src/jalview/appletgui/AnnotationLabels.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentUtils;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.Annotation;
  26 import jalview.datamodel.SequenceGroup;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.util.MessageManager;
  29 import jalview.util.ParseHtmlBodyAndLinks;
  30
  31 import java.awt.Checkbox;
  32 import java.awt.CheckboxMenuItem;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.FlowLayout;
  36 import java.awt.FontMetrics;
  37 import java.awt.Frame;
  38 import java.awt.Graphics;
  39 import java.awt.Image;
  40 import java.awt.MenuItem;
  41 import java.awt.Panel;
  42 import java.awt.PopupMenu;
  43 import java.awt.event.ActionEvent;
  44 import java.awt.event.ActionListener;
  45 import java.awt.event.InputEvent;
  46 import java.awt.event.ItemEvent;
  47 import java.awt.event.ItemListener;
  48 import java.awt.event.MouseEvent;
  49 import java.awt.event.MouseListener;
  50 import java.awt.event.MouseMotionListener;
  51 import java.util.Arrays;
  52 import java.util.Collections;
  53
  54 public class AnnotationLabels extends Panel implements ActionListener,
  55         MouseListener, MouseMotionListener
  56 {
  57   Image image;
  58
  59   boolean active = false;
  60
  61   AlignmentPanel ap;
  62
  63   AlignViewport av;
  64
  65   boolean resizing = false;
  66
  67   int oldY, mouseX;
  68
  69   static String ADDNEW = "Add New Row";
  70
  71   static String EDITNAME = "Edit Label/Description";
  72
  73   static String HIDE = "Hide This Row";
  74
  75   static String SHOWALL = "Show All Hidden Rows";
  76
  77   static String OUTPUT_TEXT = "Show Values In Textbox";
  78
  79   static String COPYCONS_SEQ = "Copy Consensus Sequence";
  80
  81   int scrollOffset = 0;
  82
  83   int selectedRow = -1;
  84
  85   Tooltip tooltip;
  86
  87   private boolean hasHiddenRows;
  88
  89   public AnnotationLabels(AlignmentPanel ap)
  90   {
  91     this.ap = ap;
  92     this.av = ap.av;
  93     setLayout(null);
  94
  95     /**
  96      * this retrieves the adjustable height glyph from resources. we don't use
  97      * it at the moment. java.net.URL url =
  98      * getClass().getResource("/images/idwidth.gif"); Image temp = null;
  99      *
 100      * if (url != null) { temp =
 101      * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
 102      *
 103      * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
 104      * mt.waitForID(0); } catch (Exception ex) { }
 105      *
 106      * BufferedImage bi = new BufferedImage(temp.getHeight(this),
 107      * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
 108      * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
 109      * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
 110      */
 111     addMouseListener(this);
 112     addMouseMotionListener(this);
 113   }
 114
 115   public AnnotationLabels(AlignViewport av)
 116   {
 117     this.av = av;
 118   }
 119
 120   public void setScrollOffset(int y, boolean repaint)
 121   {
 122     scrollOffset = y;
 123     if (repaint)
 124     {
 125       repaint();
 126     }
 127   }
 128
 129   /**
 130    *
 131    * @param y
 132    * @return -2 if no rows are visible at all, -1 if no visible rows were
 133    *         selected
 134    */
 135   int getSelectedRow(int y)
 136   {
 137     int row = -2;
 138     AlignmentAnnotation[] aa = ap.av.getAlignment()
 139             .getAlignmentAnnotation();
 140
 141     if (aa == null)
 142     {
 143       return row;
 144     }
 145     int height = 0;
 146     for (int i = 0; i < aa.length; i++)
 147     {
 148       row = -1;
 149       if (!aa[i].visible)
 150       {
 151         continue;
 152       }
 153       height += aa[i].height;
 154       if (y < height)
 155       {
 156         row = i;
 157         break;
 158       }
 159     }
 160
 161     return row;
 162   }
 163
 164   @Override
 165   public void actionPerformed(ActionEvent evt)
 166   {
 167     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 168
 169     if (evt.getActionCommand().equals(ADDNEW))
 170     {
 171       AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
 172               new Annotation[ap.av.getAlignment().getWidth()]);
 173
 174       if (!editLabelDescription(newAnnotation))
 175       {
 176         return;
 177       }
 178
 179       ap.av.getAlignment().addAnnotation(newAnnotation);
 180       ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
 181     }
 182     else if (evt.getActionCommand().equals(EDITNAME))
 183     {
 184       editLabelDescription(aa[selectedRow]);
 185     }
 186     else if (evt.getActionCommand().equals(HIDE))
 187     {
 188       aa[selectedRow].visible = false;
 189     }
 190     else if (evt.getActionCommand().equals(SHOWALL))
 191     {
 192       for (int i = 0; i < aa.length; i++)
 193       {
 194         aa[i].visible = (aa[i].annotations == null) ? false : true;
 195       }
 196     }
 197     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
 198     {
 199       CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
 200               ap.alignFrame);
 201       Frame frame = new Frame();
 202       frame.add(cap);
 203       jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
 204               + " - " + aa[selectedRow].label, 500, 100);
 205       cap.setText(aa[selectedRow].toString());
 206     }
 207     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
 208     {
 209       SequenceI cons = av.getConsensusSeq();
 210       if (cons != null)
 211       {
 212         copy_annotseqtoclipboard(cons);
 213       }
 214
 215     }
 216     refresh();
 217   }
 218
 219   /**
 220    * Adjust size and repaint
 221    */
 222   protected void refresh()
 223   {
 224     ap.annotationPanel.adjustPanelHeight();
 225     setSize(getSize().width, ap.annotationPanel.getSize().height);
 226     ap.validate();
 227     ap.paintAlignment(true);
 228   }
 229
 230   boolean editLabelDescription(AlignmentAnnotation annotation)
 231   {
 232     Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
 233             + ap.av.getGapCharacter() + "\"", annotation.padGaps);
 234
 235     EditNameDialog dialog = new EditNameDialog(annotation.label,
 236             annotation.description, "      Annotation Label",
 237             "Annotation Description", ap.alignFrame,
 238             "Edit Annotation Name / Description", 500, 180, false);
 239
 240     Panel empty = new Panel(new FlowLayout());
 241     empty.add(padGaps);
 242     dialog.add(empty);
 243     dialog.pack();
 244
 245     dialog.setVisible(true);
 246
 247     if (dialog.accept)
 248     {
 249       annotation.label = dialog.getName();
 250       annotation.description = dialog.getDescription();
 251       annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
 252       repaint();
 253       return true;
 254     }
 255     else
 256     {
 257       return false;
 258     }
 259
 260   }
 261
 262   boolean resizePanel = false;
 263
 264   @Override
 265   public void mouseMoved(MouseEvent evt)
 266   {
 267     resizePanel = evt.getY() < 10 && evt.getX() < 14;
 268     int row = getSelectedRow(evt.getY() + scrollOffset);
 269
 270     if (row > -1)
 271     {
 272       ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
 273               av.getAlignment().getAlignmentAnnotation()[row]
 274                       .getDescription(true),
 275               true, "\n");
 276       if (tooltip == null)
 277       {
 278         tooltip = new Tooltip(phb.getNonHtmlContent(), this);
 279       }
 280       else
 281       {
 282         tooltip.setTip(phb.getNonHtmlContent());
 283       }
 284     }
 285     else if (tooltip != null)
 286     {
 287       tooltip.setTip("");
 288     }
 289   }
 290
 291   /**
 292    * curent drag position
 293    */
 294   MouseEvent dragEvent = null;
 295
 296   /**
 297    * flag to indicate drag events should be ignored
 298    */
 299   private boolean dragCancelled = false;
 300
 301   /**
 302    * clear any drag events in progress
 303    */
 304   public void cancelDrag()
 305   {
 306     dragEvent = null;
 307     dragCancelled = true;
 308   }
 309
 310   @Override
 311   public void mouseDragged(MouseEvent evt)
 312   {
 313     if (dragCancelled)
 314     {
 315       return;
 316     }
 317     ;
 318     dragEvent = evt;
 319
 320     if (resizePanel)
 321     {
 322       Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
 323               .getSize(), f = ap.seqPanelHolder.getSize();
 324       int dif = evt.getY() - oldY;
 325
 326       dif /= ap.av.getCharHeight();
 327       dif *= ap.av.getCharHeight();
 328
 329       if ((d.height - dif) > 20 && (f.height + dif) > 20)
 330       {
 331         ap.annotationPanel.setSize(d.width, d.height - dif);
 332         setSize(new Dimension(e.width, d.height - dif));
 333         ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
 334                 d.height - dif));
 335         ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
 336                 - dif));
 337         ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
 338                 av.calcPanelHeight());
 339         f.height += dif;
 340         ap.seqPanelHolder.setPreferredSize(f);
 341         ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges()
 342                 .getStartSeq());
 343         ap.validate();
 344         // ap.paintAlignment(true);
 345         ap.addNotify();
 346       }
 347
 348     }
 349     else
 350     {
 351       int diff;
 352       if ((diff = 6 - evt.getY()) > 0)
 353       {
 354         // nudge scroll up
 355         ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
 356         ap.adjustmentValueChanged(null);
 357
 358       }
 359       else if ((0 < (diff = 6
 360               - ap.annotationSpaceFillerHolder.getSize().height
 361               + evt.getY())))
 362       {
 363         // nudge scroll down
 364         ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
 365         ap.adjustmentValueChanged(null);
 366       }
 367       repaint();
 368     }
 369   }
 370
 371   @Override
 372   public void mouseClicked(MouseEvent evt)
 373   {
 374   }
 375
 376   @Override
 377   public void mouseReleased(MouseEvent evt)
 378   {
 379     if (!resizePanel && !dragCancelled)
 380     {
 381       int start = selectedRow;
 382
 383       int end = getSelectedRow(evt.getY() + scrollOffset);
 384
 385       if (start > -1 && start != end)
 386       {
 387         // Swap these annotations
 388         AlignmentAnnotation startAA = ap.av.getAlignment()
 389                 .getAlignmentAnnotation()[start];
 390         if (end == -1)
 391         {
 392           end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
 393         }
 394         AlignmentAnnotation endAA = ap.av.getAlignment()
 395                 .getAlignmentAnnotation()[end];
 396
 397         ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
 398         ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
 399       }
 400     }
 401     resizePanel = false;
 402     dragEvent = null;
 403     dragCancelled = false;
 404     repaint();
 405     ap.annotationPanel.repaint();
 406   }
 407
 408   @Override
 409   public void mouseEntered(MouseEvent evt)
 410   {
 411     if (evt.getY() < 10 && evt.getX() < 14)
 412     {
 413       resizePanel = true;
 414       repaint();
 415     }
 416   }
 417
 418   @Override
 419   public void mouseExited(MouseEvent evt)
 420   {
 421     dragCancelled = false;
 422
 423     if (dragEvent == null)
 424     {
 425       resizePanel = false;
 426     }
 427     else
 428     {
 429       if (!resizePanel)
 430       {
 431         dragEvent = null;
 432       }
 433     }
 434     repaint();
 435   }
 436
 437   @Override
 438   public void mousePressed(MouseEvent evt)
 439   {
 440     oldY = evt.getY();
 441     if (resizePanel)
 442     {
 443       return;
 444     }
 445     dragCancelled = false;
 446     // todo: move below to mouseClicked ?
 447     selectedRow = getSelectedRow(evt.getY() + scrollOffset);
 448
 449     AlignmentAnnotation[] aa = ap.av.getAlignment()
 450             .getAlignmentAnnotation();
 451
 452     // DETECT RIGHT MOUSE BUTTON IN AWT
 453     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
 454     {
 455
 456       PopupMenu popup = new PopupMenu(
 457               MessageManager.getString("label.annotations"));
 458
 459       MenuItem item = new MenuItem(ADDNEW);
 460       item.addActionListener(this);
 461       popup.add(item);
 462       if (selectedRow < 0)
 463       {
 464         // this never happens at moment: - see comment on JAL-563
 465         if (hasHiddenRows)
 466         {
 467           item = new MenuItem(SHOWALL);
 468           item.addActionListener(this);
 469           popup.add(item);
 470         }
 471         this.add(popup);
 472         popup.show(this, evt.getX(), evt.getY());
 473         return;
 474       }
 475       // add the rest if there are actually rows to show
 476       item = new MenuItem(EDITNAME);
 477       item.addActionListener(this);
 478       popup.add(item);
 479       item = new MenuItem(HIDE);
 480       item.addActionListener(this);
 481       popup.add(item);
 482
 483       /*
 484        * Hide all <label>:
 485        */
 486       if (selectedRow < aa.length)
 487       {
 488         if (aa[selectedRow].sequenceRef != null)
 489         {
 490           final String label = aa[selectedRow].label;
 491           MenuItem hideType = new MenuItem(
 492                   MessageManager.getString("label.hide_all") + " " + label);
 493           hideType.addActionListener(new ActionListener()
 494           {
 495             @Override
 496             public void actionPerformed(ActionEvent e)
 497             {
 498               AlignmentUtils.showOrHideSequenceAnnotations(
 499                       ap.av.getAlignment(), Collections.singleton(label),
 500                       null, false, false);
 501               refresh();
 502             }
 503           });
 504           popup.add(hideType);
 505         }
 506       }
 507
 508       if (hasHiddenRows)
 509       {
 510         item = new MenuItem(SHOWALL);
 511         item.addActionListener(this);
 512         popup.add(item);
 513       }
 514       this.add(popup);
 515       item = new MenuItem(OUTPUT_TEXT);
 516       item.addActionListener(this);
 517       popup.add(item);
 518       if (selectedRow < aa.length)
 519       {
 520         if (aa[selectedRow].autoCalculated)
 521         {
 522           if (aa[selectedRow].label.indexOf("Consensus") > -1)
 523           {
 524             popup.addSeparator();
 525             final CheckboxMenuItem cbmi = new CheckboxMenuItem(
 526                     MessageManager.getString("label.ignore_gaps_consensus"),
 527                     (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
 528                             .getIgnoreGapsConsensus() : ap.av
 529                             .isIgnoreGapsConsensus());
 530             final AlignmentAnnotation aaa = aa[selectedRow];
 531             cbmi.addItemListener(new ItemListener()
 532             {
 533               @Override
 534               public void itemStateChanged(ItemEvent e)
 535               {
 536                 if (aaa.groupRef != null)
 537                 {
 538                   // TODO: pass on reference to ap so the view can be updated.
 539                   aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
 540                 }
 541                 else
 542                 {
 543                   ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
 544                 }
 545                 ap.paintAlignment(true);
 546               }
 547             });
 548             popup.add(cbmi);
 549             if (aaa.groupRef != null)
 550             {
 551               final CheckboxMenuItem chist = new CheckboxMenuItem(
 552                       MessageManager
 553                               .getString("label.show_group_histogram"),
 554                       aa[selectedRow].groupRef.isShowConsensusHistogram());
 555               chist.addItemListener(new ItemListener()
 556               {
 557                 @Override
 558                 public void itemStateChanged(ItemEvent e)
 559                 {
 560                   // TODO: pass on reference
 561                   // to ap
 562                   // so the
 563                   // view
 564                   // can be
 565                   // updated.
 566                   aaa.groupRef.setShowConsensusHistogram(chist.getState());
 567                   ap.repaint();
 568                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 569                 }
 570               });
 571               popup.add(chist);
 572               final CheckboxMenuItem cprofl = new CheckboxMenuItem(
 573                       MessageManager.getString("label.show_group_logo"),
 574                       aa[selectedRow].groupRef.isShowSequenceLogo());
 575               cprofl.addItemListener(new ItemListener()
 576               {
 577                 @Override
 578                 public void itemStateChanged(ItemEvent e)
 579                 {
 580                   // TODO: pass on reference
 581                   // to ap
 582                   // so the
 583                   // view
 584                   // can be
 585                   // updated.
 586                   aaa.groupRef.setshowSequenceLogo(cprofl.getState());
 587                   ap.repaint();
 588                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 589                 }
 590               });
 591
 592               popup.add(cprofl);
 593               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 594                       MessageManager
 595                               .getString("label.normalise_group_logo"),
 596                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
 597               cprofn.addItemListener(new ItemListener()
 598               {
 599                 @Override
 600                 public void itemStateChanged(ItemEvent e)
 601                 {
 602                   // TODO: pass on reference
 603                   // to ap
 604                   // so the
 605                   // view
 606                   // can be
 607                   // updated.
 608                   aaa.groupRef.setshowSequenceLogo(true);
 609                   aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
 610                   ap.repaint();
 611                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 612                 }
 613               });
 614               popup.add(cprofn);
 615             }
 616             else
 617             {
 618               final CheckboxMenuItem chist = new CheckboxMenuItem(
 619                       MessageManager.getString("label.show_histogram"),
 620                       av.isShowConsensusHistogram());
 621               chist.addItemListener(new ItemListener()
 622               {
 623                 @Override
 624                 public void itemStateChanged(ItemEvent e)
 625                 {
 626                   // TODO: pass on reference
 627                   // to ap
 628                   // so the
 629                   // view
 630                   // can be
 631                   // updated.
 632                   av.setShowConsensusHistogram(chist.getState());
 633                   ap.alignFrame.showConsensusHistogram.setState(chist
 634                           .getState()); // TODO: implement
 635                                         // ap.updateGUI()/alignFrame.updateGUI
 636                                         // for applet
 637                   ap.repaint();
 638                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 639                 }
 640               });
 641               popup.add(chist);
 642               final CheckboxMenuItem cprof = new CheckboxMenuItem(
 643                       MessageManager.getString("label.show_logo"),
 644                       av.isShowSequenceLogo());
 645               cprof.addItemListener(new ItemListener()
 646               {
 647                 @Override
 648                 public void itemStateChanged(ItemEvent e)
 649                 {
 650                   // TODO: pass on reference
 651                   // to ap
 652                   // so the
 653                   // view
 654                   // can be
 655                   // updated.
 656                   av.setShowSequenceLogo(cprof.getState());
 657                   ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
 658                                                                              // implement
 659                                                                              // ap.updateGUI()/alignFrame.updateGUI
 660                                                                              // for
 661                                                                              // applet
 662                   ap.repaint();
 663                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 664                 }
 665               });
 666               popup.add(cprof);
 667               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 668                       MessageManager.getString("label.normalise_logo"),
 669                       av.isNormaliseSequenceLogo());
 670               cprofn.addItemListener(new ItemListener()
 671               {
 672                 @Override
 673                 public void itemStateChanged(ItemEvent e)
 674                 {
 675                   // TODO: pass on reference
 676                   // to ap
 677                   // so the
 678                   // view
 679                   // can be
 680                   // updated.
 681                   av.setShowSequenceLogo(true);
 682                   ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
 683                                                                               // implement
 684                                                                               // ap.updateGUI()/alignFrame.updateGUI
 685                                                                               // for
 686                                                                               // applet
 687                   av.setNormaliseSequenceLogo(cprofn.getState());
 688                   ap.repaint();
 689                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 690                 }
 691               });
 692               popup.add(cprofn);
 693             }
 694
 695             item = new MenuItem(COPYCONS_SEQ);
 696             item.addActionListener(this);
 697             popup.add(item);
 698           }
 699         }
 700       }
 701       popup.show(this, evt.getX(), evt.getY());
 702     }
 703     else
 704     {
 705       // selection action.
 706       if (selectedRow > -1 && selectedRow < aa.length)
 707       {
 708         if (aa[selectedRow].groupRef != null)
 709         {
 710           if (evt.getClickCount() >= 2)
 711           {
 712             // todo: make the ap scroll to the selection - not necessary, first
 713             // click highlights/scrolls, second selects
 714             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 715             // process modifiers
 716             SequenceGroup sg = ap.av.getSelectionGroup();
 717             if (sg == null
 718                     || sg == aa[selectedRow].groupRef
 719                     || !(jalview.util.Platform.isControlDown(evt) || evt
 720                             .isShiftDown()))
 721             {
 722               if (jalview.util.Platform.isControlDown(evt)
 723                       || evt.isShiftDown())
 724               {
 725                 // clone a new selection group from the associated group
 726                 ap.av.setSelectionGroup(new SequenceGroup(
 727                         aa[selectedRow].groupRef));
 728               }
 729               else
 730               {
 731                 // set selection to the associated group so it can be edited
 732                 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
 733               }
 734             }
 735             else
 736             {
 737               // modify current selection with associated group
 738               int remainToAdd = aa[selectedRow].groupRef.getSize();
 739               for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
 740               {
 741                 if (jalview.util.Platform.isControlDown(evt))
 742                 {
 743                   sg.addOrRemove(sgs, --remainToAdd == 0);
 744                 }
 745                 else
 746                 {
 747                   // notionally, we should also add intermediate sequences from
 748                   // last added sequence ?
 749                   sg.addSequence(sgs, --remainToAdd == 0);
 750                 }
 751               }
 752             }
 753             ap.paintAlignment(false);
 754             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 755             ap.av.sendSelection();
 756           }
 757           else
 758           {
 759             ap.seqPanel.ap.idPanel
 760                     .highlightSearchResults(aa[selectedRow].groupRef
 761                             .getSequences(null));
 762           }
 763           return;
 764         }
 765         else if (aa[selectedRow].sequenceRef != null)
 766         {
 767           if (evt.getClickCount() == 1)
 768           {
 769             ap.seqPanel.ap.idPanel
 770                     .highlightSearchResults(Arrays
 771                             .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
 772           }
 773           else if (evt.getClickCount() >= 2)
 774           {
 775             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 776             SequenceGroup sg = ap.av.getSelectionGroup();
 777             if (sg != null)
 778             {
 779               // we make a copy rather than edit the current selection if no
 780               // modifiers pressed
 781               // see Enhancement JAL-1557
 782               if (!(jalview.util.Platform.isControlDown(evt) || evt
 783                       .isShiftDown()))
 784               {
 785                 sg = new SequenceGroup(sg);
 786                 sg.clear();
 787                 sg.addSequence(aa[selectedRow].sequenceRef, false);
 788               }
 789               else
 790               {
 791                 if (jalview.util.Platform.isControlDown(evt))
 792                 {
 793                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
 794                 }
 795                 else
 796                 {
 797                   // notionally, we should also add intermediate sequences from
 798                   // last added sequence ?
 799                   sg.addSequence(aa[selectedRow].sequenceRef, true);
 800                 }
 801               }
 802             }
 803             else
 804             {
 805               sg = new SequenceGroup();
 806               sg.setStartRes(0);
 807               sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
 808               sg.addSequence(aa[selectedRow].sequenceRef, false);
 809             }
 810             ap.av.setSelectionGroup(sg);
 811             ap.paintAlignment(false);
 812             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 813             ap.av.sendSelection();
 814           }
 815
 816         }
 817       }
 818
 819     }
 820   }
 821
 822   /**
 823    * DOCUMENT ME!
 824    *
 825    * @param e
 826    *          DOCUMENT ME!
 827    */
 828   protected void copy_annotseqtoclipboard(SequenceI sq)
 829   {
 830     if (sq == null || sq.getLength() < 1)
 831     {
 832       return;
 833     }
 834     jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
 835     jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
 836             + sq.getStart() + "\t" + sq.getEnd() + "\t"
 837             + sq.getSequenceAsString() + "\n");
 838     if (av.hasHiddenColumns())
 839     {
 840       av.getAlignment().getHiddenColumns().getHiddenColumnsCopy(
 841               jalview.appletgui.AlignFrame.copiedHiddenColumns);
 842     }
 843   }
 844
 845   @Override
 846   public void update(Graphics g)
 847   {
 848     paint(g);
 849   }
 850
 851   @Override
 852   public void paint(Graphics g)
 853   {
 854     int w = getSize().width;
 855     int h = getSize().height;
 856     if (image == null || w != image.getWidth(this)
 857             || h != image.getHeight(this))
 858     {
 859       image = createImage(w, ap.annotationPanel.getSize().height);
 860     }
 861
 862     drawComponent(image.getGraphics(), w);
 863     g.drawImage(image, 0, 0, this);
 864   }
 865
 866   public void drawComponent(Graphics g, int width)
 867   {
 868     g.setFont(av.getFont());
 869     FontMetrics fm = g.getFontMetrics(av.getFont());
 870     g.setColor(Color.white);
 871     g.fillRect(0, 0, getSize().width, getSize().height);
 872
 873     g.translate(0, -scrollOffset);
 874     g.setColor(Color.black);
 875
 876     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 877     int y = 0, fy = g.getFont().getSize();
 878     int x = 0, offset;
 879
 880     if (aa != null)
 881     {
 882       hasHiddenRows = false;
 883       for (int i = 0; i < aa.length; i++)
 884       {
 885         if (!aa[i].visible)
 886         {
 887           hasHiddenRows = true;
 888           continue;
 889         }
 890
 891         x = width - fm.stringWidth(aa[i].label) - 3;
 892
 893         y += aa[i].height;
 894         offset = -(aa[i].height - fy) / 2;
 895
 896         g.drawString(aa[i].label, x, y + offset);
 897       }
 898     }
 899     g.translate(0, +scrollOffset);
 900     if (resizePanel)
 901     {
 902       g.setColor(Color.red);
 903       g.setPaintMode();
 904       g.drawLine(2, 8, 5, 2);
 905       g.drawLine(5, 2, 8, 8);
 906     }
 907     else if (!dragCancelled && dragEvent != null && aa != null)
 908     {
 909       g.setColor(Color.lightGray);
 910       g.drawString(aa[selectedRow].label, dragEvent.getX(),
 911               dragEvent.getY());
 912     }
 913
 914     if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
 915     {
 916       g.setColor(Color.black);
 917       g.drawString(MessageManager.getString("label.right_click"), 2, 8);
 918       g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
 919               18);
 920     }
 921   }
 922 }