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