src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.FeaturesFile;
  53 import jalview.io.TCoffeeScoreFile;
  54 import jalview.schemes.Blosum62ColourScheme;
  55 import jalview.schemes.BuriedColourScheme;
  56 import jalview.schemes.ClustalxColourScheme;
  57 import jalview.schemes.ColourSchemeI;
  58 import jalview.schemes.HelixColourScheme;
  59 import jalview.schemes.HydrophobicColourScheme;
  60 import jalview.schemes.NucleotideColourScheme;
  61 import jalview.schemes.PIDColourScheme;
  62 import jalview.schemes.PurinePyrimidineColourScheme;
  63 import jalview.schemes.RNAHelicesColourChooser;
  64 import jalview.schemes.StrandColourScheme;
  65 import jalview.schemes.TCoffeeColourScheme;
  66 import jalview.schemes.TaylorColourScheme;
  67 import jalview.schemes.TurnColourScheme;
  68 import jalview.schemes.ZappoColourScheme;
  69 import jalview.structure.StructureSelectionManager;
  70 import jalview.structures.models.AAStructureBindingModel;
  71 import jalview.util.MappingUtils;
  72 import jalview.util.MessageManager;
  73 import jalview.viewmodel.AlignmentViewport;
  74
  75 import java.awt.BorderLayout;
  76 import java.awt.Canvas;
  77 import java.awt.CheckboxMenuItem;
  78 import java.awt.Color;
  79 import java.awt.FlowLayout;
  80 import java.awt.Font;
  81 import java.awt.FontMetrics;
  82 import java.awt.Frame;
  83 import java.awt.Graphics;
  84 import java.awt.Label;
  85 import java.awt.Menu;
  86 import java.awt.MenuBar;
  87 import java.awt.MenuItem;
  88 import java.awt.Panel;
  89 import java.awt.event.ActionEvent;
  90 import java.awt.event.ActionListener;
  91 import java.awt.event.FocusEvent;
  92 import java.awt.event.FocusListener;
  93 import java.awt.event.ItemEvent;
  94 import java.awt.event.ItemListener;
  95 import java.awt.event.KeyEvent;
  96 import java.awt.event.KeyListener;
  97 import java.awt.event.WindowAdapter;
  98 import java.awt.event.WindowEvent;
  99 import java.io.IOException;
 100 import java.net.URL;
 101 import java.net.URLEncoder;
 102 import java.util.Arrays;
 103 import java.util.Deque;
 104 import java.util.HashMap;
 105 import java.util.Hashtable;
 106 import java.util.List;
 107 import java.util.Map;
 108 import java.util.StringTokenizer;
 109 import java.util.Vector;
 110
 111 import org.jmol.viewer.Viewer;
 112
 113 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 114         ItemListener, KeyListener, AlignViewControllerGuiI
 115 {
 116   public AlignViewControllerI avc;
 117
 118   public AlignmentPanel alignPanel;
 119
 120   public AlignViewport viewport;
 121
 122   // width and height may be overridden by applet parameters
 123   int frameWidth = 700;
 124
 125   int frameHeight = 500;
 126
 127   String jalviewServletURL;
 128
 129   /*
 130    * Flag for showing autocalculated consensus above or below other consensus
 131    * rows
 132    */
 133   private boolean showAutoCalculatedAbove;
 134
 135   private SequenceAnnotationOrder annotationSortOrder;
 136
 137   /**
 138    * Constructor that creates the frame and adds it to the display.
 139    *
 140    * @param al
 141    * @param applet
 142    * @param title
 143    * @param embedded
 144    */
 145   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 146           boolean embedded)
 147   {
 148     this(al, applet, title, embedded, true);
 149   }
 150
 151   /**
 152    * Constructor that optionally allows the frame to be displayed or only
 153    * created.
 154    *
 155    * @param al
 156    * @param applet
 157    * @param title
 158    * @param embedded
 159    * @param addToDisplay
 160    */
 161   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 162           boolean embedded, boolean addToDisplay)
 163   {
 164     this(al, null, null, applet, title, embedded, addToDisplay);
 165   }
 166
 167   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 168           ColumnSelection columnSelection, JalviewLite applet,
 169           String title, boolean embedded)
 170   {
 171     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 172   }
 173
 174   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 175           ColumnSelection columnSelection, JalviewLite applet,
 176           String title, boolean embedded, boolean addToDisplay)
 177   {
 178     if (applet != null)
 179     {
 180       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 181     }
 182
 183     try
 184     {
 185       jbInit();
 186     } catch (Exception ex)
 187     {
 188       ex.printStackTrace();
 189     }
 190     // need to get window geometry before we calculate alignment layout
 191     if (applet != null)
 192     {
 193       String param;
 194       try
 195       {
 196         param = applet.getParameter("windowWidth");
 197         if (param != null)
 198         {
 199           int width = Integer.parseInt(param);
 200           frameWidth = width;
 201         }
 202         param = applet.getParameter("windowHeight");
 203         if (param != null)
 204         {
 205           int height = Integer.parseInt(param);
 206           frameHeight = height;
 207         }
 208       } catch (Exception ex)
 209       {
 210       }
 211     }
 212     viewport = new AlignViewport(al, applet);
 213
 214     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 215     {
 216       viewport.hideSequence(hiddenSeqs);
 217     }
 218     if (columnSelection != null)
 219     {
 220       viewport.setColumnSelection(columnSelection);
 221     }
 222     viewport.setScaleAboveWrapped(scaleAbove.getState());
 223
 224     alignPanel = new AlignmentPanel(this, viewport);
 225     avc = new jalview.controller.AlignViewController(this, viewport,
 226             alignPanel);
 227     viewport.updateConservation(alignPanel);
 228     viewport.updateConsensus(alignPanel);
 229
 230     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 231     followMouseOverFlag.setState(viewport.isFollowHighlight());
 232     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 233     showGroupConservation.setState(viewport.isShowGroupConservation());
 234     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 235     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 236     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 237     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 238     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 239     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 240     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showAlignmentAnnotations.setState(true);
 242     showSequenceAnnotations.setState(false);
 243
 244     seqLimits.setState(viewport.getShowJVSuffix());
 245
 246     if (applet != null)
 247     {
 248       String param = applet.getParameter("sortBy");
 249       if (param != null)
 250       {
 251         if (param.equalsIgnoreCase("Id"))
 252         {
 253           sortIDMenuItem_actionPerformed();
 254         }
 255         else if (param.equalsIgnoreCase("Pairwise Identity"))
 256         {
 257           sortPairwiseMenuItem_actionPerformed();
 258         }
 259         else if (param.equalsIgnoreCase("Length"))
 260         {
 261           sortLengthMenuItem_actionPerformed();
 262         }
 263       }
 264
 265       param = applet.getParameter("wrap");
 266       if (param != null)
 267       {
 268         if (param.equalsIgnoreCase("true"))
 269         {
 270           wrapMenuItem.setState(true);
 271           wrapMenuItem_actionPerformed();
 272         }
 273       }
 274       param = applet.getParameter("centrecolumnlabels");
 275       if (param != null)
 276       {
 277         centreColumnLabelFlag.setState(true);
 278         centreColumnLabelFlag_stateChanged();
 279       }
 280
 281     }
 282     if (viewport.getAlignment().isNucleotide())
 283     {
 284       viewport.updateStrucConsensus(alignPanel);
 285       if (viewport.getAlignment().hasRNAStructure())
 286       {
 287         RNAHelixColour.setEnabled(true);
 288       }
 289       else
 290       {
 291         RNAHelixColour.setEnabled(false);
 292       }
 293     }
 294     else
 295     {
 296       RNAHelixColour.setEnabled(false);
 297       purinePyrimidineColour.setEnabled(false);
 298     }
 299     // Some JVMS send keyevents to Top frame or lowest panel,
 300     // Havent worked out why yet. So add to both this frame and seqCanvas for
 301     // now
 302     this.addKeyListener(this);
 303     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 304     alignPanel.idPanel.idCanvas.addKeyListener(this);
 305     alignPanel.scalePanel.addKeyListener(this);
 306     alignPanel.annotationPanel.addKeyListener(this);
 307     alignPanel.annotationPanelHolder.addKeyListener(this);
 308     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 309     alignPanel.alabels.addKeyListener(this);
 310
 311     setAnnotationsVisibility();
 312
 313     if (addToDisplay)
 314     {
 315       addToDisplay(embedded);
 316     }
 317   }
 318
 319   /**
 320    * @param embedded
 321    */
 322   public void addToDisplay(boolean embedded)
 323   {
 324     createAlignFrameWindow(embedded);
 325     validate();
 326     alignPanel.adjustAnnotationHeight();
 327     alignPanel.paintAlignment(true);
 328   }
 329
 330   public AlignViewport getAlignViewport()
 331   {
 332     return viewport;
 333   }
 334
 335   public SeqCanvas getSeqcanvas()
 336   {
 337     return alignPanel.seqPanel.seqCanvas;
 338   }
 339
 340   /**
 341    * Load a features file onto the alignment
 342    *
 343    * @param file
 344    *          file URL, content, or other resolvable path
 345    * @param type
 346    *          is protocol for accessing data referred to by file
 347    */
 348
 349   public boolean parseFeaturesFile(String file, String type)
 350   {
 351     return parseFeaturesFile(file, type, true);
 352   }
 353
 354   /**
 355    * Load a features file onto the alignment
 356    *
 357    * @param file
 358    *          file URL, content, or other resolvable path
 359    * @param type
 360    *          is protocol for accessing data referred to by file
 361    * @param autoenabledisplay
 362    *          when true, display features flag will be automatically enabled if
 363    *          features are loaded
 364    * @return true if data parsed as a features file
 365    */
 366   public boolean parseFeaturesFile(String file, String type,
 367           boolean autoenabledisplay)
 368   {
 369     boolean featuresFile = false;
 370     try
 371     {
 372       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 373               .getFeatureRenderer().getFeatureColours();
 374       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 375               "relaxedidmatch", false);
 376       featuresFile = new FeaturesFile(file, type).parse(
 377               viewport.getAlignment(), colours, true, relaxedIdMatching);
 378     } catch (Exception ex)
 379     {
 380       ex.printStackTrace();
 381     }
 382
 383     if (featuresFile)
 384     {
 385       if (autoenabledisplay)
 386       {
 387         viewport.setShowSequenceFeatures(true);
 388         sequenceFeatures.setState(true);
 389       }
 390       if (alignPanel.seqPanel.seqCanvas.fr != null)
 391       {
 392         // update the min/max ranges where necessary
 393         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 394       }
 395       if (viewport.featureSettings != null)
 396       {
 397         viewport.featureSettings.refreshTable();
 398       }
 399       alignPanel.paintAlignment(true);
 400       statusBar.setText(MessageManager
 401               .getString("label.successfully_added_features_alignment"));
 402     }
 403     return featuresFile;
 404   }
 405
 406   @Override
 407   public void keyPressed(KeyEvent evt)
 408   {
 409     if (viewport.cursorMode
 410             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 411                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 412                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 413             && Character.isDigit(evt.getKeyChar()))
 414     {
 415       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 416     }
 417
 418     switch (evt.getKeyCode())
 419     {
 420     case 27: // escape key
 421       deselectAllSequenceMenuItem_actionPerformed();
 422
 423       alignPanel.alabels.cancelDrag();
 424       break;
 425     case KeyEvent.VK_X:
 426       if (evt.isControlDown() || evt.isMetaDown())
 427       {
 428         cut_actionPerformed();
 429       }
 430       break;
 431     case KeyEvent.VK_C:
 432       if (viewport.cursorMode && !evt.isControlDown())
 433       {
 434         alignPanel.seqPanel.setCursorColumn();
 435       }
 436       if (evt.isControlDown() || evt.isMetaDown())
 437       {
 438         copy_actionPerformed();
 439       }
 440       break;
 441     case KeyEvent.VK_V:
 442       if (evt.isControlDown())
 443       {
 444         paste(evt.isShiftDown());
 445       }
 446       break;
 447     case KeyEvent.VK_A:
 448       if (evt.isControlDown() || evt.isMetaDown())
 449       {
 450         selectAllSequenceMenuItem_actionPerformed();
 451       }
 452       break;
 453     case KeyEvent.VK_DOWN:
 454       if (viewport.cursorMode)
 455       {
 456         alignPanel.seqPanel.moveCursor(0, 1);
 457       }
 458       else
 459       {
 460         moveSelectedSequences(false);
 461       }
 462       break;
 463
 464     case KeyEvent.VK_UP:
 465       if (viewport.cursorMode)
 466       {
 467         alignPanel.seqPanel.moveCursor(0, -1);
 468       }
 469       else
 470       {
 471         moveSelectedSequences(true);
 472       }
 473       break;
 474
 475     case KeyEvent.VK_LEFT:
 476       if (evt.isAltDown() || !viewport.cursorMode)
 477       {
 478         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 479       }
 480       else
 481       {
 482         alignPanel.seqPanel.moveCursor(-1, 0);
 483       }
 484       break;
 485
 486     case KeyEvent.VK_RIGHT:
 487       if (evt.isAltDown() || !viewport.cursorMode)
 488       {
 489         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 490       }
 491       else
 492       {
 493         alignPanel.seqPanel.moveCursor(1, 0);
 494       }
 495       break;
 496
 497     case KeyEvent.VK_SPACE:
 498       if (viewport.cursorMode)
 499       {
 500         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 501                 || evt.isShiftDown() || evt.isAltDown());
 502       }
 503       break;
 504
 505     case KeyEvent.VK_DELETE:
 506     case KeyEvent.VK_BACK_SPACE:
 507       if (viewport.cursorMode)
 508       {
 509         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 510                 || evt.isShiftDown() || evt.isAltDown());
 511       }
 512       else
 513       {
 514         cut_actionPerformed();
 515         alignPanel.seqPanel.seqCanvas.repaint();
 516       }
 517       break;
 518
 519     case KeyEvent.VK_S:
 520       if (viewport.cursorMode)
 521       {
 522         alignPanel.seqPanel.setCursorRow();
 523       }
 524       break;
 525     case KeyEvent.VK_P:
 526       if (viewport.cursorMode)
 527       {
 528         alignPanel.seqPanel.setCursorPosition();
 529       }
 530       break;
 531
 532     case KeyEvent.VK_ENTER:
 533     case KeyEvent.VK_COMMA:
 534       if (viewport.cursorMode)
 535       {
 536         alignPanel.seqPanel.setCursorRowAndColumn();
 537       }
 538       break;
 539
 540     case KeyEvent.VK_Q:
 541       if (viewport.cursorMode)
 542       {
 543         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 544       }
 545       break;
 546     case KeyEvent.VK_M:
 547       if (viewport.cursorMode)
 548       {
 549         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 550       }
 551       break;
 552
 553     case KeyEvent.VK_F2:
 554       viewport.cursorMode = !viewport.cursorMode;
 555       statusBar.setText(MessageManager.formatMessage(
 556               "label.keyboard_editing_mode",
 557               new String[] { (viewport.cursorMode ? "on" : "off") }));
 558       if (viewport.cursorMode)
 559       {
 560         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 561         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 562       }
 563       break;
 564
 565     case KeyEvent.VK_F:
 566       if (evt.isControlDown())
 567       {
 568         findMenuItem_actionPerformed();
 569       }
 570       break;
 571
 572     case KeyEvent.VK_H:
 573     {
 574       boolean toggleSeqs = !evt.isControlDown();
 575       boolean toggleCols = !evt.isShiftDown();
 576       toggleHiddenRegions(toggleSeqs, toggleCols);
 577       break;
 578     }
 579
 580     case KeyEvent.VK_PAGE_UP:
 581       if (viewport.getWrapAlignment())
 582       {
 583         alignPanel.scrollUp(true);
 584       }
 585       else
 586       {
 587         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 588                 - viewport.endSeq + viewport.startSeq);
 589       }
 590       break;
 591
 592     case KeyEvent.VK_PAGE_DOWN:
 593       if (viewport.getWrapAlignment())
 594       {
 595         alignPanel.scrollUp(false);
 596       }
 597       else
 598       {
 599         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 600                 + viewport.endSeq - viewport.startSeq);
 601       }
 602       break;
 603
 604     case KeyEvent.VK_Z:
 605       if (evt.isControlDown())
 606       {
 607         undoMenuItem_actionPerformed();
 608       }
 609       break;
 610
 611     case KeyEvent.VK_Y:
 612       if (evt.isControlDown())
 613       {
 614         redoMenuItem_actionPerformed();
 615       }
 616       break;
 617
 618     case KeyEvent.VK_L:
 619       if (evt.isControlDown())
 620       {
 621         trimAlignment(true);
 622       }
 623       break;
 624
 625     case KeyEvent.VK_R:
 626       if (evt.isControlDown())
 627       {
 628         trimAlignment(false);
 629       }
 630       break;
 631
 632     case KeyEvent.VK_E:
 633       if (evt.isControlDown())
 634       {
 635         if (evt.isShiftDown())
 636         {
 637           this.removeAllGapsMenuItem_actionPerformed();
 638         }
 639         else
 640         {
 641           removeGappedColumnMenuItem_actionPerformed();
 642         }
 643       }
 644       break;
 645     case KeyEvent.VK_I:
 646       if (evt.isControlDown())
 647       {
 648         if (evt.isAltDown())
 649         {
 650           invertColSel_actionPerformed();
 651         }
 652         else
 653         {
 654           invertSequenceMenuItem_actionPerformed();
 655         }
 656       }
 657       break;
 658
 659     case KeyEvent.VK_G:
 660       if (evt.isControlDown())
 661       {
 662         if (evt.isShiftDown())
 663         {
 664           this.unGroup_actionPerformed();
 665         }
 666         else
 667         {
 668           this.createGroup_actionPerformed();
 669         }
 670       }
 671       break;
 672
 673     case KeyEvent.VK_U:
 674       if (evt.isControlDown())
 675       {
 676         this.deleteGroups_actionPerformed();
 677       }
 678       break;
 679
 680     case KeyEvent.VK_T:
 681       if (evt.isControlDown())
 682       {
 683         newView(null);
 684       }
 685       break;
 686
 687     }
 688     alignPanel.paintAlignment(true);
 689   }
 690
 691   /**
 692    * called by key handler and the hide all/show all menu items
 693    *
 694    * @param toggleSeqs
 695    * @param toggleCols
 696    */
 697   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 698   {
 699     boolean hide = false;
 700     SequenceGroup sg = viewport.getSelectionGroup();
 701     if (!toggleSeqs && !toggleCols)
 702     {
 703       // Hide everything by the current selection - this is a hack - we do the
 704       // invert and then hide
 705       // first check that there will be visible columns after the invert.
 706       if ((viewport.getColumnSelection() != null
 707               && viewport.getColumnSelection().getSelected() != null && viewport
 708               .getColumnSelection().getSelected().size() > 0)
 709               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 710                       .getEndRes()))
 711       {
 712         // now invert the sequence set, if required - empty selection implies
 713         // that no hiding is required.
 714         if (sg != null)
 715         {
 716           invertSequenceMenuItem_actionPerformed();
 717           sg = viewport.getSelectionGroup();
 718           toggleSeqs = true;
 719
 720         }
 721         viewport.expandColSelection(sg, true);
 722         // finally invert the column selection and get the new sequence
 723         // selection and indicate it should be hidden.
 724         invertColSel_actionPerformed();
 725         toggleCols = true;
 726       }
 727     }
 728
 729     if (toggleSeqs)
 730     {
 731       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 732       {
 733         hide = true;
 734         viewport.hideAllSelectedSeqs();
 735       }
 736       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 737               .size() > 0))
 738       {
 739         viewport.showAllHiddenSeqs();
 740       }
 741     }
 742
 743     if (toggleCols)
 744     {
 745       if (viewport.getColumnSelection().getSelected().size() > 0)
 746       {
 747         viewport.hideSelectedColumns();
 748         if (!toggleSeqs)
 749         {
 750           viewport.setSelectionGroup(sg);
 751         }
 752       }
 753       else if (!hide)
 754       {
 755         viewport.showAllHiddenColumns();
 756       }
 757       viewport.sendSelection();
 758     }
 759   }
 760
 761   @Override
 762   public void keyReleased(KeyEvent evt)
 763   {
 764   }
 765
 766   @Override
 767   public void keyTyped(KeyEvent evt)
 768   {
 769   }
 770
 771   @Override
 772   public void itemStateChanged(ItemEvent evt)
 773   {
 774     final Object source = evt.getSource();
 775     if (source == displayNonconservedMenuItem)
 776     {
 777       displayNonconservedMenuItem_actionPerformed();
 778     }
 779     else if (source == colourTextMenuItem)
 780     {
 781       colourTextMenuItem_actionPerformed();
 782     }
 783     else if (source == wrapMenuItem)
 784     {
 785       wrapMenuItem_actionPerformed();
 786     }
 787     else if (source == scaleAbove)
 788     {
 789       viewport.setScaleAboveWrapped(scaleAbove.getState());
 790     }
 791     else if (source == scaleLeft)
 792     {
 793       viewport.setScaleLeftWrapped(scaleLeft.getState());
 794     }
 795     else if (source == scaleRight)
 796     {
 797       viewport.setScaleRightWrapped(scaleRight.getState());
 798     }
 799     else if (source == seqLimits)
 800     {
 801       seqLimits_itemStateChanged();
 802     }
 803     else if (source == viewBoxesMenuItem)
 804     {
 805       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 806     }
 807     else if (source == viewTextMenuItem)
 808     {
 809       viewport.setShowText(viewTextMenuItem.getState());
 810     }
 811     else if (source == renderGapsMenuItem)
 812     {
 813       viewport.setRenderGaps(renderGapsMenuItem.getState());
 814     }
 815     else if (source == annotationPanelMenuItem)
 816     {
 817       boolean showAnnotations = annotationPanelMenuItem.getState();
 818       showAlignmentAnnotations.setEnabled(showAnnotations);
 819       showSequenceAnnotations.setEnabled(showAnnotations);
 820       viewport.setShowAnnotation(showAnnotations);
 821       alignPanel.setAnnotationVisible(showAnnotations);
 822     }
 823     else if (source == sequenceFeatures)
 824     {
 825       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 826       alignPanel.seqPanel.seqCanvas.repaint();
 827     }
 828     else if (source == showAlignmentAnnotations)
 829     {
 830       setAnnotationsVisibility();
 831     }
 832     else if (source == showSequenceAnnotations)
 833     {
 834       setAnnotationsVisibility();
 835     }
 836     else if (source == sortAnnBySequence)
 837     {
 838       boolean newState = sortAnnBySequence.getState();
 839       sortAnnByLabel.setState(false);
 840       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 841               : SequenceAnnotationOrder.NONE);
 842       setViewportAnnotationOrder();
 843     }
 844     else if (source == sortAnnByLabel)
 845     {
 846       boolean newState = sortAnnByLabel.getState();
 847       sortAnnBySequence.setState(false);
 848       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 849               : SequenceAnnotationOrder.NONE);
 850       setViewportAnnotationOrder();
 851     }
 852     else if (source == showAutoFirst)
 853     {
 854       showAutoLast.setState(!showAutoFirst.getState());
 855       setShowAutoCalculatedAbove(showAutoFirst.getState());
 856       setViewportAnnotationOrder();
 857     }
 858     else if (source == showAutoLast)
 859     {
 860       showAutoFirst.setState(!showAutoLast.getState());
 861       setShowAutoCalculatedAbove(showAutoFirst.getState());
 862       setViewportAnnotationOrder();
 863     }
 864     else if (source == conservationMenuItem)
 865     {
 866       conservationMenuItem_actionPerformed();
 867     }
 868     else if (source == abovePIDThreshold)
 869     {
 870       abovePIDThreshold_actionPerformed();
 871     }
 872     else if (source == applyToAllGroups)
 873     {
 874       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 875     }
 876     else if (source == autoCalculate)
 877     {
 878       viewport.autoCalculateConsensus = autoCalculate.getState();
 879     }
 880     else if (source == sortByTree)
 881     {
 882       viewport.sortByTree = sortByTree.getState();
 883     }
 884     else if (source == this.centreColumnLabelFlag)
 885     {
 886       centreColumnLabelFlag_stateChanged();
 887     }
 888     else if (source == this.followMouseOverFlag)
 889     {
 890       mouseOverFlag_stateChanged();
 891     }
 892     else if (source == showGroupConsensus)
 893     {
 894       showGroupConsensus_actionPerformed();
 895     }
 896     else if (source == showGroupConservation)
 897     {
 898       showGroupConservation_actionPerformed();
 899     }
 900     else if (source == showSequenceLogo)
 901     {
 902       showSequenceLogo_actionPerformed();
 903     }
 904     else if (source == normSequenceLogo)
 905     {
 906       normSequenceLogo_actionPerformed();
 907     }
 908     else if (source == showConsensusHistogram)
 909     {
 910       showConsensusHistogram_actionPerformed();
 911     }
 912     else if (source == applyAutoAnnotationSettings)
 913     {
 914       applyAutoAnnotationSettings_actionPerformed();
 915     }
 916     alignPanel.paintAlignment(true);
 917   }
 918
 919   /**
 920    * Set the visibility state of sequence-related and/or alignment-related
 921    * annotations depending on checkbox selections, and repaint.
 922    *
 923    * @param visible
 924    */
 925   private void setAnnotationsVisibility()
 926   {
 927     boolean showForAlignment = showAlignmentAnnotations.getState();
 928     boolean showForSequences = showSequenceAnnotations.getState();
 929     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 930     {
 931       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 932             .getAlignmentAnnotation())
 933     {
 934       boolean visible = (aa.sequenceRef == null ? showForAlignment
 935               : showForSequences);
 936       aa.visible = visible;
 937       }
 938     }
 939     alignPanel.validateAnnotationDimensions(true);
 940     validate();
 941     repaint();
 942   }
 943
 944   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 945   {
 946     this.annotationSortOrder = order;
 947   }
 948
 949   /**
 950    * Set flags on the viewport that control annotation ordering
 951    */
 952   private void setViewportAnnotationOrder()
 953   {
 954     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 955     this.alignPanel.av
 956             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 957   }
 958
 959   private void setShowAutoCalculatedAbove(boolean showAbove)
 960   {
 961     this.showAutoCalculatedAbove = showAbove;
 962   }
 963
 964   private void mouseOverFlag_stateChanged()
 965   {
 966     viewport.setFollowHighlight(followMouseOverFlag.getState());
 967     // TODO: could kick the scrollTo mechanism to reset view for current
 968     // searchresults.
 969   }
 970
 971   private void centreColumnLabelFlag_stateChanged()
 972   {
 973     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 974     this.alignPanel.annotationPanel.repaint();
 975   }
 976
 977   @Override
 978   public void actionPerformed(ActionEvent evt)
 979   {
 980     viewport.applet.currentAlignFrame = this;
 981
 982     Object source = evt.getSource();
 983
 984     if (source == inputText)
 985     {
 986       inputText_actionPerformed();
 987     }
 988     else if (source == loadTree)
 989     {
 990       loadTree_actionPerformed();
 991     }
 992     else if (source == loadApplication)
 993     {
 994       launchFullApplication();
 995     }
 996     else if (source == loadAnnotations)
 997     {
 998       loadAnnotations();
 999     }
1000     else if (source == outputAnnotations)
1001     {
1002       outputAnnotations(true);
1003     }
1004     else if (source == outputFeatures)
1005     {
1006       outputFeatures(true, "Jalview");
1007     }
1008     else if (source == closeMenuItem)
1009     {
1010       closeMenuItem_actionPerformed();
1011     }
1012     else if (source == copy)
1013     {
1014       copy_actionPerformed();
1015     }
1016     else if (source == undoMenuItem)
1017     {
1018       undoMenuItem_actionPerformed();
1019     }
1020     else if (source == redoMenuItem)
1021     {
1022       redoMenuItem_actionPerformed();
1023     }
1024     else if (source == inputText)
1025     {
1026       inputText_actionPerformed();
1027     }
1028     else if (source == closeMenuItem)
1029     {
1030       closeMenuItem_actionPerformed();
1031     }
1032     else if (source == undoMenuItem)
1033     {
1034       undoMenuItem_actionPerformed();
1035     }
1036     else if (source == redoMenuItem)
1037     {
1038       redoMenuItem_actionPerformed();
1039     }
1040     else if (source == copy)
1041     {
1042       copy_actionPerformed();
1043     }
1044     else if (source == pasteNew)
1045     {
1046       pasteNew_actionPerformed();
1047     }
1048     else if (source == pasteThis)
1049     {
1050       pasteThis_actionPerformed();
1051     }
1052     else if (source == cut)
1053     {
1054       cut_actionPerformed();
1055     }
1056     else if (source == delete)
1057     {
1058       delete_actionPerformed();
1059     }
1060     else if (source == grpsFromSelection)
1061     {
1062       makeGrpsFromSelection_actionPerformed();
1063     }
1064     else if (source == deleteGroups)
1065     {
1066       deleteGroups_actionPerformed();
1067     }
1068     else if (source == selectAllSequenceMenuItem)
1069     {
1070       selectAllSequenceMenuItem_actionPerformed();
1071     }
1072     else if (source == deselectAllSequenceMenuItem)
1073     {
1074       deselectAllSequenceMenuItem_actionPerformed();
1075     }
1076     else if (source == invertSequenceMenuItem)
1077     {
1078       invertSequenceMenuItem_actionPerformed();
1079       // uncomment to slave sequence selections in split frame
1080       // viewport.sendSelection();
1081     }
1082     else if (source == invertColSel)
1083     {
1084       viewport.invertColumnSelection();
1085       alignPanel.paintAlignment(true);
1086       viewport.sendSelection();
1087     }
1088     else if (source == remove2LeftMenuItem)
1089     {
1090       trimAlignment(true);
1091     }
1092     else if (source == remove2RightMenuItem)
1093     {
1094       trimAlignment(false);
1095     }
1096     else if (source == removeGappedColumnMenuItem)
1097     {
1098       removeGappedColumnMenuItem_actionPerformed();
1099     }
1100     else if (source == removeAllGapsMenuItem)
1101     {
1102       removeAllGapsMenuItem_actionPerformed();
1103     }
1104     else if (source == findMenuItem)
1105     {
1106       findMenuItem_actionPerformed();
1107     }
1108     else if (source == font)
1109     {
1110       new FontChooser(alignPanel);
1111     }
1112     else if (source == newView)
1113     {
1114       newView(null);
1115     }
1116     else if (source == showColumns)
1117     {
1118       viewport.showAllHiddenColumns();
1119       alignPanel.paintAlignment(true);
1120       viewport.sendSelection();
1121     }
1122     else if (source == showSeqs)
1123     {
1124       viewport.showAllHiddenSeqs();
1125       alignPanel.paintAlignment(true);
1126       // uncomment if we want to slave sequence selections in split frame
1127       // viewport.sendSelection();
1128     }
1129     else if (source == hideColumns)
1130     {
1131       viewport.hideSelectedColumns();
1132       alignPanel.paintAlignment(true);
1133       viewport.sendSelection();
1134     }
1135     else if (source == hideSequences
1136             && viewport.getSelectionGroup() != null)
1137     {
1138       viewport.hideAllSelectedSeqs();
1139       alignPanel.paintAlignment(true);
1140       // uncomment if we want to slave sequence selections in split frame
1141       // viewport.sendSelection();
1142     }
1143     else if (source == hideAllButSelection)
1144     {
1145       toggleHiddenRegions(false, false);
1146       alignPanel.paintAlignment(true);
1147       viewport.sendSelection();
1148     }
1149     else if (source == hideAllSelection)
1150     {
1151       SequenceGroup sg = viewport.getSelectionGroup();
1152       viewport.expandColSelection(sg, false);
1153       viewport.hideAllSelectedSeqs();
1154       viewport.hideSelectedColumns();
1155       alignPanel.paintAlignment(true);
1156       viewport.sendSelection();
1157     }
1158     else if (source == showAllHidden)
1159     {
1160       viewport.showAllHiddenColumns();
1161       viewport.showAllHiddenSeqs();
1162       alignPanel.paintAlignment(true);
1163       viewport.sendSelection();
1164     }
1165     else if (source == showGroupConsensus)
1166     {
1167       showGroupConsensus_actionPerformed();
1168     }
1169     else if (source == showGroupConservation)
1170     {
1171       showGroupConservation_actionPerformed();
1172     }
1173     else if (source == showSequenceLogo)
1174     {
1175       showSequenceLogo_actionPerformed();
1176     }
1177     else if (source == normSequenceLogo)
1178     {
1179       normSequenceLogo_actionPerformed();
1180     }
1181     else if (source == showConsensusHistogram)
1182     {
1183       showConsensusHistogram_actionPerformed();
1184     }
1185     else if (source == applyAutoAnnotationSettings)
1186     {
1187       applyAutoAnnotationSettings_actionPerformed();
1188     }
1189     else if (source == featureSettings)
1190     {
1191       new FeatureSettings(alignPanel);
1192     }
1193     else if (source == alProperties)
1194     {
1195       StringBuffer contents = new jalview.io.AlignmentProperties(
1196               viewport.getAlignment()).formatAsString();
1197       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1198       cap.setText(contents.toString());
1199       Frame frame = new Frame();
1200       frame.add(cap);
1201       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1202               "label.alignment_properties", new String[] { getTitle() }),
1203               400, 250);
1204     }
1205     else if (source == overviewMenuItem)
1206     {
1207       overviewMenuItem_actionPerformed();
1208     }
1209     else if (source == noColourmenuItem)
1210     {
1211       changeColour(null);
1212     }
1213     else if (source == clustalColour)
1214     {
1215       abovePIDThreshold.setState(false);
1216       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1217     }
1218     else if (source == zappoColour)
1219     {
1220       changeColour(new ZappoColourScheme());
1221     }
1222     else if (source == taylorColour)
1223     {
1224       changeColour(new TaylorColourScheme());
1225     }
1226     else if (source == hydrophobicityColour)
1227     {
1228       changeColour(new HydrophobicColourScheme());
1229     }
1230     else if (source == helixColour)
1231     {
1232       changeColour(new HelixColourScheme());
1233     }
1234     else if (source == strandColour)
1235     {
1236       changeColour(new StrandColourScheme());
1237     }
1238     else if (source == turnColour)
1239     {
1240       changeColour(new TurnColourScheme());
1241     }
1242     else if (source == buriedColour)
1243     {
1244       changeColour(new BuriedColourScheme());
1245     }
1246     else if (source == nucleotideColour)
1247     {
1248       changeColour(new NucleotideColourScheme());
1249     }
1250     else if (source == purinePyrimidineColour)
1251     {
1252       changeColour(new PurinePyrimidineColourScheme());
1253     }
1254     // else if (source == RNAInteractionColour)
1255     // {
1256     // changeColour(new RNAInteractionColourScheme());
1257     // }
1258     else if (source == RNAHelixColour)
1259     {
1260       new RNAHelicesColourChooser(viewport, alignPanel);
1261     }
1262     else if (source == modifyPID)
1263     {
1264       modifyPID_actionPerformed();
1265     }
1266     else if (source == modifyConservation)
1267     {
1268       modifyConservation_actionPerformed();
1269     }
1270     else if (source == userDefinedColour)
1271     {
1272       new UserDefinedColours(alignPanel, null);
1273     }
1274     else if (source == PIDColour)
1275     {
1276       changeColour(new PIDColourScheme());
1277     }
1278     else if (source == BLOSUM62Colour)
1279     {
1280       changeColour(new Blosum62ColourScheme());
1281     }
1282     else if (source == tcoffeeColour)
1283     {
1284       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1285     }
1286     else if (source == annotationColour)
1287     {
1288       new AnnotationColourChooser(viewport, alignPanel);
1289     }
1290     else if (source == annotationColumnSelection)
1291     {
1292       new AnnotationColumnChooser(viewport, alignPanel);
1293     }
1294     else if (source == sortPairwiseMenuItem)
1295     {
1296       sortPairwiseMenuItem_actionPerformed();
1297     }
1298     else if (source == sortIDMenuItem)
1299     {
1300       sortIDMenuItem_actionPerformed();
1301     }
1302     else if (source == sortLengthMenuItem)
1303     {
1304       sortLengthMenuItem_actionPerformed();
1305     }
1306     else if (source == sortGroupMenuItem)
1307     {
1308       sortGroupMenuItem_actionPerformed();
1309     }
1310     else if (source == removeRedundancyMenuItem)
1311     {
1312       removeRedundancyMenuItem_actionPerformed();
1313     }
1314     else if (source == pairwiseAlignmentMenuItem)
1315     {
1316       pairwiseAlignmentMenuItem_actionPerformed();
1317     }
1318     else if (source == PCAMenuItem)
1319     {
1320       PCAMenuItem_actionPerformed();
1321     }
1322     else if (source == averageDistanceTreeMenuItem)
1323     {
1324       averageDistanceTreeMenuItem_actionPerformed();
1325     }
1326     else if (source == neighbourTreeMenuItem)
1327     {
1328       neighbourTreeMenuItem_actionPerformed();
1329     }
1330     else if (source == njTreeBlosumMenuItem)
1331     {
1332       njTreeBlosumMenuItem_actionPerformed();
1333     }
1334     else if (source == avDistanceTreeBlosumMenuItem)
1335     {
1336       avTreeBlosumMenuItem_actionPerformed();
1337     }
1338     else if (source == documentation)
1339     {
1340       documentation_actionPerformed();
1341     }
1342     else if (source == about)
1343     {
1344       about_actionPerformed();
1345     }
1346
1347   }
1348
1349   public void inputText_actionPerformed()
1350   {
1351     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352     Frame frame = new Frame();
1353     frame.add(cap);
1354     jalview.bin.JalviewLite.addFrame(frame,
1355             MessageManager.getString("label.input_cut_paste"), 500, 500);
1356   }
1357
1358   protected void outputText_actionPerformed(ActionEvent e)
1359   {
1360     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1361     Frame frame = new Frame();
1362     frame.add(cap);
1363     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1364             "label.alignment_output_command",
1365             new Object[] { e.getActionCommand() }), 600, 500);
1366
1367     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1368     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1369             e.getActionCommand(), viewport.getAlignment(),
1370             viewport.getShowJVSuffix()));
1371   }
1372
1373   public void loadAnnotations()
1374   {
1375     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376     cap.setText(MessageManager
1377             .getString("label.paste_features_annotations_Tcoffee_here"));
1378     cap.setAnnotationImport();
1379     Frame frame = new Frame();
1380     frame.add(cap);
1381     jalview.bin.JalviewLite.addFrame(frame,
1382             MessageManager.getString("action.paste_annotations"), 400, 300);
1383
1384   }
1385
1386   public String outputAnnotations(boolean displayTextbox)
1387   {
1388     String annotation = new AnnotationFile()
1389             .printAnnotationsForView(viewport);
1390
1391     if (displayTextbox)
1392     {
1393       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1394       Frame frame = new Frame();
1395       frame.add(cap);
1396       jalview.bin.JalviewLite.addFrame(frame,
1397               MessageManager.getString("label.annotations"), 600, 500);
1398       cap.setText(annotation);
1399     }
1400
1401     return annotation;
1402   }
1403
1404   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1405   {
1406     if (alignPanel.getFeatureRenderer() != null
1407             && viewport.getFeaturesDisplayed() != null)
1408     {
1409       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1410
1411     }
1412     return null;
1413   }
1414
1415   public String outputFeatures(boolean displayTextbox, String format)
1416   {
1417     String features;
1418     FeaturesFile formatter = new FeaturesFile();
1419     if (format.equalsIgnoreCase("Jalview"))
1420     {
1421       features = formatter.printJalviewFormat(viewport
1422               .getAlignment().getSequencesArray(),
1423               getDisplayedFeatureCols());
1424     }
1425     else
1426     {
1427       features = formatter.printGffFormat(viewport.getAlignment()
1428               .getSequencesArray(), getDisplayedFeatureCols());
1429     }
1430
1431     if (displayTextbox)
1432     {
1433       boolean frimport = false;
1434       if (features == null || features.equals("No Features Visible"))
1435       {
1436         features = "# No features visible - paste some and import them here.";
1437         frimport = true;
1438       }
1439
1440       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1441       if (frimport)
1442       {
1443         cap.setAnnotationImport();
1444       }
1445       Frame frame = new Frame();
1446       frame.add(cap);
1447       jalview.bin.JalviewLite.addFrame(frame,
1448               MessageManager.getString("label.features"), 600, 500);
1449       cap.setText(features);
1450     }
1451     else
1452     {
1453       if (features == null)
1454       {
1455         features = "";
1456       }
1457     }
1458
1459     return features;
1460   }
1461
1462   void launchFullApplication()
1463   {
1464     StringBuffer url = new StringBuffer(jalviewServletURL);
1465
1466     // allow servlet parameters to be passed in applet parameter
1467     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1468             : "?";
1469     url.append(firstSep);
1470
1471     url.append("open="
1472             + appendProtocol(viewport.applet.getParameter("file")));
1473
1474     if (viewport.applet.getParameter("features") != null)
1475     {
1476       url.append("&features=");
1477       url.append(appendProtocol(viewport.applet.getParameter("features")));
1478     }
1479
1480     if (viewport.applet.getParameter("annotations") != null)
1481     {
1482       url.append("&annotations=");
1483       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1484     }
1485
1486     if (viewport.applet.getParameter("jnetfile") != null)
1487     {
1488       url.append("&annotations=");
1489       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1490     }
1491
1492     if (viewport.applet.getParameter("defaultColour") != null)
1493     {
1494       url.append("&colour="
1495               + removeWhiteSpace(viewport.applet
1496                       .getParameter("defaultColour")));
1497     }
1498
1499     if (viewport.applet.getParameter("userDefinedColour") != null)
1500     {
1501       url.append("&colour="
1502               + removeWhiteSpace(viewport.applet
1503                       .getParameter("userDefinedColour")));
1504     }
1505     if (viewport.applet.getParameter("tree") != null)
1506     {
1507       url.append("&tree="
1508               + appendProtocol(viewport.applet.getParameter("tree")));
1509     }
1510     if (viewport.applet.getParameter("treeFile") != null)
1511     {
1512       url.append("&tree="
1513               + appendProtocol(viewport.applet.getParameter("treeFile")));
1514     }
1515
1516     showURL(url.toString(), "FULL_APP");
1517   }
1518
1519   String removeWhiteSpace(String colour)
1520   {
1521     StringBuffer sb = new StringBuffer();
1522     for (int i = 0; i < colour.length(); i++)
1523     {
1524       if (Character.isWhitespace(colour.charAt(i)))
1525       {
1526         sb.append("%20");
1527       }
1528       else
1529       {
1530         sb.append(colour.charAt(i));
1531       }
1532     }
1533
1534     return sb.toString();
1535   }
1536
1537   String appendProtocol(String url)
1538   {
1539     try
1540     {
1541       new URL(url);
1542       url = URLEncoder.encode(url);
1543     }
1544     /*
1545      * When we finally deprecate 1.1 compatibility, we can start to use
1546      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1547      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1548      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1549      * ex.printStackTrace(); }
1550      */
1551     catch (java.net.MalformedURLException ex)
1552     {
1553       url = viewport.applet.getCodeBase() + url;
1554     }
1555     return url;
1556   }
1557
1558   public void closeMenuItem_actionPerformed()
1559   {
1560     PaintRefresher.RemoveComponent(alignPanel);
1561     if (alignPanel.seqPanel != null
1562             && alignPanel.seqPanel.seqCanvas != null)
1563     {
1564       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1565     }
1566     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1567     {
1568       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1569     }
1570
1571     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1572     {
1573       System.exit(0);
1574     }
1575     else
1576     {
1577     }
1578     viewport = null;
1579     alignPanel = null;
1580     this.dispose();
1581   }
1582
1583   /**
1584    * TODO: JAL-1104
1585    */
1586   void updateEditMenuBar()
1587   {
1588
1589     if (viewport.getHistoryList().size() > 0)
1590     {
1591       undoMenuItem.setEnabled(true);
1592       CommandI command = viewport.getHistoryList().peek();
1593       undoMenuItem.setLabel(MessageManager.formatMessage(
1594               "label.undo_command",
1595               new Object[] { command.getDescription() }));
1596     }
1597     else
1598     {
1599       undoMenuItem.setEnabled(false);
1600       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1601     }
1602
1603     if (viewport.getRedoList().size() > 0)
1604     {
1605       redoMenuItem.setEnabled(true);
1606
1607       CommandI command = viewport.getRedoList().peek();
1608       redoMenuItem.setLabel(MessageManager.formatMessage(
1609               "label.redo_command",
1610               new Object[] { command.getDescription() }));
1611     }
1612     else
1613     {
1614       redoMenuItem.setEnabled(false);
1615       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1616     }
1617   }
1618
1619   /**
1620    * TODO: JAL-1104
1621    */
1622   @Override
1623   public void addHistoryItem(CommandI command)
1624   {
1625     if (command.getSize() > 0)
1626     {
1627       viewport.addToHistoryList(command);
1628       viewport.clearRedoList();
1629       updateEditMenuBar();
1630       viewport.updateHiddenColumns();
1631     }
1632   }
1633
1634   /**
1635    * TODO: JAL-1104 DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   protected void undoMenuItem_actionPerformed()
1641   {
1642     if (viewport.getHistoryList().isEmpty())
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getHistoryList().pop();
1648     viewport.addToRedoList(command);
1649     command.undoCommand(null);
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     // JBPNote Test
1653     if (originalSource != viewport)
1654     {
1655       System.err
1656               .println("Warning: Viewport object mismatch whilst undoing");
1657     }
1658     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1659                                           // viewport.getColumnSelection().getHiddenColumns()
1660                                           // != null;
1661     updateEditMenuBar();
1662     originalSource.firePropertyChange("alignment", null, originalSource
1663             .getAlignment().getSequences());
1664   }
1665
1666   /**
1667    * TODO: JAL-1104 DOCUMENT ME!
1668    *
1669    * @param e
1670    *          DOCUMENT ME!
1671    */
1672   protected void redoMenuItem_actionPerformed()
1673   {
1674     if (viewport.getRedoList().isEmpty())
1675     {
1676       return;
1677     }
1678
1679     CommandI command = viewport.getRedoList().pop();
1680     viewport.addToHistoryList(command);
1681     command.doCommand(null);
1682
1683     AlignmentViewport originalSource = getOriginatingSource(command);
1684     // JBPNote Test
1685     if (originalSource != viewport)
1686     {
1687       System.err
1688               .println("Warning: Viewport object mismatch whilst re-doing");
1689     }
1690     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1691                                           // viewport.getColumnSelection().getHiddenColumns()
1692                                           // != null;
1693
1694     updateEditMenuBar();
1695     originalSource.firePropertyChange("alignment", null, originalSource
1696             .getAlignment().getSequences());
1697   }
1698
1699   AlignmentViewport getOriginatingSource(CommandI command)
1700   {
1701     AlignmentViewport originalSource = null;
1702     // For sequence removal and addition, we need to fire
1703     // the property change event FROM the viewport where the
1704     // original alignment was altered
1705     AlignmentI al = null;
1706     if (command instanceof EditCommand)
1707     {
1708       EditCommand editCommand = (EditCommand) command;
1709       al = editCommand.getAlignment();
1710       Vector comps = (Vector) PaintRefresher.components.get(viewport
1711               .getSequenceSetId());
1712       for (int i = 0; i < comps.size(); i++)
1713       {
1714         if (comps.elementAt(i) instanceof AlignmentPanel)
1715         {
1716           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1717           {
1718             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1719             break;
1720           }
1721         }
1722       }
1723     }
1724
1725     if (originalSource == null)
1726     {
1727       // The original view is closed, we must validate
1728       // the current view against the closed view first
1729       if (al != null)
1730       {
1731         PaintRefresher.validateSequences(al, viewport.getAlignment());
1732       }
1733
1734       originalSource = viewport;
1735     }
1736
1737     return originalSource;
1738   }
1739
1740   /**
1741    * Move the currently selected sequences up or down one position in the
1742    * alignment
1743    *
1744    * @param up
1745    */
1746   public void moveSelectedSequences(boolean up)
1747   {
1748     SequenceGroup sg = viewport.getSelectionGroup();
1749     if (sg == null)
1750     {
1751       return;
1752     }
1753     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1754             up ? null : viewport.getHiddenRepSequences(), up);
1755     alignPanel.paintAlignment(true);
1756
1757     /*
1758      * Also move cDNA/protein complement sequences
1759      */
1760     AlignViewportI complement = viewport.getCodingComplement();
1761     if (complement != null)
1762     {
1763       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1764               viewport, complement);
1765       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1766               up ? null : complement.getHiddenRepSequences(), up);
1767       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1768     }
1769   }
1770
1771   synchronized void slideSequences(boolean right, int size)
1772   {
1773     List<SequenceI> sg = new Vector<SequenceI>();
1774     if (viewport.cursorMode)
1775     {
1776       sg.add(viewport.getAlignment().getSequenceAt(
1777               alignPanel.seqPanel.seqCanvas.cursorY));
1778     }
1779     else if (viewport.getSelectionGroup() != null
1780             && viewport.getSelectionGroup().getSize() != viewport
1781                     .getAlignment().getHeight())
1782     {
1783       sg = viewport.getSelectionGroup().getSequences(
1784               viewport.getHiddenRepSequences());
1785     }
1786
1787     if (sg.size() < 1)
1788     {
1789       return;
1790     }
1791
1792     Vector<SequenceI> invertGroup = new Vector();
1793
1794     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1795     {
1796       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1797       {
1798         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1799       }
1800     }
1801
1802     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1803
1804     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1805             .size()]);
1806     for (int i = 0; i < invertGroup.size(); i++)
1807     {
1808       seqs2[i] = invertGroup.elementAt(i);
1809     }
1810
1811     SlideSequencesCommand ssc;
1812     if (right)
1813     {
1814       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1815               size, viewport.getGapCharacter());
1816     }
1817     else
1818     {
1819       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1820               size, viewport.getGapCharacter());
1821     }
1822
1823     int groupAdjustment = 0;
1824     if (ssc.getGapsInsertedBegin() && right)
1825     {
1826       if (viewport.cursorMode)
1827       {
1828         alignPanel.seqPanel.moveCursor(size, 0);
1829       }
1830       else
1831       {
1832         groupAdjustment = size;
1833       }
1834     }
1835     else if (!ssc.getGapsInsertedBegin() && !right)
1836     {
1837       if (viewport.cursorMode)
1838       {
1839         alignPanel.seqPanel.moveCursor(-size, 0);
1840       }
1841       else
1842       {
1843         groupAdjustment = -size;
1844       }
1845     }
1846
1847     if (groupAdjustment != 0)
1848     {
1849       viewport.getSelectionGroup().setStartRes(
1850               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1851       viewport.getSelectionGroup().setEndRes(
1852               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1853     }
1854
1855     boolean appendHistoryItem = false;
1856     Deque<CommandI> historyList = viewport.getHistoryList();
1857     if (historyList != null && historyList.size() > 0
1858             && historyList.peek() instanceof SlideSequencesCommand)
1859     {
1860       appendHistoryItem = ssc
1861               .appendSlideCommand((SlideSequencesCommand) historyList
1862                       .peek());
1863     }
1864
1865     if (!appendHistoryItem)
1866     {
1867       addHistoryItem(ssc);
1868     }
1869
1870     repaint();
1871   }
1872
1873   static StringBuffer copiedSequences;
1874
1875   static Vector copiedHiddenColumns;
1876
1877   protected void copy_actionPerformed()
1878   {
1879     if (viewport.getSelectionGroup() == null)
1880     {
1881       return;
1882     }
1883
1884     SequenceGroup sg = viewport.getSelectionGroup();
1885     copiedSequences = new StringBuffer();
1886     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1887     for (int i = 0; i < sg.getSize(); i++)
1888     {
1889       SequenceI seq = sg.getSequenceAt(i);
1890       int index = viewport.getAlignment().findIndex(seq);
1891       orderedSeqs.put(index, seq);
1892     }
1893
1894     int index = 0, startRes, endRes;
1895     char ch;
1896
1897     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1898     {
1899       copiedHiddenColumns = new Vector();
1900       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1901       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1902       {
1903         copiedHiddenColumns.addElement(new int[] {
1904             region[0] - hiddenOffset, region[1] - hiddenOffset });
1905       }
1906     }
1907     else
1908     {
1909       copiedHiddenColumns = null;
1910     }
1911
1912     for (int i = 0; i < sg.getSize(); i++)
1913     {
1914       SequenceI seq = null;
1915
1916       while (seq == null)
1917       {
1918         if (orderedSeqs.containsKey(index))
1919         {
1920           seq = orderedSeqs.get(index);
1921           index++;
1922           break;
1923         }
1924         else
1925         {
1926           index++;
1927         }
1928       }
1929
1930       // FIND START RES
1931       // Returns residue following index if gap
1932       startRes = seq.findPosition(sg.getStartRes());
1933
1934       // FIND END RES
1935       // Need to find the residue preceeding index if gap
1936       endRes = 0;
1937
1938       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1939       {
1940         ch = seq.getCharAt(j);
1941         if (!jalview.util.Comparison.isGap((ch)))
1942         {
1943           endRes++;
1944         }
1945       }
1946
1947       if (endRes > 0)
1948       {
1949         endRes += seq.getStart() - 1;
1950       }
1951
1952       copiedSequences.append(seq.getName()
1953               + "\t"
1954               + startRes
1955               + "\t"
1956               + endRes
1957               + "\t"
1958               + seq.getSequenceAsString(sg.getStartRes(),
1959                       sg.getEndRes() + 1) + "\n");
1960     }
1961
1962   }
1963
1964   protected void pasteNew_actionPerformed()
1965   {
1966     paste(true);
1967   }
1968
1969   protected void pasteThis_actionPerformed()
1970   {
1971     paste(false);
1972   }
1973
1974   void paste(boolean newAlignment)
1975   {
1976     try
1977     {
1978
1979       if (copiedSequences == null)
1980       {
1981         return;
1982       }
1983
1984       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1985       Vector seqs = new Vector();
1986       while (st.hasMoreElements())
1987       {
1988         String name = st.nextToken();
1989         int start = Integer.parseInt(st.nextToken());
1990         int end = Integer.parseInt(st.nextToken());
1991         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1992       }
1993       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1994       for (int i = 0; i < seqs.size(); i++)
1995       {
1996         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1997       }
1998
1999       if (newAlignment)
2000       {
2001         String newtitle = MessageManager
2002                 .getString("label.copied_sequences");
2003         if (getTitle().startsWith(
2004                 MessageManager.getString("label.copied_sequences")))
2005         {
2006           newtitle = getTitle();
2007         }
2008         else
2009         {
2010           newtitle = newtitle.concat(MessageManager.formatMessage(
2011                   "label.from_msname", new String[] { getTitle() }));
2012         }
2013         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2014                 viewport.applet, newtitle, false);
2015         if (copiedHiddenColumns != null)
2016         {
2017           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2018           {
2019             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2020             af.viewport.hideColumns(region[0], region[1]);
2021           }
2022         }
2023
2024         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2025                 frameHeight);
2026       }
2027       else
2028       {
2029         addSequences(newSeqs);
2030       }
2031
2032     } catch (Exception ex)
2033     {
2034     } // could be anything being pasted in here
2035
2036   }
2037
2038   void addSequences(SequenceI[] seqs)
2039   {
2040     for (int i = 0; i < seqs.length; i++)
2041     {
2042       viewport.getAlignment().addSequence(seqs[i]);
2043     }
2044
2045     // !newAlignment
2046     addHistoryItem(new EditCommand(
2047             MessageManager.getString("label.add_sequences"), Action.PASTE,
2048             seqs, 0, viewport.getAlignment().getWidth(),
2049             viewport.getAlignment()));
2050
2051     viewport.setEndSeq(viewport.getAlignment().getHeight());
2052     viewport.getAlignment().getWidth();
2053     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2054             .getSequences());
2055
2056   }
2057
2058   protected void cut_actionPerformed()
2059   {
2060     copy_actionPerformed();
2061     delete_actionPerformed();
2062   }
2063
2064   protected void delete_actionPerformed()
2065   {
2066
2067     SequenceGroup sg = viewport.getSelectionGroup();
2068     if (sg == null)
2069     {
2070       return;
2071     }
2072
2073     Vector seqs = new Vector();
2074     SequenceI seq;
2075     for (int i = 0; i < sg.getSize(); i++)
2076     {
2077       seq = sg.getSequenceAt(i);
2078       seqs.addElement(seq);
2079     }
2080
2081     /*
2082      * If the cut affects all sequences, warn, remove highlighted columns
2083      */
2084     if (sg.getSize() == viewport.getAlignment().getHeight())
2085     {
2086       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2087               .getAlignment().getWidth()) ? true : false;
2088       if (isEntireAlignWidth)
2089       {
2090         String title = MessageManager.getString("label.delete_all");
2091         Panel infoPanel = new Panel();
2092         infoPanel.setLayout(new FlowLayout());
2093         infoPanel
2094                 .add(new Label(MessageManager.getString("warn.delete_all")));
2095
2096         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2097         dialog.setMainPanel(infoPanel);
2098         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2099         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2100         dialog.setVisible(true);
2101
2102         if (!dialog.accept)
2103         {
2104           return;
2105         }
2106       }
2107       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2108               sg.getEndRes() + 1);
2109     }
2110
2111     SequenceI[] cut = new SequenceI[seqs.size()];
2112     for (int i = 0; i < seqs.size(); i++)
2113     {
2114       cut[i] = (SequenceI) seqs.elementAt(i);
2115     }
2116
2117     /*
2118      * //ADD HISTORY ITEM
2119      */
2120     addHistoryItem(new EditCommand(
2121             MessageManager.getString("label.cut_sequences"), Action.CUT,
2122             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2123             viewport.getAlignment()));
2124
2125     viewport.setSelectionGroup(null);
2126     viewport.getAlignment().deleteGroup(sg);
2127
2128     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2129             .getSequences());
2130
2131     if (viewport.getAlignment().getHeight() < 1)
2132     {
2133       this.setVisible(false);
2134     }
2135     viewport.sendSelection();
2136   }
2137
2138   /**
2139    * group consensus toggled
2140    *
2141    */
2142   protected void showGroupConsensus_actionPerformed()
2143   {
2144     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2145     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2146
2147   }
2148
2149   /**
2150    * group conservation toggled.
2151    */
2152   protected void showGroupConservation_actionPerformed()
2153   {
2154     viewport.setShowGroupConservation(showGroupConservation.getState());
2155     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2156   }
2157
2158   /*
2159    * (non-Javadoc)
2160    *
2161    * @see
2162    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2163    * .event.ActionEvent)
2164    */
2165   protected void showConsensusHistogram_actionPerformed()
2166   {
2167     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2168     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2169   }
2170
2171   /*
2172    * (non-Javadoc)
2173    *
2174    * @see
2175    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2176    * .event.ActionEvent)
2177    */
2178   protected void showSequenceLogo_actionPerformed()
2179   {
2180     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2181     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2182   }
2183
2184   protected void normSequenceLogo_actionPerformed()
2185   {
2186     showSequenceLogo.setState(true);
2187     viewport.setShowSequenceLogo(true);
2188     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2189     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190   }
2191
2192   protected void applyAutoAnnotationSettings_actionPerformed()
2193   {
2194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195   }
2196
2197   protected void makeGrpsFromSelection_actionPerformed()
2198   {
2199     if (avc.makeGroupsFromSelection())
2200     {
2201       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2202       alignPanel.updateAnnotation();
2203       alignPanel.paintAlignment(true);
2204     }
2205   }
2206
2207   protected void createGroup_actionPerformed()
2208   {
2209     avc.createGroup();
2210   }
2211
2212   protected void unGroup_actionPerformed()
2213   {
2214     if (avc.unGroup())
2215     {
2216       alignPanel.alignmentChanged();
2217     }
2218   }
2219
2220   protected void deleteGroups_actionPerformed()
2221   {
2222     if (avc.deleteGroups())
2223     {
2224       alignPanel.alignmentChanged();
2225     }
2226   }
2227
2228   public void selectAllSequenceMenuItem_actionPerformed()
2229   {
2230     SequenceGroup sg = new SequenceGroup();
2231     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2232     {
2233       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2234     }
2235     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2236     viewport.setSelectionGroup(sg);
2237     // JAL-2034 - should delegate to
2238     // alignPanel to decide if overview needs
2239     // updating.
2240     alignPanel.paintAlignment(false);
2241     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2242     viewport.sendSelection();
2243   }
2244
2245   public void deselectAllSequenceMenuItem_actionPerformed()
2246   {
2247     if (viewport.cursorMode)
2248     {
2249       alignPanel.seqPanel.keyboardNo1 = null;
2250       alignPanel.seqPanel.keyboardNo2 = null;
2251     }
2252     viewport.setSelectionGroup(null);
2253     viewport.getColumnSelection().clear();
2254     viewport.setSelectionGroup(null);
2255     alignPanel.idPanel.idCanvas.searchResults = null;
2256     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2257     // JAL-2034 - should delegate to
2258     // alignPanel to decide if overview needs
2259     // updating.
2260     alignPanel.paintAlignment(false);
2261     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2262     viewport.sendSelection();
2263   }
2264
2265   public void invertSequenceMenuItem_actionPerformed()
2266   {
2267     SequenceGroup sg = viewport.getSelectionGroup();
2268     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2269     {
2270       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2271     }
2272
2273     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2274     viewport.sendSelection();
2275   }
2276
2277   public void invertColSel_actionPerformed()
2278   {
2279     viewport.invertColumnSelection();
2280     alignPanel.paintAlignment(true);
2281     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2282     viewport.sendSelection();
2283   }
2284
2285   void trimAlignment(boolean trimLeft)
2286   {
2287     ColumnSelection colSel = viewport.getColumnSelection();
2288     int column;
2289
2290     if (!colSel.isEmpty())
2291     {
2292       if (trimLeft)
2293       {
2294         column = colSel.getMin();
2295       }
2296       else
2297       {
2298         column = colSel.getMax();
2299       }
2300
2301       SequenceI[] seqs;
2302       if (viewport.getSelectionGroup() != null)
2303       {
2304         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2305                 viewport.getHiddenRepSequences());
2306       }
2307       else
2308       {
2309         seqs = viewport.getAlignment().getSequencesArray();
2310       }
2311
2312       TrimRegionCommand trimRegion;
2313       if (trimLeft)
2314       {
2315         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2316                 column, viewport.getAlignment());
2317         viewport.setStartRes(0);
2318       }
2319       else
2320       {
2321         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2322                 column, viewport.getAlignment());
2323       }
2324
2325       statusBar.setText(MessageManager.formatMessage(
2326               "label.removed_columns",
2327               new String[] { Integer.valueOf(trimRegion.getSize())
2328                       .toString() }));
2329       addHistoryItem(trimRegion);
2330
2331       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2332       {
2333         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2334                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2335         {
2336           viewport.getAlignment().deleteGroup(sg);
2337         }
2338       }
2339
2340       viewport.firePropertyChange("alignment", null, viewport
2341               .getAlignment().getSequences());
2342     }
2343   }
2344
2345   public void removeGappedColumnMenuItem_actionPerformed()
2346   {
2347     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2348
2349     SequenceI[] seqs;
2350     if (viewport.getSelectionGroup() != null)
2351     {
2352       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2353               viewport.getHiddenRepSequences());
2354       start = viewport.getSelectionGroup().getStartRes();
2355       end = viewport.getSelectionGroup().getEndRes();
2356     }
2357     else
2358     {
2359       seqs = viewport.getAlignment().getSequencesArray();
2360     }
2361
2362     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2363             "Remove Gapped Columns", seqs, start, end,
2364             viewport.getAlignment());
2365
2366     addHistoryItem(removeGapCols);
2367
2368     statusBar.setText(MessageManager.formatMessage(
2369             "label.removed_empty_columns",
2370             new String[] { Integer.valueOf(removeGapCols.getSize())
2371                     .toString() }));
2372
2373     // This is to maintain viewport position on first residue
2374     // of first sequence
2375     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2376     int startRes = seq.findPosition(viewport.startRes);
2377     // ShiftList shifts;
2378     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2379     // edit.alColumnChanges=shifts.getInverse();
2380     // if (viewport.hasHiddenColumns)
2381     // viewport.getColumnSelection().compensateForEdits(shifts);
2382     viewport.setStartRes(seq.findIndex(startRes) - 1);
2383     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2384             .getSequences());
2385
2386   }
2387
2388   public void removeAllGapsMenuItem_actionPerformed()
2389   {
2390     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2391
2392     SequenceI[] seqs;
2393     if (viewport.getSelectionGroup() != null)
2394     {
2395       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2396               viewport.getHiddenRepSequences());
2397       start = viewport.getSelectionGroup().getStartRes();
2398       end = viewport.getSelectionGroup().getEndRes();
2399     }
2400     else
2401     {
2402       seqs = viewport.getAlignment().getSequencesArray();
2403     }
2404
2405     // This is to maintain viewport position on first residue
2406     // of first sequence
2407     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2408     int startRes = seq.findPosition(viewport.startRes);
2409
2410     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2411             viewport.getAlignment()));
2412
2413     viewport.setStartRes(seq.findIndex(startRes) - 1);
2414
2415     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2416             .getSequences());
2417
2418   }
2419
2420   public void findMenuItem_actionPerformed()
2421   {
2422     new Finder(alignPanel);
2423   }
2424
2425   /**
2426    * create a new view derived from the current view
2427    *
2428    * @param viewtitle
2429    * @return frame for the new view
2430    */
2431   public AlignFrame newView(String viewtitle)
2432   {
2433     AlignmentI newal;
2434     if (viewport.hasHiddenRows())
2435     {
2436       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2437               .getFullAlignment().getSequencesArray());
2438     }
2439     else
2440     {
2441       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2442     }
2443
2444     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2445     {
2446       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2447       {
2448         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2449         {
2450           newal.addAnnotation(viewport.getAlignment()
2451                   .getAlignmentAnnotation()[i]);
2452         }
2453       }
2454     }
2455
2456     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2457
2458     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2459     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2460     PaintRefresher.Register(newaf.alignPanel,
2461             newaf.alignPanel.av.getSequenceSetId());
2462
2463     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2464             newaf.alignPanel.av.getSequenceSetId());
2465     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2466             newaf.alignPanel.av.getSequenceSetId());
2467
2468     Vector comps = (Vector) PaintRefresher.components.get(viewport
2469             .getSequenceSetId());
2470     int viewSize = -1;
2471     for (int i = 0; i < comps.size(); i++)
2472     {
2473       if (comps.elementAt(i) instanceof AlignmentPanel)
2474       {
2475         viewSize++;
2476       }
2477     }
2478
2479     String title = new String(this.getTitle());
2480     if (viewtitle != null)
2481     {
2482       title = viewtitle + " ( " + title + ")";
2483     }
2484     else
2485     {
2486       if (title.indexOf("(View") > -1)
2487       {
2488         title = title.substring(0, title.indexOf("(View"));
2489       }
2490       title += "(View " + viewSize + ")";
2491     }
2492
2493     newaf.setTitle(title.toString());
2494
2495     newaf.viewport.setHistoryList(viewport.getHistoryList());
2496     newaf.viewport.setRedoList(viewport.getRedoList());
2497     return newaf;
2498   }
2499
2500   /**
2501    *
2502    * @return list of feature groups on the view
2503    */
2504   public String[] getFeatureGroups()
2505   {
2506     FeatureRenderer fr = null;
2507     if (alignPanel != null
2508             && (fr = alignPanel.getFeatureRenderer()) != null)
2509     {
2510       List<String> gps = fr.getFeatureGroups();
2511       String[] _gps = gps.toArray(new String[gps.size()]);
2512       return _gps;
2513     }
2514     return null;
2515   }
2516
2517   /**
2518    * get sequence feature groups that are hidden or shown
2519    *
2520    * @param visible
2521    *          true is visible
2522    * @return list
2523    */
2524   public String[] getFeatureGroupsOfState(boolean visible)
2525   {
2526     FeatureRenderer fr = null;
2527     if (alignPanel != null
2528             && (fr = alignPanel.getFeatureRenderer()) != null)
2529     {
2530       List<String> gps = fr.getGroups(visible);
2531       String[] _gps = gps.toArray(new String[gps.size()]);
2532       return _gps;
2533     }
2534     return null;
2535   }
2536
2537   /**
2538    * Change the display state for the given feature groups
2539    *
2540    * @param groups
2541    *          list of group strings
2542    * @param state
2543    *          visible or invisible
2544    */
2545   public void setFeatureGroupState(String[] groups, boolean state)
2546   {
2547     FeatureRenderer fr = null;
2548     this.sequenceFeatures.setState(true);
2549     viewport.setShowSequenceFeatures(true);
2550     if (alignPanel != null
2551             && (fr = alignPanel.getFeatureRenderer()) != null)
2552     {
2553
2554       fr.setGroupVisibility(Arrays.asList(groups), state);
2555       alignPanel.seqPanel.seqCanvas.repaint();
2556       if (alignPanel.overviewPanel != null)
2557       {
2558         alignPanel.overviewPanel.updateOverviewImage();
2559       }
2560     }
2561   }
2562
2563   public void seqLimits_itemStateChanged()
2564   {
2565     viewport.setShowJVSuffix(seqLimits.getState());
2566     alignPanel.fontChanged();
2567     alignPanel.paintAlignment(true);
2568   }
2569
2570   protected void colourTextMenuItem_actionPerformed()
2571   {
2572     viewport.setColourText(colourTextMenuItem.getState());
2573     alignPanel.paintAlignment(true);
2574   }
2575
2576   protected void displayNonconservedMenuItem_actionPerformed()
2577   {
2578     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2579     alignPanel.paintAlignment(true);
2580   }
2581
2582   protected void wrapMenuItem_actionPerformed()
2583   {
2584     viewport.setWrapAlignment(wrapMenuItem.getState());
2585     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2586     scaleAbove.setEnabled(wrapMenuItem.getState());
2587     scaleLeft.setEnabled(wrapMenuItem.getState());
2588     scaleRight.setEnabled(wrapMenuItem.getState());
2589     alignPanel.paintAlignment(true);
2590   }
2591
2592   public void overviewMenuItem_actionPerformed()
2593   {
2594     if (alignPanel.overviewPanel != null)
2595     {
2596       return;
2597     }
2598
2599     Frame frame = new Frame();
2600     OverviewPanel overview = new OverviewPanel(alignPanel);
2601     frame.add(overview);
2602     // +50 must allow for applet frame window
2603     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2604             "label.overview_params", new String[] { this.getTitle() }),
2605             overview.getPreferredSize().width,
2606             overview.getPreferredSize().height + 50);
2607
2608     frame.pack();
2609     final AlignmentPanel ap = alignPanel;
2610     frame.addWindowListener(new WindowAdapter()
2611     {
2612       @Override
2613       public void windowClosing(WindowEvent e)
2614       {
2615         if (ap != null)
2616         {
2617           ap.setOverviewPanel(null);
2618         }
2619       };
2620     });
2621
2622     alignPanel.setOverviewPanel(overview);
2623
2624   }
2625
2626   @Override
2627   public void changeColour(ColourSchemeI cs)
2628   {
2629
2630     if (cs != null)
2631     {
2632       if (viewport.getAbovePIDThreshold())
2633       {
2634         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2635                 cs, "Background"));
2636       }
2637
2638       if (viewport.getConservationSelected())
2639       {
2640         cs.setConservationApplied(true);
2641         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2642                 cs, "Background"));
2643       }
2644       else
2645       {
2646         cs.setConservationApplied(false);
2647       }
2648     }
2649     viewport.setGlobalColourScheme(cs);
2650
2651     alignPanel.paintAlignment(true);
2652   }
2653
2654   protected void modifyPID_actionPerformed()
2655   {
2656     if (viewport.getAbovePIDThreshold()
2657             && viewport.getGlobalColourScheme() != null)
2658     {
2659       SliderPanel.setPIDSliderSource(alignPanel,
2660               viewport.getGlobalColourScheme(), "Background");
2661       SliderPanel.showPIDSlider();
2662     }
2663   }
2664
2665   protected void modifyConservation_actionPerformed()
2666   {
2667     if (viewport.getConservationSelected()
2668             && viewport.getGlobalColourScheme() != null)
2669     {
2670       SliderPanel.setConservationSlider(alignPanel,
2671               viewport.getGlobalColourScheme(), "Background");
2672       SliderPanel.showConservationSlider();
2673     }
2674   }
2675
2676   protected void conservationMenuItem_actionPerformed()
2677   {
2678     viewport.setConservationSelected(conservationMenuItem.getState());
2679
2680     viewport.setAbovePIDThreshold(false);
2681     abovePIDThreshold.setState(false);
2682
2683     changeColour(viewport.getGlobalColourScheme());
2684
2685     modifyConservation_actionPerformed();
2686   }
2687
2688   public void abovePIDThreshold_actionPerformed()
2689   {
2690     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2691
2692     conservationMenuItem.setState(false);
2693     viewport.setConservationSelected(false);
2694
2695     changeColour(viewport.getGlobalColourScheme());
2696
2697     modifyPID_actionPerformed();
2698   }
2699
2700   public void sortPairwiseMenuItem_actionPerformed()
2701   {
2702     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2703     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2704             .getAlignment().getSequenceAt(0), null);
2705
2706     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2707             viewport.getAlignment()));
2708     alignPanel.paintAlignment(true);
2709   }
2710
2711   public void sortIDMenuItem_actionPerformed()
2712   {
2713     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2714     AlignmentSorter.sortByID(viewport.getAlignment());
2715     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2716             viewport.getAlignment()));
2717     alignPanel.paintAlignment(true);
2718   }
2719
2720   public void sortLengthMenuItem_actionPerformed()
2721   {
2722     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723     AlignmentSorter.sortByLength(viewport.getAlignment());
2724     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2725             viewport.getAlignment()));
2726     alignPanel.paintAlignment(true);
2727   }
2728
2729   public void sortGroupMenuItem_actionPerformed()
2730   {
2731     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2732     AlignmentSorter.sortByGroup(viewport.getAlignment());
2733     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2734             viewport.getAlignment()));
2735     alignPanel.paintAlignment(true);
2736
2737   }
2738
2739   public void removeRedundancyMenuItem_actionPerformed()
2740   {
2741     new RedundancyPanel(alignPanel);
2742   }
2743
2744   public void pairwiseAlignmentMenuItem_actionPerformed()
2745   {
2746     if (viewport.getSelectionGroup() != null
2747             && viewport.getSelectionGroup().getSize() > 1)
2748     {
2749       Frame frame = new Frame();
2750       frame.add(new PairwiseAlignPanel(alignPanel));
2751       jalview.bin.JalviewLite.addFrame(frame,
2752               MessageManager.getString("action.pairwise_alignment"), 600,
2753               500);
2754     }
2755   }
2756
2757   public void PCAMenuItem_actionPerformed()
2758   {
2759     // are the sequences aligned?
2760     if (!viewport.getAlignment().isAligned(false))
2761     {
2762       SequenceI current;
2763       int Width = viewport.getAlignment().getWidth();
2764
2765       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2766       {
2767         current = viewport.getAlignment().getSequenceAt(i);
2768
2769         if (current.getLength() < Width)
2770         {
2771           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2772         }
2773       }
2774       alignPanel.paintAlignment(true);
2775     }
2776
2777     if ((viewport.getSelectionGroup() != null
2778             && viewport.getSelectionGroup().getSize() < 4 && viewport
2779             .getSelectionGroup().getSize() > 0)
2780             || viewport.getAlignment().getHeight() < 4)
2781     {
2782       return;
2783     }
2784
2785     try
2786     {
2787       new PCAPanel(viewport);
2788     } catch (java.lang.OutOfMemoryError ex)
2789     {
2790     }
2791
2792   }
2793
2794   public void averageDistanceTreeMenuItem_actionPerformed()
2795   {
2796     NewTreePanel("AV", "PID", "Average distance tree using PID");
2797   }
2798
2799   public void neighbourTreeMenuItem_actionPerformed()
2800   {
2801     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2802   }
2803
2804   protected void njTreeBlosumMenuItem_actionPerformed()
2805   {
2806     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2807   }
2808
2809   protected void avTreeBlosumMenuItem_actionPerformed()
2810   {
2811     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2812   }
2813
2814   void NewTreePanel(String type, String pwType, String title)
2815   {
2816     // are the sequences aligned?
2817     if (!viewport.getAlignment().isAligned(false))
2818     {
2819       SequenceI current;
2820       int Width = viewport.getAlignment().getWidth();
2821
2822       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2823       {
2824         current = viewport.getAlignment().getSequenceAt(i);
2825
2826         if (current.getLength() < Width)
2827         {
2828           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2829         }
2830       }
2831       alignPanel.paintAlignment(true);
2832
2833     }
2834
2835     if ((viewport.getSelectionGroup() != null && viewport
2836             .getSelectionGroup().getSize() > 1)
2837             || (viewport.getAlignment().getHeight() > 1))
2838     {
2839       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2840
2841       addTreeMenuItem(tp, title);
2842
2843       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2844     }
2845   }
2846
2847   void loadTree_actionPerformed()
2848   {
2849     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2850     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2851     cap.setTreeImport();
2852     Frame frame = new Frame();
2853     frame.add(cap);
2854     jalview.bin.JalviewLite.addFrame(frame,
2855             MessageManager.getString("label.paste_newick_file"), 400, 300);
2856   }
2857
2858   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2859   {
2860     TreePanel tp = new TreePanel(alignPanel, treeFile,
2861             MessageManager.getString("label.load_tree_from_file"), tree);
2862     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2863     addTreeMenuItem(tp, treeFile);
2864   }
2865
2866   /**
2867    * sort the alignment using the given treePanel
2868    *
2869    * @param treePanel
2870    *          tree used to sort view
2871    * @param title
2872    *          string used for undo event name
2873    */
2874   public void sortByTree(TreePanel treePanel, String title)
2875   {
2876     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2877     AlignmentSorter
2878             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2879     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2880     // HistoryItem.SORT));
2881     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2882             "label.order_by_params", new String[] { title }), oldOrder,
2883             viewport.getAlignment()));
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   /**
2888    * Do any automatic reordering of the alignment and add the necessary bits to
2889    * the menu structure for the new tree
2890    *
2891    * @param treePanel
2892    * @param title
2893    */
2894   protected void addTreeMenuItem(final TreePanel treePanel,
2895           final String title)
2896   {
2897     final MenuItem item = new MenuItem(title);
2898     sortByTreeMenu.add(item);
2899     item.addActionListener(new java.awt.event.ActionListener()
2900     {
2901       @Override
2902       public void actionPerformed(ActionEvent evt)
2903       {
2904         sortByTree(treePanel, title); // treePanel.getTitle());
2905       }
2906     });
2907
2908     treePanel.addWindowListener(new WindowAdapter()
2909     {
2910       @Override
2911       public void windowOpened(WindowEvent e)
2912       {
2913         if (viewport.sortByTree)
2914         {
2915           sortByTree(treePanel, title);
2916         }
2917         super.windowOpened(e);
2918       }
2919
2920       @Override
2921       public void windowClosing(WindowEvent e)
2922       {
2923         sortByTreeMenu.remove(item);
2924       };
2925     });
2926   }
2927
2928   public boolean sortBy(AlignmentOrder alorder, String undoname)
2929   {
2930     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2931     if (viewport.applet.debug)
2932     {
2933       System.err.println("Sorting " + alorder.getOrder().size()
2934               + " in alignment '" + getTitle() + "'");
2935     }
2936     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2937     if (undoname != null)
2938     {
2939       addHistoryItem(new OrderCommand(undoname, oldOrder,
2940               viewport.getAlignment()));
2941     }
2942     alignPanel.paintAlignment(true);
2943     return true;
2944   }
2945
2946   protected void documentation_actionPerformed()
2947   {
2948     alignPanel.av.applet.openJalviewHelpUrl();
2949   }
2950
2951   protected void about_actionPerformed()
2952   {
2953
2954     class AboutPanel extends Canvas
2955     {
2956       String version;
2957
2958       String builddate;
2959
2960       public AboutPanel(String version, String builddate)
2961       {
2962         this.version = version;
2963         this.builddate = builddate;
2964       }
2965
2966       @Override
2967       public void paint(Graphics g)
2968       {
2969         g.setColor(Color.white);
2970         g.fillRect(0, 0, getSize().width, getSize().height);
2971         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2972         FontMetrics fm = g.getFontMetrics();
2973         int fh = fm.getHeight();
2974         int y = 5, x = 7;
2975         g.setColor(Color.black);
2976         // TODO: update this text for each release or centrally store it for
2977         // lite and application
2978         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2979         g.drawString(MessageManager.formatMessage(
2980                 "label.jalviewLite_release", new String[] { version }), x,
2981                 y += fh);
2982         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2983         g.drawString(MessageManager.formatMessage(
2984                 "label.jaview_build_date", new String[] { builddate }), x,
2985                 y += fh);
2986         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2987         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2988                 x, y += fh * 1.5);
2989         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2990                 x + 50, y += fh + 8);
2991         g.drawString(
2992                 MessageManager.getString("label.jalview_dev_managers"), x,
2993                 y += fh);
2994         g.drawString(MessageManager
2995                 .getString("label.jalview_distribution_lists"), x, y += fh);
2996         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2997                 x, y += fh + 8);
2998         g.drawString(
2999                 MessageManager.getString("label.jalview_cite_1_authors"),
3000                 x, y += fh);
3001         g.drawString(
3002                 MessageManager.getString("label.jalview_cite_1_title"), x,
3003                 y += fh);
3004         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3005                 x, y += fh);
3006       }
3007     }
3008
3009     Frame frame = new Frame();
3010     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3011             .getBuildDate()));
3012     jalview.bin.JalviewLite.addFrame(frame,
3013             MessageManager.getString("label.jalview"), 580, 220);
3014
3015   }
3016
3017   public void showURL(String url, String target)
3018   {
3019     if (viewport.applet == null)
3020     {
3021       System.out.println("Not running as applet - no browser available.");
3022     }
3023     else
3024     {
3025       viewport.applet.showURL(url, target);
3026     }
3027   }
3028
3029   // ////////////////////////////////////////////////////////////////////////////////
3030   // JBuilder Graphics here
3031
3032   MenuBar alignFrameMenuBar = new MenuBar();
3033
3034   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3035
3036   MenuItem loadApplication = new MenuItem(
3037           MessageManager.getString("label.view_full_application"));
3038
3039   MenuItem loadTree = new MenuItem(
3040           MessageManager.getString("label.load_associated_tree"));
3041
3042   MenuItem loadAnnotations = new MenuItem(
3043           MessageManager.getString("label.load_features_annotations"));
3044
3045   MenuItem outputFeatures = new MenuItem(
3046           MessageManager.getString("label.export_features"));
3047
3048   MenuItem outputAnnotations = new MenuItem(
3049           MessageManager.getString("label.export_annotations"));
3050
3051   MenuItem closeMenuItem = new MenuItem(
3052           MessageManager.getString("action.close"));
3053
3054   MenuItem selectAllSequenceMenuItem = new MenuItem(
3055           MessageManager.getString("action.select_all"));
3056
3057   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3058           MessageManager.getString("action.deselect_all"));
3059
3060   MenuItem invertSequenceMenuItem = new MenuItem(
3061           MessageManager.getString("action.invert_selection"));
3062
3063   MenuItem remove2LeftMenuItem = new MenuItem();
3064
3065   MenuItem remove2RightMenuItem = new MenuItem();
3066
3067   MenuItem removeGappedColumnMenuItem = new MenuItem();
3068
3069   MenuItem removeAllGapsMenuItem = new MenuItem();
3070
3071   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3072
3073   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3074
3075   MenuItem sortPairwiseMenuItem = new MenuItem();
3076
3077   MenuItem sortIDMenuItem = new MenuItem();
3078
3079   MenuItem sortLengthMenuItem = new MenuItem();
3080
3081   MenuItem sortGroupMenuItem = new MenuItem();
3082
3083   MenuItem removeRedundancyMenuItem = new MenuItem();
3084
3085   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3086
3087   MenuItem PCAMenuItem = new MenuItem();
3088
3089   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3090
3091   MenuItem neighbourTreeMenuItem = new MenuItem();
3092
3093   BorderLayout borderLayout1 = new BorderLayout();
3094
3095   public Label statusBar = new Label();
3096
3097   MenuItem clustalColour = new MenuItem();
3098
3099   MenuItem zappoColour = new MenuItem();
3100
3101   MenuItem taylorColour = new MenuItem();
3102
3103   MenuItem hydrophobicityColour = new MenuItem();
3104
3105   MenuItem helixColour = new MenuItem();
3106
3107   MenuItem strandColour = new MenuItem();
3108
3109   MenuItem turnColour = new MenuItem();
3110
3111   MenuItem buriedColour = new MenuItem();
3112
3113   MenuItem purinePyrimidineColour = new MenuItem();
3114
3115   // MenuItem RNAInteractionColour = new MenuItem();
3116
3117   MenuItem RNAHelixColour = new MenuItem();
3118
3119   MenuItem userDefinedColour = new MenuItem();
3120
3121   MenuItem PIDColour = new MenuItem();
3122
3123   MenuItem BLOSUM62Colour = new MenuItem();
3124
3125   MenuItem tcoffeeColour = new MenuItem();
3126
3127   MenuItem njTreeBlosumMenuItem = new MenuItem();
3128
3129   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3130
3131   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3132
3133   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3134
3135   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3136
3137   MenuItem alProperties = new MenuItem(
3138           MessageManager.getString("label.alignment_props"));
3139
3140   MenuItem overviewMenuItem = new MenuItem();
3141
3142   MenuItem undoMenuItem = new MenuItem();
3143
3144   MenuItem redoMenuItem = new MenuItem();
3145
3146   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3147
3148   MenuItem noColourmenuItem = new MenuItem();
3149
3150   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3151
3152   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3153
3154   MenuItem findMenuItem = new MenuItem();
3155
3156   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3157
3158   MenuItem nucleotideColour = new MenuItem();
3159
3160   MenuItem deleteGroups = new MenuItem();
3161
3162   MenuItem grpsFromSelection = new MenuItem();
3163
3164   MenuItem createGroup = new MenuItem();
3165
3166   MenuItem unGroup = new MenuItem();
3167
3168   MenuItem delete = new MenuItem();
3169
3170   MenuItem copy = new MenuItem();
3171
3172   MenuItem cut = new MenuItem();
3173
3174   Menu pasteMenu = new Menu();
3175
3176   MenuItem pasteNew = new MenuItem();
3177
3178   MenuItem pasteThis = new MenuItem();
3179
3180   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3181
3182   MenuItem font = new MenuItem();
3183
3184   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3185
3186   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3187
3188   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3189
3190   MenuItem modifyPID = new MenuItem();
3191
3192   MenuItem modifyConservation = new MenuItem();
3193
3194   CheckboxMenuItem autoCalculate = null;
3195
3196   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3197           "Sort Alignment With New Tree", true);
3198
3199   Menu sortByTreeMenu = new Menu();
3200
3201   MenuItem inputText = new MenuItem();
3202
3203   MenuItem documentation = new MenuItem();
3204
3205   MenuItem about = new MenuItem();
3206
3207   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3208
3209   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3222
3223   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3224
3225   /**
3226    * Initialise menus and other items
3227    *
3228    * @throws Exception
3229    */
3230   private void jbInit() throws Exception
3231   {
3232     setMenuBar(alignFrameMenuBar);
3233
3234     /*
3235      * Configure File menu items and actions
3236      */
3237     inputText
3238             .setLabel(MessageManager.getString("label.input_from_textbox"));
3239     inputText.addActionListener(this);
3240     Menu outputTextboxMenu = new Menu(
3241             MessageManager.getString("label.out_to_textbox"));
3242     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3243     {
3244
3245       MenuItem item = new MenuItem(
3246               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3247
3248       item.addActionListener(new java.awt.event.ActionListener()
3249       {
3250         @Override
3251         public void actionPerformed(ActionEvent e)
3252         {
3253           outputText_actionPerformed(e);
3254         }
3255       });
3256
3257       outputTextboxMenu.add(item);
3258     }
3259     closeMenuItem.addActionListener(this);
3260     loadApplication.addActionListener(this);
3261     loadTree.addActionListener(this);
3262     loadAnnotations.addActionListener(this);
3263     outputFeatures.addActionListener(this);
3264     outputAnnotations.addActionListener(this);
3265
3266     /*
3267      * Configure Edit menu items and actions
3268      */
3269     undoMenuItem.setEnabled(false);
3270     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3271     undoMenuItem.addActionListener(this);
3272     redoMenuItem.setEnabled(false);
3273     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3274     redoMenuItem.addActionListener(this);
3275     copy.setLabel(MessageManager.getString("action.copy"));
3276     copy.addActionListener(this);
3277     cut.setLabel(MessageManager.getString("action.cut"));
3278     cut.addActionListener(this);
3279     delete.setLabel(MessageManager.getString("action.delete"));
3280     delete.addActionListener(this);
3281     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3282     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3283     pasteNew.addActionListener(this);
3284     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3285     pasteThis.addActionListener(this);
3286     remove2LeftMenuItem.setLabel(MessageManager
3287             .getString("action.remove_left"));
3288     remove2LeftMenuItem.addActionListener(this);
3289     remove2RightMenuItem.setLabel(MessageManager
3290             .getString("action.remove_right"));
3291     remove2RightMenuItem.addActionListener(this);
3292     removeGappedColumnMenuItem.setLabel(MessageManager
3293             .getString("action.remove_empty_columns"));
3294     removeGappedColumnMenuItem.addActionListener(this);
3295     removeAllGapsMenuItem.setLabel(MessageManager
3296             .getString("action.remove_all_gaps"));
3297     removeAllGapsMenuItem.addActionListener(this);
3298     removeRedundancyMenuItem.setLabel(MessageManager
3299             .getString("action.remove_redundancy"));
3300     removeRedundancyMenuItem.addActionListener(this);
3301
3302     /*
3303      * Configure Select menu items and actions
3304      */
3305     findMenuItem.setLabel(MessageManager.getString("action.find"));
3306     findMenuItem.addActionListener(this);
3307     selectAllSequenceMenuItem.addActionListener(this);
3308     deselectAllSequenceMenuItem.addActionListener(this);
3309     invertSequenceMenuItem.setLabel(MessageManager
3310             .getString("action.invert_sequence_selection"));
3311     invertSequenceMenuItem.addActionListener(this);
3312     invertColSel.setLabel(MessageManager
3313             .getString("action.invert_column_selection"));
3314     invertColSel.addActionListener(this);
3315     deleteGroups.setLabel(MessageManager
3316             .getString("action.undefine_groups"));
3317     deleteGroups.addActionListener(this);
3318     grpsFromSelection.setLabel(MessageManager
3319             .getString("action.make_groups_selection"));
3320     grpsFromSelection.addActionListener(this);
3321     createGroup.setLabel(MessageManager.getString("action.create_group"));
3322     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3323     annotationColumnSelection.setLabel(MessageManager
3324             .getString("action.select_by_annotation"));
3325     annotationColumnSelection.addActionListener(this);
3326
3327     /*
3328      * Configure View menu items and actions
3329      */
3330     newView.setLabel(MessageManager.getString("action.new_view"));
3331     newView.addActionListener(this);
3332     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3333     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3334     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3335     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3336     hideColumns
3337             .setLabel(MessageManager.getString("label.selected_columns"));
3338     hideSequences.setLabel(MessageManager
3339             .getString("label.selected_sequences"));
3340     hideAllButSelection.setLabel(MessageManager
3341             .getString("label.all_but_selected_region"));
3342     hideAllSelection.setLabel(MessageManager
3343             .getString("label.selected_region"));
3344     showAllHidden.setLabel(MessageManager
3345             .getString("label.all_sequences_columns"));
3346     showColumns.addActionListener(this);
3347     showSeqs.addActionListener(this);
3348     hideColumns.addActionListener(this);
3349     hideSequences.addActionListener(this);
3350     hideAllButSelection.addActionListener(this);
3351     hideAllSelection.addActionListener(this);
3352     showAllHidden.addActionListener(this);
3353     featureSettings.setLabel(MessageManager
3354             .getString("action.feature_settings"));
3355     featureSettings.addActionListener(this);
3356     sequenceFeatures.setLabel(MessageManager
3357             .getString("label.show_sequence_features"));
3358     sequenceFeatures.addItemListener(this);
3359     sequenceFeatures.setState(false);
3360     followMouseOverFlag.setLabel(MessageManager
3361             .getString("label.automatic_scrolling"));
3362     followMouseOverFlag.addItemListener(this);
3363     alProperties.addActionListener(this);
3364     overviewMenuItem.setLabel(MessageManager
3365             .getString("label.overview_window"));
3366     overviewMenuItem.addActionListener(this);
3367
3368     /*
3369      * Configure Annotations menu items and actions
3370      */
3371     annotationPanelMenuItem.setLabel(MessageManager
3372             .getString("label.show_annotations"));
3373     annotationPanelMenuItem.addItemListener(this);
3374     showGroupConsensus.setLabel(MessageManager
3375             .getString("label.group_consensus"));
3376     showGroupConservation.setLabel(MessageManager
3377             .getString("label.group_conservation"));
3378     showConsensusHistogram.setLabel(MessageManager
3379             .getString("label.show_consensus_histogram"));
3380     showSequenceLogo.setLabel(MessageManager
3381             .getString("label.show_consensus_logo"));
3382     normSequenceLogo.setLabel(MessageManager
3383             .getString("label.norm_consensus_logo"));
3384     applyAutoAnnotationSettings.setLabel(MessageManager
3385             .getString("label.apply_all_groups"));
3386     applyAutoAnnotationSettings.setState(true);
3387     Menu autoAnnMenu = new Menu(
3388             MessageManager.getString("label.autocalculated_annotation"));
3389     showGroupConsensus.addItemListener(this);
3390     showGroupConservation.addItemListener(this);
3391     showConsensusHistogram.addItemListener(this);
3392     showSequenceLogo.addItemListener(this);
3393     normSequenceLogo.addItemListener(this);
3394     applyAutoAnnotationSettings.addItemListener(this);
3395     showAlignmentAnnotations = new CheckboxMenuItem(
3396             MessageManager.getString("label.show_all_al_annotations"));
3397     showSequenceAnnotations = new CheckboxMenuItem(
3398             MessageManager.getString("label.show_all_seq_annotations"));
3399     sortAnnBySequence = new CheckboxMenuItem(
3400             MessageManager.getString("label.sort_annotations_by_sequence"));
3401     sortAnnByLabel = new CheckboxMenuItem(
3402             MessageManager.getString("label.sort_annotations_by_label"));
3403     showAutoFirst = new CheckboxMenuItem(
3404             MessageManager.getString("label.show_first"));
3405     showAutoFirst.setState(false); // pending applet parameter
3406     setShowAutoCalculatedAbove(showAutoFirst.getState());
3407     showAutoLast = new CheckboxMenuItem(
3408             MessageManager.getString("label.show_last"));
3409     showAutoLast.setState(!showAutoFirst.getState());
3410     showAlignmentAnnotations.addItemListener(this);
3411     showSequenceAnnotations.addItemListener(this);
3412     sortAnnBySequence.addItemListener(this);
3413     sortAnnByLabel.addItemListener(this);
3414     showAutoFirst.addItemListener(this);
3415     showAutoLast.addItemListener(this);
3416
3417     /*
3418      * Configure Format menu items and actions
3419      */
3420     font.setLabel(MessageManager.getString("action.font"));
3421     font.addActionListener(this);
3422     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3423     scaleAbove.setState(true);
3424     scaleAbove.setEnabled(false);
3425     scaleAbove.addItemListener(this);
3426     scaleLeft.setEnabled(false);
3427     scaleLeft.setState(true);
3428     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3429     scaleLeft.addItemListener(this);
3430     scaleRight.setEnabled(false);
3431     scaleRight.setState(true);
3432     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3433     scaleRight.addItemListener(this);
3434     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3435     viewBoxesMenuItem.setState(true);
3436     viewBoxesMenuItem.addItemListener(this);
3437     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3438     viewTextMenuItem.setState(true);
3439     viewTextMenuItem.addItemListener(this);
3440     colourTextMenuItem.setLabel(MessageManager
3441             .getString("label.colour_text"));
3442     colourTextMenuItem.addItemListener(this);
3443     displayNonconservedMenuItem.setLabel(MessageManager
3444             .getString("label.show_non_conversed"));
3445     displayNonconservedMenuItem.addItemListener(this);
3446     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3447     wrapMenuItem.addItemListener(this);
3448     renderGapsMenuItem.setLabel(MessageManager
3449             .getString("action.show_gaps"));
3450     renderGapsMenuItem.setState(true);
3451     renderGapsMenuItem.addItemListener(this);
3452     centreColumnLabelFlag.setLabel(MessageManager
3453             .getString("label.centre_column_labels"));
3454     centreColumnLabelFlag.addItemListener(this);
3455     seqLimits.setState(true);
3456     seqLimits.setLabel(MessageManager
3457             .getString("label.show_sequence_limits"));
3458     seqLimits.addItemListener(this);
3459
3460     /*
3461      * Configure Colour menu items and actions
3462      */
3463     applyToAllGroups.setLabel(MessageManager
3464             .getString("label.apply_colour_to_all_groups"));
3465     applyToAllGroups.setState(true);
3466     applyToAllGroups.addItemListener(this);
3467     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3468     clustalColour.addActionListener(this);
3469     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3470     zappoColour.addActionListener(this);
3471     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3472     taylorColour.addActionListener(this);
3473     hydrophobicityColour.setLabel(MessageManager
3474             .getString("label.hydrophobicity"));
3475     hydrophobicityColour.addActionListener(this);
3476     helixColour
3477             .setLabel(MessageManager.getString("label.helix_propensity"));
3478     helixColour.addActionListener(this);
3479     strandColour.setLabel(MessageManager
3480             .getString("label.strand_propensity"));
3481     strandColour.addActionListener(this);
3482     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3483     turnColour.addActionListener(this);
3484     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3485     buriedColour.addActionListener(this);
3486     purinePyrimidineColour.setLabel(MessageManager
3487             .getString("label.purine_pyrimidine"));
3488     purinePyrimidineColour.addActionListener(this);
3489     // RNAInteractionColour.setLabel(MessageManager
3490     // .getString("label.rna_interaction"));
3491     // RNAInteractionColour.addActionListener(this);
3492     RNAHelixColour.setLabel(MessageManager
3493             .getString("action.by_rna_helixes"));
3494     RNAHelixColour.addActionListener(this);
3495     userDefinedColour.setLabel(MessageManager
3496             .getString("action.user_defined"));
3497     userDefinedColour.addActionListener(this);
3498     PIDColour.setLabel(MessageManager
3499             .getString("label.percentage_identity"));
3500     PIDColour.addActionListener(this);
3501     BLOSUM62Colour.setLabel(MessageManager
3502             .getString("label.blosum62_score"));
3503     BLOSUM62Colour.addActionListener(this);
3504     tcoffeeColour
3505             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3506     // it will be enabled only if a score file is provided
3507     tcoffeeColour.setEnabled(false);
3508     tcoffeeColour.addActionListener(this);
3509     conservationMenuItem.setLabel(MessageManager
3510             .getString("action.by_conservation"));
3511     conservationMenuItem.addItemListener(this);
3512     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3513     noColourmenuItem.addActionListener(this);
3514     abovePIDThreshold.setLabel(MessageManager
3515             .getString("label.above_identity_threshold"));
3516     abovePIDThreshold.addItemListener(this);
3517     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3518     nucleotideColour.addActionListener(this);
3519     modifyPID.setLabel(MessageManager
3520             .getString("label.modify_identity_thereshold"));
3521     modifyPID.addActionListener(this);
3522     modifyConservation.setLabel(MessageManager
3523             .getString("label.modify_conservation_thereshold"));
3524     modifyConservation.addActionListener(this);
3525     annotationColour.setLabel(MessageManager
3526             .getString("action.by_annotation"));
3527     annotationColour.addActionListener(this);
3528
3529     /*
3530      * Configure Calculate menu items and actions
3531      */
3532     sortPairwiseMenuItem.setLabel(MessageManager
3533             .getString("action.by_pairwise_id"));
3534     sortPairwiseMenuItem.addActionListener(this);
3535     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3536     sortIDMenuItem.addActionListener(this);
3537     sortLengthMenuItem.setLabel(MessageManager
3538             .getString("action.by_length"));
3539     sortLengthMenuItem.addActionListener(this);
3540     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3541     sortGroupMenuItem.addActionListener(this);
3542     pairwiseAlignmentMenuItem.setLabel(MessageManager
3543             .getString("action.pairwise_alignment"));
3544     pairwiseAlignmentMenuItem.addActionListener(this);
3545     PCAMenuItem.setLabel(MessageManager
3546             .getString("label.principal_component_analysis"));
3547     PCAMenuItem.addActionListener(this);
3548     autoCalculate = new CheckboxMenuItem(
3549             MessageManager.getString("label.autocalculate_consensus"), true);
3550     averageDistanceTreeMenuItem.setLabel(MessageManager
3551             .getString("label.average_distance_identity"));
3552     averageDistanceTreeMenuItem.addActionListener(this);
3553     neighbourTreeMenuItem.setLabel(MessageManager
3554             .getString("label.neighbour_joining_identity"));
3555     neighbourTreeMenuItem.addActionListener(this);
3556     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3557             .getString("label.average_distance_bloslum62"));
3558     avDistanceTreeBlosumMenuItem.addActionListener(this);
3559     njTreeBlosumMenuItem.setLabel(MessageManager
3560             .getString("label.neighbour_blosum62"));
3561     njTreeBlosumMenuItem.addActionListener(this);
3562     sortByTreeMenu.setLabel(MessageManager
3563             .getString("action.by_tree_order"));
3564     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3565     Menu calculateTreeMenu = new Menu(
3566             MessageManager.getString("action.calculate_tree"));
3567     autoCalculate.addItemListener(this);
3568     sortByTree.addItemListener(this);
3569
3570     /*
3571      * Configure Help menu items and actions
3572      */
3573     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3574     documentation.setLabel(MessageManager.getString("label.documentation"));
3575     documentation.addActionListener(this);
3576     about.setLabel(MessageManager.getString("label.about"));
3577     about.addActionListener(this);
3578
3579     /*
3580      * Add top level menus to frame
3581      */
3582     alignFrameMenuBar.add(fileMenu);
3583     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3584     alignFrameMenuBar.add(editMenu);
3585     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3586     alignFrameMenuBar.add(selectMenu);
3587     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3588     alignFrameMenuBar.add(viewMenu);
3589     Menu annotationsMenu = new Menu(
3590             MessageManager.getString("action.annotations"));
3591     alignFrameMenuBar.add(annotationsMenu);
3592     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3593     alignFrameMenuBar.add(formatMenu);
3594     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3595     alignFrameMenuBar.add(colourMenu);
3596     Menu calculateMenu = new Menu(
3597             MessageManager.getString("action.calculate"));
3598     alignFrameMenuBar.add(calculateMenu);
3599     alignFrameMenuBar.add(helpMenu);
3600
3601     /*
3602      * File menu
3603      */
3604     fileMenu.add(inputText);
3605     fileMenu.add(loadTree);
3606     fileMenu.add(loadAnnotations);
3607     fileMenu.addSeparator();
3608     fileMenu.add(outputTextboxMenu);
3609     fileMenu.add(outputFeatures);
3610     fileMenu.add(outputAnnotations);
3611     if (jalviewServletURL != null)
3612     {
3613       fileMenu.add(loadApplication);
3614     }
3615     fileMenu.addSeparator();
3616     fileMenu.add(closeMenuItem);
3617
3618     /*
3619      * Edit menu
3620      */
3621     editMenu.add(undoMenuItem);
3622     editMenu.add(redoMenuItem);
3623     editMenu.add(cut);
3624     editMenu.add(copy);
3625     pasteMenu.add(pasteNew);
3626     pasteMenu.add(pasteThis);
3627     editMenu.add(pasteMenu);
3628     editMenu.add(delete);
3629     editMenu.addSeparator();
3630     editMenu.add(remove2LeftMenuItem);
3631     editMenu.add(remove2RightMenuItem);
3632     editMenu.add(removeGappedColumnMenuItem);
3633     editMenu.add(removeAllGapsMenuItem);
3634     editMenu.add(removeRedundancyMenuItem);
3635
3636     /*
3637      * Select menu
3638      */
3639     selectMenu.add(findMenuItem);
3640     selectMenu.addSeparator();
3641     selectMenu.add(selectAllSequenceMenuItem);
3642     selectMenu.add(deselectAllSequenceMenuItem);
3643     selectMenu.add(invertSequenceMenuItem);
3644     selectMenu.add(invertColSel);
3645     selectMenu.add(createGroup);
3646     selectMenu.add(unGroup);
3647     selectMenu.add(grpsFromSelection);
3648     selectMenu.add(deleteGroups);
3649     selectMenu.add(annotationColumnSelection);
3650
3651     /*
3652      * View menu
3653      */
3654     viewMenu.add(newView);
3655     viewMenu.addSeparator();
3656     showMenu.add(showColumns);
3657     showMenu.add(showSeqs);
3658     showMenu.add(showAllHidden);
3659     viewMenu.add(showMenu);
3660     hideMenu.add(hideColumns);
3661     hideMenu.add(hideSequences);
3662     hideMenu.add(hideAllSelection);
3663     hideMenu.add(hideAllButSelection);
3664     viewMenu.add(hideMenu);
3665     viewMenu.addSeparator();
3666     viewMenu.add(followMouseOverFlag);
3667     viewMenu.addSeparator();
3668     viewMenu.add(sequenceFeatures);
3669     viewMenu.add(featureSettings);
3670     viewMenu.addSeparator();
3671     viewMenu.add(alProperties);
3672     viewMenu.addSeparator();
3673     viewMenu.add(overviewMenuItem);
3674
3675     /*
3676      * Annotations menu
3677      */
3678     annotationsMenu.add(annotationPanelMenuItem);
3679     annotationsMenu.addSeparator();
3680     annotationsMenu.add(showAlignmentAnnotations);
3681     annotationsMenu.add(showSequenceAnnotations);
3682     annotationsMenu.add(sortAnnBySequence);
3683     annotationsMenu.add(sortAnnByLabel);
3684     annotationsMenu.addSeparator();
3685     autoAnnMenu.add(showAutoFirst);
3686     autoAnnMenu.add(showAutoLast);
3687     autoAnnMenu.addSeparator();
3688     autoAnnMenu.add(applyAutoAnnotationSettings);
3689     autoAnnMenu.add(showConsensusHistogram);
3690     autoAnnMenu.add(showSequenceLogo);
3691     autoAnnMenu.add(normSequenceLogo);
3692     autoAnnMenu.addSeparator();
3693     autoAnnMenu.add(showGroupConservation);
3694     autoAnnMenu.add(showGroupConsensus);
3695     annotationsMenu.add(autoAnnMenu);
3696
3697     /*
3698      * Format menu
3699      */
3700     formatMenu.add(font);
3701     formatMenu.add(seqLimits);
3702     formatMenu.add(wrapMenuItem);
3703     formatMenu.add(scaleAbove);
3704     formatMenu.add(scaleLeft);
3705     formatMenu.add(scaleRight);
3706     formatMenu.add(viewBoxesMenuItem);
3707     formatMenu.add(viewTextMenuItem);
3708     formatMenu.add(colourTextMenuItem);
3709     formatMenu.add(displayNonconservedMenuItem);
3710     formatMenu.add(renderGapsMenuItem);
3711     formatMenu.add(centreColumnLabelFlag);
3712
3713     /*
3714      * Colour menu
3715      */
3716     colourMenu.add(applyToAllGroups);
3717     colourMenu.addSeparator();
3718     colourMenu.add(noColourmenuItem);
3719     colourMenu.add(clustalColour);
3720     colourMenu.add(BLOSUM62Colour);
3721     colourMenu.add(PIDColour);
3722     colourMenu.add(zappoColour);
3723     colourMenu.add(taylorColour);
3724     colourMenu.add(hydrophobicityColour);
3725     colourMenu.add(helixColour);
3726     colourMenu.add(strandColour);
3727     colourMenu.add(turnColour);
3728     colourMenu.add(buriedColour);
3729     colourMenu.add(nucleotideColour);
3730     colourMenu.add(purinePyrimidineColour);
3731     // colourMenu.add(RNAInteractionColour);
3732     colourMenu.add(tcoffeeColour);
3733     colourMenu.add(userDefinedColour);
3734     colourMenu.addSeparator();
3735     colourMenu.add(conservationMenuItem);
3736     colourMenu.add(modifyConservation);
3737     colourMenu.add(abovePIDThreshold);
3738     colourMenu.add(modifyPID);
3739     colourMenu.add(annotationColour);
3740     colourMenu.add(RNAHelixColour);
3741
3742     /*
3743      * Calculate menu
3744      */
3745     sortMenu.add(sortIDMenuItem);
3746     sortMenu.add(sortLengthMenuItem);
3747     sortMenu.add(sortByTreeMenu);
3748     sortMenu.add(sortGroupMenuItem);
3749     sortMenu.add(sortPairwiseMenuItem);
3750     calculateMenu.add(sortMenu);
3751     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3752     calculateTreeMenu.add(neighbourTreeMenuItem);
3753     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3754     calculateTreeMenu.add(njTreeBlosumMenuItem);
3755     calculateMenu.add(calculateTreeMenu);
3756     calculateMenu.addSeparator();
3757     calculateMenu.add(pairwiseAlignmentMenuItem);
3758     calculateMenu.add(PCAMenuItem);
3759     calculateMenu.add(autoCalculate);
3760     calculateMenu.add(sortByTree);
3761
3762     /*
3763      * Help menu
3764      */
3765     helpMenu.add(documentation);
3766     helpMenu.add(about);
3767
3768     /*
3769      * Status bar
3770      */
3771     statusBar.setBackground(Color.white);
3772     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3773     statusBar.setText(MessageManager.getString("label.status_bar"));
3774     this.add(statusBar, BorderLayout.SOUTH);
3775   }
3776
3777   @Override
3778   public void setStatus(String string)
3779   {
3780     statusBar.setText(string);
3781   };
3782
3783   MenuItem featureSettings = new MenuItem();
3784
3785   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3786
3787   MenuItem annotationColour = new MenuItem();
3788
3789   MenuItem annotationColumnSelection = new MenuItem();
3790
3791   MenuItem invertColSel = new MenuItem();
3792
3793   MenuItem showColumns = new MenuItem();
3794
3795   MenuItem showSeqs = new MenuItem();
3796
3797   MenuItem hideColumns = new MenuItem();
3798
3799   MenuItem hideSequences = new MenuItem();
3800
3801   MenuItem hideAllButSelection = new MenuItem();
3802
3803   MenuItem hideAllSelection = new MenuItem();
3804
3805   MenuItem showAllHidden = new MenuItem();
3806
3807   MenuItem newView = new MenuItem();
3808
3809   private CheckboxMenuItem showAlignmentAnnotations;
3810
3811   private CheckboxMenuItem showSequenceAnnotations;
3812
3813   private CheckboxMenuItem sortAnnBySequence;
3814
3815   private CheckboxMenuItem sortAnnByLabel;
3816
3817   private CheckboxMenuItem showAutoFirst;
3818
3819   private CheckboxMenuItem showAutoLast;
3820
3821   private SplitFrame splitFrame;
3822
3823   /**
3824    * Attach the alignFrame panels after embedding menus, if necessary. This used
3825    * to be called setEmbedded, but is now creates the dropdown menus in a
3826    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3827    *
3828    * @param reallyEmbedded
3829    *          true to attach the view to the applet area on the page rather than
3830    *          in a new window
3831    */
3832   public void createAlignFrameWindow(boolean reallyEmbedded)
3833   {
3834     if (reallyEmbedded)
3835     {
3836       embedAlignFrameInApplet(viewport.applet);
3837     }
3838     else
3839     {
3840       // //////
3841       // test and embed menu bar if necessary.
3842       //
3843       if (embedMenuIfNeeded(alignPanel))
3844       {
3845         /*
3846          * adjust for status bar height too. ? pointless as overridden by layout
3847          * manager
3848          */
3849         alignPanel.setSize(getSize().width,
3850                 getSize().height - statusBar.getHeight());
3851       }
3852       add(statusBar, BorderLayout.SOUTH);
3853       add(alignPanel, BorderLayout.CENTER);
3854       // and register with the applet so it can pass external API calls to us
3855       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3856               frameHeight);
3857     }
3858   }
3859
3860   /**
3861    * Add the components of this AlignFrame to the applet container.
3862    *
3863    * @param theApplet
3864    */
3865   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3866   {
3867     // ////
3868     // Explicitly build the embedded menu panel for the on-page applet
3869     //
3870     // view cannot be closed if its actually on the page
3871     fileMenu.remove(closeMenuItem);
3872     fileMenu.remove(3); // Remove Separator
3873     // construct embedded menu, using default font
3874     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3875     // and actually add the components to the applet area
3876     theApplet.setLayout(new BorderLayout());
3877     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3878     theApplet.add(statusBar, BorderLayout.SOUTH);
3879     // TODO should size be left to the layout manager?
3880     alignPanel.setSize(theApplet.getSize().width,
3881             theApplet.getSize().height - embeddedMenu.getHeight()
3882                     - statusBar.getHeight());
3883     theApplet.add(alignPanel, BorderLayout.CENTER);
3884     final AlignFrame me = this;
3885     theApplet.addFocusListener(new FocusListener()
3886     {
3887
3888       @Override
3889       public void focusLost(FocusEvent e)
3890       {
3891         if (theApplet.currentAlignFrame == me)
3892         {
3893           theApplet.currentAlignFrame = null;
3894         }
3895       }
3896
3897       @Override
3898       public void focusGained(FocusEvent e)
3899       {
3900         theApplet.currentAlignFrame = me;
3901       }
3902     });
3903     theApplet.validate();
3904   }
3905
3906   /**
3907    * create a new binding between structures in an existing jmol viewer instance
3908    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3909    * this does not open a new Jmol window, or modify the display of the
3910    * structures in the original jmol window. Note This method doesn't work
3911    * without an additional javascript library to exchange messages between the
3912    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3913    *
3914    * @param viewer
3915    *          JmolViewer instance
3916    * @param sequenceIds
3917    *          - sequence Ids to search for associations
3918    */
3919   public SequenceStructureBinding addStructureViewInstance(
3920           Object jmolviewer, String[] sequenceIds)
3921   {
3922     Viewer viewer = null;
3923     try
3924     {
3925       viewer = (Viewer) jmolviewer;
3926     } catch (ClassCastException ex)
3927     {
3928       System.err.println("Unsupported viewer object :"
3929               + jmolviewer.getClass());
3930     }
3931     if (viewer == null)
3932     {
3933       System.err.println("Can't use this object as a structure viewer:"
3934               + jmolviewer.getClass());
3935       return null;
3936     }
3937     SequenceI[] seqs = null;
3938     if (sequenceIds == null || sequenceIds.length == 0)
3939     {
3940       seqs = viewport.getAlignment().getSequencesArray();
3941     }
3942     else
3943     {
3944       Vector sqi = new Vector();
3945       AlignmentI al = viewport.getAlignment();
3946       for (int sid = 0; sid < sequenceIds.length; sid++)
3947       {
3948         SequenceI sq = al.findName(sequenceIds[sid]);
3949         if (sq != null)
3950         {
3951           sqi.addElement(sq);
3952         }
3953       }
3954       if (sqi.size() > 0)
3955       {
3956         seqs = new SequenceI[sqi.size()];
3957         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3958         {
3959           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3960         }
3961       }
3962       else
3963       {
3964         return null;
3965       }
3966     }
3967     AAStructureBindingModel jmv = null;
3968     // TODO: search for a jmv that involves viewer
3969     if (jmv == null)
3970     { // create a new viewer/jalview binding.
3971       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3972     }
3973     return jmv;
3974
3975   }
3976
3977   /**
3978    * bind a pdb file to a sequence in the current view
3979    *
3980    * @param sequenceId
3981    *          - sequenceId within the dataset.
3982    * @param pdbEntryString
3983    *          - the short name for the PDB file
3984    * @param pdbFile
3985    *          - pdb file - either a URL or a valid PDB file.
3986    * @return true if binding was as success TODO: consider making an exception
3987    *         structure for indicating when PDB parsing or sequenceId location
3988    *         fails.
3989    */
3990   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3991           String pdbFile)
3992   {
3993     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3994     boolean needtoadd = false;
3995     if (toaddpdb != null)
3996     {
3997       Vector pdbe = toaddpdb.getAllPDBEntries();
3998       PDBEntry pdbentry = null;
3999       if (pdbe != null && pdbe.size() > 0)
4000       {
4001         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4002         {
4003           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4004           if (!pdbentry.getId().equals(pdbEntryString)
4005                   && !pdbentry.getFile().equals(pdbFile))
4006           {
4007             pdbentry = null;
4008           }
4009           else
4010           {
4011             continue;
4012           }
4013         }
4014       }
4015       if (pdbentry == null)
4016       {
4017         pdbentry = new PDBEntry();
4018         pdbentry.setId(pdbEntryString);
4019         pdbentry.setFile(pdbFile);
4020         needtoadd = true; // add this new entry to sequence.
4021       }
4022       // resolve data source
4023       // TODO: this code should be a refactored to an io package
4024       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4025       if (protocol == null)
4026       {
4027         return false;
4028       }
4029       if (needtoadd)
4030       {
4031         // make a note of the access mode and add
4032         if (pdbentry.getProperty() == null)
4033         {
4034           pdbentry.setProperty(new Hashtable());
4035         }
4036         pdbentry.getProperty().put("protocol", protocol);
4037         toaddpdb.addPDBId(pdbentry);
4038         alignPanel.getStructureSelectionManager()
4039                 .registerPDBEntry(pdbentry);
4040       }
4041     }
4042     return true;
4043   }
4044
4045   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4046   {
4047     if (seqs != null)
4048     {
4049       Vector sequences = new Vector();
4050       for (int i = 0; i < seqs.length; i++)
4051       {
4052         if (seqs[i] != null)
4053         {
4054           sequences.addElement(new Object[] { seqs[i],
4055               (chains != null) ? chains[i] : null });
4056         }
4057       }
4058       seqs = new SequenceI[sequences.size()];
4059       chains = new String[sequences.size()];
4060       for (int i = 0, isize = sequences.size(); i < isize; i++)
4061       {
4062         Object[] oj = (Object[]) sequences.elementAt(i);
4063
4064         seqs[i] = (SequenceI) oj[0];
4065         chains[i] = (String) oj[1];
4066       }
4067     }
4068     return new Object[] { seqs, chains };
4069
4070   }
4071
4072   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4073           SequenceI[] seqs, String[] chains, String protocol)
4074   {
4075     // Scrub any null sequences from the array
4076     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4077     seqs = (SequenceI[]) sqch[0];
4078     chains = (String[]) sqch[1];
4079     if (seqs == null || seqs.length == 0)
4080     {
4081       System.err
4082               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4083     }
4084     if (protocol == null || protocol.trim().length() == 0
4085             || protocol.equals("null"))
4086     {
4087       protocol = (String) pdb.getProperty().get("protocol");
4088       if (protocol == null)
4089       {
4090         System.err.println("Couldn't work out protocol to open structure: "
4091                 + pdb.getId());
4092         return;
4093       }
4094     }
4095     if (applet.useXtrnalSviewer)
4096     {
4097       // register the association(s) and quit, don't create any windows.
4098       if (StructureSelectionManager.getStructureSelectionManager(applet)
4099               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4100       {
4101         System.err.println("Failed to map " + pdb.getFile() + " ("
4102                 + protocol + ") to any sequences");
4103       }
4104       return;
4105     }
4106     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4107     {
4108       // can only do alignments with Jmol
4109       // find the last jmol window assigned to this alignment
4110       jalview.appletgui.AppletJmol ajm = null, tajm;
4111       Vector jmols = applet
4112               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4113       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4114       {
4115         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4116         if (tajm.ap.alignFrame == this)
4117         {
4118           ajm = tajm;
4119           break;
4120         }
4121       }
4122       if (ajm != null)
4123       {
4124         System.err
4125                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4126         // try and add the pdb structure
4127         // ajm.addS
4128         ajm = null;
4129       }
4130     }
4131     // otherwise, create a new window
4132     if (applet.jmolAvailable)
4133     {
4134       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4135               protocol);
4136       applet.lastFrameX += 40;
4137       applet.lastFrameY += 40;
4138     }
4139     else
4140     {
4141       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4142     }
4143
4144   }
4145
4146   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4147           SequenceI[][] seqs, String[][] chains, String[] protocols)
4148   {
4149     // TODO Auto-generated method stub
4150     System.err.println("Aligned Structure View: Not yet implemented.");
4151   }
4152
4153   /**
4154    * modify the current selection, providing the user has not made a selection
4155    * already.
4156    *
4157    * @param sel
4158    *          - sequences from this alignment
4159    * @param csel
4160    *          - columns to be selected on the alignment
4161    */
4162   public void select(SequenceGroup sel, ColumnSelection csel)
4163   {
4164     alignPanel.seqPanel.selection(sel, csel, null);
4165   }
4166
4167   public void scrollTo(int row, int column)
4168   {
4169     alignPanel.seqPanel.scrollTo(row, column);
4170   }
4171
4172   public void scrollToRow(int row)
4173   {
4174     alignPanel.seqPanel.scrollToRow(row);
4175   }
4176
4177   public void scrollToColumn(int column)
4178   {
4179     alignPanel.seqPanel.scrollToColumn(column);
4180   }
4181
4182   /**
4183    * @return the alignments unique ID.
4184    */
4185   public String getSequenceSetId()
4186   {
4187     return viewport.getSequenceSetId();
4188   }
4189
4190   /**
4191    * Load the (T-Coffee) score file from the specified url
4192    *
4193    * @param source
4194    *          File/URL/T-COFFEE score file contents
4195    * @throws IOException
4196    * @return true if alignment was annotated with data from source
4197    */
4198   public boolean loadScoreFile(String source) throws IOException
4199   {
4200
4201     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4202             AppletFormatAdapter.checkProtocol(source));
4203     if (!file.isValid())
4204     {
4205       // TODO: raise dialog for gui
4206       System.err.println("Problems parsing T-Coffee scores: "
4207               + file.getWarningMessage());
4208       System.err.println("Origin was:\n" + source);
4209       return false;
4210     }
4211
4212     /*
4213      * check that the score matrix matches the alignment dimensions
4214      */
4215     AlignmentI aln;
4216     if ((aln = viewport.getAlignment()) != null
4217             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4218                     .getWidth()))
4219     {
4220       // TODO: raise a dialog box here rather than bomb out.
4221       System.err
4222               .println("The scores matrix does not match the alignment dimensions");
4223
4224     }
4225
4226     // TODO add parameter to indicate if matching should be done
4227     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4228     {
4229       alignPanel.fontChanged();
4230       tcoffeeColour.setEnabled(true);
4231       // switch to this color
4232       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4233       return true;
4234     }
4235     else
4236     {
4237       System.err.println("Problems resolving T-Coffee scores:");
4238       if (file.getWarningMessage() != null)
4239       {
4240         System.err.println(file.getWarningMessage());
4241       }
4242     }
4243     return false;
4244   }
4245
4246   public SplitFrame getSplitFrame()
4247   {
4248     return this.splitFrame;
4249   }
4250
4251   public void setSplitFrame(SplitFrame sf)
4252   {
4253     this.splitFrame = sf;
4254   }
4255
4256   // may not need this
4257   @Override
4258   public void setShowSeqFeatures(boolean b)
4259   {
4260     // showSeqFeatures.setSelected(b);
4261     viewport.setShowSequenceFeatures(b);
4262
4263   }
4264
4265   @Override
4266   public void setMenusForViewport()
4267   {
4268     // setMenusFromViewport(viewport);
4269
4270   }
4271
4272   @Override
4273   public void refreshFeatureUI(boolean enableIfNecessary)
4274   {
4275     if (enableIfNecessary)
4276     {
4277       sequenceFeatures.setState(true);
4278       alignPanel.av.setShowSequenceFeatures(true);
4279     }
4280   }
4281
4282   @Override
4283   public FeatureSettingsControllerI getFeatureSettingsUI()
4284   {
4285     return alignPanel.av.featureSettings;
4286   }
4287
4288 }