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
  56         implements ActionListener, 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,
 205               ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
 206               100);
 207       cap.setText(aa[selectedRow].toString());
 208     }
 209     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
 210     {
 211       SequenceI cons = av.getConsensusSeq();
 212       if (cons != null)
 213       {
 214         copy_annotseqtoclipboard(cons);
 215       }
 216
 217     }
 218     refresh();
 219   }
 220
 221   /**
 222    * Adjust size and repaint
 223    */
 224   protected void refresh()
 225   {
 226     ap.annotationPanel.adjustPanelHeight();
 227     setSize(getSize().width, ap.annotationPanel.getSize().height);
 228     ap.validate();
 229     ap.paintAlignment(true);
 230   }
 231
 232   boolean editLabelDescription(AlignmentAnnotation annotation)
 233   {
 234     Checkbox padGaps = new Checkbox(
 235             "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
 236             annotation.padGaps);
 237
 238     EditNameDialog dialog = new EditNameDialog(annotation.label,
 239             annotation.description, "      Annotation Label",
 240             "Annotation Description", ap.alignFrame,
 241             "Edit Annotation Name / Description", 500, 180, false);
 242
 243     Panel empty = new Panel(new FlowLayout());
 244     empty.add(padGaps);
 245     dialog.add(empty);
 246     dialog.pack();
 247
 248     dialog.setVisible(true);
 249
 250     if (dialog.accept)
 251     {
 252       annotation.label = dialog.getName();
 253       annotation.description = dialog.getDescription();
 254       annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
 255       repaint();
 256       return true;
 257     }
 258     else
 259     {
 260       return false;
 261     }
 262
 263   }
 264
 265   boolean resizePanel = false;
 266
 267   @Override
 268   public void mouseMoved(MouseEvent evt)
 269   {
 270     resizePanel = evt.getY() < 10 && evt.getX() < 14;
 271     int row = getSelectedRow(evt.getY() + scrollOffset);
 272
 273     if (row > -1)
 274     {
 275       ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
 276               av.getAlignment().getAlignmentAnnotation()[row]
 277                       .getDescription(true),
 278               true, "\n");
 279       if (tooltip == null)
 280       {
 281         tooltip = new Tooltip(phb.getNonHtmlContent(), this);
 282       }
 283       else
 284       {
 285         tooltip.setTip(phb.getNonHtmlContent());
 286       }
 287     }
 288     else if (tooltip != null)
 289     {
 290       tooltip.setTip("");
 291     }
 292   }
 293
 294   /**
 295    * curent drag position
 296    */
 297   MouseEvent dragEvent = null;
 298
 299   /**
 300    * flag to indicate drag events should be ignored
 301    */
 302   private boolean dragCancelled = false;
 303
 304   /**
 305    * clear any drag events in progress
 306    */
 307   public void cancelDrag()
 308   {
 309     dragEvent = null;
 310     dragCancelled = true;
 311   }
 312
 313   @Override
 314   public void mouseDragged(MouseEvent evt)
 315   {
 316     if (dragCancelled)
 317     {
 318       return;
 319     }
 320     ;
 321     dragEvent = evt;
 322
 323     if (resizePanel)
 324     {
 325       Dimension d = ap.annotationPanelHolder.getSize(),
 326               e = ap.annotationSpaceFillerHolder.getSize(),
 327               f = ap.seqPanelHolder.getSize();
 328       int dif = evt.getY() - oldY;
 329
 330       dif /= ap.av.getCharHeight();
 331       dif *= ap.av.getCharHeight();
 332
 333       if ((d.height - dif) > 20 && (f.height + dif) > 20)
 334       {
 335         ap.annotationPanel.setSize(d.width, d.height - dif);
 336         setSize(new Dimension(e.width, d.height - dif));
 337         ap.annotationSpaceFillerHolder
 338                 .setSize(new Dimension(e.width, d.height - dif));
 339         ap.annotationPanelHolder
 340                 .setSize(new Dimension(d.width, d.height - dif));
 341         ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
 342                 av.calcPanelHeight());
 343         f.height += dif;
 344         ap.seqPanelHolder.setPreferredSize(f);
 345         ap.setScrollValues(av.getRanges().getStartRes(),
 346                 av.getRanges().getStartSeq());
 347         ap.validate();
 348         // ap.paintAlignment(true);
 349         ap.addNotify();
 350       }
 351
 352     }
 353     else
 354     {
 355       int diff;
 356       if ((diff = 6 - evt.getY()) > 0)
 357       {
 358         // nudge scroll up
 359         ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
 360         ap.adjustmentValueChanged(null);
 361
 362       }
 363       else if ((0 < (diff = 6
 364               - ap.annotationSpaceFillerHolder.getSize().height
 365               + evt.getY())))
 366       {
 367         // nudge scroll down
 368         ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
 369         ap.adjustmentValueChanged(null);
 370       }
 371       repaint();
 372     }
 373   }
 374
 375   @Override
 376   public void mouseClicked(MouseEvent evt)
 377   {
 378   }
 379
 380   @Override
 381   public void mouseReleased(MouseEvent evt)
 382   {
 383     if (!resizePanel && !dragCancelled)
 384     {
 385       int start = selectedRow;
 386
 387       int end = getSelectedRow(evt.getY() + scrollOffset);
 388
 389       if (start > -1 && start != end)
 390       {
 391         // Swap these annotations
 392         AlignmentAnnotation startAA = ap.av.getAlignment()
 393                 .getAlignmentAnnotation()[start];
 394         if (end == -1)
 395         {
 396           end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
 397         }
 398         AlignmentAnnotation endAA = ap.av.getAlignment()
 399                 .getAlignmentAnnotation()[end];
 400
 401         ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
 402         ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
 403       }
 404     }
 405     resizePanel = false;
 406     dragEvent = null;
 407     dragCancelled = false;
 408     repaint();
 409     ap.annotationPanel.repaint();
 410   }
 411
 412   @Override
 413   public void mouseEntered(MouseEvent evt)
 414   {
 415     if (evt.getY() < 10 && evt.getX() < 14)
 416     {
 417       resizePanel = true;
 418       repaint();
 419     }
 420   }
 421
 422   @Override
 423   public void mouseExited(MouseEvent evt)
 424   {
 425     dragCancelled = false;
 426
 427     if (dragEvent == null)
 428     {
 429       resizePanel = false;
 430     }
 431     else
 432     {
 433       if (!resizePanel)
 434       {
 435         dragEvent = null;
 436       }
 437     }
 438     repaint();
 439   }
 440
 441   @Override
 442   public void mousePressed(MouseEvent evt)
 443   {
 444     oldY = evt.getY();
 445     if (resizePanel)
 446     {
 447       return;
 448     }
 449     dragCancelled = false;
 450     // todo: move below to mouseClicked ?
 451     selectedRow = getSelectedRow(evt.getY() + scrollOffset);
 452
 453     AlignmentAnnotation[] aa = ap.av.getAlignment()
 454             .getAlignmentAnnotation();
 455
 456     // DETECT RIGHT MOUSE BUTTON IN AWT
 457     if ((evt.getModifiers()
 458             & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
 459     {
 460
 461       PopupMenu popup = new PopupMenu(
 462               MessageManager.getString("label.annotations"));
 463
 464       MenuItem item = new MenuItem(ADDNEW);
 465       item.addActionListener(this);
 466       popup.add(item);
 467       if (selectedRow < 0)
 468       {
 469         // this never happens at moment: - see comment on JAL-563
 470         if (hasHiddenRows)
 471         {
 472           item = new MenuItem(SHOWALL);
 473           item.addActionListener(this);
 474           popup.add(item);
 475         }
 476         this.add(popup);
 477         popup.show(this, evt.getX(), evt.getY());
 478         return;
 479       }
 480       // add the rest if there are actually rows to show
 481       item = new MenuItem(EDITNAME);
 482       item.addActionListener(this);
 483       popup.add(item);
 484       item = new MenuItem(HIDE);
 485       item.addActionListener(this);
 486       popup.add(item);
 487
 488       /*
 489        * Hide all <label>:
 490        */
 491       if (selectedRow < aa.length)
 492       {
 493         if (aa[selectedRow].sequenceRef != null)
 494         {
 495           final String label = aa[selectedRow].label;
 496           MenuItem hideType = new MenuItem(
 497                   MessageManager.getString("label.hide_all") + " " + label);
 498           hideType.addActionListener(new ActionListener()
 499           {
 500             @Override
 501             public void actionPerformed(ActionEvent e)
 502             {
 503               AlignmentUtils.showOrHideSequenceAnnotations(
 504                       ap.av.getAlignment(), Collections.singleton(label),
 505                       null, false, false);
 506               refresh();
 507             }
 508           });
 509           popup.add(hideType);
 510         }
 511       }
 512
 513       if (hasHiddenRows)
 514       {
 515         item = new MenuItem(SHOWALL);
 516         item.addActionListener(this);
 517         popup.add(item);
 518       }
 519       this.add(popup);
 520       item = new MenuItem(OUTPUT_TEXT);
 521       item.addActionListener(this);
 522       popup.add(item);
 523       if (selectedRow < aa.length)
 524       {
 525         if (aa[selectedRow].autoCalculated)
 526         {
 527           if (aa[selectedRow].label.indexOf("Consensus") > -1)
 528           {
 529             popup.addSeparator();
 530             final CheckboxMenuItem cbmi = new CheckboxMenuItem(
 531                     MessageManager.getString("label.ignore_gaps_consensus"),
 532                     (aa[selectedRow].groupRef != null)
 533                             ? aa[selectedRow].groupRef
 534                                     .getIgnoreGapsConsensus()
 535                             : ap.av.isIgnoreGapsConsensus());
 536             final AlignmentAnnotation aaa = aa[selectedRow];
 537             cbmi.addItemListener(new ItemListener()
 538             {
 539               @Override
 540               public void itemStateChanged(ItemEvent e)
 541               {
 542                 if (aaa.groupRef != null)
 543                 {
 544                   // TODO: pass on reference to ap so the view can be updated.
 545                   aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
 546                 }
 547                 else
 548                 {
 549                   ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
 550                 }
 551                 ap.paintAlignment(true);
 552               }
 553             });
 554             popup.add(cbmi);
 555             if (aaa.groupRef != null)
 556             {
 557               final CheckboxMenuItem chist = new CheckboxMenuItem(
 558                       MessageManager
 559                               .getString("label.show_group_histogram"),
 560                       aa[selectedRow].groupRef.isShowConsensusHistogram());
 561               chist.addItemListener(new ItemListener()
 562               {
 563                 @Override
 564                 public void itemStateChanged(ItemEvent e)
 565                 {
 566                   // TODO: pass on reference
 567                   // to ap
 568                   // so the
 569                   // view
 570                   // can be
 571                   // updated.
 572                   aaa.groupRef.setShowConsensusHistogram(chist.getState());
 573                   ap.repaint();
 574                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 575                 }
 576               });
 577               popup.add(chist);
 578               final CheckboxMenuItem cprofl = new CheckboxMenuItem(
 579                       MessageManager.getString("label.show_group_logo"),
 580                       aa[selectedRow].groupRef.isShowSequenceLogo());
 581               cprofl.addItemListener(new ItemListener()
 582               {
 583                 @Override
 584                 public void itemStateChanged(ItemEvent e)
 585                 {
 586                   // TODO: pass on reference
 587                   // to ap
 588                   // so the
 589                   // view
 590                   // can be
 591                   // updated.
 592                   aaa.groupRef.setshowSequenceLogo(cprofl.getState());
 593                   ap.repaint();
 594                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 595                 }
 596               });
 597
 598               popup.add(cprofl);
 599               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 600                       MessageManager
 601                               .getString("label.normalise_group_logo"),
 602                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
 603               cprofn.addItemListener(new ItemListener()
 604               {
 605                 @Override
 606                 public void itemStateChanged(ItemEvent e)
 607                 {
 608                   // TODO: pass on reference
 609                   // to ap
 610                   // so the
 611                   // view
 612                   // can be
 613                   // updated.
 614                   aaa.groupRef.setshowSequenceLogo(true);
 615                   aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
 616                   ap.repaint();
 617                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 618                 }
 619               });
 620               popup.add(cprofn);
 621             }
 622             else
 623             {
 624               final CheckboxMenuItem chist = new CheckboxMenuItem(
 625                       MessageManager.getString("label.show_histogram"),
 626                       av.isShowConsensusHistogram());
 627               chist.addItemListener(new ItemListener()
 628               {
 629                 @Override
 630                 public void itemStateChanged(ItemEvent e)
 631                 {
 632                   // TODO: pass on reference
 633                   // to ap
 634                   // so the
 635                   // view
 636                   // can be
 637                   // updated.
 638                   av.setShowConsensusHistogram(chist.getState());
 639                   ap.alignFrame.showConsensusHistogram
 640                           .setState(chist.getState()); // TODO: implement
 641                                                        // ap.updateGUI()/alignFrame.updateGUI
 642                                                        // for applet
 643                   ap.repaint();
 644                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 645                 }
 646               });
 647               popup.add(chist);
 648               final CheckboxMenuItem cprof = new CheckboxMenuItem(
 649                       MessageManager.getString("label.show_logo"),
 650                       av.isShowSequenceLogo());
 651               cprof.addItemListener(new ItemListener()
 652               {
 653                 @Override
 654                 public void itemStateChanged(ItemEvent e)
 655                 {
 656                   // TODO: pass on reference
 657                   // to ap
 658                   // so the
 659                   // view
 660                   // can be
 661                   // updated.
 662                   av.setShowSequenceLogo(cprof.getState());
 663                   ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
 664                                                                              // implement
 665                                                                              // ap.updateGUI()/alignFrame.updateGUI
 666                                                                              // for
 667                                                                              // applet
 668                   ap.repaint();
 669                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 670                 }
 671               });
 672               popup.add(cprof);
 673               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 674                       MessageManager.getString("label.normalise_logo"),
 675                       av.isNormaliseSequenceLogo());
 676               cprofn.addItemListener(new ItemListener()
 677               {
 678                 @Override
 679                 public void itemStateChanged(ItemEvent e)
 680                 {
 681                   // TODO: pass on reference
 682                   // to ap
 683                   // so the
 684                   // view
 685                   // can be
 686                   // updated.
 687                   av.setShowSequenceLogo(true);
 688                   ap.alignFrame.normSequenceLogo
 689                           .setState(cprofn.getState()); // TODO:
 690                                                         // implement
 691                                                         // ap.updateGUI()/alignFrame.updateGUI
 692                                                         // for
 693                                                         // applet
 694                   av.setNormaliseSequenceLogo(cprofn.getState());
 695                   ap.repaint();
 696                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 697                 }
 698               });
 699               popup.add(cprofn);
 700             }
 701
 702             item = new MenuItem(COPYCONS_SEQ);
 703             item.addActionListener(this);
 704             popup.add(item);
 705           }
 706         }
 707       }
 708       popup.show(this, evt.getX(), evt.getY());
 709     }
 710     else
 711     {
 712       // selection action.
 713       if (selectedRow > -1 && selectedRow < aa.length)
 714       {
 715         if (aa[selectedRow].groupRef != null)
 716         {
 717           if (evt.getClickCount() >= 2)
 718           {
 719             // todo: make the ap scroll to the selection - not necessary, first
 720             // click highlights/scrolls, second selects
 721             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 722             // process modifiers
 723             SequenceGroup sg = ap.av.getSelectionGroup();
 724             if (sg == null || sg == aa[selectedRow].groupRef
 725                     || !(jalview.util.Platform.isControlDown(evt)
 726                             || evt.isShiftDown()))
 727             {
 728               if (jalview.util.Platform.isControlDown(evt)
 729                       || evt.isShiftDown())
 730               {
 731                 // clone a new selection group from the associated group
 732                 ap.av.setSelectionGroup(
 733                         new SequenceGroup(aa[selectedRow].groupRef));
 734               }
 735               else
 736               {
 737                 // set selection to the associated group so it can be edited
 738                 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
 739               }
 740             }
 741             else
 742             {
 743               // modify current selection with associated group
 744               int remainToAdd = aa[selectedRow].groupRef.getSize();
 745               for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
 746               {
 747                 if (jalview.util.Platform.isControlDown(evt))
 748                 {
 749                   sg.addOrRemove(sgs, --remainToAdd == 0);
 750                 }
 751                 else
 752                 {
 753                   // notionally, we should also add intermediate sequences from
 754                   // last added sequence ?
 755                   sg.addSequence(sgs, --remainToAdd == 0);
 756                 }
 757               }
 758             }
 759             ap.paintAlignment(false);
 760             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 761             ap.av.sendSelection();
 762           }
 763           else
 764           {
 765             ap.seqPanel.ap.idPanel.highlightSearchResults(
 766                     aa[selectedRow].groupRef.getSequences(null));
 767           }
 768           return;
 769         }
 770         else if (aa[selectedRow].sequenceRef != null)
 771         {
 772           if (evt.getClickCount() == 1)
 773           {
 774             ap.seqPanel.ap.idPanel
 775                     .highlightSearchResults(Arrays.asList(new SequenceI[]
 776                     { aa[selectedRow].sequenceRef }));
 777           }
 778           else if (evt.getClickCount() >= 2)
 779           {
 780             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 781             SequenceGroup sg = ap.av.getSelectionGroup();
 782             if (sg != null)
 783             {
 784               // we make a copy rather than edit the current selection if no
 785               // modifiers pressed
 786               // see Enhancement JAL-1557
 787               if (!(jalview.util.Platform.isControlDown(evt)
 788                       || evt.isShiftDown()))
 789               {
 790                 sg = new SequenceGroup(sg);
 791                 sg.clear();
 792                 sg.addSequence(aa[selectedRow].sequenceRef, false);
 793               }
 794               else
 795               {
 796                 if (jalview.util.Platform.isControlDown(evt))
 797                 {
 798                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
 799                 }
 800                 else
 801                 {
 802                   // notionally, we should also add intermediate sequences from
 803                   // last added sequence ?
 804                   sg.addSequence(aa[selectedRow].sequenceRef, true);
 805                 }
 806               }
 807             }
 808             else
 809             {
 810               sg = new SequenceGroup();
 811               sg.setStartRes(0);
 812               sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
 813               sg.addSequence(aa[selectedRow].sequenceRef, false);
 814             }
 815             ap.av.setSelectionGroup(sg);
 816             ap.paintAlignment(false);
 817             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 818             ap.av.sendSelection();
 819           }
 820
 821         }
 822       }
 823
 824     }
 825   }
 826
 827   /**
 828    * DOCUMENT ME!
 829    *
 830    * @param e
 831    *          DOCUMENT ME!
 832    */
 833   protected void copy_annotseqtoclipboard(SequenceI sq)
 834   {
 835     if (sq == null || sq.getLength() < 1)
 836     {
 837       return;
 838     }
 839     jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
 840     jalview.appletgui.AlignFrame.copiedSequences
 841             .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
 842                     + "\t" + sq.getSequenceAsString() + "\n");
 843     if (av.hasHiddenColumns())
 844     {
 845       jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
 846               av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
 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 }