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