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     viewport.setScaleAboveWrapped(scaleAbove.getState());
 223
 224     alignPanel = new AlignmentPanel(this, viewport);
 225     avc = new jalview.controller.AlignViewController(this, viewport,
 226             alignPanel);
 227     viewport.updateConservation(alignPanel);
 228     viewport.updateConsensus(alignPanel);
 229
 230     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 231     followMouseOverFlag.setState(viewport.isFollowHighlight());
 232     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 233     showGroupConservation.setState(viewport.isShowGroupConservation());
 234     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 235     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 236     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 237     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 238     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 239     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 240     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showAlignmentAnnotations.setState(true);
 242     showSequenceAnnotations.setState(false);
 243
 244     seqLimits.setState(viewport.getShowJVSuffix());
 245
 246     if (applet != null)
 247     {
 248       String param = applet.getParameter("sortBy");
 249       if (param != null)
 250       {
 251         if (param.equalsIgnoreCase("Id"))
 252         {
 253           sortIDMenuItem_actionPerformed();
 254         }
 255         else if (param.equalsIgnoreCase("Pairwise Identity"))
 256         {
 257           sortPairwiseMenuItem_actionPerformed();
 258         }
 259         else if (param.equalsIgnoreCase("Length"))
 260         {
 261           sortLengthMenuItem_actionPerformed();
 262         }
 263       }
 264
 265       param = applet.getParameter("wrap");
 266       if (param != null)
 267       {
 268         if (param.equalsIgnoreCase("true"))
 269         {
 270           wrapMenuItem.setState(true);
 271           wrapMenuItem_actionPerformed();
 272         }
 273       }
 274       param = applet.getParameter("centrecolumnlabels");
 275       if (param != null)
 276       {
 277         centreColumnLabelFlag.setState(true);
 278         centreColumnLabelFlag_stateChanged();
 279       }
 280
 281     }
 282     if (viewport.getAlignment().isNucleotide())
 283     {
 284       viewport.updateStrucConsensus(alignPanel);
 285       if (viewport.getAlignment().hasRNAStructure())
 286       {
 287         RNAHelixColour.setEnabled(true);
 288       }
 289       else
 290       {
 291         RNAHelixColour.setEnabled(false);
 292       }
 293     }
 294     else
 295     {
 296       RNAHelixColour.setEnabled(false);
 297       purinePyrimidineColour.setEnabled(false);
 298     }
 299     // Some JVMS send keyevents to Top frame or lowest panel,
 300     // Havent worked out why yet. So add to both this frame and seqCanvas for
 301     // now
 302     this.addKeyListener(this);
 303     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 304     alignPanel.idPanel.idCanvas.addKeyListener(this);
 305     alignPanel.scalePanel.addKeyListener(this);
 306     alignPanel.annotationPanel.addKeyListener(this);
 307     alignPanel.annotationPanelHolder.addKeyListener(this);
 308     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 309     alignPanel.alabels.addKeyListener(this);
 310
 311     setAnnotationsVisibility();
 312
 313     if (addToDisplay)
 314     {
 315       addToDisplay(embedded);
 316     }
 317   }
 318
 319   /**
 320    * @param embedded
 321    */
 322   public void addToDisplay(boolean embedded)
 323   {
 324     createAlignFrameWindow(embedded);
 325     validate();
 326     alignPanel.adjustAnnotationHeight();
 327     alignPanel.paintAlignment(true);
 328   }
 329
 330   public AlignViewport getAlignViewport()
 331   {
 332     return viewport;
 333   }
 334
 335   public SeqCanvas getSeqcanvas()
 336   {
 337     return alignPanel.seqPanel.seqCanvas;
 338   }
 339
 340   /**
 341    * Load a features file onto the alignment
 342    *
 343    * @param file
 344    *          file URL, content, or other resolvable path
 345    * @param type
 346    *          is protocol for accessing data referred to by file
 347    */
 348
 349   public boolean parseFeaturesFile(String file, String type)
 350   {
 351     return parseFeaturesFile(file, type, true);
 352   }
 353
 354   /**
 355    * Load a features file onto the alignment
 356    *
 357    * @param file
 358    *          file URL, content, or other resolvable path
 359    * @param type
 360    *          is protocol for accessing data referred to by file
 361    * @param autoenabledisplay
 362    *          when true, display features flag will be automatically enabled if
 363    *          features are loaded
 364    * @return true if data parsed as a features file
 365    */
 366   public boolean parseFeaturesFile(String file, String type,
 367           boolean autoenabledisplay)
 368   {
 369     boolean featuresFile = false;
 370     try
 371     {
 372       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 373               .getFeatureRenderer().getFeatureColours();
 374       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 375               "relaxedidmatch", false);
 376       featuresFile = new FeaturesFile(file, type).parse(
 377               viewport.getAlignment(), colours, true, relaxedIdMatching);
 378     } catch (Exception ex)
 379     {
 380       ex.printStackTrace();
 381     }
 382
 383     if (featuresFile)
 384     {
 385       if (autoenabledisplay)
 386       {
 387         viewport.setShowSequenceFeatures(true);
 388         sequenceFeatures.setState(true);
 389       }
 390       if (alignPanel.seqPanel.seqCanvas.fr != null)
 391       {
 392         // update the min/max ranges where necessary
 393         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 394       }
 395       if (viewport.featureSettings != null)
 396       {
 397         viewport.featureSettings.refreshTable();
 398       }
 399       alignPanel.paintAlignment(true);
 400       statusBar.setText(MessageManager
 401               .getString("label.successfully_added_features_alignment"));
 402     }
 403     return featuresFile;
 404   }
 405
 406   @Override
 407   public void keyPressed(KeyEvent evt)
 408   {
 409     if (viewport.cursorMode
 410             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 411                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 412                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 413             && Character.isDigit(evt.getKeyChar()))
 414     {
 415       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 416     }
 417
 418     switch (evt.getKeyCode())
 419     {
 420     case 27: // escape key
 421       deselectAllSequenceMenuItem_actionPerformed();
 422
 423       alignPanel.alabels.cancelDrag();
 424       break;
 425     case KeyEvent.VK_X:
 426       if (evt.isControlDown() || evt.isMetaDown())
 427       {
 428         cut_actionPerformed();
 429       }
 430       break;
 431     case KeyEvent.VK_C:
 432       if (viewport.cursorMode && !evt.isControlDown())
 433       {
 434         alignPanel.seqPanel.setCursorColumn();
 435       }
 436       if (evt.isControlDown() || evt.isMetaDown())
 437       {
 438         copy_actionPerformed();
 439       }
 440       break;
 441     case KeyEvent.VK_V:
 442       if (evt.isControlDown())
 443       {
 444         paste(evt.isShiftDown());
 445       }
 446       break;
 447     case KeyEvent.VK_A:
 448       if (evt.isControlDown() || evt.isMetaDown())
 449       {
 450         selectAllSequenceMenuItem_actionPerformed();
 451       }
 452       break;
 453     case KeyEvent.VK_DOWN:
 454       if (viewport.cursorMode)
 455       {
 456         alignPanel.seqPanel.moveCursor(0, 1);
 457       }
 458       else
 459       {
 460         moveSelectedSequences(false);
 461       }
 462       break;
 463
 464     case KeyEvent.VK_UP:
 465       if (viewport.cursorMode)
 466       {
 467         alignPanel.seqPanel.moveCursor(0, -1);
 468       }
 469       else
 470       {
 471         moveSelectedSequences(true);
 472       }
 473       break;
 474
 475     case KeyEvent.VK_LEFT:
 476       if (evt.isAltDown() || !viewport.cursorMode)
 477       {
 478         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 479       }
 480       else
 481       {
 482         alignPanel.seqPanel.moveCursor(-1, 0);
 483       }
 484       break;
 485
 486     case KeyEvent.VK_RIGHT:
 487       if (evt.isAltDown() || !viewport.cursorMode)
 488       {
 489         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 490       }
 491       else
 492       {
 493         alignPanel.seqPanel.moveCursor(1, 0);
 494       }
 495       break;
 496
 497     case KeyEvent.VK_SPACE:
 498       if (viewport.cursorMode)
 499       {
 500         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 501                 || evt.isShiftDown() || evt.isAltDown());
 502       }
 503       break;
 504
 505     case KeyEvent.VK_DELETE:
 506     case KeyEvent.VK_BACK_SPACE:
 507       if (viewport.cursorMode)
 508       {
 509         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 510                 || evt.isShiftDown() || evt.isAltDown());
 511       }
 512       else
 513       {
 514         cut_actionPerformed();
 515         alignPanel.seqPanel.seqCanvas.repaint();
 516       }
 517       break;
 518
 519     case KeyEvent.VK_S:
 520       if (viewport.cursorMode)
 521       {
 522         alignPanel.seqPanel.setCursorRow();
 523       }
 524       break;
 525     case KeyEvent.VK_P:
 526       if (viewport.cursorMode)
 527       {
 528         alignPanel.seqPanel.setCursorPosition();
 529       }
 530       break;
 531
 532     case KeyEvent.VK_ENTER:
 533     case KeyEvent.VK_COMMA:
 534       if (viewport.cursorMode)
 535       {
 536         alignPanel.seqPanel.setCursorRowAndColumn();
 537       }
 538       break;
 539
 540     case KeyEvent.VK_Q:
 541       if (viewport.cursorMode)
 542       {
 543         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 544       }
 545       break;
 546     case KeyEvent.VK_M:
 547       if (viewport.cursorMode)
 548       {
 549         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 550       }
 551       break;
 552
 553     case KeyEvent.VK_F2:
 554       viewport.cursorMode = !viewport.cursorMode;
 555       statusBar.setText(MessageManager.formatMessage(
 556               "label.keyboard_editing_mode",
 557               new String[] { (viewport.cursorMode ? "on" : "off") }));
 558       if (viewport.cursorMode)
 559       {
 560         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 561         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 562       }
 563       break;
 564
 565     case KeyEvent.VK_F:
 566       if (evt.isControlDown())
 567       {
 568         findMenuItem_actionPerformed();
 569       }
 570       break;
 571
 572     case KeyEvent.VK_H:
 573     {
 574       boolean toggleSeqs = !evt.isControlDown();
 575       boolean toggleCols = !evt.isShiftDown();
 576       toggleHiddenRegions(toggleSeqs, toggleCols);
 577       break;
 578     }
 579
 580     case KeyEvent.VK_PAGE_UP:
 581       if (viewport.getWrapAlignment())
 582       {
 583         alignPanel.scrollUp(true);
 584       }
 585       else
 586       {
 587         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 588                 - viewport.endSeq + viewport.startSeq);
 589       }
 590       break;
 591
 592     case KeyEvent.VK_PAGE_DOWN:
 593       if (viewport.getWrapAlignment())
 594       {
 595         alignPanel.scrollUp(false);
 596       }
 597       else
 598       {
 599         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 600                 + viewport.endSeq - viewport.startSeq);
 601       }
 602       break;
 603
 604     case KeyEvent.VK_Z:
 605       if (evt.isControlDown())
 606       {
 607         undoMenuItem_actionPerformed();
 608       }
 609       break;
 610
 611     case KeyEvent.VK_Y:
 612       if (evt.isControlDown())
 613       {
 614         redoMenuItem_actionPerformed();
 615       }
 616       break;
 617
 618     case KeyEvent.VK_L:
 619       if (evt.isControlDown())
 620       {
 621         trimAlignment(true);
 622       }
 623       break;
 624
 625     case KeyEvent.VK_R:
 626       if (evt.isControlDown())
 627       {
 628         trimAlignment(false);
 629       }
 630       break;
 631
 632     case KeyEvent.VK_E:
 633       if (evt.isControlDown())
 634       {
 635         if (evt.isShiftDown())
 636         {
 637           this.removeAllGapsMenuItem_actionPerformed();
 638         }
 639         else
 640         {
 641           removeGappedColumnMenuItem_actionPerformed();
 642         }
 643       }
 644       break;
 645     case KeyEvent.VK_I:
 646       if (evt.isControlDown())
 647       {
 648         if (evt.isAltDown())
 649         {
 650           invertColSel_actionPerformed();
 651         }
 652         else
 653         {
 654           invertSequenceMenuItem_actionPerformed();
 655         }
 656       }
 657       break;
 658
 659     case KeyEvent.VK_G:
 660       if (evt.isControlDown())
 661       {
 662         if (evt.isShiftDown())
 663         {
 664           this.unGroup_actionPerformed();
 665         }
 666         else
 667         {
 668           this.createGroup_actionPerformed();
 669         }
 670       }
 671       break;
 672
 673     case KeyEvent.VK_U:
 674       if (evt.isControlDown())
 675       {
 676         this.deleteGroups_actionPerformed();
 677       }
 678       break;
 679
 680     case KeyEvent.VK_T:
 681       if (evt.isControlDown())
 682       {
 683         newView(null);
 684       }
 685       break;
 686
 687     }
 688     alignPanel.paintAlignment(true);
 689   }
 690
 691   /**
 692    * called by key handler and the hide all/show all menu items
 693    *
 694    * @param toggleSeqs
 695    * @param toggleCols
 696    */
 697   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 698   {
 699     boolean hide = false;
 700     SequenceGroup sg = viewport.getSelectionGroup();
 701     if (!toggleSeqs && !toggleCols)
 702     {
 703       // Hide everything by the current selection - this is a hack - we do the
 704       // invert and then hide
 705       // first check that there will be visible columns after the invert.
 706       if ((viewport.getColumnSelection() != null
 707               && viewport.getColumnSelection().getSelected() != null && viewport
 708               .getColumnSelection().getSelected().size() > 0)
 709               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 710                       .getEndRes()))
 711       {
 712         // now invert the sequence set, if required - empty selection implies
 713         // that no hiding is required.
 714         if (sg != null)
 715         {
 716           invertSequenceMenuItem_actionPerformed();
 717           sg = viewport.getSelectionGroup();
 718           toggleSeqs = true;
 719
 720         }
 721         viewport.expandColSelection(sg, true);
 722         // finally invert the column selection and get the new sequence
 723         // selection and indicate it should be hidden.
 724         invertColSel_actionPerformed();
 725         toggleCols = true;
 726       }
 727     }
 728
 729     if (toggleSeqs)
 730     {
 731       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 732       {
 733         hide = true;
 734         viewport.hideAllSelectedSeqs();
 735       }
 736       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 737               .size() > 0))
 738       {
 739         viewport.showAllHiddenSeqs();
 740       }
 741     }
 742
 743     if (toggleCols)
 744     {
 745       if (viewport.getColumnSelection().getSelected().size() > 0)
 746       {
 747         viewport.hideSelectedColumns();
 748         if (!toggleSeqs)
 749         {
 750           viewport.setSelectionGroup(sg);
 751         }
 752       }
 753       else if (!hide)
 754       {
 755         viewport.showAllHiddenColumns();
 756       }
 757       viewport.sendSelection();
 758     }
 759   }
 760
 761   @Override
 762   public void keyReleased(KeyEvent evt)
 763   {
 764   }
 765
 766   @Override
 767   public void keyTyped(KeyEvent evt)
 768   {
 769   }
 770
 771   @Override
 772   public void itemStateChanged(ItemEvent evt)
 773   {
 774     final Object source = evt.getSource();
 775     if (source == displayNonconservedMenuItem)
 776     {
 777       displayNonconservedMenuItem_actionPerformed();
 778     }
 779     else if (source == colourTextMenuItem)
 780     {
 781       colourTextMenuItem_actionPerformed();
 782     }
 783     else if (source == wrapMenuItem)
 784     {
 785       wrapMenuItem_actionPerformed();
 786     }
 787     else if (source == scaleAbove)
 788     {
 789       viewport.setScaleAboveWrapped(scaleAbove.getState());
 790     }
 791     else if (source == scaleLeft)
 792     {
 793       viewport.setScaleLeftWrapped(scaleLeft.getState());
 794     }
 795     else if (source == scaleRight)
 796     {
 797       viewport.setScaleRightWrapped(scaleRight.getState());
 798     }
 799     else if (source == seqLimits)
 800     {
 801       seqLimits_itemStateChanged();
 802     }
 803     else if (source == viewBoxesMenuItem)
 804     {
 805       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 806     }
 807     else if (source == viewTextMenuItem)
 808     {
 809       viewport.setShowText(viewTextMenuItem.getState());
 810     }
 811     else if (source == renderGapsMenuItem)
 812     {
 813       viewport.setRenderGaps(renderGapsMenuItem.getState());
 814     }
 815     else if (source == annotationPanelMenuItem)
 816     {
 817       boolean showAnnotations = annotationPanelMenuItem.getState();
 818       showAlignmentAnnotations.setEnabled(showAnnotations);
 819       showSequenceAnnotations.setEnabled(showAnnotations);
 820       viewport.setShowAnnotation(showAnnotations);
 821       alignPanel.setAnnotationVisible(showAnnotations);
 822     }
 823     else if (source == sequenceFeatures)
 824     {
 825       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 826       alignPanel.seqPanel.seqCanvas.repaint();
 827     }
 828     else if (source == showAlignmentAnnotations)
 829     {
 830       setAnnotationsVisibility();
 831     }
 832     else if (source == showSequenceAnnotations)
 833     {
 834       setAnnotationsVisibility();
 835     }
 836     else if (source == sortAnnBySequence)
 837     {
 838       boolean newState = sortAnnBySequence.getState();
 839       sortAnnByLabel.setState(false);
 840       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 841               : SequenceAnnotationOrder.NONE);
 842       setViewportAnnotationOrder();
 843     }
 844     else if (source == sortAnnByLabel)
 845     {
 846       boolean newState = sortAnnByLabel.getState();
 847       sortAnnBySequence.setState(false);
 848       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 849               : SequenceAnnotationOrder.NONE);
 850       setViewportAnnotationOrder();
 851     }
 852     else if (source == showAutoFirst)
 853     {
 854       showAutoLast.setState(!showAutoFirst.getState());
 855       setShowAutoCalculatedAbove(showAutoFirst.getState());
 856       setViewportAnnotationOrder();
 857     }
 858     else if (source == showAutoLast)
 859     {
 860       showAutoFirst.setState(!showAutoLast.getState());
 861       setShowAutoCalculatedAbove(showAutoFirst.getState());
 862       setViewportAnnotationOrder();
 863     }
 864     else if (source == conservationMenuItem)
 865     {
 866       conservationMenuItem_actionPerformed();
 867     }
 868     else if (source == abovePIDThreshold)
 869     {
 870       abovePIDThreshold_actionPerformed();
 871     }
 872     else if (source == applyToAllGroups)
 873     {
 874       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 875     }
 876     else if (source == autoCalculate)
 877     {
 878       viewport.autoCalculateConsensus = autoCalculate.getState();
 879     }
 880     else if (source == sortByTree)
 881     {
 882       viewport.sortByTree = sortByTree.getState();
 883     }
 884     else if (source == this.centreColumnLabelFlag)
 885     {
 886       centreColumnLabelFlag_stateChanged();
 887     }
 888     else if (source == this.followMouseOverFlag)
 889     {
 890       mouseOverFlag_stateChanged();
 891     }
 892     else if (source == showGroupConsensus)
 893     {
 894       showGroupConsensus_actionPerformed();
 895     }
 896     else if (source == showGroupConservation)
 897     {
 898       showGroupConservation_actionPerformed();
 899     }
 900     else if (source == showSequenceLogo)
 901     {
 902       showSequenceLogo_actionPerformed();
 903     }
 904     else if (source == normSequenceLogo)
 905     {
 906       normSequenceLogo_actionPerformed();
 907     }
 908     else if (source == showConsensusHistogram)
 909     {
 910       showConsensusHistogram_actionPerformed();
 911     }
 912     else if (source == applyAutoAnnotationSettings)
 913     {
 914       applyAutoAnnotationSettings_actionPerformed();
 915     }
 916     alignPanel.paintAlignment(true);
 917   }
 918
 919   /**
 920    * Set the visibility state of sequence-related and/or alignment-related
 921    * annotations depending on checkbox selections, and repaint.
 922    *
 923    * @param visible
 924    */
 925   private void setAnnotationsVisibility()
 926   {
 927     boolean showForAlignment = showAlignmentAnnotations.getState();
 928     boolean showForSequences = showSequenceAnnotations.getState();
 929     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 930     {
 931       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 932             .getAlignmentAnnotation())
 933     {
 934       boolean visible = (aa.sequenceRef == null ? showForAlignment
 935               : showForSequences);
 936       aa.visible = visible;
 937       }
 938     }
 939     alignPanel.validateAnnotationDimensions(true);
 940     validate();
 941     repaint();
 942   }
 943
 944   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 945   {
 946     this.annotationSortOrder = order;
 947   }
 948
 949   /**
 950    * Set flags on the viewport that control annotation ordering
 951    */
 952   private void setViewportAnnotationOrder()
 953   {
 954     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 955     this.alignPanel.av
 956             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 957   }
 958
 959   private void setShowAutoCalculatedAbove(boolean showAbove)
 960   {
 961     this.showAutoCalculatedAbove = showAbove;
 962   }
 963
 964   private void mouseOverFlag_stateChanged()
 965   {
 966     viewport.setFollowHighlight(followMouseOverFlag.getState());
 967     // TODO: could kick the scrollTo mechanism to reset view for current
 968     // searchresults.
 969   }
 970
 971   private void centreColumnLabelFlag_stateChanged()
 972   {
 973     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 974     this.alignPanel.annotationPanel.repaint();
 975   }
 976
 977   @Override
 978   public void actionPerformed(ActionEvent evt)
 979   {
 980     viewport.applet.currentAlignFrame = this;
 981
 982     Object source = evt.getSource();
 983
 984     if (source == inputText)
 985     {
 986       inputText_actionPerformed();
 987     }
 988     else if (source == loadTree)
 989     {
 990       loadTree_actionPerformed();
 991     }
 992     else if (source == loadApplication)
 993     {
 994       launchFullApplication();
 995     }
 996     else if (source == loadAnnotations)
 997     {
 998       loadAnnotations();
 999     }
1000     else if (source == outputAnnotations)
1001     {
1002       outputAnnotations(true);
1003     }
1004     else if (source == outputFeatures)
1005     {
1006       outputFeatures(true, "Jalview");
1007     }
1008     else if (source == closeMenuItem)
1009     {
1010       closeMenuItem_actionPerformed();
1011     }
1012     else if (source == copy)
1013     {
1014       copy_actionPerformed();
1015     }
1016     else if (source == undoMenuItem)
1017     {
1018       undoMenuItem_actionPerformed();
1019     }
1020     else if (source == redoMenuItem)
1021     {
1022       redoMenuItem_actionPerformed();
1023     }
1024     else if (source == inputText)
1025     {
1026       inputText_actionPerformed();
1027     }
1028     else if (source == closeMenuItem)
1029     {
1030       closeMenuItem_actionPerformed();
1031     }
1032     else if (source == undoMenuItem)
1033     {
1034       undoMenuItem_actionPerformed();
1035     }
1036     else if (source == redoMenuItem)
1037     {
1038       redoMenuItem_actionPerformed();
1039     }
1040     else if (source == copy)
1041     {
1042       copy_actionPerformed();
1043     }
1044     else if (source == pasteNew)
1045     {
1046       pasteNew_actionPerformed();
1047     }
1048     else if (source == pasteThis)
1049     {
1050       pasteThis_actionPerformed();
1051     }
1052     else if (source == cut)
1053     {
1054       cut_actionPerformed();
1055     }
1056     else if (source == delete)
1057     {
1058       delete_actionPerformed();
1059     }
1060     else if (source == grpsFromSelection)
1061     {
1062       makeGrpsFromSelection_actionPerformed();
1063     }
1064     else if (source == deleteGroups)
1065     {
1066       deleteGroups_actionPerformed();
1067     }
1068     else if (source == selectAllSequenceMenuItem)
1069     {
1070       selectAllSequenceMenuItem_actionPerformed();
1071     }
1072     else if (source == deselectAllSequenceMenuItem)
1073     {
1074       deselectAllSequenceMenuItem_actionPerformed();
1075     }
1076     else if (source == invertSequenceMenuItem)
1077     {
1078       invertSequenceMenuItem_actionPerformed();
1079       // uncomment to slave sequence selections in split frame
1080       // viewport.sendSelection();
1081     }
1082     else if (source == invertColSel)
1083     {
1084       viewport.invertColumnSelection();
1085       alignPanel.paintAlignment(true);
1086       viewport.sendSelection();
1087     }
1088     else if (source == remove2LeftMenuItem)
1089     {
1090       trimAlignment(true);
1091     }
1092     else if (source == remove2RightMenuItem)
1093     {
1094       trimAlignment(false);
1095     }
1096     else if (source == removeGappedColumnMenuItem)
1097     {
1098       removeGappedColumnMenuItem_actionPerformed();
1099     }
1100     else if (source == removeAllGapsMenuItem)
1101     {
1102       removeAllGapsMenuItem_actionPerformed();
1103     }
1104     else if (source == findMenuItem)
1105     {
1106       findMenuItem_actionPerformed();
1107     }
1108     else if (source == font)
1109     {
1110       new FontChooser(alignPanel);
1111     }
1112     else if (source == newView)
1113     {
1114       newView(null);
1115     }
1116     else if (source == showColumns)
1117     {
1118       viewport.showAllHiddenColumns();
1119       alignPanel.paintAlignment(true);
1120       viewport.sendSelection();
1121     }
1122     else if (source == showSeqs)
1123     {
1124       viewport.showAllHiddenSeqs();
1125       alignPanel.paintAlignment(true);
1126       // uncomment if we want to slave sequence selections in split frame
1127       // viewport.sendSelection();
1128     }
1129     else if (source == hideColumns)
1130     {
1131       viewport.hideSelectedColumns();
1132       alignPanel.paintAlignment(true);
1133       viewport.sendSelection();
1134     }
1135     else if (source == hideSequences
1136             && viewport.getSelectionGroup() != null)
1137     {
1138       viewport.hideAllSelectedSeqs();
1139       alignPanel.paintAlignment(true);
1140       // uncomment if we want to slave sequence selections in split frame
1141       // viewport.sendSelection();
1142     }
1143     else if (source == hideAllButSelection)
1144     {
1145       toggleHiddenRegions(false, false);
1146       alignPanel.paintAlignment(true);
1147       viewport.sendSelection();
1148     }
1149     else if (source == hideAllSelection)
1150     {
1151       SequenceGroup sg = viewport.getSelectionGroup();
1152       viewport.expandColSelection(sg, false);
1153       viewport.hideAllSelectedSeqs();
1154       viewport.hideSelectedColumns();
1155       alignPanel.paintAlignment(true);
1156       viewport.sendSelection();
1157     }
1158     else if (source == showAllHidden)
1159     {
1160       viewport.showAllHiddenColumns();
1161       viewport.showAllHiddenSeqs();
1162       alignPanel.paintAlignment(true);
1163       viewport.sendSelection();
1164     }
1165     else if (source == showGroupConsensus)
1166     {
1167       showGroupConsensus_actionPerformed();
1168     }
1169     else if (source == showGroupConservation)
1170     {
1171       showGroupConservation_actionPerformed();
1172     }
1173     else if (source == showSequenceLogo)
1174     {
1175       showSequenceLogo_actionPerformed();
1176     }
1177     else if (source == normSequenceLogo)
1178     {
1179       normSequenceLogo_actionPerformed();
1180     }
1181     else if (source == showConsensusHistogram)
1182     {
1183       showConsensusHistogram_actionPerformed();
1184     }
1185     else if (source == applyAutoAnnotationSettings)
1186     {
1187       applyAutoAnnotationSettings_actionPerformed();
1188     }
1189     else if (source == featureSettings)
1190     {
1191       new FeatureSettings(alignPanel);
1192     }
1193     else if (source == alProperties)
1194     {
1195       StringBuffer contents = new jalview.io.AlignmentProperties(
1196               viewport.getAlignment()).formatAsString();
1197       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1198       cap.setText(contents.toString());
1199       Frame frame = new Frame();
1200       frame.add(cap);
1201       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1202               "label.alignment_properties", new String[] { getTitle() }),
1203               400, 250);
1204     }
1205     else if (source == overviewMenuItem)
1206     {
1207       overviewMenuItem_actionPerformed();
1208     }
1209     else if (source == noColourmenuItem)
1210     {
1211       changeColour(null);
1212     }
1213     else if (source == clustalColour)
1214     {
1215       abovePIDThreshold.setState(false);
1216       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1217     }
1218     else if (source == zappoColour)
1219     {
1220       changeColour(new ZappoColourScheme());
1221     }
1222     else if (source == taylorColour)
1223     {
1224       changeColour(new TaylorColourScheme());
1225     }
1226     else if (source == hydrophobicityColour)
1227     {
1228       changeColour(new HydrophobicColourScheme());
1229     }
1230     else if (source == helixColour)
1231     {
1232       changeColour(new HelixColourScheme());
1233     }
1234     else if (source == strandColour)
1235     {
1236       changeColour(new StrandColourScheme());
1237     }
1238     else if (source == turnColour)
1239     {
1240       changeColour(new TurnColourScheme());
1241     }
1242     else if (source == buriedColour)
1243     {
1244       changeColour(new BuriedColourScheme());
1245     }
1246     else if (source == nucleotideColour)
1247     {
1248       changeColour(new NucleotideColourScheme());
1249     }
1250     else if (source == purinePyrimidineColour)
1251     {
1252       changeColour(new PurinePyrimidineColourScheme());
1253     }
1254     // else if (source == RNAInteractionColour)
1255     // {
1256     // changeColour(new RNAInteractionColourScheme());
1257     // }
1258     else if (source == RNAHelixColour)
1259     {
1260       new RNAHelicesColourChooser(viewport, alignPanel);
1261     }
1262     else if (source == modifyPID)
1263     {
1264       modifyPID_actionPerformed();
1265     }
1266     else if (source == modifyConservation)
1267     {
1268       modifyConservation_actionPerformed();
1269     }
1270     else if (source == userDefinedColour)
1271     {
1272       new UserDefinedColours(alignPanel, null);
1273     }
1274     else if (source == PIDColour)
1275     {
1276       changeColour(new PIDColourScheme());
1277     }
1278     else if (source == BLOSUM62Colour)
1279     {
1280       changeColour(new Blosum62ColourScheme());
1281     }
1282     else if (source == tcoffeeColour)
1283     {
1284       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1285     }
1286     else if (source == annotationColour)
1287     {
1288       new AnnotationColourChooser(viewport, alignPanel);
1289     }
1290     else if (source == annotationColumnSelection)
1291     {
1292       new AnnotationColumnChooser(viewport, alignPanel);
1293     }
1294     else if (source == sortPairwiseMenuItem)
1295     {
1296       sortPairwiseMenuItem_actionPerformed();
1297     }
1298     else if (source == sortIDMenuItem)
1299     {
1300       sortIDMenuItem_actionPerformed();
1301     }
1302     else if (source == sortLengthMenuItem)
1303     {
1304       sortLengthMenuItem_actionPerformed();
1305     }
1306     else if (source == sortGroupMenuItem)
1307     {
1308       sortGroupMenuItem_actionPerformed();
1309     }
1310     else if (source == removeRedundancyMenuItem)
1311     {
1312       removeRedundancyMenuItem_actionPerformed();
1313     }
1314     else if (source == pairwiseAlignmentMenuItem)
1315     {
1316       pairwiseAlignmentMenuItem_actionPerformed();
1317     }
1318     else if (source == PCAMenuItem)
1319     {
1320       PCAMenuItem_actionPerformed();
1321     }
1322     else if (source == averageDistanceTreeMenuItem)
1323     {
1324       averageDistanceTreeMenuItem_actionPerformed();
1325     }
1326     else if (source == neighbourTreeMenuItem)
1327     {
1328       neighbourTreeMenuItem_actionPerformed();
1329     }
1330     else if (source == njTreeBlosumMenuItem)
1331     {
1332       njTreeBlosumMenuItem_actionPerformed();
1333     }
1334     else if (source == avDistanceTreeBlosumMenuItem)
1335     {
1336       avTreeBlosumMenuItem_actionPerformed();
1337     }
1338     else if (source == documentation)
1339     {
1340       documentation_actionPerformed();
1341     }
1342     else if (source == about)
1343     {
1344       about_actionPerformed();
1345     }
1346
1347   }
1348
1349   public void inputText_actionPerformed()
1350   {
1351     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352     Frame frame = new Frame();
1353     frame.add(cap);
1354     jalview.bin.JalviewLite.addFrame(frame,
1355             MessageManager.getString("label.input_cut_paste"), 500, 500);
1356   }
1357
1358   protected void outputText_actionPerformed(ActionEvent e)
1359   {
1360     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1361     Frame frame = new Frame();
1362     frame.add(cap);
1363     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1364             "label.alignment_output_command",
1365             new Object[] { e.getActionCommand() }), 600, 500);
1366
1367     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1368     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1369             e.getActionCommand(), viewport.getAlignment(),
1370             viewport.getShowJVSuffix()));
1371   }
1372
1373   public void loadAnnotations()
1374   {
1375     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376     cap.setText(MessageManager
1377             .getString("label.paste_features_annotations_Tcoffee_here"));
1378     cap.setAnnotationImport();
1379     Frame frame = new Frame();
1380     frame.add(cap);
1381     jalview.bin.JalviewLite.addFrame(frame,
1382             MessageManager.getString("action.paste_annotations"), 400, 300);
1383
1384   }
1385
1386   public String outputAnnotations(boolean displayTextbox)
1387   {
1388     String annotation = new AnnotationFile()
1389             .printAnnotationsForView(viewport);
1390
1391     if (displayTextbox)
1392     {
1393       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1394       Frame frame = new Frame();
1395       frame.add(cap);
1396       jalview.bin.JalviewLite.addFrame(frame,
1397               MessageManager.getString("label.annotations"), 600, 500);
1398       cap.setText(annotation);
1399     }
1400
1401     return annotation;
1402   }
1403
1404   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1405   {
1406     if (alignPanel.getFeatureRenderer() != null
1407             && viewport.getFeaturesDisplayed() != null)
1408     {
1409       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1410
1411     }
1412     return null;
1413   }
1414
1415   public String outputFeatures(boolean displayTextbox, String format)
1416   {
1417     String features;
1418     FeaturesFile formatter = new FeaturesFile();
1419     if (format.equalsIgnoreCase("Jalview"))
1420     {
1421       features = formatter.printJalviewFormat(viewport
1422               .getAlignment().getSequencesArray(),
1423               getDisplayedFeatureCols());
1424     }
1425     else
1426     {
1427       features = formatter.printGffFormat(viewport.getAlignment()
1428               .getSequencesArray(), getDisplayedFeatureCols());
1429     }
1430
1431     if (displayTextbox)
1432     {
1433       boolean frimport = false;
1434       if (features == null || features.equals("No Features Visible"))
1435       {
1436         features = "# No features visible - paste some and import them here.";
1437         frimport = true;
1438       }
1439
1440       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1441       if (frimport)
1442       {
1443         cap.setAnnotationImport();
1444       }
1445       Frame frame = new Frame();
1446       frame.add(cap);
1447       jalview.bin.JalviewLite.addFrame(frame,
1448               MessageManager.getString("label.features"), 600, 500);
1449       cap.setText(features);
1450     }
1451     else
1452     {
1453       if (features == null)
1454       {
1455         features = "";
1456       }
1457     }
1458
1459     return features;
1460   }
1461
1462   void launchFullApplication()
1463   {
1464     StringBuffer url = new StringBuffer(jalviewServletURL);
1465
1466     // allow servlet parameters to be passed in applet parameter
1467     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1468             : "?";
1469     url.append(firstSep);
1470
1471     url.append("open="
1472             + appendProtocol(viewport.applet.getParameter("file")));
1473
1474     if (viewport.applet.getParameter("features") != null)
1475     {
1476       url.append("&features=");
1477       url.append(appendProtocol(viewport.applet.getParameter("features")));
1478     }
1479
1480     if (viewport.applet.getParameter("annotations") != null)
1481     {
1482       url.append("&annotations=");
1483       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1484     }
1485
1486     if (viewport.applet.getParameter("jnetfile") != null)
1487     {
1488       url.append("&annotations=");
1489       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1490     }
1491
1492     if (viewport.applet.getParameter("defaultColour") != null)
1493     {
1494       url.append("&colour="
1495               + removeWhiteSpace(viewport.applet
1496                       .getParameter("defaultColour")));
1497     }
1498
1499     if (viewport.applet.getParameter("userDefinedColour") != null)
1500     {
1501       url.append("&colour="
1502               + removeWhiteSpace(viewport.applet
1503                       .getParameter("userDefinedColour")));
1504     }
1505     if (viewport.applet.getParameter("tree") != null)
1506     {
1507       url.append("&tree="
1508               + appendProtocol(viewport.applet.getParameter("tree")));
1509     }
1510     if (viewport.applet.getParameter("treeFile") != null)
1511     {
1512       url.append("&tree="
1513               + appendProtocol(viewport.applet.getParameter("treeFile")));
1514     }
1515
1516     showURL(url.toString(), "FULL_APP");
1517   }
1518
1519   String removeWhiteSpace(String colour)
1520   {
1521     StringBuffer sb = new StringBuffer();
1522     for (int i = 0; i < colour.length(); i++)
1523     {
1524       if (Character.isWhitespace(colour.charAt(i)))
1525       {
1526         sb.append("%20");
1527       }
1528       else
1529       {
1530         sb.append(colour.charAt(i));
1531       }
1532     }
1533
1534     return sb.toString();
1535   }
1536
1537   String appendProtocol(String url)
1538   {
1539     try
1540     {
1541       new URL(url);
1542       url = URLEncoder.encode(url);
1543     }
1544     /*
1545      * When we finally deprecate 1.1 compatibility, we can start to use
1546      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1547      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1548      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1549      * ex.printStackTrace(); }
1550      */
1551     catch (java.net.MalformedURLException ex)
1552     {
1553       url = viewport.applet.getCodeBase() + url;
1554     }
1555     return url;
1556   }
1557
1558   public void closeMenuItem_actionPerformed()
1559   {
1560     PaintRefresher.RemoveComponent(alignPanel);
1561     if (alignPanel.seqPanel != null
1562             && alignPanel.seqPanel.seqCanvas != null)
1563     {
1564       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1565     }
1566     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1567     {
1568       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1569     }
1570
1571     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1572     {
1573       System.exit(0);
1574     }
1575     else
1576     {
1577     }
1578     viewport = null;
1579     alignPanel = null;
1580     this.dispose();
1581   }
1582
1583   /**
1584    * TODO: JAL-1104
1585    */
1586   void updateEditMenuBar()
1587   {
1588
1589     if (viewport.getHistoryList().size() > 0)
1590     {
1591       undoMenuItem.setEnabled(true);
1592       CommandI command = viewport.getHistoryList().peek();
1593       undoMenuItem.setLabel(MessageManager.formatMessage(
1594               "label.undo_command",
1595               new Object[] { command.getDescription() }));
1596     }
1597     else
1598     {
1599       undoMenuItem.setEnabled(false);
1600       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1601     }
1602
1603     if (viewport.getRedoList().size() > 0)
1604     {
1605       redoMenuItem.setEnabled(true);
1606
1607       CommandI command = viewport.getRedoList().peek();
1608       redoMenuItem.setLabel(MessageManager.formatMessage(
1609               "label.redo_command",
1610               new Object[] { command.getDescription() }));
1611     }
1612     else
1613     {
1614       redoMenuItem.setEnabled(false);
1615       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1616     }
1617   }
1618
1619   /**
1620    * TODO: JAL-1104
1621    */
1622   @Override
1623   public void addHistoryItem(CommandI command)
1624   {
1625     if (command.getSize() > 0)
1626     {
1627       viewport.addToHistoryList(command);
1628       viewport.clearRedoList();
1629       updateEditMenuBar();
1630       viewport.updateHiddenColumns();
1631     }
1632   }
1633
1634   /**
1635    * TODO: JAL-1104 DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   protected void undoMenuItem_actionPerformed()
1641   {
1642     if (viewport.getHistoryList().isEmpty())
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getHistoryList().pop();
1648     viewport.addToRedoList(command);
1649     command.undoCommand(null);
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     // JBPNote Test
1653     if (originalSource != viewport)
1654     {
1655       System.err
1656               .println("Warning: Viewport object mismatch whilst undoing");
1657     }
1658     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1659                                           // viewport.getColumnSelection().getHiddenColumns()
1660                                           // != null;
1661     updateEditMenuBar();
1662     originalSource.firePropertyChange("alignment", null, originalSource
1663             .getAlignment().getSequences());
1664   }
1665
1666   /**
1667    * TODO: JAL-1104 DOCUMENT ME!
1668    *
1669    * @param e
1670    *          DOCUMENT ME!
1671    */
1672   protected void redoMenuItem_actionPerformed()
1673   {
1674     if (viewport.getRedoList().isEmpty())
1675     {
1676       return;
1677     }
1678
1679     CommandI command = viewport.getRedoList().pop();
1680     viewport.addToHistoryList(command);
1681     command.doCommand(null);
1682
1683     AlignmentViewport originalSource = getOriginatingSource(command);
1684     // JBPNote Test
1685     if (originalSource != viewport)
1686     {
1687       System.err
1688               .println("Warning: Viewport object mismatch whilst re-doing");
1689     }
1690     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1691                                           // viewport.getColumnSelection().getHiddenColumns()
1692                                           // != null;
1693
1694     updateEditMenuBar();
1695     originalSource.firePropertyChange("alignment", null, originalSource
1696             .getAlignment().getSequences());
1697   }
1698
1699   AlignmentViewport getOriginatingSource(CommandI command)
1700   {
1701     AlignmentViewport originalSource = null;
1702     // For sequence removal and addition, we need to fire
1703     // the property change event FROM the viewport where the
1704     // original alignment was altered
1705     AlignmentI al = null;
1706     if (command instanceof EditCommand)
1707     {
1708       EditCommand editCommand = (EditCommand) command;
1709       al = editCommand.getAlignment();
1710       Vector comps = (Vector) PaintRefresher.components.get(viewport
1711               .getSequenceSetId());
1712       for (int i = 0; i < comps.size(); i++)
1713       {
1714         if (comps.elementAt(i) instanceof AlignmentPanel)
1715         {
1716           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1717           {
1718             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1719             break;
1720           }
1721         }
1722       }
1723     }
1724
1725     if (originalSource == null)
1726     {
1727       // The original view is closed, we must validate
1728       // the current view against the closed view first
1729       if (al != null)
1730       {
1731         PaintRefresher.validateSequences(al, viewport.getAlignment());
1732       }
1733
1734       originalSource = viewport;
1735     }
1736
1737     return originalSource;
1738   }
1739
1740   /**
1741    * Move the currently selected sequences up or down one position in the
1742    * alignment
1743    *
1744    * @param up
1745    */
1746   public void moveSelectedSequences(boolean up)
1747   {
1748     SequenceGroup sg = viewport.getSelectionGroup();
1749     if (sg == null)
1750     {
1751       return;
1752     }
1753     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1754             up ? null : viewport.getHiddenRepSequences(), up);
1755     alignPanel.paintAlignment(true);
1756
1757     /*
1758      * Also move cDNA/protein complement sequences
1759      */
1760     AlignViewportI complement = viewport.getCodingComplement();
1761     if (complement != null)
1762     {
1763       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1764               viewport, complement);
1765       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1766               up ? null : complement.getHiddenRepSequences(), up);
1767       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1768     }
1769   }
1770
1771   synchronized void slideSequences(boolean right, int size)
1772   {
1773     List<SequenceI> sg = new Vector<SequenceI>();
1774     if (viewport.cursorMode)
1775     {
1776       sg.add(viewport.getAlignment().getSequenceAt(
1777               alignPanel.seqPanel.seqCanvas.cursorY));
1778     }
1779     else if (viewport.getSelectionGroup() != null
1780             && viewport.getSelectionGroup().getSize() != viewport
1781                     .getAlignment().getHeight())
1782     {
1783       sg = viewport.getSelectionGroup().getSequences(
1784               viewport.getHiddenRepSequences());
1785     }
1786
1787     if (sg.size() < 1)
1788     {
1789       return;
1790     }
1791
1792     Vector<SequenceI> invertGroup = new Vector();
1793
1794     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1795     {
1796       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1797       {
1798         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1799       }
1800     }
1801
1802     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1803
1804     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1805             .size()]);
1806     for (int i = 0; i < invertGroup.size(); i++)
1807     {
1808       seqs2[i] = invertGroup.elementAt(i);
1809     }
1810
1811     SlideSequencesCommand ssc;
1812     if (right)
1813     {
1814       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1815               size, viewport.getGapCharacter());
1816     }
1817     else
1818     {
1819       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1820               size, viewport.getGapCharacter());
1821     }
1822
1823     int groupAdjustment = 0;
1824     if (ssc.getGapsInsertedBegin() && right)
1825     {
1826       if (viewport.cursorMode)
1827       {
1828         alignPanel.seqPanel.moveCursor(size, 0);
1829       }
1830       else
1831       {
1832         groupAdjustment = size;
1833       }
1834     }
1835     else if (!ssc.getGapsInsertedBegin() && !right)
1836     {
1837       if (viewport.cursorMode)
1838       {
1839         alignPanel.seqPanel.moveCursor(-size, 0);
1840       }
1841       else
1842       {
1843         groupAdjustment = -size;
1844       }
1845     }
1846
1847     if (groupAdjustment != 0)
1848     {
1849       viewport.getSelectionGroup().setStartRes(
1850               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1851       viewport.getSelectionGroup().setEndRes(
1852               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1853     }
1854
1855     boolean appendHistoryItem = false;
1856     Deque<CommandI> historyList = viewport.getHistoryList();
1857     if (historyList != null && historyList.size() > 0
1858             && historyList.peek() instanceof SlideSequencesCommand)
1859     {
1860       appendHistoryItem = ssc
1861               .appendSlideCommand((SlideSequencesCommand) historyList
1862                       .peek());
1863     }
1864
1865     if (!appendHistoryItem)
1866     {
1867       addHistoryItem(ssc);
1868     }
1869
1870     repaint();
1871   }
1872
1873   static StringBuffer copiedSequences;
1874
1875   static Vector copiedHiddenColumns;
1876
1877   protected void copy_actionPerformed()
1878   {
1879     if (viewport.getSelectionGroup() == null)
1880     {
1881       return;
1882     }
1883
1884     SequenceGroup sg = viewport.getSelectionGroup();
1885     copiedSequences = new StringBuffer();
1886     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1887     for (int i = 0; i < sg.getSize(); i++)
1888     {
1889       SequenceI seq = sg.getSequenceAt(i);
1890       int index = viewport.getAlignment().findIndex(seq);
1891       orderedSeqs.put(index, seq);
1892     }
1893
1894     int index = 0, startRes, endRes;
1895     char ch;
1896
1897     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1898     {
1899       copiedHiddenColumns = new Vector();
1900       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1901       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1902       {
1903         copiedHiddenColumns.addElement(new int[] {
1904             region[0] - hiddenOffset, region[1] - hiddenOffset });
1905       }
1906     }
1907     else
1908     {
1909       copiedHiddenColumns = null;
1910     }
1911
1912     for (int i = 0; i < sg.getSize(); i++)
1913     {
1914       SequenceI seq = null;
1915
1916       while (seq == null)
1917       {
1918         if (orderedSeqs.containsKey(index))
1919         {
1920           seq = orderedSeqs.get(index);
1921           index++;
1922           break;
1923         }
1924         else
1925         {
1926           index++;
1927         }
1928       }
1929
1930       // FIND START RES
1931       // Returns residue following index if gap
1932       startRes = seq.findPosition(sg.getStartRes());
1933
1934       // FIND END RES
1935       // Need to find the residue preceeding index if gap
1936       endRes = 0;
1937
1938       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1939       {
1940         ch = seq.getCharAt(j);
1941         if (!jalview.util.Comparison.isGap((ch)))
1942         {
1943           endRes++;
1944         }
1945       }
1946
1947       if (endRes > 0)
1948       {
1949         endRes += seq.getStart() - 1;
1950       }
1951
1952       copiedSequences.append(seq.getName()
1953               + "\t"
1954               + startRes
1955               + "\t"
1956               + endRes
1957               + "\t"
1958               + seq.getSequenceAsString(sg.getStartRes(),
1959                       sg.getEndRes() + 1) + "\n");
1960     }
1961
1962   }
1963
1964   protected void pasteNew_actionPerformed()
1965   {
1966     paste(true);
1967   }
1968
1969   protected void pasteThis_actionPerformed()
1970   {
1971     paste(false);
1972   }
1973
1974   void paste(boolean newAlignment)
1975   {
1976     try
1977     {
1978
1979       if (copiedSequences == null)
1980       {
1981         return;
1982       }
1983
1984       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1985       Vector seqs = new Vector();
1986       while (st.hasMoreElements())
1987       {
1988         String name = st.nextToken();
1989         int start = Integer.parseInt(st.nextToken());
1990         int end = Integer.parseInt(st.nextToken());
1991         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1992       }
1993       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1994       for (int i = 0; i < seqs.size(); i++)
1995       {
1996         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1997       }
1998
1999       if (newAlignment)
2000       {
2001         String newtitle = MessageManager
2002                 .getString("label.copied_sequences");
2003         if (getTitle().startsWith(
2004                 MessageManager.getString("label.copied_sequences")))
2005         {
2006           newtitle = getTitle();
2007         }
2008         else
2009         {
2010           newtitle = newtitle.concat(MessageManager.formatMessage(
2011                   "label.from_msname", new String[] { getTitle() }));
2012         }
2013         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2014                 viewport.applet, newtitle, false);
2015         if (copiedHiddenColumns != null)
2016         {
2017           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2018           {
2019             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2020             af.viewport.hideColumns(region[0], region[1]);
2021           }
2022         }
2023
2024         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2025                 frameHeight);
2026       }
2027       else
2028       {
2029         addSequences(newSeqs);
2030       }
2031
2032     } catch (Exception ex)
2033     {
2034     } // could be anything being pasted in here
2035
2036   }
2037
2038   void addSequences(SequenceI[] seqs)
2039   {
2040     for (int i = 0; i < seqs.length; i++)
2041     {
2042       viewport.getAlignment().addSequence(seqs[i]);
2043     }
2044
2045     // !newAlignment
2046     addHistoryItem(new EditCommand(
2047             MessageManager.getString("label.add_sequences"), Action.PASTE,
2048             seqs, 0, viewport.getAlignment().getWidth(),
2049             viewport.getAlignment()));
2050
2051     viewport.setEndSeq(viewport.getAlignment().getHeight());
2052     viewport.getAlignment().getWidth();
2053     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2054             .getSequences());
2055
2056   }
2057
2058   protected void cut_actionPerformed()
2059   {
2060     copy_actionPerformed();
2061     delete_actionPerformed();
2062   }
2063
2064   protected void delete_actionPerformed()
2065   {
2066
2067     SequenceGroup sg = viewport.getSelectionGroup();
2068     if (sg == null)
2069     {
2070       return;
2071     }
2072
2073     Vector seqs = new Vector();
2074     SequenceI seq;
2075     for (int i = 0; i < sg.getSize(); i++)
2076     {
2077       seq = sg.getSequenceAt(i);
2078       seqs.addElement(seq);
2079     }
2080
2081     /*
2082      * If the cut affects all sequences, warn, remove highlighted columns
2083      */
2084     if (sg.getSize() == viewport.getAlignment().getHeight())
2085     {
2086       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2087               .getAlignment().getWidth()) ? true : false;
2088       if (isEntireAlignWidth)
2089       {
2090         String title = MessageManager.getString("label.delete_all");
2091         Panel infoPanel = new Panel();
2092         infoPanel.setLayout(new FlowLayout());
2093         infoPanel
2094                 .add(new Label(MessageManager.getString("warn.delete_all")));
2095
2096         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2097         dialog.setMainPanel(infoPanel);
2098         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2099         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2100         dialog.setVisible(true);
2101
2102         if (!dialog.accept)
2103         {
2104           return;
2105         }
2106       }
2107       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2108               sg.getEndRes() + 1);
2109     }
2110
2111     SequenceI[] cut = new SequenceI[seqs.size()];
2112     for (int i = 0; i < seqs.size(); i++)
2113     {
2114       cut[i] = (SequenceI) seqs.elementAt(i);
2115     }
2116
2117     /*
2118      * //ADD HISTORY ITEM
2119      */
2120     addHistoryItem(new EditCommand(
2121             MessageManager.getString("label.cut_sequences"), Action.CUT,
2122             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2123             viewport.getAlignment()));
2124
2125     viewport.setSelectionGroup(null);
2126     viewport.getAlignment().deleteGroup(sg);
2127
2128     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2129             .getSequences());
2130
2131     if (viewport.getAlignment().getHeight() < 1)
2132     {
2133       this.setVisible(false);
2134     }
2135     viewport.sendSelection();
2136   }
2137
2138   /**
2139    * group consensus toggled
2140    *
2141    */
2142   protected void showGroupConsensus_actionPerformed()
2143   {
2144     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2145     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2146
2147   }
2148
2149   /**
2150    * group conservation toggled.
2151    */
2152   protected void showGroupConservation_actionPerformed()
2153   {
2154     viewport.setShowGroupConservation(showGroupConservation.getState());
2155     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2156   }
2157
2158   /*
2159    * (non-Javadoc)
2160    *
2161    * @see
2162    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2163    * .event.ActionEvent)
2164    */
2165   protected void showConsensusHistogram_actionPerformed()
2166   {
2167     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2168     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2169   }
2170
2171   /*
2172    * (non-Javadoc)
2173    *
2174    * @see
2175    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2176    * .event.ActionEvent)
2177    */
2178   protected void showSequenceLogo_actionPerformed()
2179   {
2180     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2181     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2182   }
2183
2184   protected void normSequenceLogo_actionPerformed()
2185   {
2186     showSequenceLogo.setState(true);
2187     viewport.setShowSequenceLogo(true);
2188     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2189     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190   }
2191
2192   protected void applyAutoAnnotationSettings_actionPerformed()
2193   {
2194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195   }
2196
2197   protected void makeGrpsFromSelection_actionPerformed()
2198   {
2199     if (avc.makeGroupsFromSelection())
2200     {
2201       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2202       alignPanel.updateAnnotation();
2203       alignPanel.paintAlignment(true);
2204     }
2205   }
2206
2207   protected void createGroup_actionPerformed()
2208   {
2209     avc.createGroup();
2210   }
2211
2212   protected void unGroup_actionPerformed()
2213   {
2214     if (avc.unGroup())
2215     {
2216       alignPanel.alignmentChanged();
2217     }
2218   }
2219
2220   protected void deleteGroups_actionPerformed()
2221   {
2222     if (avc.deleteGroups())
2223     {
2224       alignPanel.alignmentChanged();
2225     }
2226   }
2227
2228   public void selectAllSequenceMenuItem_actionPerformed()
2229   {
2230     SequenceGroup sg = new SequenceGroup();
2231     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2232     {
2233       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2234     }
2235     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2236     viewport.setSelectionGroup(sg);
2237     alignPanel.paintAlignment(true);
2238     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2239     viewport.sendSelection();
2240   }
2241
2242   public void deselectAllSequenceMenuItem_actionPerformed()
2243   {
2244     if (viewport.cursorMode)
2245     {
2246       alignPanel.seqPanel.keyboardNo1 = null;
2247       alignPanel.seqPanel.keyboardNo2 = null;
2248     }
2249     viewport.setSelectionGroup(null);
2250     viewport.getColumnSelection().clear();
2251     viewport.setSelectionGroup(null);
2252     alignPanel.idPanel.idCanvas.searchResults = null;
2253     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2254     alignPanel.paintAlignment(true);
2255     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2256     viewport.sendSelection();
2257   }
2258
2259   public void invertSequenceMenuItem_actionPerformed()
2260   {
2261     SequenceGroup sg = viewport.getSelectionGroup();
2262     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2263     {
2264       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2265     }
2266
2267     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2268     viewport.sendSelection();
2269   }
2270
2271   public void invertColSel_actionPerformed()
2272   {
2273     viewport.invertColumnSelection();
2274     alignPanel.paintAlignment(true);
2275     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2276     viewport.sendSelection();
2277   }
2278
2279   void trimAlignment(boolean trimLeft)
2280   {
2281     ColumnSelection colSel = viewport.getColumnSelection();
2282     int column;
2283
2284     if (!colSel.isEmpty())
2285     {
2286       if (trimLeft)
2287       {
2288         column = colSel.getMin();
2289       }
2290       else
2291       {
2292         column = colSel.getMax();
2293       }
2294
2295       SequenceI[] seqs;
2296       if (viewport.getSelectionGroup() != null)
2297       {
2298         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2299                 viewport.getHiddenRepSequences());
2300       }
2301       else
2302       {
2303         seqs = viewport.getAlignment().getSequencesArray();
2304       }
2305
2306       TrimRegionCommand trimRegion;
2307       if (trimLeft)
2308       {
2309         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2310                 column, viewport.getAlignment());
2311         viewport.setStartRes(0);
2312       }
2313       else
2314       {
2315         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2316                 column, viewport.getAlignment());
2317       }
2318
2319       statusBar.setText(MessageManager.formatMessage(
2320               "label.removed_columns",
2321               new String[] { Integer.valueOf(trimRegion.getSize())
2322                       .toString() }));
2323       addHistoryItem(trimRegion);
2324
2325       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2326       {
2327         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2328                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2329         {
2330           viewport.getAlignment().deleteGroup(sg);
2331         }
2332       }
2333
2334       viewport.firePropertyChange("alignment", null, viewport
2335               .getAlignment().getSequences());
2336     }
2337   }
2338
2339   public void removeGappedColumnMenuItem_actionPerformed()
2340   {
2341     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2342
2343     SequenceI[] seqs;
2344     if (viewport.getSelectionGroup() != null)
2345     {
2346       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2347               viewport.getHiddenRepSequences());
2348       start = viewport.getSelectionGroup().getStartRes();
2349       end = viewport.getSelectionGroup().getEndRes();
2350     }
2351     else
2352     {
2353       seqs = viewport.getAlignment().getSequencesArray();
2354     }
2355
2356     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2357             "Remove Gapped Columns", seqs, start, end,
2358             viewport.getAlignment());
2359
2360     addHistoryItem(removeGapCols);
2361
2362     statusBar.setText(MessageManager.formatMessage(
2363             "label.removed_empty_columns",
2364             new String[] { Integer.valueOf(removeGapCols.getSize())
2365                     .toString() }));
2366
2367     // This is to maintain viewport position on first residue
2368     // of first sequence
2369     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2370     int startRes = seq.findPosition(viewport.startRes);
2371     // ShiftList shifts;
2372     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2373     // edit.alColumnChanges=shifts.getInverse();
2374     // if (viewport.hasHiddenColumns)
2375     // viewport.getColumnSelection().compensateForEdits(shifts);
2376     viewport.setStartRes(seq.findIndex(startRes) - 1);
2377     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2378             .getSequences());
2379
2380   }
2381
2382   public void removeAllGapsMenuItem_actionPerformed()
2383   {
2384     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2385
2386     SequenceI[] seqs;
2387     if (viewport.getSelectionGroup() != null)
2388     {
2389       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2390               viewport.getHiddenRepSequences());
2391       start = viewport.getSelectionGroup().getStartRes();
2392       end = viewport.getSelectionGroup().getEndRes();
2393     }
2394     else
2395     {
2396       seqs = viewport.getAlignment().getSequencesArray();
2397     }
2398
2399     // This is to maintain viewport position on first residue
2400     // of first sequence
2401     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2402     int startRes = seq.findPosition(viewport.startRes);
2403
2404     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2405             viewport.getAlignment()));
2406
2407     viewport.setStartRes(seq.findIndex(startRes) - 1);
2408
2409     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2410             .getSequences());
2411
2412   }
2413
2414   public void findMenuItem_actionPerformed()
2415   {
2416     new Finder(alignPanel);
2417   }
2418
2419   /**
2420    * create a new view derived from the current view
2421    *
2422    * @param viewtitle
2423    * @return frame for the new view
2424    */
2425   public AlignFrame newView(String viewtitle)
2426   {
2427     AlignmentI newal;
2428     if (viewport.hasHiddenRows())
2429     {
2430       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2431               .getFullAlignment().getSequencesArray());
2432     }
2433     else
2434     {
2435       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2436     }
2437
2438     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2439     {
2440       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2441       {
2442         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2443         {
2444           newal.addAnnotation(viewport.getAlignment()
2445                   .getAlignmentAnnotation()[i]);
2446         }
2447       }
2448     }
2449
2450     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2451
2452     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2453     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2454     PaintRefresher.Register(newaf.alignPanel,
2455             newaf.alignPanel.av.getSequenceSetId());
2456
2457     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2458             newaf.alignPanel.av.getSequenceSetId());
2459     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2460             newaf.alignPanel.av.getSequenceSetId());
2461
2462     Vector comps = (Vector) PaintRefresher.components.get(viewport
2463             .getSequenceSetId());
2464     int viewSize = -1;
2465     for (int i = 0; i < comps.size(); i++)
2466     {
2467       if (comps.elementAt(i) instanceof AlignmentPanel)
2468       {
2469         viewSize++;
2470       }
2471     }
2472
2473     String title = new String(this.getTitle());
2474     if (viewtitle != null)
2475     {
2476       title = viewtitle + " ( " + title + ")";
2477     }
2478     else
2479     {
2480       if (title.indexOf("(View") > -1)
2481       {
2482         title = title.substring(0, title.indexOf("(View"));
2483       }
2484       title += "(View " + viewSize + ")";
2485     }
2486
2487     newaf.setTitle(title.toString());
2488
2489     newaf.viewport.setHistoryList(viewport.getHistoryList());
2490     newaf.viewport.setRedoList(viewport.getRedoList());
2491     return newaf;
2492   }
2493
2494   /**
2495    *
2496    * @return list of feature groups on the view
2497    */
2498   public String[] getFeatureGroups()
2499   {
2500     FeatureRenderer fr = null;
2501     if (alignPanel != null
2502             && (fr = alignPanel.getFeatureRenderer()) != null)
2503     {
2504       List<String> gps = fr.getFeatureGroups();
2505       String[] _gps = gps.toArray(new String[gps.size()]);
2506       return _gps;
2507     }
2508     return null;
2509   }
2510
2511   /**
2512    * get sequence feature groups that are hidden or shown
2513    *
2514    * @param visible
2515    *          true is visible
2516    * @return list
2517    */
2518   public String[] getFeatureGroupsOfState(boolean visible)
2519   {
2520     FeatureRenderer fr = null;
2521     if (alignPanel != null
2522             && (fr = alignPanel.getFeatureRenderer()) != null)
2523     {
2524       List<String> gps = fr.getGroups(visible);
2525       String[] _gps = gps.toArray(new String[gps.size()]);
2526       return _gps;
2527     }
2528     return null;
2529   }
2530
2531   /**
2532    * Change the display state for the given feature groups
2533    *
2534    * @param groups
2535    *          list of group strings
2536    * @param state
2537    *          visible or invisible
2538    */
2539   public void setFeatureGroupState(String[] groups, boolean state)
2540   {
2541     FeatureRenderer fr = null;
2542     this.sequenceFeatures.setState(true);
2543     viewport.setShowSequenceFeatures(true);
2544     if (alignPanel != null
2545             && (fr = alignPanel.getFeatureRenderer()) != null)
2546     {
2547
2548       fr.setGroupVisibility(Arrays.asList(groups), state);
2549       alignPanel.seqPanel.seqCanvas.repaint();
2550       if (alignPanel.overviewPanel != null)
2551       {
2552         alignPanel.overviewPanel.updateOverviewImage();
2553       }
2554     }
2555   }
2556
2557   public void seqLimits_itemStateChanged()
2558   {
2559     viewport.setShowJVSuffix(seqLimits.getState());
2560     alignPanel.fontChanged();
2561     alignPanel.paintAlignment(true);
2562   }
2563
2564   protected void colourTextMenuItem_actionPerformed()
2565   {
2566     viewport.setColourText(colourTextMenuItem.getState());
2567     alignPanel.paintAlignment(true);
2568   }
2569
2570   protected void displayNonconservedMenuItem_actionPerformed()
2571   {
2572     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2573     alignPanel.paintAlignment(true);
2574   }
2575
2576   protected void wrapMenuItem_actionPerformed()
2577   {
2578     viewport.setWrapAlignment(wrapMenuItem.getState());
2579     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2580     scaleAbove.setEnabled(wrapMenuItem.getState());
2581     scaleLeft.setEnabled(wrapMenuItem.getState());
2582     scaleRight.setEnabled(wrapMenuItem.getState());
2583     alignPanel.paintAlignment(true);
2584   }
2585
2586   public void overviewMenuItem_actionPerformed()
2587   {
2588     if (alignPanel.overviewPanel != null)
2589     {
2590       return;
2591     }
2592
2593     Frame frame = new Frame();
2594     OverviewPanel overview = new OverviewPanel(alignPanel);
2595     frame.add(overview);
2596     // +50 must allow for applet frame window
2597     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2598             "label.overview_params", new String[] { this.getTitle() }),
2599             overview.getPreferredSize().width,
2600             overview.getPreferredSize().height + 50);
2601
2602     frame.pack();
2603     final AlignmentPanel ap = alignPanel;
2604     frame.addWindowListener(new WindowAdapter()
2605     {
2606       @Override
2607       public void windowClosing(WindowEvent e)
2608       {
2609         if (ap != null)
2610         {
2611           ap.setOverviewPanel(null);
2612         }
2613       };
2614     });
2615
2616     alignPanel.setOverviewPanel(overview);
2617
2618   }
2619
2620   @Override
2621   public void changeColour(ColourSchemeI cs)
2622   {
2623
2624     if (cs != null)
2625     {
2626       if (viewport.getAbovePIDThreshold())
2627       {
2628         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2629                 cs, "Background"));
2630       }
2631
2632       if (viewport.getConservationSelected())
2633       {
2634         cs.setConservationApplied(true);
2635         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2636                 cs, "Background"));
2637       }
2638       else
2639       {
2640         cs.setConservationApplied(false);
2641       }
2642     }
2643     viewport.setGlobalColourScheme(cs);
2644
2645     alignPanel.paintAlignment(true);
2646   }
2647
2648   protected void modifyPID_actionPerformed()
2649   {
2650     if (viewport.getAbovePIDThreshold()
2651             && viewport.getGlobalColourScheme() != null)
2652     {
2653       SliderPanel.setPIDSliderSource(alignPanel,
2654               viewport.getGlobalColourScheme(), "Background");
2655       SliderPanel.showPIDSlider();
2656     }
2657   }
2658
2659   protected void modifyConservation_actionPerformed()
2660   {
2661     if (viewport.getConservationSelected()
2662             && viewport.getGlobalColourScheme() != null)
2663     {
2664       SliderPanel.setConservationSlider(alignPanel,
2665               viewport.getGlobalColourScheme(), "Background");
2666       SliderPanel.showConservationSlider();
2667     }
2668   }
2669
2670   protected void conservationMenuItem_actionPerformed()
2671   {
2672     viewport.setConservationSelected(conservationMenuItem.getState());
2673
2674     viewport.setAbovePIDThreshold(false);
2675     abovePIDThreshold.setState(false);
2676
2677     changeColour(viewport.getGlobalColourScheme());
2678
2679     modifyConservation_actionPerformed();
2680   }
2681
2682   public void abovePIDThreshold_actionPerformed()
2683   {
2684     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2685
2686     conservationMenuItem.setState(false);
2687     viewport.setConservationSelected(false);
2688
2689     changeColour(viewport.getGlobalColourScheme());
2690
2691     modifyPID_actionPerformed();
2692   }
2693
2694   public void sortPairwiseMenuItem_actionPerformed()
2695   {
2696     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2697     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2698             .getAlignment().getSequenceAt(0), null);
2699
2700     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2701             viewport.getAlignment()));
2702     alignPanel.paintAlignment(true);
2703   }
2704
2705   public void sortIDMenuItem_actionPerformed()
2706   {
2707     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2708     AlignmentSorter.sortByID(viewport.getAlignment());
2709     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2710             viewport.getAlignment()));
2711     alignPanel.paintAlignment(true);
2712   }
2713
2714   public void sortLengthMenuItem_actionPerformed()
2715   {
2716     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2717     AlignmentSorter.sortByLength(viewport.getAlignment());
2718     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2719             viewport.getAlignment()));
2720     alignPanel.paintAlignment(true);
2721   }
2722
2723   public void sortGroupMenuItem_actionPerformed()
2724   {
2725     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2726     AlignmentSorter.sortByGroup(viewport.getAlignment());
2727     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2728             viewport.getAlignment()));
2729     alignPanel.paintAlignment(true);
2730
2731   }
2732
2733   public void removeRedundancyMenuItem_actionPerformed()
2734   {
2735     new RedundancyPanel(alignPanel);
2736   }
2737
2738   public void pairwiseAlignmentMenuItem_actionPerformed()
2739   {
2740     if (viewport.getSelectionGroup() != null
2741             && viewport.getSelectionGroup().getSize() > 1)
2742     {
2743       Frame frame = new Frame();
2744       frame.add(new PairwiseAlignPanel(alignPanel));
2745       jalview.bin.JalviewLite.addFrame(frame,
2746               MessageManager.getString("action.pairwise_alignment"), 600,
2747               500);
2748     }
2749   }
2750
2751   public void PCAMenuItem_actionPerformed()
2752   {
2753     // are the sequences aligned?
2754     if (!viewport.getAlignment().isAligned(false))
2755     {
2756       SequenceI current;
2757       int Width = viewport.getAlignment().getWidth();
2758
2759       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2760       {
2761         current = viewport.getAlignment().getSequenceAt(i);
2762
2763         if (current.getLength() < Width)
2764         {
2765           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2766         }
2767       }
2768       alignPanel.paintAlignment(true);
2769     }
2770
2771     if ((viewport.getSelectionGroup() != null
2772             && viewport.getSelectionGroup().getSize() < 4 && viewport
2773             .getSelectionGroup().getSize() > 0)
2774             || viewport.getAlignment().getHeight() < 4)
2775     {
2776       return;
2777     }
2778
2779     try
2780     {
2781       new PCAPanel(viewport);
2782     } catch (java.lang.OutOfMemoryError ex)
2783     {
2784     }
2785
2786   }
2787
2788   public void averageDistanceTreeMenuItem_actionPerformed()
2789   {
2790     NewTreePanel("AV", "PID", "Average distance tree using PID");
2791   }
2792
2793   public void neighbourTreeMenuItem_actionPerformed()
2794   {
2795     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2796   }
2797
2798   protected void njTreeBlosumMenuItem_actionPerformed()
2799   {
2800     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2801   }
2802
2803   protected void avTreeBlosumMenuItem_actionPerformed()
2804   {
2805     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2806   }
2807
2808   void NewTreePanel(String type, String pwType, String title)
2809   {
2810     // are the sequences aligned?
2811     if (!viewport.getAlignment().isAligned(false))
2812     {
2813       SequenceI current;
2814       int Width = viewport.getAlignment().getWidth();
2815
2816       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2817       {
2818         current = viewport.getAlignment().getSequenceAt(i);
2819
2820         if (current.getLength() < Width)
2821         {
2822           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2823         }
2824       }
2825       alignPanel.paintAlignment(true);
2826
2827     }
2828
2829     if ((viewport.getSelectionGroup() != null && viewport
2830             .getSelectionGroup().getSize() > 1)
2831             || (viewport.getAlignment().getHeight() > 1))
2832     {
2833       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2834
2835       addTreeMenuItem(tp, title);
2836
2837       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2838     }
2839   }
2840
2841   void loadTree_actionPerformed()
2842   {
2843     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2844     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2845     cap.setTreeImport();
2846     Frame frame = new Frame();
2847     frame.add(cap);
2848     jalview.bin.JalviewLite.addFrame(frame,
2849             MessageManager.getString("label.paste_newick_file"), 400, 300);
2850   }
2851
2852   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2853   {
2854     TreePanel tp = new TreePanel(alignPanel, treeFile,
2855             MessageManager.getString("label.load_tree_from_file"), tree);
2856     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2857     addTreeMenuItem(tp, treeFile);
2858   }
2859
2860   /**
2861    * sort the alignment using the given treePanel
2862    *
2863    * @param treePanel
2864    *          tree used to sort view
2865    * @param title
2866    *          string used for undo event name
2867    */
2868   public void sortByTree(TreePanel treePanel, String title)
2869   {
2870     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2871     AlignmentSorter
2872             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2873     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2874     // HistoryItem.SORT));
2875     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2876             "label.order_by_params", new String[] { title }), oldOrder,
2877             viewport.getAlignment()));
2878     alignPanel.paintAlignment(true);
2879   }
2880
2881   /**
2882    * Do any automatic reordering of the alignment and add the necessary bits to
2883    * the menu structure for the new tree
2884    *
2885    * @param treePanel
2886    * @param title
2887    */
2888   protected void addTreeMenuItem(final TreePanel treePanel,
2889           final String title)
2890   {
2891     final MenuItem item = new MenuItem(title);
2892     sortByTreeMenu.add(item);
2893     item.addActionListener(new java.awt.event.ActionListener()
2894     {
2895       @Override
2896       public void actionPerformed(ActionEvent evt)
2897       {
2898         sortByTree(treePanel, title); // treePanel.getTitle());
2899       }
2900     });
2901
2902     treePanel.addWindowListener(new WindowAdapter()
2903     {
2904       @Override
2905       public void windowOpened(WindowEvent e)
2906       {
2907         if (viewport.sortByTree)
2908         {
2909           sortByTree(treePanel, title);
2910         }
2911         super.windowOpened(e);
2912       }
2913
2914       @Override
2915       public void windowClosing(WindowEvent e)
2916       {
2917         sortByTreeMenu.remove(item);
2918       };
2919     });
2920   }
2921
2922   public boolean sortBy(AlignmentOrder alorder, String undoname)
2923   {
2924     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2925     if (viewport.applet.debug)
2926     {
2927       System.err.println("Sorting " + alorder.getOrder().size()
2928               + " in alignment '" + getTitle() + "'");
2929     }
2930     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2931     if (undoname != null)
2932     {
2933       addHistoryItem(new OrderCommand(undoname, oldOrder,
2934               viewport.getAlignment()));
2935     }
2936     alignPanel.paintAlignment(true);
2937     return true;
2938   }
2939
2940   protected void documentation_actionPerformed()
2941   {
2942     alignPanel.av.applet.openJalviewHelpUrl();
2943   }
2944
2945   protected void about_actionPerformed()
2946   {
2947
2948     class AboutPanel extends Canvas
2949     {
2950       String version;
2951
2952       String builddate;
2953
2954       public AboutPanel(String version, String builddate)
2955       {
2956         this.version = version;
2957         this.builddate = builddate;
2958       }
2959
2960       @Override
2961       public void paint(Graphics g)
2962       {
2963         g.setColor(Color.white);
2964         g.fillRect(0, 0, getSize().width, getSize().height);
2965         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2966         FontMetrics fm = g.getFontMetrics();
2967         int fh = fm.getHeight();
2968         int y = 5, x = 7;
2969         g.setColor(Color.black);
2970         // TODO: update this text for each release or centrally store it for
2971         // lite and application
2972         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2973         g.drawString(MessageManager.formatMessage(
2974                 "label.jalviewLite_release", new String[] { version }), x,
2975                 y += fh);
2976         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2977         g.drawString(MessageManager.formatMessage(
2978                 "label.jaview_build_date", new String[] { builddate }), x,
2979                 y += fh);
2980         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2981         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2982                 x, y += fh * 1.5);
2983         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2984                 x + 50, y += fh + 8);
2985         g.drawString(
2986                 MessageManager.getString("label.jalview_dev_managers"), x,
2987                 y += fh);
2988         g.drawString(MessageManager
2989                 .getString("label.jalview_distribution_lists"), x, y += fh);
2990         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2991                 x, y += fh + 8);
2992         g.drawString(
2993                 MessageManager.getString("label.jalview_cite_1_authors"),
2994                 x, y += fh);
2995         g.drawString(
2996                 MessageManager.getString("label.jalview_cite_1_title"), x,
2997                 y += fh);
2998         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2999                 x, y += fh);
3000       }
3001     }
3002
3003     Frame frame = new Frame();
3004     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3005             .getBuildDate()));
3006     jalview.bin.JalviewLite.addFrame(frame,
3007             MessageManager.getString("label.jalview"), 580, 220);
3008
3009   }
3010
3011   public void showURL(String url, String target)
3012   {
3013     if (viewport.applet == null)
3014     {
3015       System.out.println("Not running as applet - no browser available.");
3016     }
3017     else
3018     {
3019       viewport.applet.showURL(url, target);
3020     }
3021   }
3022
3023   // ////////////////////////////////////////////////////////////////////////////////
3024   // JBuilder Graphics here
3025
3026   MenuBar alignFrameMenuBar = new MenuBar();
3027
3028   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3029
3030   MenuItem loadApplication = new MenuItem(
3031           MessageManager.getString("label.view_full_application"));
3032
3033   MenuItem loadTree = new MenuItem(
3034           MessageManager.getString("label.load_associated_tree"));
3035
3036   MenuItem loadAnnotations = new MenuItem(
3037           MessageManager.getString("label.load_features_annotations"));
3038
3039   MenuItem outputFeatures = new MenuItem(
3040           MessageManager.getString("label.export_features"));
3041
3042   MenuItem outputAnnotations = new MenuItem(
3043           MessageManager.getString("label.export_annotations"));
3044
3045   MenuItem closeMenuItem = new MenuItem(
3046           MessageManager.getString("action.close"));
3047
3048   MenuItem selectAllSequenceMenuItem = new MenuItem(
3049           MessageManager.getString("action.select_all"));
3050
3051   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3052           MessageManager.getString("action.deselect_all"));
3053
3054   MenuItem invertSequenceMenuItem = new MenuItem(
3055           MessageManager.getString("action.invert_selection"));
3056
3057   MenuItem remove2LeftMenuItem = new MenuItem();
3058
3059   MenuItem remove2RightMenuItem = new MenuItem();
3060
3061   MenuItem removeGappedColumnMenuItem = new MenuItem();
3062
3063   MenuItem removeAllGapsMenuItem = new MenuItem();
3064
3065   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3066
3067   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3068
3069   MenuItem sortPairwiseMenuItem = new MenuItem();
3070
3071   MenuItem sortIDMenuItem = new MenuItem();
3072
3073   MenuItem sortLengthMenuItem = new MenuItem();
3074
3075   MenuItem sortGroupMenuItem = new MenuItem();
3076
3077   MenuItem removeRedundancyMenuItem = new MenuItem();
3078
3079   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3080
3081   MenuItem PCAMenuItem = new MenuItem();
3082
3083   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3084
3085   MenuItem neighbourTreeMenuItem = new MenuItem();
3086
3087   BorderLayout borderLayout1 = new BorderLayout();
3088
3089   public Label statusBar = new Label();
3090
3091   MenuItem clustalColour = new MenuItem();
3092
3093   MenuItem zappoColour = new MenuItem();
3094
3095   MenuItem taylorColour = new MenuItem();
3096
3097   MenuItem hydrophobicityColour = new MenuItem();
3098
3099   MenuItem helixColour = new MenuItem();
3100
3101   MenuItem strandColour = new MenuItem();
3102
3103   MenuItem turnColour = new MenuItem();
3104
3105   MenuItem buriedColour = new MenuItem();
3106
3107   MenuItem purinePyrimidineColour = new MenuItem();
3108
3109   // MenuItem RNAInteractionColour = new MenuItem();
3110
3111   MenuItem RNAHelixColour = new MenuItem();
3112
3113   MenuItem userDefinedColour = new MenuItem();
3114
3115   MenuItem PIDColour = new MenuItem();
3116
3117   MenuItem BLOSUM62Colour = new MenuItem();
3118
3119   MenuItem tcoffeeColour = new MenuItem();
3120
3121   MenuItem njTreeBlosumMenuItem = new MenuItem();
3122
3123   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3124
3125   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3126
3127   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3128
3129   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3130
3131   MenuItem alProperties = new MenuItem(
3132           MessageManager.getString("label.alignment_props"));
3133
3134   MenuItem overviewMenuItem = new MenuItem();
3135
3136   MenuItem undoMenuItem = new MenuItem();
3137
3138   MenuItem redoMenuItem = new MenuItem();
3139
3140   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3141
3142   MenuItem noColourmenuItem = new MenuItem();
3143
3144   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3145
3146   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3147
3148   MenuItem findMenuItem = new MenuItem();
3149
3150   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3151
3152   MenuItem nucleotideColour = new MenuItem();
3153
3154   MenuItem deleteGroups = new MenuItem();
3155
3156   MenuItem grpsFromSelection = new MenuItem();
3157
3158   MenuItem createGroup = new MenuItem();
3159
3160   MenuItem unGroup = new MenuItem();
3161
3162   MenuItem delete = new MenuItem();
3163
3164   MenuItem copy = new MenuItem();
3165
3166   MenuItem cut = new MenuItem();
3167
3168   Menu pasteMenu = new Menu();
3169
3170   MenuItem pasteNew = new MenuItem();
3171
3172   MenuItem pasteThis = new MenuItem();
3173
3174   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3175
3176   MenuItem font = new MenuItem();
3177
3178   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3179
3180   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3181
3182   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3183
3184   MenuItem modifyPID = new MenuItem();
3185
3186   MenuItem modifyConservation = new MenuItem();
3187
3188   CheckboxMenuItem autoCalculate = null;
3189
3190   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3191           "Sort Alignment With New Tree", true);
3192
3193   Menu sortByTreeMenu = new Menu();
3194
3195   MenuItem inputText = new MenuItem();
3196
3197   MenuItem documentation = new MenuItem();
3198
3199   MenuItem about = new MenuItem();
3200
3201   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3202
3203   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3204
3205   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3206
3207   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3208
3209   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3218
3219   /**
3220    * Initialise menus and other items
3221    *
3222    * @throws Exception
3223    */
3224   private void jbInit() throws Exception
3225   {
3226     setMenuBar(alignFrameMenuBar);
3227
3228     /*
3229      * Configure File menu items and actions
3230      */
3231     inputText
3232             .setLabel(MessageManager.getString("label.input_from_textbox"));
3233     inputText.addActionListener(this);
3234     Menu outputTextboxMenu = new Menu(
3235             MessageManager.getString("label.out_to_textbox"));
3236     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3237     {
3238
3239       MenuItem item = new MenuItem(
3240               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3241
3242       item.addActionListener(new java.awt.event.ActionListener()
3243       {
3244         @Override
3245         public void actionPerformed(ActionEvent e)
3246         {
3247           outputText_actionPerformed(e);
3248         }
3249       });
3250
3251       outputTextboxMenu.add(item);
3252     }
3253     closeMenuItem.addActionListener(this);
3254     loadApplication.addActionListener(this);
3255     loadTree.addActionListener(this);
3256     loadAnnotations.addActionListener(this);
3257     outputFeatures.addActionListener(this);
3258     outputAnnotations.addActionListener(this);
3259
3260     /*
3261      * Configure Edit menu items and actions
3262      */
3263     undoMenuItem.setEnabled(false);
3264     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3265     undoMenuItem.addActionListener(this);
3266     redoMenuItem.setEnabled(false);
3267     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3268     redoMenuItem.addActionListener(this);
3269     copy.setLabel(MessageManager.getString("action.copy"));
3270     copy.addActionListener(this);
3271     cut.setLabel(MessageManager.getString("action.cut"));
3272     cut.addActionListener(this);
3273     delete.setLabel(MessageManager.getString("action.delete"));
3274     delete.addActionListener(this);
3275     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3276     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3277     pasteNew.addActionListener(this);
3278     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3279     pasteThis.addActionListener(this);
3280     remove2LeftMenuItem.setLabel(MessageManager
3281             .getString("action.remove_left"));
3282     remove2LeftMenuItem.addActionListener(this);
3283     remove2RightMenuItem.setLabel(MessageManager
3284             .getString("action.remove_right"));
3285     remove2RightMenuItem.addActionListener(this);
3286     removeGappedColumnMenuItem.setLabel(MessageManager
3287             .getString("action.remove_empty_columns"));
3288     removeGappedColumnMenuItem.addActionListener(this);
3289     removeAllGapsMenuItem.setLabel(MessageManager
3290             .getString("action.remove_all_gaps"));
3291     removeAllGapsMenuItem.addActionListener(this);
3292     removeRedundancyMenuItem.setLabel(MessageManager
3293             .getString("action.remove_redundancy"));
3294     removeRedundancyMenuItem.addActionListener(this);
3295
3296     /*
3297      * Configure Select menu items and actions
3298      */
3299     findMenuItem.setLabel(MessageManager.getString("action.find"));
3300     findMenuItem.addActionListener(this);
3301     selectAllSequenceMenuItem.addActionListener(this);
3302     deselectAllSequenceMenuItem.addActionListener(this);
3303     invertSequenceMenuItem.setLabel(MessageManager
3304             .getString("action.invert_sequence_selection"));
3305     invertSequenceMenuItem.addActionListener(this);
3306     invertColSel.setLabel(MessageManager
3307             .getString("action.invert_column_selection"));
3308     invertColSel.addActionListener(this);
3309     deleteGroups.setLabel(MessageManager
3310             .getString("action.undefine_groups"));
3311     deleteGroups.addActionListener(this);
3312     grpsFromSelection.setLabel(MessageManager
3313             .getString("action.make_groups_selection"));
3314     grpsFromSelection.addActionListener(this);
3315     createGroup.setLabel(MessageManager.getString("action.create_group"));
3316     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3317     annotationColumnSelection.setLabel(MessageManager
3318             .getString("action.select_by_annotation"));
3319     annotationColumnSelection.addActionListener(this);
3320
3321     /*
3322      * Configure View menu items and actions
3323      */
3324     newView.setLabel(MessageManager.getString("action.new_view"));
3325     newView.addActionListener(this);
3326     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3327     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3328     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3329     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3330     hideColumns
3331             .setLabel(MessageManager.getString("label.selected_columns"));
3332     hideSequences.setLabel(MessageManager
3333             .getString("label.selected_sequences"));
3334     hideAllButSelection.setLabel(MessageManager
3335             .getString("label.all_but_selected_region"));
3336     hideAllSelection.setLabel(MessageManager
3337             .getString("label.selected_region"));
3338     showAllHidden.setLabel(MessageManager
3339             .getString("label.all_sequences_columns"));
3340     showColumns.addActionListener(this);
3341     showSeqs.addActionListener(this);
3342     hideColumns.addActionListener(this);
3343     hideSequences.addActionListener(this);
3344     hideAllButSelection.addActionListener(this);
3345     hideAllSelection.addActionListener(this);
3346     showAllHidden.addActionListener(this);
3347     featureSettings.setLabel(MessageManager
3348             .getString("action.feature_settings"));
3349     featureSettings.addActionListener(this);
3350     sequenceFeatures.setLabel(MessageManager
3351             .getString("label.show_sequence_features"));
3352     sequenceFeatures.addItemListener(this);
3353     sequenceFeatures.setState(false);
3354     followMouseOverFlag.setLabel(MessageManager
3355             .getString("label.automatic_scrolling"));
3356     followMouseOverFlag.addItemListener(this);
3357     alProperties.addActionListener(this);
3358     overviewMenuItem.setLabel(MessageManager
3359             .getString("label.overview_window"));
3360     overviewMenuItem.addActionListener(this);
3361
3362     /*
3363      * Configure Annotations menu items and actions
3364      */
3365     annotationPanelMenuItem.setLabel(MessageManager
3366             .getString("label.show_annotations"));
3367     annotationPanelMenuItem.addItemListener(this);
3368     showGroupConsensus.setLabel(MessageManager
3369             .getString("label.group_consensus"));
3370     showGroupConservation.setLabel(MessageManager
3371             .getString("label.group_conservation"));
3372     showConsensusHistogram.setLabel(MessageManager
3373             .getString("label.show_consensus_histogram"));
3374     showSequenceLogo.setLabel(MessageManager
3375             .getString("label.show_consensus_logo"));
3376     normSequenceLogo.setLabel(MessageManager
3377             .getString("label.norm_consensus_logo"));
3378     applyAutoAnnotationSettings.setLabel(MessageManager
3379             .getString("label.apply_all_groups"));
3380     applyAutoAnnotationSettings.setState(true);
3381     Menu autoAnnMenu = new Menu(
3382             MessageManager.getString("label.autocalculated_annotation"));
3383     showGroupConsensus.addItemListener(this);
3384     showGroupConservation.addItemListener(this);
3385     showConsensusHistogram.addItemListener(this);
3386     showSequenceLogo.addItemListener(this);
3387     normSequenceLogo.addItemListener(this);
3388     applyAutoAnnotationSettings.addItemListener(this);
3389     showAlignmentAnnotations = new CheckboxMenuItem(
3390             MessageManager.getString("label.show_all_al_annotations"));
3391     showSequenceAnnotations = new CheckboxMenuItem(
3392             MessageManager.getString("label.show_all_seq_annotations"));
3393     sortAnnBySequence = new CheckboxMenuItem(
3394             MessageManager.getString("label.sort_annotations_by_sequence"));
3395     sortAnnByLabel = new CheckboxMenuItem(
3396             MessageManager.getString("label.sort_annotations_by_label"));
3397     showAutoFirst = new CheckboxMenuItem(
3398             MessageManager.getString("label.show_first"));
3399     showAutoFirst.setState(false); // pending applet parameter
3400     setShowAutoCalculatedAbove(showAutoFirst.getState());
3401     showAutoLast = new CheckboxMenuItem(
3402             MessageManager.getString("label.show_last"));
3403     showAutoLast.setState(!showAutoFirst.getState());
3404     showAlignmentAnnotations.addItemListener(this);
3405     showSequenceAnnotations.addItemListener(this);
3406     sortAnnBySequence.addItemListener(this);
3407     sortAnnByLabel.addItemListener(this);
3408     showAutoFirst.addItemListener(this);
3409     showAutoLast.addItemListener(this);
3410
3411     /*
3412      * Configure Format menu items and actions
3413      */
3414     font.setLabel(MessageManager.getString("action.font"));
3415     font.addActionListener(this);
3416     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3417     scaleAbove.setState(true);
3418     scaleAbove.setEnabled(false);
3419     scaleAbove.addItemListener(this);
3420     scaleLeft.setEnabled(false);
3421     scaleLeft.setState(true);
3422     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3423     scaleLeft.addItemListener(this);
3424     scaleRight.setEnabled(false);
3425     scaleRight.setState(true);
3426     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3427     scaleRight.addItemListener(this);
3428     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3429     viewBoxesMenuItem.setState(true);
3430     viewBoxesMenuItem.addItemListener(this);
3431     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3432     viewTextMenuItem.setState(true);
3433     viewTextMenuItem.addItemListener(this);
3434     colourTextMenuItem.setLabel(MessageManager
3435             .getString("label.colour_text"));
3436     colourTextMenuItem.addItemListener(this);
3437     displayNonconservedMenuItem.setLabel(MessageManager
3438             .getString("label.show_non_conversed"));
3439     displayNonconservedMenuItem.addItemListener(this);
3440     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3441     wrapMenuItem.addItemListener(this);
3442     renderGapsMenuItem.setLabel(MessageManager
3443             .getString("action.show_gaps"));
3444     renderGapsMenuItem.setState(true);
3445     renderGapsMenuItem.addItemListener(this);
3446     centreColumnLabelFlag.setLabel(MessageManager
3447             .getString("label.centre_column_labels"));
3448     centreColumnLabelFlag.addItemListener(this);
3449     seqLimits.setState(true);
3450     seqLimits.setLabel(MessageManager
3451             .getString("label.show_sequence_limits"));
3452     seqLimits.addItemListener(this);
3453
3454     /*
3455      * Configure Colour menu items and actions
3456      */
3457     applyToAllGroups.setLabel(MessageManager
3458             .getString("label.apply_colour_to_all_groups"));
3459     applyToAllGroups.setState(true);
3460     applyToAllGroups.addItemListener(this);
3461     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3462     clustalColour.addActionListener(this);
3463     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3464     zappoColour.addActionListener(this);
3465     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3466     taylorColour.addActionListener(this);
3467     hydrophobicityColour.setLabel(MessageManager
3468             .getString("label.hydrophobicity"));
3469     hydrophobicityColour.addActionListener(this);
3470     helixColour
3471             .setLabel(MessageManager.getString("label.helix_propensity"));
3472     helixColour.addActionListener(this);
3473     strandColour.setLabel(MessageManager
3474             .getString("label.strand_propensity"));
3475     strandColour.addActionListener(this);
3476     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3477     turnColour.addActionListener(this);
3478     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3479     buriedColour.addActionListener(this);
3480     purinePyrimidineColour.setLabel(MessageManager
3481             .getString("label.purine_pyrimidine"));
3482     purinePyrimidineColour.addActionListener(this);
3483     // RNAInteractionColour.setLabel(MessageManager
3484     // .getString("label.rna_interaction"));
3485     // RNAInteractionColour.addActionListener(this);
3486     RNAHelixColour.setLabel(MessageManager
3487             .getString("action.by_rna_helixes"));
3488     RNAHelixColour.addActionListener(this);
3489     userDefinedColour.setLabel(MessageManager
3490             .getString("action.user_defined"));
3491     userDefinedColour.addActionListener(this);
3492     PIDColour.setLabel(MessageManager
3493             .getString("label.percentage_identity"));
3494     PIDColour.addActionListener(this);
3495     BLOSUM62Colour.setLabel(MessageManager
3496             .getString("label.blosum62_score"));
3497     BLOSUM62Colour.addActionListener(this);
3498     tcoffeeColour
3499             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3500     // it will be enabled only if a score file is provided
3501     tcoffeeColour.setEnabled(false);
3502     tcoffeeColour.addActionListener(this);
3503     conservationMenuItem.setLabel(MessageManager
3504             .getString("action.by_conservation"));
3505     conservationMenuItem.addItemListener(this);
3506     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3507     noColourmenuItem.addActionListener(this);
3508     abovePIDThreshold.setLabel(MessageManager
3509             .getString("label.above_identity_threshold"));
3510     abovePIDThreshold.addItemListener(this);
3511     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3512     nucleotideColour.addActionListener(this);
3513     modifyPID.setLabel(MessageManager
3514             .getString("label.modify_identity_thereshold"));
3515     modifyPID.addActionListener(this);
3516     modifyConservation.setLabel(MessageManager
3517             .getString("label.modify_conservation_thereshold"));
3518     modifyConservation.addActionListener(this);
3519     annotationColour.setLabel(MessageManager
3520             .getString("action.by_annotation"));
3521     annotationColour.addActionListener(this);
3522
3523     /*
3524      * Configure Calculate menu items and actions
3525      */
3526     sortPairwiseMenuItem.setLabel(MessageManager
3527             .getString("action.by_pairwise_id"));
3528     sortPairwiseMenuItem.addActionListener(this);
3529     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3530     sortIDMenuItem.addActionListener(this);
3531     sortLengthMenuItem.setLabel(MessageManager
3532             .getString("action.by_length"));
3533     sortLengthMenuItem.addActionListener(this);
3534     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3535     sortGroupMenuItem.addActionListener(this);
3536     pairwiseAlignmentMenuItem.setLabel(MessageManager
3537             .getString("action.pairwise_alignment"));
3538     pairwiseAlignmentMenuItem.addActionListener(this);
3539     PCAMenuItem.setLabel(MessageManager
3540             .getString("label.principal_component_analysis"));
3541     PCAMenuItem.addActionListener(this);
3542     autoCalculate = new CheckboxMenuItem(
3543             MessageManager.getString("label.autocalculate_consensus"), true);
3544     averageDistanceTreeMenuItem.setLabel(MessageManager
3545             .getString("label.average_distance_identity"));
3546     averageDistanceTreeMenuItem.addActionListener(this);
3547     neighbourTreeMenuItem.setLabel(MessageManager
3548             .getString("label.neighbour_joining_identity"));
3549     neighbourTreeMenuItem.addActionListener(this);
3550     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3551             .getString("label.average_distance_bloslum62"));
3552     avDistanceTreeBlosumMenuItem.addActionListener(this);
3553     njTreeBlosumMenuItem.setLabel(MessageManager
3554             .getString("label.neighbour_blosum62"));
3555     njTreeBlosumMenuItem.addActionListener(this);
3556     sortByTreeMenu.setLabel(MessageManager
3557             .getString("action.by_tree_order"));
3558     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3559     Menu calculateTreeMenu = new Menu(
3560             MessageManager.getString("action.calculate_tree"));
3561     autoCalculate.addItemListener(this);
3562     sortByTree.addItemListener(this);
3563
3564     /*
3565      * Configure Help menu items and actions
3566      */
3567     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3568     documentation.setLabel(MessageManager.getString("label.documentation"));
3569     documentation.addActionListener(this);
3570     about.setLabel(MessageManager.getString("label.about"));
3571     about.addActionListener(this);
3572
3573     /*
3574      * Add top level menus to frame
3575      */
3576     alignFrameMenuBar.add(fileMenu);
3577     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3578     alignFrameMenuBar.add(editMenu);
3579     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3580     alignFrameMenuBar.add(selectMenu);
3581     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3582     alignFrameMenuBar.add(viewMenu);
3583     Menu annotationsMenu = new Menu(
3584             MessageManager.getString("action.annotations"));
3585     alignFrameMenuBar.add(annotationsMenu);
3586     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3587     alignFrameMenuBar.add(formatMenu);
3588     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3589     alignFrameMenuBar.add(colourMenu);
3590     Menu calculateMenu = new Menu(
3591             MessageManager.getString("action.calculate"));
3592     alignFrameMenuBar.add(calculateMenu);
3593     alignFrameMenuBar.add(helpMenu);
3594
3595     /*
3596      * File menu
3597      */
3598     fileMenu.add(inputText);
3599     fileMenu.add(loadTree);
3600     fileMenu.add(loadAnnotations);
3601     fileMenu.addSeparator();
3602     fileMenu.add(outputTextboxMenu);
3603     fileMenu.add(outputFeatures);
3604     fileMenu.add(outputAnnotations);
3605     if (jalviewServletURL != null)
3606     {
3607       fileMenu.add(loadApplication);
3608     }
3609     fileMenu.addSeparator();
3610     fileMenu.add(closeMenuItem);
3611
3612     /*
3613      * Edit menu
3614      */
3615     editMenu.add(undoMenuItem);
3616     editMenu.add(redoMenuItem);
3617     editMenu.add(cut);
3618     editMenu.add(copy);
3619     pasteMenu.add(pasteNew);
3620     pasteMenu.add(pasteThis);
3621     editMenu.add(pasteMenu);
3622     editMenu.add(delete);
3623     editMenu.addSeparator();
3624     editMenu.add(remove2LeftMenuItem);
3625     editMenu.add(remove2RightMenuItem);
3626     editMenu.add(removeGappedColumnMenuItem);
3627     editMenu.add(removeAllGapsMenuItem);
3628     editMenu.add(removeRedundancyMenuItem);
3629
3630     /*
3631      * Select menu
3632      */
3633     selectMenu.add(findMenuItem);
3634     selectMenu.addSeparator();
3635     selectMenu.add(selectAllSequenceMenuItem);
3636     selectMenu.add(deselectAllSequenceMenuItem);
3637     selectMenu.add(invertSequenceMenuItem);
3638     selectMenu.add(invertColSel);
3639     selectMenu.add(createGroup);
3640     selectMenu.add(unGroup);
3641     selectMenu.add(grpsFromSelection);
3642     selectMenu.add(deleteGroups);
3643     selectMenu.add(annotationColumnSelection);
3644
3645     /*
3646      * View menu
3647      */
3648     viewMenu.add(newView);
3649     viewMenu.addSeparator();
3650     showMenu.add(showColumns);
3651     showMenu.add(showSeqs);
3652     showMenu.add(showAllHidden);
3653     viewMenu.add(showMenu);
3654     hideMenu.add(hideColumns);
3655     hideMenu.add(hideSequences);
3656     hideMenu.add(hideAllSelection);
3657     hideMenu.add(hideAllButSelection);
3658     viewMenu.add(hideMenu);
3659     viewMenu.addSeparator();
3660     viewMenu.add(followMouseOverFlag);
3661     viewMenu.addSeparator();
3662     viewMenu.add(sequenceFeatures);
3663     viewMenu.add(featureSettings);
3664     viewMenu.addSeparator();
3665     viewMenu.add(alProperties);
3666     viewMenu.addSeparator();
3667     viewMenu.add(overviewMenuItem);
3668
3669     /*
3670      * Annotations menu
3671      */
3672     annotationsMenu.add(annotationPanelMenuItem);
3673     annotationsMenu.addSeparator();
3674     annotationsMenu.add(showAlignmentAnnotations);
3675     annotationsMenu.add(showSequenceAnnotations);
3676     annotationsMenu.add(sortAnnBySequence);
3677     annotationsMenu.add(sortAnnByLabel);
3678     annotationsMenu.addSeparator();
3679     autoAnnMenu.add(showAutoFirst);
3680     autoAnnMenu.add(showAutoLast);
3681     autoAnnMenu.addSeparator();
3682     autoAnnMenu.add(applyAutoAnnotationSettings);
3683     autoAnnMenu.add(showConsensusHistogram);
3684     autoAnnMenu.add(showSequenceLogo);
3685     autoAnnMenu.add(normSequenceLogo);
3686     autoAnnMenu.addSeparator();
3687     autoAnnMenu.add(showGroupConservation);
3688     autoAnnMenu.add(showGroupConsensus);
3689     annotationsMenu.add(autoAnnMenu);
3690
3691     /*
3692      * Format menu
3693      */
3694     formatMenu.add(font);
3695     formatMenu.add(seqLimits);
3696     formatMenu.add(wrapMenuItem);
3697     formatMenu.add(scaleAbove);
3698     formatMenu.add(scaleLeft);
3699     formatMenu.add(scaleRight);
3700     formatMenu.add(viewBoxesMenuItem);
3701     formatMenu.add(viewTextMenuItem);
3702     formatMenu.add(colourTextMenuItem);
3703     formatMenu.add(displayNonconservedMenuItem);
3704     formatMenu.add(renderGapsMenuItem);
3705     formatMenu.add(centreColumnLabelFlag);
3706
3707     /*
3708      * Colour menu
3709      */
3710     colourMenu.add(applyToAllGroups);
3711     colourMenu.addSeparator();
3712     colourMenu.add(noColourmenuItem);
3713     colourMenu.add(clustalColour);
3714     colourMenu.add(BLOSUM62Colour);
3715     colourMenu.add(PIDColour);
3716     colourMenu.add(zappoColour);
3717     colourMenu.add(taylorColour);
3718     colourMenu.add(hydrophobicityColour);
3719     colourMenu.add(helixColour);
3720     colourMenu.add(strandColour);
3721     colourMenu.add(turnColour);
3722     colourMenu.add(buriedColour);
3723     colourMenu.add(nucleotideColour);
3724     colourMenu.add(purinePyrimidineColour);
3725     // colourMenu.add(RNAInteractionColour);
3726     colourMenu.add(tcoffeeColour);
3727     colourMenu.add(userDefinedColour);
3728     colourMenu.addSeparator();
3729     colourMenu.add(conservationMenuItem);
3730     colourMenu.add(modifyConservation);
3731     colourMenu.add(abovePIDThreshold);
3732     colourMenu.add(modifyPID);
3733     colourMenu.add(annotationColour);
3734     colourMenu.add(RNAHelixColour);
3735
3736     /*
3737      * Calculate menu
3738      */
3739     sortMenu.add(sortIDMenuItem);
3740     sortMenu.add(sortLengthMenuItem);
3741     sortMenu.add(sortByTreeMenu);
3742     sortMenu.add(sortGroupMenuItem);
3743     sortMenu.add(sortPairwiseMenuItem);
3744     calculateMenu.add(sortMenu);
3745     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3746     calculateTreeMenu.add(neighbourTreeMenuItem);
3747     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3748     calculateTreeMenu.add(njTreeBlosumMenuItem);
3749     calculateMenu.add(calculateTreeMenu);
3750     calculateMenu.addSeparator();
3751     calculateMenu.add(pairwiseAlignmentMenuItem);
3752     calculateMenu.add(PCAMenuItem);
3753     calculateMenu.add(autoCalculate);
3754     calculateMenu.add(sortByTree);
3755
3756     /*
3757      * Help menu
3758      */
3759     helpMenu.add(documentation);
3760     helpMenu.add(about);
3761
3762     /*
3763      * Status bar
3764      */
3765     statusBar.setBackground(Color.white);
3766     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3767     statusBar.setText(MessageManager.getString("label.status_bar"));
3768     this.add(statusBar, BorderLayout.SOUTH);
3769   }
3770
3771   @Override
3772   public void setStatus(String string)
3773   {
3774     statusBar.setText(string);
3775   };
3776
3777   MenuItem featureSettings = new MenuItem();
3778
3779   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3780
3781   MenuItem annotationColour = new MenuItem();
3782
3783   MenuItem annotationColumnSelection = new MenuItem();
3784
3785   MenuItem invertColSel = new MenuItem();
3786
3787   MenuItem showColumns = new MenuItem();
3788
3789   MenuItem showSeqs = new MenuItem();
3790
3791   MenuItem hideColumns = new MenuItem();
3792
3793   MenuItem hideSequences = new MenuItem();
3794
3795   MenuItem hideAllButSelection = new MenuItem();
3796
3797   MenuItem hideAllSelection = new MenuItem();
3798
3799   MenuItem showAllHidden = new MenuItem();
3800
3801   MenuItem newView = new MenuItem();
3802
3803   private CheckboxMenuItem showAlignmentAnnotations;
3804
3805   private CheckboxMenuItem showSequenceAnnotations;
3806
3807   private CheckboxMenuItem sortAnnBySequence;
3808
3809   private CheckboxMenuItem sortAnnByLabel;
3810
3811   private CheckboxMenuItem showAutoFirst;
3812
3813   private CheckboxMenuItem showAutoLast;
3814
3815   private SplitFrame splitFrame;
3816
3817   /**
3818    * Attach the alignFrame panels after embedding menus, if necessary. This used
3819    * to be called setEmbedded, but is now creates the dropdown menus in a
3820    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3821    *
3822    * @param reallyEmbedded
3823    *          true to attach the view to the applet area on the page rather than
3824    *          in a new window
3825    */
3826   public void createAlignFrameWindow(boolean reallyEmbedded)
3827   {
3828     if (reallyEmbedded)
3829     {
3830       embedAlignFrameInApplet(viewport.applet);
3831     }
3832     else
3833     {
3834       // //////
3835       // test and embed menu bar if necessary.
3836       //
3837       if (embedMenuIfNeeded(alignPanel))
3838       {
3839         /*
3840          * adjust for status bar height too. ? pointless as overridden by layout
3841          * manager
3842          */
3843         alignPanel.setSize(getSize().width,
3844                 getSize().height - statusBar.getHeight());
3845       }
3846       add(statusBar, BorderLayout.SOUTH);
3847       add(alignPanel, BorderLayout.CENTER);
3848       // and register with the applet so it can pass external API calls to us
3849       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3850               frameHeight);
3851     }
3852   }
3853
3854   /**
3855    * Add the components of this AlignFrame to the applet container.
3856    *
3857    * @param theApplet
3858    */
3859   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3860   {
3861     // ////
3862     // Explicitly build the embedded menu panel for the on-page applet
3863     //
3864     // view cannot be closed if its actually on the page
3865     fileMenu.remove(closeMenuItem);
3866     fileMenu.remove(3); // Remove Separator
3867     // construct embedded menu, using default font
3868     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3869     // and actually add the components to the applet area
3870     theApplet.setLayout(new BorderLayout());
3871     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3872     theApplet.add(statusBar, BorderLayout.SOUTH);
3873     // TODO should size be left to the layout manager?
3874     alignPanel.setSize(theApplet.getSize().width,
3875             theApplet.getSize().height - embeddedMenu.getHeight()
3876                     - statusBar.getHeight());
3877     theApplet.add(alignPanel, BorderLayout.CENTER);
3878     final AlignFrame me = this;
3879     theApplet.addFocusListener(new FocusListener()
3880     {
3881
3882       @Override
3883       public void focusLost(FocusEvent e)
3884       {
3885         if (theApplet.currentAlignFrame == me)
3886         {
3887           theApplet.currentAlignFrame = null;
3888         }
3889       }
3890
3891       @Override
3892       public void focusGained(FocusEvent e)
3893       {
3894         theApplet.currentAlignFrame = me;
3895       }
3896     });
3897     theApplet.validate();
3898   }
3899
3900   /**
3901    * create a new binding between structures in an existing jmol viewer instance
3902    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3903    * this does not open a new Jmol window, or modify the display of the
3904    * structures in the original jmol window. Note This method doesn't work
3905    * without an additional javascript library to exchange messages between the
3906    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3907    *
3908    * @param viewer
3909    *          JmolViewer instance
3910    * @param sequenceIds
3911    *          - sequence Ids to search for associations
3912    */
3913   public SequenceStructureBinding addStructureViewInstance(
3914           Object jmolviewer, String[] sequenceIds)
3915   {
3916     Viewer viewer = null;
3917     try
3918     {
3919       viewer = (Viewer) jmolviewer;
3920     } catch (ClassCastException ex)
3921     {
3922       System.err.println("Unsupported viewer object :"
3923               + jmolviewer.getClass());
3924     }
3925     if (viewer == null)
3926     {
3927       System.err.println("Can't use this object as a structure viewer:"
3928               + jmolviewer.getClass());
3929       return null;
3930     }
3931     SequenceI[] seqs = null;
3932     if (sequenceIds == null || sequenceIds.length == 0)
3933     {
3934       seqs = viewport.getAlignment().getSequencesArray();
3935     }
3936     else
3937     {
3938       Vector sqi = new Vector();
3939       AlignmentI al = viewport.getAlignment();
3940       for (int sid = 0; sid < sequenceIds.length; sid++)
3941       {
3942         SequenceI sq = al.findName(sequenceIds[sid]);
3943         if (sq != null)
3944         {
3945           sqi.addElement(sq);
3946         }
3947       }
3948       if (sqi.size() > 0)
3949       {
3950         seqs = new SequenceI[sqi.size()];
3951         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3952         {
3953           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3954         }
3955       }
3956       else
3957       {
3958         return null;
3959       }
3960     }
3961     AAStructureBindingModel jmv = null;
3962     // TODO: search for a jmv that involves viewer
3963     if (jmv == null)
3964     { // create a new viewer/jalview binding.
3965       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3966     }
3967     return jmv;
3968
3969   }
3970
3971   /**
3972    * bind a pdb file to a sequence in the current view
3973    *
3974    * @param sequenceId
3975    *          - sequenceId within the dataset.
3976    * @param pdbEntryString
3977    *          - the short name for the PDB file
3978    * @param pdbFile
3979    *          - pdb file - either a URL or a valid PDB file.
3980    * @return true if binding was as success TODO: consider making an exception
3981    *         structure for indicating when PDB parsing or sequenceId location
3982    *         fails.
3983    */
3984   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3985           String pdbFile)
3986   {
3987     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3988     boolean needtoadd = false;
3989     if (toaddpdb != null)
3990     {
3991       Vector pdbe = toaddpdb.getAllPDBEntries();
3992       PDBEntry pdbentry = null;
3993       if (pdbe != null && pdbe.size() > 0)
3994       {
3995         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3996         {
3997           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3998           if (!pdbentry.getId().equals(pdbEntryString)
3999                   && !pdbentry.getFile().equals(pdbFile))
4000           {
4001             pdbentry = null;
4002           }
4003           else
4004           {
4005             continue;
4006           }
4007         }
4008       }
4009       if (pdbentry == null)
4010       {
4011         pdbentry = new PDBEntry();
4012         pdbentry.setId(pdbEntryString);
4013         pdbentry.setFile(pdbFile);
4014         needtoadd = true; // add this new entry to sequence.
4015       }
4016       // resolve data source
4017       // TODO: this code should be a refactored to an io package
4018       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4019       if (protocol == null)
4020       {
4021         return false;
4022       }
4023       if (needtoadd)
4024       {
4025         // make a note of the access mode and add
4026         if (pdbentry.getProperty() == null)
4027         {
4028           pdbentry.setProperty(new Hashtable());
4029         }
4030         pdbentry.getProperty().put("protocol", protocol);
4031         toaddpdb.addPDBId(pdbentry);
4032         alignPanel.getStructureSelectionManager()
4033                 .registerPDBEntry(pdbentry);
4034       }
4035     }
4036     return true;
4037   }
4038
4039   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4040   {
4041     if (seqs != null)
4042     {
4043       Vector sequences = new Vector();
4044       for (int i = 0; i < seqs.length; i++)
4045       {
4046         if (seqs[i] != null)
4047         {
4048           sequences.addElement(new Object[] { seqs[i],
4049               (chains != null) ? chains[i] : null });
4050         }
4051       }
4052       seqs = new SequenceI[sequences.size()];
4053       chains = new String[sequences.size()];
4054       for (int i = 0, isize = sequences.size(); i < isize; i++)
4055       {
4056         Object[] oj = (Object[]) sequences.elementAt(i);
4057
4058         seqs[i] = (SequenceI) oj[0];
4059         chains[i] = (String) oj[1];
4060       }
4061     }
4062     return new Object[] { seqs, chains };
4063
4064   }
4065
4066   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4067           SequenceI[] seqs, String[] chains, String protocol)
4068   {
4069     // Scrub any null sequences from the array
4070     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4071     seqs = (SequenceI[]) sqch[0];
4072     chains = (String[]) sqch[1];
4073     if (seqs == null || seqs.length == 0)
4074     {
4075       System.err
4076               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4077     }
4078     if (protocol == null || protocol.trim().length() == 0
4079             || protocol.equals("null"))
4080     {
4081       protocol = (String) pdb.getProperty().get("protocol");
4082       if (protocol == null)
4083       {
4084         System.err.println("Couldn't work out protocol to open structure: "
4085                 + pdb.getId());
4086         return;
4087       }
4088     }
4089     if (applet.useXtrnalSviewer)
4090     {
4091       // register the association(s) and quit, don't create any windows.
4092       if (StructureSelectionManager.getStructureSelectionManager(applet)
4093               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4094       {
4095         System.err.println("Failed to map " + pdb.getFile() + " ("
4096                 + protocol + ") to any sequences");
4097       }
4098       return;
4099     }
4100     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4101     {
4102       // can only do alignments with Jmol
4103       // find the last jmol window assigned to this alignment
4104       jalview.appletgui.AppletJmol ajm = null, tajm;
4105       Vector jmols = applet
4106               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4107       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4108       {
4109         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4110         if (tajm.ap.alignFrame == this)
4111         {
4112           ajm = tajm;
4113           break;
4114         }
4115       }
4116       if (ajm != null)
4117       {
4118         System.err
4119                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4120         // try and add the pdb structure
4121         // ajm.addS
4122         ajm = null;
4123       }
4124     }
4125     // otherwise, create a new window
4126     if (applet.jmolAvailable)
4127     {
4128       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4129               protocol);
4130       applet.lastFrameX += 40;
4131       applet.lastFrameY += 40;
4132     }
4133     else
4134     {
4135       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4136     }
4137
4138   }
4139
4140   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4141           SequenceI[][] seqs, String[][] chains, String[] protocols)
4142   {
4143     // TODO Auto-generated method stub
4144     System.err.println("Aligned Structure View: Not yet implemented.");
4145   }
4146
4147   /**
4148    * modify the current selection, providing the user has not made a selection
4149    * already.
4150    *
4151    * @param sel
4152    *          - sequences from this alignment
4153    * @param csel
4154    *          - columns to be selected on the alignment
4155    */
4156   public void select(SequenceGroup sel, ColumnSelection csel)
4157   {
4158     alignPanel.seqPanel.selection(sel, csel, null);
4159   }
4160
4161   public void scrollTo(int row, int column)
4162   {
4163     alignPanel.seqPanel.scrollTo(row, column);
4164   }
4165
4166   public void scrollToRow(int row)
4167   {
4168     alignPanel.seqPanel.scrollToRow(row);
4169   }
4170
4171   public void scrollToColumn(int column)
4172   {
4173     alignPanel.seqPanel.scrollToColumn(column);
4174   }
4175
4176   /**
4177    * @return the alignments unique ID.
4178    */
4179   public String getSequenceSetId()
4180   {
4181     return viewport.getSequenceSetId();
4182   }
4183
4184   /**
4185    * Load the (T-Coffee) score file from the specified url
4186    *
4187    * @param source
4188    *          File/URL/T-COFFEE score file contents
4189    * @throws IOException
4190    * @return true if alignment was annotated with data from source
4191    */
4192   public boolean loadScoreFile(String source) throws IOException
4193   {
4194
4195     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4196             AppletFormatAdapter.checkProtocol(source));
4197     if (!file.isValid())
4198     {
4199       // TODO: raise dialog for gui
4200       System.err.println("Problems parsing T-Coffee scores: "
4201               + file.getWarningMessage());
4202       System.err.println("Origin was:\n" + source);
4203       return false;
4204     }
4205
4206     /*
4207      * check that the score matrix matches the alignment dimensions
4208      */
4209     AlignmentI aln;
4210     if ((aln = viewport.getAlignment()) != null
4211             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4212                     .getWidth()))
4213     {
4214       // TODO: raise a dialog box here rather than bomb out.
4215       System.err
4216               .println("The scores matrix does not match the alignment dimensions");
4217
4218     }
4219
4220     // TODO add parameter to indicate if matching should be done
4221     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4222     {
4223       alignPanel.fontChanged();
4224       tcoffeeColour.setEnabled(true);
4225       // switch to this color
4226       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4227       return true;
4228     }
4229     else
4230     {
4231       System.err.println("Problems resolving T-Coffee scores:");
4232       if (file.getWarningMessage() != null)
4233       {
4234         System.err.println(file.getWarningMessage());
4235       }
4236     }
4237     return false;
4238   }
4239
4240   public SplitFrame getSplitFrame()
4241   {
4242     return this.splitFrame;
4243   }
4244
4245   public void setSplitFrame(SplitFrame sf)
4246   {
4247     this.splitFrame = sf;
4248   }
4249
4250   // may not need this
4251   @Override
4252   public void setShowSeqFeatures(boolean b)
4253   {
4254     // showSeqFeatures.setSelected(b);
4255     viewport.setShowSequenceFeatures(b);
4256
4257   }
4258
4259   @Override
4260   public void setMenusForViewport()
4261   {
4262     // setMenusFromViewport(viewport);
4263
4264   }
4265
4266   @Override
4267   public void refreshFeatureUI(boolean enableIfNecessary)
4268   {
4269     if (enableIfNecessary)
4270     {
4271       sequenceFeatures.setState(true);
4272       alignPanel.av.setShowSequenceFeatures(true);
4273     }
4274   }
4275
4276   @Override
4277   public FeatureSettingsControllerI getFeatureSettingsUI()
4278   {
4279     return alignPanel.av.featureSettings;
4280   }
4281
4282 }