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