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     // TODO: only paint if we needed to
 230     ap.paintAlignment(true, true);
 231   }
 232
 233   boolean editLabelDescription(AlignmentAnnotation annotation)
 234   {
 235     Checkbox padGaps = new Checkbox(
 236             "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
 237             annotation.padGaps);
 238
 239     EditNameDialog dialog = new EditNameDialog(annotation.label,
 240             annotation.description, "      Annotation Label",
 241             "Annotation Description", ap.alignFrame,
 242             "Edit Annotation Name / Description", 500, 180, false);
 243
 244     Panel empty = new Panel(new FlowLayout());
 245     empty.add(padGaps);
 246     dialog.add(empty);
 247     dialog.pack();
 248
 249     dialog.setVisible(true);
 250
 251     if (dialog.accept)
 252     {
 253       annotation.label = dialog.getName();
 254       annotation.description = dialog.getDescription();
 255       annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
 256       repaint();
 257       return true;
 258     }
 259     else
 260     {
 261       return false;
 262     }
 263
 264   }
 265
 266   boolean resizePanel = false;
 267
 268   @Override
 269   public void mouseMoved(MouseEvent evt)
 270   {
 271     resizePanel = evt.getY() < 10 && evt.getX() < 14;
 272     int row = getSelectedRow(evt.getY() + scrollOffset);
 273
 274     if (row > -1)
 275     {
 276       ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
 277               av.getAlignment().getAlignmentAnnotation()[row]
 278                       .getDescription(true),
 279               true, "\n");
 280       if (tooltip == null)
 281       {
 282         tooltip = new Tooltip(phb.getNonHtmlContent(), this);
 283       }
 284       else
 285       {
 286         tooltip.setTip(phb.getNonHtmlContent());
 287       }
 288     }
 289     else if (tooltip != null)
 290     {
 291       tooltip.setTip("");
 292     }
 293   }
 294
 295   /**
 296    * curent drag position
 297    */
 298   MouseEvent dragEvent = null;
 299
 300   /**
 301    * flag to indicate drag events should be ignored
 302    */
 303   private boolean dragCancelled = false;
 304
 305   /**
 306    * clear any drag events in progress
 307    */
 308   public void cancelDrag()
 309   {
 310     dragEvent = null;
 311     dragCancelled = true;
 312   }
 313
 314   @Override
 315   public void mouseDragged(MouseEvent evt)
 316   {
 317     if (dragCancelled)
 318     {
 319       return;
 320     }
 321     ;
 322     dragEvent = evt;
 323
 324     if (resizePanel)
 325     {
 326       Dimension d = ap.annotationPanelHolder.getSize(),
 327               e = ap.annotationSpaceFillerHolder.getSize(),
 328               f = ap.seqPanelHolder.getSize();
 329       int dif = evt.getY() - oldY;
 330
 331       dif /= ap.av.getCharHeight();
 332       dif *= ap.av.getCharHeight();
 333
 334       if ((d.height - dif) > 20 && (f.height + dif) > 20)
 335       {
 336         ap.annotationPanel.setSize(d.width, d.height - dif);
 337         setSize(new Dimension(e.width, d.height - dif));
 338         ap.annotationSpaceFillerHolder
 339                 .setSize(new Dimension(e.width, d.height - dif));
 340         ap.annotationPanelHolder
 341                 .setSize(new Dimension(d.width, d.height - dif));
 342         ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
 343                 av.calcPanelHeight());
 344         f.height += dif;
 345         ap.seqPanelHolder.setPreferredSize(f);
 346         ap.setScrollValues(av.getRanges().getStartRes(),
 347                 av.getRanges().getStartSeq());
 348         ap.validate();
 349         // ap.paintAlignment(true);
 350         ap.addNotify();
 351       }
 352
 353     }
 354     else
 355     {
 356       int diff;
 357       if ((diff = 6 - evt.getY()) > 0)
 358       {
 359         // nudge scroll up
 360         ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
 361         ap.adjustmentValueChanged(null);
 362
 363       }
 364       else if ((0 < (diff = 6
 365               - ap.annotationSpaceFillerHolder.getSize().height
 366               + evt.getY())))
 367       {
 368         // nudge scroll down
 369         ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
 370         ap.adjustmentValueChanged(null);
 371       }
 372       repaint();
 373     }
 374   }
 375
 376   @Override
 377   public void mouseClicked(MouseEvent evt)
 378   {
 379   }
 380
 381   @Override
 382   public void mouseReleased(MouseEvent evt)
 383   {
 384     if (!resizePanel && !dragCancelled)
 385     {
 386       int start = selectedRow;
 387
 388       int end = getSelectedRow(evt.getY() + scrollOffset);
 389
 390       if (start > -1 && start != end)
 391       {
 392         // Swap these annotations
 393         AlignmentAnnotation startAA = ap.av.getAlignment()
 394                 .getAlignmentAnnotation()[start];
 395         if (end == -1)
 396         {
 397           end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
 398         }
 399         AlignmentAnnotation endAA = ap.av.getAlignment()
 400                 .getAlignmentAnnotation()[end];
 401
 402         ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
 403         ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
 404       }
 405     }
 406     resizePanel = false;
 407     dragEvent = null;
 408     dragCancelled = false;
 409     repaint();
 410     ap.annotationPanel.repaint();
 411   }
 412
 413   @Override
 414   public void mouseEntered(MouseEvent evt)
 415   {
 416     if (evt.getY() < 10 && evt.getX() < 14)
 417     {
 418       resizePanel = true;
 419       repaint();
 420     }
 421   }
 422
 423   @Override
 424   public void mouseExited(MouseEvent evt)
 425   {
 426     dragCancelled = false;
 427
 428     if (dragEvent == null)
 429     {
 430       resizePanel = false;
 431     }
 432     else
 433     {
 434       if (!resizePanel)
 435       {
 436         dragEvent = null;
 437       }
 438     }
 439     repaint();
 440   }
 441
 442   @Override
 443   public void mousePressed(MouseEvent evt)
 444   {
 445     oldY = evt.getY();
 446     if (resizePanel)
 447     {
 448       return;
 449     }
 450     dragCancelled = false;
 451     // todo: move below to mouseClicked ?
 452     selectedRow = getSelectedRow(evt.getY() + scrollOffset);
 453
 454     AlignmentAnnotation[] aa = ap.av.getAlignment()
 455             .getAlignmentAnnotation();
 456
 457     // DETECT RIGHT MOUSE BUTTON IN AWT
 458     if ((evt.getModifiers()
 459             & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
 460     {
 461
 462       PopupMenu popup = new PopupMenu(
 463               MessageManager.getString("label.annotations"));
 464
 465       MenuItem item = new MenuItem(ADDNEW);
 466       item.addActionListener(this);
 467       popup.add(item);
 468       if (selectedRow < 0)
 469       {
 470         // this never happens at moment: - see comment on JAL-563
 471         if (hasHiddenRows)
 472         {
 473           item = new MenuItem(SHOWALL);
 474           item.addActionListener(this);
 475           popup.add(item);
 476         }
 477         this.add(popup);
 478         popup.show(this, evt.getX(), evt.getY());
 479         return;
 480       }
 481       // add the rest if there are actually rows to show
 482       item = new MenuItem(EDITNAME);
 483       item.addActionListener(this);
 484       popup.add(item);
 485       item = new MenuItem(HIDE);
 486       item.addActionListener(this);
 487       popup.add(item);
 488
 489       /*
 490        * Hide all <label>:
 491        */
 492       if (selectedRow < aa.length)
 493       {
 494         if (aa[selectedRow].sequenceRef != null)
 495         {
 496           final String label = aa[selectedRow].label;
 497           MenuItem hideType = new MenuItem(
 498                   MessageManager.getString("label.hide_all") + " " + label);
 499           hideType.addActionListener(new ActionListener()
 500           {
 501             @Override
 502             public void actionPerformed(ActionEvent e)
 503             {
 504               AlignmentUtils.showOrHideSequenceAnnotations(
 505                       ap.av.getAlignment(), Collections.singleton(label),
 506                       null, false, false);
 507               refresh();
 508             }
 509           });
 510           popup.add(hideType);
 511         }
 512       }
 513
 514       if (hasHiddenRows)
 515       {
 516         item = new MenuItem(SHOWALL);
 517         item.addActionListener(this);
 518         popup.add(item);
 519       }
 520       this.add(popup);
 521       item = new MenuItem(OUTPUT_TEXT);
 522       item.addActionListener(this);
 523       popup.add(item);
 524       if (selectedRow < aa.length)
 525       {
 526         if (aa[selectedRow].autoCalculated)
 527         {
 528           if (aa[selectedRow].label.indexOf("Consensus") > -1)
 529           {
 530             popup.addSeparator();
 531             final CheckboxMenuItem cbmi = new CheckboxMenuItem(
 532                     MessageManager.getString("label.ignore_gaps_consensus"),
 533                     (aa[selectedRow].groupRef != null)
 534                             ? aa[selectedRow].groupRef
 535                                     .getIgnoreGapsConsensus()
 536                             : ap.av.isIgnoreGapsConsensus());
 537             final AlignmentAnnotation aaa = aa[selectedRow];
 538             cbmi.addItemListener(new ItemListener()
 539             {
 540               @Override
 541               public void itemStateChanged(ItemEvent e)
 542               {
 543                 if (aaa.groupRef != null)
 544                 {
 545                   // TODO: pass on reference to ap so the view can be updated.
 546                   aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
 547                 }
 548                 else
 549                 {
 550                   ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
 551                 }
 552                 ap.paintAlignment(true, true);
 553               }
 554             });
 555             popup.add(cbmi);
 556             if (aaa.groupRef != null)
 557             {
 558               final CheckboxMenuItem chist = new CheckboxMenuItem(
 559                       MessageManager
 560                               .getString("label.show_group_histogram"),
 561                       aa[selectedRow].groupRef.isShowConsensusHistogram());
 562               chist.addItemListener(new ItemListener()
 563               {
 564                 @Override
 565                 public void itemStateChanged(ItemEvent e)
 566                 {
 567                   // TODO: pass on reference
 568                   // to ap
 569                   // so the
 570                   // view
 571                   // can be
 572                   // updated.
 573                   aaa.groupRef.setShowConsensusHistogram(chist.getState());
 574                   ap.repaint();
 575                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 576                 }
 577               });
 578               popup.add(chist);
 579               final CheckboxMenuItem cprofl = new CheckboxMenuItem(
 580                       MessageManager.getString("label.show_group_logo"),
 581                       aa[selectedRow].groupRef.isShowSequenceLogo());
 582               cprofl.addItemListener(new ItemListener()
 583               {
 584                 @Override
 585                 public void itemStateChanged(ItemEvent e)
 586                 {
 587                   // TODO: pass on reference
 588                   // to ap
 589                   // so the
 590                   // view
 591                   // can be
 592                   // updated.
 593                   aaa.groupRef.setshowSequenceLogo(cprofl.getState());
 594                   ap.repaint();
 595                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 596                 }
 597               });
 598
 599               popup.add(cprofl);
 600               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 601                       MessageManager
 602                               .getString("label.normalise_group_logo"),
 603                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
 604               cprofn.addItemListener(new ItemListener()
 605               {
 606                 @Override
 607                 public void itemStateChanged(ItemEvent e)
 608                 {
 609                   // TODO: pass on reference
 610                   // to ap
 611                   // so the
 612                   // view
 613                   // can be
 614                   // updated.
 615                   aaa.groupRef.setshowSequenceLogo(true);
 616                   aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
 617                   ap.repaint();
 618                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 619                 }
 620               });
 621               popup.add(cprofn);
 622             }
 623             else
 624             {
 625               final CheckboxMenuItem chist = new CheckboxMenuItem(
 626                       MessageManager.getString("label.show_histogram"),
 627                       av.isShowConsensusHistogram());
 628               chist.addItemListener(new ItemListener()
 629               {
 630                 @Override
 631                 public void itemStateChanged(ItemEvent e)
 632                 {
 633                   // TODO: pass on reference
 634                   // to ap
 635                   // so the
 636                   // view
 637                   // can be
 638                   // updated.
 639                   av.setShowConsensusHistogram(chist.getState());
 640                   ap.alignFrame.showConsensusHistogram
 641                           .setState(chist.getState()); // TODO: implement
 642                                                        // ap.updateGUI()/alignFrame.updateGUI
 643                                                        // for applet
 644                   ap.repaint();
 645                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 646                 }
 647               });
 648               popup.add(chist);
 649               final CheckboxMenuItem cprof = new CheckboxMenuItem(
 650                       MessageManager.getString("label.show_logo"),
 651                       av.isShowSequenceLogo());
 652               cprof.addItemListener(new ItemListener()
 653               {
 654                 @Override
 655                 public void itemStateChanged(ItemEvent e)
 656                 {
 657                   // TODO: pass on reference
 658                   // to ap
 659                   // so the
 660                   // view
 661                   // can be
 662                   // updated.
 663                   av.setShowSequenceLogo(cprof.getState());
 664                   ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
 665                                                                              // implement
 666                                                                              // ap.updateGUI()/alignFrame.updateGUI
 667                                                                              // for
 668                                                                              // applet
 669                   ap.repaint();
 670                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 671                 }
 672               });
 673               popup.add(cprof);
 674               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
 675                       MessageManager.getString("label.normalise_logo"),
 676                       av.isNormaliseSequenceLogo());
 677               cprofn.addItemListener(new ItemListener()
 678               {
 679                 @Override
 680                 public void itemStateChanged(ItemEvent e)
 681                 {
 682                   // TODO: pass on reference
 683                   // to ap
 684                   // so the
 685                   // view
 686                   // can be
 687                   // updated.
 688                   av.setShowSequenceLogo(true);
 689                   ap.alignFrame.normSequenceLogo
 690                           .setState(cprofn.getState()); // TODO:
 691                                                         // implement
 692                                                         // ap.updateGUI()/alignFrame.updateGUI
 693                                                         // for
 694                                                         // applet
 695                   av.setNormaliseSequenceLogo(cprofn.getState());
 696                   ap.repaint();
 697                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
 698                 }
 699               });
 700               popup.add(cprofn);
 701             }
 702
 703             item = new MenuItem(COPYCONS_SEQ);
 704             item.addActionListener(this);
 705             popup.add(item);
 706           }
 707         }
 708       }
 709       popup.show(this, evt.getX(), evt.getY());
 710     }
 711     else
 712     {
 713       // selection action.
 714       if (selectedRow > -1 && selectedRow < aa.length)
 715       {
 716         if (aa[selectedRow].groupRef != null)
 717         {
 718           if (evt.getClickCount() >= 2)
 719           {
 720             // todo: make the ap scroll to the selection - not necessary, first
 721             // click highlights/scrolls, second selects
 722             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 723             // process modifiers
 724             SequenceGroup sg = ap.av.getSelectionGroup();
 725             if (sg == null || sg == aa[selectedRow].groupRef
 726                     || !(jalview.util.Platform.isControlDown(evt)
 727                             || evt.isShiftDown()))
 728             {
 729               if (jalview.util.Platform.isControlDown(evt)
 730                       || evt.isShiftDown())
 731               {
 732                 // clone a new selection group from the associated group
 733                 ap.av.setSelectionGroup(
 734                         new SequenceGroup(aa[selectedRow].groupRef));
 735               }
 736               else
 737               {
 738                 // set selection to the associated group so it can be edited
 739                 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
 740               }
 741             }
 742             else
 743             {
 744               // modify current selection with associated group
 745               int remainToAdd = aa[selectedRow].groupRef.getSize();
 746               for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
 747               {
 748                 if (jalview.util.Platform.isControlDown(evt))
 749                 {
 750                   sg.addOrRemove(sgs, --remainToAdd == 0);
 751                 }
 752                 else
 753                 {
 754                   // notionally, we should also add intermediate sequences from
 755                   // last added sequence ?
 756                   sg.addSequence(sgs, --remainToAdd == 0);
 757                 }
 758               }
 759             }
 760             ap.paintAlignment(false, false);
 761             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 762             ap.av.sendSelection();
 763           }
 764           else
 765           {
 766             ap.seqPanel.ap.idPanel.highlightSearchResults(
 767                     aa[selectedRow].groupRef.getSequences(null));
 768           }
 769           return;
 770         }
 771         else if (aa[selectedRow].sequenceRef != null)
 772         {
 773           if (evt.getClickCount() == 1)
 774           {
 775             ap.seqPanel.ap.idPanel
 776                     .highlightSearchResults(Arrays.asList(new SequenceI[]
 777                     { aa[selectedRow].sequenceRef }));
 778           }
 779           else if (evt.getClickCount() >= 2)
 780           {
 781             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
 782             SequenceGroup sg = ap.av.getSelectionGroup();
 783             if (sg != null)
 784             {
 785               // we make a copy rather than edit the current selection if no
 786               // modifiers pressed
 787               // see Enhancement JAL-1557
 788               if (!(jalview.util.Platform.isControlDown(evt)
 789                       || evt.isShiftDown()))
 790               {
 791                 sg = new SequenceGroup(sg);
 792                 sg.clear();
 793                 sg.addSequence(aa[selectedRow].sequenceRef, false);
 794               }
 795               else
 796               {
 797                 if (jalview.util.Platform.isControlDown(evt))
 798                 {
 799                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
 800                 }
 801                 else
 802                 {
 803                   // notionally, we should also add intermediate sequences from
 804                   // last added sequence ?
 805                   sg.addSequence(aa[selectedRow].sequenceRef, true);
 806                 }
 807               }
 808             }
 809             else
 810             {
 811               sg = new SequenceGroup();
 812               sg.setStartRes(0);
 813               sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
 814               sg.addSequence(aa[selectedRow].sequenceRef, false);
 815             }
 816             ap.av.setSelectionGroup(sg);
 817             ap.paintAlignment(false, false);
 818             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
 819             ap.av.sendSelection();
 820           }
 821
 822         }
 823       }
 824
 825     }
 826   }
 827
 828   /**
 829    * DOCUMENT ME!
 830    *
 831    * @param e
 832    *          DOCUMENT ME!
 833    */
 834   protected void copy_annotseqtoclipboard(SequenceI sq)
 835   {
 836     if (sq == null || sq.getLength() < 1)
 837     {
 838       return;
 839     }
 840     jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
 841     jalview.appletgui.AlignFrame.copiedSequences
 842             .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
 843                     + "\t" + sq.getSequenceAsString() + "\n");
 844     if (av.hasHiddenColumns())
 845     {
 846       jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
 847               av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
 848     }
 849   }
 850
 851   @Override
 852   public void update(Graphics g)
 853   {
 854     paint(g);
 855   }
 856
 857   @Override
 858   public void paint(Graphics g)
 859   {
 860     int w = getSize().width;
 861     int h = getSize().height;
 862     if (image == null || w != image.getWidth(this)
 863             || h != image.getHeight(this))
 864     {
 865       image = createImage(w, ap.annotationPanel.getSize().height);
 866     }
 867
 868     drawComponent(image.getGraphics(), w);
 869     g.drawImage(image, 0, 0, this);
 870   }
 871
 872   public void drawComponent(Graphics g, int width)
 873   {
 874     g.setFont(av.getFont());
 875     FontMetrics fm = g.getFontMetrics(av.getFont());
 876     g.setColor(Color.white);
 877     g.fillRect(0, 0, getSize().width, getSize().height);
 878
 879     g.translate(0, -scrollOffset);
 880     g.setColor(Color.black);
 881
 882     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 883     int y = 0, fy = g.getFont().getSize();
 884     int x = 0, offset;
 885
 886     if (aa != null)
 887     {
 888       hasHiddenRows = false;
 889       for (int i = 0; i < aa.length; i++)
 890       {
 891         if (!aa[i].visible)
 892         {
 893           hasHiddenRows = true;
 894           continue;
 895         }
 896
 897         x = width - fm.stringWidth(aa[i].label) - 3;
 898
 899         y += aa[i].height;
 900         offset = -(aa[i].height - fy) / 2;
 901
 902         g.drawString(aa[i].label, x, y + offset);
 903       }
 904     }
 905     g.translate(0, +scrollOffset);
 906     if (resizePanel)
 907     {
 908       g.setColor(Color.red);
 909       g.setPaintMode();
 910       g.drawLine(2, 8, 5, 2);
 911       g.drawLine(5, 2, 8, 8);
 912     }
 913     else if (!dragCancelled && dragEvent != null && aa != null)
 914     {
 915       g.setColor(Color.lightGray);
 916       g.drawString(aa[selectedRow].label, dragEvent.getX(),
 917               dragEvent.getY());
 918     }
 919
 920     if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
 921     {
 922       g.setColor(Color.black);
 923       g.drawString(MessageManager.getString("label.right_click"), 2, 8);
 924       g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
 925               18);
 926     }
 927   }
 928 }