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 static jalview.gui.FeatureSettings.FeatureTableModel.COLOUR_COLUMN;
  24 import static jalview.gui.FeatureSettings.FeatureTableModel.FILTER_COLUMN;
  25 import static jalview.gui.FeatureSettings.FeatureTableModel.SHOW_COLUMN;
  26 import static jalview.gui.FeatureSettings.FeatureTableModel.TYPE_COLUMN;
  27
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureSettingsControllerI;
  30 import jalview.bin.Cache;
  31 import jalview.datamodel.AlignmentI;
  32 import jalview.datamodel.SequenceI;
  33 import jalview.gui.Help.HelpId;
  34 import jalview.io.JalviewFileChooser;
  35 import jalview.io.JalviewFileView;
  36 import jalview.schemabinding.version2.JalviewUserColours;
  37 import jalview.schemes.FeatureColour;
  38 import jalview.util.Format;
  39 import jalview.util.MessageManager;
  40 import jalview.util.Platform;
  41 import jalview.util.QuickSort;
  42 import jalview.util.matcher.KeyedMatcherSet;
  43 import jalview.util.matcher.KeyedMatcherSetI;
  44 import jalview.viewmodel.AlignmentViewport;
  45 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
  46 import jalview.ws.DasSequenceFeatureFetcher;
  47 import jalview.ws.dbsources.das.api.jalviewSourceI;
  48
  49 import java.awt.BorderLayout;
  50 import java.awt.Color;
  51 import java.awt.Component;
  52 import java.awt.Dimension;
  53 import java.awt.Font;
  54 import java.awt.Graphics;
  55 import java.awt.GridLayout;
  56 import java.awt.Point;
  57 import java.awt.Rectangle;
  58 import java.awt.event.ActionEvent;
  59 import java.awt.event.ActionListener;
  60 import java.awt.event.ItemEvent;
  61 import java.awt.event.ItemListener;
  62 import java.awt.event.MouseAdapter;
  63 import java.awt.event.MouseEvent;
  64 import java.awt.event.MouseMotionAdapter;
  65 import java.beans.PropertyChangeEvent;
  66 import java.beans.PropertyChangeListener;
  67 import java.io.File;
  68 import java.io.FileInputStream;
  69 import java.io.FileOutputStream;
  70 import java.io.InputStreamReader;
  71 import java.io.OutputStreamWriter;
  72 import java.io.PrintWriter;
  73 import java.util.Arrays;
  74 import java.util.HashSet;
  75 import java.util.Hashtable;
  76 import java.util.Iterator;
  77 import java.util.List;
  78 import java.util.Map;
  79 import java.util.Set;
  80 import java.util.Vector;
  81
  82 import javax.help.HelpSetException;
  83 import javax.swing.AbstractCellEditor;
  84 import javax.swing.BorderFactory;
  85 import javax.swing.Icon;
  86 import javax.swing.JButton;
  87 import javax.swing.JCheckBox;
  88 import javax.swing.JCheckBoxMenuItem;
  89 import javax.swing.JColorChooser;
  90 import javax.swing.JDialog;
  91 import javax.swing.JInternalFrame;
  92 import javax.swing.JLabel;
  93 import javax.swing.JLayeredPane;
  94 import javax.swing.JMenuItem;
  95 import javax.swing.JPanel;
  96 import javax.swing.JPopupMenu;
  97 import javax.swing.JScrollPane;
  98 import javax.swing.JSlider;
  99 import javax.swing.JTable;
 100 import javax.swing.ListSelectionModel;
 101 import javax.swing.SwingConstants;
 102 import javax.swing.SwingUtilities;
 103 import javax.swing.event.ChangeEvent;
 104 import javax.swing.event.ChangeListener;
 105 import javax.swing.table.AbstractTableModel;
 106 import javax.swing.table.TableCellEditor;
 107 import javax.swing.table.TableCellRenderer;
 108 import javax.swing.table.TableColumn;
 109
 110 public class FeatureSettings extends JPanel
 111         implements FeatureSettingsControllerI
 112 {
 113   private static final int COLUMN_COUNT = 4;
 114
 115   private static final int MIN_WIDTH = 400;
 116
 117   private static final int MIN_HEIGHT = 400;
 118
 119   DasSourceBrowser dassourceBrowser;
 120
 121   DasSequenceFeatureFetcher dasFeatureFetcher;
 122
 123   JPanel dasSettingsPane = new JPanel();
 124
 125   final FeatureRenderer fr;
 126
 127   public final AlignFrame af;
 128
 129   /*
 130    * 'original' fields hold settings to restore on Cancel
 131    */
 132   Object[][] originalData;
 133
 134   private float originalTransparency;
 135
 136   private Map<String, KeyedMatcherSetI> originalFilters;
 137
 138   final JInternalFrame frame;
 139
 140   JScrollPane scrollPane = new JScrollPane();
 141
 142   JTable table;
 143
 144   JPanel groupPanel;
 145
 146   JSlider transparency = new JSlider();
 147
 148   /*
 149    * when true, constructor is still executing - so ignore UI events
 150    */
 151   protected volatile boolean inConstruction = true;
 152
 153   int selectedRow = -1;
 154
 155   JButton fetchDAS = new JButton();
 156
 157   JButton saveDAS = new JButton();
 158
 159   JButton cancelDAS = new JButton();
 160
 161   boolean resettingTable = false;
 162
 163   /*
 164    * true when Feature Settings are updating from feature renderer
 165    */
 166   private boolean handlingUpdate = false;
 167
 168   /*
 169    * holds {featureCount, totalExtent} for each feature type
 170    */
 171   Map<String, float[]> typeWidth = null;
 172
 173   /**
 174    * Constructor
 175    *
 176    * @param af
 177    */
 178   public FeatureSettings(AlignFrame alignFrame)
 179   {
 180     this.af = alignFrame;
 181     fr = af.getFeatureRenderer();
 182
 183     // save transparency for restore on Cancel
 184     originalTransparency = fr.getTransparency();
 185     int originalTransparencyAsPercent = (int) (originalTransparency * 100);
 186     transparency.setMaximum(100 - originalTransparencyAsPercent);
 187
 188     originalFilters = fr.getFeatureFilters();
 189
 190     try
 191     {
 192       jbInit();
 193     } catch (Exception ex)
 194     {
 195       ex.printStackTrace();
 196     }
 197
 198     table = new JTable()
 199     {
 200       @Override
 201       public String getToolTipText(MouseEvent e)
 202       {
 203         String tip = null;
 204         int column = table.columnAtPoint(e.getPoint());
 205         switch (column)
 206         {
 207         case TYPE_COLUMN:
 208           tip = JvSwingUtils.wrapTooltip(true, MessageManager
 209                   .getString("label.feature_settings_click_drag"));
 210           break;
 211         case FILTER_COLUMN:
 212           int row = table.rowAtPoint(e.getPoint());
 213           KeyedMatcherSet o = (KeyedMatcherSet) table.getValueAt(row,
 214                   column);
 215           tip = o.isEmpty()
 216                   ? MessageManager.getString("label.filters_tooltip")
 217                   : o.toString();
 218           break;
 219         default:
 220           break;
 221         }
 222         return tip;
 223       }
 224     };
 225     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
 226     table.setFont(new Font("Verdana", Font.PLAIN, 12));
 227
 228     // table.setDefaultRenderer(Color.class, new ColorRenderer());
 229     // table.setDefaultEditor(Color.class, new ColorEditor(this));
 230     //
 231     table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
 232     table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
 233
 234     table.setDefaultEditor(KeyedMatcherSet.class, new FilterEditor(this));
 235     table.setDefaultRenderer(KeyedMatcherSet.class, new FilterRenderer());
 236
 237     TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
 238             new ColorRenderer(), new ColorEditor(this));
 239     table.addColumn(colourColumn);
 240
 241     TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
 242             new FilterRenderer(), new FilterEditor(this));
 243     table.addColumn(filterColumn);
 244
 245     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 246
 247     table.addMouseListener(new MouseAdapter()
 248     {
 249       @Override
 250       public void mousePressed(MouseEvent evt)
 251       {
 252         selectedRow = table.rowAtPoint(evt.getPoint());
 253         String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
 254         if (evt.isPopupTrigger())
 255         {
 256           Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
 257           popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
 258                   evt.getY());
 259         }
 260         else if (evt.getClickCount() == 2)
 261         {
 262           boolean invertSelection = evt.isAltDown();
 263           boolean toggleSelection = Platform.isControlDown(evt);
 264           boolean extendSelection = evt.isShiftDown();
 265           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
 266                   invertSelection, extendSelection, toggleSelection, type);
 267         }
 268       }
 269
 270       // isPopupTrigger fires on mouseReleased on Windows
 271       @Override
 272       public void mouseReleased(MouseEvent evt)
 273       {
 274         selectedRow = table.rowAtPoint(evt.getPoint());
 275         if (evt.isPopupTrigger())
 276         {
 277           String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
 278           Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
 279           popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
 280                   evt.getY());
 281         }
 282       }
 283     });
 284
 285     table.addMouseMotionListener(new MouseMotionAdapter()
 286     {
 287       @Override
 288       public void mouseDragged(MouseEvent evt)
 289       {
 290         int newRow = table.rowAtPoint(evt.getPoint());
 291         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
 292         {
 293           /*
 294            * reposition 'selectedRow' to 'newRow' (the dragged to location)
 295            * this could be more than one row away for a very fast drag action
 296            * so just swap it with adjacent rows until we get it there
 297            */
 298           Object[][] data = ((FeatureTableModel) table.getModel())
 299                   .getData();
 300           int direction = newRow < selectedRow ? -1 : 1;
 301           for (int i = selectedRow; i != newRow; i += direction)
 302           {
 303             Object[] temp = data[i];
 304             data[i] = data[i + direction];
 305             data[i + direction] = temp;
 306           }
 307           updateFeatureRenderer(data);
 308           table.repaint();
 309           selectedRow = newRow;
 310         }
 311       }
 312     });
 313     // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
 314     // MessageManager.getString("label.feature_settings_click_drag")));
 315     scrollPane.setViewportView(table);
 316
 317     dassourceBrowser = new DasSourceBrowser(this);
 318     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 319
 320     if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
 321     {
 322       fr.findAllFeatures(true); // display everything!
 323     }
 324
 325     discoverAllFeatureData();
 326     final PropertyChangeListener change;
 327     final FeatureSettings fs = this;
 328     fr.addPropertyChangeListener(change = new PropertyChangeListener()
 329     {
 330       @Override
 331       public void propertyChange(PropertyChangeEvent evt)
 332       {
 333         if (!fs.resettingTable && !fs.handlingUpdate)
 334         {
 335           fs.handlingUpdate = true;
 336           fs.resetTable(null);
 337           // new groups may be added with new sequence feature types only
 338           fs.handlingUpdate = false;
 339         }
 340       }
 341
 342     });
 343
 344     frame = new JInternalFrame();
 345     frame.setContentPane(this);
 346     if (Platform.isAMac())
 347     {
 348       Desktop.addInternalFrame(frame,
 349               MessageManager.getString("label.sequence_feature_settings"),
 350               600, 480);
 351     }
 352     else
 353     {
 354       Desktop.addInternalFrame(frame,
 355               MessageManager.getString("label.sequence_feature_settings"),
 356               600, 450);
 357     }
 358     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 359
 360     frame.addInternalFrameListener(
 361             new javax.swing.event.InternalFrameAdapter()
 362             {
 363               @Override
 364               public void internalFrameClosed(
 365                       javax.swing.event.InternalFrameEvent evt)
 366               {
 367                 fr.removePropertyChangeListener(change);
 368                 dassourceBrowser.fs = null;
 369               };
 370             });
 371     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 372     inConstruction = false;
 373   }
 374
 375   protected void popupSort(final int rowSelected, final String type,
 376           final Object typeCol, final Map<String, float[][]> minmax, int x,
 377           int y)
 378   {
 379     final FeatureColourI featureColour = (FeatureColourI) typeCol;
 380
 381     JPopupMenu men = new JPopupMenu(MessageManager
 382             .formatMessage("label.settings_for_param", new String[]
 383             { type }));
 384     JMenuItem scr = new JMenuItem(
 385             MessageManager.getString("label.sort_by_score"));
 386     men.add(scr);
 387     final FeatureSettings me = this;
 388     scr.addActionListener(new ActionListener()
 389     {
 390
 391       @Override
 392       public void actionPerformed(ActionEvent e)
 393       {
 394         me.af.avc
 395                 .sortAlignmentByFeatureScore(Arrays.asList(new String[]
 396                 { type }));
 397       }
 398
 399     });
 400     JMenuItem dens = new JMenuItem(
 401             MessageManager.getString("label.sort_by_density"));
 402     dens.addActionListener(new ActionListener()
 403     {
 404
 405       @Override
 406       public void actionPerformed(ActionEvent e)
 407       {
 408         me.af.avc
 409                 .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
 410                 { type }));
 411       }
 412
 413     });
 414     men.add(dens);
 415
 416     /*
 417      * variable colour options include colour by label, by score,
 418      * by selected attribute text, or attribute value
 419      */
 420     final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
 421             MessageManager.getString("label.variable_colour"));
 422     mxcol.setSelected(!featureColour.isSimpleColour());
 423     men.add(mxcol);
 424     mxcol.addActionListener(new ActionListener()
 425     {
 426       JColorChooser colorChooser;
 427
 428       @Override
 429       public void actionPerformed(ActionEvent e)
 430       {
 431         if (e.getSource() == mxcol)
 432         {
 433           if (featureColour.isSimpleColour())
 434           {
 435             FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
 436             fc.addActionListener(this);
 437           }
 438           else
 439           {
 440             // bring up simple color chooser
 441             colorChooser = new JColorChooser();
 442             String title = MessageManager
 443                     .getString("label.select_colour");
 444             JDialog dialog = JColorChooser.createDialog(me,
 445                     title, true, // modal
 446                     colorChooser, this, // OK button handler
 447                     null); // no CANCEL button handler
 448             colorChooser.setColor(featureColour.getMaxColour());
 449             dialog.setVisible(true);
 450           }
 451         }
 452         else
 453         {
 454           if (e.getSource() instanceof FeatureTypeSettings)
 455           {
 456             /*
 457              * update after OK in feature colour dialog; the updated
 458              * colour will have already been set in the FeatureRenderer
 459              */
 460             FeatureColourI fci = fr.getFeatureColours().get(type);
 461             table.setValueAt(fci, rowSelected, 1);
 462             table.validate();
 463           }
 464           else
 465           {
 466             // probably the color chooser!
 467             table.setValueAt(new FeatureColour(colorChooser.getColor()),
 468                     rowSelected, 1);
 469             table.validate();
 470             me.updateFeatureRenderer(
 471                     ((FeatureTableModel) table.getModel()).getData(),
 472                     false);
 473           }
 474         }
 475       }
 476
 477     });
 478
 479     JMenuItem selCols = new JMenuItem(
 480             MessageManager.getString("label.select_columns_containing"));
 481     selCols.addActionListener(new ActionListener()
 482     {
 483       @Override
 484       public void actionPerformed(ActionEvent arg0)
 485       {
 486         fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
 487                 false, type);
 488       }
 489     });
 490     JMenuItem clearCols = new JMenuItem(MessageManager
 491             .getString("label.select_columns_not_containing"));
 492     clearCols.addActionListener(new ActionListener()
 493     {
 494       @Override
 495       public void actionPerformed(ActionEvent arg0)
 496       {
 497         fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
 498                 false, type);
 499       }
 500     });
 501     JMenuItem hideCols = new JMenuItem(
 502             MessageManager.getString("label.hide_columns_containing"));
 503     hideCols.addActionListener(new ActionListener()
 504     {
 505       @Override
 506       public void actionPerformed(ActionEvent arg0)
 507       {
 508         fr.ap.alignFrame.hideFeatureColumns(type, true);
 509       }
 510     });
 511     JMenuItem hideOtherCols = new JMenuItem(
 512             MessageManager.getString("label.hide_columns_not_containing"));
 513     hideOtherCols.addActionListener(new ActionListener()
 514     {
 515       @Override
 516       public void actionPerformed(ActionEvent arg0)
 517       {
 518         fr.ap.alignFrame.hideFeatureColumns(type, false);
 519       }
 520     });
 521     men.add(selCols);
 522     men.add(clearCols);
 523     men.add(hideCols);
 524     men.add(hideOtherCols);
 525     men.show(table, x, y);
 526   }
 527
 528   @Override
 529   synchronized public void discoverAllFeatureData()
 530   {
 531     Set<String> allGroups = new HashSet<>();
 532     AlignmentI alignment = af.getViewport().getAlignment();
 533
 534     for (int i = 0; i < alignment.getHeight(); i++)
 535     {
 536       SequenceI seq = alignment.getSequenceAt(i);
 537       for (String group : seq.getFeatures().getFeatureGroups(true))
 538       {
 539         if (group != null && !allGroups.contains(group))
 540         {
 541           allGroups.add(group);
 542           checkGroupState(group);
 543         }
 544       }
 545     }
 546
 547     resetTable(null);
 548
 549     validate();
 550   }
 551
 552   /**
 553    * Synchronise gui group list and check visibility of group
 554    *
 555    * @param group
 556    * @return true if group is visible
 557    */
 558   private boolean checkGroupState(String group)
 559   {
 560     boolean visible = fr.checkGroupVisibility(group, true);
 561
 562     for (int g = 0; g < groupPanel.getComponentCount(); g++)
 563     {
 564       if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
 565       {
 566         ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
 567         return visible;
 568       }
 569     }
 570
 571     final String grp = group;
 572     final JCheckBox check = new JCheckBox(group, visible);
 573     check.setFont(new Font("Serif", Font.BOLD, 12));
 574     check.setToolTipText(group);
 575     check.addItemListener(new ItemListener()
 576     {
 577       @Override
 578       public void itemStateChanged(ItemEvent evt)
 579       {
 580         fr.setGroupVisibility(check.getText(), check.isSelected());
 581         resetTable(new String[] { grp });
 582         af.alignPanel.paintAlignment(true, true);
 583       }
 584     });
 585     groupPanel.add(check);
 586     return visible;
 587   }
 588
 589   synchronized void resetTable(String[] groupChanged)
 590   {
 591     if (resettingTable)
 592     {
 593       return;
 594     }
 595     resettingTable = true;
 596     typeWidth = new Hashtable<>();
 597     // TODO: change avWidth calculation to 'per-sequence' average and use long
 598     // rather than float
 599
 600     Set<String> displayableTypes = new HashSet<>();
 601     Set<String> foundGroups = new HashSet<>();
 602
 603     /*
 604      * determine which feature types may be visible depending on
 605      * which groups are selected, and recompute average width data
 606      */
 607     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 608     {
 609
 610       SequenceI seq = af.getViewport().getAlignment().getSequenceAt(i);
 611
 612       /*
 613        * get the sequence's groups for positional features
 614        * and keep track of which groups are visible
 615        */
 616       Set<String> groups = seq.getFeatures().getFeatureGroups(true);
 617       Set<String> visibleGroups = new HashSet<>();
 618       for (String group : groups)
 619       {
 620         if (group == null || checkGroupState(group))
 621         {
 622           visibleGroups.add(group);
 623         }
 624       }
 625       foundGroups.addAll(groups);
 626
 627       /*
 628        * get distinct feature types for visible groups
 629        * record distinct visible types, and their count and total length
 630        */
 631       Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
 632               visibleGroups.toArray(new String[visibleGroups.size()]));
 633       for (String type : types)
 634       {
 635         displayableTypes.add(type);
 636         float[] avWidth = typeWidth.get(type);
 637         if (avWidth == null)
 638         {
 639           avWidth = new float[2];
 640           typeWidth.put(type, avWidth);
 641         }
 642         // todo this could include features with a non-visible group
 643         // - do we greatly care?
 644         // todo should we include non-displayable features here, and only
 645         // update when features are added?
 646         avWidth[0] += seq.getFeatures().getFeatureCount(true, type);
 647         avWidth[1] += seq.getFeatures().getTotalFeatureLength(type);
 648       }
 649     }
 650
 651     int columnCount = COLUMN_COUNT;
 652     Object[][] data = new Object[displayableTypes.size()][columnCount];
 653     int dataIndex = 0;
 654
 655     if (fr.hasRenderOrder())
 656     {
 657       if (!handlingUpdate)
 658       {
 659         fr.findAllFeatures(groupChanged != null); // prod to update
 660         // colourschemes. but don't
 661         // affect display
 662         // First add the checks in the previous render order,
 663         // in case the window has been closed and reopened
 664       }
 665       List<String> frl = fr.getRenderOrder();
 666       for (int ro = frl.size() - 1; ro > -1; ro--)
 667       {
 668         String type = frl.get(ro);
 669
 670         if (!displayableTypes.contains(type))
 671         {
 672           continue;
 673         }
 674
 675         data[dataIndex][TYPE_COLUMN] = type;
 676         data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
 677         KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type);
 678         data[dataIndex][FILTER_COLUMN] = featureFilter == null
 679                 ? new KeyedMatcherSet()
 680                 : featureFilter;
 681         data[dataIndex][SHOW_COLUMN] = new Boolean(
 682                 af.getViewport().getFeaturesDisplayed().isVisible(type));
 683         dataIndex++;
 684         displayableTypes.remove(type);
 685       }
 686     }
 687
 688     /*
 689      * process any extra features belonging only to
 690      * a group which was just selected
 691      */
 692     while (!displayableTypes.isEmpty())
 693     {
 694       String type = displayableTypes.iterator().next();
 695       data[dataIndex][TYPE_COLUMN] = type;
 696
 697       data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
 698       if (data[dataIndex][COLOUR_COLUMN] == null)
 699       {
 700         // "Colour has been updated in another view!!"
 701         fr.clearRenderOrder();
 702         return;
 703       }
 704       KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type);
 705       data[dataIndex][FILTER_COLUMN] = featureFilter == null
 706               ? new KeyedMatcherSet()
 707               : featureFilter;
 708       data[dataIndex][SHOW_COLUMN] = new Boolean(true);
 709       dataIndex++;
 710       displayableTypes.remove(type);
 711     }
 712
 713     if (originalData == null)
 714     {
 715       int size = data[0].length;
 716       originalData = new Object[data.length][size];
 717       for (int i = 0; i < data.length; i++)
 718       {
 719         System.arraycopy(data[i], 0, originalData[i], 0, size);
 720       }
 721     }
 722     else
 723     {
 724       updateOriginalData(data);
 725     }
 726
 727     table.setModel(new FeatureTableModel(data));
 728     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 729
 730     groupPanel.setLayout(
 731             new GridLayout(fr.getFeatureGroupsSize() / 4 + 1, 4));
 732     pruneGroups(foundGroups);
 733     groupPanel.validate();
 734
 735     updateFeatureRenderer(data, groupChanged != null);
 736     resettingTable = false;
 737   }
 738
 739   /**
 740    * Updates 'originalData' (used for restore on Cancel) if we detect that changes
 741    * have been made outwith this dialog
 742    * <ul>
 743    * <li>a new feature type added (and made visible)</li>
 744    * <li>a feature colour changed (in the Amend Features dialog)</li>
 745    * </ul>
 746    *
 747    * @param foundData
 748    */
 749   protected void updateOriginalData(Object[][] foundData)
 750   {
 751     // todo LinkedHashMap instead of Object[][] would be nice
 752
 753     Object[][] currentData = ((FeatureTableModel) table.getModel())
 754             .getData();
 755     for (Object[] row : foundData)
 756     {
 757       String type = (String) row[TYPE_COLUMN];
 758       boolean found = false;
 759       for (Object[] current : currentData)
 760       {
 761         if (type.equals(current[TYPE_COLUMN]))
 762         {
 763           found = true;
 764           /*
 765            * currently dependent on object equality here;
 766            * really need an equals method on FeatureColour
 767            */
 768           if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN]))
 769           {
 770             /*
 771              * feature colour has changed externally - update originalData
 772              */
 773             for (Object[] original : originalData)
 774             {
 775               if (type.equals(original[TYPE_COLUMN]))
 776               {
 777                 original[COLOUR_COLUMN] = row[COLOUR_COLUMN];
 778                 break;
 779               }
 780             }
 781           }
 782           break;
 783         }
 784       }
 785       if (!found)
 786       {
 787         /*
 788          * new feature detected - add to original data (on top)
 789          */
 790         int size = currentData[0].length;
 791         Object[][] newData = new Object[originalData.length + 1][size];
 792         for (int i = 0; i < originalData.length; i++)
 793         {
 794           System.arraycopy(originalData[i], 0, newData[i + 1], 0, size);
 795         }
 796         newData[0] = row;
 797         originalData = newData;
 798       }
 799     }
 800   }
 801
 802   /**
 803    * Remove from the groups panel any checkboxes for groups that are not in the
 804    * foundGroups set. This enables removing a group from the display when the last
 805    * feature in that group is deleted.
 806    *
 807    * @param foundGroups
 808    */
 809   protected void pruneGroups(Set<String> foundGroups)
 810   {
 811     for (int g = 0; g < groupPanel.getComponentCount(); g++)
 812     {
 813       JCheckBox checkbox = (JCheckBox) groupPanel.getComponent(g);
 814       if (!foundGroups.contains(checkbox.getText()))
 815       {
 816         groupPanel.remove(checkbox);
 817       }
 818     }
 819   }
 820
 821   /**
 822    * reorder data based on the featureRenderers global priority list.
 823    *
 824    * @param data
 825    */
 826   private void ensureOrder(Object[][] data)
 827   {
 828     boolean sort = false;
 829     float[] order = new float[data.length];
 830     for (int i = 0; i < order.length; i++)
 831     {
 832       order[i] = fr.getOrder(data[i][0].toString());
 833       if (order[i] < 0)
 834       {
 835         order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
 836       }
 837       if (i > 1)
 838       {
 839         sort = sort || order[i - 1] > order[i];
 840       }
 841     }
 842     if (sort)
 843     {
 844       jalview.util.QuickSort.sort(order, data);
 845     }
 846   }
 847
 848   void load()
 849   {
 850     JalviewFileChooser chooser = new JalviewFileChooser("fc",
 851             "Sequence Feature Colours");
 852     chooser.setFileView(new JalviewFileView());
 853     chooser.setDialogTitle(
 854             MessageManager.getString("label.load_feature_colours"));
 855     chooser.setToolTipText(MessageManager.getString("action.load"));
 856
 857     int value = chooser.showOpenDialog(this);
 858
 859     if (value == JalviewFileChooser.APPROVE_OPTION)
 860     {
 861       File file = chooser.getSelectedFile();
 862
 863       try
 864       {
 865         InputStreamReader in = new InputStreamReader(
 866                 new FileInputStream(file), "UTF-8");
 867
 868         JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 869
 870         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
 871         {
 872           String name;
 873           jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
 874           if (newcol.hasMax())
 875           {
 876             Color mincol = null, maxcol = null;
 877             try
 878             {
 879               mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
 880               maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
 881
 882             } catch (Exception e)
 883             {
 884               Cache.log.warn("Couldn't parse out graduated feature color.",
 885                       e);
 886             }
 887             FeatureColourI gcol = new FeatureColour(mincol, maxcol,
 888                     newcol.getMin(), newcol.getMax());
 889             if (newcol.hasAutoScale())
 890             {
 891               gcol.setAutoScaled(newcol.getAutoScale());
 892             }
 893             if (newcol.hasColourByLabel())
 894             {
 895               gcol.setColourByLabel(newcol.getColourByLabel());
 896             }
 897             if (newcol.hasThreshold())
 898             {
 899               gcol.setThreshold(newcol.getThreshold());
 900             }
 901             if (newcol.getThreshType().length() > 0)
 902             {
 903               String ttyp = newcol.getThreshType();
 904               if (ttyp.equalsIgnoreCase("ABOVE"))
 905               {
 906                 gcol.setAboveThreshold(true);
 907               }
 908               if (ttyp.equalsIgnoreCase("BELOW"))
 909               {
 910                 gcol.setBelowThreshold(true);
 911               }
 912             }
 913             fr.setColour(name = newcol.getName(), gcol);
 914           }
 915           else
 916           {
 917             Color color = new Color(
 918                     Integer.parseInt(jucs.getColour(i).getRGB(), 16));
 919             fr.setColour(name = jucs.getColour(i).getName(),
 920                     new FeatureColour(color));
 921           }
 922           fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
 923         }
 924         if (table != null)
 925         {
 926           resetTable(null);
 927           Object[][] data = ((FeatureTableModel) table.getModel())
 928                   .getData();
 929           ensureOrder(data);
 930           updateFeatureRenderer(data, false);
 931           table.repaint();
 932         }
 933       } catch (Exception ex)
 934       {
 935         System.out.println("Error loading User Colour File\n" + ex);
 936       }
 937     }
 938   }
 939
 940   void save()
 941   {
 942     JalviewFileChooser chooser = new JalviewFileChooser("fc",
 943             "Sequence Feature Colours");
 944     chooser.setFileView(new JalviewFileView());
 945     chooser.setDialogTitle(
 946             MessageManager.getString("label.save_feature_colours"));
 947     chooser.setToolTipText(MessageManager.getString("action.save"));
 948
 949     int value = chooser.showSaveDialog(this);
 950
 951     if (value == JalviewFileChooser.APPROVE_OPTION)
 952     {
 953       String choice = chooser.getSelectedFile().getPath();
 954       jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 955       ucs.setSchemeName("Sequence Features");
 956       try
 957       {
 958         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 959                 new FileOutputStream(choice), "UTF-8"));
 960
 961         Set<String> fr_colours = fr.getAllFeatureColours();
 962         Iterator<String> e = fr_colours.iterator();
 963         float[] sortOrder = new float[fr_colours.size()];
 964         String[] sortTypes = new String[fr_colours.size()];
 965         int i = 0;
 966         while (e.hasNext())
 967         {
 968           sortTypes[i] = e.next();
 969           sortOrder[i] = fr.getOrder(sortTypes[i]);
 970           i++;
 971         }
 972         QuickSort.sort(sortOrder, sortTypes);
 973         sortOrder = null;
 974         for (i = 0; i < sortTypes.length; i++)
 975         {
 976           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 977           col.setName(sortTypes[i]);
 978           FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
 979           if (fcol.isSimpleColour())
 980           {
 981             col.setRGB(Format.getHexString(fcol.getColour()));
 982           }
 983           else
 984           {
 985             col.setRGB(Format.getHexString(fcol.getMaxColour()));
 986             col.setMin(fcol.getMin());
 987             col.setMax(fcol.getMax());
 988             col.setMinRGB(
 989                     jalview.util.Format.getHexString(fcol.getMinColour()));
 990             col.setAutoScale(fcol.isAutoScaled());
 991             col.setThreshold(fcol.getThreshold());
 992             col.setColourByLabel(fcol.isColourByLabel());
 993             col.setThreshType(fcol.isAboveThreshold() ? "ABOVE"
 994                     : (fcol.isBelowThreshold() ? "BELOW" : "NONE"));
 995           }
 996           ucs.addColour(col);
 997         }
 998         ucs.marshal(out);
 999         out.close();
1000       } catch (Exception ex)
1001       {
1002         ex.printStackTrace();
1003       }
1004     }
1005   }
1006
1007   public void invertSelection()
1008   {
1009     for (int i = 0; i < table.getRowCount(); i++)
1010     {
1011       Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
1012
1013       table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
1014     }
1015   }
1016
1017   public void orderByAvWidth()
1018   {
1019     if (table == null || table.getModel() == null)
1020     {
1021       return;
1022     }
1023     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
1024     float[] width = new float[data.length];
1025     float[] awidth;
1026     float max = 0;
1027
1028     for (int i = 0; i < data.length; i++)
1029     {
1030       awidth = typeWidth.get(data[i][TYPE_COLUMN]);
1031       if (awidth[0] > 0)
1032       {
1033         width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
1034         // weight - but have to make per
1035         // sequence, too (awidth[2])
1036         // if (width[i]==1) // hack to distinguish single width sequences.
1037       }
1038       else
1039       {
1040         width[i] = 0;
1041       }
1042       if (max < width[i])
1043       {
1044         max = width[i];
1045       }
1046     }
1047     boolean sort = false;
1048     for (int i = 0; i < width.length; i++)
1049     {
1050       // awidth = (float[]) typeWidth.get(data[i][0]);
1051       if (width[i] == 0)
1052       {
1053         width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString());
1054         if (width[i] < 0)
1055         {
1056           width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(),
1057                   i / data.length);
1058         }
1059       }
1060       else
1061       {
1062         width[i] /= max; // normalize
1063         fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later
1064       }
1065       if (i > 0)
1066       {
1067         sort = sort || width[i - 1] > width[i];
1068       }
1069     }
1070     if (sort)
1071     {
1072       jalview.util.QuickSort.sort(width, data);
1073       // update global priority order
1074     }
1075
1076     updateFeatureRenderer(data, false);
1077     table.repaint();
1078   }
1079
1080   public void close()
1081   {
1082     try
1083     {
1084       frame.setClosed(true);
1085     } catch (Exception exe)
1086     {
1087     }
1088
1089   }
1090
1091   public void updateFeatureRenderer(Object[][] data)
1092   {
1093     updateFeatureRenderer(data, true);
1094   }
1095
1096   /**
1097    * Update the priority order of features; only repaint if this changed the order
1098    * of visible features
1099    *
1100    * @param data
1101    * @param visibleNew
1102    */
1103   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
1104   {
1105     FeatureSettingsBean[] rowData = getTableAsBeans(data);
1106
1107     if (fr.setFeaturePriority(rowData, visibleNew))
1108     {
1109       af.alignPanel.paintAlignment(true, true);
1110     }
1111   }
1112
1113   /**
1114    * Converts table data into an array of data beans
1115    */
1116   private FeatureSettingsBean[] getTableAsBeans(Object[][] data)
1117   {
1118     FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length];
1119     for (int i = 0; i < data.length; i++)
1120     {
1121       String type = (String) data[i][TYPE_COLUMN];
1122       FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN];
1123       KeyedMatcherSetI theFilter = (KeyedMatcherSetI) data[i][FILTER_COLUMN];
1124       Boolean isShown = (Boolean) data[i][SHOW_COLUMN];
1125       rowData[i] = new FeatureSettingsBean(type, colour, theFilter,
1126               isShown);
1127     }
1128     return rowData;
1129   }
1130
1131   private void jbInit() throws Exception
1132   {
1133     this.setLayout(new BorderLayout());
1134
1135     JPanel settingsPane = new JPanel();
1136     settingsPane.setLayout(new BorderLayout());
1137
1138     dasSettingsPane.setLayout(new BorderLayout());
1139
1140     JPanel bigPanel = new JPanel();
1141     bigPanel.setLayout(new BorderLayout());
1142
1143     groupPanel = new JPanel();
1144     bigPanel.add(groupPanel, BorderLayout.NORTH);
1145
1146     JButton invert = new JButton(
1147             MessageManager.getString("label.invert_selection"));
1148     invert.setFont(JvSwingUtils.getLabelFont());
1149     invert.addActionListener(new ActionListener()
1150     {
1151       @Override
1152       public void actionPerformed(ActionEvent e)
1153       {
1154         invertSelection();
1155       }
1156     });
1157
1158     JButton optimizeOrder = new JButton(
1159             MessageManager.getString("label.optimise_order"));
1160     optimizeOrder.setFont(JvSwingUtils.getLabelFont());
1161     optimizeOrder.addActionListener(new ActionListener()
1162     {
1163       @Override
1164       public void actionPerformed(ActionEvent e)
1165       {
1166         orderByAvWidth();
1167       }
1168     });
1169
1170     JButton sortByScore = new JButton(
1171             MessageManager.getString("label.seq_sort_by_score"));
1172     sortByScore.setFont(JvSwingUtils.getLabelFont());
1173     sortByScore.addActionListener(new ActionListener()
1174     {
1175       @Override
1176       public void actionPerformed(ActionEvent e)
1177       {
1178         af.avc.sortAlignmentByFeatureScore(null);
1179       }
1180     });
1181     JButton sortByDens = new JButton(
1182             MessageManager.getString("label.sequence_sort_by_density"));
1183     sortByDens.setFont(JvSwingUtils.getLabelFont());
1184     sortByDens.addActionListener(new ActionListener()
1185     {
1186       @Override
1187       public void actionPerformed(ActionEvent e)
1188       {
1189         af.avc.sortAlignmentByFeatureDensity(null);
1190       }
1191     });
1192
1193     JButton help = new JButton(MessageManager.getString("action.help"));
1194     help.setFont(JvSwingUtils.getLabelFont());
1195     help.addActionListener(new ActionListener()
1196     {
1197       @Override
1198       public void actionPerformed(ActionEvent e)
1199       {
1200         try
1201         {
1202           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1203         } catch (HelpSetException e1)
1204         {
1205           e1.printStackTrace();
1206         }
1207       }
1208     });
1209     help.setFont(JvSwingUtils.getLabelFont());
1210     help.setText(MessageManager.getString("action.help"));
1211     help.addActionListener(new ActionListener()
1212     {
1213       @Override
1214       public void actionPerformed(ActionEvent e)
1215       {
1216         try
1217         {
1218           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1219         } catch (HelpSetException e1)
1220         {
1221           e1.printStackTrace();
1222         }
1223       }
1224     });
1225
1226     JButton cancel = new JButton(MessageManager.getString("action.cancel"));
1227     cancel.setFont(JvSwingUtils.getLabelFont());
1228     cancel.addActionListener(new ActionListener()
1229     {
1230       @Override
1231       public void actionPerformed(ActionEvent e)
1232       {
1233         fr.setTransparency(originalTransparency);
1234         fr.setFeatureFilters(originalFilters);
1235         updateFeatureRenderer(originalData);
1236         close();
1237       }
1238     });
1239
1240     JButton ok = new JButton(MessageManager.getString("action.ok"));
1241     ok.setFont(JvSwingUtils.getLabelFont());
1242     ok.addActionListener(new ActionListener()
1243     {
1244       @Override
1245       public void actionPerformed(ActionEvent e)
1246       {
1247         close();
1248       }
1249     });
1250
1251     JButton loadColours = new JButton(
1252             MessageManager.getString("label.load_colours"));
1253     loadColours.setFont(JvSwingUtils.getLabelFont());
1254     loadColours.addActionListener(new ActionListener()
1255     {
1256       @Override
1257       public void actionPerformed(ActionEvent e)
1258       {
1259         load();
1260       }
1261     });
1262
1263     JButton saveColours = new JButton(
1264             MessageManager.getString("label.save_colours"));
1265     saveColours.setFont(JvSwingUtils.getLabelFont());
1266     saveColours.addActionListener(new ActionListener()
1267     {
1268       @Override
1269       public void actionPerformed(ActionEvent e)
1270       {
1271         save();
1272       }
1273     });
1274     transparency.addChangeListener(new ChangeListener()
1275     {
1276       @Override
1277       public void stateChanged(ChangeEvent evt)
1278       {
1279         if (!inConstruction)
1280         {
1281           fr.setTransparency((100 - transparency.getValue()) / 100f);
1282           af.alignPanel.paintAlignment(true, true);
1283         }
1284       }
1285     });
1286
1287     transparency.setMaximum(70);
1288     transparency.setToolTipText(
1289             MessageManager.getString("label.transparency_tip"));
1290     fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
1291     fetchDAS.addActionListener(new ActionListener()
1292     {
1293       @Override
1294       public void actionPerformed(ActionEvent e)
1295       {
1296         fetchDAS_actionPerformed(e);
1297       }
1298     });
1299     saveDAS.setText(MessageManager.getString("action.save_as_default"));
1300     saveDAS.addActionListener(new ActionListener()
1301     {
1302       @Override
1303       public void actionPerformed(ActionEvent e)
1304       {
1305         saveDAS_actionPerformed(e);
1306       }
1307     });
1308
1309     JPanel dasButtonPanel = new JPanel();
1310     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
1311     dasSettingsPane.setBorder(null);
1312     cancelDAS.setEnabled(false);
1313     cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
1314     cancelDAS.addActionListener(new ActionListener()
1315     {
1316       @Override
1317       public void actionPerformed(ActionEvent e)
1318       {
1319         cancelDAS_actionPerformed(e);
1320       }
1321     });
1322
1323     JPanel transPanel = new JPanel(new GridLayout(1, 2));
1324     bigPanel.add(transPanel, BorderLayout.SOUTH);
1325
1326     JPanel transbuttons = new JPanel(new GridLayout(5, 1));
1327     transbuttons.add(optimizeOrder);
1328     transbuttons.add(invert);
1329     transbuttons.add(sortByScore);
1330     transbuttons.add(sortByDens);
1331     transbuttons.add(help);
1332     transPanel.add(transparency);
1333     transPanel.add(transbuttons);
1334
1335     JPanel buttonPanel = new JPanel();
1336     buttonPanel.add(ok);
1337     buttonPanel.add(cancel);
1338     buttonPanel.add(loadColours);
1339     buttonPanel.add(saveColours);
1340     bigPanel.add(scrollPane, BorderLayout.CENTER);
1341     dasSettingsPane.add(dasButtonPanel, BorderLayout.SOUTH);
1342     dasButtonPanel.add(fetchDAS);
1343     dasButtonPanel.add(cancelDAS);
1344     dasButtonPanel.add(saveDAS);
1345     settingsPane.add(bigPanel, BorderLayout.CENTER);
1346     settingsPane.add(buttonPanel, BorderLayout.SOUTH);
1347     this.add(settingsPane);
1348   }
1349
1350   public void fetchDAS_actionPerformed(ActionEvent e)
1351   {
1352     fetchDAS.setEnabled(false);
1353     cancelDAS.setEnabled(true);
1354     dassourceBrowser.setGuiEnabled(false);
1355     Vector<jalviewSourceI> selectedSources = dassourceBrowser
1356             .getSelectedSources();
1357     doDasFeatureFetch(selectedSources, true, true);
1358   }
1359
1360   /**
1361    * get the features from selectedSources for all or the current selection
1362    *
1363    * @param selectedSources
1364    * @param checkDbRefs
1365    * @param promptFetchDbRefs
1366    */
1367   private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
1368           boolean checkDbRefs, boolean promptFetchDbRefs)
1369   {
1370     SequenceI[] dataset, seqs;
1371     int iSize;
1372     AlignmentViewport vp = af.getViewport();
1373     if (vp.getSelectionGroup() != null
1374             && vp.getSelectionGroup().getSize() > 0)
1375     {
1376       iSize = vp.getSelectionGroup().getSize();
1377       dataset = new SequenceI[iSize];
1378       seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
1379     }
1380     else
1381     {
1382       iSize = vp.getAlignment().getHeight();
1383       seqs = vp.getAlignment().getSequencesArray();
1384     }
1385
1386     dataset = new SequenceI[iSize];
1387     for (int i = 0; i < iSize; i++)
1388     {
1389       dataset[i] = seqs[i].getDatasetSequence();
1390     }
1391
1392     cancelDAS.setEnabled(true);
1393     dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
1394             this, selectedSources, checkDbRefs, promptFetchDbRefs);
1395     af.getViewport().setShowSequenceFeatures(true);
1396     af.showSeqFeatures.setSelected(true);
1397   }
1398
1399   /**
1400    * blocking call to initialise the das source browser
1401    */
1402   public void initDasSources()
1403   {
1404     dassourceBrowser.initDasSources();
1405   }
1406
1407   /**
1408    * examine the current list of das sources and return any matching the given
1409    * nicknames in sources
1410    *
1411    * @param sources
1412    *          Vector of Strings to resolve to DAS source nicknames.
1413    * @return sources that are present in source list.
1414    */
1415   public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
1416   {
1417     return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
1418   }
1419
1420   /**
1421    * get currently selected das sources. ensure you have called initDasSources
1422    * before calling this.
1423    *
1424    * @return vector of selected das source nicknames
1425    */
1426   public Vector<jalviewSourceI> getSelectedSources()
1427   {
1428     return dassourceBrowser.getSelectedSources();
1429   }
1430
1431   /**
1432    * properly initialise DAS fetcher and then initiate a new thread to fetch
1433    * features from the named sources (rather than any turned on by default)
1434    *
1435    * @param sources
1436    * @param block
1437    *          if true then runs in same thread, otherwise passes to the Swing
1438    *          executor
1439    */
1440   public void fetchDasFeatures(Vector<String> sources, boolean block)
1441   {
1442     initDasSources();
1443     List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
1444             .resolveSourceNicknames(sources);
1445     if (resolved.size() == 0)
1446     {
1447       resolved = dassourceBrowser.getSelectedSources();
1448     }
1449     if (resolved.size() > 0)
1450     {
1451       final List<jalviewSourceI> dassources = resolved;
1452       fetchDAS.setEnabled(false);
1453       // cancelDAS.setEnabled(true); doDasFetch does this.
1454       Runnable fetcher = new Runnable()
1455       {
1456
1457         @Override
1458         public void run()
1459         {
1460           doDasFeatureFetch(dassources, true, false);
1461
1462         }
1463       };
1464       if (block)
1465       {
1466         fetcher.run();
1467       }
1468       else
1469       {
1470         SwingUtilities.invokeLater(fetcher);
1471       }
1472     }
1473   }
1474
1475   public void saveDAS_actionPerformed(ActionEvent e)
1476   {
1477     dassourceBrowser
1478             .saveProperties(jalview.bin.Cache.applicationProperties);
1479   }
1480
1481   public void complete()
1482   {
1483     fetchDAS.setEnabled(true);
1484     cancelDAS.setEnabled(false);
1485     dassourceBrowser.setGuiEnabled(true);
1486
1487   }
1488
1489   public void cancelDAS_actionPerformed(ActionEvent e)
1490   {
1491     if (dasFeatureFetcher != null)
1492     {
1493       dasFeatureFetcher.cancel();
1494     }
1495     complete();
1496   }
1497
1498   public void noDasSourceActive()
1499   {
1500     complete();
1501     JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
1502             MessageManager.getString("label.no_das_sources_selected_warn"),
1503             MessageManager.getString("label.no_das_sources_selected_title"),
1504             JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
1505   }
1506
1507   // ///////////////////////////////////////////////////////////////////////
1508   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
1509   // ///////////////////////////////////////////////////////////////////////
1510   class FeatureTableModel extends AbstractTableModel
1511   {
1512     /*
1513      * column indices of fields in Feature Settings table
1514      */
1515     static final int TYPE_COLUMN = 0;
1516
1517     static final int COLOUR_COLUMN = 1;
1518
1519     static final int FILTER_COLUMN = 2;
1520
1521     static final int SHOW_COLUMN = 3;
1522
1523     private String[] columnNames = {
1524         MessageManager.getString("label.feature_type"),
1525         MessageManager.getString("action.colour"),
1526         MessageManager.getString("label.filter"),
1527         MessageManager.getString("label.show") };
1528
1529     private Object[][] data;
1530
1531     FeatureTableModel(Object[][] data)
1532     {
1533       this.data = data;
1534     }
1535
1536     public Object[][] getData()
1537     {
1538       return data;
1539     }
1540
1541     public void setData(Object[][] data)
1542     {
1543       this.data = data;
1544     }
1545
1546     @Override
1547     public int getColumnCount()
1548     {
1549       return columnNames.length;
1550     }
1551
1552     public Object[] getRow(int row)
1553     {
1554       return data[row];
1555     }
1556
1557     @Override
1558     public int getRowCount()
1559     {
1560       return data.length;
1561     }
1562
1563     @Override
1564     public String getColumnName(int col)
1565     {
1566       return columnNames[col];
1567     }
1568
1569     @Override
1570     public Object getValueAt(int row, int col)
1571     {
1572       return data[row][col];
1573     }
1574
1575     /**
1576      * Answers the class of the object in column c of the first row of the table
1577      */
1578     @Override
1579     public Class<?> getColumnClass(int c)
1580     {
1581       Object v = getValueAt(0, c);
1582       return v == null ? null : v.getClass();
1583     }
1584
1585     @Override
1586     public boolean isCellEditable(int row, int col)
1587     {
1588       return col == 0 ? false : true;
1589     }
1590
1591     @Override
1592     public void setValueAt(Object value, int row, int col)
1593     {
1594       data[row][col] = value;
1595       fireTableCellUpdated(row, col);
1596       updateFeatureRenderer(data);
1597     }
1598
1599   }
1600
1601   class ColorRenderer extends JLabel implements TableCellRenderer
1602   {
1603     javax.swing.border.Border unselectedBorder = null;
1604
1605     javax.swing.border.Border selectedBorder = null;
1606
1607     final String baseTT = "Click to edit, right/apple click for menu.";
1608
1609     public ColorRenderer()
1610     {
1611       setOpaque(true); // MUST do this for background to show up.
1612       setHorizontalTextPosition(SwingConstants.CENTER);
1613       setVerticalTextPosition(SwingConstants.CENTER);
1614     }
1615
1616     @Override
1617     public Component getTableCellRendererComponent(JTable tbl, Object color,
1618             boolean isSelected, boolean hasFocus, int row, int column)
1619     {
1620       FeatureColourI cellColour = (FeatureColourI) color;
1621       setOpaque(true);
1622       setToolTipText(baseTT);
1623       setBackground(tbl.getBackground());
1624       if (!cellColour.isSimpleColour())
1625       {
1626         Rectangle cr = tbl.getCellRect(row, column, false);
1627         FeatureSettings.renderGraduatedColor(this, cellColour,
1628                 (int) cr.getWidth(), (int) cr.getHeight());
1629       }
1630       else
1631       {
1632         this.setText("");
1633         this.setIcon(null);
1634         setBackground(cellColour.getColour());
1635       }
1636       if (isSelected)
1637       {
1638         if (selectedBorder == null)
1639         {
1640           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1641                   tbl.getSelectionBackground());
1642         }
1643         setBorder(selectedBorder);
1644       }
1645       else
1646       {
1647         if (unselectedBorder == null)
1648         {
1649           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1650                   tbl.getBackground());
1651         }
1652         setBorder(unselectedBorder);
1653       }
1654
1655       return this;
1656     }
1657   }
1658
1659   class FilterRenderer extends JLabel implements TableCellRenderer
1660   {
1661     javax.swing.border.Border unselectedBorder = null;
1662
1663     javax.swing.border.Border selectedBorder = null;
1664
1665     public FilterRenderer()
1666     {
1667       setOpaque(true); // MUST do this for background to show up.
1668       setHorizontalTextPosition(SwingConstants.CENTER);
1669       setVerticalTextPosition(SwingConstants.CENTER);
1670     }
1671
1672     @Override
1673     public Component getTableCellRendererComponent(JTable tbl,
1674             Object filter, boolean isSelected, boolean hasFocus, int row,
1675             int column)
1676     {
1677       KeyedMatcherSetI theFilter = (KeyedMatcherSetI) filter;
1678       setOpaque(true);
1679       String asText = theFilter.toString();
1680       setBackground(tbl.getBackground());
1681       this.setText(asText);
1682       this.setIcon(null);
1683
1684       if (isSelected)
1685       {
1686         if (selectedBorder == null)
1687         {
1688           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1689                   tbl.getSelectionBackground());
1690         }
1691         setBorder(selectedBorder);
1692       }
1693       else
1694       {
1695         if (unselectedBorder == null)
1696         {
1697           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1698                   tbl.getBackground());
1699         }
1700         setBorder(unselectedBorder);
1701       }
1702
1703       return this;
1704     }
1705   }
1706
1707   /**
1708    * update comp using rendering settings from gcol
1709    *
1710    * @param comp
1711    * @param gcol
1712    */
1713   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
1714   {
1715     int w = comp.getWidth(), h = comp.getHeight();
1716     if (w < 20)
1717     {
1718       w = (int) comp.getPreferredSize().getWidth();
1719       h = (int) comp.getPreferredSize().getHeight();
1720       if (w < 20)
1721       {
1722         w = 80;
1723         h = 12;
1724       }
1725     }
1726     renderGraduatedColor(comp, gcol, w, h);
1727   }
1728
1729   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
1730           int w, int h)
1731   {
1732     boolean thr = false;
1733     StringBuilder tt = new StringBuilder();
1734     StringBuilder tx = new StringBuilder();
1735
1736     if (gcol.isColourByAttribute())
1737     {
1738       tx.append(String.join(":", gcol.getAttributeName()));
1739     }
1740     else if (!gcol.isColourByLabel())
1741     {
1742       tx.append(MessageManager.getString("label.score"));
1743     }
1744     tx.append(" ");
1745     if (gcol.isAboveThreshold())
1746     {
1747       thr = true;
1748       tx.append(">");
1749       tt.append("Thresholded (Above ").append(gcol.getThreshold())
1750               .append(") ");
1751     }
1752     if (gcol.isBelowThreshold())
1753     {
1754       thr = true;
1755       tx.append("<");
1756       tt.append("Thresholded (Below ").append(gcol.getThreshold())
1757               .append(") ");
1758     }
1759     if (gcol.isColourByLabel())
1760     {
1761       tt.append("Coloured by label text. ").append(tt);
1762       if (thr)
1763       {
1764         tx.append(" ");
1765       }
1766       if (!gcol.isColourByAttribute())
1767       {
1768         tx.append("Label");
1769       }
1770       comp.setIcon(null);
1771     }
1772     else
1773     {
1774       Color newColor = gcol.getMaxColour();
1775       comp.setBackground(newColor);
1776       // System.err.println("Width is " + w / 2);
1777       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
1778       comp.setIcon(ficon);
1779       // tt+="RGB value: Max (" + newColor.getRed() + ", "
1780       // + newColor.getGreen() + ", " + newColor.getBlue()
1781       // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
1782       // + ", " + minCol.getBlue() + ")");
1783     }
1784     comp.setHorizontalAlignment(SwingConstants.CENTER);
1785     comp.setText(tx.toString());
1786     if (tt.length() > 0)
1787     {
1788       if (comp.getToolTipText() == null)
1789       {
1790         comp.setToolTipText(tt.toString());
1791       }
1792       else
1793       {
1794         comp.setToolTipText(
1795                 tt.append(" ").append(comp.getToolTipText()).toString());
1796       }
1797     }
1798   }
1799
1800   class ColorEditor extends AbstractCellEditor
1801           implements TableCellEditor, ActionListener
1802   {
1803     FeatureSettings me;
1804
1805     FeatureColourI currentColor;
1806
1807     FeatureTypeSettings chooser;
1808
1809     String type;
1810
1811     JButton button;
1812
1813     JColorChooser colorChooser;
1814
1815     JDialog dialog;
1816
1817     protected static final String EDIT = "edit";
1818
1819     int rowSelected = 0;
1820
1821     public ColorEditor(FeatureSettings me)
1822     {
1823       this.me = me;
1824       // Set up the editor (from the table's point of view),
1825       // which is a button.
1826       // This button brings up the color chooser dialog,
1827       // which is the editor from the user's point of view.
1828       button = new JButton();
1829       button.setActionCommand(EDIT);
1830       button.addActionListener(this);
1831       button.setBorderPainted(false);
1832       // Set up the dialog that the button brings up.
1833       colorChooser = new JColorChooser();
1834       dialog = JColorChooser.createDialog(button,
1835               MessageManager.getString("label.select_colour"), true, // modal
1836               colorChooser, this, // OK button handler
1837               null); // no CANCEL button handler
1838     }
1839
1840     /**
1841      * Handles events from the editor button and from the dialog's OK button.
1842      */
1843     @Override
1844     public void actionPerformed(ActionEvent e)
1845     {
1846       // todo test e.getSource() instead here
1847       if (EDIT.equals(e.getActionCommand()))
1848       {
1849         // The user has clicked the cell, so
1850         // bring up the dialog.
1851         if (currentColor.isSimpleColour())
1852         {
1853           // bring up simple color chooser
1854           button.setBackground(currentColor.getColour());
1855           colorChooser.setColor(currentColor.getColour());
1856           dialog.setVisible(true);
1857         }
1858         else
1859         {
1860           // bring up graduated chooser.
1861           chooser = new FeatureTypeSettings(me.fr, type);
1862           chooser.setRequestFocusEnabled(true);
1863           chooser.requestFocus();
1864           chooser.addActionListener(this);
1865           chooser.showTab(true);
1866         }
1867         // Make the renderer reappear.
1868         fireEditingStopped();
1869
1870       }
1871       else
1872       {
1873         if (currentColor.isSimpleColour())
1874         {
1875           /*
1876            * read off colour picked in colour chooser after OK pressed
1877            */
1878           currentColor = new FeatureColour(colorChooser.getColor());
1879           me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
1880         }
1881         else
1882         {
1883           /*
1884            * after OK in variable colour dialog, any changes to colour
1885            * (or filters!) are already set in FeatureRenderer, so just
1886            * update table data without triggering updateFeatureRenderer
1887            */
1888           currentColor = fr.getFeatureColours().get(type);
1889           KeyedMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
1890           if (currentFilter == null)
1891           {
1892             currentFilter = new KeyedMatcherSet();
1893           }
1894           Object[] data = ((FeatureTableModel) table.getModel())
1895                   .getData()[rowSelected];
1896           data[COLOUR_COLUMN] = currentColor;
1897           data[FILTER_COLUMN] = currentFilter;
1898         }
1899         fireEditingStopped();
1900         me.table.validate();
1901       }
1902     }
1903
1904     // Implement the one CellEditor method that AbstractCellEditor doesn't.
1905     @Override
1906     public Object getCellEditorValue()
1907     {
1908       return currentColor;
1909     }
1910
1911     // Implement the one method defined by TableCellEditor.
1912     @Override
1913     public Component getTableCellEditorComponent(JTable theTable, Object value,
1914             boolean isSelected, int row, int column)
1915     {
1916       currentColor = (FeatureColourI) value;
1917       this.rowSelected = row;
1918       type = me.table.getValueAt(row, TYPE_COLUMN).toString();
1919       button.setOpaque(true);
1920       button.setBackground(me.getBackground());
1921       if (!currentColor.isSimpleColour())
1922       {
1923         JLabel btn = new JLabel();
1924         btn.setSize(button.getSize());
1925         FeatureSettings.renderGraduatedColor(btn, currentColor);
1926         button.setBackground(btn.getBackground());
1927         button.setIcon(btn.getIcon());
1928         button.setText(btn.getText());
1929       }
1930       else
1931       {
1932         button.setText("");
1933         button.setIcon(null);
1934         button.setBackground(currentColor.getColour());
1935       }
1936       return button;
1937     }
1938   }
1939
1940   /**
1941    * The cell editor for the Filter column. It displays the text of any filters
1942    * for the feature type in that row (in full as a tooltip, possible abbreviated
1943    * as display text). On click in the cell, opens the Feature Display Settings
1944    * dialog at the Filters tab.
1945    */
1946   class FilterEditor extends AbstractCellEditor
1947           implements TableCellEditor, ActionListener
1948   {
1949     FeatureSettings me;
1950
1951     KeyedMatcherSetI currentFilter;
1952
1953     Point lastLocation;
1954
1955     String type;
1956
1957     JButton button;
1958
1959     protected static final String EDIT = "edit";
1960
1961     int rowSelected = 0;
1962
1963     public FilterEditor(FeatureSettings me)
1964     {
1965       this.me = me;
1966       button = new JButton();
1967       button.setActionCommand(EDIT);
1968       button.addActionListener(this);
1969       button.setBorderPainted(false);
1970     }
1971
1972     /**
1973      * Handles events from the editor button
1974      */
1975     @Override
1976     public void actionPerformed(ActionEvent e)
1977     {
1978       if (button == e.getSource())
1979       {
1980         FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
1981         chooser.addActionListener(this);
1982         chooser.setRequestFocusEnabled(true);
1983         chooser.requestFocus();
1984         if (lastLocation != null)
1985         {
1986           // todo open at its last position on screen
1987           chooser.setBounds(lastLocation.x, lastLocation.y,
1988                   chooser.getWidth(), chooser.getHeight());
1989           chooser.validate();
1990         }
1991         chooser.showTab(false);
1992         fireEditingStopped();
1993       }
1994       else if (e.getSource() instanceof Component)
1995       {
1996
1997         /*
1998          * after OK in variable colour dialog, any changes to filter
1999          * (or colours!) are already set in FeatureRenderer, so just
2000          * update table data without triggering updateFeatureRenderer
2001          */
2002         FeatureColourI currentColor = fr.getFeatureColours().get(type);
2003         currentFilter = me.fr.getFeatureFilter(type);
2004         if (currentFilter == null)
2005         {
2006           currentFilter = new KeyedMatcherSet();
2007         }
2008         Object[] data = ((FeatureTableModel) table.getModel())
2009                 .getData()[rowSelected];
2010         data[COLOUR_COLUMN] = currentColor;
2011         data[FILTER_COLUMN] = currentFilter;
2012         fireEditingStopped();
2013         me.table.validate();
2014       }
2015     }
2016
2017     @Override
2018     public Object getCellEditorValue()
2019     {
2020       return currentFilter;
2021     }
2022
2023     @Override
2024     public Component getTableCellEditorComponent(JTable theTable, Object value,
2025             boolean isSelected, int row, int column)
2026     {
2027       currentFilter = (KeyedMatcherSetI) value;
2028       this.rowSelected = row;
2029       type = me.table.getValueAt(row, TYPE_COLUMN).toString();
2030       button.setOpaque(true);
2031       button.setBackground(me.getBackground());
2032       button.setText(currentFilter.toString());
2033       button.setToolTipText(currentFilter.toString());
2034       button.setIcon(null);
2035       return button;
2036     }
2037   }
2038 }
2039
2040 class FeatureIcon implements Icon
2041 {
2042   FeatureColourI gcol;
2043
2044   Color backg;
2045
2046   boolean midspace = false;
2047
2048   int width = 50, height = 20;
2049
2050   int s1, e1; // start and end of midpoint band for thresholded symbol
2051
2052   Color mpcolour = Color.white;
2053
2054   FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
2055   {
2056     gcol = gfc;
2057     backg = bg;
2058     width = w;
2059     height = h;
2060     midspace = mspace;
2061     if (midspace)
2062     {
2063       s1 = width / 3;
2064       e1 = s1 * 2;
2065     }
2066     else
2067     {
2068       s1 = width / 2;
2069       e1 = s1;
2070     }
2071   }
2072
2073   @Override
2074   public int getIconWidth()
2075   {
2076     return width;
2077   }
2078
2079   @Override
2080   public int getIconHeight()
2081   {
2082     return height;
2083   }
2084
2085   @Override
2086   public void paintIcon(Component c, Graphics g, int x, int y)
2087   {
2088
2089     if (gcol.isColourByLabel())
2090     {
2091       g.setColor(backg);
2092       g.fillRect(0, 0, width, height);
2093       // need an icon here.
2094       g.setColor(gcol.getMaxColour());
2095
2096       g.setFont(new Font("Verdana", Font.PLAIN, 9));
2097
2098       // g.setFont(g.getFont().deriveFont(
2099       // AffineTransform.getScaleInstance(
2100       // width/g.getFontMetrics().stringWidth("Label"),
2101       // height/g.getFontMetrics().getHeight())));
2102
2103       g.drawString(MessageManager.getString("label.label"), 0, 0);
2104
2105     }
2106     else
2107     {
2108       Color minCol = gcol.getMinColour();
2109       g.setColor(minCol);
2110       g.fillRect(0, 0, s1, height);
2111       if (midspace)
2112       {
2113         g.setColor(Color.white);
2114         g.fillRect(s1, 0, e1 - s1, height);
2115       }
2116       g.setColor(gcol.getMaxColour());
2117       g.fillRect(0, e1, width - e1, height);
2118     }
2119   }
2120 }