src/jalview/appletgui/AlignFrame.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.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.FeaturesFile;
  53 import jalview.io.TCoffeeScoreFile;
  54 import jalview.schemes.Blosum62ColourScheme;
  55 import jalview.schemes.BuriedColourScheme;
  56 import jalview.schemes.ClustalxColourScheme;
  57 import jalview.schemes.ColourSchemeI;
  58 import jalview.schemes.HelixColourScheme;
  59 import jalview.schemes.HydrophobicColourScheme;
  60 import jalview.schemes.NucleotideColourScheme;
  61 import jalview.schemes.PIDColourScheme;
  62 import jalview.schemes.PurinePyrimidineColourScheme;
  63 import jalview.schemes.RNAHelicesColourChooser;
  64 import jalview.schemes.StrandColourScheme;
  65 import jalview.schemes.TCoffeeColourScheme;
  66 import jalview.schemes.TaylorColourScheme;
  67 import jalview.schemes.TurnColourScheme;
  68 import jalview.schemes.ZappoColourScheme;
  69 import jalview.structure.StructureSelectionManager;
  70 import jalview.structures.models.AAStructureBindingModel;
  71 import jalview.util.MappingUtils;
  72 import jalview.util.MessageManager;
  73 import jalview.viewmodel.AlignmentViewport;
  74
  75 import java.awt.BorderLayout;
  76 import java.awt.Canvas;
  77 import java.awt.CheckboxMenuItem;
  78 import java.awt.Color;
  79 import java.awt.FlowLayout;
  80 import java.awt.Font;
  81 import java.awt.FontMetrics;
  82 import java.awt.Frame;
  83 import java.awt.Graphics;
  84 import java.awt.Label;
  85 import java.awt.Menu;
  86 import java.awt.MenuBar;
  87 import java.awt.MenuItem;
  88 import java.awt.Panel;
  89 import java.awt.event.ActionEvent;
  90 import java.awt.event.ActionListener;
  91 import java.awt.event.FocusEvent;
  92 import java.awt.event.FocusListener;
  93 import java.awt.event.ItemEvent;
  94 import java.awt.event.ItemListener;
  95 import java.awt.event.KeyEvent;
  96 import java.awt.event.KeyListener;
  97 import java.awt.event.WindowAdapter;
  98 import java.awt.event.WindowEvent;
  99 import java.io.IOException;
 100 import java.net.URL;
 101 import java.net.URLEncoder;
 102 import java.util.Arrays;
 103 import java.util.Deque;
 104 import java.util.HashMap;
 105 import java.util.Hashtable;
 106 import java.util.List;
 107 import java.util.Map;
 108 import java.util.StringTokenizer;
 109 import java.util.Vector;
 110
 111 import org.jmol.viewer.Viewer;
 112
 113 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 114         ItemListener, KeyListener, AlignViewControllerGuiI
 115 {
 116   public AlignViewControllerI avc;
 117
 118   public AlignmentPanel alignPanel;
 119
 120   public AlignViewport viewport;
 121
 122   // width and height may be overridden by applet parameters
 123   int frameWidth = 700;
 124
 125   int frameHeight = 500;
 126
 127   String jalviewServletURL;
 128
 129   /*
 130    * Flag for showing autocalculated consensus above or below other consensus
 131    * rows
 132    */
 133   private boolean showAutoCalculatedAbove;
 134
 135   private SequenceAnnotationOrder annotationSortOrder;
 136
 137   /**
 138    * Constructor that creates the frame and adds it to the display.
 139    *
 140    * @param al
 141    * @param applet
 142    * @param title
 143    * @param embedded
 144    */
 145   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 146           boolean embedded)
 147   {
 148     this(al, applet, title, embedded, true);
 149   }
 150
 151   /**
 152    * Constructor that optionally allows the frame to be displayed or only
 153    * created.
 154    *
 155    * @param al
 156    * @param applet
 157    * @param title
 158    * @param embedded
 159    * @param addToDisplay
 160    */
 161   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 162           boolean embedded, boolean addToDisplay)
 163   {
 164     this(al, null, null, applet, title, embedded, addToDisplay);
 165   }
 166
 167   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 168           ColumnSelection columnSelection, JalviewLite applet,
 169           String title, boolean embedded)
 170   {
 171     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 172   }
 173
 174   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 175           ColumnSelection columnSelection, JalviewLite applet,
 176           String title, boolean embedded, boolean addToDisplay)
 177   {
 178     if (applet != null)
 179     {
 180       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 181     }
 182
 183     try
 184     {
 185       jbInit();
 186     } catch (Exception ex)
 187     {
 188       ex.printStackTrace();
 189     }
 190     // need to get window geometry before we calculate alignment layout
 191     if (applet != null)
 192     {
 193       String param;
 194       try
 195       {
 196         param = applet.getParameter("windowWidth");
 197         if (param != null)
 198         {
 199           int width = Integer.parseInt(param);
 200           frameWidth = width;
 201         }
 202         param = applet.getParameter("windowHeight");
 203         if (param != null)
 204         {
 205           int height = Integer.parseInt(param);
 206           frameHeight = height;
 207         }
 208       } catch (Exception ex)
 209       {
 210       }
 211     }
 212     viewport = new AlignViewport(al, applet);
 213
 214     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 215     {
 216       viewport.hideSequence(hiddenSeqs);
 217     }
 218     if (columnSelection != null)
 219     {
 220       viewport.setColumnSelection(columnSelection);
 221     }
 222
 223     alignPanel = new AlignmentPanel(this, viewport);
 224     avc = new jalview.controller.AlignViewController(this, viewport,
 225             alignPanel);
 226     viewport.updateConservation(alignPanel);
 227     viewport.updateConsensus(alignPanel);
 228
 229     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 230     followMouseOverFlag.setState(viewport.isFollowHighlight());
 231     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 232     showGroupConservation.setState(viewport.isShowGroupConservation());
 233     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 234     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 235     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 236     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 237     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 238     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 239     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 240     showAlignmentAnnotations.setState(true);
 241     showSequenceAnnotations.setState(false);
 242
 243     seqLimits.setState(viewport.getShowJVSuffix());
 244
 245     if (applet != null)
 246     {
 247       String param = applet.getParameter("sortBy");
 248       if (param != null)
 249       {
 250         if (param.equalsIgnoreCase("Id"))
 251         {
 252           sortIDMenuItem_actionPerformed();
 253         }
 254         else if (param.equalsIgnoreCase("Pairwise Identity"))
 255         {
 256           sortPairwiseMenuItem_actionPerformed();
 257         }
 258         else if (param.equalsIgnoreCase("Length"))
 259         {
 260           sortLengthMenuItem_actionPerformed();
 261         }
 262       }
 263
 264       param = applet.getParameter("wrap");
 265       if (param != null)
 266       {
 267         if (param.equalsIgnoreCase("true"))
 268         {
 269           wrapMenuItem.setState(true);
 270           wrapMenuItem_actionPerformed();
 271         }
 272       }
 273       param = applet.getParameter("centrecolumnlabels");
 274       if (param != null)
 275       {
 276         centreColumnLabelFlag.setState(true);
 277         centreColumnLabelFlag_stateChanged();
 278       }
 279
 280     }
 281     if (viewport.getAlignment().isNucleotide())
 282     {
 283       viewport.updateStrucConsensus(alignPanel);
 284       if (viewport.getAlignment().hasRNAStructure())
 285       {
 286         RNAHelixColour.setEnabled(true);
 287       }
 288       else
 289       {
 290         RNAHelixColour.setEnabled(false);
 291       }
 292     }
 293     else
 294     {
 295       RNAHelixColour.setEnabled(false);
 296       purinePyrimidineColour.setEnabled(false);
 297     }
 298     // Some JVMS send keyevents to Top frame or lowest panel,
 299     // Havent worked out why yet. So add to both this frame and seqCanvas for
 300     // now
 301     this.addKeyListener(this);
 302     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 303     alignPanel.idPanel.idCanvas.addKeyListener(this);
 304     alignPanel.scalePanel.addKeyListener(this);
 305     alignPanel.annotationPanel.addKeyListener(this);
 306     alignPanel.annotationPanelHolder.addKeyListener(this);
 307     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 308     alignPanel.alabels.addKeyListener(this);
 309
 310     setAnnotationsVisibility();
 311
 312     if (addToDisplay)
 313     {
 314       addToDisplay(embedded);
 315     }
 316   }
 317
 318   /**
 319    * @param embedded
 320    */
 321   public void addToDisplay(boolean embedded)
 322   {
 323     createAlignFrameWindow(embedded);
 324     validate();
 325     alignPanel.adjustAnnotationHeight();
 326     alignPanel.paintAlignment(true);
 327   }
 328
 329   public AlignViewport getAlignViewport()
 330   {
 331     return viewport;
 332   }
 333
 334   public SeqCanvas getSeqcanvas()
 335   {
 336     return alignPanel.seqPanel.seqCanvas;
 337   }
 338
 339   /**
 340    * Load a features file onto the alignment
 341    *
 342    * @param file
 343    *          file URL, content, or other resolvable path
 344    * @param type
 345    *          is protocol for accessing data referred to by file
 346    */
 347
 348   public boolean parseFeaturesFile(String file, String type)
 349   {
 350     return parseFeaturesFile(file, type, true);
 351   }
 352
 353   /**
 354    * Load a features file onto the alignment
 355    *
 356    * @param file
 357    *          file URL, content, or other resolvable path
 358    * @param type
 359    *          is protocol for accessing data referred to by file
 360    * @param autoenabledisplay
 361    *          when true, display features flag will be automatically enabled if
 362    *          features are loaded
 363    * @return true if data parsed as a features file
 364    */
 365   public boolean parseFeaturesFile(String file, String type,
 366           boolean autoenabledisplay)
 367   {
 368     boolean featuresFile = false;
 369     try
 370     {
 371       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 372               .getFeatureRenderer().getFeatureColours();
 373       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 374               "relaxedidmatch", false);
 375       featuresFile = new FeaturesFile(file, type).parse(
 376               viewport.getAlignment(), colours, true, relaxedIdMatching);
 377     } catch (Exception ex)
 378     {
 379       ex.printStackTrace();
 380     }
 381
 382     if (featuresFile)
 383     {
 384       if (autoenabledisplay)
 385       {
 386         viewport.setShowSequenceFeatures(true);
 387         sequenceFeatures.setState(true);
 388       }
 389       if (alignPanel.seqPanel.seqCanvas.fr != null)
 390       {
 391         // update the min/max ranges where necessary
 392         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 393       }
 394       if (viewport.featureSettings != null)
 395       {
 396         viewport.featureSettings.refreshTable();
 397       }
 398       alignPanel.paintAlignment(true);
 399       statusBar.setText(MessageManager
 400               .getString("label.successfully_added_features_alignment"));
 401     }
 402     return featuresFile;
 403   }
 404
 405   @Override
 406   public void keyPressed(KeyEvent evt)
 407   {
 408     if (viewport.cursorMode
 409             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 410                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 411                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 412             && Character.isDigit(evt.getKeyChar()))
 413     {
 414       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 415     }
 416
 417     switch (evt.getKeyCode())
 418     {
 419     case 27: // escape key
 420       deselectAllSequenceMenuItem_actionPerformed();
 421
 422       alignPanel.alabels.cancelDrag();
 423       break;
 424     case KeyEvent.VK_X:
 425       if (evt.isControlDown() || evt.isMetaDown())
 426       {
 427         cut_actionPerformed();
 428       }
 429       break;
 430     case KeyEvent.VK_C:
 431       if (viewport.cursorMode && !evt.isControlDown())
 432       {
 433         alignPanel.seqPanel.setCursorColumn();
 434       }
 435       if (evt.isControlDown() || evt.isMetaDown())
 436       {
 437         copy_actionPerformed();
 438       }
 439       break;
 440     case KeyEvent.VK_V:
 441       if (evt.isControlDown())
 442       {
 443         paste(evt.isShiftDown());
 444       }
 445       break;
 446     case KeyEvent.VK_A:
 447       if (evt.isControlDown() || evt.isMetaDown())
 448       {
 449         selectAllSequenceMenuItem_actionPerformed();
 450       }
 451       break;
 452     case KeyEvent.VK_DOWN:
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.moveCursor(0, 1);
 456       }
 457       else
 458       {
 459         moveSelectedSequences(false);
 460       }
 461       break;
 462
 463     case KeyEvent.VK_UP:
 464       if (viewport.cursorMode)
 465       {
 466         alignPanel.seqPanel.moveCursor(0, -1);
 467       }
 468       else
 469       {
 470         moveSelectedSequences(true);
 471       }
 472       break;
 473
 474     case KeyEvent.VK_LEFT:
 475       if (evt.isAltDown() || !viewport.cursorMode)
 476       {
 477         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 478       }
 479       else
 480       {
 481         alignPanel.seqPanel.moveCursor(-1, 0);
 482       }
 483       break;
 484
 485     case KeyEvent.VK_RIGHT:
 486       if (evt.isAltDown() || !viewport.cursorMode)
 487       {
 488         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 489       }
 490       else
 491       {
 492         alignPanel.seqPanel.moveCursor(1, 0);
 493       }
 494       break;
 495
 496     case KeyEvent.VK_SPACE:
 497       if (viewport.cursorMode)
 498       {
 499         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 500                 || evt.isShiftDown() || evt.isAltDown());
 501       }
 502       break;
 503
 504     case KeyEvent.VK_DELETE:
 505     case KeyEvent.VK_BACK_SPACE:
 506       if (viewport.cursorMode)
 507       {
 508         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 509                 || evt.isShiftDown() || evt.isAltDown());
 510       }
 511       else
 512       {
 513         cut_actionPerformed();
 514         alignPanel.seqPanel.seqCanvas.repaint();
 515       }
 516       break;
 517
 518     case KeyEvent.VK_S:
 519       if (viewport.cursorMode)
 520       {
 521         alignPanel.seqPanel.setCursorRow();
 522       }
 523       break;
 524     case KeyEvent.VK_P:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorPosition();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_ENTER:
 532     case KeyEvent.VK_COMMA:
 533       if (viewport.cursorMode)
 534       {
 535         alignPanel.seqPanel.setCursorRowAndColumn();
 536       }
 537       break;
 538
 539     case KeyEvent.VK_Q:
 540       if (viewport.cursorMode)
 541       {
 542         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 543       }
 544       break;
 545     case KeyEvent.VK_M:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_F2:
 553       viewport.cursorMode = !viewport.cursorMode;
 554       statusBar.setText(MessageManager.formatMessage(
 555               "label.keyboard_editing_mode",
 556               new String[] { (viewport.cursorMode ? "on" : "off") }));
 557       if (viewport.cursorMode)
 558       {
 559         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 560         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 561       }
 562       break;
 563
 564     case KeyEvent.VK_F:
 565       if (evt.isControlDown())
 566       {
 567         findMenuItem_actionPerformed();
 568       }
 569       break;
 570
 571     case KeyEvent.VK_H:
 572     {
 573       boolean toggleSeqs = !evt.isControlDown();
 574       boolean toggleCols = !evt.isShiftDown();
 575       toggleHiddenRegions(toggleSeqs, toggleCols);
 576       break;
 577     }
 578
 579     case KeyEvent.VK_PAGE_UP:
 580       if (viewport.getWrapAlignment())
 581       {
 582         alignPanel.scrollUp(true);
 583       }
 584       else
 585       {
 586         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 587                 - viewport.endSeq + viewport.startSeq);
 588       }
 589       break;
 590
 591     case KeyEvent.VK_PAGE_DOWN:
 592       if (viewport.getWrapAlignment())
 593       {
 594         alignPanel.scrollUp(false);
 595       }
 596       else
 597       {
 598         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 599                 + viewport.endSeq - viewport.startSeq);
 600       }
 601       break;
 602
 603     case KeyEvent.VK_Z:
 604       if (evt.isControlDown())
 605       {
 606         undoMenuItem_actionPerformed();
 607       }
 608       break;
 609
 610     case KeyEvent.VK_Y:
 611       if (evt.isControlDown())
 612       {
 613         redoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_L:
 618       if (evt.isControlDown())
 619       {
 620         trimAlignment(true);
 621       }
 622       break;
 623
 624     case KeyEvent.VK_R:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(false);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_E:
 632       if (evt.isControlDown())
 633       {
 634         if (evt.isShiftDown())
 635         {
 636           this.removeAllGapsMenuItem_actionPerformed();
 637         }
 638         else
 639         {
 640           removeGappedColumnMenuItem_actionPerformed();
 641         }
 642       }
 643       break;
 644     case KeyEvent.VK_I:
 645       if (evt.isControlDown())
 646       {
 647         if (evt.isAltDown())
 648         {
 649           invertColSel_actionPerformed();
 650         }
 651         else
 652         {
 653           invertSequenceMenuItem_actionPerformed();
 654         }
 655       }
 656       break;
 657
 658     case KeyEvent.VK_G:
 659       if (evt.isControlDown())
 660       {
 661         if (evt.isShiftDown())
 662         {
 663           this.unGroup_actionPerformed();
 664         }
 665         else
 666         {
 667           this.createGroup_actionPerformed();
 668         }
 669       }
 670       break;
 671
 672     case KeyEvent.VK_U:
 673       if (evt.isControlDown())
 674       {
 675         this.deleteGroups_actionPerformed();
 676       }
 677       break;
 678
 679     case KeyEvent.VK_T:
 680       if (evt.isControlDown())
 681       {
 682         newView(null);
 683       }
 684       break;
 685
 686     }
 687     alignPanel.paintAlignment(true);
 688   }
 689
 690   /**
 691    * called by key handler and the hide all/show all menu items
 692    *
 693    * @param toggleSeqs
 694    * @param toggleCols
 695    */
 696   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 697   {
 698     boolean hide = false;
 699     SequenceGroup sg = viewport.getSelectionGroup();
 700     if (!toggleSeqs && !toggleCols)
 701     {
 702       // Hide everything by the current selection - this is a hack - we do the
 703       // invert and then hide
 704       // first check that there will be visible columns after the invert.
 705       if ((viewport.getColumnSelection() != null
 706               && viewport.getColumnSelection().getSelected() != null && viewport
 707               .getColumnSelection().getSelected().size() > 0)
 708               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 709                       .getEndRes()))
 710       {
 711         // now invert the sequence set, if required - empty selection implies
 712         // that no hiding is required.
 713         if (sg != null)
 714         {
 715           invertSequenceMenuItem_actionPerformed();
 716           sg = viewport.getSelectionGroup();
 717           toggleSeqs = true;
 718
 719         }
 720         viewport.expandColSelection(sg, true);
 721         // finally invert the column selection and get the new sequence
 722         // selection and indicate it should be hidden.
 723         invertColSel_actionPerformed();
 724         toggleCols = true;
 725       }
 726     }
 727
 728     if (toggleSeqs)
 729     {
 730       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 731       {
 732         hide = true;
 733         viewport.hideAllSelectedSeqs();
 734       }
 735       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 736               .size() > 0))
 737       {
 738         viewport.showAllHiddenSeqs();
 739       }
 740     }
 741
 742     if (toggleCols)
 743     {
 744       if (viewport.getColumnSelection().getSelected().size() > 0)
 745       {
 746         viewport.hideSelectedColumns();
 747         if (!toggleSeqs)
 748         {
 749           viewport.setSelectionGroup(sg);
 750         }
 751       }
 752       else if (!hide)
 753       {
 754         viewport.showAllHiddenColumns();
 755       }
 756       viewport.sendSelection();
 757     }
 758   }
 759
 760   @Override
 761   public void keyReleased(KeyEvent evt)
 762   {
 763   }
 764
 765   @Override
 766   public void keyTyped(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void itemStateChanged(ItemEvent evt)
 772   {
 773     final Object source = evt.getSource();
 774     if (source == displayNonconservedMenuItem)
 775     {
 776       displayNonconservedMenuItem_actionPerformed();
 777     }
 778     else if (source == colourTextMenuItem)
 779     {
 780       colourTextMenuItem_actionPerformed();
 781     }
 782     else if (source == wrapMenuItem)
 783     {
 784       wrapMenuItem_actionPerformed();
 785     }
 786     else if (source == scaleAbove)
 787     {
 788       viewport.setScaleAboveWrapped(scaleAbove.getState());
 789     }
 790     else if (source == scaleLeft)
 791     {
 792       viewport.setScaleLeftWrapped(scaleLeft.getState());
 793     }
 794     else if (source == scaleRight)
 795     {
 796       viewport.setScaleRightWrapped(scaleRight.getState());
 797     }
 798     else if (source == seqLimits)
 799     {
 800       seqLimits_itemStateChanged();
 801     }
 802     else if (source == viewBoxesMenuItem)
 803     {
 804       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 805     }
 806     else if (source == viewTextMenuItem)
 807     {
 808       viewport.setShowText(viewTextMenuItem.getState());
 809     }
 810     else if (source == renderGapsMenuItem)
 811     {
 812       viewport.setRenderGaps(renderGapsMenuItem.getState());
 813     }
 814     else if (source == annotationPanelMenuItem)
 815     {
 816       boolean showAnnotations = annotationPanelMenuItem.getState();
 817       showAlignmentAnnotations.setEnabled(showAnnotations);
 818       showSequenceAnnotations.setEnabled(showAnnotations);
 819       viewport.setShowAnnotation(showAnnotations);
 820       alignPanel.setAnnotationVisible(showAnnotations);
 821     }
 822     else if (source == sequenceFeatures)
 823     {
 824       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 825       alignPanel.seqPanel.seqCanvas.repaint();
 826     }
 827     else if (source == showAlignmentAnnotations)
 828     {
 829       setAnnotationsVisibility();
 830     }
 831     else if (source == showSequenceAnnotations)
 832     {
 833       setAnnotationsVisibility();
 834     }
 835     else if (source == sortAnnBySequence)
 836     {
 837       boolean newState = sortAnnBySequence.getState();
 838       sortAnnByLabel.setState(false);
 839       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 840               : SequenceAnnotationOrder.NONE);
 841       setViewportAnnotationOrder();
 842     }
 843     else if (source == sortAnnByLabel)
 844     {
 845       boolean newState = sortAnnByLabel.getState();
 846       sortAnnBySequence.setState(false);
 847       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 848               : SequenceAnnotationOrder.NONE);
 849       setViewportAnnotationOrder();
 850     }
 851     else if (source == showAutoFirst)
 852     {
 853       showAutoLast.setState(!showAutoFirst.getState());
 854       setShowAutoCalculatedAbove(showAutoFirst.getState());
 855       setViewportAnnotationOrder();
 856     }
 857     else if (source == showAutoLast)
 858     {
 859       showAutoFirst.setState(!showAutoLast.getState());
 860       setShowAutoCalculatedAbove(showAutoFirst.getState());
 861       setViewportAnnotationOrder();
 862     }
 863     else if (source == conservationMenuItem)
 864     {
 865       conservationMenuItem_actionPerformed();
 866     }
 867     else if (source == abovePIDThreshold)
 868     {
 869       abovePIDThreshold_actionPerformed();
 870     }
 871     else if (source == applyToAllGroups)
 872     {
 873       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 874     }
 875     else if (source == autoCalculate)
 876     {
 877       viewport.autoCalculateConsensus = autoCalculate.getState();
 878     }
 879     else if (source == sortByTree)
 880     {
 881       viewport.sortByTree = sortByTree.getState();
 882     }
 883     else if (source == this.centreColumnLabelFlag)
 884     {
 885       centreColumnLabelFlag_stateChanged();
 886     }
 887     else if (source == this.followMouseOverFlag)
 888     {
 889       mouseOverFlag_stateChanged();
 890     }
 891     else if (source == showGroupConsensus)
 892     {
 893       showGroupConsensus_actionPerformed();
 894     }
 895     else if (source == showGroupConservation)
 896     {
 897       showGroupConservation_actionPerformed();
 898     }
 899     else if (source == showSequenceLogo)
 900     {
 901       showSequenceLogo_actionPerformed();
 902     }
 903     else if (source == normSequenceLogo)
 904     {
 905       normSequenceLogo_actionPerformed();
 906     }
 907     else if (source == showConsensusHistogram)
 908     {
 909       showConsensusHistogram_actionPerformed();
 910     }
 911     else if (source == applyAutoAnnotationSettings)
 912     {
 913       applyAutoAnnotationSettings_actionPerformed();
 914     }
 915     alignPanel.paintAlignment(true);
 916   }
 917
 918   /**
 919    * Set the visibility state of sequence-related and/or alignment-related
 920    * annotations depending on checkbox selections, and repaint.
 921    *
 922    * @param visible
 923    */
 924   private void setAnnotationsVisibility()
 925   {
 926     boolean showForAlignment = showAlignmentAnnotations.getState();
 927     boolean showForSequences = showSequenceAnnotations.getState();
 928     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 929     {
 930       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 931             .getAlignmentAnnotation())
 932     {
 933       boolean visible = (aa.sequenceRef == null ? showForAlignment
 934               : showForSequences);
 935       aa.visible = visible;
 936       }
 937     }
 938     alignPanel.validateAnnotationDimensions(true);
 939     validate();
 940     repaint();
 941   }
 942
 943   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 944   {
 945     this.annotationSortOrder = order;
 946   }
 947
 948   /**
 949    * Set flags on the viewport that control annotation ordering
 950    */
 951   private void setViewportAnnotationOrder()
 952   {
 953     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 954     this.alignPanel.av
 955             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 956   }
 957
 958   private void setShowAutoCalculatedAbove(boolean showAbove)
 959   {
 960     this.showAutoCalculatedAbove = showAbove;
 961   }
 962
 963   private void mouseOverFlag_stateChanged()
 964   {
 965     viewport.setFollowHighlight(followMouseOverFlag.getState());
 966     // TODO: could kick the scrollTo mechanism to reset view for current
 967     // searchresults.
 968   }
 969
 970   private void centreColumnLabelFlag_stateChanged()
 971   {
 972     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 973     this.alignPanel.annotationPanel.repaint();
 974   }
 975
 976   @Override
 977   public void actionPerformed(ActionEvent evt)
 978   {
 979     viewport.applet.currentAlignFrame = this;
 980
 981     Object source = evt.getSource();
 982
 983     if (source == inputText)
 984     {
 985       inputText_actionPerformed();
 986     }
 987     else if (source == loadTree)
 988     {
 989       loadTree_actionPerformed();
 990     }
 991     else if (source == loadApplication)
 992     {
 993       launchFullApplication();
 994     }
 995     else if (source == loadAnnotations)
 996     {
 997       loadAnnotations();
 998     }
 999     else if (source == outputAnnotations)
1000     {
1001       outputAnnotations(true);
1002     }
1003     else if (source == outputFeatures)
1004     {
1005       outputFeatures(true, "Jalview");
1006     }
1007     else if (source == closeMenuItem)
1008     {
1009       closeMenuItem_actionPerformed();
1010     }
1011     else if (source == copy)
1012     {
1013       copy_actionPerformed();
1014     }
1015     else if (source == undoMenuItem)
1016     {
1017       undoMenuItem_actionPerformed();
1018     }
1019     else if (source == redoMenuItem)
1020     {
1021       redoMenuItem_actionPerformed();
1022     }
1023     else if (source == inputText)
1024     {
1025       inputText_actionPerformed();
1026     }
1027     else if (source == closeMenuItem)
1028     {
1029       closeMenuItem_actionPerformed();
1030     }
1031     else if (source == undoMenuItem)
1032     {
1033       undoMenuItem_actionPerformed();
1034     }
1035     else if (source == redoMenuItem)
1036     {
1037       redoMenuItem_actionPerformed();
1038     }
1039     else if (source == copy)
1040     {
1041       copy_actionPerformed();
1042     }
1043     else if (source == pasteNew)
1044     {
1045       pasteNew_actionPerformed();
1046     }
1047     else if (source == pasteThis)
1048     {
1049       pasteThis_actionPerformed();
1050     }
1051     else if (source == cut)
1052     {
1053       cut_actionPerformed();
1054     }
1055     else if (source == delete)
1056     {
1057       delete_actionPerformed();
1058     }
1059     else if (source == grpsFromSelection)
1060     {
1061       makeGrpsFromSelection_actionPerformed();
1062     }
1063     else if (source == deleteGroups)
1064     {
1065       deleteGroups_actionPerformed();
1066     }
1067     else if (source == selectAllSequenceMenuItem)
1068     {
1069       selectAllSequenceMenuItem_actionPerformed();
1070     }
1071     else if (source == deselectAllSequenceMenuItem)
1072     {
1073       deselectAllSequenceMenuItem_actionPerformed();
1074     }
1075     else if (source == invertSequenceMenuItem)
1076     {
1077       invertSequenceMenuItem_actionPerformed();
1078       // uncomment to slave sequence selections in split frame
1079       // viewport.sendSelection();
1080     }
1081     else if (source == invertColSel)
1082     {
1083       viewport.invertColumnSelection();
1084       alignPanel.paintAlignment(true);
1085       viewport.sendSelection();
1086     }
1087     else if (source == remove2LeftMenuItem)
1088     {
1089       trimAlignment(true);
1090     }
1091     else if (source == remove2RightMenuItem)
1092     {
1093       trimAlignment(false);
1094     }
1095     else if (source == removeGappedColumnMenuItem)
1096     {
1097       removeGappedColumnMenuItem_actionPerformed();
1098     }
1099     else if (source == removeAllGapsMenuItem)
1100     {
1101       removeAllGapsMenuItem_actionPerformed();
1102     }
1103     else if (source == findMenuItem)
1104     {
1105       findMenuItem_actionPerformed();
1106     }
1107     else if (source == font)
1108     {
1109       new FontChooser(alignPanel);
1110     }
1111     else if (source == newView)
1112     {
1113       newView(null);
1114     }
1115     else if (source == showColumns)
1116     {
1117       viewport.showAllHiddenColumns();
1118       alignPanel.paintAlignment(true);
1119       viewport.sendSelection();
1120     }
1121     else if (source == showSeqs)
1122     {
1123       viewport.showAllHiddenSeqs();
1124       alignPanel.paintAlignment(true);
1125       // uncomment if we want to slave sequence selections in split frame
1126       // viewport.sendSelection();
1127     }
1128     else if (source == hideColumns)
1129     {
1130       viewport.hideSelectedColumns();
1131       alignPanel.paintAlignment(true);
1132       viewport.sendSelection();
1133     }
1134     else if (source == hideSequences
1135             && viewport.getSelectionGroup() != null)
1136     {
1137       viewport.hideAllSelectedSeqs();
1138       alignPanel.paintAlignment(true);
1139       // uncomment if we want to slave sequence selections in split frame
1140       // viewport.sendSelection();
1141     }
1142     else if (source == hideAllButSelection)
1143     {
1144       toggleHiddenRegions(false, false);
1145       alignPanel.paintAlignment(true);
1146       viewport.sendSelection();
1147     }
1148     else if (source == hideAllSelection)
1149     {
1150       SequenceGroup sg = viewport.getSelectionGroup();
1151       viewport.expandColSelection(sg, false);
1152       viewport.hideAllSelectedSeqs();
1153       viewport.hideSelectedColumns();
1154       alignPanel.paintAlignment(true);
1155       viewport.sendSelection();
1156     }
1157     else if (source == showAllHidden)
1158     {
1159       viewport.showAllHiddenColumns();
1160       viewport.showAllHiddenSeqs();
1161       alignPanel.paintAlignment(true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == showGroupConsensus)
1165     {
1166       showGroupConsensus_actionPerformed();
1167     }
1168     else if (source == showGroupConservation)
1169     {
1170       showGroupConservation_actionPerformed();
1171     }
1172     else if (source == showSequenceLogo)
1173     {
1174       showSequenceLogo_actionPerformed();
1175     }
1176     else if (source == normSequenceLogo)
1177     {
1178       normSequenceLogo_actionPerformed();
1179     }
1180     else if (source == showConsensusHistogram)
1181     {
1182       showConsensusHistogram_actionPerformed();
1183     }
1184     else if (source == applyAutoAnnotationSettings)
1185     {
1186       applyAutoAnnotationSettings_actionPerformed();
1187     }
1188     else if (source == featureSettings)
1189     {
1190       new FeatureSettings(alignPanel);
1191     }
1192     else if (source == alProperties)
1193     {
1194       StringBuffer contents = new jalview.io.AlignmentProperties(
1195               viewport.getAlignment()).formatAsString();
1196       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1197       cap.setText(contents.toString());
1198       Frame frame = new Frame();
1199       frame.add(cap);
1200       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1201               "label.alignment_properties", new String[] { getTitle() }),
1202               400, 250);
1203     }
1204     else if (source == overviewMenuItem)
1205     {
1206       overviewMenuItem_actionPerformed();
1207     }
1208     else if (source == noColourmenuItem)
1209     {
1210       changeColour(null);
1211     }
1212     else if (source == clustalColour)
1213     {
1214       abovePIDThreshold.setState(false);
1215       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1216     }
1217     else if (source == zappoColour)
1218     {
1219       changeColour(new ZappoColourScheme());
1220     }
1221     else if (source == taylorColour)
1222     {
1223       changeColour(new TaylorColourScheme());
1224     }
1225     else if (source == hydrophobicityColour)
1226     {
1227       changeColour(new HydrophobicColourScheme());
1228     }
1229     else if (source == helixColour)
1230     {
1231       changeColour(new HelixColourScheme());
1232     }
1233     else if (source == strandColour)
1234     {
1235       changeColour(new StrandColourScheme());
1236     }
1237     else if (source == turnColour)
1238     {
1239       changeColour(new TurnColourScheme());
1240     }
1241     else if (source == buriedColour)
1242     {
1243       changeColour(new BuriedColourScheme());
1244     }
1245     else if (source == nucleotideColour)
1246     {
1247       changeColour(new NucleotideColourScheme());
1248     }
1249     else if (source == purinePyrimidineColour)
1250     {
1251       changeColour(new PurinePyrimidineColourScheme());
1252     }
1253     // else if (source == RNAInteractionColour)
1254     // {
1255     // changeColour(new RNAInteractionColourScheme());
1256     // }
1257     else if (source == RNAHelixColour)
1258     {
1259       new RNAHelicesColourChooser(viewport, alignPanel);
1260     }
1261     else if (source == modifyPID)
1262     {
1263       modifyPID_actionPerformed();
1264     }
1265     else if (source == modifyConservation)
1266     {
1267       modifyConservation_actionPerformed();
1268     }
1269     else if (source == userDefinedColour)
1270     {
1271       new UserDefinedColours(alignPanel, null);
1272     }
1273     else if (source == PIDColour)
1274     {
1275       changeColour(new PIDColourScheme());
1276     }
1277     else if (source == BLOSUM62Colour)
1278     {
1279       changeColour(new Blosum62ColourScheme());
1280     }
1281     else if (source == tcoffeeColour)
1282     {
1283       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1284     }
1285     else if (source == annotationColour)
1286     {
1287       new AnnotationColourChooser(viewport, alignPanel);
1288     }
1289     else if (source == annotationColumnSelection)
1290     {
1291       new AnnotationColumnChooser(viewport, alignPanel);
1292     }
1293     else if (source == sortPairwiseMenuItem)
1294     {
1295       sortPairwiseMenuItem_actionPerformed();
1296     }
1297     else if (source == sortIDMenuItem)
1298     {
1299       sortIDMenuItem_actionPerformed();
1300     }
1301     else if (source == sortLengthMenuItem)
1302     {
1303       sortLengthMenuItem_actionPerformed();
1304     }
1305     else if (source == sortGroupMenuItem)
1306     {
1307       sortGroupMenuItem_actionPerformed();
1308     }
1309     else if (source == removeRedundancyMenuItem)
1310     {
1311       removeRedundancyMenuItem_actionPerformed();
1312     }
1313     else if (source == pairwiseAlignmentMenuItem)
1314     {
1315       pairwiseAlignmentMenuItem_actionPerformed();
1316     }
1317     else if (source == PCAMenuItem)
1318     {
1319       PCAMenuItem_actionPerformed();
1320     }
1321     else if (source == averageDistanceTreeMenuItem)
1322     {
1323       averageDistanceTreeMenuItem_actionPerformed();
1324     }
1325     else if (source == neighbourTreeMenuItem)
1326     {
1327       neighbourTreeMenuItem_actionPerformed();
1328     }
1329     else if (source == njTreeBlosumMenuItem)
1330     {
1331       njTreeBlosumMenuItem_actionPerformed();
1332     }
1333     else if (source == avDistanceTreeBlosumMenuItem)
1334     {
1335       avTreeBlosumMenuItem_actionPerformed();
1336     }
1337     else if (source == documentation)
1338     {
1339       documentation_actionPerformed();
1340     }
1341     else if (source == about)
1342     {
1343       about_actionPerformed();
1344     }
1345
1346   }
1347
1348   public void inputText_actionPerformed()
1349   {
1350     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1351     Frame frame = new Frame();
1352     frame.add(cap);
1353     jalview.bin.JalviewLite.addFrame(frame,
1354             MessageManager.getString("label.input_cut_paste"), 500, 500);
1355   }
1356
1357   protected void outputText_actionPerformed(ActionEvent e)
1358   {
1359     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1360     Frame frame = new Frame();
1361     frame.add(cap);
1362     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1363             "label.alignment_output_command",
1364             new Object[] { e.getActionCommand() }), 600, 500);
1365
1366     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1367     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1368             e.getActionCommand(), viewport.getAlignment(),
1369             viewport.getShowJVSuffix()));
1370   }
1371
1372   public void loadAnnotations()
1373   {
1374     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1375     cap.setText(MessageManager
1376             .getString("label.paste_features_annotations_Tcoffee_here"));
1377     cap.setAnnotationImport();
1378     Frame frame = new Frame();
1379     frame.add(cap);
1380     jalview.bin.JalviewLite.addFrame(frame,
1381             MessageManager.getString("action.paste_annotations"), 400, 300);
1382
1383   }
1384
1385   public String outputAnnotations(boolean displayTextbox)
1386   {
1387     String annotation = new AnnotationFile()
1388             .printAnnotationsForView(viewport);
1389
1390     if (displayTextbox)
1391     {
1392       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1393       Frame frame = new Frame();
1394       frame.add(cap);
1395       jalview.bin.JalviewLite.addFrame(frame,
1396               MessageManager.getString("label.annotations"), 600, 500);
1397       cap.setText(annotation);
1398     }
1399
1400     return annotation;
1401   }
1402
1403   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1404   {
1405     if (alignPanel.getFeatureRenderer() != null
1406             && viewport.getFeaturesDisplayed() != null)
1407     {
1408       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1409
1410     }
1411     return null;
1412   }
1413
1414   public String outputFeatures(boolean displayTextbox, String format)
1415   {
1416     String features;
1417     FeaturesFile formatter = new FeaturesFile();
1418     if (format.equalsIgnoreCase("Jalview"))
1419     {
1420       features = formatter.printJalviewFormat(viewport
1421               .getAlignment().getSequencesArray(),
1422               getDisplayedFeatureCols());
1423     }
1424     else
1425     {
1426       features = formatter.printGffFormat(viewport.getAlignment()
1427               .getSequencesArray(), getDisplayedFeatureCols());
1428     }
1429
1430     if (displayTextbox)
1431     {
1432       boolean frimport = false;
1433       if (features == null || features.equals("No Features Visible"))
1434       {
1435         features = "# No features visible - paste some and import them here.";
1436         frimport = true;
1437       }
1438
1439       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1440       if (frimport)
1441       {
1442         cap.setAnnotationImport();
1443       }
1444       Frame frame = new Frame();
1445       frame.add(cap);
1446       jalview.bin.JalviewLite.addFrame(frame,
1447               MessageManager.getString("label.features"), 600, 500);
1448       cap.setText(features);
1449     }
1450     else
1451     {
1452       if (features == null)
1453       {
1454         features = "";
1455       }
1456     }
1457
1458     return features;
1459   }
1460
1461   void launchFullApplication()
1462   {
1463     StringBuffer url = new StringBuffer(jalviewServletURL);
1464
1465     // allow servlet parameters to be passed in applet parameter
1466     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1467             : "?";
1468     url.append(firstSep);
1469
1470     url.append("open="
1471             + appendProtocol(viewport.applet.getParameter("file")));
1472
1473     if (viewport.applet.getParameter("features") != null)
1474     {
1475       url.append("&features=");
1476       url.append(appendProtocol(viewport.applet.getParameter("features")));
1477     }
1478
1479     if (viewport.applet.getParameter("annotations") != null)
1480     {
1481       url.append("&annotations=");
1482       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1483     }
1484
1485     if (viewport.applet.getParameter("jnetfile") != null)
1486     {
1487       url.append("&annotations=");
1488       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1489     }
1490
1491     if (viewport.applet.getParameter("defaultColour") != null)
1492     {
1493       url.append("&colour="
1494               + removeWhiteSpace(viewport.applet
1495                       .getParameter("defaultColour")));
1496     }
1497
1498     if (viewport.applet.getParameter("userDefinedColour") != null)
1499     {
1500       url.append("&colour="
1501               + removeWhiteSpace(viewport.applet
1502                       .getParameter("userDefinedColour")));
1503     }
1504     if (viewport.applet.getParameter("tree") != null)
1505     {
1506       url.append("&tree="
1507               + appendProtocol(viewport.applet.getParameter("tree")));
1508     }
1509     if (viewport.applet.getParameter("treeFile") != null)
1510     {
1511       url.append("&tree="
1512               + appendProtocol(viewport.applet.getParameter("treeFile")));
1513     }
1514
1515     showURL(url.toString(), "FULL_APP");
1516   }
1517
1518   String removeWhiteSpace(String colour)
1519   {
1520     StringBuffer sb = new StringBuffer();
1521     for (int i = 0; i < colour.length(); i++)
1522     {
1523       if (Character.isWhitespace(colour.charAt(i)))
1524       {
1525         sb.append("%20");
1526       }
1527       else
1528       {
1529         sb.append(colour.charAt(i));
1530       }
1531     }
1532
1533     return sb.toString();
1534   }
1535
1536   String appendProtocol(String url)
1537   {
1538     try
1539     {
1540       new URL(url);
1541       url = URLEncoder.encode(url);
1542     }
1543     /*
1544      * When we finally deprecate 1.1 compatibility, we can start to use
1545      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1546      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1547      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1548      * ex.printStackTrace(); }
1549      */
1550     catch (java.net.MalformedURLException ex)
1551     {
1552       url = viewport.applet.getCodeBase() + url;
1553     }
1554     return url;
1555   }
1556
1557   public void closeMenuItem_actionPerformed()
1558   {
1559     PaintRefresher.RemoveComponent(alignPanel);
1560     if (alignPanel.seqPanel != null
1561             && alignPanel.seqPanel.seqCanvas != null)
1562     {
1563       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1564     }
1565     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1566     {
1567       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1568     }
1569
1570     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1571     {
1572       System.exit(0);
1573     }
1574     else
1575     {
1576     }
1577     viewport = null;
1578     alignPanel = null;
1579     this.dispose();
1580   }
1581
1582   /**
1583    * TODO: JAL-1104
1584    */
1585   void updateEditMenuBar()
1586   {
1587
1588     if (viewport.getHistoryList().size() > 0)
1589     {
1590       undoMenuItem.setEnabled(true);
1591       CommandI command = viewport.getHistoryList().peek();
1592       undoMenuItem.setLabel(MessageManager.formatMessage(
1593               "label.undo_command",
1594               new Object[] { command.getDescription() }));
1595     }
1596     else
1597     {
1598       undoMenuItem.setEnabled(false);
1599       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1600     }
1601
1602     if (viewport.getRedoList().size() > 0)
1603     {
1604       redoMenuItem.setEnabled(true);
1605
1606       CommandI command = viewport.getRedoList().peek();
1607       redoMenuItem.setLabel(MessageManager.formatMessage(
1608               "label.redo_command",
1609               new Object[] { command.getDescription() }));
1610     }
1611     else
1612     {
1613       redoMenuItem.setEnabled(false);
1614       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1615     }
1616   }
1617
1618   /**
1619    * TODO: JAL-1104
1620    */
1621   @Override
1622   public void addHistoryItem(CommandI command)
1623   {
1624     if (command.getSize() > 0)
1625     {
1626       viewport.addToHistoryList(command);
1627       viewport.clearRedoList();
1628       updateEditMenuBar();
1629       viewport.updateHiddenColumns();
1630     }
1631   }
1632
1633   /**
1634    * TODO: JAL-1104 DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   protected void undoMenuItem_actionPerformed()
1640   {
1641     if (viewport.getHistoryList().isEmpty())
1642     {
1643       return;
1644     }
1645
1646     CommandI command = viewport.getHistoryList().pop();
1647     viewport.addToRedoList(command);
1648     command.undoCommand(null);
1649
1650     AlignmentViewport originalSource = getOriginatingSource(command);
1651     // JBPNote Test
1652     if (originalSource != viewport)
1653     {
1654       System.err
1655               .println("Warning: Viewport object mismatch whilst undoing");
1656     }
1657     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1658                                           // viewport.getColumnSelection().getHiddenColumns()
1659                                           // != null;
1660     updateEditMenuBar();
1661     originalSource.firePropertyChange("alignment", null, originalSource
1662             .getAlignment().getSequences());
1663   }
1664
1665   /**
1666    * TODO: JAL-1104 DOCUMENT ME!
1667    *
1668    * @param e
1669    *          DOCUMENT ME!
1670    */
1671   protected void redoMenuItem_actionPerformed()
1672   {
1673     if (viewport.getRedoList().isEmpty())
1674     {
1675       return;
1676     }
1677
1678     CommandI command = viewport.getRedoList().pop();
1679     viewport.addToHistoryList(command);
1680     command.doCommand(null);
1681
1682     AlignmentViewport originalSource = getOriginatingSource(command);
1683     // JBPNote Test
1684     if (originalSource != viewport)
1685     {
1686       System.err
1687               .println("Warning: Viewport object mismatch whilst re-doing");
1688     }
1689     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1690                                           // viewport.getColumnSelection().getHiddenColumns()
1691                                           // != null;
1692
1693     updateEditMenuBar();
1694     originalSource.firePropertyChange("alignment", null, originalSource
1695             .getAlignment().getSequences());
1696   }
1697
1698   AlignmentViewport getOriginatingSource(CommandI command)
1699   {
1700     AlignmentViewport originalSource = null;
1701     // For sequence removal and addition, we need to fire
1702     // the property change event FROM the viewport where the
1703     // original alignment was altered
1704     AlignmentI al = null;
1705     if (command instanceof EditCommand)
1706     {
1707       EditCommand editCommand = (EditCommand) command;
1708       al = editCommand.getAlignment();
1709       Vector comps = (Vector) PaintRefresher.components.get(viewport
1710               .getSequenceSetId());
1711       for (int i = 0; i < comps.size(); i++)
1712       {
1713         if (comps.elementAt(i) instanceof AlignmentPanel)
1714         {
1715           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1716           {
1717             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1718             break;
1719           }
1720         }
1721       }
1722     }
1723
1724     if (originalSource == null)
1725     {
1726       // The original view is closed, we must validate
1727       // the current view against the closed view first
1728       if (al != null)
1729       {
1730         PaintRefresher.validateSequences(al, viewport.getAlignment());
1731       }
1732
1733       originalSource = viewport;
1734     }
1735
1736     return originalSource;
1737   }
1738
1739   /**
1740    * Move the currently selected sequences up or down one position in the
1741    * alignment
1742    *
1743    * @param up
1744    */
1745   public void moveSelectedSequences(boolean up)
1746   {
1747     SequenceGroup sg = viewport.getSelectionGroup();
1748     if (sg == null)
1749     {
1750       return;
1751     }
1752     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753             up ? null : viewport.getHiddenRepSequences(), up);
1754     alignPanel.paintAlignment(true);
1755
1756     /*
1757      * Also move cDNA/protein complement sequences
1758      */
1759     AlignViewportI complement = viewport.getCodingComplement();
1760     if (complement != null)
1761     {
1762       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1763               viewport, complement);
1764       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1765               up ? null : complement.getHiddenRepSequences(), up);
1766       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1767     }
1768   }
1769
1770   synchronized void slideSequences(boolean right, int size)
1771   {
1772     List<SequenceI> sg = new Vector<SequenceI>();
1773     if (viewport.cursorMode)
1774     {
1775       sg.add(viewport.getAlignment().getSequenceAt(
1776               alignPanel.seqPanel.seqCanvas.cursorY));
1777     }
1778     else if (viewport.getSelectionGroup() != null
1779             && viewport.getSelectionGroup().getSize() != viewport
1780                     .getAlignment().getHeight())
1781     {
1782       sg = viewport.getSelectionGroup().getSequences(
1783               viewport.getHiddenRepSequences());
1784     }
1785
1786     if (sg.size() < 1)
1787     {
1788       return;
1789     }
1790
1791     Vector<SequenceI> invertGroup = new Vector();
1792
1793     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1794     {
1795       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1796       {
1797         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1798       }
1799     }
1800
1801     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1802
1803     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1804             .size()]);
1805     for (int i = 0; i < invertGroup.size(); i++)
1806     {
1807       seqs2[i] = invertGroup.elementAt(i);
1808     }
1809
1810     SlideSequencesCommand ssc;
1811     if (right)
1812     {
1813       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1814               size, viewport.getGapCharacter());
1815     }
1816     else
1817     {
1818       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1819               size, viewport.getGapCharacter());
1820     }
1821
1822     int groupAdjustment = 0;
1823     if (ssc.getGapsInsertedBegin() && right)
1824     {
1825       if (viewport.cursorMode)
1826       {
1827         alignPanel.seqPanel.moveCursor(size, 0);
1828       }
1829       else
1830       {
1831         groupAdjustment = size;
1832       }
1833     }
1834     else if (!ssc.getGapsInsertedBegin() && !right)
1835     {
1836       if (viewport.cursorMode)
1837       {
1838         alignPanel.seqPanel.moveCursor(-size, 0);
1839       }
1840       else
1841       {
1842         groupAdjustment = -size;
1843       }
1844     }
1845
1846     if (groupAdjustment != 0)
1847     {
1848       viewport.getSelectionGroup().setStartRes(
1849               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1850       viewport.getSelectionGroup().setEndRes(
1851               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1852     }
1853
1854     boolean appendHistoryItem = false;
1855     Deque<CommandI> historyList = viewport.getHistoryList();
1856     if (historyList != null && historyList.size() > 0
1857             && historyList.peek() instanceof SlideSequencesCommand)
1858     {
1859       appendHistoryItem = ssc
1860               .appendSlideCommand((SlideSequencesCommand) historyList
1861                       .peek());
1862     }
1863
1864     if (!appendHistoryItem)
1865     {
1866       addHistoryItem(ssc);
1867     }
1868
1869     repaint();
1870   }
1871
1872   static StringBuffer copiedSequences;
1873
1874   static Vector copiedHiddenColumns;
1875
1876   protected void copy_actionPerformed()
1877   {
1878     if (viewport.getSelectionGroup() == null)
1879     {
1880       return;
1881     }
1882
1883     SequenceGroup sg = viewport.getSelectionGroup();
1884     copiedSequences = new StringBuffer();
1885     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1886     for (int i = 0; i < sg.getSize(); i++)
1887     {
1888       SequenceI seq = sg.getSequenceAt(i);
1889       int index = viewport.getAlignment().findIndex(seq);
1890       orderedSeqs.put(index, seq);
1891     }
1892
1893     int index = 0, startRes, endRes;
1894     char ch;
1895
1896     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1897     {
1898       copiedHiddenColumns = new Vector();
1899       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1900       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1901       {
1902         copiedHiddenColumns.addElement(new int[] {
1903             region[0] - hiddenOffset, region[1] - hiddenOffset });
1904       }
1905     }
1906     else
1907     {
1908       copiedHiddenColumns = null;
1909     }
1910
1911     for (int i = 0; i < sg.getSize(); i++)
1912     {
1913       SequenceI seq = null;
1914
1915       while (seq == null)
1916       {
1917         if (orderedSeqs.containsKey(index))
1918         {
1919           seq = orderedSeqs.get(index);
1920           index++;
1921           break;
1922         }
1923         else
1924         {
1925           index++;
1926         }
1927       }
1928
1929       // FIND START RES
1930       // Returns residue following index if gap
1931       startRes = seq.findPosition(sg.getStartRes());
1932
1933       // FIND END RES
1934       // Need to find the residue preceeding index if gap
1935       endRes = 0;
1936
1937       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1938       {
1939         ch = seq.getCharAt(j);
1940         if (!jalview.util.Comparison.isGap((ch)))
1941         {
1942           endRes++;
1943         }
1944       }
1945
1946       if (endRes > 0)
1947       {
1948         endRes += seq.getStart() - 1;
1949       }
1950
1951       copiedSequences.append(seq.getName()
1952               + "\t"
1953               + startRes
1954               + "\t"
1955               + endRes
1956               + "\t"
1957               + seq.getSequenceAsString(sg.getStartRes(),
1958                       sg.getEndRes() + 1) + "\n");
1959     }
1960
1961   }
1962
1963   protected void pasteNew_actionPerformed()
1964   {
1965     paste(true);
1966   }
1967
1968   protected void pasteThis_actionPerformed()
1969   {
1970     paste(false);
1971   }
1972
1973   void paste(boolean newAlignment)
1974   {
1975     try
1976     {
1977
1978       if (copiedSequences == null)
1979       {
1980         return;
1981       }
1982
1983       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1984       Vector seqs = new Vector();
1985       while (st.hasMoreElements())
1986       {
1987         String name = st.nextToken();
1988         int start = Integer.parseInt(st.nextToken());
1989         int end = Integer.parseInt(st.nextToken());
1990         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1991       }
1992       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1993       for (int i = 0; i < seqs.size(); i++)
1994       {
1995         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1996       }
1997
1998       if (newAlignment)
1999       {
2000         String newtitle = MessageManager
2001                 .getString("label.copied_sequences");
2002         if (getTitle().startsWith(
2003                 MessageManager.getString("label.copied_sequences")))
2004         {
2005           newtitle = getTitle();
2006         }
2007         else
2008         {
2009           newtitle = newtitle.concat(MessageManager.formatMessage(
2010                   "label.from_msname", new String[] { getTitle() }));
2011         }
2012         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2013                 viewport.applet, newtitle, false);
2014         if (copiedHiddenColumns != null)
2015         {
2016           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2017           {
2018             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2019             af.viewport.hideColumns(region[0], region[1]);
2020           }
2021         }
2022
2023         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2024                 frameHeight);
2025       }
2026       else
2027       {
2028         addSequences(newSeqs);
2029       }
2030
2031     } catch (Exception ex)
2032     {
2033     } // could be anything being pasted in here
2034
2035   }
2036
2037   void addSequences(SequenceI[] seqs)
2038   {
2039     for (int i = 0; i < seqs.length; i++)
2040     {
2041       viewport.getAlignment().addSequence(seqs[i]);
2042     }
2043
2044     // !newAlignment
2045     addHistoryItem(new EditCommand(
2046             MessageManager.getString("label.add_sequences"), Action.PASTE,
2047             seqs, 0, viewport.getAlignment().getWidth(),
2048             viewport.getAlignment()));
2049
2050     viewport.setEndSeq(viewport.getAlignment().getHeight());
2051     viewport.getAlignment().getWidth();
2052     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2053             .getSequences());
2054
2055   }
2056
2057   protected void cut_actionPerformed()
2058   {
2059     copy_actionPerformed();
2060     delete_actionPerformed();
2061   }
2062
2063   protected void delete_actionPerformed()
2064   {
2065
2066     SequenceGroup sg = viewport.getSelectionGroup();
2067     if (sg == null)
2068     {
2069       return;
2070     }
2071
2072     Vector seqs = new Vector();
2073     SequenceI seq;
2074     for (int i = 0; i < sg.getSize(); i++)
2075     {
2076       seq = sg.getSequenceAt(i);
2077       seqs.addElement(seq);
2078     }
2079
2080     /*
2081      * If the cut affects all sequences, warn, remove highlighted columns
2082      */
2083     if (sg.getSize() == viewport.getAlignment().getHeight())
2084     {
2085       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2086               .getAlignment().getWidth()) ? true : false;
2087       if (isEntireAlignWidth)
2088       {
2089         String title = MessageManager.getString("label.delete_all");
2090         Panel infoPanel = new Panel();
2091         infoPanel.setLayout(new FlowLayout());
2092         infoPanel
2093                 .add(new Label(MessageManager.getString("warn.delete_all")));
2094
2095         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2096         dialog.setMainPanel(infoPanel);
2097         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2098         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2099         dialog.setVisible(true);
2100
2101         if (!dialog.accept)
2102         {
2103           return;
2104         }
2105       }
2106       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2107               sg.getEndRes() + 1);
2108     }
2109
2110     SequenceI[] cut = new SequenceI[seqs.size()];
2111     for (int i = 0; i < seqs.size(); i++)
2112     {
2113       cut[i] = (SequenceI) seqs.elementAt(i);
2114     }
2115
2116     /*
2117      * //ADD HISTORY ITEM
2118      */
2119     addHistoryItem(new EditCommand(
2120             MessageManager.getString("label.cut_sequences"), Action.CUT,
2121             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2122             viewport.getAlignment()));
2123
2124     viewport.setSelectionGroup(null);
2125     viewport.getAlignment().deleteGroup(sg);
2126
2127     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2128             .getSequences());
2129
2130     if (viewport.getAlignment().getHeight() < 1)
2131     {
2132       this.setVisible(false);
2133     }
2134     viewport.sendSelection();
2135   }
2136
2137   /**
2138    * group consensus toggled
2139    *
2140    */
2141   protected void showGroupConsensus_actionPerformed()
2142   {
2143     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2144     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145
2146   }
2147
2148   /**
2149    * group conservation toggled.
2150    */
2151   protected void showGroupConservation_actionPerformed()
2152   {
2153     viewport.setShowGroupConservation(showGroupConservation.getState());
2154     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2155   }
2156
2157   /*
2158    * (non-Javadoc)
2159    *
2160    * @see
2161    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2162    * .event.ActionEvent)
2163    */
2164   protected void showConsensusHistogram_actionPerformed()
2165   {
2166     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2167     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2168   }
2169
2170   /*
2171    * (non-Javadoc)
2172    *
2173    * @see
2174    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2175    * .event.ActionEvent)
2176    */
2177   protected void showSequenceLogo_actionPerformed()
2178   {
2179     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2180     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181   }
2182
2183   protected void normSequenceLogo_actionPerformed()
2184   {
2185     showSequenceLogo.setState(true);
2186     viewport.setShowSequenceLogo(true);
2187     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2188     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2189   }
2190
2191   protected void applyAutoAnnotationSettings_actionPerformed()
2192   {
2193     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2194   }
2195
2196   protected void makeGrpsFromSelection_actionPerformed()
2197   {
2198     if (avc.makeGroupsFromSelection())
2199     {
2200       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2201       alignPanel.updateAnnotation();
2202       alignPanel.paintAlignment(true);
2203     }
2204   }
2205
2206   protected void createGroup_actionPerformed()
2207   {
2208     avc.createGroup();
2209   }
2210
2211   protected void unGroup_actionPerformed()
2212   {
2213     if (avc.unGroup())
2214     {
2215       alignPanel.alignmentChanged();
2216     }
2217   }
2218
2219   protected void deleteGroups_actionPerformed()
2220   {
2221     if (avc.deleteGroups())
2222     {
2223       alignPanel.alignmentChanged();
2224     }
2225   }
2226
2227   public void selectAllSequenceMenuItem_actionPerformed()
2228   {
2229     SequenceGroup sg = new SequenceGroup();
2230     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2231     {
2232       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2233     }
2234     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2235     viewport.setSelectionGroup(sg);
2236     alignPanel.paintAlignment(true);
2237     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2238     viewport.sendSelection();
2239   }
2240
2241   public void deselectAllSequenceMenuItem_actionPerformed()
2242   {
2243     if (viewport.cursorMode)
2244     {
2245       alignPanel.seqPanel.keyboardNo1 = null;
2246       alignPanel.seqPanel.keyboardNo2 = null;
2247     }
2248     viewport.setSelectionGroup(null);
2249     viewport.getColumnSelection().clear();
2250     viewport.setSelectionGroup(null);
2251     alignPanel.idPanel.idCanvas.searchResults = null;
2252     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2253     alignPanel.paintAlignment(true);
2254     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2255     viewport.sendSelection();
2256   }
2257
2258   public void invertSequenceMenuItem_actionPerformed()
2259   {
2260     SequenceGroup sg = viewport.getSelectionGroup();
2261     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2262     {
2263       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2264     }
2265
2266     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2267     viewport.sendSelection();
2268   }
2269
2270   public void invertColSel_actionPerformed()
2271   {
2272     viewport.invertColumnSelection();
2273     alignPanel.paintAlignment(true);
2274     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2275     viewport.sendSelection();
2276   }
2277
2278   void trimAlignment(boolean trimLeft)
2279   {
2280     ColumnSelection colSel = viewport.getColumnSelection();
2281     int column;
2282
2283     if (!colSel.isEmpty())
2284     {
2285       if (trimLeft)
2286       {
2287         column = colSel.getMin();
2288       }
2289       else
2290       {
2291         column = colSel.getMax();
2292       }
2293
2294       SequenceI[] seqs;
2295       if (viewport.getSelectionGroup() != null)
2296       {
2297         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2298                 viewport.getHiddenRepSequences());
2299       }
2300       else
2301       {
2302         seqs = viewport.getAlignment().getSequencesArray();
2303       }
2304
2305       TrimRegionCommand trimRegion;
2306       if (trimLeft)
2307       {
2308         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2309                 column, viewport.getAlignment());
2310         viewport.setStartRes(0);
2311       }
2312       else
2313       {
2314         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2315                 column, viewport.getAlignment());
2316       }
2317
2318       statusBar.setText(MessageManager.formatMessage(
2319               "label.removed_columns",
2320               new String[] { Integer.valueOf(trimRegion.getSize())
2321                       .toString() }));
2322       addHistoryItem(trimRegion);
2323
2324       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2325       {
2326         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2327                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2328         {
2329           viewport.getAlignment().deleteGroup(sg);
2330         }
2331       }
2332
2333       viewport.firePropertyChange("alignment", null, viewport
2334               .getAlignment().getSequences());
2335     }
2336   }
2337
2338   public void removeGappedColumnMenuItem_actionPerformed()
2339   {
2340     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2341
2342     SequenceI[] seqs;
2343     if (viewport.getSelectionGroup() != null)
2344     {
2345       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2346               viewport.getHiddenRepSequences());
2347       start = viewport.getSelectionGroup().getStartRes();
2348       end = viewport.getSelectionGroup().getEndRes();
2349     }
2350     else
2351     {
2352       seqs = viewport.getAlignment().getSequencesArray();
2353     }
2354
2355     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2356             "Remove Gapped Columns", seqs, start, end,
2357             viewport.getAlignment());
2358
2359     addHistoryItem(removeGapCols);
2360
2361     statusBar.setText(MessageManager.formatMessage(
2362             "label.removed_empty_columns",
2363             new String[] { Integer.valueOf(removeGapCols.getSize())
2364                     .toString() }));
2365
2366     // This is to maintain viewport position on first residue
2367     // of first sequence
2368     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2369     int startRes = seq.findPosition(viewport.startRes);
2370     // ShiftList shifts;
2371     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2372     // edit.alColumnChanges=shifts.getInverse();
2373     // if (viewport.hasHiddenColumns)
2374     // viewport.getColumnSelection().compensateForEdits(shifts);
2375     viewport.setStartRes(seq.findIndex(startRes) - 1);
2376     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2377             .getSequences());
2378
2379   }
2380
2381   public void removeAllGapsMenuItem_actionPerformed()
2382   {
2383     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2384
2385     SequenceI[] seqs;
2386     if (viewport.getSelectionGroup() != null)
2387     {
2388       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2389               viewport.getHiddenRepSequences());
2390       start = viewport.getSelectionGroup().getStartRes();
2391       end = viewport.getSelectionGroup().getEndRes();
2392     }
2393     else
2394     {
2395       seqs = viewport.getAlignment().getSequencesArray();
2396     }
2397
2398     // This is to maintain viewport position on first residue
2399     // of first sequence
2400     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2401     int startRes = seq.findPosition(viewport.startRes);
2402
2403     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2404             viewport.getAlignment()));
2405
2406     viewport.setStartRes(seq.findIndex(startRes) - 1);
2407
2408     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2409             .getSequences());
2410
2411   }
2412
2413   public void findMenuItem_actionPerformed()
2414   {
2415     new Finder(alignPanel);
2416   }
2417
2418   /**
2419    * create a new view derived from the current view
2420    *
2421    * @param viewtitle
2422    * @return frame for the new view
2423    */
2424   public AlignFrame newView(String viewtitle)
2425   {
2426     AlignmentI newal;
2427     if (viewport.hasHiddenRows())
2428     {
2429       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2430               .getFullAlignment().getSequencesArray());
2431     }
2432     else
2433     {
2434       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2435     }
2436
2437     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2438     {
2439       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2440       {
2441         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2442         {
2443           newal.addAnnotation(viewport.getAlignment()
2444                   .getAlignmentAnnotation()[i]);
2445         }
2446       }
2447     }
2448
2449     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2450
2451     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2452     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2453     PaintRefresher.Register(newaf.alignPanel,
2454             newaf.alignPanel.av.getSequenceSetId());
2455
2456     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2457             newaf.alignPanel.av.getSequenceSetId());
2458     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2459             newaf.alignPanel.av.getSequenceSetId());
2460
2461     Vector comps = (Vector) PaintRefresher.components.get(viewport
2462             .getSequenceSetId());
2463     int viewSize = -1;
2464     for (int i = 0; i < comps.size(); i++)
2465     {
2466       if (comps.elementAt(i) instanceof AlignmentPanel)
2467       {
2468         viewSize++;
2469       }
2470     }
2471
2472     String title = new String(this.getTitle());
2473     if (viewtitle != null)
2474     {
2475       title = viewtitle + " ( " + title + ")";
2476     }
2477     else
2478     {
2479       if (title.indexOf("(View") > -1)
2480       {
2481         title = title.substring(0, title.indexOf("(View"));
2482       }
2483       title += "(View " + viewSize + ")";
2484     }
2485
2486     newaf.setTitle(title.toString());
2487
2488     newaf.viewport.setHistoryList(viewport.getHistoryList());
2489     newaf.viewport.setRedoList(viewport.getRedoList());
2490     return newaf;
2491   }
2492
2493   /**
2494    *
2495    * @return list of feature groups on the view
2496    */
2497   public String[] getFeatureGroups()
2498   {
2499     FeatureRenderer fr = null;
2500     if (alignPanel != null
2501             && (fr = alignPanel.getFeatureRenderer()) != null)
2502     {
2503       List<String> gps = fr.getFeatureGroups();
2504       String[] _gps = gps.toArray(new String[gps.size()]);
2505       return _gps;
2506     }
2507     return null;
2508   }
2509
2510   /**
2511    * get sequence feature groups that are hidden or shown
2512    *
2513    * @param visible
2514    *          true is visible
2515    * @return list
2516    */
2517   public String[] getFeatureGroupsOfState(boolean visible)
2518   {
2519     FeatureRenderer fr = null;
2520     if (alignPanel != null
2521             && (fr = alignPanel.getFeatureRenderer()) != null)
2522     {
2523       List<String> gps = fr.getGroups(visible);
2524       String[] _gps = gps.toArray(new String[gps.size()]);
2525       return _gps;
2526     }
2527     return null;
2528   }
2529
2530   /**
2531    * Change the display state for the given feature groups
2532    *
2533    * @param groups
2534    *          list of group strings
2535    * @param state
2536    *          visible or invisible
2537    */
2538   public void setFeatureGroupState(String[] groups, boolean state)
2539   {
2540     FeatureRenderer fr = null;
2541     this.sequenceFeatures.setState(true);
2542     viewport.setShowSequenceFeatures(true);
2543     if (alignPanel != null
2544             && (fr = alignPanel.getFeatureRenderer()) != null)
2545     {
2546
2547       fr.setGroupVisibility(Arrays.asList(groups), state);
2548       alignPanel.seqPanel.seqCanvas.repaint();
2549       if (alignPanel.overviewPanel != null)
2550       {
2551         alignPanel.overviewPanel.updateOverviewImage();
2552       }
2553     }
2554   }
2555
2556   public void seqLimits_itemStateChanged()
2557   {
2558     viewport.setShowJVSuffix(seqLimits.getState());
2559     alignPanel.fontChanged();
2560     alignPanel.paintAlignment(true);
2561   }
2562
2563   protected void colourTextMenuItem_actionPerformed()
2564   {
2565     viewport.setColourText(colourTextMenuItem.getState());
2566     alignPanel.paintAlignment(true);
2567   }
2568
2569   protected void displayNonconservedMenuItem_actionPerformed()
2570   {
2571     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2572     alignPanel.paintAlignment(true);
2573   }
2574
2575   protected void wrapMenuItem_actionPerformed()
2576   {
2577     viewport.setWrapAlignment(wrapMenuItem.getState());
2578     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2579     scaleAbove.setEnabled(wrapMenuItem.getState());
2580     scaleLeft.setEnabled(wrapMenuItem.getState());
2581     scaleRight.setEnabled(wrapMenuItem.getState());
2582     alignPanel.paintAlignment(true);
2583   }
2584
2585   public void overviewMenuItem_actionPerformed()
2586   {
2587     if (alignPanel.overviewPanel != null)
2588     {
2589       return;
2590     }
2591
2592     Frame frame = new Frame();
2593     OverviewPanel overview = new OverviewPanel(alignPanel);
2594     frame.add(overview);
2595     // +50 must allow for applet frame window
2596     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2597             "label.overview_params", new String[] { this.getTitle() }),
2598             overview.getPreferredSize().width,
2599             overview.getPreferredSize().height + 50);
2600
2601     frame.pack();
2602     final AlignmentPanel ap = alignPanel;
2603     frame.addWindowListener(new WindowAdapter()
2604     {
2605       @Override
2606       public void windowClosing(WindowEvent e)
2607       {
2608         if (ap != null)
2609         {
2610           ap.setOverviewPanel(null);
2611         }
2612       };
2613     });
2614
2615     alignPanel.setOverviewPanel(overview);
2616
2617   }
2618
2619   @Override
2620   public void changeColour(ColourSchemeI cs)
2621   {
2622
2623     if (cs != null)
2624     {
2625       if (viewport.getAbovePIDThreshold())
2626       {
2627         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2628                 cs, "Background"));
2629       }
2630
2631       if (viewport.getConservationSelected())
2632       {
2633         cs.setConservationApplied(true);
2634         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2635                 cs, "Background"));
2636       }
2637       else
2638       {
2639         cs.setConservationApplied(false);
2640       }
2641     }
2642     viewport.setGlobalColourScheme(cs);
2643
2644     alignPanel.paintAlignment(true);
2645   }
2646
2647   protected void modifyPID_actionPerformed()
2648   {
2649     if (viewport.getAbovePIDThreshold()
2650             && viewport.getGlobalColourScheme() != null)
2651     {
2652       SliderPanel.setPIDSliderSource(alignPanel,
2653               viewport.getGlobalColourScheme(), "Background");
2654       SliderPanel.showPIDSlider();
2655     }
2656   }
2657
2658   protected void modifyConservation_actionPerformed()
2659   {
2660     if (viewport.getConservationSelected()
2661             && viewport.getGlobalColourScheme() != null)
2662     {
2663       SliderPanel.setConservationSlider(alignPanel,
2664               viewport.getGlobalColourScheme(), "Background");
2665       SliderPanel.showConservationSlider();
2666     }
2667   }
2668
2669   protected void conservationMenuItem_actionPerformed()
2670   {
2671     viewport.setConservationSelected(conservationMenuItem.getState());
2672
2673     viewport.setAbovePIDThreshold(false);
2674     abovePIDThreshold.setState(false);
2675
2676     changeColour(viewport.getGlobalColourScheme());
2677
2678     modifyConservation_actionPerformed();
2679   }
2680
2681   public void abovePIDThreshold_actionPerformed()
2682   {
2683     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2684
2685     conservationMenuItem.setState(false);
2686     viewport.setConservationSelected(false);
2687
2688     changeColour(viewport.getGlobalColourScheme());
2689
2690     modifyPID_actionPerformed();
2691   }
2692
2693   public void sortPairwiseMenuItem_actionPerformed()
2694   {
2695     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2696     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2697             .getAlignment().getSequenceAt(0), null);
2698
2699     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2700             viewport.getAlignment()));
2701     alignPanel.paintAlignment(true);
2702   }
2703
2704   public void sortIDMenuItem_actionPerformed()
2705   {
2706     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2707     AlignmentSorter.sortByID(viewport.getAlignment());
2708     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2709             viewport.getAlignment()));
2710     alignPanel.paintAlignment(true);
2711   }
2712
2713   public void sortLengthMenuItem_actionPerformed()
2714   {
2715     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2716     AlignmentSorter.sortByLength(viewport.getAlignment());
2717     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2718             viewport.getAlignment()));
2719     alignPanel.paintAlignment(true);
2720   }
2721
2722   public void sortGroupMenuItem_actionPerformed()
2723   {
2724     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2725     AlignmentSorter.sortByGroup(viewport.getAlignment());
2726     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2727             viewport.getAlignment()));
2728     alignPanel.paintAlignment(true);
2729
2730   }
2731
2732   public void removeRedundancyMenuItem_actionPerformed()
2733   {
2734     new RedundancyPanel(alignPanel);
2735   }
2736
2737   public void pairwiseAlignmentMenuItem_actionPerformed()
2738   {
2739     if (viewport.getSelectionGroup() != null
2740             && viewport.getSelectionGroup().getSize() > 1)
2741     {
2742       Frame frame = new Frame();
2743       frame.add(new PairwiseAlignPanel(alignPanel));
2744       jalview.bin.JalviewLite.addFrame(frame,
2745               MessageManager.getString("action.pairwise_alignment"), 600,
2746               500);
2747     }
2748   }
2749
2750   public void PCAMenuItem_actionPerformed()
2751   {
2752     // are the sequences aligned?
2753     if (!viewport.getAlignment().isAligned(false))
2754     {
2755       SequenceI current;
2756       int Width = viewport.getAlignment().getWidth();
2757
2758       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2759       {
2760         current = viewport.getAlignment().getSequenceAt(i);
2761
2762         if (current.getLength() < Width)
2763         {
2764           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2765         }
2766       }
2767       alignPanel.paintAlignment(true);
2768     }
2769
2770     if ((viewport.getSelectionGroup() != null
2771             && viewport.getSelectionGroup().getSize() < 4 && viewport
2772             .getSelectionGroup().getSize() > 0)
2773             || viewport.getAlignment().getHeight() < 4)
2774     {
2775       return;
2776     }
2777
2778     try
2779     {
2780       new PCAPanel(viewport);
2781     } catch (java.lang.OutOfMemoryError ex)
2782     {
2783     }
2784
2785   }
2786
2787   public void averageDistanceTreeMenuItem_actionPerformed()
2788   {
2789     NewTreePanel("AV", "PID", "Average distance tree using PID");
2790   }
2791
2792   public void neighbourTreeMenuItem_actionPerformed()
2793   {
2794     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2795   }
2796
2797   protected void njTreeBlosumMenuItem_actionPerformed()
2798   {
2799     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2800   }
2801
2802   protected void avTreeBlosumMenuItem_actionPerformed()
2803   {
2804     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2805   }
2806
2807   void NewTreePanel(String type, String pwType, String title)
2808   {
2809     // are the sequences aligned?
2810     if (!viewport.getAlignment().isAligned(false))
2811     {
2812       SequenceI current;
2813       int Width = viewport.getAlignment().getWidth();
2814
2815       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2816       {
2817         current = viewport.getAlignment().getSequenceAt(i);
2818
2819         if (current.getLength() < Width)
2820         {
2821           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2822         }
2823       }
2824       alignPanel.paintAlignment(true);
2825
2826     }
2827
2828     if ((viewport.getSelectionGroup() != null && viewport
2829             .getSelectionGroup().getSize() > 1)
2830             || (viewport.getAlignment().getHeight() > 1))
2831     {
2832       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2833
2834       addTreeMenuItem(tp, title);
2835
2836       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2837     }
2838   }
2839
2840   void loadTree_actionPerformed()
2841   {
2842     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2843     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2844     cap.setTreeImport();
2845     Frame frame = new Frame();
2846     frame.add(cap);
2847     jalview.bin.JalviewLite.addFrame(frame,
2848             MessageManager.getString("label.paste_newick_file"), 400, 300);
2849   }
2850
2851   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2852   {
2853     TreePanel tp = new TreePanel(alignPanel, treeFile,
2854             MessageManager.getString("label.load_tree_from_file"), tree);
2855     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2856     addTreeMenuItem(tp, treeFile);
2857   }
2858
2859   /**
2860    * sort the alignment using the given treePanel
2861    *
2862    * @param treePanel
2863    *          tree used to sort view
2864    * @param title
2865    *          string used for undo event name
2866    */
2867   public void sortByTree(TreePanel treePanel, String title)
2868   {
2869     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2870     AlignmentSorter
2871             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2872     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2873     // HistoryItem.SORT));
2874     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2875             "label.order_by_params", new String[] { title }), oldOrder,
2876             viewport.getAlignment()));
2877     alignPanel.paintAlignment(true);
2878   }
2879
2880   /**
2881    * Do any automatic reordering of the alignment and add the necessary bits to
2882    * the menu structure for the new tree
2883    *
2884    * @param treePanel
2885    * @param title
2886    */
2887   protected void addTreeMenuItem(final TreePanel treePanel,
2888           final String title)
2889   {
2890     final MenuItem item = new MenuItem(title);
2891     sortByTreeMenu.add(item);
2892     item.addActionListener(new java.awt.event.ActionListener()
2893     {
2894       @Override
2895       public void actionPerformed(ActionEvent evt)
2896       {
2897         sortByTree(treePanel, title); // treePanel.getTitle());
2898       }
2899     });
2900
2901     treePanel.addWindowListener(new WindowAdapter()
2902     {
2903       @Override
2904       public void windowOpened(WindowEvent e)
2905       {
2906         if (viewport.sortByTree)
2907         {
2908           sortByTree(treePanel, title);
2909         }
2910         super.windowOpened(e);
2911       }
2912
2913       @Override
2914       public void windowClosing(WindowEvent e)
2915       {
2916         sortByTreeMenu.remove(item);
2917       };
2918     });
2919   }
2920
2921   public boolean sortBy(AlignmentOrder alorder, String undoname)
2922   {
2923     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2924     if (viewport.applet.debug)
2925     {
2926       System.err.println("Sorting " + alorder.getOrder().size()
2927               + " in alignment '" + getTitle() + "'");
2928     }
2929     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2930     if (undoname != null)
2931     {
2932       addHistoryItem(new OrderCommand(undoname, oldOrder,
2933               viewport.getAlignment()));
2934     }
2935     alignPanel.paintAlignment(true);
2936     return true;
2937   }
2938
2939   protected void documentation_actionPerformed()
2940   {
2941     alignPanel.av.applet.openJalviewHelpUrl();
2942   }
2943
2944   protected void about_actionPerformed()
2945   {
2946
2947     class AboutPanel extends Canvas
2948     {
2949       String version;
2950
2951       String builddate;
2952
2953       public AboutPanel(String version, String builddate)
2954       {
2955         this.version = version;
2956         this.builddate = builddate;
2957       }
2958
2959       @Override
2960       public void paint(Graphics g)
2961       {
2962         g.setColor(Color.white);
2963         g.fillRect(0, 0, getSize().width, getSize().height);
2964         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2965         FontMetrics fm = g.getFontMetrics();
2966         int fh = fm.getHeight();
2967         int y = 5, x = 7;
2968         g.setColor(Color.black);
2969         // TODO: update this text for each release or centrally store it for
2970         // lite and application
2971         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2972         g.drawString(MessageManager.formatMessage(
2973                 "label.jalviewLite_release", new String[] { version }), x,
2974                 y += fh);
2975         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2976         g.drawString(MessageManager.formatMessage(
2977                 "label.jaview_build_date", new String[] { builddate }), x,
2978                 y += fh);
2979         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2980         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2981                 x, y += fh * 1.5);
2982         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2983                 x + 50, y += fh + 8);
2984         g.drawString(
2985                 MessageManager.getString("label.jalview_dev_managers"), x,
2986                 y += fh);
2987         g.drawString(MessageManager
2988                 .getString("label.jalview_distribution_lists"), x, y += fh);
2989         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2990                 x, y += fh + 8);
2991         g.drawString(
2992                 MessageManager.getString("label.jalview_cite_1_authors"),
2993                 x, y += fh);
2994         g.drawString(
2995                 MessageManager.getString("label.jalview_cite_1_title"), x,
2996                 y += fh);
2997         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2998                 x, y += fh);
2999       }
3000     }
3001
3002     Frame frame = new Frame();
3003     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3004             .getBuildDate()));
3005     jalview.bin.JalviewLite.addFrame(frame,
3006             MessageManager.getString("label.jalview"), 580, 220);
3007
3008   }
3009
3010   public void showURL(String url, String target)
3011   {
3012     if (viewport.applet == null)
3013     {
3014       System.out.println("Not running as applet - no browser available.");
3015     }
3016     else
3017     {
3018       viewport.applet.showURL(url, target);
3019     }
3020   }
3021
3022   // ////////////////////////////////////////////////////////////////////////////////
3023   // JBuilder Graphics here
3024
3025   MenuBar alignFrameMenuBar = new MenuBar();
3026
3027   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3028
3029   MenuItem loadApplication = new MenuItem(
3030           MessageManager.getString("label.view_full_application"));
3031
3032   MenuItem loadTree = new MenuItem(
3033           MessageManager.getString("label.load_associated_tree"));
3034
3035   MenuItem loadAnnotations = new MenuItem(
3036           MessageManager.getString("label.load_features_annotations"));
3037
3038   MenuItem outputFeatures = new MenuItem(
3039           MessageManager.getString("label.export_features"));
3040
3041   MenuItem outputAnnotations = new MenuItem(
3042           MessageManager.getString("label.export_annotations"));
3043
3044   MenuItem closeMenuItem = new MenuItem(
3045           MessageManager.getString("action.close"));
3046
3047   MenuItem selectAllSequenceMenuItem = new MenuItem(
3048           MessageManager.getString("action.select_all"));
3049
3050   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3051           MessageManager.getString("action.deselect_all"));
3052
3053   MenuItem invertSequenceMenuItem = new MenuItem(
3054           MessageManager.getString("action.invert_selection"));
3055
3056   MenuItem remove2LeftMenuItem = new MenuItem();
3057
3058   MenuItem remove2RightMenuItem = new MenuItem();
3059
3060   MenuItem removeGappedColumnMenuItem = new MenuItem();
3061
3062   MenuItem removeAllGapsMenuItem = new MenuItem();
3063
3064   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3065
3066   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3067
3068   MenuItem sortPairwiseMenuItem = new MenuItem();
3069
3070   MenuItem sortIDMenuItem = new MenuItem();
3071
3072   MenuItem sortLengthMenuItem = new MenuItem();
3073
3074   MenuItem sortGroupMenuItem = new MenuItem();
3075
3076   MenuItem removeRedundancyMenuItem = new MenuItem();
3077
3078   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3079
3080   MenuItem PCAMenuItem = new MenuItem();
3081
3082   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3083
3084   MenuItem neighbourTreeMenuItem = new MenuItem();
3085
3086   BorderLayout borderLayout1 = new BorderLayout();
3087
3088   public Label statusBar = new Label();
3089
3090   MenuItem clustalColour = new MenuItem();
3091
3092   MenuItem zappoColour = new MenuItem();
3093
3094   MenuItem taylorColour = new MenuItem();
3095
3096   MenuItem hydrophobicityColour = new MenuItem();
3097
3098   MenuItem helixColour = new MenuItem();
3099
3100   MenuItem strandColour = new MenuItem();
3101
3102   MenuItem turnColour = new MenuItem();
3103
3104   MenuItem buriedColour = new MenuItem();
3105
3106   MenuItem purinePyrimidineColour = new MenuItem();
3107
3108   // MenuItem RNAInteractionColour = new MenuItem();
3109
3110   MenuItem RNAHelixColour = new MenuItem();
3111
3112   MenuItem userDefinedColour = new MenuItem();
3113
3114   MenuItem PIDColour = new MenuItem();
3115
3116   MenuItem BLOSUM62Colour = new MenuItem();
3117
3118   MenuItem tcoffeeColour = new MenuItem();
3119
3120   MenuItem njTreeBlosumMenuItem = new MenuItem();
3121
3122   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3123
3124   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3125
3126   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3127
3128   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3129
3130   MenuItem alProperties = new MenuItem(
3131           MessageManager.getString("label.alignment_props"));
3132
3133   MenuItem overviewMenuItem = new MenuItem();
3134
3135   MenuItem undoMenuItem = new MenuItem();
3136
3137   MenuItem redoMenuItem = new MenuItem();
3138
3139   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3140
3141   MenuItem noColourmenuItem = new MenuItem();
3142
3143   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3144
3145   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3146
3147   MenuItem findMenuItem = new MenuItem();
3148
3149   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3150
3151   MenuItem nucleotideColour = new MenuItem();
3152
3153   MenuItem deleteGroups = new MenuItem();
3154
3155   MenuItem grpsFromSelection = new MenuItem();
3156
3157   MenuItem createGroup = new MenuItem();
3158
3159   MenuItem unGroup = new MenuItem();
3160
3161   MenuItem delete = new MenuItem();
3162
3163   MenuItem copy = new MenuItem();
3164
3165   MenuItem cut = new MenuItem();
3166
3167   Menu pasteMenu = new Menu();
3168
3169   MenuItem pasteNew = new MenuItem();
3170
3171   MenuItem pasteThis = new MenuItem();
3172
3173   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3174
3175   MenuItem font = new MenuItem();
3176
3177   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3178
3179   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3180
3181   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3182
3183   MenuItem modifyPID = new MenuItem();
3184
3185   MenuItem modifyConservation = new MenuItem();
3186
3187   CheckboxMenuItem autoCalculate = null;
3188
3189   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3190           "Sort Alignment With New Tree", true);
3191
3192   Menu sortByTreeMenu = new Menu();
3193
3194   MenuItem inputText = new MenuItem();
3195
3196   MenuItem documentation = new MenuItem();
3197
3198   MenuItem about = new MenuItem();
3199
3200   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3201
3202   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3203
3204   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3205
3206   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3209
3210   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3211
3212   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3213
3214   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3215
3216   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3217
3218   /**
3219    * Initialise menus and other items
3220    *
3221    * @throws Exception
3222    */
3223   private void jbInit() throws Exception
3224   {
3225     setMenuBar(alignFrameMenuBar);
3226
3227     /*
3228      * Configure File menu items and actions
3229      */
3230     inputText
3231             .setLabel(MessageManager.getString("label.input_from_textbox"));
3232     inputText.addActionListener(this);
3233     Menu outputTextboxMenu = new Menu(
3234             MessageManager.getString("label.out_to_textbox"));
3235     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3236     {
3237
3238       MenuItem item = new MenuItem(
3239               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3240
3241       item.addActionListener(new java.awt.event.ActionListener()
3242       {
3243         @Override
3244         public void actionPerformed(ActionEvent e)
3245         {
3246           outputText_actionPerformed(e);
3247         }
3248       });
3249
3250       outputTextboxMenu.add(item);
3251     }
3252     closeMenuItem.addActionListener(this);
3253     loadApplication.addActionListener(this);
3254     loadTree.addActionListener(this);
3255     loadAnnotations.addActionListener(this);
3256     outputFeatures.addActionListener(this);
3257     outputAnnotations.addActionListener(this);
3258
3259     /*
3260      * Configure Edit menu items and actions
3261      */
3262     undoMenuItem.setEnabled(false);
3263     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3264     undoMenuItem.addActionListener(this);
3265     redoMenuItem.setEnabled(false);
3266     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3267     redoMenuItem.addActionListener(this);
3268     copy.setLabel(MessageManager.getString("action.copy"));
3269     copy.addActionListener(this);
3270     cut.setLabel(MessageManager.getString("action.cut"));
3271     cut.addActionListener(this);
3272     delete.setLabel(MessageManager.getString("action.delete"));
3273     delete.addActionListener(this);
3274     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3275     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3276     pasteNew.addActionListener(this);
3277     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3278     pasteThis.addActionListener(this);
3279     remove2LeftMenuItem.setLabel(MessageManager
3280             .getString("action.remove_left"));
3281     remove2LeftMenuItem.addActionListener(this);
3282     remove2RightMenuItem.setLabel(MessageManager
3283             .getString("action.remove_right"));
3284     remove2RightMenuItem.addActionListener(this);
3285     removeGappedColumnMenuItem.setLabel(MessageManager
3286             .getString("action.remove_empty_columns"));
3287     removeGappedColumnMenuItem.addActionListener(this);
3288     removeAllGapsMenuItem.setLabel(MessageManager
3289             .getString("action.remove_all_gaps"));
3290     removeAllGapsMenuItem.addActionListener(this);
3291     removeRedundancyMenuItem.setLabel(MessageManager
3292             .getString("action.remove_redundancy"));
3293     removeRedundancyMenuItem.addActionListener(this);
3294
3295     /*
3296      * Configure Select menu items and actions
3297      */
3298     findMenuItem.setLabel(MessageManager.getString("action.find"));
3299     findMenuItem.addActionListener(this);
3300     selectAllSequenceMenuItem.addActionListener(this);
3301     deselectAllSequenceMenuItem.addActionListener(this);
3302     invertSequenceMenuItem.setLabel(MessageManager
3303             .getString("action.invert_sequence_selection"));
3304     invertSequenceMenuItem.addActionListener(this);
3305     invertColSel.setLabel(MessageManager
3306             .getString("action.invert_column_selection"));
3307     invertColSel.addActionListener(this);
3308     deleteGroups.setLabel(MessageManager
3309             .getString("action.undefine_groups"));
3310     deleteGroups.addActionListener(this);
3311     grpsFromSelection.setLabel(MessageManager
3312             .getString("action.make_groups_selection"));
3313     grpsFromSelection.addActionListener(this);
3314     createGroup.setLabel(MessageManager.getString("action.create_group"));
3315     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3316     annotationColumnSelection.setLabel(MessageManager
3317             .getString("action.select_by_annotation"));
3318     annotationColumnSelection.addActionListener(this);
3319
3320     /*
3321      * Configure View menu items and actions
3322      */
3323     newView.setLabel(MessageManager.getString("action.new_view"));
3324     newView.addActionListener(this);
3325     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3326     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3327     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3328     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3329     hideColumns
3330             .setLabel(MessageManager.getString("label.selected_columns"));
3331     hideSequences.setLabel(MessageManager
3332             .getString("label.selected_sequences"));
3333     hideAllButSelection.setLabel(MessageManager
3334             .getString("label.all_but_selected_region"));
3335     hideAllSelection.setLabel(MessageManager
3336             .getString("label.selected_region"));
3337     showAllHidden.setLabel(MessageManager
3338             .getString("label.all_sequences_columns"));
3339     showColumns.addActionListener(this);
3340     showSeqs.addActionListener(this);
3341     hideColumns.addActionListener(this);
3342     hideSequences.addActionListener(this);
3343     hideAllButSelection.addActionListener(this);
3344     hideAllSelection.addActionListener(this);
3345     showAllHidden.addActionListener(this);
3346     featureSettings.setLabel(MessageManager
3347             .getString("action.feature_settings"));
3348     featureSettings.addActionListener(this);
3349     sequenceFeatures.setLabel(MessageManager
3350             .getString("label.show_sequence_features"));
3351     sequenceFeatures.addItemListener(this);
3352     sequenceFeatures.setState(false);
3353     followMouseOverFlag.setLabel(MessageManager
3354             .getString("label.automatic_scrolling"));
3355     followMouseOverFlag.addItemListener(this);
3356     alProperties.addActionListener(this);
3357     overviewMenuItem.setLabel(MessageManager
3358             .getString("label.overview_window"));
3359     overviewMenuItem.addActionListener(this);
3360
3361     /*
3362      * Configure Annotations menu items and actions
3363      */
3364     annotationPanelMenuItem.setLabel(MessageManager
3365             .getString("label.show_annotations"));
3366     annotationPanelMenuItem.addItemListener(this);
3367     showGroupConsensus.setLabel(MessageManager
3368             .getString("label.group_consensus"));
3369     showGroupConservation.setLabel(MessageManager
3370             .getString("label.group_conservation"));
3371     showConsensusHistogram.setLabel(MessageManager
3372             .getString("label.show_consensus_histogram"));
3373     showSequenceLogo.setLabel(MessageManager
3374             .getString("label.show_consensus_logo"));
3375     normSequenceLogo.setLabel(MessageManager
3376             .getString("label.norm_consensus_logo"));
3377     applyAutoAnnotationSettings.setLabel(MessageManager
3378             .getString("label.apply_all_groups"));
3379     applyAutoAnnotationSettings.setState(true);
3380     Menu autoAnnMenu = new Menu(
3381             MessageManager.getString("label.autocalculated_annotation"));
3382     showGroupConsensus.addItemListener(this);
3383     showGroupConservation.addItemListener(this);
3384     showConsensusHistogram.addItemListener(this);
3385     showSequenceLogo.addItemListener(this);
3386     normSequenceLogo.addItemListener(this);
3387     applyAutoAnnotationSettings.addItemListener(this);
3388     showAlignmentAnnotations = new CheckboxMenuItem(
3389             MessageManager.getString("label.show_all_al_annotations"));
3390     showSequenceAnnotations = new CheckboxMenuItem(
3391             MessageManager.getString("label.show_all_seq_annotations"));
3392     sortAnnBySequence = new CheckboxMenuItem(
3393             MessageManager.getString("label.sort_annotations_by_sequence"));
3394     sortAnnByLabel = new CheckboxMenuItem(
3395             MessageManager.getString("label.sort_annotations_by_label"));
3396     showAutoFirst = new CheckboxMenuItem(
3397             MessageManager.getString("label.show_first"));
3398     showAutoFirst.setState(false); // pending applet parameter
3399     setShowAutoCalculatedAbove(showAutoFirst.getState());
3400     showAutoLast = new CheckboxMenuItem(
3401             MessageManager.getString("label.show_last"));
3402     showAutoLast.setState(!showAutoFirst.getState());
3403     showAlignmentAnnotations.addItemListener(this);
3404     showSequenceAnnotations.addItemListener(this);
3405     sortAnnBySequence.addItemListener(this);
3406     sortAnnByLabel.addItemListener(this);
3407     showAutoFirst.addItemListener(this);
3408     showAutoLast.addItemListener(this);
3409
3410     /*
3411      * Configure Format menu items and actions
3412      */
3413     font.setLabel(MessageManager.getString("action.font"));
3414     font.addActionListener(this);
3415     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3416     scaleAbove.setState(true);
3417     scaleAbove.setEnabled(false);
3418     scaleAbove.addItemListener(this);
3419     scaleLeft.setEnabled(false);
3420     scaleLeft.setState(true);
3421     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3422     scaleLeft.addItemListener(this);
3423     scaleRight.setEnabled(false);
3424     scaleRight.setState(true);
3425     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3426     scaleRight.addItemListener(this);
3427     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3428     viewBoxesMenuItem.setState(true);
3429     viewBoxesMenuItem.addItemListener(this);
3430     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3431     viewTextMenuItem.setState(true);
3432     viewTextMenuItem.addItemListener(this);
3433     colourTextMenuItem.setLabel(MessageManager
3434             .getString("label.colour_text"));
3435     colourTextMenuItem.addItemListener(this);
3436     displayNonconservedMenuItem.setLabel(MessageManager
3437             .getString("label.show_non_conversed"));
3438     displayNonconservedMenuItem.addItemListener(this);
3439     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3440     wrapMenuItem.addItemListener(this);
3441     renderGapsMenuItem.setLabel(MessageManager
3442             .getString("action.show_gaps"));
3443     renderGapsMenuItem.setState(true);
3444     renderGapsMenuItem.addItemListener(this);
3445     centreColumnLabelFlag.setLabel(MessageManager
3446             .getString("label.centre_column_labels"));
3447     centreColumnLabelFlag.addItemListener(this);
3448     seqLimits.setState(true);
3449     seqLimits.setLabel(MessageManager
3450             .getString("label.show_sequence_limits"));
3451     seqLimits.addItemListener(this);
3452
3453     /*
3454      * Configure Colour menu items and actions
3455      */
3456     applyToAllGroups.setLabel(MessageManager
3457             .getString("label.apply_colour_to_all_groups"));
3458     applyToAllGroups.setState(true);
3459     applyToAllGroups.addItemListener(this);
3460     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3461     clustalColour.addActionListener(this);
3462     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3463     zappoColour.addActionListener(this);
3464     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3465     taylorColour.addActionListener(this);
3466     hydrophobicityColour.setLabel(MessageManager
3467             .getString("label.hydrophobicity"));
3468     hydrophobicityColour.addActionListener(this);
3469     helixColour
3470             .setLabel(MessageManager.getString("label.helix_propensity"));
3471     helixColour.addActionListener(this);
3472     strandColour.setLabel(MessageManager
3473             .getString("label.strand_propensity"));
3474     strandColour.addActionListener(this);
3475     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3476     turnColour.addActionListener(this);
3477     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3478     buriedColour.addActionListener(this);
3479     purinePyrimidineColour.setLabel(MessageManager
3480             .getString("label.purine_pyrimidine"));
3481     purinePyrimidineColour.addActionListener(this);
3482     // RNAInteractionColour.setLabel(MessageManager
3483     // .getString("label.rna_interaction"));
3484     // RNAInteractionColour.addActionListener(this);
3485     RNAHelixColour.setLabel(MessageManager
3486             .getString("action.by_rna_helixes"));
3487     RNAHelixColour.addActionListener(this);
3488     userDefinedColour.setLabel(MessageManager
3489             .getString("action.user_defined"));
3490     userDefinedColour.addActionListener(this);
3491     PIDColour.setLabel(MessageManager
3492             .getString("label.percentage_identity"));
3493     PIDColour.addActionListener(this);
3494     BLOSUM62Colour.setLabel(MessageManager
3495             .getString("label.blosum62_score"));
3496     BLOSUM62Colour.addActionListener(this);
3497     tcoffeeColour
3498             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3499     // it will be enabled only if a score file is provided
3500     tcoffeeColour.setEnabled(false);
3501     tcoffeeColour.addActionListener(this);
3502     conservationMenuItem.setLabel(MessageManager
3503             .getString("action.by_conservation"));
3504     conservationMenuItem.addItemListener(this);
3505     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3506     noColourmenuItem.addActionListener(this);
3507     abovePIDThreshold.setLabel(MessageManager
3508             .getString("label.above_identity_threshold"));
3509     abovePIDThreshold.addItemListener(this);
3510     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3511     nucleotideColour.addActionListener(this);
3512     modifyPID.setLabel(MessageManager
3513             .getString("label.modify_identity_thereshold"));
3514     modifyPID.addActionListener(this);
3515     modifyConservation.setLabel(MessageManager
3516             .getString("label.modify_conservation_thereshold"));
3517     modifyConservation.addActionListener(this);
3518     annotationColour.setLabel(MessageManager
3519             .getString("action.by_annotation"));
3520     annotationColour.addActionListener(this);
3521
3522     /*
3523      * Configure Calculate menu items and actions
3524      */
3525     sortPairwiseMenuItem.setLabel(MessageManager
3526             .getString("action.by_pairwise_id"));
3527     sortPairwiseMenuItem.addActionListener(this);
3528     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3529     sortIDMenuItem.addActionListener(this);
3530     sortLengthMenuItem.setLabel(MessageManager
3531             .getString("action.by_length"));
3532     sortLengthMenuItem.addActionListener(this);
3533     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3534     sortGroupMenuItem.addActionListener(this);
3535     pairwiseAlignmentMenuItem.setLabel(MessageManager
3536             .getString("action.pairwise_alignment"));
3537     pairwiseAlignmentMenuItem.addActionListener(this);
3538     PCAMenuItem.setLabel(MessageManager
3539             .getString("label.principal_component_analysis"));
3540     PCAMenuItem.addActionListener(this);
3541     autoCalculate = new CheckboxMenuItem(
3542             MessageManager.getString("label.autocalculate_consensus"), true);
3543     averageDistanceTreeMenuItem.setLabel(MessageManager
3544             .getString("label.average_distance_identity"));
3545     averageDistanceTreeMenuItem.addActionListener(this);
3546     neighbourTreeMenuItem.setLabel(MessageManager
3547             .getString("label.neighbour_joining_identity"));
3548     neighbourTreeMenuItem.addActionListener(this);
3549     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3550             .getString("label.average_distance_bloslum62"));
3551     avDistanceTreeBlosumMenuItem.addActionListener(this);
3552     njTreeBlosumMenuItem.setLabel(MessageManager
3553             .getString("label.neighbour_blosum62"));
3554     njTreeBlosumMenuItem.addActionListener(this);
3555     sortByTreeMenu.setLabel(MessageManager
3556             .getString("action.by_tree_order"));
3557     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3558     Menu calculateTreeMenu = new Menu(
3559             MessageManager.getString("action.calculate_tree"));
3560     autoCalculate.addItemListener(this);
3561     sortByTree.addItemListener(this);
3562
3563     /*
3564      * Configure Help menu items and actions
3565      */
3566     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3567     documentation.setLabel(MessageManager.getString("label.documentation"));
3568     documentation.addActionListener(this);
3569     about.setLabel(MessageManager.getString("label.about"));
3570     about.addActionListener(this);
3571
3572     /*
3573      * Add top level menus to frame
3574      */
3575     alignFrameMenuBar.add(fileMenu);
3576     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3577     alignFrameMenuBar.add(editMenu);
3578     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3579     alignFrameMenuBar.add(selectMenu);
3580     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3581     alignFrameMenuBar.add(viewMenu);
3582     Menu annotationsMenu = new Menu(
3583             MessageManager.getString("action.annotations"));
3584     alignFrameMenuBar.add(annotationsMenu);
3585     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3586     alignFrameMenuBar.add(formatMenu);
3587     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3588     alignFrameMenuBar.add(colourMenu);
3589     Menu calculateMenu = new Menu(
3590             MessageManager.getString("action.calculate"));
3591     alignFrameMenuBar.add(calculateMenu);
3592     alignFrameMenuBar.add(helpMenu);
3593
3594     /*
3595      * File menu
3596      */
3597     fileMenu.add(inputText);
3598     fileMenu.add(loadTree);
3599     fileMenu.add(loadAnnotations);
3600     fileMenu.addSeparator();
3601     fileMenu.add(outputTextboxMenu);
3602     fileMenu.add(outputFeatures);
3603     fileMenu.add(outputAnnotations);
3604     if (jalviewServletURL != null)
3605     {
3606       fileMenu.add(loadApplication);
3607     }
3608     fileMenu.addSeparator();
3609     fileMenu.add(closeMenuItem);
3610
3611     /*
3612      * Edit menu
3613      */
3614     editMenu.add(undoMenuItem);
3615     editMenu.add(redoMenuItem);
3616     editMenu.add(cut);
3617     editMenu.add(copy);
3618     pasteMenu.add(pasteNew);
3619     pasteMenu.add(pasteThis);
3620     editMenu.add(pasteMenu);
3621     editMenu.add(delete);
3622     editMenu.addSeparator();
3623     editMenu.add(remove2LeftMenuItem);
3624     editMenu.add(remove2RightMenuItem);
3625     editMenu.add(removeGappedColumnMenuItem);
3626     editMenu.add(removeAllGapsMenuItem);
3627     editMenu.add(removeRedundancyMenuItem);
3628
3629     /*
3630      * Select menu
3631      */
3632     selectMenu.add(findMenuItem);
3633     selectMenu.addSeparator();
3634     selectMenu.add(selectAllSequenceMenuItem);
3635     selectMenu.add(deselectAllSequenceMenuItem);
3636     selectMenu.add(invertSequenceMenuItem);
3637     selectMenu.add(invertColSel);
3638     selectMenu.add(createGroup);
3639     selectMenu.add(unGroup);
3640     selectMenu.add(grpsFromSelection);
3641     selectMenu.add(deleteGroups);
3642     selectMenu.add(annotationColumnSelection);
3643
3644     /*
3645      * View menu
3646      */
3647     viewMenu.add(newView);
3648     viewMenu.addSeparator();
3649     showMenu.add(showColumns);
3650     showMenu.add(showSeqs);
3651     showMenu.add(showAllHidden);
3652     viewMenu.add(showMenu);
3653     hideMenu.add(hideColumns);
3654     hideMenu.add(hideSequences);
3655     hideMenu.add(hideAllSelection);
3656     hideMenu.add(hideAllButSelection);
3657     viewMenu.add(hideMenu);
3658     viewMenu.addSeparator();
3659     viewMenu.add(followMouseOverFlag);
3660     viewMenu.addSeparator();
3661     viewMenu.add(sequenceFeatures);
3662     viewMenu.add(featureSettings);
3663     viewMenu.addSeparator();
3664     viewMenu.add(alProperties);
3665     viewMenu.addSeparator();
3666     viewMenu.add(overviewMenuItem);
3667
3668     /*
3669      * Annotations menu
3670      */
3671     annotationsMenu.add(annotationPanelMenuItem);
3672     annotationsMenu.addSeparator();
3673     annotationsMenu.add(showAlignmentAnnotations);
3674     annotationsMenu.add(showSequenceAnnotations);
3675     annotationsMenu.add(sortAnnBySequence);
3676     annotationsMenu.add(sortAnnByLabel);
3677     annotationsMenu.addSeparator();
3678     autoAnnMenu.add(showAutoFirst);
3679     autoAnnMenu.add(showAutoLast);
3680     autoAnnMenu.addSeparator();
3681     autoAnnMenu.add(applyAutoAnnotationSettings);
3682     autoAnnMenu.add(showConsensusHistogram);
3683     autoAnnMenu.add(showSequenceLogo);
3684     autoAnnMenu.add(normSequenceLogo);
3685     autoAnnMenu.addSeparator();
3686     autoAnnMenu.add(showGroupConservation);
3687     autoAnnMenu.add(showGroupConsensus);
3688     annotationsMenu.add(autoAnnMenu);
3689
3690     /*
3691      * Format menu
3692      */
3693     formatMenu.add(font);
3694     formatMenu.add(seqLimits);
3695     formatMenu.add(wrapMenuItem);
3696     formatMenu.add(scaleAbove);
3697     formatMenu.add(scaleLeft);
3698     formatMenu.add(scaleRight);
3699     formatMenu.add(viewBoxesMenuItem);
3700     formatMenu.add(viewTextMenuItem);
3701     formatMenu.add(colourTextMenuItem);
3702     formatMenu.add(displayNonconservedMenuItem);
3703     formatMenu.add(renderGapsMenuItem);
3704     formatMenu.add(centreColumnLabelFlag);
3705
3706     /*
3707      * Colour menu
3708      */
3709     colourMenu.add(applyToAllGroups);
3710     colourMenu.addSeparator();
3711     colourMenu.add(noColourmenuItem);
3712     colourMenu.add(clustalColour);
3713     colourMenu.add(BLOSUM62Colour);
3714     colourMenu.add(PIDColour);
3715     colourMenu.add(zappoColour);
3716     colourMenu.add(taylorColour);
3717     colourMenu.add(hydrophobicityColour);
3718     colourMenu.add(helixColour);
3719     colourMenu.add(strandColour);
3720     colourMenu.add(turnColour);
3721     colourMenu.add(buriedColour);
3722     colourMenu.add(nucleotideColour);
3723     colourMenu.add(purinePyrimidineColour);
3724     // colourMenu.add(RNAInteractionColour);
3725     colourMenu.add(tcoffeeColour);
3726     colourMenu.add(userDefinedColour);
3727     colourMenu.addSeparator();
3728     colourMenu.add(conservationMenuItem);
3729     colourMenu.add(modifyConservation);
3730     colourMenu.add(abovePIDThreshold);
3731     colourMenu.add(modifyPID);
3732     colourMenu.add(annotationColour);
3733     colourMenu.add(RNAHelixColour);
3734
3735     /*
3736      * Calculate menu
3737      */
3738     sortMenu.add(sortIDMenuItem);
3739     sortMenu.add(sortLengthMenuItem);
3740     sortMenu.add(sortByTreeMenu);
3741     sortMenu.add(sortGroupMenuItem);
3742     sortMenu.add(sortPairwiseMenuItem);
3743     calculateMenu.add(sortMenu);
3744     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3745     calculateTreeMenu.add(neighbourTreeMenuItem);
3746     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3747     calculateTreeMenu.add(njTreeBlosumMenuItem);
3748     calculateMenu.add(calculateTreeMenu);
3749     calculateMenu.addSeparator();
3750     calculateMenu.add(pairwiseAlignmentMenuItem);
3751     calculateMenu.add(PCAMenuItem);
3752     calculateMenu.add(autoCalculate);
3753     calculateMenu.add(sortByTree);
3754
3755     /*
3756      * Help menu
3757      */
3758     helpMenu.add(documentation);
3759     helpMenu.add(about);
3760
3761     /*
3762      * Status bar
3763      */
3764     statusBar.setBackground(Color.white);
3765     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3766     statusBar.setText(MessageManager.getString("label.status_bar"));
3767     this.add(statusBar, BorderLayout.SOUTH);
3768   }
3769
3770   @Override
3771   public void setStatus(String string)
3772   {
3773     statusBar.setText(string);
3774   };
3775
3776   MenuItem featureSettings = new MenuItem();
3777
3778   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3779
3780   MenuItem annotationColour = new MenuItem();
3781
3782   MenuItem annotationColumnSelection = new MenuItem();
3783
3784   MenuItem invertColSel = new MenuItem();
3785
3786   MenuItem showColumns = new MenuItem();
3787
3788   MenuItem showSeqs = new MenuItem();
3789
3790   MenuItem hideColumns = new MenuItem();
3791
3792   MenuItem hideSequences = new MenuItem();
3793
3794   MenuItem hideAllButSelection = new MenuItem();
3795
3796   MenuItem hideAllSelection = new MenuItem();
3797
3798   MenuItem showAllHidden = new MenuItem();
3799
3800   MenuItem newView = new MenuItem();
3801
3802   private CheckboxMenuItem showAlignmentAnnotations;
3803
3804   private CheckboxMenuItem showSequenceAnnotations;
3805
3806   private CheckboxMenuItem sortAnnBySequence;
3807
3808   private CheckboxMenuItem sortAnnByLabel;
3809
3810   private CheckboxMenuItem showAutoFirst;
3811
3812   private CheckboxMenuItem showAutoLast;
3813
3814   private SplitFrame splitFrame;
3815
3816   /**
3817    * Attach the alignFrame panels after embedding menus, if necessary. This used
3818    * to be called setEmbedded, but is now creates the dropdown menus in a
3819    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3820    *
3821    * @param reallyEmbedded
3822    *          true to attach the view to the applet area on the page rather than
3823    *          in a new window
3824    */
3825   public void createAlignFrameWindow(boolean reallyEmbedded)
3826   {
3827     if (reallyEmbedded)
3828     {
3829       embedAlignFrameInApplet(viewport.applet);
3830     }
3831     else
3832     {
3833       // //////
3834       // test and embed menu bar if necessary.
3835       //
3836       if (embedMenuIfNeeded(alignPanel))
3837       {
3838         /*
3839          * adjust for status bar height too. ? pointless as overridden by layout
3840          * manager
3841          */
3842         alignPanel.setSize(getSize().width,
3843                 getSize().height - statusBar.getHeight());
3844       }
3845       add(statusBar, BorderLayout.SOUTH);
3846       add(alignPanel, BorderLayout.CENTER);
3847       // and register with the applet so it can pass external API calls to us
3848       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3849               frameHeight);
3850     }
3851   }
3852
3853   /**
3854    * Add the components of this AlignFrame to the applet container.
3855    *
3856    * @param theApplet
3857    */
3858   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3859   {
3860     // ////
3861     // Explicitly build the embedded menu panel for the on-page applet
3862     //
3863     // view cannot be closed if its actually on the page
3864     fileMenu.remove(closeMenuItem);
3865     fileMenu.remove(3); // Remove Separator
3866     // construct embedded menu, using default font
3867     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3868     // and actually add the components to the applet area
3869     theApplet.setLayout(new BorderLayout());
3870     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3871     theApplet.add(statusBar, BorderLayout.SOUTH);
3872     // TODO should size be left to the layout manager?
3873     alignPanel.setSize(theApplet.getSize().width,
3874             theApplet.getSize().height - embeddedMenu.getHeight()
3875                     - statusBar.getHeight());
3876     theApplet.add(alignPanel, BorderLayout.CENTER);
3877     final AlignFrame me = this;
3878     theApplet.addFocusListener(new FocusListener()
3879     {
3880
3881       @Override
3882       public void focusLost(FocusEvent e)
3883       {
3884         if (theApplet.currentAlignFrame == me)
3885         {
3886           theApplet.currentAlignFrame = null;
3887         }
3888       }
3889
3890       @Override
3891       public void focusGained(FocusEvent e)
3892       {
3893         theApplet.currentAlignFrame = me;
3894       }
3895     });
3896     theApplet.validate();
3897   }
3898
3899   /**
3900    * create a new binding between structures in an existing jmol viewer instance
3901    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3902    * this does not open a new Jmol window, or modify the display of the
3903    * structures in the original jmol window. Note This method doesn't work
3904    * without an additional javascript library to exchange messages between the
3905    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3906    *
3907    * @param viewer
3908    *          JmolViewer instance
3909    * @param sequenceIds
3910    *          - sequence Ids to search for associations
3911    */
3912   public SequenceStructureBinding addStructureViewInstance(
3913           Object jmolviewer, String[] sequenceIds)
3914   {
3915     Viewer viewer = null;
3916     try
3917     {
3918       viewer = (Viewer) jmolviewer;
3919     } catch (ClassCastException ex)
3920     {
3921       System.err.println("Unsupported viewer object :"
3922               + jmolviewer.getClass());
3923     }
3924     if (viewer == null)
3925     {
3926       System.err.println("Can't use this object as a structure viewer:"
3927               + jmolviewer.getClass());
3928       return null;
3929     }
3930     SequenceI[] seqs = null;
3931     if (sequenceIds == null || sequenceIds.length == 0)
3932     {
3933       seqs = viewport.getAlignment().getSequencesArray();
3934     }
3935     else
3936     {
3937       Vector sqi = new Vector();
3938       AlignmentI al = viewport.getAlignment();
3939       for (int sid = 0; sid < sequenceIds.length; sid++)
3940       {
3941         SequenceI sq = al.findName(sequenceIds[sid]);
3942         if (sq != null)
3943         {
3944           sqi.addElement(sq);
3945         }
3946       }
3947       if (sqi.size() > 0)
3948       {
3949         seqs = new SequenceI[sqi.size()];
3950         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3951         {
3952           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3953         }
3954       }
3955       else
3956       {
3957         return null;
3958       }
3959     }
3960     AAStructureBindingModel jmv = null;
3961     // TODO: search for a jmv that involves viewer
3962     if (jmv == null)
3963     { // create a new viewer/jalview binding.
3964       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3965     }
3966     return jmv;
3967
3968   }
3969
3970   /**
3971    * bind a pdb file to a sequence in the current view
3972    *
3973    * @param sequenceId
3974    *          - sequenceId within the dataset.
3975    * @param pdbEntryString
3976    *          - the short name for the PDB file
3977    * @param pdbFile
3978    *          - pdb file - either a URL or a valid PDB file.
3979    * @return true if binding was as success TODO: consider making an exception
3980    *         structure for indicating when PDB parsing or sequenceId location
3981    *         fails.
3982    */
3983   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3984           String pdbFile)
3985   {
3986     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3987     boolean needtoadd = false;
3988     if (toaddpdb != null)
3989     {
3990       Vector pdbe = toaddpdb.getAllPDBEntries();
3991       PDBEntry pdbentry = null;
3992       if (pdbe != null && pdbe.size() > 0)
3993       {
3994         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3995         {
3996           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3997           if (!pdbentry.getId().equals(pdbEntryString)
3998                   && !pdbentry.getFile().equals(pdbFile))
3999           {
4000             pdbentry = null;
4001           }
4002           else
4003           {
4004             continue;
4005           }
4006         }
4007       }
4008       if (pdbentry == null)
4009       {
4010         pdbentry = new PDBEntry();
4011         pdbentry.setId(pdbEntryString);
4012         pdbentry.setFile(pdbFile);
4013         needtoadd = true; // add this new entry to sequence.
4014       }
4015       // resolve data source
4016       // TODO: this code should be a refactored to an io package
4017       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4018       if (protocol == null)
4019       {
4020         return false;
4021       }
4022       if (needtoadd)
4023       {
4024         // make a note of the access mode and add
4025         if (pdbentry.getProperty() == null)
4026         {
4027           pdbentry.setProperty(new Hashtable());
4028         }
4029         pdbentry.getProperty().put("protocol", protocol);
4030         toaddpdb.addPDBId(pdbentry);
4031         alignPanel.getStructureSelectionManager()
4032                 .registerPDBEntry(pdbentry);
4033       }
4034     }
4035     return true;
4036   }
4037
4038   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4039   {
4040     if (seqs != null)
4041     {
4042       Vector sequences = new Vector();
4043       for (int i = 0; i < seqs.length; i++)
4044       {
4045         if (seqs[i] != null)
4046         {
4047           sequences.addElement(new Object[] { seqs[i],
4048               (chains != null) ? chains[i] : null });
4049         }
4050       }
4051       seqs = new SequenceI[sequences.size()];
4052       chains = new String[sequences.size()];
4053       for (int i = 0, isize = sequences.size(); i < isize; i++)
4054       {
4055         Object[] oj = (Object[]) sequences.elementAt(i);
4056
4057         seqs[i] = (SequenceI) oj[0];
4058         chains[i] = (String) oj[1];
4059       }
4060     }
4061     return new Object[] { seqs, chains };
4062
4063   }
4064
4065   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4066           SequenceI[] seqs, String[] chains, String protocol)
4067   {
4068     // Scrub any null sequences from the array
4069     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4070     seqs = (SequenceI[]) sqch[0];
4071     chains = (String[]) sqch[1];
4072     if (seqs == null || seqs.length == 0)
4073     {
4074       System.err
4075               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4076     }
4077     if (protocol == null || protocol.trim().length() == 0
4078             || protocol.equals("null"))
4079     {
4080       protocol = (String) pdb.getProperty().get("protocol");
4081       if (protocol == null)
4082       {
4083         System.err.println("Couldn't work out protocol to open structure: "
4084                 + pdb.getId());
4085         return;
4086       }
4087     }
4088     if (applet.useXtrnalSviewer)
4089     {
4090       // register the association(s) and quit, don't create any windows.
4091       if (StructureSelectionManager.getStructureSelectionManager(applet)
4092               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4093       {
4094         System.err.println("Failed to map " + pdb.getFile() + " ("
4095                 + protocol + ") to any sequences");
4096       }
4097       return;
4098     }
4099     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4100     {
4101       // can only do alignments with Jmol
4102       // find the last jmol window assigned to this alignment
4103       jalview.appletgui.AppletJmol ajm = null, tajm;
4104       Vector jmols = applet
4105               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4106       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4107       {
4108         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4109         if (tajm.ap.alignFrame == this)
4110         {
4111           ajm = tajm;
4112           break;
4113         }
4114       }
4115       if (ajm != null)
4116       {
4117         System.err
4118                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4119         // try and add the pdb structure
4120         // ajm.addS
4121         ajm = null;
4122       }
4123     }
4124     // otherwise, create a new window
4125     if (applet.jmolAvailable)
4126     {
4127       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4128               protocol);
4129       applet.lastFrameX += 40;
4130       applet.lastFrameY += 40;
4131     }
4132     else
4133     {
4134       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4135     }
4136
4137   }
4138
4139   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4140           SequenceI[][] seqs, String[][] chains, String[] protocols)
4141   {
4142     // TODO Auto-generated method stub
4143     System.err.println("Aligned Structure View: Not yet implemented.");
4144   }
4145
4146   /**
4147    * modify the current selection, providing the user has not made a selection
4148    * already.
4149    *
4150    * @param sel
4151    *          - sequences from this alignment
4152    * @param csel
4153    *          - columns to be selected on the alignment
4154    */
4155   public void select(SequenceGroup sel, ColumnSelection csel)
4156   {
4157     alignPanel.seqPanel.selection(sel, csel, null);
4158   }
4159
4160   public void scrollTo(int row, int column)
4161   {
4162     alignPanel.seqPanel.scrollTo(row, column);
4163   }
4164
4165   public void scrollToRow(int row)
4166   {
4167     alignPanel.seqPanel.scrollToRow(row);
4168   }
4169
4170   public void scrollToColumn(int column)
4171   {
4172     alignPanel.seqPanel.scrollToColumn(column);
4173   }
4174
4175   /**
4176    * @return the alignments unique ID.
4177    */
4178   public String getSequenceSetId()
4179   {
4180     return viewport.getSequenceSetId();
4181   }
4182
4183   /**
4184    * Load the (T-Coffee) score file from the specified url
4185    *
4186    * @param source
4187    *          File/URL/T-COFFEE score file contents
4188    * @throws IOException
4189    * @return true if alignment was annotated with data from source
4190    */
4191   public boolean loadScoreFile(String source) throws IOException
4192   {
4193
4194     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4195             AppletFormatAdapter.checkProtocol(source));
4196     if (!file.isValid())
4197     {
4198       // TODO: raise dialog for gui
4199       System.err.println("Problems parsing T-Coffee scores: "
4200               + file.getWarningMessage());
4201       System.err.println("Origin was:\n" + source);
4202       return false;
4203     }
4204
4205     /*
4206      * check that the score matrix matches the alignment dimensions
4207      */
4208     AlignmentI aln;
4209     if ((aln = viewport.getAlignment()) != null
4210             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4211                     .getWidth()))
4212     {
4213       // TODO: raise a dialog box here rather than bomb out.
4214       System.err
4215               .println("The scores matrix does not match the alignment dimensions");
4216
4217     }
4218
4219     // TODO add parameter to indicate if matching should be done
4220     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4221     {
4222       alignPanel.fontChanged();
4223       tcoffeeColour.setEnabled(true);
4224       // switch to this color
4225       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4226       return true;
4227     }
4228     else
4229     {
4230       System.err.println("Problems resolving T-Coffee scores:");
4231       if (file.getWarningMessage() != null)
4232       {
4233         System.err.println(file.getWarningMessage());
4234       }
4235     }
4236     return false;
4237   }
4238
4239   public SplitFrame getSplitFrame()
4240   {
4241     return this.splitFrame;
4242   }
4243
4244   public void setSplitFrame(SplitFrame sf)
4245   {
4246     this.splitFrame = sf;
4247   }
4248
4249   // may not need this
4250   @Override
4251   public void setShowSeqFeatures(boolean b)
4252   {
4253     // showSeqFeatures.setSelected(b);
4254     viewport.setShowSequenceFeatures(b);
4255
4256   }
4257
4258   @Override
4259   public void setMenusForViewport()
4260   {
4261     // setMenusFromViewport(viewport);
4262
4263   }
4264
4265   @Override
4266   public void refreshFeatureUI(boolean enableIfNecessary)
4267   {
4268     if (enableIfNecessary)
4269     {
4270       sequenceFeatures.setState(true);
4271       alignPanel.av.setShowSequenceFeatures(true);
4272     }
4273   }
4274
4275   @Override
4276   public FeatureSettingsControllerI getFeatureSettingsUI()
4277   {
4278     return alignPanel.av.featureSettings;
4279   }
4280
4281 }