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               index++;
 467               continue;
 468             }
 469           }
 470
 471
 472           if (! (features[index].begin == 0 && features[index].end == 0))
 473           {
 474             // If beginning and end are 0, the feature is for the whole sequence
 475             // and we don't want to render the feature in the normal way
 476
 477             if (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
 478               // this is a new feature type on the alignment. Mark it for
 479               // display.
 480               av.featuresDisplayed.put(features[index].getType(),
 481                                      new Integer(getColour(features[index].
 482                 getType()).getRGB()));
 483               setOrder(features[index].getType(),0);
 484             }
 485            }
 486         }
 487         if (!allfeatures.contains(features[index].getType()))
 488         {
 489           allfeatures.addElement(features[index].getType());
 490         }
 491         index++;
 492       }
 493     }
 494     updateRenderOrder(allfeatures);
 495     findingFeatures = false;
 496   }
 497   protected boolean firing=false;
 498   /**
 499    * replaces the current renderOrder with the unordered features in allfeatures.
 500    * The ordering of any types in both renderOrder and allfeatures is preserved,
 501    * and all new feature types are rendered on top of the existing types, in
 502    * the order given by getOrder or the order given in allFeatures.
 503    * Note. this operates directly on the featureOrder hash for efficiency. TODO:
 504    * eliminate the float storage for computing/recalling the persistent ordering
 505    *
 506    * @param allFeatures
 507    */
 508   private void updateRenderOrder(Vector allFeatures) {
 509     Vector allfeatures = new Vector(allFeatures);
 510     String[] oldRender = renderOrder;
 511     renderOrder = new String[allfeatures.size()];
 512     boolean initOrders=(featureOrder==null);
 513     int opos=0;
 514     if (oldRender!=null && oldRender.length>0)
 515     {
 516       for (int j=0; j<oldRender.length; j++)
 517       {
 518         if (oldRender[j]!=null)
 519           {
 520             if (initOrders)
 521             {
 522               setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
 523             }
 524             if (allfeatures.contains(oldRender[j])) {
 525               renderOrder[opos++]  = oldRender[j]; // existing features always
 526                                                     // appear below new features
 527               allfeatures.removeElement(oldRender[j]);
 528             }
 529           }
 530         }
 531     }
 532     if (allfeatures.size()==0) {
 533       // no new features - leave order unchanged.
 534       return;
 535     }
 536     int i=allfeatures.size()-1;
 537     int iSize=i;
 538     boolean sort=false;
 539     String[] newf = new String[allfeatures.size()];
 540     float[] sortOrder = new float[allfeatures.size()];
 541     Enumeration en = allfeatures.elements();
 542     // sort remaining elements
 543     while (en.hasMoreElements())
 544     {
 545       newf[i] = en.nextElement().toString();
 546       if (initOrders || !featureOrder.containsKey(newf[i]))
 547       {
 548         int denom = initOrders ? allfeatures.size() : featureOrder.size();
 549           // new unordered feature - compute persistent ordering at head of
 550           // existing features.
 551         setOrder(newf[i], i/(float) denom);
 552       }
 553       // set order from newly found feature from persisted ordering.
 554       sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
 555       if (i<iSize)
 556       {
 557         // only sort if we need to
 558         sort = sort || sortOrder[i]>sortOrder[i+1];
 559       }
 560       i--;
 561     }
 562     if (iSize>1 && sort)
 563       jalview.util.QuickSort.sort(sortOrder, newf);
 564     sortOrder=null;
 565     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
 566   }
 567   public Color getColour(String featureType)
 568   {
 569     if (!featureColours.containsKey(featureType))
 570     {
 571       jalview.schemes.UserColourScheme ucs = new
 572           jalview.schemes.UserColourScheme();
 573       Color col = ucs.createColourFromName(featureType);
 574       featureColours.put(featureType, col);
 575       return col;
 576     }
 577     else
 578       return (Color) featureColours.get(featureType);
 579   }
 580
 581   static String lastFeatureAdded;
 582   static String lastFeatureGroupAdded;
 583   static String lastDescriptionAdded;
 584
 585   int featureIndex = 0;
 586   boolean amendFeatures(final SequenceI[] sequences,
 587                         final SequenceFeature[] features,
 588                         boolean newFeatures,
 589                         final AlignmentPanel ap)
 590   {
 591
 592     featureIndex = 0;
 593
 594     JPanel bigPanel = new JPanel(new BorderLayout());
 595     final JComboBox overlaps;
 596     final JTextField name = new JTextField(25);
 597     final JTextField source = new JTextField(25);
 598     final JTextArea description = new JTextArea(3, 25);
 599     final JSpinner start = new JSpinner();
 600     final JSpinner end = new JSpinner();
 601     start.setPreferredSize(new Dimension(80, 20));
 602     end.setPreferredSize(new Dimension(80, 20));
 603
 604     final JPanel colour = new JPanel();
 605     colour.setBorder(BorderFactory.createEtchedBorder());
 606     colour.setMaximumSize(new Dimension(40, 10));
 607     colour.addMouseListener(new MouseAdapter()
 608     {
 609       public void mousePressed(MouseEvent evt)
 610       {
 611         Color col = JColorChooser.showDialog(Desktop.desktop,
 612                                              "Select Feature Colour",
 613                                              colour.getBackground());
 614         if (col != null)
 615           colour.setBackground(col);
 616
 617       }
 618     });
 619
 620     JPanel tmp = new JPanel();
 621     JPanel panel = new JPanel(new GridLayout(3, 1));
 622
 623     ///////////////////////////////////////
 624     ///MULTIPLE FEATURES AT SELECTED RESIDUE
 625     if(!newFeatures && features.length>1)
 626     {
 627      panel = new JPanel(new GridLayout(4, 1));
 628      tmp = new JPanel();
 629      tmp.add(new JLabel("Select Feature: "));
 630      overlaps = new JComboBox();
 631      for(int i=0; i<features.length; i++)
 632      {
 633        overlaps.addItem(features[i].getType()
 634         +"/"+features[i].getBegin()+"-"+features[i].getEnd()
 635         +" ("+features[i].getFeatureGroup()+")");
 636      }
 637
 638      tmp.add(overlaps);
 639
 640      overlaps.addItemListener(new ItemListener()
 641      {
 642        public void itemStateChanged(ItemEvent e)
 643        {
 644          int index = overlaps.getSelectedIndex();
 645          if (index != -1)
 646          {
 647            featureIndex = index;
 648            name.setText(features[index].getType());
 649            description.setText(features[index].getDescription());
 650            source.setText(features[index].getFeatureGroup());
 651            start.setValue(new Integer(features[index].getBegin()));
 652            end.setValue(new Integer(features[index].getEnd()));
 653
 654            SearchResults highlight = new SearchResults();
 655            highlight.addResult(sequences[0],
 656                                features[index].getBegin(),
 657                                features[index].getEnd());
 658
 659            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 660
 661          }
 662          Color col = getColour(name.getText());
 663          if (col == null)
 664          {
 665            col = new
 666                jalview.schemes.UserColourScheme()
 667                .createColourFromName(name.getText());
 668          }
 669
 670          colour.setBackground(col);
 671        }
 672      });
 673
 674
 675      panel.add(tmp);
 676     }
 677     //////////
 678     //////////////////////////////////////
 679
 680     tmp = new JPanel();
 681     panel.add(tmp);
 682     tmp.add(new JLabel("Name: ", JLabel.RIGHT));
 683     tmp.add(name);
 684
 685     tmp = new JPanel();
 686     panel.add(tmp);
 687     tmp.add(new JLabel("Group: ", JLabel.RIGHT));
 688     tmp.add(source);
 689
 690     tmp = new JPanel();
 691     panel.add(tmp);
 692     tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
 693     tmp.add(colour);
 694     colour.setPreferredSize(new Dimension(150, 15));
 695
 696     bigPanel.add(panel, BorderLayout.NORTH);
 697
 698     panel = new JPanel();
 699     panel.add(new JLabel("Description: ", JLabel.RIGHT));
 700     description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 701     description.setLineWrap(true);
 702     panel.add(new JScrollPane(description));
 703
 704     if (!newFeatures)
 705     {
 706       bigPanel.add(panel, BorderLayout.SOUTH);
 707
 708       panel = new JPanel();
 709       panel.add(new JLabel(" Start:", JLabel.RIGHT));
 710       panel.add(start);
 711       panel.add(new JLabel("  End:", JLabel.RIGHT));
 712       panel.add(end);
 713       bigPanel.add(panel, BorderLayout.CENTER);
 714     }
 715     else
 716     {
 717       bigPanel.add(panel, BorderLayout.CENTER);
 718     }
 719
 720     if (lastFeatureAdded == null)
 721     {
 722       if (features[0].type != null)
 723       {
 724         lastFeatureAdded = features[0].type;
 725       }
 726       else
 727       {
 728         lastFeatureAdded = "feature_1";
 729       }
 730     }
 731
 732     if (lastFeatureGroupAdded == null)
 733     {
 734       if (features[0].featureGroup != null)
 735       {
 736         lastFeatureGroupAdded = features[0].featureGroup;
 737       }
 738       else
 739       {
 740         lastFeatureGroupAdded = "Jalview";
 741       }
 742     }
 743
 744     if(newFeatures)
 745     {
 746       name.setText(lastFeatureAdded);
 747       source.setText(lastFeatureGroupAdded);
 748     }
 749     else
 750     {
 751       name.setText(features[0].getType());
 752       source.setText(features[0].getFeatureGroup());
 753     }
 754
 755     start.setValue(new Integer(features[0].getBegin()));
 756     end.setValue(new Integer(features[0].getEnd()));
 757     description.setText(features[0].getDescription());
 758     colour.setBackground(getColour(name.getText()));
 759
 760
 761     Object[] options;
 762     if (!newFeatures)
 763     {
 764       options = new Object[]
 765           {
 766           "Amend", "Delete", "Cancel"};
 767     }
 768     else
 769     {
 770       options = new Object[]
 771           {
 772           "OK", "Cancel"};
 773     }
 774
 775     String title = newFeatures ? "Create New Sequence Feature(s)" :
 776         "Amend/Delete Features for "
 777         + sequences[0].getName();
 778
 779     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 780         bigPanel,
 781         title,
 782         JOptionPane.YES_NO_CANCEL_OPTION,
 783         JOptionPane.QUESTION_MESSAGE,
 784         null,
 785         options, "OK");
 786
 787     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 788
 789     if (reply == JOptionPane.OK_OPTION && name.getText().length()>0)
 790     {
 791       // This ensures that the last sequence
 792       // is refreshed and new features are rendered
 793       lastSeq = null;
 794       lastFeatureAdded = name.getText().trim();
 795       lastFeatureGroupAdded = source.getText().trim();
 796       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 797
 798       if(lastFeatureGroupAdded.length()<1)
 799         lastFeatureGroupAdded = null;
 800     }
 801
 802     if (!newFeatures)
 803     {
 804       SequenceFeature sf = features[featureIndex];
 805
 806       if (reply == JOptionPane.NO_OPTION)
 807       {
 808         sequences[0].getDatasetSequence().deleteFeature(sf);
 809       }
 810       else if (reply == JOptionPane.YES_OPTION)
 811       {
 812         sf.type = lastFeatureAdded;
 813         sf.featureGroup = lastFeatureGroupAdded;
 814         sf.description = lastDescriptionAdded;
 815
 816         setColour(sf.type, colour.getBackground());
 817         av.featuresDisplayed.put(sf.type,
 818                                  new Integer(colour.getBackground().getRGB()));
 819
 820         try
 821         {
 822           sf.begin = ( (Integer) start.getValue()).intValue();
 823           sf.end = ( (Integer) end.getValue()).intValue();
 824         }
 825         catch (NumberFormatException ex)
 826         {}
 827
 828         ffile.parseDescriptionHTML(sf, false);
 829       }
 830     }
 831     else //NEW FEATURES ADDED
 832     {
 833       if (reply == JOptionPane.OK_OPTION
 834           && lastFeatureAdded.length()>0)
 835       {
 836         for (int i = 0; i < sequences.length; i++)
 837         {
 838           features[i].type = lastFeatureAdded;
 839           if (lastFeatureGroupAdded!=null)
 840             features[i].featureGroup = lastFeatureGroupAdded;
 841           features[i].description = lastDescriptionAdded;
 842           sequences[i].addSequenceFeature(features[i]);
 843           ffile.parseDescriptionHTML(features[i], false);
 844         }
 845
 846         if (av.featuresDisplayed == null)
 847         {
 848           av.featuresDisplayed = new Hashtable();
 849         }
 850
 851         if (lastFeatureGroupAdded != null)
 852         {
 853           if (featureGroups == null)
 854             featureGroups = new Hashtable();
 855           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 856         }
 857
 858         Color col = colour.getBackground();
 859         setColour(lastFeatureAdded, colour.getBackground());
 860         av.featuresDisplayed.put(lastFeatureAdded,
 861                                    new Integer(col.getRGB()));
 862
 863         findAllFeatures(false);
 864
 865         ap.paintAlignment(true);
 866
 867
 868         return true;
 869       }
 870       else
 871       {
 872         return false;
 873       }
 874     }
 875
 876     ap.paintAlignment(true);
 877
 878     return true;
 879   }
 880
 881   public void setColour(String featureType, Color col)
 882   {
 883     featureColours.put(featureType, col);
 884   }
 885
 886   public void setTransparency(float value)
 887   {
 888     transparency = value;
 889   }
 890
 891   public float getTransparency()
 892   {
 893     return transparency;
 894   }
 895   /**
 896    * Replace current ordering with new ordering
 897    * @param data { String(Type), Colour(Type), Boolean(Displayed) }
 898    */
 899   public void setFeaturePriority(Object[][] data)
 900   {
 901     setFeaturePriority(data, true);
 902   }
 903   /**
 904    *
 905    * @param data { String(Type), Colour(Type), Boolean(Displayed) }
 906    * @param visibleNew when true current featureDisplay list will be cleared
 907    */
 908   public void setFeaturePriority(Object[][] data, boolean visibleNew)
 909   {
 910     if (visibleNew)
 911       {
 912       if (av.featuresDisplayed != null)
 913       {
 914         av.featuresDisplayed.clear();
 915       }
 916       else
 917       {
 918         av.featuresDisplayed = new Hashtable();
 919       }
 920     }
 921     if (data==null)
 922     {
 923       return;
 924     }
 925
 926     // The feature table will display high priority
 927     // features at the top, but theses are the ones
 928     // we need to render last, so invert the data
 929     renderOrder = new String[data.length];
 930
 931     if (data.length > 0)
 932     {
 933       for (int i = 0; i < data.length; i++)
 934       {
 935         String type = data[i][0].toString();
 936         setColour(type, (Color) data[i][1]);
 937         if ( ( (Boolean) data[i][2]).booleanValue())
 938         {
 939           av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
 940         }
 941
 942         renderOrder[data.length - i - 1] = type;
 943       }
 944     }
 945
 946   }
 947   Hashtable featureOrder=null;
 948   /**
 949    * analogous to colour - store a normalized ordering for all feature types in
 950    * this rendering context.
 951    *
 952    * @param type
 953    *          Feature type string
 954    * @param position
 955    *          normalized priority - 0 means always appears on top, 1 means
 956    *          always last.
 957    */
 958   public float setOrder(String type, float position)
 959   {
 960     if (featureOrder==null)
 961     {
 962       featureOrder = new Hashtable();
 963     }
 964     featureOrder.put(type, new Float(position));
 965     return position;
 966   }
 967   /**
 968    * get the global priority (0 (top) to 1 (bottom))
 969    *
 970    * @param type
 971    * @return [0,1] or -1 for a type without a priority
 972    */
 973   public float getOrder(String type) {
 974     if (featureOrder!=null)
 975     {
 976       if (featureOrder.containsKey(type))
 977       {
 978         return ((Float)featureOrder.get(type)).floatValue();
 979       }
 980     }
 981     return -1;
 982   }
 983
 984   /**
 985    * @param listener
 986    * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
 987    */
 988   public void addPropertyChangeListener(PropertyChangeListener listener)
 989   {
 990     changeSupport.addPropertyChangeListener(listener);
 991   }
 992
 993   /**
 994    * @param listener
 995    * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
 996    */
 997   public void removePropertyChangeListener(PropertyChangeListener listener)
 998   {
 999     changeSupport.removePropertyChangeListener(listener);
1000   }
1001 }