src/jalview/appletgui/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.appletgui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23
  24 import java.awt.event.*;
  25
  26 import jalview.appletgui.FeatureSettings.MyCheckbox;
  27 import jalview.datamodel.*;
  28 import jalview.schemes.AnnotationColourGradient;
  29 import jalview.schemes.GraduatedColor;
  30
  31 /**
  32  * DOCUMENT ME!
  33  *
  34  * @author $author$
  35  * @version $Revision$
  36  */
  37 public class FeatureRenderer implements jalview.api.FeatureRenderer
  38 {
  39   AlignViewport av;
  40
  41   Hashtable featureColours = new Hashtable();
  42
  43   // A higher level for grouping features of a
  44   // particular type
  45   Hashtable featureGroups = null;
  46
  47   // Holds web links for feature groups and feature types
  48   // in the form label|link
  49   Hashtable featureLinks = null;
  50
  51   // This is actually an Integer held in the hashtable,
  52   // Retrieved using the key feature type
  53   Object currentColour;
  54
  55   String[] renderOrder;
  56
  57   FontMetrics fm;
  58
  59   int charOffset;
  60
  61   float transparency = 1f;
  62
  63   TransparencySetter transparencySetter = null;
  64
  65   /**
  66    * Creates a new FeatureRenderer object.
  67    *
  68    * @param av
  69    *          DOCUMENT ME!
  70    */
  71   public FeatureRenderer(AlignViewport av)
  72   {
  73     this.av = av;
  74
  75     if (!System.getProperty("java.version").startsWith("1.1"))
  76     {
  77       transparencySetter = new TransparencySetter();
  78     }
  79   }
  80
  81   public void transferSettings(FeatureRenderer fr)
  82   {
  83     renderOrder = fr.renderOrder;
  84     featureGroups = fr.featureGroups;
  85     featureColours = fr.featureColours;
  86     transparency = fr.transparency;
  87     if (av!=null && fr.av!=null && fr.av!=av)
  88     {
  89       if (fr.av.featuresDisplayed!=null)
  90       {
  91         if (av.featuresDisplayed==null)
  92         {
  93           av.featuresDisplayed = new Hashtable();
  94         } else {
  95           av.featuresDisplayed.clear();
  96         }
  97         Enumeration en=fr.av.featuresDisplayed.keys();
  98         while (en.hasMoreElements())
  99         {
 100           av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
 101         }
 102       }
 103     }
 104   }
 105
 106   static String lastFeatureAdded;
 107
 108   static String lastFeatureGroupAdded;
 109
 110   static String lastDescriptionAdded;
 111
 112   int featureIndex = 0;
 113
 114   boolean deleteFeature = false;
 115
 116   FeatureColourPanel colourPanel;
 117
 118   class FeatureColourPanel extends Panel
 119   {
 120     String label = "";
 121
 122     private Color maxCol;
 123
 124     private boolean isColourByLabel, isGcol;
 125
 126     /**
 127      * render a feature style in the amend feature dialog box
 128      */
 129     public void updateColor(Object newcol)
 130     {
 131
 132       Color bg, col = null;
 133       GraduatedColor gcol = null;
 134       String vlabel = "";
 135       if (newcol instanceof Color)
 136       {
 137         isGcol = false;
 138         col = (Color) newcol;
 139         gcol = null;
 140       }
 141       else if (newcol instanceof GraduatedColor)
 142       {
 143         isGcol = true;
 144         gcol = (GraduatedColor) newcol;
 145         col = null;
 146       }
 147       else
 148       {
 149         throw new Error("Invalid color for MyCheckBox");
 150       }
 151       if (col != null)
 152       {
 153         setBackground(bg = col);
 154       }
 155       else
 156       {
 157         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 158         {
 159           vlabel += " "
 160                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 161                           : "(<)");
 162         }
 163         if (isColourByLabel = gcol.isColourByLabel())
 164         {
 165           setBackground(bg = Color.white);
 166           vlabel += " (by Label)";
 167         }
 168         else
 169         {
 170           setBackground(bg = gcol.getMinColor());
 171           maxCol = gcol.getMaxColor();
 172         }
 173       }
 174       label = vlabel;
 175       setBackground(bg);
 176       repaint();
 177     }
 178
 179     FeatureColourPanel()
 180     {
 181       super(null);
 182     }
 183
 184     public void paint(Graphics g)
 185     {
 186       Dimension d = getSize();
 187       if (isGcol)
 188       {
 189         if (isColourByLabel)
 190         {
 191           g.setColor(Color.white);
 192           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 193           g.setColor(Color.black);
 194           Font f = new Font("Verdana", Font.PLAIN, 10);
 195           g.setFont(f);
 196           g.drawString("Label", 0, 0);
 197         }
 198         else
 199         {
 200           g.setColor(maxCol);
 201           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 202
 203         }
 204       }
 205     }
 206
 207   }
 208
 209   boolean amendFeatures(final SequenceI[] sequences,
 210           final SequenceFeature[] features, boolean newFeatures,
 211           final AlignmentPanel ap)
 212   {
 213     Panel bigPanel = new Panel(new BorderLayout());
 214     final TextField name = new TextField(16);
 215     final TextField source = new TextField(16);
 216     final TextArea description = new TextArea(3, 35);
 217     final TextField start = new TextField(8);
 218     final TextField end = new TextField(8);
 219     final Choice overlaps;
 220     Button deleteButton = new Button("Delete");
 221     deleteFeature = false;
 222
 223     colourPanel = new FeatureColourPanel();
 224     colourPanel.setSize(110, 15);
 225     final FeatureRenderer fr = this;
 226
 227     Panel panel = new Panel(new GridLayout(3, 1));
 228
 229     featureIndex = 0; // feature to be amended.
 230     Panel tmp;
 231
 232     // /////////////////////////////////////
 233     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 234     if (!newFeatures && features.length > 1)
 235     {
 236       panel = new Panel(new GridLayout(4, 1));
 237       tmp = new Panel();
 238       tmp.add(new Label("Select Feature: "));
 239       overlaps = new Choice();
 240       for (int i = 0; i < features.length; i++)
 241       {
 242         String item = features[i].getType() + "/" + features[i].getBegin()
 243                 + "-" + features[i].getEnd();
 244
 245         if (features[i].getFeatureGroup() != null)
 246           item += " (" + features[i].getFeatureGroup() + ")";
 247
 248         overlaps.addItem(item);
 249       }
 250
 251       tmp.add(overlaps);
 252
 253       overlaps.addItemListener(new java.awt.event.ItemListener()
 254       {
 255         public void itemStateChanged(java.awt.event.ItemEvent e)
 256         {
 257           int index = overlaps.getSelectedIndex();
 258           if (index != -1)
 259           {
 260             featureIndex = index;
 261             name.setText(features[index].getType());
 262             description.setText(features[index].getDescription());
 263             source.setText(features[index].getFeatureGroup());
 264             start.setText(features[index].getBegin() + "");
 265             end.setText(features[index].getEnd() + "");
 266
 267             SearchResults highlight = new SearchResults();
 268             highlight.addResult(sequences[0], features[index].getBegin(),
 269                     features[index].getEnd());
 270
 271             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 272
 273           }
 274           Object col = getFeatureStyle(name.getText());
 275           if (col == null)
 276           {
 277             col = new jalview.schemes.UserColourScheme()
 278                     .createColourFromName(name.getText());
 279           }
 280
 281           colourPanel.updateColor(col);
 282         }
 283       });
 284
 285       panel.add(tmp);
 286     }
 287     // ////////
 288     // ////////////////////////////////////
 289
 290     tmp = new Panel();
 291     panel.add(tmp);
 292     tmp.add(new Label("Name: ", Label.RIGHT));
 293     tmp.add(name);
 294
 295     tmp = new Panel();
 296     panel.add(tmp);
 297     tmp.add(new Label("Group: ", Label.RIGHT));
 298     tmp.add(source);
 299
 300     tmp = new Panel();
 301     panel.add(tmp);
 302     tmp.add(new Label("Colour: ", Label.RIGHT));
 303     tmp.add(colourPanel);
 304
 305     bigPanel.add(panel, BorderLayout.NORTH);
 306
 307     panel = new Panel();
 308     panel.add(new Label("Description: ", Label.RIGHT));
 309     panel.add(new ScrollPane().add(description));
 310
 311     if (!newFeatures)
 312     {
 313       bigPanel.add(panel, BorderLayout.SOUTH);
 314
 315       panel = new Panel();
 316       panel.add(new Label(" Start:", Label.RIGHT));
 317       panel.add(start);
 318       panel.add(new Label("  End:", Label.RIGHT));
 319       panel.add(end);
 320       bigPanel.add(panel, BorderLayout.CENTER);
 321     }
 322     else
 323     {
 324       bigPanel.add(panel, BorderLayout.CENTER);
 325     }
 326
 327     if (lastFeatureAdded == null)
 328     {
 329       if (features[0].type != null)
 330       {
 331         lastFeatureAdded = features[0].type;
 332       }
 333       else
 334       {
 335         lastFeatureAdded = "feature_1";
 336       }
 337     }
 338
 339     if (lastFeatureGroupAdded == null)
 340     {
 341       if (features[0].featureGroup != null)
 342       {
 343         lastFeatureGroupAdded = features[0].featureGroup;
 344       }
 345       else
 346       {
 347         lastFeatureAdded = "Jalview";
 348       }
 349     }
 350
 351     String title = newFeatures ? "Create New Sequence Feature(s)"
 352             : "Amend/Delete Features for " + sequences[0].getName();
 353
 354     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 355             240);
 356
 357     dialog.setMainPanel(bigPanel);
 358
 359     if (newFeatures)
 360     {
 361       name.setText(lastFeatureAdded);
 362       source.setText(lastFeatureGroupAdded);
 363     }
 364     else
 365     {
 366       dialog.ok.setLabel("Amend");
 367       dialog.buttonPanel.add(deleteButton, 1);
 368       deleteButton.addActionListener(new ActionListener()
 369       {
 370         public void actionPerformed(ActionEvent evt)
 371         {
 372           deleteFeature = true;
 373           dialog.setVisible(false);
 374         }
 375       });
 376       name.setText(features[0].getType());
 377       source.setText(features[0].getFeatureGroup());
 378     }
 379
 380     start.setText(features[0].getBegin() + "");
 381     end.setText(features[0].getEnd() + "");
 382     description.setText(features[0].getDescription());
 383     Color col = getColour(name.getText());
 384     if (col == null)
 385     {
 386       col = new jalview.schemes.UserColourScheme()
 387               .createColourFromName(name.getText());
 388     }
 389     Object fcol = getFeatureStyle(name.getText());
 390     // simply display the feature color in a box
 391     colourPanel.updateColor(fcol);
 392     dialog.setResizable(true);
 393     // TODO: render the graduated color in the box.
 394     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 395     {
 396       public void mousePressed(java.awt.event.MouseEvent evt)
 397       {
 398         if (!colourPanel.isGcol)
 399         {
 400           new UserDefinedColours(fr, ap.alignFrame);
 401         }
 402         else
 403         {
 404           FeatureColourChooser fcc = new FeatureColourChooser(
 405                   ap.alignFrame, name.getText());
 406           dialog.transferFocus();
 407         }
 408       }
 409     });
 410     dialog.setVisible(true);
 411
 412     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 413
 414     if (dialog.accept)
 415     {
 416       // This ensures that the last sequence
 417       // is refreshed and new features are rendered
 418       lastSeq = null;
 419       lastFeatureAdded = name.getText().trim();
 420       lastFeatureGroupAdded = source.getText().trim();
 421       lastDescriptionAdded = description.getText().replace('\n', ' ');
 422     }
 423
 424     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 425       lastFeatureGroupAdded = null;
 426
 427     if (!newFeatures)
 428     {
 429
 430       SequenceFeature sf = features[featureIndex];
 431       if (dialog.accept)
 432       {
 433         sf.type = lastFeatureAdded;
 434         sf.featureGroup = lastFeatureGroupAdded;
 435         sf.description = lastDescriptionAdded;
 436         if (!colourPanel.isGcol)
 437         {
 438           // update colour - otherwise its already done.
 439           setColour(sf.type, colourPanel.getBackground());
 440         }
 441         try
 442         {
 443           sf.begin = Integer.parseInt(start.getText());
 444           sf.end = Integer.parseInt(end.getText());
 445         } catch (NumberFormatException ex)
 446         {
 447         }
 448
 449         ffile.parseDescriptionHTML(sf, false);
 450       }
 451       if (deleteFeature)
 452       {
 453         sequences[0].deleteFeature(sf);
 454       }
 455
 456     }
 457     else
 458     {
 459       if (dialog.accept && name.getText().length() > 0)
 460       {
 461         for (int i = 0; i < sequences.length; i++)
 462         {
 463           features[i].type = lastFeatureAdded;
 464           features[i].featureGroup = lastFeatureGroupAdded;
 465           features[i].description = lastDescriptionAdded;
 466           sequences[i].addSequenceFeature(features[i]);
 467           ffile.parseDescriptionHTML(features[i], false);
 468         }
 469
 470         if (av.featuresDisplayed == null)
 471         {
 472           av.featuresDisplayed = new Hashtable();
 473         }
 474
 475         if (featureGroups == null)
 476         {
 477           featureGroups = new Hashtable();
 478         }
 479
 480         col = colourPanel.getBackground();
 481         // setColour(lastFeatureAdded, fcol);
 482
 483         if (lastFeatureGroupAdded != null)
 484         {
 485           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 486         }
 487         if (fcol instanceof Color)
 488         {
 489           setColour(lastFeatureAdded, fcol);
 490         }
 491         av.featuresDisplayed.put(lastFeatureAdded,
 492                 getFeatureStyle(lastFeatureAdded));
 493
 494         findAllFeatures();
 495
 496         String[] tro = new String[renderOrder.length];
 497         tro[0] = renderOrder[renderOrder.length - 1];
 498         System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1);
 499         renderOrder = tro;
 500       }
 501       else
 502       {
 503         // no update to the alignment
 504         return false;
 505       }
 506     }
 507     // refresh the alignment and the feature settings dialog
 508     if (av.featureSettings != null)
 509     {
 510       av.featureSettings.refreshTable();
 511     }
 512     // findAllFeatures();
 513
 514     ap.paintAlignment(true);
 515
 516     return true;
 517   }
 518
 519   public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
 520   {
 521     overview = true;
 522     if (!av.showSequenceFeatures)
 523     {
 524       return initialCol;
 525     }
 526
 527     lastSeq = seq;
 528     sequenceFeatures = lastSeq.getSequenceFeatures();
 529     if (sequenceFeatures == null)
 530     {
 531       return initialCol;
 532     }
 533
 534     sfSize = sequenceFeatures.length;
 535
 536     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))
 537     {
 538       return Color.white;
 539     }
 540
 541     currentColour = null;
 542
 543     drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);
 544
 545     if (currentColour == null)
 546     {
 547       return initialCol;
 548     }
 549
 550     return new Color(((Integer) currentColour).intValue());
 551   }
 552
 553   /**
 554    * This is used by the Molecule Viewer to get the accurate colour of the
 555    * rendered sequence
 556    */
 557   boolean overview = false;
 558
 559   /**
 560    * DOCUMENT ME!
 561    *
 562    * @param g
 563    *          DOCUMENT ME!
 564    * @param seq
 565    *          DOCUMENT ME!
 566    * @param sg
 567    *          DOCUMENT ME!
 568    * @param start
 569    *          DOCUMENT ME!
 570    * @param end
 571    *          DOCUMENT ME!
 572    * @param x1
 573    *          DOCUMENT ME!
 574    * @param y1
 575    *          DOCUMENT ME!
 576    * @param width
 577    *          DOCUMENT ME!
 578    * @param height
 579    *          DOCUMENT ME!
 580    */
 581   // String type;
 582   // SequenceFeature sf;
 583   SequenceI lastSeq;
 584
 585   SequenceFeature[] sequenceFeatures;
 586
 587   int sfSize, sfindex, spos, epos;
 588
 589   synchronized public void drawSequence(Graphics g, SequenceI seq,
 590           int start, int end, int y1)
 591   {
 592     if (seq.getSequenceFeatures() == null
 593             || seq.getSequenceFeatures().length == 0)
 594     {
 595       return;
 596     }
 597
 598     if (transparencySetter != null && g != null)
 599     {
 600       transparencySetter.setTransparency(g, transparency);
 601     }
 602
 603     if (lastSeq == null || seq != lastSeq
 604             || sequenceFeatures != seq.getSequenceFeatures())
 605     {
 606       lastSeq = seq;
 607       sequenceFeatures = seq.getSequenceFeatures();
 608       sfSize = sequenceFeatures.length;
 609     }
 610
 611     if (av.featuresDisplayed == null || renderOrder == null)
 612     {
 613       findAllFeatures();
 614       if (av.featuresDisplayed.size() < 1)
 615       {
 616         return;
 617       }
 618
 619       sequenceFeatures = seq.getSequenceFeatures();
 620       sfSize = sequenceFeatures.length;
 621     }
 622     if (!overview)
 623     {
 624       spos = lastSeq.findPosition(start);
 625       epos = lastSeq.findPosition(end);
 626       if (g != null)
 627       {
 628         fm = g.getFontMetrics();
 629       }
 630     }
 631     String type;
 632     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 633     {
 634       type = renderOrder[renderIndex];
 635       if (!av.featuresDisplayed.containsKey(type))
 636       {
 637         continue;
 638       }
 639
 640       // loop through all features in sequence to find
 641       // current feature to render
 642       for (sfindex = 0; sfindex < sfSize; sfindex++)
 643       {
 644         if (!sequenceFeatures[sfindex].type.equals(type))
 645         {
 646           continue;
 647         }
 648
 649         if (featureGroups != null
 650                 && sequenceFeatures[sfindex].featureGroup != null
 651                 && featureGroups
 652                         .containsKey(sequenceFeatures[sfindex].featureGroup)
 653                 && !((Boolean) featureGroups
 654                         .get(sequenceFeatures[sfindex].featureGroup))
 655                         .booleanValue())
 656         {
 657           continue;
 658         }
 659
 660         if (!overview
 661                 && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
 662                         .getEnd() < spos))
 663         {
 664           continue;
 665         }
 666
 667         if (overview)
 668         {
 669           if (sequenceFeatures[sfindex].begin <= start
 670                   && sequenceFeatures[sfindex].end >= start)
 671           {
 672             currentColour = new Integer(
 673                     getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed
 674             // .get(sequenceFeatures[sfindex].type);
 675           }
 676
 677         }
 678         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
 679         {
 680
 681           renderFeature(g, seq,
 682                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 683                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 684                   getColour(sequenceFeatures[sfindex])
 685                   // new Color(((Integer) av.featuresDisplayed
 686                   // .get(sequenceFeatures[sfindex].type)).intValue())
 687                   , start, end, y1);
 688           renderFeature(g, seq,
 689                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 690                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 691                   getColour(sequenceFeatures[sfindex])
 692                   // new Color(((Integer) av.featuresDisplayed
 693                   // .get(sequenceFeatures[sfindex].type)).intValue())
 694                   , start, end, y1);
 695
 696         }
 697         else
 698         {
 699           if (showFeature(sequenceFeatures[sfindex]))
 700           {
 701             renderFeature(g, seq,
 702                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 703                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 704                     getColour(sequenceFeatures[sfindex]), start, end, y1);
 705           }
 706         }
 707
 708       }
 709     }
 710
 711     if (transparencySetter != null && g != null)
 712     {
 713       transparencySetter.setTransparency(g, 1.0f);
 714     }
 715   }
 716
 717   char s;
 718
 719   int i;
 720
 721   void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
 722           Color featureColour, int start, int end, int y1)
 723   {
 724
 725     if (((fstart <= end) && (fend >= start)))
 726     {
 727       if (fstart < start)
 728       { // fix for if the feature we have starts before the sequence start,
 729         fstart = start; // but the feature end is still valid!!
 730       }
 731
 732       if (fend >= end)
 733       {
 734         fend = end;
 735       }
 736
 737       for (i = fstart; i <= fend; i++)
 738       {
 739         s = seq.getCharAt(i);
 740
 741         if (jalview.util.Comparison.isGap(s))
 742         {
 743           continue;
 744         }
 745
 746         g.setColor(featureColour);
 747
 748         g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
 749                 av.charHeight);
 750
 751         if (!av.validCharWidth)
 752         {
 753           continue;
 754         }
 755
 756         g.setColor(Color.white);
 757         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 758         g.drawString(String.valueOf(s), charOffset
 759                 + (av.charWidth * (i - start)), (y1 + av.charHeight)
 760                 - av.charHeight / 5); // pady = height / 5;
 761
 762       }
 763     }
 764   }
 765
 766   Hashtable minmax = null;
 767
 768   /**
 769    * Called when alignment in associated view has new/modified features to
 770    * discover and display.
 771    *
 772    */
 773   public void featuresAdded()
 774   {
 775     lastSeq = null;
 776     findAllFeatures();
 777   }
 778
 779   /**
 780    * find all features on the alignment
 781    */
 782   void findAllFeatures()
 783   {
 784     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
 785
 786     av.featuresDisplayed = new Hashtable();
 787     Vector allfeatures = new Vector();
 788     minmax = new Hashtable();
 789     AlignmentI alignment=av.getAlignment();
 790     for (int i = 0; i < alignment.getHeight(); i++)
 791     {
 792       SequenceFeature[] features = alignment.getSequenceAt(i)
 793               .getSequenceFeatures();
 794
 795       if (features == null)
 796       {
 797         continue;
 798       }
 799
 800       int index = 0;
 801       while (index < features.length)
 802       {
 803         if (features[index].begin == 0 && features[index].end == 0)
 804         {
 805           index++;
 806           continue;
 807         }
 808         if (!av.featuresDisplayed.containsKey(features[index].getType()))
 809         {
 810           if (getColour(features[index].getType()) == null)
 811           {
 812             featureColours.put(features[index].getType(),
 813                     ucs.createColourFromName(features[index].getType()));
 814           }
 815
 816           av.featuresDisplayed.put(features[index].getType(), new Integer(
 817                   getColour(features[index].getType()).getRGB()));
 818           allfeatures.addElement(features[index].getType());
 819         }
 820         if (features[index].score != Float.NaN)
 821         {
 822           int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
 823           float[][] mm = (float[][]) minmax.get(features[index].getType());
 824           if (mm == null)
 825           {
 826             mm = new float[][]
 827             { null, null };
 828             minmax.put(features[index].getType(), mm);
 829           }
 830           if (mm[nonpos] == null)
 831           {
 832             mm[nonpos] = new float[]
 833             { features[index].score, features[index].score };
 834
 835           }
 836           else
 837           {
 838             if (mm[nonpos][0] > features[index].score)
 839             {
 840               mm[nonpos][0] = features[index].score;
 841             }
 842             if (mm[nonpos][1] < features[index].score)
 843             {
 844               mm[nonpos][1] = features[index].score;
 845             }
 846           }
 847         }
 848
 849         index++;
 850       }
 851     }
 852
 853     renderOrder = new String[allfeatures.size()];
 854     Enumeration en = allfeatures.elements();
 855     int i = allfeatures.size() - 1;
 856     while (en.hasMoreElements())
 857     {
 858       renderOrder[i] = en.nextElement().toString();
 859       i--;
 860     }
 861   }
 862
 863   /**
 864    * get a feature style object for the given type string. Creates a
 865    * java.awt.Color for a featureType with no existing colourscheme. TODO:
 866    * replace return type with object implementing standard abstract colour/style
 867    * interface
 868    *
 869    * @param featureType
 870    * @return java.awt.Color or GraduatedColor
 871    */
 872   public Object getFeatureStyle(String featureType)
 873   {
 874     Object fc = featureColours.get(featureType);
 875     if (fc == null)
 876     {
 877       jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
 878       Color col = ucs.createColourFromName(featureType);
 879       featureColours.put(featureType, fc = col);
 880     }
 881     return fc;
 882   }
 883
 884   public Color getColour(String featureType)
 885   {
 886     Object fc = getFeatureStyle(featureType);
 887
 888     if (fc instanceof Color)
 889     {
 890       return (Color) fc;
 891     }
 892     else
 893     {
 894       if (fc instanceof GraduatedColor)
 895       {
 896         return ((GraduatedColor) fc).getMaxColor();
 897       }
 898     }
 899     throw new Error("Implementation Error: Unrecognised render object "
 900             + fc.getClass() + " for features of type " + featureType);
 901   }
 902
 903   /**
 904    *
 905    * @param sequenceFeature
 906    * @return true if feature is visible.
 907    */
 908   private boolean showFeature(SequenceFeature sequenceFeature)
 909   {
 910     Object fc = getFeatureStyle(sequenceFeature.type);
 911     if (fc instanceof GraduatedColor)
 912     {
 913       return ((GraduatedColor) fc).isColored(sequenceFeature);
 914     }
 915     else
 916     {
 917       return true;
 918     }
 919   }
 920
 921   /**
 922    * implement graduated colouring for features with scores
 923    *
 924    * @param feature
 925    * @return render colour for the given feature
 926    */
 927   public Color getColour(SequenceFeature feature)
 928   {
 929     Object fc = getFeatureStyle(feature.getType());
 930     if (fc instanceof Color)
 931     {
 932       return (Color) fc;
 933     }
 934     else
 935     {
 936       if (fc instanceof GraduatedColor)
 937       {
 938         return ((GraduatedColor) fc).findColor(feature);
 939       }
 940     }
 941     throw new Error("Implementation Error: Unrecognised render object "
 942             + fc.getClass() + " for features of type " + feature.getType());
 943   }
 944
 945   public void setColour(String featureType, Object col)
 946   {
 947     // overwrite
 948     // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
 949     // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
 950     // Object c = featureColours.get(featureType);
 951     // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
 952     // !((GraduatedColor)c).getMaxColor().equals(_col)))
 953     {
 954       featureColours.put(featureType, col);
 955     }
 956   }
 957
 958   public void setFeaturePriority(Object[][] data)
 959   {
 960     // The feature table will display high priority
 961     // features at the top, but theses are the ones
 962     // we need to render last, so invert the data
 963     if (av.featuresDisplayed != null)
 964     {
 965       av.featuresDisplayed.clear();
 966     }
 967
 968     /*
 969      * if (visibleNew) { if (av.featuresDisplayed != null) {
 970      * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new
 971      * Hashtable(); } } if (data == null) { return; }
 972      */
 973
 974     renderOrder = new String[data.length];
 975
 976     if (data.length > 0)
 977     {
 978       for (int i = 0; i < data.length; i++)
 979       {
 980         String type = data[i][0].toString();
 981         setColour(type, data[i][1]);
 982         if (((Boolean) data[i][2]).booleanValue())
 983         {
 984           av.featuresDisplayed.put(type, new Integer(getColour(type)
 985                   .getRGB()));
 986         }
 987
 988         renderOrder[data.length - i - 1] = type;
 989       }
 990     }
 991   }
 992
 993   /**
 994    * @return a simple list of feature group names or null
 995    */
 996   public String[] getGroups()
 997   {
 998     buildGroupHash();
 999     if (featureGroups != null)
1000     {
1001       String[] gps = new String[featureGroups.size()];
1002       Enumeration gn = featureGroups.keys();
1003       int i = 0;
1004       while (gn.hasMoreElements())
1005       {
1006         gps[i++] = (String) gn.nextElement();
1007       }
1008       return gps;
1009     }
1010     return null;
1011   }
1012
1013   /**
1014    * get visible or invisible groups
1015    *
1016    * @param visible
1017    *          true to return visible groups, false to return hidden ones.
1018    * @return list of groups
1019    */
1020   public String[] getGroups(boolean visible)
1021   {
1022     buildGroupHash();
1023     if (featureGroups != null)
1024     {
1025       Vector gp = new Vector();
1026
1027       Enumeration gn = featureGroups.keys();
1028       while (gn.hasMoreElements())
1029       {
1030         String nm = (String) gn.nextElement();
1031         Boolean state = (Boolean) featureGroups.get(nm);
1032         if (state.booleanValue() == visible)
1033         {
1034           gp.addElement(nm);
1035         }
1036       }
1037       String[] gps = new String[gp.size()];
1038       gp.copyInto(gps);
1039
1040       int i = 0;
1041       while (gn.hasMoreElements())
1042       {
1043         gps[i++] = (String) gn.nextElement();
1044       }
1045       return gps;
1046     }
1047     return null;
1048   }
1049
1050   /**
1051    * set all feature groups in toset to be visible or invisible
1052    *
1053    * @param toset
1054    *          group names
1055    * @param visible
1056    *          the state of the named groups to set
1057    */
1058   public void setGroupState(String[] toset, boolean visible)
1059   {
1060     buildGroupHash();
1061     if (toset != null && toset.length > 0 && featureGroups != null)
1062     {
1063       boolean rdrw = false;
1064       for (int i = 0; i < toset.length; i++)
1065       {
1066         Object st = featureGroups.get(toset[i]);
1067         featureGroups.put(toset[i], new Boolean(visible));
1068         if (st != null)
1069         {
1070           rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
1071         }
1072       }
1073       if (rdrw)
1074       {
1075         if (this.av != null)
1076           if (this.av.featureSettings != null)
1077           {
1078             av.featureSettings.rebuildGroups();
1079             this.av.featureSettings.resetTable(true);
1080           }
1081           else
1082           {
1083             buildFeatureHash();
1084           }
1085         if (av != null)
1086         {
1087           av.alignmentChanged(null);
1088         }
1089       }
1090     }
1091   }
1092
1093   ArrayList<String> hiddenGroups=new ArrayList<String>();
1094   /**
1095    * analyse alignment for groups and hash tables (used to be embedded in
1096    * FeatureSettings.setTableData)
1097    *
1098    * @return true if features are on the alignment
1099    */
1100   public boolean buildGroupHash()
1101   {
1102     boolean alignmentHasFeatures = false;
1103     if (featureGroups == null)
1104     {
1105       featureGroups = new Hashtable();
1106     }
1107     hiddenGroups =new ArrayList<String>();
1108     hiddenGroups.addAll(featureGroups.keySet());
1109     ArrayList allFeatures = new ArrayList();
1110     ArrayList allGroups = new ArrayList();
1111     SequenceFeature[] tmpfeatures;
1112     String group;
1113     AlignmentI alignment=av.getAlignment();
1114     for (int i = 0; i < alignment.getHeight(); i++)
1115     {
1116       if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
1117       {
1118         continue;
1119       }
1120
1121       alignmentHasFeatures = true;
1122
1123       tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
1124       int index = 0;
1125       while (index < tmpfeatures.length)
1126       {
1127         if (tmpfeatures[index].getFeatureGroup() != null)
1128         {
1129           group = tmpfeatures[index].featureGroup;
1130           // Remove group from the hiddenGroup list
1131           hiddenGroups.remove(group);
1132           if (!allGroups.contains(group))
1133           {
1134             allGroups.add(group);
1135
1136             boolean visible = true;
1137             if (featureGroups.containsKey(group))
1138             {
1139               visible = ((Boolean) featureGroups.get(group)).booleanValue();
1140             }
1141             else
1142             {
1143               featureGroups.put(group, new Boolean(visible));
1144             }
1145           }
1146         }
1147
1148         if (!allFeatures.contains(tmpfeatures[index].getType()))
1149         {
1150           allFeatures.add(tmpfeatures[index].getType());
1151         }
1152         index++;
1153       }
1154     }
1155
1156     return alignmentHasFeatures;
1157   }
1158
1159   /**
1160    * rebuild the featuresDisplayed and renderorder list based on the
1161    * featureGroups hash and any existing display state and force a repaint if
1162    * necessary
1163    *
1164    * @return true if alignment has visible features
1165    */
1166   public boolean buildFeatureHash()
1167   {
1168     boolean alignmentHasFeatures = false;
1169     if (featureGroups == null)
1170     {
1171       alignmentHasFeatures = buildGroupHash();
1172     }
1173     if (!alignmentHasFeatures)
1174       return false;
1175     Hashtable fdisp = av.featuresDisplayed;
1176     Vector allFeatures = new Vector();
1177     SequenceFeature[] tmpfeatures;
1178     String group;
1179     AlignmentI alignment=av.getAlignment();
1180     for (int i = 0; i < alignment.getHeight(); i++)
1181     {
1182       if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
1183       {
1184         continue;
1185       }
1186
1187       alignmentHasFeatures = true;
1188
1189       tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
1190       int index = 0;
1191       while (index < tmpfeatures.length)
1192       {
1193         boolean visible = true;
1194         if (tmpfeatures[index].getFeatureGroup() != null)
1195         {
1196           group = tmpfeatures[index].featureGroup;
1197           if (featureGroups.containsKey(group))
1198           {
1199             visible = ((Boolean) featureGroups.get(group)).booleanValue();
1200           }
1201         }
1202
1203         if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
1204         {
1205           allFeatures.addElement(tmpfeatures[index].getType());
1206         }
1207         index++;
1208       }
1209     }
1210     if (allFeatures.size() > 0)
1211     {
1212       String[] neworder = new String[allFeatures.size()];
1213       int p = neworder.length - 1;
1214       for (int i = renderOrder.length - 1; i >= 0; i--)
1215       {
1216         if (allFeatures.contains(renderOrder[i]))
1217         {
1218           neworder[p--] = renderOrder[i];
1219           allFeatures.removeElement(renderOrder[i]);
1220         }
1221         else
1222         {
1223           av.featuresDisplayed.remove(renderOrder[i]);
1224         }
1225       }
1226       for (int i = allFeatures.size() - 1; i > 0; i++)
1227       {
1228         Object e = allFeatures.elementAt(i);
1229         if (e != null)
1230         {
1231           neworder[p--] = (String) e;
1232           av.featuresDisplayed.put(e, getColour((String) e));
1233         }
1234       }
1235       renderOrder = neworder;
1236       return true;
1237     }
1238
1239     return alignmentHasFeatures;
1240   }
1241
1242   /**
1243    *
1244    * @return the displayed feature type as an array of strings
1245    */
1246   protected String[] getDisplayedFeatureTypes()
1247   {
1248     String[] typ = null;
1249     synchronized (renderOrder)
1250     {
1251       typ = new String[renderOrder.length];
1252       System.arraycopy(renderOrder, 0, typ, 0, typ.length);
1253       for (int i = 0; i < typ.length; i++)
1254       {
1255         if (av.featuresDisplayed.get(typ[i]) == null)
1256         {
1257           typ[i] = null;
1258         }
1259       }
1260     }
1261     return typ;
1262   }
1263 }
1264
1265 class TransparencySetter
1266 {
1267   void setTransparency(Graphics g, float value)
1268   {
1269     Graphics2D g2 = (Graphics2D) g;
1270     g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
1271             value));
1272   }
1273 }