src/jalview/gui/FeatureSettings.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import java.io.*;
  22 import java.util.*;
  23
  24 import java.awt.*;
  25 import java.awt.event.*;
  26 import java.beans.PropertyChangeEvent;
  27 import java.beans.PropertyChangeListener;
  28
  29 import javax.swing.*;
  30 import javax.swing.event.*;
  31 import javax.swing.table.*;
  32
  33 import jalview.datamodel.*;
  34 import jalview.io.*;
  35
  36 public class FeatureSettings
  37     extends JPanel
  38 {
  39   DasSourceBrowser dassourceBrowser;
  40   jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
  41   JPanel settingsPane = new JPanel();
  42   JPanel dasSettingsPane = new JPanel();
  43
  44   final FeatureRenderer fr;
  45   public final AlignFrame af;
  46   Object[][] originalData;
  47   final JInternalFrame frame;
  48   JScrollPane scrollPane = new JScrollPane();
  49   JTable table;
  50   JPanel groupPanel;
  51   JSlider transparency = new JSlider();
  52
  53   JPanel transPanel = new JPanel(new FlowLayout());
  54
  55   public FeatureSettings(AlignFrame af)
  56   {
  57     this.af = af;
  58     fr = af.getFeatureRenderer();
  59
  60     transparency.setMaximum(100 - (int) (fr.transparency * 100));
  61
  62     try
  63     {
  64       jbInit();
  65     }
  66     catch (Exception ex)
  67     {
  68       ex.printStackTrace();
  69     }
  70
  71     table = new JTable();
  72     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
  73     table.setFont(new Font("Verdana", Font.PLAIN, 12));
  74     table.setDefaultRenderer(Color.class,
  75                              new ColorRenderer());
  76
  77     table.setDefaultEditor(Color.class,
  78                            new ColorEditor());
  79
  80     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
  81
  82     table.addMouseListener(new MouseAdapter()
  83     {
  84       public void mousePressed(MouseEvent evt)
  85       {
  86         selectedRow = table.rowAtPoint(evt.getPoint());
  87       }
  88     });
  89
  90     table.addMouseMotionListener(new MouseMotionAdapter()
  91     {
  92       public void mouseDragged(MouseEvent evt)
  93       {
  94         int newRow = table.rowAtPoint(evt.getPoint());
  95         if (newRow != selectedRow
  96             && selectedRow != -1
  97             && newRow != -1)
  98         {
  99           Object[] temp = new Object[3];
 100           temp[0] = table.getValueAt(selectedRow, 0);
 101           temp[1] = table.getValueAt(selectedRow, 1);
 102           temp[2] = table.getValueAt(selectedRow, 2);
 103
 104           table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
 105           table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
 106           table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
 107
 108           table.setValueAt(temp[0], newRow, 0);
 109           table.setValueAt(temp[1], newRow, 1);
 110           table.setValueAt(temp[2], newRow, 2);
 111
 112           selectedRow = newRow;
 113         }
 114       }
 115     });
 116
 117     scrollPane.setViewportView(table);
 118
 119     dassourceBrowser = new DasSourceBrowser();
 120     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 121
 122     if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
 123     {
 124       fr.findAllFeatures(true); // display everything!
 125     }
 126
 127     setTableData();
 128     final PropertyChangeListener change;
 129     final FeatureSettings fs=this;
 130     fr.addPropertyChangeListener(change=new PropertyChangeListener() {
 131       public void propertyChange(PropertyChangeEvent evt)
 132       {
 133         if (!fs.resettingTable && !fs.handlingUpdate) {
 134           fs.handlingUpdate=true;
 135           fs.resetTable(new String[] {}); // groups may be added
 136           fs.handlingUpdate=false;
 137         }
 138       }
 139
 140     });
 141
 142     frame = new JInternalFrame();
 143     frame.setContentPane(this);
 144     Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
 145     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 146     {
 147       public void internalFrameClosed(
 148           javax.swing.event.InternalFrameEvent evt)
 149       {
 150         fr.removePropertyChangeListener(change);
 151       }
 152       ;
 153     });
 154     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 155   }
 156   /**
 157    * true when Feature Settings are updating from feature renderer
 158    */
 159   private boolean handlingUpdate=false;
 160
 161   /**
 162    * contains a float[3] for each feature type string. created by setTableData
 163    */
 164   Hashtable typeWidth=null;
 165   synchronized public void setTableData()
 166   {
 167     if (fr.featureGroups == null)
 168     {
 169       fr.featureGroups = new Hashtable();
 170     }
 171     Vector allFeatures = new Vector();
 172     Vector allGroups = new Vector();
 173     SequenceFeature[] tmpfeatures;
 174     String group;
 175     for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
 176     {
 177       if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().
 178           getSequenceFeatures() == null)
 179       {
 180         continue;
 181       }
 182
 183       tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
 184           getDatasetSequence().getSequenceFeatures();
 185
 186       int index = 0;
 187       while (index < tmpfeatures.length)
 188       {
 189         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 190         {
 191           index++;
 192           continue;
 193         }
 194
 195         if (tmpfeatures[index].getFeatureGroup() != null)
 196         {
 197           group = tmpfeatures[index].featureGroup;
 198           if (!allGroups.contains(group))
 199           {
 200             allGroups.addElement(group);
 201
 202             boolean visible;
 203             if (fr.featureGroups.containsKey(group))
 204             {
 205               visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
 206             } else {
 207               visible=true; //initGroups || fr.av.featuresDisplayed.containsKey(tmpfeatures[index].getType());
 208             }
 209
 210             if (groupPanel == null)
 211             {
 212               groupPanel = new JPanel();
 213             }
 214
 215             boolean alreadyAdded = false;
 216             for (int g = 0; g < groupPanel.getComponentCount(); g++)
 217             {
 218               if ( ( (JCheckBox) groupPanel.getComponent(g))
 219                   .getText().equals(group))
 220               {
 221                 alreadyAdded = true;
 222                 break;
 223               }
 224             }
 225
 226             if (alreadyAdded)
 227             {
 228
 229               continue;
 230             }
 231
 232             fr.featureGroups.put(group, new Boolean(visible));
 233             final String grp = group;
 234             final JCheckBox check = new JCheckBox(group, visible);
 235             check.setFont(new Font("Serif", Font.BOLD, 12));
 236             check.addItemListener(new ItemListener()
 237             {
 238               public void itemStateChanged(ItemEvent evt)
 239               {
 240                 fr.featureGroups.put(check.getText(),
 241                                      new Boolean(check.isSelected()));
 242                 af.alignPanel.seqPanel.seqCanvas.repaint();
 243                 if (af.alignPanel.overviewPanel != null)
 244                 {
 245                   af.alignPanel.overviewPanel.updateOverviewImage();
 246                 }
 247
 248                 resetTable(new String[] { grp } );
 249               }
 250             });
 251             groupPanel.add(check);
 252           }
 253         }
 254
 255         if (!allFeatures.contains(tmpfeatures[index].getType()))
 256         {
 257           allFeatures.addElement(tmpfeatures[index].getType());
 258         }
 259         index++;
 260       }
 261     }
 262
 263     resetTable(null);
 264
 265     validate();
 266   }
 267   boolean resettingTable=false;
 268   void resetTable(String[] groupChanged)
 269   {
 270     resettingTable=true;
 271     typeWidth=new Hashtable();
 272     Vector groupchanged = new Vector();
 273     // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
 274     float[] avWidth=null;
 275     SequenceFeature[] tmpfeatures;
 276     String group = null, type;
 277     Vector visibleChecks = new Vector();
 278
 279     //Find out which features should be visible depending on which groups
 280     //are selected / deselected
 281     //and recompute average width ordering
 282     for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
 283     {
 284
 285       tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
 286           getDatasetSequence().getSequenceFeatures();
 287       if (tmpfeatures == null)
 288       {
 289         continue;
 290       }
 291
 292       int index = 0;
 293       while (index < tmpfeatures.length)
 294       {
 295         group = tmpfeatures[index].featureGroup;
 296
 297         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 298         {
 299           index++;
 300           continue;
 301         }
 302
 303         if (group == null || fr.featureGroups.get(group) == null ||
 304             ( (Boolean) fr.featureGroups.get(group)).booleanValue())
 305         {
 306           type = tmpfeatures[index].getType();
 307           if (!visibleChecks.contains(type))
 308           {
 309             visibleChecks.addElement(type);
 310           }
 311         }
 312         if (!typeWidth.containsKey(tmpfeatures[index].getType())) {
 313           typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]);
 314         } else {
 315           avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
 316         }
 317         avWidth[0]++;
 318         if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
 319         {
 320           avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
 321         } else {
 322           avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
 323         }
 324         index++;
 325       }
 326     }
 327
 328     int fSize = visibleChecks.size();
 329     Object[][] data = new Object[fSize][3];
 330     int dataIndex = 0;
 331
 332     if (fr.renderOrder != null)
 333     {
 334       if (!handlingUpdate)
 335         fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
 336       //First add the checks in the previous render order,
 337       //in case the window has been closed and reopened
 338       for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
 339       {
 340         type = fr.renderOrder[ro];
 341
 342         if (!visibleChecks.contains(type))
 343         {
 344           continue;
 345         }
 346
 347         data[dataIndex][0] = type;
 348         data[dataIndex][1] = fr.getColour(type);
 349         data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
 350         dataIndex++;
 351         visibleChecks.removeElement(type);
 352       }
 353     }
 354
 355     fSize = visibleChecks.size();
 356     for (int i = 0; i < fSize; i++)
 357     {
 358       //These must be extra features belonging to the group
 359       //which was just selected
 360       type = visibleChecks.elementAt(i).toString();
 361       data[dataIndex][0] = type;
 362
 363       data[dataIndex][1] = fr.getColour(type);
 364       if (data[dataIndex][1] == null)
 365       {
 366         //"Colour has been updated in another view!!"
 367         fr.renderOrder = null;
 368         return;
 369       }
 370
 371       data[dataIndex][2] = new Boolean(true);
 372       dataIndex++;
 373     }
 374
 375     if (originalData == null)
 376     {
 377       originalData = new Object[data.length][3];
 378       System.arraycopy(data, 0, originalData, 0, data.length);
 379     }
 380
 381     table.setModel(new FeatureTableModel(data));
 382     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 383
 384     if (groupPanel != null)
 385     {
 386       groupPanel.setLayout(
 387           new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
 388
 389       groupPanel.validate();
 390       bigPanel.add(groupPanel, BorderLayout.NORTH);
 391     }
 392
 393     updateFeatureRenderer(data, groupChanged!=null);
 394     resettingTable=false;
 395   }
 396   /**
 397    * reorder data based on the featureRenderers global priority list.
 398    * @param data
 399    */
 400   private void ensureOrder(Object[][] data)
 401   {
 402     boolean sort=false;
 403     float[] order = new float[data.length];
 404     for (int i=0;i<order.length; i++)
 405     {
 406       order[i] = fr.getOrder(data[i][0].toString());
 407       if (order[i]<0)
 408         order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
 409       if (i>1)
 410         sort = sort || order[i-1]>order[i];
 411     }
 412     if (sort)
 413       jalview.util.QuickSort.sort(order, data);
 414   }
 415
 416   void load()
 417   {
 418     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 419         getProperty(
 420             "LAST_DIRECTORY"), new String[]
 421         {"fc"},
 422         new String[]
 423         {"Sequence Feature Colours"}, "Sequence Feature Colours");
 424     chooser.setFileView(new jalview.io.JalviewFileView());
 425     chooser.setDialogTitle("Load Feature Colours");
 426     chooser.setToolTipText("Load");
 427
 428     int value = chooser.showOpenDialog(this);
 429
 430     if (value == JalviewFileChooser.APPROVE_OPTION)
 431     {
 432       File file = chooser.getSelectedFile();
 433
 434       try
 435       {
 436         InputStreamReader in = new InputStreamReader(new FileInputStream(
 437             file), "UTF-8");
 438
 439         jalview.binding.JalviewUserColours jucs = new jalview.binding.
 440             JalviewUserColours();
 441         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 442
 443         for (int i = jucs.getColourCount()-1; i >=0; i--)
 444         {
 445           String name;
 446           fr.setColour(name=jucs.getColour(i).getName(),
 447                        new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
 448                                                   16)));
 449           fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
 450         }
 451         if (table!=null) {
 452           resetTable(null);
 453           Object[][] data=((FeatureTableModel) table.getModel()).getData();
 454           ensureOrder(data);
 455           updateFeatureRenderer(data,false);
 456           table.repaint();
 457         }
 458       }
 459       catch (Exception ex)
 460       {
 461         System.out.println("Error loading User Colour File\n" + ex);
 462       }
 463     }
 464   }
 465
 466   void save()
 467   {
 468     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 469         getProperty(
 470             "LAST_DIRECTORY"), new String[]
 471         {"fc"},
 472         new String[]
 473         {"Sequence Feature Colours"}, "Sequence Feature Colours");
 474     chooser.setFileView(new jalview.io.JalviewFileView());
 475     chooser.setDialogTitle("Save Feature Colour Scheme");
 476     chooser.setToolTipText("Save");
 477
 478     int value = chooser.showSaveDialog(this);
 479
 480     if (value == JalviewFileChooser.APPROVE_OPTION)
 481     {
 482       String choice = chooser.getSelectedFile().getPath();
 483       jalview.binding.JalviewUserColours ucs = new jalview.binding.
 484           JalviewUserColours();
 485       ucs.setSchemeName("Sequence Features");
 486       try
 487       {
 488         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 489             new FileOutputStream(choice), "UTF-8"));
 490
 491         Enumeration e = fr.featureColours.keys();
 492         float[] sortOrder = new float[fr.featureColours.size()];
 493         String[] sortTypes = new String[fr.featureColours.size()];
 494         int i=0;
 495         while (e.hasMoreElements())
 496         {
 497           sortTypes[i] = e.nextElement().toString();
 498           sortOrder[i]  = fr.getOrder(sortTypes[i]);
 499           i++;
 500         }
 501         jalview.util.QuickSort.sort(sortOrder, sortTypes);
 502         sortOrder=null;
 503         for (i=0; i<sortTypes.length; i++) {
 504           jalview.binding.Colour col = new jalview.binding.Colour();
 505           col.setName(sortTypes[i]);
 506           col.setRGB(jalview.util.Format.getHexString(
 507               fr.getColour(col.getName())));
 508           ucs.addColour(col);
 509         }
 510         ucs.marshal(out);
 511         out.close();
 512       }
 513       catch (Exception ex)
 514       {
 515         ex.printStackTrace();
 516       }
 517     }
 518   }
 519
 520   public void invertSelection()
 521   {
 522     for (int i = 0; i < table.getRowCount(); i++)
 523     {
 524       Boolean value = (Boolean) table.getValueAt(i, 2);
 525
 526       table.setValueAt(
 527           new Boolean(!value.booleanValue()),
 528           i, 2);
 529     }
 530   }
 531   public void orderByAvWidth() {
 532     if (table==null || table.getModel()==null)
 533       return;
 534     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
 535     float[] width = new float[data.length];
 536     float[] awidth;
 537     float max=0;
 538     int num=0;
 539     for (int i=0;i<data.length;i++) {
 540        awidth = (float[]) typeWidth.get(data[i][0]);
 541        if (awidth[0]>0) {
 542          width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2])
 543          //if (width[i]==1) // hack to distinguish single width sequences.
 544          num++;
 545        } else {
 546          width[i]=0;
 547        }
 548        if (max<width[i])
 549          max=width[i];
 550     }
 551     boolean sort=false;
 552     for (int i=0;i<width.length; i++) {
 553       //awidth = (float[]) typeWidth.get(data[i][0]);
 554       if (width[i]==0)
 555       {
 556         width[i] = fr.getOrder(data[i][0].toString());
 557         if (width[i]<0)
 558         {
 559           width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
 560         }
 561       } else {
 562         width[i] /=max; // normalize
 563         fr.setOrder(data[i][0].toString(), width[i]); // store for later
 564       }
 565       if (i>0)
 566         sort = sort || width[i-1]>width[i];
 567     }
 568     if (sort)
 569       jalview.util.QuickSort.sort(width, data);
 570     // update global priority order
 571
 572     updateFeatureRenderer(data,false);
 573     table.repaint();
 574   }
 575   public void close()
 576   {
 577     try
 578     {
 579       frame.setClosed(true);
 580     }
 581     catch (Exception exe)
 582     {}
 583
 584   }
 585
 586   public void updateFeatureRenderer(Object[][] data)
 587   {
 588     updateFeatureRenderer(data, true);
 589   }
 590   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
 591   {
 592     fr.setFeaturePriority(data, visibleNew);
 593     af.alignPanel.paintAlignment(true);
 594
 595     if (af.alignPanel.overviewPanel != null)
 596     {
 597       af.alignPanel.overviewPanel.updateOverviewImage();
 598     }
 599   }
 600
 601   int selectedRow = -1;
 602   JTabbedPane tabbedPane = new JTabbedPane();
 603   BorderLayout borderLayout1 = new BorderLayout();
 604   BorderLayout borderLayout2 = new BorderLayout();
 605   BorderLayout borderLayout3 = new BorderLayout();
 606   JPanel bigPanel = new JPanel();
 607   BorderLayout borderLayout4 = new BorderLayout();
 608   JButton invert = new JButton();
 609   JPanel buttonPanel = new JPanel();
 610   JButton cancel = new JButton();
 611   JButton ok = new JButton();
 612   JButton loadColours = new JButton();
 613   JButton saveColours = new JButton();
 614   JPanel dasButtonPanel = new JPanel();
 615   JButton fetchDAS = new JButton();
 616   JButton saveDAS = new JButton();
 617   JButton cancelDAS = new JButton();
 618   JButton optimizeOrder = new JButton();
 619   JPanel transbuttons = new JPanel(new BorderLayout());
 620   private void jbInit()
 621       throws Exception
 622   {
 623     this.setLayout(borderLayout1);
 624     settingsPane.setLayout(borderLayout2);
 625     dasSettingsPane.setLayout(borderLayout3);
 626     bigPanel.setLayout(borderLayout4);
 627     invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 628     invert.setText("Invert Selection");
 629     invert.addActionListener(new ActionListener()
 630     {
 631       public void actionPerformed(ActionEvent e)
 632       {
 633         invertSelection();
 634       }
 635     });
 636     optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 637     optimizeOrder.setText("Optimise Order");
 638     optimizeOrder.addActionListener(new ActionListener() {
 639       public void actionPerformed(ActionEvent e) {
 640         orderByAvWidth();
 641       }
 642     });
 643     cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 644     cancel.setText("Cancel");
 645     cancel.addActionListener(new ActionListener()
 646     {
 647       public void actionPerformed(ActionEvent e)
 648       {
 649         updateFeatureRenderer(originalData);
 650         close();
 651       }
 652     });
 653     ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 654     ok.setText("OK");
 655     ok.addActionListener(new ActionListener()
 656     {
 657       public void actionPerformed(ActionEvent e)
 658       {
 659         close();
 660       }
 661     });
 662     loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 663     loadColours.setText("Load Colours");
 664     loadColours.addActionListener(new ActionListener()
 665     {
 666       public void actionPerformed(ActionEvent e)
 667       {
 668         load();
 669       }
 670     });
 671     saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 672     saveColours.setText("Save Colours");
 673     saveColours.addActionListener(new ActionListener()
 674     {
 675       public void actionPerformed(ActionEvent e)
 676       {
 677         save();
 678       }
 679     });
 680     transparency.addChangeListener(new ChangeListener()
 681     {
 682       public void stateChanged(ChangeEvent evt)
 683       {
 684         fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
 685         af.alignPanel.paintAlignment(true);
 686       }
 687     });
 688
 689     transparency.setMaximum(70);
 690     fetchDAS.setText("Fetch DAS Features");
 691     fetchDAS.addActionListener(new ActionListener()
 692     {
 693       public void actionPerformed(ActionEvent e)
 694       {
 695         fetchDAS_actionPerformed(e);
 696       }
 697     });
 698     saveDAS.setText("Save as default");
 699     saveDAS.addActionListener(new ActionListener()
 700     {
 701       public void actionPerformed(ActionEvent e)
 702       {
 703         saveDAS_actionPerformed(e);
 704       }
 705     });
 706     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
 707     dasSettingsPane.setBorder(null);
 708     cancelDAS.setEnabled(false);
 709     cancelDAS.setText("Cancel Fetch");
 710     cancelDAS.addActionListener(new ActionListener()
 711     {
 712       public void actionPerformed(ActionEvent e)
 713       {
 714         cancelDAS_actionPerformed(e);
 715       }
 716     });
 717     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 718     tabbedPane.addTab("Feature Settings", settingsPane);
 719     tabbedPane.addTab("DAS Settings", dasSettingsPane);
 720     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
 721     transPanel.add(transparency);
 722     transbuttons.add(invert, java.awt.BorderLayout.NORTH);
 723     transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH);
 724     transPanel.add(transbuttons);
 725     buttonPanel.add(ok);
 726     buttonPanel.add(cancel);
 727     buttonPanel.add(loadColours);
 728     buttonPanel.add(saveColours);
 729     bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
 730     dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
 731     dasButtonPanel.add(fetchDAS);
 732     dasButtonPanel.add(cancelDAS);
 733     dasButtonPanel.add(saveDAS);
 734     settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
 735     settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
 736   }
 737
 738   public void fetchDAS_actionPerformed(ActionEvent e)
 739   {
 740     fetchDAS.setEnabled(false);
 741     cancelDAS.setEnabled(true);
 742     Vector selectedSources = dassourceBrowser.getSelectedSources();
 743
 744     SequenceI[] dataset, seqs;
 745     int iSize;
 746
 747     if (af.getViewport().getSelectionGroup() != null
 748         && af.getViewport().getSelectionGroup().getSize() > 0)
 749     {
 750       iSize = af.getViewport().getSelectionGroup().getSize();
 751       dataset = new SequenceI[iSize];
 752       seqs = af.getViewport().getSelectionGroup().
 753           getSequencesInOrder(
 754               af.getViewport().getAlignment());
 755     }
 756     else
 757     {
 758       iSize = af.getViewport().getAlignment().getHeight();
 759       seqs = af.getViewport().getAlignment().getSequencesArray();
 760     }
 761
 762     dataset = new SequenceI[iSize];
 763     for (int i = 0; i < iSize; i++)
 764     {
 765       dataset[i] = seqs[i].getDatasetSequence();
 766     }
 767
 768     dasFeatureFetcher =
 769         new jalview.io.DasSequenceFeatureFetcher(
 770             dataset,
 771             this,
 772             selectedSources);
 773     cancelDAS.setEnabled(true);
 774     af.getViewport().setShowSequenceFeatures(true);
 775     af.showSeqFeatures.setSelected(true);
 776   }
 777
 778   public void saveDAS_actionPerformed(ActionEvent e)
 779   {
 780     dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);
 781   }
 782
 783   public void complete()
 784   {
 785     fetchDAS.setEnabled(true);
 786     cancelDAS.setEnabled(false);
 787   }
 788
 789   public void cancelDAS_actionPerformed(ActionEvent e)
 790   {
 791     dasFeatureFetcher.cancel();
 792     fetchDAS.setEnabled(true);
 793     cancelDAS.setEnabled(false);
 794   }
 795
 796   /////////////////////////////////////////////////////////////////////////
 797   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
 798   /////////////////////////////////////////////////////////////////////////
 799   class FeatureTableModel
 800       extends AbstractTableModel
 801   {
 802     FeatureTableModel(Object[][] data)
 803     {
 804       this.data = data;
 805     }
 806
 807     private String[] columnNames =
 808         {
 809         "Feature Type", "Colour", "Display"};
 810     private Object[][] data;
 811
 812     public Object[][] getData()
 813     {
 814       return data;
 815     }
 816
 817     public void setData(Object[][] data)
 818     {
 819       this.data = data;
 820     }
 821
 822     public int getColumnCount()
 823     {
 824       return columnNames.length;
 825     }
 826
 827     public Object[] getRow(int row)
 828     {
 829       return data[row];
 830     }
 831
 832     public int getRowCount()
 833     {
 834       return data.length;
 835     }
 836
 837     public String getColumnName(int col)
 838     {
 839       return columnNames[col];
 840     }
 841
 842     public Object getValueAt(int row, int col)
 843     {
 844       return data[row][col];
 845     }
 846
 847     public Class getColumnClass(int c)
 848     {
 849       return getValueAt(0, c).getClass();
 850     }
 851
 852     public boolean isCellEditable(int row, int col)
 853     {
 854       return col == 0 ? false : true;
 855     }
 856
 857     public void setValueAt(Object value, int row, int col)
 858     {
 859       data[row][col] = value;
 860       fireTableCellUpdated(row, col);
 861       updateFeatureRenderer(data);
 862     }
 863
 864   }
 865
 866   class ColorRenderer
 867       extends JLabel implements TableCellRenderer
 868   {
 869     javax.swing.border.Border unselectedBorder = null;
 870     javax.swing.border.Border selectedBorder = null;
 871
 872     public ColorRenderer()
 873     {
 874       setOpaque(true); //MUST do this for background to show up.
 875     }
 876
 877     public Component getTableCellRendererComponent(
 878         JTable table, Object color,
 879         boolean isSelected, boolean hasFocus,
 880         int row, int column)
 881     {
 882       Color newColor = (Color) color;
 883       setBackground(newColor);
 884       if (isSelected)
 885       {
 886         if (selectedBorder == null)
 887         {
 888           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
 889               table.getSelectionBackground());
 890         }
 891         setBorder(selectedBorder);
 892       }
 893       else
 894       {
 895         if (unselectedBorder == null)
 896         {
 897           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
 898               table.getBackground());
 899         }
 900         setBorder(unselectedBorder);
 901       }
 902
 903       setToolTipText("RGB value: " + newColor.getRed() + ", "
 904                      + newColor.getGreen() + ", "
 905                      + newColor.getBlue());
 906       return this;
 907     }
 908   }
 909 }
 910
 911 class ColorEditor
 912     extends AbstractCellEditor implements TableCellEditor,
 913     ActionListener
 914 {
 915   Color currentColor;
 916   JButton button;
 917   JColorChooser colorChooser;
 918   JDialog dialog;
 919   protected static final String EDIT = "edit";
 920
 921   public ColorEditor()
 922   {
 923     //Set up the editor (from the table's point of view),
 924     //which is a button.
 925     //This button brings up the color chooser dialog,
 926     //which is the editor from the user's point of view.
 927     button = new JButton();
 928     button.setActionCommand(EDIT);
 929     button.addActionListener(this);
 930     button.setBorderPainted(false);
 931     //Set up the dialog that the button brings up.
 932     colorChooser = new JColorChooser();
 933     dialog = JColorChooser.createDialog(button,
 934                                         "Select new Colour",
 935                                         true, //modal
 936                                         colorChooser,
 937                                         this, //OK button handler
 938                                         null); //no CANCEL button handler
 939   }
 940
 941   /**
 942    * Handles events from the editor button and from
 943    * the dialog's OK button.
 944    */
 945   public void actionPerformed(ActionEvent e)
 946   {
 947
 948     if (EDIT.equals(e.getActionCommand()))
 949     {
 950       //The user has clicked the cell, so
 951       //bring up the dialog.
 952       button.setBackground(currentColor);
 953       colorChooser.setColor(currentColor);
 954       dialog.setVisible(true);
 955
 956       //Make the renderer reappear.
 957       fireEditingStopped();
 958
 959     }
 960     else
 961     { //User pressed dialog's "OK" button.
 962       currentColor = colorChooser.getColor();
 963     }
 964   }
 965
 966   //Implement the one CellEditor method that AbstractCellEditor doesn't.
 967   public Object getCellEditorValue()
 968   {
 969     return currentColor;
 970   }
 971
 972   //Implement the one method defined by TableCellEditor.
 973   public Component getTableCellEditorComponent(JTable table,
 974                                                Object value,
 975                                                boolean isSelected,
 976                                                int row,
 977                                                int column)
 978   {
 979     currentColor = (Color) value;
 980     return button;
 981   }
 982 }