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