src/jalview/gui/FeatureRenderer.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.util.*;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import java.awt.image.*;
  26 import java.beans.PropertyChangeListener;
  27 import java.beans.PropertyChangeSupport;
  28
  29 import javax.swing.*;
  30
  31 import jalview.datamodel.*;
  32
  33 /**
  34  * DOCUMENT ME!
  35  *
  36  * @author $author$
  37  * @version $Revision$
  38  */
  39 public class FeatureRenderer
  40 {
  41   AlignmentPanel ap;
  42   AlignViewport av;
  43   Color resBoxColour;
  44   float transparency = 1.0f;
  45   FontMetrics fm;
  46   int charOffset;
  47
  48   Hashtable featureColours = new Hashtable();
  49
  50   // A higher level for grouping features of a
  51   // particular type
  52   Hashtable featureGroups = new Hashtable();
  53
  54   // This is actually an Integer held in the hashtable,
  55   // Retrieved using the key feature type
  56   Object currentColour;
  57
  58   String[] renderOrder;
  59   PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
  60
  61   Vector allfeatures;
  62
  63   /**
  64    * Creates a new FeatureRenderer object.
  65    *
  66    * @param av
  67    *          DOCUMENT ME!
  68    */
  69   public FeatureRenderer(AlignmentPanel ap)
  70   {
  71     this.ap = ap;
  72     this.av = ap.av;
  73   }
  74
  75
  76   public void transferSettings(FeatureRenderer fr)
  77   {
  78     this.renderOrder = fr.renderOrder;
  79     this.featureGroups = fr.featureGroups;
  80     this.featureColours = fr.featureColours;
  81     this.transparency = fr.transparency;
  82     this.featureOrder = fr.featureOrder;
  83   }
  84
  85   BufferedImage offscreenImage;
  86   boolean offscreenRender = false;
  87   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
  88   {
  89     return new Color(findFeatureColour(initialCol.getRGB(),
  90                                        seq, res));
  91   }
  92
  93   /**
  94    * This is used by the Molecule Viewer and Overview to get the accurate
  95    * colourof the rendered sequence
  96    */
  97   public int findFeatureColour(int initialCol, SequenceI seq, int column)
  98   {
  99     if (!av.showSequenceFeatures)
 100     {
 101       return initialCol;
 102     }
 103
 104     if (seq != lastSeq)
 105     {
 106       lastSeq = seq;
 107       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
 108       if (sequenceFeatures!=null)
 109       {
 110         sfSize = sequenceFeatures.length;
 111       }
 112     }
 113
 114     if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
 115       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
 116       if (sequenceFeatures != null)
 117       {
 118         sfSize = sequenceFeatures.length;
 119       }
 120     }
 121
 122     if (sequenceFeatures == null || sfSize==0)
 123     {
 124       return initialCol;
 125     }
 126
 127
 128     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
 129     {
 130       return Color.white.getRGB();
 131     }
 132
 133     // Only bother making an offscreen image if transparency is applied
 134     if (transparency != 1.0f && offscreenImage == null)
 135     {
 136       offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
 137     }
 138
 139     currentColour = null;
 140
 141     offscreenRender = true;
 142
 143     if (offscreenImage != null)
 144     {
 145       offscreenImage.setRGB(0, 0, initialCol);
 146       drawSequence(offscreenImage.getGraphics(),
 147                    lastSeq,
 148                    column, column, 0);
 149
 150       return offscreenImage.getRGB(0, 0);
 151     }
 152     else
 153     {
 154       drawSequence(null,
 155                    lastSeq,
 156                    lastSeq.findPosition(column),
 157                    -1, -1);
 158
 159       if (currentColour == null)
 160       {
 161         return initialCol;
 162       }
 163       else
 164       {
 165         return ( (Integer) currentColour).intValue();
 166       }
 167     }
 168
 169   }
 170
 171   /**
 172    * DOCUMENT ME!
 173    *
 174    * @param g
 175    *          DOCUMENT ME!
 176    * @param seq
 177    *          DOCUMENT ME!
 178    * @param sg
 179    *          DOCUMENT ME!
 180    * @param start
 181    *          DOCUMENT ME!
 182    * @param end
 183    *          DOCUMENT ME!
 184    * @param x1
 185    *          DOCUMENT ME!
 186    * @param y1
 187    *          DOCUMENT ME!
 188    * @param width
 189    *          DOCUMENT ME!
 190    * @param height
 191    *          DOCUMENT ME!
 192    */
 193   // String type;
 194   // SequenceFeature sf;
 195   SequenceI lastSeq;
 196   SequenceFeature[] sequenceFeatures;
 197   int sfSize, sfindex, spos, epos;
 198
 199   synchronized public void drawSequence(Graphics g, SequenceI seq,
 200                            int start, int end, int y1)
 201   {
 202
 203     if (seq.getDatasetSequence().getSequenceFeatures() == null
 204         || seq.getDatasetSequence().getSequenceFeatures().length == 0)
 205     {
 206       return;
 207     }
 208
 209     if (g != null)
 210     {
 211       fm = g.getFontMetrics();
 212     }
 213
 214     if (av.featuresDisplayed == null
 215         || renderOrder == null
 216         || newFeatureAdded)
 217     {
 218       findAllFeatures();
 219       if (av.featuresDisplayed.size() < 1)
 220       {
 221         return;
 222       }
 223
 224       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
 225     }
 226
 227     if (lastSeq == null || seq != lastSeq
 228         || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
 229     {
 230       lastSeq = seq;
 231       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
 232     }
 233
 234     if (transparency != 1 && g != null)
 235     {
 236       Graphics2D g2 = (Graphics2D) g;
 237       g2.setComposite(
 238           AlphaComposite.getInstance(
 239               AlphaComposite.SRC_OVER, transparency));
 240     }
 241
 242     if (!offscreenRender)
 243     {
 244       spos = lastSeq.findPosition(start);
 245       epos = lastSeq.findPosition(end);
 246     }
 247
 248     sfSize = sequenceFeatures.length;
 249     String type;
 250     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 251     {
 252       type = renderOrder[renderIndex];
 253
 254       if (type == null || !av.featuresDisplayed.containsKey(type))
 255       {
 256         continue;
 257       }
 258
 259       // loop through all features in sequence to find
 260       // current feature to render
 261       for (sfindex = 0; sfindex < sfSize; sfindex++)
 262       {
 263         if (!sequenceFeatures[sfindex].type.equals(type))
 264         {
 265           continue;
 266         }
 267
 268         if (featureGroups != null
 269             && sequenceFeatures[sfindex].featureGroup != null
 270             &&
 271             sequenceFeatures[sfindex].featureGroup.length()!=0
 272             && featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
 273             &&
 274             ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
 275                                             featureGroup)).
 276             booleanValue())
 277         {
 278           continue;
 279         }
 280
 281         if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
 282                                  || sequenceFeatures[sfindex].getEnd() < spos))
 283         {
 284           continue;
 285         }
 286
 287         if (offscreenRender && offscreenImage == null)
 288         {
 289           if (sequenceFeatures[sfindex].begin <= start &&
 290               sequenceFeatures[sfindex].end >= start)
 291           {
 292             currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
 293                 type);
 294           }
 295         }
 296         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
 297         {
 298
 299           renderFeature(g, seq,
 300                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 301                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 302                         new Color( ( (Integer) av.featuresDisplayed.get(
 303                             sequenceFeatures[sfindex].type)).intValue()),
 304                         start, end, y1);
 305           renderFeature(g, seq,
 306                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 307                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 308                         new Color( ( (Integer) av.featuresDisplayed.get(
 309                             sequenceFeatures[sfindex].type)).intValue()),
 310                         start, end, y1);
 311
 312         }
 313         else
 314         {
 315           renderFeature(g, seq,
 316                         seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 317                         seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 318                         getColour(sequenceFeatures[sfindex].type),
 319                         start, end, y1);
 320         }
 321
 322       }
 323
 324     }
 325
 326     if (transparency != 1.0f && g != null)
 327     {
 328       Graphics2D g2 = (Graphics2D) g;
 329       g2.setComposite(
 330           AlphaComposite.getInstance(
 331               AlphaComposite.SRC_OVER, 1.0f));
 332     }
 333   }
 334
 335   char s;
 336   int i;
 337   void renderFeature(Graphics g, SequenceI seq,
 338                      int fstart, int fend, Color featureColour, int start,
 339                      int end, int y1)
 340   {
 341
 342     if ( ( (fstart <= end) && (fend >= start)))
 343     {
 344       if (fstart < start)
 345       { // fix for if the feature we have starts before the sequence start,
 346         fstart = start; // but the feature end is still valid!!
 347       }
 348
 349       if (fend >= end)
 350       {
 351         fend = end;
 352       }
 353       int pady = (y1 + av.charHeight) - av.charHeight / 5;
 354       for (i = fstart; i <= fend; i++)
 355       {
 356         s = seq.getCharAt(i);
 357
 358         if (jalview.util.Comparison.isGap(s))
 359         {
 360           continue;
 361         }
 362
 363         g.setColor(featureColour);
 364
 365         g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
 366
 367         if (offscreenRender || !av.validCharWidth)
 368         {
 369           continue;
 370         }
 371
 372         g.setColor(Color.white);
 373         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 374         g.drawString(String.valueOf(s),
 375                      charOffset + (av.charWidth * (i - start)),
 376                      pady);
 377
 378       }
 379     }
 380   }
 381
 382   boolean newFeatureAdded = false;
 383   /**
 384    * Called when alignment in associated view has new/modified features
 385    * to discover and display.
 386    *
 387    */
 388   public void featuresAdded()
 389   {
 390     lastSeq=null;
 391     findAllFeatures();
 392   }
 393
 394   boolean findingFeatures = false;
 395   /**
 396    * search the alignment for all new features, give them a colour and display
 397    * them. Then fires a PropertyChangeEvent on the changeSupport object.
 398    *
 399    */
 400   synchronized void findAllFeatures()
 401   {
 402     findAllFeatures(true); // add all new features as visible
 403     if (!firing) {
 404       firing=true;
 405       changeSupport.firePropertyChange("changeSupport",null,null);
 406       firing=false;
 407     }
 408   }
 409   /**
 410    * Searches alignment for all features and updates colours
 411    *
 412    * @param newMadeVisible
 413    *          if true newly added feature types will be rendered immediatly
 414    */
 415   synchronized void findAllFeatures(boolean newMadeVisible) {
 416     newFeatureAdded = false;
 417
 418     if (findingFeatures)
 419     {
 420       newFeatureAdded = true;
 421       return;
 422     }
 423
 424     findingFeatures = true;
 425
 426     if (av.featuresDisplayed == null)
 427     {
 428       av.featuresDisplayed = new Hashtable();
 429     }
 430
 431     allfeatures = new Vector();
 432     Vector oldfeatures = new Vector();
 433     if (renderOrder!=null)
 434     {
 435       for (int i=0; i<renderOrder.length; i++) {
 436         if (renderOrder[i]!=null)
 437         {
 438           oldfeatures.addElement(renderOrder[i]);
 439         }
 440       }
 441     }
 442     for (int i = 0; i < av.alignment.getHeight(); i++)
 443     {
 444       SequenceFeature[] features
 445           = av.alignment.getSequenceAt(i).getDatasetSequence().
 446           getSequenceFeatures();
 447
 448       if (features == null)
 449       {
 450         continue;
 451       }
 452
 453       int index = 0;
 454       while (index < features.length)
 455       {
 456         if (!av.featuresDisplayed.containsKey(features[index].getType()))
 457         {
 458
 459           if(featureGroups.containsKey(features[index].getType()))
 460           {
 461             boolean visible = ( (Boolean) featureGroups.get(
 462                 features[index].featureGroup)).booleanValue();
 463
 464             if(!visible)
 465             {
 466               System.out.println(features[index].featureGroup
 467                                  +" not visible");
 468               index++;
 469               continue;
 470             }
 471           }
 472
 473
 474           if (! (features[index].begin == 0 && features[index].end == 0))
 475           {
 476             // If beginning and end are 0, the feature is for the whole sequence
 477             // and we don't want to render the feature in the normal way
 478
 479             if (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
 480               // this is a new feature type on the alignment. Mark it for
 481               // display.
 482               av.featuresDisplayed.put(features[index].getType(),
 483                                      new Integer(getColour(features[index].
 484                 getType()).getRGB()));
 485               setOrder(features[index].getType(),0);
 486             }
 487            }
 488         }
 489         if (!allfeatures.contains(features[index].getType()))
 490         {
 491           allfeatures.addElement(features[index].getType());
 492         }
 493         index++;
 494       }
 495     }
 496     updateRenderOrder(allfeatures);
 497     findingFeatures = false;
 498   }
 499   protected boolean firing=false;
 500   /**
 501    * replaces the current renderOrder with the unordered features in allfeatures.
 502    * The ordering of any types in both renderOrder and allfeatures is preserved,
 503    * and all new feature types are rendered on top of the existing types, in
 504    * the order given by getOrder or the order given in allFeatures.
 505    * Note. this operates directly on the featureOrder hash for efficiency. TODO:
 506    * eliminate the float storage for computing/recalling the persistent ordering
 507    *
 508    * @param allFeatures
 509    */
 510   private void updateRenderOrder(Vector allFeatures) {
 511     Vector allfeatures = new Vector(allFeatures);
 512     String[] oldRender = renderOrder;
 513     renderOrder = new String[allfeatures.size()];
 514     boolean initOrders=(featureOrder==null);
 515     int opos=0;
 516     if (oldRender!=null && oldRender.length>0)
 517     {
 518       for (int j=0; j<oldRender.length; j++)
 519       {
 520         if (oldRender[j]!=null)
 521           {
 522             if (initOrders)
 523             {
 524               setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
 525             }
 526             if (allfeatures.contains(oldRender[j])) {
 527               renderOrder[opos++]  = oldRender[j]; // existing features always
 528                                                     // appear below new features
 529               allfeatures.removeElement(oldRender[j]);
 530             }
 531           }
 532         }
 533     }
 534     if (allfeatures.size()==0) {
 535       // no new features - leave order unchanged.
 536       return;
 537     }
 538     int i=allfeatures.size()-1;
 539     int iSize=i;
 540     boolean sort=false;
 541     String[] newf = new String[allfeatures.size()];
 542     float[] sortOrder = new float[allfeatures.size()];
 543     Enumeration en = allfeatures.elements();
 544     // sort remaining elements
 545     while (en.hasMoreElements())
 546     {
 547       newf[i] = en.nextElement().toString();
 548       if (initOrders || !featureOrder.containsKey(newf[i]))
 549       {
 550         int denom = initOrders ? allfeatures.size() : featureOrder.size();
 551           // new unordered feature - compute persistent ordering at head of
 552           // existing features.
 553         setOrder(newf[i], i/(float) denom);
 554       }
 555       // set order from newly found feature from persisted ordering.
 556       sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
 557       if (i<iSize)
 558       {
 559         // only sort if we need to
 560         sort = sort || sortOrder[i]>sortOrder[i+1];
 561       }
 562       i--;
 563     }
 564     if (iSize>1 && sort)
 565       jalview.util.QuickSort.sort(sortOrder, newf);
 566     sortOrder=null;
 567     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
 568   }
 569   public Color getColour(String featureType)
 570   {
 571     if (!featureColours.containsKey(featureType))
 572     {
 573       jalview.schemes.UserColourScheme ucs = new
 574           jalview.schemes.UserColourScheme();
 575       Color col = ucs.createColourFromName(featureType);
 576       featureColours.put(featureType, col);
 577       return col;
 578     }
 579     else
 580       return (Color) featureColours.get(featureType);
 581   }
 582
 583   static String lastFeatureAdded;
 584   static String lastFeatureGroupAdded;
 585   static String lastDescriptionAdded;
 586
 587   int featureIndex = 0;
 588   boolean amendFeatures(final SequenceI[] sequences,
 589                         final SequenceFeature[] features,
 590                         boolean newFeatures,
 591                         final AlignmentPanel ap)
 592   {
 593
 594     featureIndex = 0;
 595
 596     JPanel bigPanel = new JPanel(new BorderLayout());
 597     final JComboBox overlaps;
 598     final JTextField name = new JTextField(25);
 599     final JTextField source = new JTextField(25);
 600     final JTextArea description = new JTextArea(3, 25);
 601     final JSpinner start = new JSpinner();
 602     final JSpinner end = new JSpinner();
 603     start.setPreferredSize(new Dimension(80, 20));
 604     end.setPreferredSize(new Dimension(80, 20));
 605
 606     final JPanel colour = new JPanel();
 607     colour.setBorder(BorderFactory.createEtchedBorder());
 608     colour.setMaximumSize(new Dimension(40, 10));
 609     colour.addMouseListener(new MouseAdapter()
 610     {
 611       public void mousePressed(MouseEvent evt)
 612       {
 613         Color col = JColorChooser.showDialog(Desktop.desktop,
 614                                              "Select Feature Colour",
 615                                              colour.getBackground());
 616         if (col != null)
 617           colour.setBackground(col);
 618
 619       }
 620     });
 621
 622     JPanel tmp = new JPanel();
 623     JPanel panel = new JPanel(new GridLayout(3, 1));
 624
 625     ///////////////////////////////////////
 626     ///MULTIPLE FEATURES AT SELECTED RESIDUE
 627     if(!newFeatures && features.length>1)
 628     {
 629      panel = new JPanel(new GridLayout(4, 1));
 630      tmp = new JPanel();
 631      tmp.add(new JLabel("Select Feature: "));
 632      overlaps = new JComboBox();
 633      for(int i=0; i<features.length; i++)
 634      {
 635        overlaps.addItem(features[i].getType()
 636         +"/"+features[i].getBegin()+"-"+features[i].getEnd()
 637         +" ("+features[i].getFeatureGroup()+")");
 638      }
 639
 640      tmp.add(overlaps);
 641
 642      overlaps.addItemListener(new ItemListener()
 643      {
 644        public void itemStateChanged(ItemEvent e)
 645        {
 646          int index = overlaps.getSelectedIndex();
 647          if (index != -1)
 648          {
 649            featureIndex = index;
 650            name.setText(features[index].getType());
 651            description.setText(features[index].getDescription());
 652            source.setText(features[index].getFeatureGroup());
 653            start.setValue(new Integer(features[index].getBegin()));
 654            end.setValue(new Integer(features[index].getEnd()));
 655
 656            SearchResults highlight = new SearchResults();
 657            highlight.addResult(sequences[0],
 658                                features[index].getBegin(),
 659                                features[index].getEnd());
 660
 661            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 662
 663          }
 664          Color col = getColour(name.getText());
 665          if (col == null)
 666          {
 667            col = new
 668                jalview.schemes.UserColourScheme()
 669                .createColourFromName(name.getText());
 670          }
 671
 672          colour.setBackground(col);
 673        }
 674      });
 675
 676
 677      panel.add(tmp);
 678     }
 679     //////////
 680     //////////////////////////////////////
 681
 682     tmp = new JPanel();
 683     panel.add(tmp);
 684     tmp.add(new JLabel("Name: ", JLabel.RIGHT));
 685     tmp.add(name);
 686
 687     tmp = new JPanel();
 688     panel.add(tmp);
 689     tmp.add(new JLabel("Group: ", JLabel.RIGHT));
 690     tmp.add(source);
 691
 692     tmp = new JPanel();
 693     panel.add(tmp);
 694     tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
 695     tmp.add(colour);
 696     colour.setPreferredSize(new Dimension(150, 15));
 697
 698     bigPanel.add(panel, BorderLayout.NORTH);
 699
 700     panel = new JPanel();
 701     panel.add(new JLabel("Description: ", JLabel.RIGHT));
 702     description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 703     description.setLineWrap(true);
 704     panel.add(new JScrollPane(description));
 705
 706     if (!newFeatures)
 707     {
 708       bigPanel.add(panel, BorderLayout.SOUTH);
 709
 710       panel = new JPanel();
 711       panel.add(new JLabel(" Start:", JLabel.RIGHT));
 712       panel.add(start);
 713       panel.add(new JLabel("  End:", JLabel.RIGHT));
 714       panel.add(end);
 715       bigPanel.add(panel, BorderLayout.CENTER);
 716     }
 717     else
 718     {
 719       bigPanel.add(panel, BorderLayout.CENTER);
 720     }
 721
 722     if (lastFeatureAdded == null)
 723     {
 724       if (features[0].type != null)
 725       {
 726         lastFeatureAdded = features[0].type;
 727       }
 728       else
 729       {
 730         lastFeatureAdded = "feature_1";
 731       }
 732     }
 733
 734     if (lastFeatureGroupAdded == null)
 735     {
 736       if (features[0].featureGroup != null)
 737       {
 738         lastFeatureGroupAdded = features[0].featureGroup;
 739       }
 740       else
 741       {
 742         lastFeatureGroupAdded = "Jalview";
 743       }
 744     }
 745
 746     if(newFeatures)
 747     {
 748       name.setText(lastFeatureAdded);
 749       source.setText(lastFeatureGroupAdded);
 750     }
 751     else
 752     {
 753       name.setText(features[0].getType());
 754       source.setText(features[0].getFeatureGroup());
 755     }
 756
 757     start.setValue(new Integer(features[0].getBegin()));
 758     end.setValue(new Integer(features[0].getEnd()));
 759     description.setText(features[0].getDescription());
 760     colour.setBackground(getColour(name.getText()));
 761
 762
 763     Object[] options;
 764     if (!newFeatures)
 765     {
 766       options = new Object[]
 767           {
 768           "Amend", "Delete", "Cancel"};
 769     }
 770     else
 771     {
 772       options = new Object[]
 773           {
 774           "OK", "Cancel"};
 775     }
 776
 777     String title = newFeatures ? "Create New Sequence Feature(s)" :
 778         "Amend/Delete Features for "
 779         + sequences[0].getName();
 780
 781     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 782         bigPanel,
 783         title,
 784         JOptionPane.YES_NO_CANCEL_OPTION,
 785         JOptionPane.QUESTION_MESSAGE,
 786         null,
 787         options, "OK");
 788
 789     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 790
 791     if (reply == JOptionPane.OK_OPTION && name.getText().length()>0)
 792     {
 793       // This ensures that the last sequence
 794       // is refreshed and new features are rendered
 795       lastSeq = null;
 796       lastFeatureAdded = name.getText().trim();
 797       lastFeatureGroupAdded = source.getText().trim();
 798       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 799
 800       if(lastFeatureGroupAdded.length()<1)
 801         lastFeatureGroupAdded = null;
 802     }
 803
 804     if (!newFeatures)
 805     {
 806       SequenceFeature sf = features[featureIndex];
 807
 808       if (reply == JOptionPane.NO_OPTION)
 809       {
 810         sequences[0].getDatasetSequence().deleteFeature(sf);
 811       }
 812       else if (reply == JOptionPane.YES_OPTION)
 813       {
 814         sf.type = lastFeatureAdded;
 815         sf.featureGroup = lastFeatureGroupAdded;
 816         sf.description = lastDescriptionAdded;
 817
 818         setColour(sf.type, colour.getBackground());
 819         av.featuresDisplayed.put(sf.type,
 820                                  new Integer(colour.getBackground().getRGB()));
 821
 822         try
 823         {
 824           sf.begin = ( (Integer) start.getValue()).intValue();
 825           sf.end = ( (Integer) end.getValue()).intValue();
 826         }
 827         catch (NumberFormatException ex)
 828         {}
 829
 830         ffile.parseDescriptionHTML(sf, false);
 831       }
 832     }
 833     else //NEW FEATURES ADDED
 834     {
 835       if (reply == JOptionPane.OK_OPTION
 836           && lastFeatureAdded.length()>0)
 837       {
 838         for (int i = 0; i < sequences.length; i++)
 839         {
 840           features[i].type = lastFeatureAdded;
 841           if (lastFeatureGroupAdded!=null)
 842             features[i].featureGroup = lastFeatureGroupAdded;
 843           features[i].description = lastDescriptionAdded;
 844           sequences[i].addSequenceFeature(features[i]);
 845           ffile.parseDescriptionHTML(features[i], false);
 846         }
 847
 848         if (av.featuresDisplayed == null)
 849         {
 850           av.featuresDisplayed = new Hashtable();
 851         }
 852
 853         if (lastFeatureGroupAdded != null)
 854         {
 855           if (featureGroups == null)
 856             featureGroups = new Hashtable();
 857           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 858         }
 859
 860         Color col = colour.getBackground();
 861         setColour(lastFeatureAdded, colour.getBackground());
 862         av.featuresDisplayed.put(lastFeatureAdded,
 863                                    new Integer(col.getRGB()));
 864
 865         findAllFeatures(false);
 866
 867         ap.paintAlignment(true);
 868
 869
 870         return true;
 871       }
 872       else
 873       {
 874         return false;
 875       }
 876     }
 877
 878     ap.paintAlignment(true);
 879
 880     return true;
 881   }
 882
 883   public void setColour(String featureType, Color col)
 884   {
 885     featureColours.put(featureType, col);
 886   }
 887
 888   public void setTransparency(float value)
 889   {
 890     transparency = value;
 891   }
 892
 893   public float getTransparency()
 894   {
 895     return transparency;
 896   }
 897   /**
 898    * Replace current ordering with new ordering
 899    * @param data { String(Type), Colour(Type), Boolean(Displayed) }
 900    */
 901   public void setFeaturePriority(Object[][] data)
 902   {
 903     setFeaturePriority(data, true);
 904   }
 905   /**
 906    *
 907    * @param data { String(Type), Colour(Type), Boolean(Displayed) }
 908    * @param visibleNew when true current featureDisplay list will be cleared
 909    */
 910   public void setFeaturePriority(Object[][] data, boolean visibleNew)
 911   {
 912     if (visibleNew)
 913       {
 914       if (av.featuresDisplayed != null)
 915       {
 916         av.featuresDisplayed.clear();
 917       }
 918       else
 919       {
 920         av.featuresDisplayed = new Hashtable();
 921       }
 922     }
 923     if (data==null)
 924     {
 925       return;
 926     }
 927
 928     // The feature table will display high priority
 929     // features at the top, but theses are the ones
 930     // we need to render last, so invert the data
 931     renderOrder = new String[data.length];
 932
 933     if (data.length > 0)
 934     {
 935       for (int i = 0; i < data.length; i++)
 936       {
 937         String type = data[i][0].toString();
 938         setColour(type, (Color) data[i][1]);
 939         if ( ( (Boolean) data[i][2]).booleanValue())
 940         {
 941           av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
 942         }
 943
 944         renderOrder[data.length - i - 1] = type;
 945       }
 946     }
 947
 948   }
 949   Hashtable featureOrder=null;
 950   /**
 951    * analogous to colour - store a normalized ordering for all feature types in
 952    * this rendering context.
 953    *
 954    * @param type
 955    *          Feature type string
 956    * @param position
 957    *          normalized priority - 0 means always appears on top, 1 means
 958    *          always last.
 959    */
 960   public float setOrder(String type, float position)
 961   {
 962     if (featureOrder==null)
 963     {
 964       featureOrder = new Hashtable();
 965     }
 966     featureOrder.put(type, new Float(position));
 967     return position;
 968   }
 969   /**
 970    * get the global priority (0 (top) to 1 (bottom))
 971    *
 972    * @param type
 973    * @return [0,1] or -1 for a type without a priority
 974    */
 975   public float getOrder(String type) {
 976     if (featureOrder!=null)
 977     {
 978       if (featureOrder.containsKey(type))
 979       {
 980         return ((Float)featureOrder.get(type)).floatValue();
 981       }
 982     }
 983     return -1;
 984   }
 985
 986   /**
 987    * @param listener
 988    * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
 989    */
 990   public void addPropertyChangeListener(PropertyChangeListener listener)
 991   {
 992     changeSupport.addPropertyChangeListener(listener);
 993   }
 994
 995   /**
 996    * @param listener
 997    * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
 998    */
 999   public void removePropertyChangeListener(PropertyChangeListener listener)
1000   {
1001     changeSupport.removePropertyChangeListener(listener);
1002   }
1003 }