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 import java.util.Vector;
  54
  55 public class AnnotationLabels extends Panel implements ActionListener,
  56         MouseListener, MouseMotionListener
  57 {
  58   Image image;
  59
  60   boolean active = false;
  61
  62   AlignmentPanel ap;
  63
  64   AlignViewport av;
  65
  66   boolean resizing = false;
  67
  68   int oldY, mouseX;
  69
  70   static String ADDNEW = "Add New Row";
  71
  72   static String EDITNAME = "Edit Label/Description";
  73
  74   static String HIDE = "Hide This Row";
  75
  76   static String SHOWALL = "Show All Hidden Rows";
  77
  78   static String OUTPUT_TEXT = "Show Values In Textbox";
  79
  80   static String COPYCONS_SEQ = "Copy Consensus Sequence";
  81
  82   int scrollOffset = 0;
  83
  84   int selectedRow = -1;
  85
  86   Tooltip tooltip;
  87
  88   private boolean hasHiddenRows;
  89
  90   public AnnotationLabels(AlignmentPanel ap)
  91   {
  92     this.ap = ap;
  93     this.av = ap.av;
  94     setLayout(null);
  95
  96     /**
  97      * this retrieves the adjustable height glyph from resources. we don't use
  98      * it at the moment. java.net.URL url =
  99      * getClass().getResource("/images/idwidth.gif"); Image temp = null;
 100      *
 101      * if (url != null) { temp =
 102      * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
 103      *
 104      * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
 105      * mt.waitForID(0); } catch (Exception ex) { }
 106      *
 107      * BufferedImage bi = new BufferedImage(temp.getHeight(this),
 108      * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
 109      * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
 110      * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
 111      */
 112     addMouseListener(this);
 113     addMouseMotionListener(this);
 114   }
 115
 116   public AnnotationLabels(AlignViewport av)
 117   {
 118     this.av = av;
 119   }
 120
 121   public void setScrollOffset(int y, boolean repaint)
 122   {
 123     scrollOffset = y;
 124     if (repaint)
 125     {
 126       repaint();
 127     }
 128   }
 129
 130   /**
 131    *
 132    * @param y
 133    * @return -2 if no rows are visible at all, -1 if no visible rows were
 134    *         selected
 135    */
 136   int getSelectedRow(int y)
 137   {
 138     int row = -2;
 139     AlignmentAnnotation[] aa = ap.av.getAlignment()
 140             .getAlignmentAnnotation();
 141
 142     if (aa == null)
 143     {
 144       return row;
 145     }
 146     int height = 0;
 147     for (int i = 0; i < aa.length; i++)
 148     {
 149       row = -1;
 150       if (!aa[i].visible)
 151       {
 152         continue;
 153       }
 154       height += aa[i].height;
 155       if (y < height)
 156       {
 157         row = i;
 158         break;
 159       }
 160     }
 161
 162     return row;
 163   }
 164
 165   @Override
 166   public void actionPerformed(ActionEvent evt)
 167   {
 168     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 169
 170     if (evt.getActionCommand().equals(ADDNEW))
 171     {
 172       AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
 173               new Annotation[ap.av.getAlignment().getWidth()]);
 174
 175       if (!editLabelDescription(newAnnotation))
 176       {
 177         return;
 178       }
 179
 180       ap.av.getAlignment().addAnnotation(newAnnotation);
 181       ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
 182     }
 183     else if (evt.getActionCommand().equals(EDITNAME))
 184     {
 185       editLabelDescription(aa[selectedRow]);
 186     }
 187     else if (evt.getActionCommand().equals(HIDE))
 188     {
 189       aa[selectedRow].visible = false;
 190     }
 191     else if (evt.getActionCommand().equals(SHOWALL))
 192     {
 193       for (int i = 0; i < aa.length; i++)
 194       {
 195         aa[i].visible = (aa[i].annotations == null) ? false : true;
 196       }
 197     }
 198     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
 199     {
 200       CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
 201               ap.alignFrame);
 202       Frame frame = new Frame();
 203       frame.add(cap);
 204       jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
 205               + " - " + aa[selectedRow].label, 500, 100);
 206       cap.setText(aa[selectedRow].toString());
 207     }
 208     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
 209     {
 210       SequenceI cons = av.getConsensusSeq();
 211       if (cons != null)
 212       {
 213         copy_annotseqtoclipboard(cons);
 214       }
 215
 216     }
 217     refresh();
 218   }
 219
 220   /**
 221    * Adjust size and repaint
 222    */
 223   protected void refresh()
 224   {
 225     ap.annotationPanel.adjustPanelHeight();
 226     setSize(getSize().width, ap.annotationPanel.getSize().height);
 227     ap.validate();
 228     ap.paintAlignment(true);
 229   }
 230
 231   boolean editLabelDescription(AlignmentAnnotation annotation)
 232   {
 233     Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
 234             + ap.av.getGapCharacter() + "\"", annotation.padGaps);
 235
 236     EditNameDialog dialog = new EditNameDialog(annotation.label,
 237             annotation.description, "      Annotation Label",
 238             "Annotation Description", ap.alignFrame,
 239             "Edit Annotation Name / Description", 500, 180, false);
 240
 241     Panel empty = new Panel(new FlowLayout());
 242     empty.add(padGaps);
 243     dialog.add(empty);
 244     dialog.pack();
 245
 246     dialog.setVisible(true);
 247
 248     if (dialog.accept)
 249     {
 250       annotation.label = dialog.getName();
 251       annotation.description = dialog.getDescription();
 252       annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
 253       repaint();
 254       return true;
 255     }
 256     else
 257     {
 258       return false;
 259     }
 260
 261   }
 262
 263   boolean resizePanel = false;
 264
 265   @Override
 266   public void mouseMoved(MouseEvent evt)
 267   {
 268     resizePanel = evt.getY() < 10 && evt.getX() < 14;
 269     int row = getSelectedRow(evt.getY() + scrollOffset);
 270
 271     if (row > -1)
 272     {
 273       ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
 274               av.getAlignment().getAlignmentAnnotation()[row]
 275                       .getDescription(true),
 276               true, "\n");
 277       if (tooltip == null)
 278       {
 279         tooltip = new Tooltip(phb.getNonHtmlContent(), this);
 280       }
 281       else
 282       {
 283         tooltip.setTip(phb.getNonHtmlContent());
 284       }
 285     }
 286     else if (tooltip != null)
 287     {
 288       tooltip.setTip("");
 289     }
 290   }
 291
 292   /**
 293    * curent drag position
 294    */
 295   MouseEvent dragEvent = null;
 296
 297   /**
 298    * flag to indicate drag events should be ignored
 299    */
 300   private boolean dragCancelled = false;
 301
 302   /**
 303    * clear any drag events in progress
 304    */
 305   public void cancelDrag()
 306   {
 307     dragEvent = null;
 308     dragCancelled = true;
 309   }
 310
 311   @Override
 312   public void mouseDragged(MouseEvent evt)
 313   {
 314     if (dragCancelled)
 315     {
 316       return;
 317     }
 318     ;
 319     dragEvent = evt;
 320
 321     if (resizePanel)
 322     {
 323       Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
 324               .getSize(), f = ap.seqPanelHolder.getSize();
 325       int dif = evt.getY() - oldY;
 326
 327       dif /= ap.av.getCharHeight();
 328       dif *= ap.av.getCharHeight();
 329
 330       if ((d.height - dif) > 20 && (f.height + dif) > 20)
 331       {
 332         ap.annotationPanel.setSize(d.width, d.height - dif);
 333         setSize(new Dimension(e.width, d.height - dif));
 334         ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
 335                 d.height - dif));
 336         ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
 337                 - dif));
 338         ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
 339                 av.calcPanelHeight());
 340         f.height += dif;
 341         ap.seqPanelHolder.setPreferredSize(f);
 342         ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges()
 343                 .getStartSeq());
 344         ap.validate();
 345         // ap.paintAlignment(true);
 346         ap.addNotify();
 347       }
 348
 349     }
 350     else
 351     {
 352       int diff;
 353       if ((diff = 6 - evt.getY()) > 0)
 354       {
 355         // nudge scroll up
 356         ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
 357         ap.adjustmentValueChanged(null);
 358
 359       }
 360       else if ((0 < (diff = 6
 361               - ap.annotationSpaceFillerHolder.getSize().height
 362               + evt.getY())))
 363       {
 364         // nudge scroll down
 365         ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
 366         ap.adjustmentValueChanged(null);
 367       }
 368       repaint();
 369     }
 370   }
 371
 372   @Override
 373   public void mouseClicked(MouseEvent evt)
 374   {
 375   }
 376
 377   @Override
 378   public void mouseReleased(MouseEvent evt)
 379   {
 380     if (!resizePanel && !dragCancelled)
 381     {
 382       int start = selectedRow;
 383
 384       int end = getSelectedRow(evt.getY() + scrollOffset);
 385
 386       if (start > -1 && start != end)
 387       {
 388         // Swap these annotations
 389         AlignmentAnnotation startAA = ap.av.getAlignment()
 390                 .getAlignmentAnnotation()[start];
 391         if (end == -1)
 392         {
 393           end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
 394         }
 395         AlignmentAnnotation endAA = ap.av.getAlignment()
 396                 .getAlignmentAnnotation()[end];
 397
 398         ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
 399         ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
 400       }
 401     }
 402     resizePanel = false;
 403     dragEvent = null;
 404     dragCancelled = false;
 405     repaint();
 406     ap.annotationPanel.repaint();
 407   }
 408
 409   @Override
 410   public void mouseEntered(MouseEvent evt)
 411   {
 412     if (evt.getY() < 10 && evt.getX() < 14)
 413     {
 414       resizePanel = true;
 415       repaint();
 416     }
 417   }
 418
 419   @Override
 420   public void mouseExited(MouseEvent evt)
 421   {
 422     dragCancelled = false;
 423
 424     if (dragEvent == null)
 425     {
 426       resizePanel = false;
 427     }
 428     else
 429     {
 430       if (!resizePanel)
 431       {
 432         dragEvent = null;
 433       }
 434     }
 435     repaint();
 436   }
 437
 438   @Override
 439   public void mousePressed(MouseEvent evt)
 440   {
 441     oldY = evt.getY();
 442     if (resizePanel)
 443     {
 444       return;
 445     }
 446     dragCancelled = false;
 447     // todo: move below to mouseClicked ?
 448     selectedRow = getSelectedRow(evt.getY() + scrollOffset);
 449
 450     AlignmentAnnotation[] aa = ap.av.getAlignment()
 451             .getAlignmentAnnotation();
 452
 453     // DETECT RIGHT MOUSE BUTTON IN AWT
 454     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
 455     {
 456
 457       PopupMenu popup = new PopupMenu(
 458               MessageManager.getString("label.annotations"));
 459
 460       MenuItem item = new MenuItem(ADDNEW);
 461       item.addActionListener(this);
 462       popup.add(item);
 463       if (selectedRow < 0)
 464       {
 465         // this never happens at moment: - see comment on JAL-563
 466         if (hasHiddenRows)
 467         {
 468           item = new MenuItem(SHOWALL);
 469           item.addActionListener(this);
 470           popup.add(item);
 471         }
 472         this.add(popup);
 473         popup.show(this, evt.getX(), evt.getY());
 474         return;
 475       }
 476       // add the rest if there are actually rows to show
 477       item = new MenuItem(EDITNAME);
 478       item.addActionListener(this);
 479       popup.add(item);
 480       item = new MenuItem(HIDE);
 481       item.addActionListener(this);
 482       popup.add(item);
 483
 484       /*
 485        * Hide all <label>:
 486        */
 487       if (selectedRow < aa.length)
 488       {
 489         if (aa[selectedRow].sequenceRef != null)
 490         {
 491           final String label = aa[selectedRow].label;
 492           MenuItem hideType = new MenuItem(
 493                   MessageManager.getString("label.hide_all") + " " + label);
 494           hideType.addActionListener(new ActionListener()
 495           {
 496             @Override
 497             public void actionPerformed(ActionEvent e)
 498             {
 499               AlignmentUtils.showOrHideSequenceAnnotations(
 500                       ap.av.getAlignment(), Collections.singleton(label),
 501                       null, false, false);
 502               refresh();
 503             }
 504           });
 505           popup.add(hideType);
 506         }
 507       }
 508
 509       if (hasHiddenRows)
 510       {
 511         item = new MenuItem(SHOWALL);
 512         item.addActionListener(this);
 513         popup.add(item);
 514       }
 515       this.add(popup);
 516       item = new MenuItem(OUTPUT_TEXT);
 517       item.addActionListener(this);
 518       popup.add(item);
 519       if (selectedRow < aa.length)
 520       {
 521         if (aa[selectedRow].autoCalculated)
 522         {
 523           if (aa[selectedRow].label.indexOf("Consensus") > -1)
 524           {
 525             popup.addSeparator();
 526             final CheckboxMenuItem cbmi = new CheckboxMenuItem(
 527                     MessageManager.getString("label.ignore_gaps_consensus"),
 528                     (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
 529                             .getIgnoreGapsConsensus() : ap.av
 530                             .isIgnoreGapsConsensus());
 531             final AlignmentAnnotation aaa = aa[selectedRow];
 532             cbmi.addItemListener(new ItemListener()
 533             {
 534               @Override
 535               public void itemStateChanged(ItemEvent e)
 536               {
 537                 if (aaa.groupRef != null)
 538                 {
 539                   // TODO: pass on reference to ap so the view can be updated.
 540                   aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
 541                 }
 542                 else
 543                 {
 544                   ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
 545                 }
 546                 ap.paintAlignment(true);
 547               }
 548             });
 549             popup.add(cbmi);
 550             if (aaa.groupRef != null)
 551             {
 552               final CheckboxMenuItem chist = new CheckboxMenuItem(
 553                       MessageManager
 554                               .getString("label.show_group_histogram"),
 555                       aa[selectedRow].groupRef.isShowConsensusHistogram());
 556               chist.addItemListener(new ItemListener()
 557               {
 558                 @Override
 559                 public void itemStateChanged(ItemEvent e)
 560                 {
 561                   // TODO: pass on reference
 562                   // to ap
 563                   // so the
 564                   // view
 565                   // can be
 566                   // updated.
 567                   aaa.groupRef.setShowConsensusHistogram(chist.getState());
 568                   ap.repaint();
 569                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 570                 }
 571               });
 572               popup.add(chist);
 573               final CheckboxMenuItem cprofl = new CheckboxMenuItem(
 574                       MessageManager.getString("label.show_group_logo"),
 575                       aa[selectedRow].groupRef.isShowSequenceLogo());
 576               cprofl.addItemListener(new ItemListener()
 577               {
 578                 @Override
 579                 public void itemStateChanged(ItemEvent e)
 580                 {
 581                   // TODO: pass on reference
 582                   // to ap
 583                   // so the
 584                   // view
 585                   // can be
 586                   // updated.
 587                   aaa.groupRef.setshowSequenceLogo(cprofl.getState());
 588                   ap.repaint();
 589                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 590                 }
 591               });
 592
 593               popup.add(cprofl);
 594               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 595                       MessageManager
 596                               .getString("label.normalise_group_logo"),
 597                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
 598               cprofn.addItemListener(new ItemListener()
 599               {
 600                 @Override
 601                 public void itemStateChanged(ItemEvent e)
 602                 {
 603                   // TODO: pass on reference
 604                   // to ap
 605                   // so the
 606                   // view
 607                   // can be
 608                   // updated.
 609                   aaa.groupRef.setshowSequenceLogo(true);
 610                   aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
 611                   ap.repaint();
 612                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 613                 }
 614               });
 615               popup.add(cprofn);
 616             }
 617             else
 618             {
 619               final CheckboxMenuItem chist = new CheckboxMenuItem(
 620                       MessageManager.getString("label.show_histogram"),
 621                       av.isShowConsensusHistogram());
 622               chist.addItemListener(new ItemListener()
 623               {
 624                 @Override
 625                 public void itemStateChanged(ItemEvent e)
 626                 {
 627                   // TODO: pass on reference
 628                   // to ap
 629                   // so the
 630                   // view
 631                   // can be
 632                   // updated.
 633                   av.setShowConsensusHistogram(chist.getState());
 634                   ap.alignFrame.showConsensusHistogram.setState(chist
 635                           .getState()); // TODO: implement
 636                                         // ap.updateGUI()/alignFrame.updateGUI
 637                                         // for applet
 638                   ap.repaint();
 639                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 640                 }
 641               });
 642               popup.add(chist);
 643               final CheckboxMenuItem cprof = new CheckboxMenuItem(
 644                       MessageManager.getString("label.show_logo"),
 645                       av.isShowSequenceLogo());
 646               cprof.addItemListener(new ItemListener()
 647               {
 648                 @Override
 649                 public void itemStateChanged(ItemEvent e)
 650                 {
 651                   // TODO: pass on reference
 652                   // to ap
 653                   // so the
 654                   // view
 655                   // can be
 656                   // updated.
 657                   av.setShowSequenceLogo(cprof.getState());
 658                   ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
 659                                                                              // implement
 660                                                                              // ap.updateGUI()/alignFrame.updateGUI
 661                                                                              // for
 662                                                                              // applet
 663                   ap.repaint();
 664                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 665                 }
 666               });
 667               popup.add(cprof);
 668               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 669                       MessageManager.getString("label.normalise_logo"),
 670                       av.isNormaliseSequenceLogo());
 671               cprofn.addItemListener(new ItemListener()
 672               {
 673                 @Override
 674                 public void itemStateChanged(ItemEvent e)
 675                 {
 676                   // TODO: pass on reference
 677                   // to ap
 678                   // so the
 679                   // view
 680                   // can be
 681                   // updated.
 682                   av.setShowSequenceLogo(true);
 683                   ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
 684                                                                               // implement
 685                                                                               // ap.updateGUI()/alignFrame.updateGUI
 686                                                                               // for
 687                                                                               // applet
 688                   av.setNormaliseSequenceLogo(cprofn.getState());
 689                   ap.repaint();
 690                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 691                 }
 692               });
 693               popup.add(cprofn);
 694             }
 695
 696             item = new MenuItem(COPYCONS_SEQ);
 697             item.addActionListener(this);
 698             popup.add(item);
 699           }
 700         }
 701       }
 702       popup.show(this, evt.getX(), evt.getY());
 703     }
 704     else
 705     {
 706       // selection action.
 707       if (selectedRow > -1 && selectedRow < aa.length)
 708       {
 709         if (aa[selectedRow].groupRef != null)
 710         {
 711           if (evt.getClickCount() >= 2)
 712           {
 713             // todo: make the ap scroll to the selection - not necessary, first
 714             // click highlights/scrolls, second selects
 715             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 716             // process modifiers
 717             SequenceGroup sg = ap.av.getSelectionGroup();
 718             if (sg == null
 719                     || sg == aa[selectedRow].groupRef
 720                     || !(jalview.util.Platform.isControlDown(evt) || evt
 721                             .isShiftDown()))
 722             {
 723               if (jalview.util.Platform.isControlDown(evt)
 724                       || evt.isShiftDown())
 725               {
 726                 // clone a new selection group from the associated group
 727                 ap.av.setSelectionGroup(new SequenceGroup(
 728                         aa[selectedRow].groupRef));
 729               }
 730               else
 731               {
 732                 // set selection to the associated group so it can be edited
 733                 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
 734               }
 735             }
 736             else
 737             {
 738               // modify current selection with associated group
 739               int remainToAdd = aa[selectedRow].groupRef.getSize();
 740               for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
 741               {
 742                 if (jalview.util.Platform.isControlDown(evt))
 743                 {
 744                   sg.addOrRemove(sgs, --remainToAdd == 0);
 745                 }
 746                 else
 747                 {
 748                   // notionally, we should also add intermediate sequences from
 749                   // last added sequence ?
 750                   sg.addSequence(sgs, --remainToAdd == 0);
 751                 }
 752               }
 753             }
 754             ap.paintAlignment(false);
 755             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 756             ap.av.sendSelection();
 757           }
 758           else
 759           {
 760             ap.seqPanel.ap.idPanel
 761                     .highlightSearchResults(aa[selectedRow].groupRef
 762                             .getSequences(null));
 763           }
 764           return;
 765         }
 766         else if (aa[selectedRow].sequenceRef != null)
 767         {
 768           if (evt.getClickCount() == 1)
 769           {
 770             ap.seqPanel.ap.idPanel
 771                     .highlightSearchResults(Arrays
 772                             .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
 773           }
 774           else if (evt.getClickCount() >= 2)
 775           {
 776             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 777             SequenceGroup sg = ap.av.getSelectionGroup();
 778             if (sg != null)
 779             {
 780               // we make a copy rather than edit the current selection if no
 781               // modifiers pressed
 782               // see Enhancement JAL-1557
 783               if (!(jalview.util.Platform.isControlDown(evt) || evt
 784                       .isShiftDown()))
 785               {
 786                 sg = new SequenceGroup(sg);
 787                 sg.clear();
 788                 sg.addSequence(aa[selectedRow].sequenceRef, false);
 789               }
 790               else
 791               {
 792                 if (jalview.util.Platform.isControlDown(evt))
 793                 {
 794                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
 795                 }
 796                 else
 797                 {
 798                   // notionally, we should also add intermediate sequences from
 799                   // last added sequence ?
 800                   sg.addSequence(aa[selectedRow].sequenceRef, true);
 801                 }
 802               }
 803             }
 804             else
 805             {
 806               sg = new SequenceGroup();
 807               sg.setStartRes(0);
 808               sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
 809               sg.addSequence(aa[selectedRow].sequenceRef, false);
 810             }
 811             ap.av.setSelectionGroup(sg);
 812             ap.paintAlignment(false);
 813             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 814             ap.av.sendSelection();
 815           }
 816
 817         }
 818       }
 819
 820     }
 821   }
 822
 823   /**
 824    * DOCUMENT ME!
 825    *
 826    * @param e
 827    *          DOCUMENT ME!
 828    */
 829   protected void copy_annotseqtoclipboard(SequenceI sq)
 830   {
 831     if (sq == null || sq.getLength() < 1)
 832     {
 833       return;
 834     }
 835     jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
 836     jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
 837             + sq.getStart() + "\t" + sq.getEnd() + "\t"
 838             + sq.getSequenceAsString() + "\n");
 839     if (av.hasHiddenColumns())
 840     {
 841       jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
 842       for (int[] region : av.getColumnSelection().getHiddenColumns())
 843       {
 844         jalview.appletgui.AlignFrame.copiedHiddenColumns
 845                 .addElement(new int[] { region[0], region[1] });
 846       }
 847     }
 848   }
 849
 850   @Override
 851   public void update(Graphics g)
 852   {
 853     paint(g);
 854   }
 855
 856   @Override
 857   public void paint(Graphics g)
 858   {
 859     int w = getSize().width;
 860     int h = getSize().height;
 861     if (image == null || w != image.getWidth(this)
 862             || h != image.getHeight(this))
 863     {
 864       image = createImage(w, ap.annotationPanel.getSize().height);
 865     }
 866
 867     drawComponent(image.getGraphics(), w);
 868     g.drawImage(image, 0, 0, this);
 869   }
 870
 871   public void drawComponent(Graphics g, int width)
 872   {
 873     g.setFont(av.getFont());
 874     FontMetrics fm = g.getFontMetrics(av.getFont());
 875     g.setColor(Color.white);
 876     g.fillRect(0, 0, getSize().width, getSize().height);
 877
 878     g.translate(0, -scrollOffset);
 879     g.setColor(Color.black);
 880
 881     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 882     int y = 0, fy = g.getFont().getSize();
 883     int x = 0, offset;
 884
 885     if (aa != null)
 886     {
 887       hasHiddenRows = false;
 888       for (int i = 0; i < aa.length; i++)
 889       {
 890         if (!aa[i].visible)
 891         {
 892           hasHiddenRows = true;
 893           continue;
 894         }
 895
 896         x = width - fm.stringWidth(aa[i].label) - 3;
 897
 898         y += aa[i].height;
 899         offset = -(aa[i].height - fy) / 2;
 900
 901         g.drawString(aa[i].label, x, y + offset);
 902       }
 903     }
 904     g.translate(0, +scrollOffset);
 905     if (resizePanel)
 906     {
 907       g.setColor(Color.red);
 908       g.setPaintMode();
 909       g.drawLine(2, 8, 5, 2);
 910       g.drawLine(5, 2, 8, 8);
 911     }
 912     else if (!dragCancelled && dragEvent != null && aa != null)
 913     {
 914       g.setColor(Color.lightGray);
 915       g.drawString(aa[selectedRow].label, dragEvent.getX(),
 916               dragEvent.getY());
 917     }
 918
 919     if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
 920     {
 921       g.setColor(Color.black);
 922       g.drawString(MessageManager.getString("label.right_click"), 2, 8);
 923       g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
 924               18);
 925     }
 926   }
 927 }