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(null); // new groups may be added with new seuqence feature types only
 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             if (checkGroupState(group))
 202             {
 203               // continue; // skip this group's feature - we've done it already ?
 204             }
 205           }
 206         }
 207
 208         if (!allFeatures.contains(tmpfeatures[index].getType()))
 209         {
 210           allFeatures.addElement(tmpfeatures[index].getType());
 211         }
 212         index++;
 213       }
 214     }
 215
 216     resetTable(null);
 217
 218     validate();
 219   }
 220   /**
 221    *
 222    * @param group
 223    * @return true if group has been seen before and is already added to set.
 224    */
 225   private boolean checkGroupState(String group) {
 226     boolean visible;
 227     if (fr.featureGroups.containsKey(group))
 228     {
 229       visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
 230         } else {
 231         visible=true; // new group is always made visible
 232       }
 233
 234       if (groupPanel == null)
 235       {
 236         groupPanel = new JPanel();
 237       }
 238
 239       boolean alreadyAdded = false;
 240       for (int g = 0; g < groupPanel.getComponentCount(); g++)
 241       {
 242         if ( ( (JCheckBox) groupPanel.getComponent(g))
 243             .getText().equals(group))
 244         {
 245           alreadyAdded = true;
 246           ((JCheckBox)groupPanel.getComponent(g)).setSelected(visible);
 247           break;
 248         }
 249       }
 250
 251       if (alreadyAdded)
 252       {
 253
 254         return true;
 255       }
 256
 257       fr.featureGroups.put(group, new Boolean(visible));
 258       final String grp = group;
 259       final JCheckBox check = new JCheckBox(group, visible);
 260       check.setFont(new Font("Serif", Font.BOLD, 12));
 261       check.addItemListener(new ItemListener()
 262       {
 263         public void itemStateChanged(ItemEvent evt)
 264         {
 265           fr.featureGroups.put(check.getText(),
 266                                new Boolean(check.isSelected()));
 267           af.alignPanel.seqPanel.seqCanvas.repaint();
 268           if (af.alignPanel.overviewPanel != null)
 269           {
 270             af.alignPanel.overviewPanel.updateOverviewImage();
 271           }
 272
 273           resetTable(new String[] { grp } );
 274         }
 275       });
 276       groupPanel.add(check);
 277       return false;
 278   }
 279   boolean resettingTable=false;
 280   void resetTable(String[] groupChanged)
 281   {
 282     resettingTable=true;
 283     typeWidth=new Hashtable();
 284     // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
 285     float[] avWidth=null;
 286     SequenceFeature[] tmpfeatures;
 287     String group = null, type;
 288     Vector visibleChecks = new Vector();
 289
 290     //Find out which features should be visible depending on which groups
 291     //are selected / deselected
 292     //and recompute average width ordering
 293     for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
 294     {
 295
 296       tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
 297           getDatasetSequence().getSequenceFeatures();
 298       if (tmpfeatures == null)
 299       {
 300         continue;
 301       }
 302
 303       int index = 0;
 304       while (index < tmpfeatures.length)
 305       {
 306         group = tmpfeatures[index].featureGroup;
 307
 308         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 309         {
 310           index++;
 311           continue;
 312         }
 313
 314         if (group == null || fr.featureGroups.get(group) == null ||
 315             ( (Boolean) fr.featureGroups.get(group)).booleanValue())
 316         {
 317           checkGroupState(group);
 318           type = tmpfeatures[index].getType();
 319           if (!visibleChecks.contains(type))
 320           {
 321             visibleChecks.addElement(type);
 322           }
 323         }
 324         if (!typeWidth.containsKey(tmpfeatures[index].getType())) {
 325           typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]);
 326         } else {
 327           avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
 328         }
 329         avWidth[0]++;
 330         if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
 331         {
 332           avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
 333         } else {
 334           avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
 335         }
 336         index++;
 337       }
 338     }
 339
 340     int fSize = visibleChecks.size();
 341     Object[][] data = new Object[fSize][3];
 342     int dataIndex = 0;
 343
 344     if (fr.renderOrder != null)
 345     {
 346       if (!handlingUpdate)
 347         fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
 348       //First add the checks in the previous render order,
 349       //in case the window has been closed and reopened
 350       for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
 351       {
 352         type = fr.renderOrder[ro];
 353
 354         if (!visibleChecks.contains(type))
 355         {
 356           continue;
 357         }
 358
 359         data[dataIndex][0] = type;
 360         data[dataIndex][1] = fr.getColour(type);
 361         data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
 362         dataIndex++;
 363         visibleChecks.removeElement(type);
 364       }
 365     }
 366
 367     fSize = visibleChecks.size();
 368     for (int i = 0; i < fSize; i++)
 369     {
 370       //These must be extra features belonging to the group
 371       //which was just selected
 372       type = visibleChecks.elementAt(i).toString();
 373       data[dataIndex][0] = type;
 374
 375       data[dataIndex][1] = fr.getColour(type);
 376       if (data[dataIndex][1] == null)
 377       {
 378         //"Colour has been updated in another view!!"
 379         fr.renderOrder = null;
 380         return;
 381       }
 382
 383       data[dataIndex][2] = new Boolean(true);
 384       dataIndex++;
 385     }
 386
 387     if (originalData == null)
 388     {
 389       originalData = new Object[data.length][3];
 390       System.arraycopy(data, 0, originalData, 0, data.length);
 391     }
 392
 393     table.setModel(new FeatureTableModel(data));
 394     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 395
 396     if (groupPanel != null)
 397     {
 398       groupPanel.setLayout(
 399           new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
 400
 401       groupPanel.validate();
 402       bigPanel.add(groupPanel, BorderLayout.NORTH);
 403     }
 404
 405     updateFeatureRenderer(data, groupChanged!=null);
 406     resettingTable=false;
 407   }
 408   /**
 409    * reorder data based on the featureRenderers global priority list.
 410    * @param data
 411    */
 412   private void ensureOrder(Object[][] data)
 413   {
 414     boolean sort=false;
 415     float[] order = new float[data.length];
 416     for (int i=0;i<order.length; i++)
 417     {
 418       order[i] = fr.getOrder(data[i][0].toString());
 419       if (order[i]<0)
 420         order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
 421       if (i>1)
 422         sort = sort || order[i-1]>order[i];
 423     }
 424     if (sort)
 425       jalview.util.QuickSort.sort(order, data);
 426   }
 427
 428   void load()
 429   {
 430     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 431         getProperty(
 432             "LAST_DIRECTORY"), new String[]
 433         {"fc"},
 434         new String[]
 435         {"Sequence Feature Colours"}, "Sequence Feature Colours");
 436     chooser.setFileView(new jalview.io.JalviewFileView());
 437     chooser.setDialogTitle("Load Feature Colours");
 438     chooser.setToolTipText("Load");
 439
 440     int value = chooser.showOpenDialog(this);
 441
 442     if (value == JalviewFileChooser.APPROVE_OPTION)
 443     {
 444       File file = chooser.getSelectedFile();
 445
 446       try
 447       {
 448         InputStreamReader in = new InputStreamReader(new FileInputStream(
 449             file), "UTF-8");
 450
 451         jalview.binding.JalviewUserColours jucs = new jalview.binding.
 452             JalviewUserColours();
 453         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 454
 455         for (int i = jucs.getColourCount()-1; i >=0; i--)
 456         {
 457           String name;
 458           fr.setColour(name=jucs.getColour(i).getName(),
 459                        new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
 460                                                   16)));
 461           fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
 462         }
 463         if (table!=null) {
 464           resetTable(null);
 465           Object[][] data=((FeatureTableModel) table.getModel()).getData();
 466           ensureOrder(data);
 467           updateFeatureRenderer(data,false);
 468           table.repaint();
 469         }
 470       }
 471       catch (Exception ex)
 472       {
 473         System.out.println("Error loading User Colour File\n" + ex);
 474       }
 475     }
 476   }
 477
 478   void save()
 479   {
 480     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 481         getProperty(
 482             "LAST_DIRECTORY"), new String[]
 483         {"fc"},
 484         new String[]
 485         {"Sequence Feature Colours"}, "Sequence Feature Colours");
 486     chooser.setFileView(new jalview.io.JalviewFileView());
 487     chooser.setDialogTitle("Save Feature Colour Scheme");
 488     chooser.setToolTipText("Save");
 489
 490     int value = chooser.showSaveDialog(this);
 491
 492     if (value == JalviewFileChooser.APPROVE_OPTION)
 493     {
 494       String choice = chooser.getSelectedFile().getPath();
 495       jalview.binding.JalviewUserColours ucs = new jalview.binding.
 496           JalviewUserColours();
 497       ucs.setSchemeName("Sequence Features");
 498       try
 499       {
 500         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 501             new FileOutputStream(choice), "UTF-8"));
 502
 503         Enumeration e = fr.featureColours.keys();
 504         float[] sortOrder = new float[fr.featureColours.size()];
 505         String[] sortTypes = new String[fr.featureColours.size()];
 506         int i=0;
 507         while (e.hasMoreElements())
 508         {
 509           sortTypes[i] = e.nextElement().toString();
 510           sortOrder[i]  = fr.getOrder(sortTypes[i]);
 511           i++;
 512         }
 513         jalview.util.QuickSort.sort(sortOrder, sortTypes);
 514         sortOrder=null;
 515         for (i=0; i<sortTypes.length; i++) {
 516           jalview.binding.Colour col = new jalview.binding.Colour();
 517           col.setName(sortTypes[i]);
 518           col.setRGB(jalview.util.Format.getHexString(
 519               fr.getColour(col.getName())));
 520           ucs.addColour(col);
 521         }
 522         ucs.marshal(out);
 523         out.close();
 524       }
 525       catch (Exception ex)
 526       {
 527         ex.printStackTrace();
 528       }
 529     }
 530   }
 531
 532   public void invertSelection()
 533   {
 534     for (int i = 0; i < table.getRowCount(); i++)
 535     {
 536       Boolean value = (Boolean) table.getValueAt(i, 2);
 537
 538       table.setValueAt(
 539           new Boolean(!value.booleanValue()),
 540           i, 2);
 541     }
 542   }
 543   public void orderByAvWidth() {
 544     if (table==null || table.getModel()==null)
 545       return;
 546     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
 547     float[] width = new float[data.length];
 548     float[] awidth;
 549     float max=0;
 550     int num=0;
 551     for (int i=0;i<data.length;i++) {
 552        awidth = (float[]) typeWidth.get(data[i][0]);
 553        if (awidth[0]>0) {
 554          width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2])
 555          //if (width[i]==1) // hack to distinguish single width sequences.
 556          num++;
 557        } else {
 558          width[i]=0;
 559        }
 560        if (max<width[i])
 561          max=width[i];
 562     }
 563     boolean sort=false;
 564     for (int i=0;i<width.length; i++) {
 565       //awidth = (float[]) typeWidth.get(data[i][0]);
 566       if (width[i]==0)
 567       {
 568         width[i] = fr.getOrder(data[i][0].toString());
 569         if (width[i]<0)
 570         {
 571           width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
 572         }
 573       } else {
 574         width[i] /=max; // normalize
 575         fr.setOrder(data[i][0].toString(), width[i]); // store for later
 576       }
 577       if (i>0)
 578         sort = sort || width[i-1]>width[i];
 579     }
 580     if (sort)
 581       jalview.util.QuickSort.sort(width, data);
 582     // update global priority order
 583
 584     updateFeatureRenderer(data,false);
 585     table.repaint();
 586   }
 587   public void close()
 588   {
 589     try
 590     {
 591       frame.setClosed(true);
 592     }
 593     catch (Exception exe)
 594     {}
 595
 596   }
 597
 598   public void updateFeatureRenderer(Object[][] data)
 599   {
 600     updateFeatureRenderer(data, true);
 601   }
 602   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
 603   {
 604     fr.setFeaturePriority(data, visibleNew);
 605     af.alignPanel.paintAlignment(true);
 606
 607     if (af.alignPanel.overviewPanel != null)
 608     {
 609       af.alignPanel.overviewPanel.updateOverviewImage();
 610     }
 611   }
 612
 613   int selectedRow = -1;
 614   JTabbedPane tabbedPane = new JTabbedPane();
 615   BorderLayout borderLayout1 = new BorderLayout();
 616   BorderLayout borderLayout2 = new BorderLayout();
 617   BorderLayout borderLayout3 = new BorderLayout();
 618   JPanel bigPanel = new JPanel();
 619   BorderLayout borderLayout4 = new BorderLayout();
 620   JButton invert = new JButton();
 621   JPanel buttonPanel = new JPanel();
 622   JButton cancel = new JButton();
 623   JButton ok = new JButton();
 624   JButton loadColours = new JButton();
 625   JButton saveColours = new JButton();
 626   JPanel dasButtonPanel = new JPanel();
 627   JButton fetchDAS = new JButton();
 628   JButton saveDAS = new JButton();
 629   JButton cancelDAS = new JButton();
 630   JButton optimizeOrder = new JButton();
 631   JPanel transbuttons = new JPanel(new BorderLayout());
 632   private void jbInit()
 633       throws Exception
 634   {
 635     this.setLayout(borderLayout1);
 636     settingsPane.setLayout(borderLayout2);
 637     dasSettingsPane.setLayout(borderLayout3);
 638     bigPanel.setLayout(borderLayout4);
 639     invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 640     invert.setText("Invert Selection");
 641     invert.addActionListener(new ActionListener()
 642     {
 643       public void actionPerformed(ActionEvent e)
 644       {
 645         invertSelection();
 646       }
 647     });
 648     optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 649     optimizeOrder.setText("Optimise Order");
 650     optimizeOrder.addActionListener(new ActionListener() {
 651       public void actionPerformed(ActionEvent e) {
 652         orderByAvWidth();
 653       }
 654     });
 655     cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 656     cancel.setText("Cancel");
 657     cancel.addActionListener(new ActionListener()
 658     {
 659       public void actionPerformed(ActionEvent e)
 660       {
 661         updateFeatureRenderer(originalData);
 662         close();
 663       }
 664     });
 665     ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 666     ok.setText("OK");
 667     ok.addActionListener(new ActionListener()
 668     {
 669       public void actionPerformed(ActionEvent e)
 670       {
 671         close();
 672       }
 673     });
 674     loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 675     loadColours.setText("Load Colours");
 676     loadColours.addActionListener(new ActionListener()
 677     {
 678       public void actionPerformed(ActionEvent e)
 679       {
 680         load();
 681       }
 682     });
 683     saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 684     saveColours.setText("Save Colours");
 685     saveColours.addActionListener(new ActionListener()
 686     {
 687       public void actionPerformed(ActionEvent e)
 688       {
 689         save();
 690       }
 691     });
 692     transparency.addChangeListener(new ChangeListener()
 693     {
 694       public void stateChanged(ChangeEvent evt)
 695       {
 696         fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
 697         af.alignPanel.paintAlignment(true);
 698       }
 699     });
 700
 701     transparency.setMaximum(70);
 702     fetchDAS.setText("Fetch DAS Features");
 703     fetchDAS.addActionListener(new ActionListener()
 704     {
 705       public void actionPerformed(ActionEvent e)
 706       {
 707         fetchDAS_actionPerformed(e);
 708       }
 709     });
 710     saveDAS.setText("Save as default");
 711     saveDAS.addActionListener(new ActionListener()
 712     {
 713       public void actionPerformed(ActionEvent e)
 714       {
 715         saveDAS_actionPerformed(e);
 716       }
 717     });
 718     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
 719     dasSettingsPane.setBorder(null);
 720     cancelDAS.setEnabled(false);
 721     cancelDAS.setText("Cancel Fetch");
 722     cancelDAS.addActionListener(new ActionListener()
 723     {
 724       public void actionPerformed(ActionEvent e)
 725       {
 726         cancelDAS_actionPerformed(e);
 727       }
 728     });
 729     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
 730     tabbedPane.addTab("Feature Settings", settingsPane);
 731     tabbedPane.addTab("DAS Settings", dasSettingsPane);
 732     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
 733     transPanel.add(transparency);
 734     transbuttons.add(invert, java.awt.BorderLayout.NORTH);
 735     transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH);
 736     transPanel.add(transbuttons);
 737     buttonPanel.add(ok);
 738     buttonPanel.add(cancel);
 739     buttonPanel.add(loadColours);
 740     buttonPanel.add(saveColours);
 741     bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
 742     dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
 743     dasButtonPanel.add(fetchDAS);
 744     dasButtonPanel.add(cancelDAS);
 745     dasButtonPanel.add(saveDAS);
 746     settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
 747     settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
 748   }
 749
 750   public void fetchDAS_actionPerformed(ActionEvent e)
 751   {
 752     fetchDAS.setEnabled(false);
 753     cancelDAS.setEnabled(true);
 754     Vector selectedSources = dassourceBrowser.getSelectedSources();
 755
 756     SequenceI[] dataset, seqs;
 757     int iSize;
 758
 759     if (af.getViewport().getSelectionGroup() != null
 760         && af.getViewport().getSelectionGroup().getSize() > 0)
 761     {
 762       iSize = af.getViewport().getSelectionGroup().getSize();
 763       dataset = new SequenceI[iSize];
 764       seqs = af.getViewport().getSelectionGroup().
 765           getSequencesInOrder(
 766               af.getViewport().getAlignment());
 767     }
 768     else
 769     {
 770       iSize = af.getViewport().getAlignment().getHeight();
 771       seqs = af.getViewport().getAlignment().getSequencesArray();
 772     }
 773
 774     dataset = new SequenceI[iSize];
 775     for (int i = 0; i < iSize; i++)
 776     {
 777       dataset[i] = seqs[i].getDatasetSequence();
 778     }
 779
 780     dasFeatureFetcher =
 781         new jalview.io.DasSequenceFeatureFetcher(
 782             dataset,
 783             this,
 784             selectedSources);
 785     cancelDAS.setEnabled(true);
 786     af.getViewport().setShowSequenceFeatures(true);
 787     af.showSeqFeatures.setSelected(true);
 788   }
 789
 790   public void saveDAS_actionPerformed(ActionEvent e)
 791   {
 792     dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);
 793   }
 794
 795   public void complete()
 796   {
 797     fetchDAS.setEnabled(true);
 798     cancelDAS.setEnabled(false);
 799   }
 800
 801   public void cancelDAS_actionPerformed(ActionEvent e)
 802   {
 803     dasFeatureFetcher.cancel();
 804     fetchDAS.setEnabled(true);
 805     cancelDAS.setEnabled(false);
 806   }
 807
 808   /////////////////////////////////////////////////////////////////////////
 809   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
 810   /////////////////////////////////////////////////////////////////////////
 811   class FeatureTableModel
 812       extends AbstractTableModel
 813   {
 814     FeatureTableModel(Object[][] data)
 815     {
 816       this.data = data;
 817     }
 818
 819     private String[] columnNames =
 820         {
 821         "Feature Type", "Colour", "Display"};
 822     private Object[][] data;
 823
 824     public Object[][] getData()
 825     {
 826       return data;
 827     }
 828
 829     public void setData(Object[][] data)
 830     {
 831       this.data = data;
 832     }
 833
 834     public int getColumnCount()
 835     {
 836       return columnNames.length;
 837     }
 838
 839     public Object[] getRow(int row)
 840     {
 841       return data[row];
 842     }
 843
 844     public int getRowCount()
 845     {
 846       return data.length;
 847     }
 848
 849     public String getColumnName(int col)
 850     {
 851       return columnNames[col];
 852     }
 853
 854     public Object getValueAt(int row, int col)
 855     {
 856       return data[row][col];
 857     }
 858
 859     public Class getColumnClass(int c)
 860     {
 861       return getValueAt(0, c).getClass();
 862     }
 863
 864     public boolean isCellEditable(int row, int col)
 865     {
 866       return col == 0 ? false : true;
 867     }
 868
 869     public void setValueAt(Object value, int row, int col)
 870     {
 871       data[row][col] = value;
 872       fireTableCellUpdated(row, col);
 873       updateFeatureRenderer(data);
 874     }
 875
 876   }
 877
 878   class ColorRenderer
 879       extends JLabel implements TableCellRenderer
 880   {
 881     javax.swing.border.Border unselectedBorder = null;
 882     javax.swing.border.Border selectedBorder = null;
 883
 884     public ColorRenderer()
 885     {
 886       setOpaque(true); //MUST do this for background to show up.
 887     }
 888
 889     public Component getTableCellRendererComponent(
 890         JTable table, Object color,
 891         boolean isSelected, boolean hasFocus,
 892         int row, int column)
 893     {
 894       Color newColor = (Color) color;
 895       setBackground(newColor);
 896       if (isSelected)
 897       {
 898         if (selectedBorder == null)
 899         {
 900           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
 901               table.getSelectionBackground());
 902         }
 903         setBorder(selectedBorder);
 904       }
 905       else
 906       {
 907         if (unselectedBorder == null)
 908         {
 909           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
 910               table.getBackground());
 911         }
 912         setBorder(unselectedBorder);
 913       }
 914
 915       setToolTipText("RGB value: " + newColor.getRed() + ", "
 916                      + newColor.getGreen() + ", "
 917                      + newColor.getBlue());
 918       return this;
 919     }
 920   }
 921 }
 922
 923 class ColorEditor
 924     extends AbstractCellEditor implements TableCellEditor,
 925     ActionListener
 926 {
 927   Color currentColor;
 928   JButton button;
 929   JColorChooser colorChooser;
 930   JDialog dialog;
 931   protected static final String EDIT = "edit";
 932
 933   public ColorEditor()
 934   {
 935     //Set up the editor (from the table's point of view),
 936     //which is a button.
 937     //This button brings up the color chooser dialog,
 938     //which is the editor from the user's point of view.
 939     button = new JButton();
 940     button.setActionCommand(EDIT);
 941     button.addActionListener(this);
 942     button.setBorderPainted(false);
 943     //Set up the dialog that the button brings up.
 944     colorChooser = new JColorChooser();
 945     dialog = JColorChooser.createDialog(button,
 946                                         "Select new Colour",
 947                                         true, //modal
 948                                         colorChooser,
 949                                         this, //OK button handler
 950                                         null); //no CANCEL button handler
 951   }
 952
 953   /**
 954    * Handles events from the editor button and from
 955    * the dialog's OK button.
 956    */
 957   public void actionPerformed(ActionEvent e)
 958   {
 959
 960     if (EDIT.equals(e.getActionCommand()))
 961     {
 962       //The user has clicked the cell, so
 963       //bring up the dialog.
 964       button.setBackground(currentColor);
 965       colorChooser.setColor(currentColor);
 966       dialog.setVisible(true);
 967
 968       //Make the renderer reappear.
 969       fireEditingStopped();
 970
 971     }
 972     else
 973     { //User pressed dialog's "OK" button.
 974       currentColor = colorChooser.getColor();
 975     }
 976   }
 977
 978   //Implement the one CellEditor method that AbstractCellEditor doesn't.
 979   public Object getCellEditorValue()
 980   {
 981     return currentColor;
 982   }
 983
 984   //Implement the one method defined by TableCellEditor.
 985   public Component getTableCellEditorComponent(JTable table,
 986                                                Object value,
 987                                                boolean isSelected,
 988                                                int row,
 989                                                int column)
 990   {
 991     currentColor = (Color) value;
 992     return button;
 993   }
 994 }