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 = null;
  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           if(featureGroups.containsKey(features[index].getType()))
 459           {
 460             boolean visible = ( (Boolean) featureGroups.get(
 461                 features[index].featureGroup)).booleanValue();
 462
 463             if(!visible)
 464             {
 465               System.out.println(features[index].featureGroup
 466                                  +" not visible");
 467               index++;
 468               continue;
 469             }
 470           }
 471
 472
 473           if (! (features[index].begin == 0 && features[index].end == 0))
 474           {
 475             // If beginning and end are 0, the feature is for the whole sequence
 476             // and we don't want to render the feature in the normal way
 477
 478             if (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
 479               // this is a new feature type on the alignment. Mark it for
 480               // display.
 481               av.featuresDisplayed.put(features[index].getType(),
 482                                      new Integer(getColour(features[index].
 483                 getType()).getRGB()));
 484               setOrder(features[index].getType(),0);
 485             }
 486            }
 487         }
 488         if (!allfeatures.contains(features[index].getType()))
 489         {
 490           allfeatures.addElement(features[index].getType());
 491         }
 492         index++;
 493       }
 494     }
 495     updateRenderOrder(allfeatures);
 496     findingFeatures = false;
 497   }
 498   protected boolean firing=false;
 499   /**
 500    * replaces the current renderOrder with the unordered features in allfeatures.
 501    * The ordering of any types in both renderOrder and allfeatures is preserved,
 502    * and all new feature types are rendered on top of the existing types, in
 503    * the order given by getOrder or the order given in allFeatures.
 504    * Note. this operates directly on the featureOrder hash for efficiency. TODO:
 505    * eliminate the float storage for computing/recalling the persistent ordering
 506    *
 507    * @param allFeatures
 508    */
 509   private void updateRenderOrder(Vector allFeatures) {
 510     Vector allfeatures = new Vector(allFeatures);
 511     String[] oldRender = renderOrder;
 512     renderOrder = new String[allfeatures.size()];
 513     boolean initOrders=(featureOrder==null);
 514     int opos=0;
 515     if (oldRender!=null && oldRender.length>0)
 516     {
 517       for (int j=0; j<oldRender.length; j++)
 518       {
 519         if (oldRender[j]!=null)
 520           {
 521             if (initOrders)
 522             {
 523               setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
 524             }
 525             if (allfeatures.contains(oldRender[j])) {
 526               renderOrder[opos++]  = oldRender[j]; // existing features always
 527                                                     // appear below new features
 528               allfeatures.removeElement(oldRender[j]);
 529             }
 530           }
 531         }
 532     }
 533     if (allfeatures.size()==0) {
 534       // no new features - leave order unchanged.
 535       return;
 536     }
 537     int i=allfeatures.size()-1;
 538     int iSize=i;
 539     boolean sort=false;
 540     String[] newf = new String[allfeatures.size()];
 541     float[] sortOrder = new float[allfeatures.size()];
 542     Enumeration en = allfeatures.elements();
 543     // sort remaining elements
 544     while (en.hasMoreElements())
 545     {
 546       newf[i] = en.nextElement().toString();
 547       if (initOrders || !featureOrder.containsKey(newf[i]))
 548       {
 549         int denom = initOrders ? allfeatures.size() : featureOrder.size();
 550           // new unordered feature - compute persistent ordering at head of
 551           // existing features.
 552         setOrder(newf[i], i/(float) denom);
 553       }
 554       // set order from newly found feature from persisted ordering.
 555       sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
 556       if (i<iSize)
 557       {
 558         // only sort if we need to
 559         sort = sort || sortOrder[i]>sortOrder[i+1];
 560       }
 561       i--;
 562     }
 563     if (iSize>1 && sort)
 564       jalview.util.QuickSort.sort(sortOrder, newf);
 565     sortOrder=null;
 566     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
 567   }
 568   public Color getColour(String featureType)
 569   {
 570     if (!featureColours.containsKey(featureType))
 571     {
 572       jalview.schemes.UserColourScheme ucs = new
 573           jalview.schemes.UserColourScheme();
 574       Color col = ucs.createColourFromName(featureType);
 575       featureColours.put(featureType, col);
 576       return col;
 577     }
 578     else
 579       return (Color) featureColours.get(featureType);
 580   }
 581
 582   static String lastFeatureAdded;
 583   static String lastFeatureGroupAdded;
 584   static String lastDescriptionAdded;
 585
 586   int featureIndex = 0;
 587   boolean amendFeatures(final SequenceI[] sequences,
 588                         final SequenceFeature[] features,
 589                         boolean newFeatures,
 590                         final AlignmentPanel ap)
 591   {
 592
 593     featureIndex = 0;
 594
 595     JPanel bigPanel = new JPanel(new BorderLayout());
 596     final JComboBox overlaps;
 597     final JTextField name = new JTextField(25);
 598     final JTextField source = new JTextField(25);
 599     final JTextArea description = new JTextArea(3, 25);
 600     final JSpinner start = new JSpinner();
 601     final JSpinner end = new JSpinner();
 602     start.setPreferredSize(new Dimension(80, 20));
 603     end.setPreferredSize(new Dimension(80, 20));
 604
 605     final JPanel colour = new JPanel();
 606     colour.setBorder(BorderFactory.createEtchedBorder());
 607     colour.setMaximumSize(new Dimension(40, 10));
 608     colour.addMouseListener(new MouseAdapter()
 609     {
 610       public void mousePressed(MouseEvent evt)
 611       {
 612         Color col = JColorChooser.showDialog(Desktop.desktop,
 613                                              "Select Feature Colour",
 614                                              colour.getBackground());
 615         if (col != null)
 616           colour.setBackground(col);
 617
 618       }
 619     });
 620
 621     JPanel tmp = new JPanel();
 622     JPanel panel = new JPanel(new GridLayout(3, 1));
 623
 624     ///////////////////////////////////////
 625     ///MULTIPLE FEATURES AT SELECTED RESIDUE
 626     if(!newFeatures && features.length>1)
 627     {
 628      panel = new JPanel(new GridLayout(4, 1));
 629      tmp = new JPanel();
 630      tmp.add(new JLabel("Select Feature: "));
 631      overlaps = new JComboBox();
 632      for(int i=0; i<features.length; i++)
 633      {
 634        overlaps.addItem(features[i].getType()
 635         +"/"+features[i].getBegin()+"-"+features[i].getEnd()
 636         +" ("+features[i].getFeatureGroup()+")");
 637      }
 638
 639      tmp.add(overlaps);
 640
 641      overlaps.addItemListener(new ItemListener()
 642      {
 643        public void itemStateChanged(ItemEvent e)
 644        {
 645          int index = overlaps.getSelectedIndex();
 646          if (index != -1)
 647          {
 648            featureIndex = index;
 649            name.setText(features[index].getType());
 650            description.setText(features[index].getDescription());
 651            source.setText(features[index].getFeatureGroup());
 652            start.setValue(new Integer(features[index].getBegin()));
 653            end.setValue(new Integer(features[index].getEnd()));
 654
 655            SearchResults highlight = new SearchResults();
 656            highlight.addResult(sequences[0],
 657                                features[index].getBegin(),
 658                                features[index].getEnd());
 659
 660            ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 661
 662          }
 663          Color col = getColour(name.getText());
 664          if (col == null)
 665          {
 666            col = new
 667                jalview.schemes.UserColourScheme()
 668                .createColourFromName(name.getText());
 669          }
 670
 671          colour.setBackground(col);
 672        }
 673      });
 674
 675
 676      panel.add(tmp);
 677     }
 678     //////////
 679     //////////////////////////////////////
 680
 681     tmp = new JPanel();
 682     panel.add(tmp);
 683     tmp.add(new JLabel("Name: ", JLabel.RIGHT));
 684     tmp.add(name);
 685
 686     tmp = new JPanel();
 687     panel.add(tmp);
 688     tmp.add(new JLabel("Group: ", JLabel.RIGHT));
 689     tmp.add(source);
 690
 691     tmp = new JPanel();
 692     panel.add(tmp);
 693     tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
 694     tmp.add(colour);
 695     colour.setPreferredSize(new Dimension(150, 15));
 696
 697     bigPanel.add(panel, BorderLayout.NORTH);
 698
 699     panel = new JPanel();
 700     panel.add(new JLabel("Description: ", JLabel.RIGHT));
 701     description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 702     description.setLineWrap(true);
 703     panel.add(new JScrollPane(description));
 704
 705     if (!newFeatures)
 706     {
 707       bigPanel.add(panel, BorderLayout.SOUTH);
 708
 709       panel = new JPanel();
 710       panel.add(new JLabel(" Start:", JLabel.RIGHT));
 711       panel.add(start);
 712       panel.add(new JLabel("  End:", JLabel.RIGHT));
 713       panel.add(end);
 714       bigPanel.add(panel, BorderLayout.CENTER);
 715     }
 716     else
 717     {
 718       bigPanel.add(panel, BorderLayout.CENTER);
 719     }
 720
 721     if (lastFeatureAdded == null)
 722     {
 723       if (features[0].type != null)
 724       {
 725         lastFeatureAdded = features[0].type;
 726       }
 727       else
 728       {
 729         lastFeatureAdded = "feature_1";
 730       }
 731     }
 732
 733     if (lastFeatureGroupAdded == null)
 734     {
 735       if (features[0].featureGroup != null)
 736       {
 737         lastFeatureGroupAdded = features[0].featureGroup;
 738       }
 739       else
 740       {
 741         lastFeatureGroupAdded = "Jalview";
 742       }
 743     }
 744
 745     if(newFeatures)
 746     {
 747       name.setText(lastFeatureAdded);
 748       source.setText(lastFeatureGroupAdded);
 749     }
 750     else
 751     {
 752       name.setText(features[0].getType());
 753       source.setText(features[0].getFeatureGroup());
 754     }
 755
 756     start.setValue(new Integer(features[0].getBegin()));
 757     end.setValue(new Integer(features[0].getEnd()));
 758     description.setText(features[0].getDescription());
 759     colour.setBackground(getColour(name.getText()));
 760
 761
 762     Object[] options;
 763     if (!newFeatures)
 764     {
 765       options = new Object[]
 766           {
 767           "Amend", "Delete", "Cancel"};
 768     }
 769     else
 770     {
 771       options = new Object[]
 772           {
 773           "OK", "Cancel"};
 774     }
 775
 776     String title = newFeatures ? "Create New Sequence Feature(s)" :
 777         "Amend/Delete Features for "
 778         + sequences[0].getName();
 779
 780     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 781         bigPanel,
 782         title,
 783         JOptionPane.YES_NO_CANCEL_OPTION,
 784         JOptionPane.QUESTION_MESSAGE,
 785         null,
 786         options, "OK");
 787
 788     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 789
 790     if (reply == JOptionPane.OK_OPTION && name.getText().length()>0)
 791     {
 792       // This ensures that the last sequence
 793       // is refreshed and new features are rendered
 794       lastSeq = null;
 795       lastFeatureAdded = name.getText().trim();
 796       lastFeatureGroupAdded = source.getText().trim();
 797       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 798
 799       if(lastFeatureGroupAdded.length()<1)
 800         lastFeatureGroupAdded = null;
 801     }
 802
 803     if (!newFeatures)
 804     {
 805       SequenceFeature sf = features[featureIndex];
 806
 807       if (reply == JOptionPane.NO_OPTION)
 808       {
 809         sequences[0].getDatasetSequence().deleteFeature(sf);
 810       }
 811       else if (reply == JOptionPane.YES_OPTION)
 812       {
 813         sf.type = lastFeatureAdded;
 814         sf.featureGroup = lastFeatureGroupAdded;
 815         sf.description = lastDescriptionAdded;
 816
 817         setColour(sf.type, colour.getBackground());
 818         av.featuresDisplayed.put(sf.type,
 819                                  new Integer(colour.getBackground().getRGB()));
 820
 821         try
 822         {
 823           sf.begin = ( (Integer) start.getValue()).intValue();
 824           sf.end = ( (Integer) end.getValue()).intValue();
 825         }
 826         catch (NumberFormatException ex)
 827         {}
 828
 829         ffile.parseDescriptionHTML(sf, false);
 830       }
 831     }
 832     else //NEW FEATURES ADDED
 833     {
 834       if (reply == JOptionPane.OK_OPTION
 835           && lastFeatureAdded.length()>0)
 836       {
 837         for (int i = 0; i < sequences.length; i++)
 838         {
 839           features[i].type = lastFeatureAdded;
 840           if (lastFeatureGroupAdded!=null)
 841             features[i].featureGroup = lastFeatureGroupAdded;
 842           features[i].description = lastDescriptionAdded;
 843           sequences[i].addSequenceFeature(features[i]);
 844           ffile.parseDescriptionHTML(features[i], false);
 845         }
 846
 847         if (av.featuresDisplayed == null)
 848         {
 849           av.featuresDisplayed = new Hashtable();
 850         }
 851
 852         if (lastFeatureGroupAdded != null)
 853         {
 854           if (featureGroups == null)
 855             featureGroups = new Hashtable();
 856           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 857         }
 858
 859         Color col = colour.getBackground();
 860         setColour(lastFeatureAdded, colour.getBackground());
 861         av.featuresDisplayed.put(lastFeatureAdded,
 862                                    new Integer(col.getRGB()));
 863
 864         findAllFeatures(false);
 865
 866         ap.paintAlignment(true);
 867
 868
 869         return true;
 870       }
 871       else
 872       {
 873         return false;
 874       }
 875     }
 876
 877     ap.paintAlignment(true);
 878
 879     return true;
 880   }
 881
 882   public void setColour(String featureType, Color col)
 883   {
 884     featureColours.put(featureType, col);
 885   }
 886
 887   public void setTransparency(float value)
 888   {
 889     transparency = value;
 890   }
 891
 892   public float getTransparency()
 893   {
 894     return transparency;
 895   }
 896   /**
 897    * Replace current ordering with new ordering
 898    * @param data { String(Type), Colour(Type), Boolean(Displayed) }
 899    */
 900   public void setFeaturePriority(Object[][] data)
 901   {
 902     setFeaturePriority(data, true);
 903   }
 904   /**
 905    *
 906    * @param data { String(Type), Colour(Type), Boolean(Displayed) }
 907    * @param visibleNew when true current featureDisplay list will be cleared
 908    */
 909   public void setFeaturePriority(Object[][] data, boolean visibleNew)
 910   {
 911     if (visibleNew)
 912       {
 913       if (av.featuresDisplayed != null)
 914       {
 915         av.featuresDisplayed.clear();
 916       }
 917       else
 918       {
 919         av.featuresDisplayed = new Hashtable();
 920       }
 921     }
 922     if (data==null)
 923     {
 924       return;
 925     }
 926
 927     // The feature table will display high priority
 928     // features at the top, but theses are the ones
 929     // we need to render last, so invert the data
 930     renderOrder = new String[data.length];
 931
 932     if (data.length > 0)
 933     {
 934       for (int i = 0; i < data.length; i++)
 935       {
 936         String type = data[i][0].toString();
 937         setColour(type, (Color) data[i][1]);
 938         if ( ( (Boolean) data[i][2]).booleanValue())
 939         {
 940           av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
 941         }
 942
 943         renderOrder[data.length - i - 1] = type;
 944       }
 945     }
 946
 947   }
 948   Hashtable featureOrder=null;
 949   /**
 950    * analogous to colour - store a normalized ordering for all feature types in
 951    * this rendering context.
 952    *
 953    * @param type
 954    *          Feature type string
 955    * @param position
 956    *          normalized priority - 0 means always appears on top, 1 means
 957    *          always last.
 958    */
 959   public float setOrder(String type, float position)
 960   {
 961     if (featureOrder==null)
 962     {
 963       featureOrder = new Hashtable();
 964     }
 965     featureOrder.put(type, new Float(position));
 966     return position;
 967   }
 968   /**
 969    * get the global priority (0 (top) to 1 (bottom))
 970    *
 971    * @param type
 972    * @return [0,1] or -1 for a type without a priority
 973    */
 974   public float getOrder(String type) {
 975     if (featureOrder!=null)
 976     {
 977       if (featureOrder.containsKey(type))
 978       {
 979         return ((Float)featureOrder.get(type)).floatValue();
 980       }
 981     }
 982     return -1;
 983   }
 984
 985   /**
 986    * @param listener
 987    * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
 988    */
 989   public void addPropertyChangeListener(PropertyChangeListener listener)
 990   {
 991     changeSupport.addPropertyChangeListener(listener);
 992   }
 993
 994   /**
 995    * @param listener
 996    * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
 997    */
 998   public void removePropertyChangeListener(PropertyChangeListener listener)
 999   {
1000     changeSupport.removePropertyChangeListener(listener);
1001   }
1002 }