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.ws.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 (group!=null)
 202             {
 203               checkGroupState(group);
 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   synchronized void resetTable(String[] groupChanged)
 281   {
 282     if (resettingTable==true)
 283     {
 284       return;
 285     }
 286     resettingTable=true;
 287     typeWidth=new Hashtable();
 288     // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
 289     float[] avWidth=null;
 290     SequenceFeature[] tmpfeatures;
 291     String group = null, type;
 292     Vector visibleChecks = new Vector();
 293
 294     //Find out which features should be visible depending on which groups
 295     //are selected / deselected
 296     //and recompute average width ordering
 297     for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
 298     {
 299
 300       tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
 301           getDatasetSequence().getSequenceFeatures();
 302       if (tmpfeatures == null)
 303       {
 304         continue;
 305       }
 306
 307       int index = 0;
 308       while (index < tmpfeatures.length)
 309       {
 310         group = tmpfeatures[index].featureGroup;
 311
 312         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 313         {
 314           index++;
 315           continue;
 316         }
 317
 318         if (group == null || fr.featureGroups.get(group) == null ||
 319             ( (Boolean) fr.featureGroups.get(group)).booleanValue())
 320         {
 321           if (group!=null)
 322             checkGroupState(group);
 323           type = tmpfeatures[index].getType();
 324           if (!visibleChecks.contains(type))
 325           {
 326             visibleChecks.addElement(type);
 327           }
 328         }
 329         if (!typeWidth.containsKey(tmpfeatures[index].getType())) {
 330           typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]);
 331         } else {
 332           avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
 333         }
 334         avWidth[0]++;
 335         if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
 336         {
 337           avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
 338         } else {
 339           avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
 340         }
 341         index++;
 342       }
 343     }
 344
 345     int fSize = visibleChecks.size();
 346     Object[][] data = new Object[fSize][3];
 347     int dataIndex = 0;
 348
 349     if (fr.renderOrder != null)
 350     {
 351       if (!handlingUpdate)
 352         fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
 353       //First add the checks in the previous render order,
 354       //in case the window has been closed and reopened
 355       for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
 356       {
 357         type = fr.renderOrder[ro];
 358
 359         if (!visibleChecks.contains(type))
 360         {
 361           continue;
 362         }
 363
 364         data[dataIndex][0] = type;
 365         data[dataIndex][1] = fr.getColour(type);
 366         data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
 367         dataIndex++;
 368         visibleChecks.removeElement(type);
 369       }
 370     }
 371
 372     fSize = visibleChecks.size();
 373     for (int i = 0; i < fSize; i++)
 374     {
 375       //These must be extra features belonging to the group
 376       //which was just selected
 377       type = visibleChecks.elementAt(i).toString();
 378       data[dataIndex][0] = type;
 379
 380       data[dataIndex][1] = fr.getColour(type);
 381       if (data[dataIndex][1] == null)
 382       {
 383         //"Colour has been updated in another view!!"
 384         fr.renderOrder = null;
 385         return;
 386       }
 387
 388       data[dataIndex][2] = new Boolean(true);
 389       dataIndex++;
 390     }
 391
 392     if (originalData == null)
 393     {
 394       originalData = new Object[data.length][3];
 395       System.arraycopy(data, 0, originalData, 0, data.length);
 396     }
 397
 398     table.setModel(new FeatureTableModel(data));
 399     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 400
 401     if (groupPanel != null)
 402     {
 403       groupPanel.setLayout(
 404           new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
 405
 406       groupPanel.validate();
 407       bigPanel.add(groupPanel, BorderLayout.NORTH);
 408     }
 409
 410     updateFeatureRenderer(data, groupChanged!=null);
 411     resettingTable=false;
 412   }
 413   /**
 414    * reorder data based on the featureRenderers global priority list.
 415    * @param data
 416    */
 417   private void ensureOrder(Object[][] data)
 418   {
 419     boolean sort=false;
 420     float[] order = new float[data.length];
 421     for (int i=0;i<order.length; i++)
 422     {
 423       order[i] = fr.getOrder(data[i][0].toString());
 424       if (order[i]<0)
 425         order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
 426       if (i>1)
 427         sort = sort || order[i-1]>order[i];
 428     }
 429     if (sort)
 430       jalview.util.QuickSort.sort(order, data);
 431   }
 432
 433   void load()
 434   {
 435     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 436         getProperty(
 437             "LAST_DIRECTORY"), new String[]
 438         {"fc"},
 439         new String[]
 440         {"Sequence Feature Colours"}, "Sequence Feature Colours");
 441     chooser.setFileView(new jalview.io.JalviewFileView());
 442     chooser.setDialogTitle("Load Feature Colours");
 443     chooser.setToolTipText("Load");
 444
 445     int value = chooser.showOpenDialog(this);
 446
 447     if (value == JalviewFileChooser.APPROVE_OPTION)
 448     {
 449       File file = chooser.getSelectedFile();
 450
 451       try
 452       {
 453         InputStreamReader in = new InputStreamReader(new FileInputStream(
 454             file), "UTF-8");
 455
 456         jalview.binding.JalviewUserColours jucs = new jalview.binding.
 457             JalviewUserColours();
 458         jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 459
 460         for (int i = jucs.getColourCount()-1; i >=0; i--)
 461         {
 462           String name;
 463           fr.setColour(name=jucs.getColour(i).getName(),
 464                        new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
 465                                                   16)));
 466           fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
 467         }
 468         if (table!=null) {
 469           resetTable(null);
 470           Object[][] data=((FeatureTableModel) table.getModel()).getData();
 471           ensureOrder(data);
 472           updateFeatureRenderer(data,false);
 473           table.repaint();
 474         }
 475       }
 476       catch (Exception ex)
 477       {
 478         System.out.println("Error loading User Colour File\n" + ex);
 479       }
 480     }
 481   }
 482
 483   void save()
 484   {
 485     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
 486         getProperty(
 487             "LAST_DIRECTORY"), new String[]
 488         {"fc"},
 489         new String[]
 490         {"Sequence Feature Colours"}, "Sequence Feature Colours");
 491     chooser.setFileView(new jalview.io.JalviewFileView());
 492     chooser.setDialogTitle("Save Feature Colour Scheme");
 493     chooser.setToolTipText("Save");
 494
 495     int value = chooser.showSaveDialog(this);
 496
 497     if (value == JalviewFileChooser.APPROVE_OPTION)
 498     {
 499       String choice = chooser.getSelectedFile().getPath();
 500       jalview.binding.JalviewUserColours ucs = new jalview.binding.
 501           JalviewUserColours();
 502       ucs.setSchemeName("Sequence Features");
 503       try
 504       {
 505         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 506             new FileOutputStream(choice), "UTF-8"));
 507
 508         Enumeration e = fr.featureColours.keys();
 509         float[] sortOrder = new float[fr.featureColours.size()];
 510         String[] sortTypes = new String[fr.featureColours.size()];
 511         int i=0;
 512         while (e.hasMoreElements())
 513         {
 514           sortTypes[i] = e.nextElement().toString();
 515           sortOrder[i]  = fr.getOrder(sortTypes[i]);
 516           i++;
 517         }
 518         jalview.util.QuickSort.sort(sortOrder, sortTypes);
 519         sortOrder=null;
 520         for (i=0; i<sortTypes.length; i++) {
 521           jalview.binding.Colour col = new jalview.binding.Colour();
 522           col.setName(sortTypes[i]);
 523           col.setRGB(jalview.util.Format.getHexString(
 524               fr.getColour(col.getName())));
 525           ucs.addColour(col);
 526         }
 527         ucs.marshal(out);
 528         out.close();
 529       }
 530       catch (Exception ex)
 531       {
 532         ex.printStackTrace();
 533       }
 534     }
 535   }
 536
 537   public void invertSelection()
 538   {
 539     for (int i = 0; i < table.getRowCount(); i++)
 540     {
 541       Boolean value = (Boolean) table.getValueAt(i, 2);
 542
 543       table.setValueAt(
 544           new Boolean(!value.booleanValue()),
 545           i, 2);
 546     }
 547   }
 548   public void orderByAvWidth() {
 549     if (table==null || table.getModel()==null)
 550       return;
 551     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
 552     float[] width = new float[data.length];
 553     float[] awidth;
 554     float max=0;
 555     int num=0;
 556     for (int i=0;i<data.length;i++) {
 557        awidth = (float[]) typeWidth.get(data[i][0]);
 558        if (awidth[0]>0) {
 559          width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2])
 560          //if (width[i]==1) // hack to distinguish single width sequences.
 561          num++;
 562        } else {
 563          width[i]=0;
 564        }
 565        if (max<width[i])
 566          max=width[i];
 567     }
 568     boolean sort=false;
 569     for (int i=0;i<width.length; i++) {
 570       //awidth = (float[]) typeWidth.get(data[i][0]);
 571       if (width[i]==0)
 572       {
 573         width[i] = fr.getOrder(data[i][0].toString());
 574         if (width[i]<0)
 575         {
 576           width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
 577         }
 578       } else {
 579         width[i] /=max; // normalize
 580         fr.setOrder(data[i][0].toString(), width[i]); // store for later
 581       }
 582       if (i>0)
 583         sort = sort || width[i-1]>width[i];
 584     }
 585     if (sort)
 586       jalview.util.QuickSort.sort(width, data);
 587     // update global priority order
 588
 589     updateFeatureRenderer(data,false);
 590     table.repaint();
 591   }
 592   public void close()
 593   {
 594     try
 595     {
 596       frame.setClosed(true);
 597     }
 598     catch (Exception exe)
 599     {}
 600
 601   }
 602
 603   public void updateFeatureRenderer(Object[][] data)
 604   {
 605     updateFeatureRenderer(data, true);
 606   }
 607   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
 608   {
 609     fr.setFeaturePriority(data, visibleNew);
 610     af.alignPanel.paintAlignment(true);
 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.ws.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   public void noDasSourceActive()
 808   {
 809     JOptionPane.showInternalConfirmDialog(Desktop.desktop,
 810             "No das sources were selected.\n"
 811             + "Please select some sources and\n"
 812             +" try again.",
 813             "No Sources Selected",
 814             JOptionPane.DEFAULT_OPTION,
 815             JOptionPane.INFORMATION_MESSAGE);
 816     complete();
 817   }
 818
 819   /////////////////////////////////////////////////////////////////////////
 820   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
 821   /////////////////////////////////////////////////////////////////////////
 822   class FeatureTableModel
 823       extends AbstractTableModel
 824   {
 825     FeatureTableModel(Object[][] data)
 826     {
 827       this.data = data;
 828     }
 829
 830     private String[] columnNames =
 831         {
 832         "Feature Type", "Colour", "Display"};
 833     private Object[][] data;
 834
 835     public Object[][] getData()
 836     {
 837       return data;
 838     }
 839
 840     public void setData(Object[][] data)
 841     {
 842       this.data = data;
 843     }
 844
 845     public int getColumnCount()
 846     {
 847       return columnNames.length;
 848     }
 849
 850     public Object[] getRow(int row)
 851     {
 852       return data[row];
 853     }
 854
 855     public int getRowCount()
 856     {
 857       return data.length;
 858     }
 859
 860     public String getColumnName(int col)
 861     {
 862       return columnNames[col];
 863     }
 864
 865     public Object getValueAt(int row, int col)
 866     {
 867       return data[row][col];
 868     }
 869
 870     public Class getColumnClass(int c)
 871     {
 872       return getValueAt(0, c).getClass();
 873     }
 874
 875     public boolean isCellEditable(int row, int col)
 876     {
 877       return col == 0 ? false : true;
 878     }
 879
 880     public void setValueAt(Object value, int row, int col)
 881     {
 882       data[row][col] = value;
 883       fireTableCellUpdated(row, col);
 884       updateFeatureRenderer(data);
 885     }
 886
 887   }
 888
 889   class ColorRenderer
 890       extends JLabel implements TableCellRenderer
 891   {
 892     javax.swing.border.Border unselectedBorder = null;
 893     javax.swing.border.Border selectedBorder = null;
 894
 895     public ColorRenderer()
 896     {
 897       setOpaque(true); //MUST do this for background to show up.
 898     }
 899
 900     public Component getTableCellRendererComponent(
 901         JTable table, Object color,
 902         boolean isSelected, boolean hasFocus,
 903         int row, int column)
 904     {
 905       Color newColor = (Color) color;
 906       setBackground(newColor);
 907       if (isSelected)
 908       {
 909         if (selectedBorder == null)
 910         {
 911           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
 912               table.getSelectionBackground());
 913         }
 914         setBorder(selectedBorder);
 915       }
 916       else
 917       {
 918         if (unselectedBorder == null)
 919         {
 920           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
 921               table.getBackground());
 922         }
 923         setBorder(unselectedBorder);
 924       }
 925
 926       setToolTipText("RGB value: " + newColor.getRed() + ", "
 927                      + newColor.getGreen() + ", "
 928                      + newColor.getBlue());
 929       return this;
 930     }
 931   }
 932
 933 }
 934
 935 class ColorEditor
 936     extends AbstractCellEditor implements TableCellEditor,
 937     ActionListener
 938 {
 939   Color currentColor;
 940   JButton button;
 941   JColorChooser colorChooser;
 942   JDialog dialog;
 943   protected static final String EDIT = "edit";
 944
 945   public ColorEditor()
 946   {
 947     //Set up the editor (from the table's point of view),
 948     //which is a button.
 949     //This button brings up the color chooser dialog,
 950     //which is the editor from the user's point of view.
 951     button = new JButton();
 952     button.setActionCommand(EDIT);
 953     button.addActionListener(this);
 954     button.setBorderPainted(false);
 955     //Set up the dialog that the button brings up.
 956     colorChooser = new JColorChooser();
 957     dialog = JColorChooser.createDialog(button,
 958                                         "Select new Colour",
 959                                         true, //modal
 960                                         colorChooser,
 961                                         this, //OK button handler
 962                                         null); //no CANCEL button handler
 963   }
 964
 965   /**
 966    * Handles events from the editor button and from
 967    * the dialog's OK button.
 968    */
 969   public void actionPerformed(ActionEvent e)
 970   {
 971
 972     if (EDIT.equals(e.getActionCommand()))
 973     {
 974       //The user has clicked the cell, so
 975       //bring up the dialog.
 976       button.setBackground(currentColor);
 977       colorChooser.setColor(currentColor);
 978       dialog.setVisible(true);
 979
 980       //Make the renderer reappear.
 981       fireEditingStopped();
 982
 983     }
 984     else
 985     { //User pressed dialog's "OK" button.
 986       currentColor = colorChooser.getColor();
 987     }
 988   }
 989
 990   //Implement the one CellEditor method that AbstractCellEditor doesn't.
 991   public Object getCellEditorValue()
 992   {
 993     return currentColor;
 994   }
 995
 996   //Implement the one method defined by TableCellEditor.
 997   public Component getTableCellEditorComponent(JTable table,
 998                                                Object value,
 999                                                boolean isSelected,
1000                                                int row,
1001                                                int column)
1002   {
1003     currentColor = (Color) value;
1004     return button;
1005   }
1006 }