 379                         colorChooser, this, // OK button handler
 380                         null); // no CANCEL button handler
 381                 colorChooser.setColor(featureColour.getMaxColour());
 382                 dialog.setVisible(true);
 383               }
 384             }
 385             else
 386             {
 387               if (e.getSource() instanceof FeatureColourChooser)
 388               {
 389                 FeatureColourChooser fc = (FeatureColourChooser) e
 390                         .getSource();
 391                 table.setValueAt(fc.getLastColour(), selectedRow, 1);
 392                 table.validate();
 393               }
 394               else
 395               {
 396                 // probably the color chooser!
 397                 table.setValueAt(
 398                         new FeatureColour(colorChooser.getColor()),
 399                         selectedRow, 1);
 400                 table.validate();
 401                 me.updateFeatureRenderer(
 402                         ((FeatureTableModel) table.getModel()).getData(),
 403                         false);
 404               }
 405             }
 406           }
 407
 408         });
 409       }
 410     }
 411     JMenuItem selCols = new JMenuItem(
 412             MessageManager.getString("label.select_columns_containing"));
 413     selCols.addActionListener(new ActionListener()
 414     {
 415       @Override
 416       public void actionPerformed(ActionEvent arg0)
 417       {
 418         fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
 419                 false, type);
 420       }
 421     });
 422     JMenuItem clearCols = new JMenuItem(
 423             MessageManager.getString("label.select_columns_not_containing"));
 424     clearCols.addActionListener(new ActionListener()
 425     {
 426       @Override
 427       public void actionPerformed(ActionEvent arg0)
 428       {
 429         fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
 430                 false, type);
 431       }
 432     });
 433     JMenuItem hideCols = new JMenuItem(
 434             MessageManager.getString("label.hide_columns_containing"));
 435     hideCols.addActionListener(new ActionListener()
 436     {
 437       @Override
 438       public void actionPerformed(ActionEvent arg0)
 439       {
 440         fr.ap.alignFrame.hideFeatureColumns(type, true);
 441       }
 442     });
 443     JMenuItem hideOtherCols = new JMenuItem(
 444             MessageManager.getString("label.hide_columns_not_containing"));
 445     hideOtherCols.addActionListener(new ActionListener()
 446     {
 447       @Override
 448       public void actionPerformed(ActionEvent arg0)
 449       {
 450         fr.ap.alignFrame.hideFeatureColumns(type, false);
 451       }
 452     });
 453     men.add(selCols);
 454     men.add(clearCols);
 455     men.add(hideCols);
 456     men.add(hideOtherCols);
 457     men.show(table, x, y);
 458   }
 459
 460   /**
 461    * true when Feature Settings are updating from feature renderer
 462    */
 463   private boolean handlingUpdate = false;
 464
 465   /**
 466    * contains a float[3] for each feature type string. created by setTableData
 467    */
 468   Map<String, float[]> typeWidth = null;
 469
 470   @Override
 471   synchronized public void discoverAllFeatureData()
 472   {
 473     Vector<String> allFeatures = new Vector<String>();
 474     Vector<String> allGroups = new Vector<String>();
 475     SequenceFeature[] tmpfeatures;
 476     String group;
 477     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 478     {
 479       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 480               .getSequenceFeatures();
 481       if (tmpfeatures == null)
 482       {
 483         continue;
 484       }
 485
 486       int index = 0;
 487       while (index < tmpfeatures.length)
 488       {
 489         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 490         {
 491           index++;
 492           continue;
 493         }
 494
 495         if (tmpfeatures[index].getFeatureGroup() != null)
 496         {
 497           group = tmpfeatures[index].featureGroup;
 498           if (!allGroups.contains(group))
 499           {
 500             allGroups.addElement(group);
 501             checkGroupState(group);
 502           }
 503         }
 504
 505         if (!allFeatures.contains(tmpfeatures[index].getType()))
 506         {
 507           allFeatures.addElement(tmpfeatures[index].getType());
 508         }
 509         index++;
 510       }
 511     }
 512
 513     resetTable(null);
 514
 515     validate();
 516   }
 517
 518   /**
 519    * Synchronise gui group list and check visibility of group
 520    *
 521    * @param group
 522    * @return true if group is visible
 523    */
 524   private boolean checkGroupState(String group)
 525   {
 526     boolean visible = fr.checkGroupVisibility(group, true);
 527
 528     if (groupPanel == null)
 529     {
 530       groupPanel = new JPanel();
 531     }
 532
 533     boolean alreadyAdded = false;
 534     for (int g = 0; g < groupPanel.getComponentCount(); g++)
 535     {
 536       if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
 537       {
 538         alreadyAdded = true;
 539         ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
 540         break;
 541       }
 542     }
 543
 544     if (alreadyAdded)
 545     {
 546
 547       return visible;
 548     }
 549     final String grp = group;
 550     final JCheckBox check = new JCheckBox(group, visible);
 551     check.setFont(new Font("Serif", Font.BOLD, 12));
 552     check.addItemListener(new ItemListener()
 553     {
 554       @Override
 555       public void itemStateChanged(ItemEvent evt)
 556       {
 557         fr.setGroupVisibility(check.getText(), check.isSelected());
 558         af.alignPanel.getSeqPanel().seqCanvas.repaint();
 559         if (af.alignPanel.overviewPanel != null)
 560         {
 561           af.alignPanel.overviewPanel.updateOverviewImage();
 562         }
 563
 564         resetTable(new String[] { grp });
 565       }
 566     });
 567     groupPanel.add(check);
 568     return visible;
 569   }
 570
 571   boolean resettingTable = false;
 572
 573   synchronized void resetTable(String[] groupChanged)
 574   {
 575     if (resettingTable == true)
 576     {
 577       return;
 578     }
 579     resettingTable = true;
 580     typeWidth = new Hashtable<String, float[]>();
 581     // TODO: change avWidth calculation to 'per-sequence' average and use long
 582     // rather than float
 583     float[] avWidth = null;
 584     SequenceFeature[] tmpfeatures;
 585     String group = null, type;
 586     Vector<String> visibleChecks = new Vector<String>();
 587
 588     // Find out which features should be visible depending on which groups
 589     // are selected / deselected
 590     // and recompute average width ordering
 591     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 592     {
 593
 594       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 595               .getSequenceFeatures();
 596       if (tmpfeatures == null)
 597       {
 598         continue;
 599       }
 600
 601       int index = 0;
 602       while (index < tmpfeatures.length)
 603       {
 604         group = tmpfeatures[index].featureGroup;
 605
 606         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 607         {
 608           index++;
 609           continue;
 610         }
 611
 612         if (group == null || checkGroupState(group))
 613         {
 614           type = tmpfeatures[index].getType();
 615           if (!visibleChecks.contains(type))
 616           {
 617             visibleChecks.addElement(type);
 618           }
 619         }
 620         if (!typeWidth.containsKey(tmpfeatures[index].getType()))
 621         {
 622           typeWidth.put(tmpfeatures[index].getType(),
 623                   avWidth = new float[3]);
 624         }
 625         else
 626         {
 627           avWidth = typeWidth.get(tmpfeatures[index].getType());
 628         }
 629         avWidth[0]++;
 630         if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
 631         {
 632           avWidth[1] += 1 + tmpfeatures[index].getBegin()
 633                   - tmpfeatures[index].getEnd();
 634         }
 635         else
 636         {
 637           avWidth[1] += 1 + tmpfeatures[index].getEnd()
 638                   - tmpfeatures[index].getBegin();
 639         }
 640         index++;
 641       }
 642     }
 643
 644     int fSize = visibleChecks.size();
 645     Object[][] data = new Object[fSize][3];
 646     int dataIndex = 0;
 647
 648     if (fr.hasRenderOrder())
 649     {
 650       if (!handlingUpdate)
 651       {
 652         fr.findAllFeatures(groupChanged != null); // prod to update
 653         // colourschemes. but don't
 654         // affect display
 655         // First add the checks in the previous render order,
 656         // in case the window has been closed and reopened
 657       }
 658       List<String> frl = fr.getRenderOrder();
 659       for (int ro = frl.size() - 1; ro > -1; ro--)
 660       {
 661         type = frl.get(ro);
 662
 663         if (!visibleChecks.contains(type))
 664         {
 665           continue;
 666         }
 667
 668         data[dataIndex][0] = type;
 669         data[dataIndex][1] = fr.getFeatureStyle(type);
 670         data[dataIndex][2] = new Boolean(af.getViewport()
 671                 .getFeaturesDisplayed().isVisible(type));
 672         dataIndex++;
 673         visibleChecks.removeElement(type);
 674       }
 675     }
 676
 677     fSize = visibleChecks.size();
 678     for (int i = 0; i < fSize; i++)
 679     {
 680       // These must be extra features belonging to the group
 681       // which was just selected
 682       type = visibleChecks.elementAt(i).toString();
 683       data[dataIndex][0] = type;
 684
 685       data[dataIndex][1] = fr.getFeatureStyle(type);
 686       if (data[dataIndex][1] == null)
 687       {
 688         // "Colour has been updated in another view!!"
 689         fr.clearRenderOrder();
 690         return;
 691       }
 692
 693       data[dataIndex][2] = new Boolean(true);
 694       dataIndex++;
 695     }
 696
 697     if (originalData == null)
 698     {
 699       originalData = new Object[data.length][3];
 700       for (int i = 0; i < data.length; i++)
 701       {
 702         System.arraycopy(data[i], 0, originalData[i], 0, 3);
 703       }
 704     }
 705
 706     table.setModel(new FeatureTableModel(data));
 707     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 708
 709     if (groupPanel != null)
 710     {
 711       groupPanel.setLayout(new GridLayout(
 712               fr.getFeatureGroupsSize() / 4 + 1, 4));
 713
 714       groupPanel.validate();
 715       bigPanel.add(groupPanel, BorderLayout.NORTH);
 716     }
 717
 718     updateFeatureRenderer(data, groupChanged != null);
 719     resettingTable = false;
 720   }
 721
 722   /**
 723    * reorder data based on the featureRenderers global priority list.
 724    *
 725    * @param data
 726    */
 727   private void ensureOrder(Object[][] data)
 728   {
 729     boolean sort = false;
 730     float[] order = new float[data.length];
 731     for (int i = 0; i < order.length; i++)
 732     {
 733       order[i] = fr.getOrder(data[i][0].toString());
 734       if (order[i] < 0)
 735       {
 736         order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
 737       }
 738       if (i > 1)
 739       {
 740         sort = sort || order[i - 1] > order[i];
 741       }
 742     }
 743     if (sort)
 744     {
 745       jalview.util.QuickSort.sort(order, data);
 746     }
 747   }
 748
 749   void load()
 750   {
 751     JalviewFileChooser chooser = new JalviewFileChooser("fc",
 752             "Sequence Feature Colours");
 753     chooser.setFileView(new JalviewFileView());
 754     chooser.setDialogTitle(MessageManager
 755             .getString("label.load_feature_colours"));
 756     chooser.setToolTipText(MessageManager.getString("action.load"));
 757
 758     int value = chooser.showOpenDialog(this);
 759
 760     if (value == JalviewFileChooser.APPROVE_OPTION)
 761     {
 762       File file = chooser.getSelectedFile();
 763
 764       try
 765       {
 766         InputStreamReader in = new InputStreamReader(new FileInputStream(
 767                 file), "UTF-8");
 768
 769         JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 770
 771         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
 772         {
 773           String name;
 774           jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
 775           if (newcol.hasMax())
 776           {
 777             Color mincol = null, maxcol = null;
 778             try
 779             {
 780               mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
 781               maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
 782
 783             } catch (Exception e)
 784             {
 785               Cache.log.warn("Couldn't parse out graduated feature color.",
 786                       e);
 787             }
 788             FeatureColourI gcol = new FeatureColour(mincol, maxcol,
 789                     newcol.getMin(), newcol.getMax());
 790             if (newcol.hasAutoScale())
 791             {
 792               gcol.setAutoScaled(newcol.getAutoScale());
 793             }
 794             if (newcol.hasColourByLabel())
 795             {
 796               gcol.setColourByLabel(newcol.getColourByLabel());
 797             }
 798             if (newcol.hasThreshold())
 799             {
 800               gcol.setThreshold(newcol.getThreshold());
 801             }
 802             if (newcol.getThreshType().length() > 0)
 803             {
 804               String ttyp = newcol.getThreshType();
 805               if (ttyp.equalsIgnoreCase("ABOVE"))
 806               {
 807                 gcol.setAboveThreshold(true);
 808               }
 809               if (ttyp.equalsIgnoreCase("BELOW"))
 810               {
 811                 gcol.setBelowThreshold(true);
 812               }
 813             }
 814             fr.setColour(name = newcol.getName(), gcol);
 815           }
 816           else
 817           {
 818             Color color = new Color(
 819                     Integer.parseInt(jucs.getColour(i).getRGB(), 16));
 820             fr.setColour(name = jucs.getColour(i).getName(),
 821                     new FeatureColour(color));
 822           }
 823           fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
 824         }
 825         if (table != null)
 826         {
 827           resetTable(null);
 828           Object[][] data = ((FeatureTableModel) table.getModel())
 829                   .getData();
 830           ensureOrder(data);
 831           updateFeatureRenderer(data, false);
 832           table.repaint();
 833         }
 834       } catch (Exception ex)
 835       {
 836         System.out.println("Error loading User Colour File\n" + ex);
 837       }
 838     }
 839   }
 840
 841   void save()
 842   {
 843     JalviewFileChooser chooser = new JalviewFileChooser("fc",
 844             "Sequence Feature Colours");
 845     chooser.setFileView(new JalviewFileView());
 846     chooser.setDialogTitle(MessageManager
 847             .getString("label.save_feature_colours"));
 848     chooser.setToolTipText(MessageManager.getString("action.save"));
 849
 850     int value = chooser.showSaveDialog(this);
 851
 852     if (value == JalviewFileChooser.APPROVE_OPTION)
 853     {
 854       String choice = chooser.getSelectedFile().getPath();
 855       jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 856       ucs.setSchemeName("Sequence Features");
 857       try
 858       {
 859         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 860                 new FileOutputStream(choice), "UTF-8"));
 861
 862         Set<String> fr_colours = fr.getAllFeatureColours();
 863         Iterator<String> e = fr_colours.iterator();
 864         float[] sortOrder = new float[fr_colours.size()];
 865         String[] sortTypes = new String[fr_colours.size()];
 866         int i = 0;
 867         while (e.hasNext())
 868         {
 869           sortTypes[i] = e.next();
 870           sortOrder[i] = fr.getOrder(sortTypes[i]);
 871           i++;
 872         }
 873         QuickSort.sort(sortOrder, sortTypes);
 874         sortOrder = null;
 875         for (i = 0; i < sortTypes.length; i++)
 876         {
 877           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 878           col.setName(sortTypes[i]);
 879           FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
 880           if (fcol.isSimpleColour())
 881           {
 882             col.setRGB(Format.getHexString(fcol.getColour()));
 883           }
 884           else
 885           {
 886             col.setRGB(Format.getHexString(fcol.getMaxColour()));
 887             col.setMin(fcol.getMin());
 888             col.setMax(fcol.getMax());
 889             col.setMinRGB(jalview.util.Format.getHexString(fcol
 890                     .getMinColour()));
 891             col.setAutoScale(fcol.isAutoScaled());
 892             col.setThreshold(fcol.getThreshold());
 893             col.setColourByLabel(fcol.isColourByLabel());
 894             col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol
 895                     .isBelowThreshold() ? "BELOW" : "NONE"));
 896           }
 897           ucs.addColour(col);
 898         }
 899         ucs.marshal(out);
 900         out.close();
 901       } catch (Exception ex)
 902       {
 903         ex.printStackTrace();
 904       }
 905     }
 906   }
 907
 908   public void invertSelection()
 909   {
 910     for (int i = 0; i < table.getRowCount(); i++)
 911     {
 912       Boolean value = (Boolean) table.getValueAt(i, 2);
 913
 914       table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
 915     }
 916   }
 917
 918   public void orderByAvWidth()
 919   {
 920     if (table == null || table.getModel() == null)
 921     {
 922       return;
 923     }
 924     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
 925     float[] width = new float[data.length];
 926     float[] awidth;
 927     float max = 0;
 928     int num = 0;
 929     for (int i = 0; i < data.length; i++)
 930     {
 931       awidth = typeWidth.get(data[i][0]);
 932       if (awidth[0] > 0)
 933       {
 934         width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
 935         // weight - but have to make per
 936         // sequence, too (awidth[2])
 937         // if (width[i]==1) // hack to distinguish single width sequences.
 938         num++;
 939       }
 940       else
 941       {
 942         width[i] = 0;
 943       }
 944       if (max < width[i])
 945       {
 946         max = width[i];
 947       }
 948     }
 949     boolean sort = false;
 950     for (int i = 0; i < width.length; i++)
 951     {
 952       // awidth = (float[]) typeWidth.get(data[i][0]);
 953       if (width[i] == 0)
 954       {
 955         width[i] = fr.getOrder(data[i][0].toString());
 956         if (width[i] < 0)
 957         {
 958           width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
 959         }
 960       }
 961       else
 962       {
 963         width[i] /= max; // normalize
 964         fr.setOrder(data[i][0].toString(), width[i]); // store for later
 965       }
 966       if (i > 0)
 967       {
 968         sort = sort || width[i - 1] > width[i];
 969       }
 970     }
 971     if (sort)
 972     {
 973       jalview.util.QuickSort.sort(width, data);
 974       // update global priority order
 975     }
 976
 977     updateFeatureRenderer(data, false);
 978     table.repaint();
 979   }
 980
 981   public void close()
 982   {
 983     try
 984     {
 985       frame.setClosed(true);
 986     } catch (Exception exe)
 987     {
 988     }
 989
 990   }
 991
 992   public void updateFeatureRenderer(Object[][] data)
 993   {
 994     updateFeatureRenderer(data, true);
 995   }
 996
 997   /**
 998    * Update the priority order of features; only repaint if this changed the
 999    * order of visible features
1000    *
1001    * @param data
1002    * @param visibleNew
1003    */
1004   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
1005   {
1006     if (fr.setFeaturePriority(data, visibleNew))
1007     {
1008       af.alignPanel.paintAlignment(true);
1009     }
1010   }
1011
1012   int selectedRow = -1;
1013
1014   JTabbedPane tabbedPane = new JTabbedPane();
1015
1016   BorderLayout borderLayout1 = new BorderLayout();
1017
1018   BorderLayout borderLayout2 = new BorderLayout();
1019
1020   BorderLayout borderLayout3 = new BorderLayout();
1021
1022   JPanel bigPanel = new JPanel();
1023
1024   BorderLayout borderLayout4 = new BorderLayout();
1025
1026   JButton invert = new JButton();
1027
1028   JPanel buttonPanel = new JPanel();
1029
1030   JButton cancel = new JButton();
1031
1032   JButton ok = new JButton();
1033
1034   JButton loadColours = new JButton();
1035
1036   JButton saveColours = new JButton();
1037
1038   JPanel dasButtonPanel = new JPanel();
1039
1040   JButton fetchDAS = new JButton();
1041
1042   JButton saveDAS = new JButton();
1043
1044   JButton cancelDAS = new JButton();
1045
1046   JButton optimizeOrder = new JButton();
1047
1048   JButton sortByScore = new JButton();
1049
1050   JButton sortByDens = new JButton();
1051
1052   JButton help = new JButton();
1053
1054   JPanel transbuttons = new JPanel(new GridLayout(5, 1));
1055
1056   private void jbInit() throws Exception
1057   {
1058     this.setLayout(borderLayout1);
1059     settingsPane.setLayout(borderLayout2);
1060     dasSettingsPane.setLayout(borderLayout3);
1061     bigPanel.setLayout(borderLayout4);
1062     invert.setFont(JvSwingUtils.getLabelFont());
1063     invert.setText(MessageManager.getString("label.invert_selection"));
1064     invert.addActionListener(new ActionListener()
1065     {
1066       @Override
1067       public void actionPerformed(ActionEvent e)
1068       {
1069         invertSelection();
1070       }
1071     });
1072     optimizeOrder.setFont(JvSwingUtils.getLabelFont());
1073     optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
1074     optimizeOrder.addActionListener(new ActionListener()
1075     {
1076       @Override
1077       public void actionPerformed(ActionEvent e)
1078       {
1079         orderByAvWidth();
1080       }
1081     });
1082     sortByScore.setFont(JvSwingUtils.getLabelFont());
1083     sortByScore
1084             .setText(MessageManager.getString("label.seq_sort_by_score"));
1085     sortByScore.addActionListener(new ActionListener()
1086     {
1087       @Override
1088       public void actionPerformed(ActionEvent e)
1089       {
1090         af.avc.sortAlignmentByFeatureScore(null);
1091       }
1092     });
1093     sortByDens.setFont(JvSwingUtils.getLabelFont());
1094     sortByDens.setText(MessageManager
1095             .getString("label.sequence_sort_by_density"));
1096     sortByDens.addActionListener(new ActionListener()
1097     {
1098       @Override
1099       public void actionPerformed(ActionEvent e)
1100       {
1101         af.avc.sortAlignmentByFeatureDensity(null);
1102       }
1103     });
1104     help.setFont(JvSwingUtils.getLabelFont());
1105     help.setText(MessageManager.getString("action.help"));
1106     help.addActionListener(new ActionListener()
1107     {
1108       @Override
1109       public void actionPerformed(ActionEvent e)
1110       {
1111         try
1112         {
1113           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1114         } catch (HelpSetException e1)
1115         {
1116           e1.printStackTrace();
1117         }
1118       }
1119     });
1120     help.setFont(JvSwingUtils.getLabelFont());
1121     help.setText(MessageManager.getString("action.help"));
1122     help.addActionListener(new ActionListener()
1123     {
1124       @Override
1125       public void actionPerformed(ActionEvent e)
1126       {
1127         try
1128         {
1129           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1130         } catch (HelpSetException e1)
1131         {
1132           e1.printStackTrace();
1133         }
1134       }
1135     });
1136     cancel.setFont(JvSwingUtils.getLabelFont());
1137     cancel.setText(MessageManager.getString("action.cancel"));
1138     cancel.addActionListener(new ActionListener()
1139     {
1140       @Override
1141       public void actionPerformed(ActionEvent e)
1142       {
1143         fr.setTransparency(originalTransparency);
1144         updateFeatureRenderer(originalData);
1145         close();
1146       }
1147     });
1148     ok.setFont(JvSwingUtils.getLabelFont());
1149     ok.setText(MessageManager.getString("action.ok"));
1150     ok.addActionListener(new ActionListener()
1151     {
1152       @Override
1153       public void actionPerformed(ActionEvent e)
1154       {
1155         close();
1156       }
1157     });
1158     loadColours.setFont(JvSwingUtils.getLabelFont());
1159     loadColours.setText(MessageManager.getString("label.load_colours"));
1160     loadColours.addActionListener(new ActionListener()
1161     {
1162       @Override
1163       public void actionPerformed(ActionEvent e)
1164       {
1165         load();
1166       }
1167     });
1168     saveColours.setFont(JvSwingUtils.getLabelFont());
1169     saveColours.setText(MessageManager.getString("label.save_colours"));
1170     saveColours.addActionListener(new ActionListener()
1171     {
1172       @Override
1173       public void actionPerformed(ActionEvent e)
1174       {
1175         save();
1176       }
1177     });
1178     transparency.addChangeListener(new ChangeListener()
1179     {
1180       @Override
1181       public void stateChanged(ChangeEvent evt)
1182       {
1183         fr.setTransparency((100 - transparency.getValue()) / 100f);
1184         af.alignPanel.paintAlignment(true);
1185       }
1186     });
1187
1188     transparency.setMaximum(70);
1189     transparency.setToolTipText(MessageManager
1190             .getString("label.transparency_tip"));
1191     fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
1192     fetchDAS.addActionListener(new ActionListener()
1193     {
1194       @Override
1195       public void actionPerformed(ActionEvent e)
1196       {
1197         fetchDAS_actionPerformed(e);
1198       }
1199     });
1200     saveDAS.setText(MessageManager.getString("action.save_as_default"));
1201     saveDAS.addActionListener(new ActionListener()
1202     {
1203       @Override
1204       public void actionPerformed(ActionEvent e)
1205       {
1206         saveDAS_actionPerformed(e);
1207       }
1208     });
1209     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
1210     dasSettingsPane.setBorder(null);
1211     cancelDAS.setEnabled(false);
1212     cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
1213     cancelDAS.addActionListener(new ActionListener()
1214     {
1215       @Override
1216       public void actionPerformed(ActionEvent e)
1217       {
1218         cancelDAS_actionPerformed(e);
1219       }
1220     });
1221     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
1222     tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
1223             settingsPane);
1224     tabbedPane.addTab(MessageManager.getString("label.das_settings"),
1225             dasSettingsPane);
1226     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
1227     transbuttons.add(optimizeOrder);
1228     transbuttons.add(invert);
1229     transbuttons.add(sortByScore);
1230     transbuttons.add(sortByDens);
1231     transbuttons.add(help);
1232     JPanel sliderPanel = new JPanel();
1233     sliderPanel.add(transparency);
1234     transPanel.add(transparency);
1235     transPanel.add(transbuttons);
1236     buttonPanel.add(ok);
1237     buttonPanel.add(cancel);
1238     buttonPanel.add(loadColours);
1239     buttonPanel.add(saveColours);
1240     bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
1241     dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
1242     dasButtonPanel.add(fetchDAS);
1243     dasButtonPanel.add(cancelDAS);
1244     dasButtonPanel.add(saveDAS);
1245     settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
1246     settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
1247   }
1248
1249   public void fetchDAS_actionPerformed(ActionEvent e)
1250   {
1251     fetchDAS.setEnabled(false);
1252     cancelDAS.setEnabled(true);
1253     dassourceBrowser.setGuiEnabled(false);
1254     Vector<jalviewSourceI> selectedSources = dassourceBrowser
1255             .getSelectedSources();
1256     doDasFeatureFetch(selectedSources, true, true);
1257   }
1258
1259   /**
1260    * get the features from selectedSources for all or the current selection
1261    *
1262    * @param selectedSources
1263    * @param checkDbRefs
1264    * @param promptFetchDbRefs
1265    */
1266   private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
1267           boolean checkDbRefs, boolean promptFetchDbRefs)
1268   {
1269     SequenceI[] dataset, seqs;
1270     int iSize;
1271     AlignmentViewport vp = af.getViewport();
1272     if (vp.getSelectionGroup() != null
1273             && vp.getSelectionGroup().getSize() > 0)
1274     {
1275       iSize = vp.getSelectionGroup().getSize();
1276       dataset = new SequenceI[iSize];
1277       seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
1278     }
1279     else
1280     {
1281       iSize = vp.getAlignment().getHeight();
1282       seqs = vp.getAlignment().getSequencesArray();
1283     }
1284
1285     dataset = new SequenceI[iSize];
1286     for (int i = 0; i < iSize; i++)
1287     {
1288       dataset[i] = seqs[i].getDatasetSequence();
1289     }
1290
1291     cancelDAS.setEnabled(true);
1292     dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
1293             this, selectedSources, checkDbRefs, promptFetchDbRefs);
1294     af.getViewport().setShowSequenceFeatures(true);
1295     af.showSeqFeatures.setSelected(true);
1296   }
1297
1298   /**
1299    * blocking call to initialise the das source browser
1300    */
1301   public void initDasSources()
1302   {
1303     dassourceBrowser.initDasSources();
1304   }
1305
1306   /**
1307    * examine the current list of das sources and return any matching the given
1308    * nicknames in sources
1309    *
1310    * @param sources
1311    *          Vector of Strings to resolve to DAS source nicknames.
1312    * @return sources that are present in source list.
1313    */
1314   public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
1315   {
1316     return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
1317   }
1318
1319   /**
1320    * get currently selected das sources. ensure you have called initDasSources
1321    * before calling this.
1322    *
1323    * @return vector of selected das source nicknames
1324    */
1325   public Vector<jalviewSourceI> getSelectedSources()
1326   {
1327     return dassourceBrowser.getSelectedSources();
1328   }
1329
1330   /**
1331    * properly initialise DAS fetcher and then initiate a new thread to fetch
1332    * features from the named sources (rather than any turned on by default)
1333    *
1334    * @param sources
1335    * @param block
1336    *          if true then runs in same thread, otherwise passes to the Swing
1337    *          executor
1338    */
1339   public void fetchDasFeatures(Vector<String> sources, boolean block)
1340   {
1341     initDasSources();
1342     List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
1343             .resolveSourceNicknames(sources);
1344     if (resolved.size() == 0)
1345     {
1346       resolved = dassourceBrowser.getSelectedSources();
1347     }
1348     if (resolved.size() > 0)
1349     {
1350       final List<jalviewSourceI> dassources = resolved;
1351       fetchDAS.setEnabled(false);
1352       // cancelDAS.setEnabled(true); doDasFetch does this.
1353       Runnable fetcher = new Runnable()
1354       {
1355
1356         @Override
1357         public void run()
1358         {
1359           doDasFeatureFetch(dassources, true, false);
1360
1361         }
1362       };
1363       if (block)
1364       {
1365         fetcher.run();
1366       }
1367       else
1368       {
1369         SwingUtilities.invokeLater(fetcher);
1370       }
1371     }
1372   }
1373
1374   public void saveDAS_actionPerformed(ActionEvent e)
1375   {
1376     dassourceBrowser
1377             .saveProperties(jalview.bin.Cache.applicationProperties);
1378   }
1379
1380   public void complete()
1381   {
1382     fetchDAS.setEnabled(true);
1383     cancelDAS.setEnabled(false);
1384     dassourceBrowser.setGuiEnabled(true);
1385
1386   }
1387
1388   public void cancelDAS_actionPerformed(ActionEvent e)
1389   {
1390     if (dasFeatureFetcher != null)
1391     {
1392       dasFeatureFetcher.cancel();
1393     }
1394     complete();
1395   }
1396
1397   public void noDasSourceActive()
1398   {
1399     complete();
1400     JvOptionPane
1401             .showInternalConfirmDialog(
1402                     Desktop.desktop,
1403                     MessageManager
1404                             .getString("label.no_das_sources_selected_warn"),
1405                     MessageManager
1406                             .getString("label.no_das_sources_selected_title"),
1407                     JvOptionPane.DEFAULT_OPTION,
1408                     JvOptionPane.INFORMATION_MESSAGE);
1409   }
1410
1411   // ///////////////////////////////////////////////////////////////////////
1412   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
1413   // ///////////////////////////////////////////////////////////////////////
1414   class FeatureTableModel extends AbstractTableModel
1415   {
1416     FeatureTableModel(Object[][] data)
1417     {
1418       this.data = data;
1419     }
1420
1421     private String[] columnNames = {
1422         MessageManager.getString("label.feature_type"),
1423         MessageManager.getString("action.colour"),
1424         MessageManager.getString("label.display") };
1425
1426     private Object[][] data;
1427
1428     public Object[][] getData()
1429     {
1430       return data;
1431     }
1432
1433     public void setData(Object[][] data)
1434     {
1435       this.data = data;
1436     }
1437
1438     @Override
1439     public int getColumnCount()
1440     {
1441       return columnNames.length;
1442     }
1443
1444     public Object[] getRow(int row)
1445     {
1446       return data[row];
1447     }
1448
1449     @Override
1450     public int getRowCount()
1451     {
1452       return data.length;
1453     }
1454
1455     @Override
1456     public String getColumnName(int col)
1457     {
1458       return columnNames[col];
1459     }
1460
1461     @Override
1462     public Object getValueAt(int row, int col)
1463     {
1464       return data[row][col];
1465     }
1466
1467     @Override
1468     public Class getColumnClass(int c)
1469     {
1470       return getValueAt(0, c).getClass();
1471     }
1472
1473     @Override
1474     public boolean isCellEditable(int row, int col)
1475     {
1476       return col == 0 ? false : true;
1477     }
1478
1479     @Override
1480     public void setValueAt(Object value, int row, int col)
1481     {
1482       data[row][col] = value;
1483       fireTableCellUpdated(row, col);
1484       updateFeatureRenderer(data);
1485     }
1486
1487   }
1488
1489   class ColorRenderer extends JLabel implements TableCellRenderer
1490   {
1491     javax.swing.border.Border unselectedBorder = null;
1492
1493     javax.swing.border.Border selectedBorder = null;
1494
1495     final String baseTT = "Click to edit, right/apple click for menu.";
1496
1497     public ColorRenderer()
1498     {
1499       setOpaque(true); // MUST do this for background to show up.
1500       setHorizontalTextPosition(SwingConstants.CENTER);
1501       setVerticalTextPosition(SwingConstants.CENTER);
1502     }
1503
1504     @Override
1505     public Component getTableCellRendererComponent(JTable tbl,
1506             Object color, boolean isSelected, boolean hasFocus, int row,
1507             int column)
1508     {
1509       FeatureColourI cellColour = (FeatureColourI) color;
1510       // JLabel comp = new JLabel();
1511       // comp.
1512       setOpaque(true);
1513       // comp.
1514       // setBounds(getBounds());
1515       Color newColor;
1516       setToolTipText(baseTT);
1517       setBackground(tbl.getBackground());
1518       if (!cellColour.isSimpleColour())
1519       {
1520         Rectangle cr = tbl.getCellRect(row, column, false);
1521         FeatureSettings.renderGraduatedColor(this, cellColour,
1522                 (int) cr.getWidth(), (int) cr.getHeight());
1523
1524       }
1525       else
1526       {
1527         this.setText("");
1528         this.setIcon(null);
1529         newColor = cellColour.getColour();
1530         setBackground(newColor);
1531       }
1532       if (isSelected)
1533       {
1534         if (selectedBorder == null)
1535         {
1536           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1537                   tbl.getSelectionBackground());
1538         }
1539         setBorder(selectedBorder);
1540       }
1541       else
1542       {
1543         if (unselectedBorder == null)
1544         {
1545           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1546                   tbl.getBackground());
1547         }
1548         setBorder(unselectedBorder);
1549       }
1550
1551       return this;
1552     }
1553   }
1554
1555   /**
1556    * update comp using rendering settings from gcol
1557    *
1558    * @param comp
1559    * @param gcol
1560    */
1561   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
1562   {
1563     int w = comp.getWidth(), h = comp.getHeight();
1564     if (w < 20)
1565     {
1566       w = (int) comp.getPreferredSize().getWidth();
1567       h = (int) comp.getPreferredSize().getHeight();
1568       if (w < 20)
1569       {
1570         w = 80;
1571         h = 12;
1572       }
1573     }
1574     renderGraduatedColor(comp, gcol, w, h);
1575   }
1576
1577   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
1578           int w, int h)
1579   {
1580     boolean thr = false;
1581     String tt = "";
1582     String tx = "";
1583     if (gcol.isAboveThreshold())
1584     {
1585       thr = true;
1586       tx += ">";
1587       tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
1588     }
1589     if (gcol.isBelowThreshold())
1590     {
1591       thr = true;
1592       tx += "<";
1593       tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
1594     }
1595     if (gcol.isColourByLabel())
1596     {
1597       tt = "Coloured by label text. " + tt;
1598       if (thr)
1599       {
1600         tx += " ";
1601       }
1602       tx += "Label";
1603       comp.setIcon(null);
1604     }
1605     else
1606     {
1607       Color newColor = gcol.getMaxColour();
1608       comp.setBackground(newColor);
1609       // System.err.println("Width is " + w / 2);
1610       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
1611       comp.setIcon(ficon);
1612       // tt+="RGB value: Max (" + newColor.getRed() + ", "
1613       // + newColor.getGreen() + ", " + newColor.getBlue()
1614       // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
1615       // + ", " + minCol.getBlue() + ")");
1616     }
1617     comp.setHorizontalAlignment(SwingConstants.CENTER);
1618     comp.setText(tx);
1619     if (tt.length() > 0)
1620     {
1621       if (comp.getToolTipText() == null)
1622       {
1623         comp.setToolTipText(tt);
1624       }
1625       else
1626       {
1627         comp.setToolTipText(tt + " " + comp.getToolTipText());
1628       }
1629     }
1630   }
1631 }
1632
1633 class FeatureIcon implements Icon
1634 {
1635   FeatureColourI gcol;
1636
1637   Color backg;
1638
1639   boolean midspace = false;
1640
1641   int width = 50, height = 20;
1642
1643   int s1, e1; // start and end of midpoint band for thresholded symbol
1644
1645   Color mpcolour = Color.white;
1646
1647   FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
1648   {
1649     gcol = gfc;
1650     backg = bg;
1651     width = w;
1652     height = h;
1653     midspace = mspace;
1654     if (midspace)
1655     {
1656       s1 = width / 3;
1657       e1 = s1 * 2;
1658     }
1659     else
1660     {
1661       s1 = width / 2;
1662       e1 = s1;
1663     }
1664   }
1665
1666   @Override
1667   public int getIconWidth()
1668   {
1669     return width;
1670   }
1671
1672   @Override
1673   public int getIconHeight()
1674   {
1675     return height;
1676   }
1677
1678   @Override
1679   public void paintIcon(Component c, Graphics g, int x, int y)
1680   {
1681
1682     if (gcol.isColourByLabel())
1683     {
1684       g.setColor(backg);
1685       g.fillRect(0, 0, width, height);
1686       // need an icon here.
1687       g.setColor(gcol.getMaxColour());
1688
1689       g.setFont(new Font("Verdana", Font.PLAIN, 9));
1690
1691       // g.setFont(g.getFont().deriveFont(
1692       // AffineTransform.getScaleInstance(
1693       // width/g.getFontMetrics().stringWidth("Label"),
1694       // height/g.getFontMetrics().getHeight())));
1695
1696       g.drawString(MessageManager.getString("label.label"), 0, 0);
1697
1698     }
1699     else
1700     {
1701       Color minCol = gcol.getMinColour();
1702       g.setColor(minCol);
1703       g.fillRect(0, 0, s1, height);
1704       if (midspace)
1705       {
1706         g.setColor(Color.white);
1707         g.fillRect(s1, 0, e1 - s1, height);
1708       }
1709       g.setColor(gcol.getMaxColour());
1710       g.fillRect(0, e1, width - e1, height);
1711     }
1712   }
1713 }
1714
1715 class ColorEditor extends AbstractCellEditor implements TableCellEditor,
1716         ActionListener
1717 {
1718   FeatureSettings me;
1719
1720   FeatureColourI currentColor;
1721
1722   FeatureColourChooser chooser;
1723
1724   String type;
1725
1726   JButton button;
1727
1728   JColorChooser colorChooser;
1729
1730   JDialog dialog;
1731
1732   protected static final String EDIT = "edit";
1733
1734   int selectedRow = 0;
1735
1736   public ColorEditor(FeatureSettings me)
1737   {
1738     this.me = me;
1739     // Set up the editor (from the table's point of view),
1740     // which is a button.
1741     // This button brings up the color chooser dialog,
1742     // which is the editor from the user's point of view.
1743     button = new JButton();
1744     button.setActionCommand(EDIT);
1745     button.addActionListener(this);
1746     button.setBorderPainted(false);
1747     // Set up the dialog that the button brings up.
1748     colorChooser = new JColorChooser();
1749     dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal
1750             colorChooser, this, // OK button handler
1751             null); // no CANCEL button handler
1752   }
1753
1754   /**
1755    * Handles events from the editor button and from the dialog's OK button.
1756    */
1757   @Override
1758   public void actionPerformed(ActionEvent e)
1759   {
1760
1761     if (EDIT.equals(e.getActionCommand()))
1762     {
1763       // The user has clicked the cell, so
1764       // bring up the dialog.
1765       if (currentColor.isSimpleColour())
1766       {
1767         // bring up simple color chooser
1768         button.setBackground(currentColor.getColour());
1769         colorChooser.setColor(currentColor.getColour());
1770         dialog.setVisible(true);
1771       }
1772       else
1773       {
1774         // bring up graduated chooser.
1775         chooser = new FeatureColourChooser(me.fr, type);
1776         chooser.setRequestFocusEnabled(true);
1777         chooser.requestFocus();
1778         chooser.addActionListener(this);
1779       }
1780       // Make the renderer reappear.
1781       fireEditingStopped();
1782
1783     }
1784     else
1785     { // User pressed dialog's "OK" button.
1786       if (currentColor.isSimpleColour())
1787       {
1788         currentColor = new FeatureColour(colorChooser.getColor());
1789       }
1790       else
1791       {
1792         currentColor = chooser.getLastColour();
1793       }
1794       me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
1795       fireEditingStopped();
1796       me.table.validate();
1797     }
1798   }
1799
1800   // Implement the one CellEditor method that AbstractCellEditor doesn't.
1801   @Override
1802   public Object getCellEditorValue()
1803   {
1804     return currentColor;
1805   }
1806
1807   // Implement the one method defined by TableCellEditor.
1808   @Override
1809   public Component getTableCellEditorComponent(JTable table, Object value,
1810           boolean isSelected, int row, int column)
1811   {
1812     currentColor = (FeatureColourI) value;
1813     this.selectedRow = row;
1814     type = me.table.getValueAt(row, 0).toString();
1815     button.setOpaque(true);
1816     button.setBackground(me.getBackground());
1817     if (!currentColor.isSimpleColour())
1818     {
1819       JLabel btn = new JLabel();
1820       btn.setSize(button.getSize());
1821       FeatureSettings.renderGraduatedColor(btn, currentColor);
1822       button.setBackground(btn.getBackground());
1823       button.setIcon(btn.getIcon());
1824       button.setText(btn.getText());
1825     }
1826     else
1827     {
1828       button.setText("");
1829       button.setIcon(null);
1830       button.setBackground(currentColor.getColour());
1831     }
1832     return button;
1833   }
1834 }