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