src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
   3  * Copyright (C) 2015 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.FeatureRenderer;
  29 import jalview.api.FeatureSettingsControllerI;
  30 import jalview.api.SequenceStructureBinding;
  31 import jalview.bin.JalviewLite;
  32 import jalview.commands.CommandI;
  33 import jalview.commands.EditCommand;
  34 import jalview.commands.EditCommand.Action;
  35 import jalview.commands.OrderCommand;
  36 import jalview.commands.RemoveGapColCommand;
  37 import jalview.commands.RemoveGapsCommand;
  38 import jalview.commands.SlideSequencesCommand;
  39 import jalview.commands.TrimRegionCommand;
  40 import jalview.datamodel.Alignment;
  41 import jalview.datamodel.AlignmentAnnotation;
  42 import jalview.datamodel.AlignmentI;
  43 import jalview.datamodel.AlignmentOrder;
  44 import jalview.datamodel.ColumnSelection;
  45 import jalview.datamodel.PDBEntry;
  46 import jalview.datamodel.Sequence;
  47 import jalview.datamodel.SequenceGroup;
  48 import jalview.datamodel.SequenceI;
  49 import jalview.io.AnnotationFile;
  50 import jalview.io.AppletFormatAdapter;
  51 import jalview.io.FeaturesFile;
  52 import jalview.io.TCoffeeScoreFile;
  53 import jalview.schemes.Blosum62ColourScheme;
  54 import jalview.schemes.BuriedColourScheme;
  55 import jalview.schemes.ClustalxColourScheme;
  56 import jalview.schemes.ColourSchemeI;
  57 import jalview.schemes.HelixColourScheme;
  58 import jalview.schemes.HydrophobicColourScheme;
  59 import jalview.schemes.NucleotideColourScheme;
  60 import jalview.schemes.PIDColourScheme;
  61 import jalview.schemes.PurinePyrimidineColourScheme;
  62 import jalview.schemes.RNAHelicesColourChooser;
  63 import jalview.schemes.StrandColourScheme;
  64 import jalview.schemes.TCoffeeColourScheme;
  65 import jalview.schemes.TaylorColourScheme;
  66 import jalview.schemes.TurnColourScheme;
  67 import jalview.schemes.ZappoColourScheme;
  68 import jalview.structure.StructureSelectionManager;
  69 import jalview.structures.models.AAStructureBindingModel;
  70 import jalview.util.MappingUtils;
  71 import jalview.util.MessageManager;
  72 import jalview.viewmodel.AlignmentViewport;
  73
  74 import java.awt.BorderLayout;
  75 import java.awt.Canvas;
  76 import java.awt.CheckboxMenuItem;
  77 import java.awt.Color;
  78 import java.awt.FlowLayout;
  79 import java.awt.Font;
  80 import java.awt.FontMetrics;
  81 import java.awt.Frame;
  82 import java.awt.Graphics;
  83 import java.awt.Label;
  84 import java.awt.Menu;
  85 import java.awt.MenuBar;
  86 import java.awt.MenuItem;
  87 import java.awt.Panel;
  88 import java.awt.event.ActionEvent;
  89 import java.awt.event.ActionListener;
  90 import java.awt.event.FocusEvent;
  91 import java.awt.event.FocusListener;
  92 import java.awt.event.ItemEvent;
  93 import java.awt.event.ItemListener;
  94 import java.awt.event.KeyEvent;
  95 import java.awt.event.KeyListener;
  96 import java.awt.event.WindowAdapter;
  97 import java.awt.event.WindowEvent;
  98 import java.io.IOException;
  99 import java.net.URL;
 100 import java.net.URLEncoder;
 101 import java.util.Arrays;
 102 import java.util.Deque;
 103 import java.util.HashMap;
 104 import java.util.Hashtable;
 105 import java.util.List;
 106 import java.util.Map;
 107 import java.util.StringTokenizer;
 108 import java.util.Vector;
 109
 110 import org.jmol.viewer.Viewer;
 111
 112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 113         ItemListener, KeyListener, AlignViewControllerGuiI
 114 {
 115   public AlignViewControllerI avc;
 116
 117   public AlignmentPanel alignPanel;
 118
 119   public AlignViewport viewport;
 120
 121   // width and height may be overridden by applet parameters
 122   int frameWidth = 700;
 123
 124   int frameHeight = 500;
 125
 126   String jalviewServletURL;
 127
 128   /*
 129    * Flag for showing autocalculated consensus above or below other consensus
 130    * rows
 131    */
 132   private boolean showAutoCalculatedAbove;
 133
 134   private SequenceAnnotationOrder annotationSortOrder;
 135
 136   /**
 137    * Constructor that creates the frame and adds it to the display.
 138    *
 139    * @param al
 140    * @param applet
 141    * @param title
 142    * @param embedded
 143    */
 144   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 145           boolean embedded)
 146   {
 147     this(al, applet, title, embedded, true);
 148   }
 149
 150   /**
 151    * Constructor that optionally allows the frame to be displayed or only
 152    * created.
 153    *
 154    * @param al
 155    * @param applet
 156    * @param title
 157    * @param embedded
 158    * @param addToDisplay
 159    */
 160   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 161           boolean embedded, boolean addToDisplay)
 162   {
 163     this(al, null, null, applet, title, embedded, addToDisplay);
 164   }
 165
 166   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 167           ColumnSelection columnSelection, JalviewLite applet,
 168           String title, boolean embedded)
 169   {
 170     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 171   }
 172
 173   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 174           ColumnSelection columnSelection, JalviewLite applet,
 175           String title, boolean embedded, boolean addToDisplay)
 176   {
 177     if (applet != null)
 178     {
 179       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 180     }
 181
 182     try
 183     {
 184       jbInit();
 185     } catch (Exception ex)
 186     {
 187       ex.printStackTrace();
 188     }
 189     // need to get window geometry before we calculate alignment layout
 190     if (applet != null)
 191     {
 192       String param;
 193       try
 194       {
 195         param = applet.getParameter("windowWidth");
 196         if (param != null)
 197         {
 198           int width = Integer.parseInt(param);
 199           frameWidth = width;
 200         }
 201         param = applet.getParameter("windowHeight");
 202         if (param != null)
 203         {
 204           int height = Integer.parseInt(param);
 205           frameHeight = height;
 206         }
 207       } catch (Exception ex)
 208       {
 209       }
 210     }
 211     viewport = new AlignViewport(al, applet);
 212
 213     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 214     {
 215       viewport.hideSequence(hiddenSeqs);
 216     }
 217     if (columnSelection != null)
 218     {
 219       viewport.setColumnSelection(columnSelection);
 220     }
 221
 222     alignPanel = new AlignmentPanel(this, viewport);
 223     avc = new jalview.controller.AlignViewController(this, viewport,
 224             alignPanel);
 225     viewport.updateConservation(alignPanel);
 226     viewport.updateConsensus(alignPanel);
 227
 228     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 229     followMouseOverFlag.setState(viewport.isFollowHighlight());
 230     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 231     showGroupConservation.setState(viewport.isShowGroupConservation());
 232     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 233     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 234     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 235     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 236     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 237     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 238     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 239     showAlignmentAnnotations.setState(true);
 240     showSequenceAnnotations.setState(false);
 241
 242     seqLimits.setState(viewport.getShowJVSuffix());
 243
 244     if (applet != null)
 245     {
 246       String param = applet.getParameter("sortBy");
 247       if (param != null)
 248       {
 249         if (param.equalsIgnoreCase("Id"))
 250         {
 251           sortIDMenuItem_actionPerformed();
 252         }
 253         else if (param.equalsIgnoreCase("Pairwise Identity"))
 254         {
 255           sortPairwiseMenuItem_actionPerformed();
 256         }
 257         else if (param.equalsIgnoreCase("Length"))
 258         {
 259           sortLengthMenuItem_actionPerformed();
 260         }
 261       }
 262
 263       param = applet.getParameter("wrap");
 264       if (param != null)
 265       {
 266         if (param.equalsIgnoreCase("true"))
 267         {
 268           wrapMenuItem.setState(true);
 269           wrapMenuItem_actionPerformed();
 270         }
 271       }
 272       param = applet.getParameter("centrecolumnlabels");
 273       if (param != null)
 274       {
 275         centreColumnLabelFlag.setState(true);
 276         centreColumnLabelFlag_stateChanged();
 277       }
 278
 279     }
 280     if (viewport.getAlignment().isNucleotide())
 281     {
 282       viewport.updateStrucConsensus(alignPanel);
 283       if (viewport.getAlignment().hasRNAStructure())
 284       {
 285         RNAHelixColour.setEnabled(true);
 286       }
 287       else
 288       {
 289         RNAHelixColour.setEnabled(false);
 290       }
 291     }
 292     else
 293     {
 294       RNAHelixColour.setEnabled(false);
 295       purinePyrimidineColour.setEnabled(false);
 296     }
 297     // Some JVMS send keyevents to Top frame or lowest panel,
 298     // Havent worked out why yet. So add to both this frame and seqCanvas for
 299     // now
 300     this.addKeyListener(this);
 301     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 302     alignPanel.idPanel.idCanvas.addKeyListener(this);
 303     alignPanel.scalePanel.addKeyListener(this);
 304     alignPanel.annotationPanel.addKeyListener(this);
 305     alignPanel.annotationPanelHolder.addKeyListener(this);
 306     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 307     alignPanel.alabels.addKeyListener(this);
 308
 309     setAnnotationsVisibility();
 310
 311     if (addToDisplay)
 312     {
 313       addToDisplay(embedded);
 314     }
 315   }
 316
 317   /**
 318    * @param embedded
 319    */
 320   public void addToDisplay(boolean embedded)
 321   {
 322     createAlignFrameWindow(embedded);
 323     validate();
 324     alignPanel.adjustAnnotationHeight();
 325     alignPanel.paintAlignment(true);
 326   }
 327
 328   public AlignViewport getAlignViewport()
 329   {
 330     return viewport;
 331   }
 332
 333   public SeqCanvas getSeqcanvas()
 334   {
 335     return alignPanel.seqPanel.seqCanvas;
 336   }
 337
 338   /**
 339    * Load a features file onto the alignment
 340    *
 341    * @param file
 342    *          file URL, content, or other resolvable path
 343    * @param type
 344    *          is protocol for accessing data referred to by file
 345    */
 346
 347   public boolean parseFeaturesFile(String file, String type)
 348   {
 349     return parseFeaturesFile(file, type, true);
 350   }
 351
 352   /**
 353    * Load a features file onto the alignment
 354    *
 355    * @param file
 356    *          file URL, content, or other resolvable path
 357    * @param type
 358    *          is protocol for accessing data referred to by file
 359    * @param autoenabledisplay
 360    *          when true, display features flag will be automatically enabled if
 361    *          features are loaded
 362    * @return true if data parsed as a features file
 363    */
 364   public boolean parseFeaturesFile(String file, String type,
 365           boolean autoenabledisplay)
 366   {
 367     // TODO: test if importing a features file onto an alignment which already
 368     // has features with links overwrites the original links.
 369
 370     Hashtable featureLinks = new Hashtable();
 371     boolean featuresFile = false;
 372     try
 373     {
 374       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
 375               .getAlignment(), alignPanel.seqPanel.seqCanvas
 376               .getFeatureRenderer().getFeatureColours(), featureLinks,
 377               true, viewport.applet.getDefaultParameter("relaxedidmatch",
 378                       false));
 379     } catch (Exception ex)
 380     {
 381       ex.printStackTrace();
 382     }
 383
 384     if (featuresFile)
 385     {
 386       if (featureLinks.size() > 0)
 387       {
 388         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 389       }
 390       if (autoenabledisplay)
 391       {
 392         viewport.setShowSequenceFeatures(true);
 393         sequenceFeatures.setState(true);
 394       }
 395       if (alignPanel.seqPanel.seqCanvas.fr != null)
 396       {
 397         // update the min/max ranges where necessary
 398         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 399       }
 400       if (viewport.featureSettings != null)
 401       {
 402         viewport.featureSettings.refreshTable();
 403       }
 404       alignPanel.paintAlignment(true);
 405       statusBar.setText(MessageManager
 406               .getString("label.successfully_added_features_alignment"));
 407     }
 408     return featuresFile;
 409   }
 410
 411   @Override
 412   public void keyPressed(KeyEvent evt)
 413   {
 414     if (viewport.cursorMode
 415             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 416                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 417                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 418             && Character.isDigit(evt.getKeyChar()))
 419     {
 420       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 421     }
 422
 423     switch (evt.getKeyCode())
 424     {
 425     case 27: // escape key
 426       deselectAllSequenceMenuItem_actionPerformed();
 427
 428       alignPanel.alabels.cancelDrag();
 429       break;
 430     case KeyEvent.VK_X:
 431       if (evt.isControlDown() || evt.isMetaDown())
 432       {
 433         cut_actionPerformed();
 434       }
 435       break;
 436     case KeyEvent.VK_C:
 437       if (viewport.cursorMode && !evt.isControlDown())
 438       {
 439         alignPanel.seqPanel.setCursorColumn();
 440       }
 441       if (evt.isControlDown() || evt.isMetaDown())
 442       {
 443         copy_actionPerformed();
 444       }
 445       break;
 446     case KeyEvent.VK_V:
 447       if (evt.isControlDown())
 448       {
 449         paste(evt.isShiftDown());
 450       }
 451       break;
 452     case KeyEvent.VK_A:
 453       if (evt.isControlDown() || evt.isMetaDown())
 454       {
 455         selectAllSequenceMenuItem_actionPerformed();
 456       }
 457       break;
 458     case KeyEvent.VK_DOWN:
 459       if (viewport.cursorMode)
 460       {
 461         alignPanel.seqPanel.moveCursor(0, 1);
 462       }
 463       else
 464       {
 465         moveSelectedSequences(false);
 466       }
 467       break;
 468
 469     case KeyEvent.VK_UP:
 470       if (viewport.cursorMode)
 471       {
 472         alignPanel.seqPanel.moveCursor(0, -1);
 473       }
 474       else
 475       {
 476         moveSelectedSequences(true);
 477       }
 478       break;
 479
 480     case KeyEvent.VK_LEFT:
 481       if (evt.isAltDown() || !viewport.cursorMode)
 482       {
 483         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 484       }
 485       else
 486       {
 487         alignPanel.seqPanel.moveCursor(-1, 0);
 488       }
 489       break;
 490
 491     case KeyEvent.VK_RIGHT:
 492       if (evt.isAltDown() || !viewport.cursorMode)
 493       {
 494         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 495       }
 496       else
 497       {
 498         alignPanel.seqPanel.moveCursor(1, 0);
 499       }
 500       break;
 501
 502     case KeyEvent.VK_SPACE:
 503       if (viewport.cursorMode)
 504       {
 505         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 506                 || evt.isShiftDown() || evt.isAltDown());
 507       }
 508       break;
 509
 510     case KeyEvent.VK_DELETE:
 511     case KeyEvent.VK_BACK_SPACE:
 512       if (viewport.cursorMode)
 513       {
 514         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 515                 || evt.isShiftDown() || evt.isAltDown());
 516       }
 517       else
 518       {
 519         cut_actionPerformed();
 520         alignPanel.seqPanel.seqCanvas.repaint();
 521       }
 522       break;
 523
 524     case KeyEvent.VK_S:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorRow();
 528       }
 529       break;
 530     case KeyEvent.VK_P:
 531       if (viewport.cursorMode)
 532       {
 533         alignPanel.seqPanel.setCursorPosition();
 534       }
 535       break;
 536
 537     case KeyEvent.VK_ENTER:
 538     case KeyEvent.VK_COMMA:
 539       if (viewport.cursorMode)
 540       {
 541         alignPanel.seqPanel.setCursorRowAndColumn();
 542       }
 543       break;
 544
 545     case KeyEvent.VK_Q:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 549       }
 550       break;
 551     case KeyEvent.VK_M:
 552       if (viewport.cursorMode)
 553       {
 554         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 555       }
 556       break;
 557
 558     case KeyEvent.VK_F2:
 559       viewport.cursorMode = !viewport.cursorMode;
 560       statusBar.setText(MessageManager.formatMessage(
 561               "label.keyboard_editing_mode",
 562               new String[] { (viewport.cursorMode ? "on" : "off") }));
 563       if (viewport.cursorMode)
 564       {
 565         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 566         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 567       }
 568       break;
 569
 570     case KeyEvent.VK_F:
 571       if (evt.isControlDown())
 572       {
 573         findMenuItem_actionPerformed();
 574       }
 575       break;
 576
 577     case KeyEvent.VK_H:
 578     {
 579       boolean toggleSeqs = !evt.isControlDown();
 580       boolean toggleCols = !evt.isShiftDown();
 581       toggleHiddenRegions(toggleSeqs, toggleCols);
 582       break;
 583     }
 584
 585     case KeyEvent.VK_PAGE_UP:
 586       if (viewport.getWrapAlignment())
 587       {
 588         alignPanel.scrollUp(true);
 589       }
 590       else
 591       {
 592         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 593                 - viewport.endSeq + viewport.startSeq);
 594       }
 595       break;
 596
 597     case KeyEvent.VK_PAGE_DOWN:
 598       if (viewport.getWrapAlignment())
 599       {
 600         alignPanel.scrollUp(false);
 601       }
 602       else
 603       {
 604         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 605                 + viewport.endSeq - viewport.startSeq);
 606       }
 607       break;
 608
 609     case KeyEvent.VK_Z:
 610       if (evt.isControlDown())
 611       {
 612         undoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_Y:
 617       if (evt.isControlDown())
 618       {
 619         redoMenuItem_actionPerformed();
 620       }
 621       break;
 622
 623     case KeyEvent.VK_L:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(true);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_R:
 631       if (evt.isControlDown())
 632       {
 633         trimAlignment(false);
 634       }
 635       break;
 636
 637     case KeyEvent.VK_E:
 638       if (evt.isControlDown())
 639       {
 640         if (evt.isShiftDown())
 641         {
 642           this.removeAllGapsMenuItem_actionPerformed();
 643         }
 644         else
 645         {
 646           removeGappedColumnMenuItem_actionPerformed();
 647         }
 648       }
 649       break;
 650     case KeyEvent.VK_I:
 651       if (evt.isControlDown())
 652       {
 653         if (evt.isAltDown())
 654         {
 655           invertColSel_actionPerformed();
 656         }
 657         else
 658         {
 659           invertSequenceMenuItem_actionPerformed();
 660         }
 661       }
 662       break;
 663
 664     case KeyEvent.VK_G:
 665       if (evt.isControlDown())
 666       {
 667         if (evt.isShiftDown())
 668         {
 669           this.unGroup_actionPerformed();
 670         }
 671         else
 672         {
 673           this.createGroup_actionPerformed();
 674         }
 675       }
 676       break;
 677
 678     case KeyEvent.VK_U:
 679       if (evt.isControlDown())
 680       {
 681         this.deleteGroups_actionPerformed();
 682       }
 683       break;
 684
 685     case KeyEvent.VK_T:
 686       if (evt.isControlDown())
 687       {
 688         newView(null);
 689       }
 690       break;
 691
 692     }
 693     alignPanel.paintAlignment(true);
 694   }
 695
 696   /**
 697    * called by key handler and the hide all/show all menu items
 698    *
 699    * @param toggleSeqs
 700    * @param toggleCols
 701    */
 702   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 703   {
 704     boolean hide = false;
 705     SequenceGroup sg = viewport.getSelectionGroup();
 706     if (!toggleSeqs && !toggleCols)
 707     {
 708       // Hide everything by the current selection - this is a hack - we do the
 709       // invert and then hide
 710       // first check that there will be visible columns after the invert.
 711       if ((viewport.getColumnSelection() != null
 712               && viewport.getColumnSelection().getSelected() != null && viewport
 713               .getColumnSelection().getSelected().size() > 0)
 714               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 715                       .getEndRes()))
 716       {
 717         // now invert the sequence set, if required - empty selection implies
 718         // that no hiding is required.
 719         if (sg != null)
 720         {
 721           invertSequenceMenuItem_actionPerformed();
 722           sg = viewport.getSelectionGroup();
 723           toggleSeqs = true;
 724
 725         }
 726         viewport.expandColSelection(sg, true);
 727         // finally invert the column selection and get the new sequence
 728         // selection and indicate it should be hidden.
 729         invertColSel_actionPerformed();
 730         toggleCols = true;
 731       }
 732     }
 733
 734     if (toggleSeqs)
 735     {
 736       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 737       {
 738         hide = true;
 739         viewport.hideAllSelectedSeqs();
 740       }
 741       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 742               .size() > 0))
 743       {
 744         viewport.showAllHiddenSeqs();
 745       }
 746     }
 747
 748     if (toggleCols)
 749     {
 750       if (viewport.getColumnSelection().getSelected().size() > 0)
 751       {
 752         viewport.hideSelectedColumns();
 753         if (!toggleSeqs)
 754         {
 755           viewport.setSelectionGroup(sg);
 756         }
 757       }
 758       else if (!hide)
 759       {
 760         viewport.showAllHiddenColumns();
 761       }
 762     }
 763   }
 764
 765   @Override
 766   public void keyReleased(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void keyTyped(KeyEvent evt)
 772   {
 773   }
 774
 775   @Override
 776   public void itemStateChanged(ItemEvent evt)
 777   {
 778     final Object source = evt.getSource();
 779     if (source == displayNonconservedMenuItem)
 780     {
 781       displayNonconservedMenuItem_actionPerformed();
 782     }
 783     else if (source == colourTextMenuItem)
 784     {
 785       colourTextMenuItem_actionPerformed();
 786     }
 787     else if (source == wrapMenuItem)
 788     {
 789       wrapMenuItem_actionPerformed();
 790     }
 791     else if (source == scaleAbove)
 792     {
 793       viewport.setScaleAboveWrapped(scaleAbove.getState());
 794     }
 795     else if (source == scaleLeft)
 796     {
 797       viewport.setScaleLeftWrapped(scaleLeft.getState());
 798     }
 799     else if (source == scaleRight)
 800     {
 801       viewport.setScaleRightWrapped(scaleRight.getState());
 802     }
 803     else if (source == seqLimits)
 804     {
 805       seqLimits_itemStateChanged();
 806     }
 807     else if (source == viewBoxesMenuItem)
 808     {
 809       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 810     }
 811     else if (source == viewTextMenuItem)
 812     {
 813       viewport.setShowText(viewTextMenuItem.getState());
 814     }
 815     else if (source == renderGapsMenuItem)
 816     {
 817       viewport.setRenderGaps(renderGapsMenuItem.getState());
 818     }
 819     else if (source == annotationPanelMenuItem)
 820     {
 821       boolean showAnnotations = annotationPanelMenuItem.getState();
 822       showAlignmentAnnotations.setEnabled(showAnnotations);
 823       showSequenceAnnotations.setEnabled(showAnnotations);
 824       viewport.setShowAnnotation(showAnnotations);
 825       alignPanel.setAnnotationVisible(showAnnotations);
 826     }
 827     else if (source == sequenceFeatures)
 828     {
 829       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 830       alignPanel.seqPanel.seqCanvas.repaint();
 831     }
 832     else if (source == showAlignmentAnnotations)
 833     {
 834       setAnnotationsVisibility();
 835     }
 836     else if (source == showSequenceAnnotations)
 837     {
 838       setAnnotationsVisibility();
 839     }
 840     else if (source == sortAnnBySequence)
 841     {
 842       boolean newState = sortAnnBySequence.getState();
 843       sortAnnByLabel.setState(false);
 844       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 845               : SequenceAnnotationOrder.NONE);
 846       setViewportAnnotationOrder();
 847     }
 848     else if (source == sortAnnByLabel)
 849     {
 850       boolean newState = sortAnnByLabel.getState();
 851       sortAnnBySequence.setState(false);
 852       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 853               : SequenceAnnotationOrder.NONE);
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == showAutoFirst)
 857     {
 858       showAutoLast.setState(!showAutoFirst.getState());
 859       setShowAutoCalculatedAbove(showAutoFirst.getState());
 860       setViewportAnnotationOrder();
 861     }
 862     else if (source == showAutoLast)
 863     {
 864       showAutoFirst.setState(!showAutoLast.getState());
 865       setShowAutoCalculatedAbove(showAutoFirst.getState());
 866       setViewportAnnotationOrder();
 867     }
 868     else if (source == conservationMenuItem)
 869     {
 870       conservationMenuItem_actionPerformed();
 871     }
 872     else if (source == abovePIDThreshold)
 873     {
 874       abovePIDThreshold_actionPerformed();
 875     }
 876     else if (source == applyToAllGroups)
 877     {
 878       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 879     }
 880     else if (source == autoCalculate)
 881     {
 882       viewport.autoCalculateConsensus = autoCalculate.getState();
 883     }
 884     else if (source == sortByTree)
 885     {
 886       viewport.sortByTree = sortByTree.getState();
 887     }
 888     else if (source == this.centreColumnLabelFlag)
 889     {
 890       centreColumnLabelFlag_stateChanged();
 891     }
 892     else if (source == this.followMouseOverFlag)
 893     {
 894       mouseOverFlag_stateChanged();
 895     }
 896     else if (source == showGroupConsensus)
 897     {
 898       showGroupConsensus_actionPerformed();
 899     }
 900     else if (source == showGroupConservation)
 901     {
 902       showGroupConservation_actionPerformed();
 903     }
 904     else if (source == showSequenceLogo)
 905     {
 906       showSequenceLogo_actionPerformed();
 907     }
 908     else if (source == normSequenceLogo)
 909     {
 910       normSequenceLogo_actionPerformed();
 911     }
 912     else if (source == showConsensusHistogram)
 913     {
 914       showConsensusHistogram_actionPerformed();
 915     }
 916     else if (source == applyAutoAnnotationSettings)
 917     {
 918       applyAutoAnnotationSettings_actionPerformed();
 919     }
 920     alignPanel.paintAlignment(true);
 921   }
 922
 923   /**
 924    * Set the visibility state of sequence-related and/or alignment-related
 925    * annotations depending on checkbox selections, and repaint.
 926    *
 927    * @param visible
 928    */
 929   private void setAnnotationsVisibility()
 930   {
 931     boolean showForAlignment = showAlignmentAnnotations.getState();
 932     boolean showForSequences = showSequenceAnnotations.getState();
 933     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 934     {
 935       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 936             .getAlignmentAnnotation())
 937     {
 938       boolean visible = (aa.sequenceRef == null ? showForAlignment
 939               : showForSequences);
 940       aa.visible = visible;
 941       }
 942     }
 943     alignPanel.validateAnnotationDimensions(true);
 944     validate();
 945     repaint();
 946   }
 947
 948   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 949   {
 950     this.annotationSortOrder = order;
 951   }
 952
 953   /**
 954    * Set flags on the viewport that control annotation ordering
 955    */
 956   private void setViewportAnnotationOrder()
 957   {
 958     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 959     this.alignPanel.av
 960             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 961   }
 962
 963   private void setShowAutoCalculatedAbove(boolean showAbove)
 964   {
 965     this.showAutoCalculatedAbove = showAbove;
 966   }
 967
 968   private void mouseOverFlag_stateChanged()
 969   {
 970     viewport.setFollowHighlight(followMouseOverFlag.getState());
 971     // TODO: could kick the scrollTo mechanism to reset view for current
 972     // searchresults.
 973   }
 974
 975   private void centreColumnLabelFlag_stateChanged()
 976   {
 977     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 978     this.alignPanel.annotationPanel.repaint();
 979   }
 980
 981   @Override
 982   public void actionPerformed(ActionEvent evt)
 983   {
 984     viewport.applet.currentAlignFrame = this;
 985
 986     Object source = evt.getSource();
 987
 988     if (source == inputText)
 989     {
 990       inputText_actionPerformed();
 991     }
 992     else if (source == loadTree)
 993     {
 994       loadTree_actionPerformed();
 995     }
 996     else if (source == loadApplication)
 997     {
 998       launchFullApplication();
 999     }
1000     else if (source == loadAnnotations)
1001     {
1002       loadAnnotations();
1003     }
1004     else if (source == outputAnnotations)
1005     {
1006       outputAnnotations(true);
1007     }
1008     else if (source == outputFeatures)
1009     {
1010       outputFeatures(true, "Jalview");
1011     }
1012     else if (source == closeMenuItem)
1013     {
1014       closeMenuItem_actionPerformed();
1015     }
1016     else if (source == copy)
1017     {
1018       copy_actionPerformed();
1019     }
1020     else if (source == undoMenuItem)
1021     {
1022       undoMenuItem_actionPerformed();
1023     }
1024     else if (source == redoMenuItem)
1025     {
1026       redoMenuItem_actionPerformed();
1027     }
1028     else if (source == inputText)
1029     {
1030       inputText_actionPerformed();
1031     }
1032     else if (source == closeMenuItem)
1033     {
1034       closeMenuItem_actionPerformed();
1035     }
1036     else if (source == undoMenuItem)
1037     {
1038       undoMenuItem_actionPerformed();
1039     }
1040     else if (source == redoMenuItem)
1041     {
1042       redoMenuItem_actionPerformed();
1043     }
1044     else if (source == copy)
1045     {
1046       copy_actionPerformed();
1047     }
1048     else if (source == pasteNew)
1049     {
1050       pasteNew_actionPerformed();
1051     }
1052     else if (source == pasteThis)
1053     {
1054       pasteThis_actionPerformed();
1055     }
1056     else if (source == cut)
1057     {
1058       cut_actionPerformed();
1059     }
1060     else if (source == delete)
1061     {
1062       delete_actionPerformed();
1063     }
1064     else if (source == grpsFromSelection)
1065     {
1066       makeGrpsFromSelection_actionPerformed();
1067     }
1068     else if (source == deleteGroups)
1069     {
1070       deleteGroups_actionPerformed();
1071     }
1072     else if (source == selectAllSequenceMenuItem)
1073     {
1074       selectAllSequenceMenuItem_actionPerformed();
1075     }
1076     else if (source == deselectAllSequenceMenuItem)
1077     {
1078       deselectAllSequenceMenuItem_actionPerformed();
1079     }
1080     else if (source == invertSequenceMenuItem)
1081     {
1082       invertSequenceMenuItem_actionPerformed();
1083     }
1084     else if (source == invertColSel)
1085     {
1086       viewport.invertColumnSelection();
1087       alignPanel.paintAlignment(true);
1088     }
1089     else if (source == remove2LeftMenuItem)
1090     {
1091       trimAlignment(true);
1092     }
1093     else if (source == remove2RightMenuItem)
1094     {
1095       trimAlignment(false);
1096     }
1097     else if (source == removeGappedColumnMenuItem)
1098     {
1099       removeGappedColumnMenuItem_actionPerformed();
1100     }
1101     else if (source == removeAllGapsMenuItem)
1102     {
1103       removeAllGapsMenuItem_actionPerformed();
1104     }
1105     else if (source == findMenuItem)
1106     {
1107       findMenuItem_actionPerformed();
1108     }
1109     else if (source == font)
1110     {
1111       new FontChooser(alignPanel);
1112     }
1113     else if (source == newView)
1114     {
1115       newView(null);
1116     }
1117     else if (source == showColumns)
1118     {
1119       viewport.showAllHiddenColumns();
1120       alignPanel.paintAlignment(true);
1121     }
1122     else if (source == showSeqs)
1123     {
1124       viewport.showAllHiddenSeqs();
1125       alignPanel.paintAlignment(true);
1126     }
1127     else if (source == hideColumns)
1128     {
1129       viewport.hideSelectedColumns();
1130       alignPanel.paintAlignment(true);
1131     }
1132     else if (source == hideSequences
1133             && viewport.getSelectionGroup() != null)
1134     {
1135       viewport.hideAllSelectedSeqs();
1136       alignPanel.paintAlignment(true);
1137     }
1138     else if (source == hideAllButSelection)
1139     {
1140       toggleHiddenRegions(false, false);
1141       alignPanel.paintAlignment(true);
1142     }
1143     else if (source == hideAllSelection)
1144     {
1145       SequenceGroup sg = viewport.getSelectionGroup();
1146       viewport.expandColSelection(sg, false);
1147       viewport.hideAllSelectedSeqs();
1148       viewport.hideSelectedColumns();
1149       alignPanel.paintAlignment(true);
1150     }
1151     else if (source == showAllHidden)
1152     {
1153       viewport.showAllHiddenColumns();
1154       viewport.showAllHiddenSeqs();
1155       alignPanel.paintAlignment(true);
1156     }
1157     else if (source == showGroupConsensus)
1158     {
1159       showGroupConsensus_actionPerformed();
1160     }
1161     else if (source == showGroupConservation)
1162     {
1163       showGroupConservation_actionPerformed();
1164     }
1165     else if (source == showSequenceLogo)
1166     {
1167       showSequenceLogo_actionPerformed();
1168     }
1169     else if (source == normSequenceLogo)
1170     {
1171       normSequenceLogo_actionPerformed();
1172     }
1173     else if (source == showConsensusHistogram)
1174     {
1175       showConsensusHistogram_actionPerformed();
1176     }
1177     else if (source == applyAutoAnnotationSettings)
1178     {
1179       applyAutoAnnotationSettings_actionPerformed();
1180     }
1181     else if (source == featureSettings)
1182     {
1183       new FeatureSettings(alignPanel);
1184     }
1185     else if (source == alProperties)
1186     {
1187       StringBuffer contents = new jalview.io.AlignmentProperties(
1188               viewport.getAlignment()).formatAsString();
1189       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1190       cap.setText(contents.toString());
1191       Frame frame = new Frame();
1192       frame.add(cap);
1193       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1194               "label.alignment_properties", new String[] { getTitle() }),
1195               400, 250);
1196     }
1197     else if (source == overviewMenuItem)
1198     {
1199       overviewMenuItem_actionPerformed();
1200     }
1201     else if (source == noColourmenuItem)
1202     {
1203       changeColour(null);
1204     }
1205     else if (source == clustalColour)
1206     {
1207       abovePIDThreshold.setState(false);
1208       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1209     }
1210     else if (source == zappoColour)
1211     {
1212       changeColour(new ZappoColourScheme());
1213     }
1214     else if (source == taylorColour)
1215     {
1216       changeColour(new TaylorColourScheme());
1217     }
1218     else if (source == hydrophobicityColour)
1219     {
1220       changeColour(new HydrophobicColourScheme());
1221     }
1222     else if (source == helixColour)
1223     {
1224       changeColour(new HelixColourScheme());
1225     }
1226     else if (source == strandColour)
1227     {
1228       changeColour(new StrandColourScheme());
1229     }
1230     else if (source == turnColour)
1231     {
1232       changeColour(new TurnColourScheme());
1233     }
1234     else if (source == buriedColour)
1235     {
1236       changeColour(new BuriedColourScheme());
1237     }
1238     else if (source == nucleotideColour)
1239     {
1240       changeColour(new NucleotideColourScheme());
1241     }
1242     else if (source == purinePyrimidineColour)
1243     {
1244       changeColour(new PurinePyrimidineColourScheme());
1245     }
1246     // else if (source == RNAInteractionColour)
1247     // {
1248     // changeColour(new RNAInteractionColourScheme());
1249     // }
1250     else if (source == RNAHelixColour)
1251     {
1252       new RNAHelicesColourChooser(viewport, alignPanel);
1253     }
1254     else if (source == modifyPID)
1255     {
1256       modifyPID_actionPerformed();
1257     }
1258     else if (source == modifyConservation)
1259     {
1260       modifyConservation_actionPerformed();
1261     }
1262     else if (source == userDefinedColour)
1263     {
1264       new UserDefinedColours(alignPanel, null);
1265     }
1266     else if (source == PIDColour)
1267     {
1268       changeColour(new PIDColourScheme());
1269     }
1270     else if (source == BLOSUM62Colour)
1271     {
1272       changeColour(new Blosum62ColourScheme());
1273     }
1274     else if (source == tcoffeeColour)
1275     {
1276       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1277     }
1278     else if (source == annotationColour)
1279     {
1280       new AnnotationColourChooser(viewport, alignPanel);
1281     }
1282     else if (source == annotationColumnSelection)
1283     {
1284       new AnnotationColumnChooser(viewport, alignPanel);
1285     }
1286     else if (source == sortPairwiseMenuItem)
1287     {
1288       sortPairwiseMenuItem_actionPerformed();
1289     }
1290     else if (source == sortIDMenuItem)
1291     {
1292       sortIDMenuItem_actionPerformed();
1293     }
1294     else if (source == sortLengthMenuItem)
1295     {
1296       sortLengthMenuItem_actionPerformed();
1297     }
1298     else if (source == sortGroupMenuItem)
1299     {
1300       sortGroupMenuItem_actionPerformed();
1301     }
1302     else if (source == removeRedundancyMenuItem)
1303     {
1304       removeRedundancyMenuItem_actionPerformed();
1305     }
1306     else if (source == pairwiseAlignmentMenuItem)
1307     {
1308       pairwiseAlignmentMenuItem_actionPerformed();
1309     }
1310     else if (source == PCAMenuItem)
1311     {
1312       PCAMenuItem_actionPerformed();
1313     }
1314     else if (source == averageDistanceTreeMenuItem)
1315     {
1316       averageDistanceTreeMenuItem_actionPerformed();
1317     }
1318     else if (source == neighbourTreeMenuItem)
1319     {
1320       neighbourTreeMenuItem_actionPerformed();
1321     }
1322     else if (source == njTreeBlosumMenuItem)
1323     {
1324       njTreeBlosumMenuItem_actionPerformed();
1325     }
1326     else if (source == avDistanceTreeBlosumMenuItem)
1327     {
1328       avTreeBlosumMenuItem_actionPerformed();
1329     }
1330     else if (source == documentation)
1331     {
1332       documentation_actionPerformed();
1333     }
1334     else if (source == about)
1335     {
1336       about_actionPerformed();
1337     }
1338
1339   }
1340
1341   public void inputText_actionPerformed()
1342   {
1343     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1344     Frame frame = new Frame();
1345     frame.add(cap);
1346     jalview.bin.JalviewLite.addFrame(frame,
1347             MessageManager.getString("label.input_cut_paste"), 500, 500);
1348   }
1349
1350   protected void outputText_actionPerformed(ActionEvent e)
1351   {
1352     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1353     Frame frame = new Frame();
1354     frame.add(cap);
1355     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1356             "label.alignment_output_command",
1357             new Object[] { e.getActionCommand() }), 600, 500);
1358
1359     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1360     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1361             e.getActionCommand(), viewport.getAlignment(),
1362             viewport.getShowJVSuffix()));
1363   }
1364
1365   public void loadAnnotations()
1366   {
1367     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1368     cap.setText(MessageManager
1369             .getString("label.paste_features_annotations_Tcoffee_here"));
1370     cap.setAnnotationImport();
1371     Frame frame = new Frame();
1372     frame.add(cap);
1373     jalview.bin.JalviewLite.addFrame(frame,
1374             MessageManager.getString("action.paste_annotations"), 400, 300);
1375
1376   }
1377
1378   public String outputAnnotations(boolean displayTextbox)
1379   {
1380     String annotation = new AnnotationFile()
1381             .printAnnotationsForView(viewport);
1382
1383     if (displayTextbox)
1384     {
1385       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1386       Frame frame = new Frame();
1387       frame.add(cap);
1388       jalview.bin.JalviewLite.addFrame(frame,
1389               MessageManager.getString("label.annotations"), 600, 500);
1390       cap.setText(annotation);
1391     }
1392
1393     return annotation;
1394   }
1395
1396   private Map<String, Object> getDisplayedFeatureCols()
1397   {
1398     if (alignPanel.getFeatureRenderer() != null
1399             && viewport.getFeaturesDisplayed() != null)
1400     {
1401       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1402
1403     }
1404     return null;
1405   }
1406
1407   public String outputFeatures(boolean displayTextbox, String format)
1408   {
1409     String features;
1410     if (format.equalsIgnoreCase("Jalview"))
1411     {
1412       features = new FeaturesFile().printJalviewFormat(viewport
1413               .getAlignment().getSequencesArray(),
1414               getDisplayedFeatureCols());
1415     }
1416     else
1417     {
1418       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1419               .getSequencesArray(), getDisplayedFeatureCols());
1420     }
1421
1422     if (displayTextbox)
1423     {
1424       boolean frimport = false;
1425       if (features == null || features.equals("No Features Visible"))
1426       {
1427         features = "# No features visible - paste some and import them here.";
1428         frimport = true;
1429       }
1430
1431       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1432       if (frimport)
1433       {
1434         cap.setAnnotationImport();
1435       }
1436       Frame frame = new Frame();
1437       frame.add(cap);
1438       jalview.bin.JalviewLite.addFrame(frame,
1439               MessageManager.getString("label.features"), 600, 500);
1440       cap.setText(features);
1441     }
1442     else
1443     {
1444       if (features == null)
1445       {
1446         features = "";
1447       }
1448     }
1449
1450     return features;
1451   }
1452
1453   void launchFullApplication()
1454   {
1455     StringBuffer url = new StringBuffer(jalviewServletURL);
1456
1457     // allow servlet parameters to be passed in applet parameter
1458     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1459             : "?";
1460     url.append(firstSep);
1461
1462     url.append("open="
1463             + appendProtocol(viewport.applet.getParameter("file")));
1464
1465     if (viewport.applet.getParameter("features") != null)
1466     {
1467       url.append("&features=");
1468       url.append(appendProtocol(viewport.applet.getParameter("features")));
1469     }
1470
1471     if (viewport.applet.getParameter("annotations") != null)
1472     {
1473       url.append("&annotations=");
1474       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1475     }
1476
1477     if (viewport.applet.getParameter("jnetfile") != null)
1478     {
1479       url.append("&annotations=");
1480       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1481     }
1482
1483     if (viewport.applet.getParameter("defaultColour") != null)
1484     {
1485       url.append("&colour="
1486               + removeWhiteSpace(viewport.applet
1487                       .getParameter("defaultColour")));
1488     }
1489
1490     if (viewport.applet.getParameter("userDefinedColour") != null)
1491     {
1492       url.append("&colour="
1493               + removeWhiteSpace(viewport.applet
1494                       .getParameter("userDefinedColour")));
1495     }
1496     if (viewport.applet.getParameter("tree") != null)
1497     {
1498       url.append("&tree="
1499               + appendProtocol(viewport.applet.getParameter("tree")));
1500     }
1501     if (viewport.applet.getParameter("treeFile") != null)
1502     {
1503       url.append("&tree="
1504               + appendProtocol(viewport.applet.getParameter("treeFile")));
1505     }
1506
1507     showURL(url.toString(), "FULL_APP");
1508   }
1509
1510   String removeWhiteSpace(String colour)
1511   {
1512     StringBuffer sb = new StringBuffer();
1513     for (int i = 0; i < colour.length(); i++)
1514     {
1515       if (Character.isWhitespace(colour.charAt(i)))
1516       {
1517         sb.append("%20");
1518       }
1519       else
1520       {
1521         sb.append(colour.charAt(i));
1522       }
1523     }
1524
1525     return sb.toString();
1526   }
1527
1528   String appendProtocol(String url)
1529   {
1530     try
1531     {
1532       new URL(url);
1533       url = URLEncoder.encode(url);
1534     }
1535     /*
1536      * When we finally deprecate 1.1 compatibility, we can start to use
1537      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1538      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1539      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1540      * ex.printStackTrace(); }
1541      */
1542     catch (java.net.MalformedURLException ex)
1543     {
1544       url = viewport.applet.getCodeBase() + url;
1545     }
1546     return url;
1547   }
1548
1549   public void closeMenuItem_actionPerformed()
1550   {
1551     PaintRefresher.RemoveComponent(alignPanel);
1552     if (alignPanel.seqPanel != null
1553             && alignPanel.seqPanel.seqCanvas != null)
1554     {
1555       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1556     }
1557     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1558     {
1559       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1560     }
1561
1562     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1563     {
1564       System.exit(0);
1565     }
1566     else
1567     {
1568     }
1569     viewport = null;
1570     alignPanel = null;
1571     this.dispose();
1572   }
1573
1574   /**
1575    * TODO: JAL-1104
1576    */
1577   void updateEditMenuBar()
1578   {
1579
1580     if (viewport.getHistoryList().size() > 0)
1581     {
1582       undoMenuItem.setEnabled(true);
1583       CommandI command = viewport.getHistoryList().peek();
1584       undoMenuItem.setLabel(MessageManager.formatMessage(
1585               "label.undo_command",
1586               new Object[] { command.getDescription() }));
1587     }
1588     else
1589     {
1590       undoMenuItem.setEnabled(false);
1591       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1592     }
1593
1594     if (viewport.getRedoList().size() > 0)
1595     {
1596       redoMenuItem.setEnabled(true);
1597
1598       CommandI command = viewport.getRedoList().peek();
1599       redoMenuItem.setLabel(MessageManager.formatMessage(
1600               "label.redo_command",
1601               new Object[] { command.getDescription() }));
1602     }
1603     else
1604     {
1605       redoMenuItem.setEnabled(false);
1606       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1607     }
1608   }
1609
1610   /**
1611    * TODO: JAL-1104
1612    */
1613   @Override
1614   public void addHistoryItem(CommandI command)
1615   {
1616     if (command.getSize() > 0)
1617     {
1618       viewport.addToHistoryList(command);
1619       viewport.clearRedoList();
1620       updateEditMenuBar();
1621       viewport.updateHiddenColumns();
1622     }
1623   }
1624
1625   /**
1626    * TODO: JAL-1104 DOCUMENT ME!
1627    *
1628    * @param e
1629    *          DOCUMENT ME!
1630    */
1631   protected void undoMenuItem_actionPerformed()
1632   {
1633     if (viewport.getHistoryList().isEmpty())
1634     {
1635       return;
1636     }
1637
1638     CommandI command = viewport.getHistoryList().pop();
1639     viewport.addToRedoList(command);
1640     command.undoCommand(null);
1641
1642     AlignmentViewport originalSource = getOriginatingSource(command);
1643     // JBPNote Test
1644     if (originalSource != viewport)
1645     {
1646       System.err
1647               .println("Warning: Viewport object mismatch whilst undoing");
1648     }
1649     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1650                                           // viewport.getColumnSelection().getHiddenColumns()
1651                                           // != null;
1652     updateEditMenuBar();
1653     originalSource.firePropertyChange("alignment", null, originalSource
1654             .getAlignment().getSequences());
1655   }
1656
1657   /**
1658    * TODO: JAL-1104 DOCUMENT ME!
1659    *
1660    * @param e
1661    *          DOCUMENT ME!
1662    */
1663   protected void redoMenuItem_actionPerformed()
1664   {
1665     if (viewport.getRedoList().isEmpty())
1666     {
1667       return;
1668     }
1669
1670     CommandI command = viewport.getRedoList().pop();
1671     viewport.addToHistoryList(command);
1672     command.doCommand(null);
1673
1674     AlignmentViewport originalSource = getOriginatingSource(command);
1675     // JBPNote Test
1676     if (originalSource != viewport)
1677     {
1678       System.err
1679               .println("Warning: Viewport object mismatch whilst re-doing");
1680     }
1681     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1682                                           // viewport.getColumnSelection().getHiddenColumns()
1683                                           // != null;
1684
1685     updateEditMenuBar();
1686     originalSource.firePropertyChange("alignment", null, originalSource
1687             .getAlignment().getSequences());
1688   }
1689
1690   AlignmentViewport getOriginatingSource(CommandI command)
1691   {
1692     AlignmentViewport originalSource = null;
1693     // For sequence removal and addition, we need to fire
1694     // the property change event FROM the viewport where the
1695     // original alignment was altered
1696     AlignmentI al = null;
1697     if (command instanceof EditCommand)
1698     {
1699       EditCommand editCommand = (EditCommand) command;
1700       al = editCommand.getAlignment();
1701       Vector comps = (Vector) PaintRefresher.components.get(viewport
1702               .getSequenceSetId());
1703       for (int i = 0; i < comps.size(); i++)
1704       {
1705         if (comps.elementAt(i) instanceof AlignmentPanel)
1706         {
1707           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1708           {
1709             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1710             break;
1711           }
1712         }
1713       }
1714     }
1715
1716     if (originalSource == null)
1717     {
1718       // The original view is closed, we must validate
1719       // the current view against the closed view first
1720       if (al != null)
1721       {
1722         PaintRefresher.validateSequences(al, viewport.getAlignment());
1723       }
1724
1725       originalSource = viewport;
1726     }
1727
1728     return originalSource;
1729   }
1730
1731   /**
1732    * Move the currently selected sequences up or down one position in the
1733    * alignment
1734    *
1735    * @param up
1736    */
1737   public void moveSelectedSequences(boolean up)
1738   {
1739     SequenceGroup sg = viewport.getSelectionGroup();
1740     if (sg == null)
1741     {
1742       return;
1743     }
1744     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1745             up ? null : viewport.getHiddenRepSequences(), up);
1746     alignPanel.paintAlignment(true);
1747
1748     /*
1749      * Also move cDNA/protein complement sequences
1750      */
1751     AlignViewportI complement = viewport.getCodingComplement();
1752     if (complement != null)
1753     {
1754       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1755               viewport, complement);
1756       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1757               up ? null : complement.getHiddenRepSequences(), up);
1758       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1759     }
1760   }
1761
1762   synchronized void slideSequences(boolean right, int size)
1763   {
1764     List<SequenceI> sg = new Vector<SequenceI>();
1765     if (viewport.cursorMode)
1766     {
1767       sg.add(viewport.getAlignment().getSequenceAt(
1768               alignPanel.seqPanel.seqCanvas.cursorY));
1769     }
1770     else if (viewport.getSelectionGroup() != null
1771             && viewport.getSelectionGroup().getSize() != viewport
1772                     .getAlignment().getHeight())
1773     {
1774       sg = viewport.getSelectionGroup().getSequences(
1775               viewport.getHiddenRepSequences());
1776     }
1777
1778     if (sg.size() < 1)
1779     {
1780       return;
1781     }
1782
1783     Vector<SequenceI> invertGroup = new Vector();
1784
1785     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1786     {
1787       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1788       {
1789         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1790       }
1791     }
1792
1793     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1794
1795     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1796             .size()]);
1797     for (int i = 0; i < invertGroup.size(); i++)
1798     {
1799       seqs2[i] = invertGroup.elementAt(i);
1800     }
1801
1802     SlideSequencesCommand ssc;
1803     if (right)
1804     {
1805       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1806               size, viewport.getGapCharacter());
1807     }
1808     else
1809     {
1810       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1811               size, viewport.getGapCharacter());
1812     }
1813
1814     int groupAdjustment = 0;
1815     if (ssc.getGapsInsertedBegin() && right)
1816     {
1817       if (viewport.cursorMode)
1818       {
1819         alignPanel.seqPanel.moveCursor(size, 0);
1820       }
1821       else
1822       {
1823         groupAdjustment = size;
1824       }
1825     }
1826     else if (!ssc.getGapsInsertedBegin() && !right)
1827     {
1828       if (viewport.cursorMode)
1829       {
1830         alignPanel.seqPanel.moveCursor(-size, 0);
1831       }
1832       else
1833       {
1834         groupAdjustment = -size;
1835       }
1836     }
1837
1838     if (groupAdjustment != 0)
1839     {
1840       viewport.getSelectionGroup().setStartRes(
1841               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1842       viewport.getSelectionGroup().setEndRes(
1843               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1844     }
1845
1846     boolean appendHistoryItem = false;
1847     Deque<CommandI> historyList = viewport.getHistoryList();
1848     if (historyList != null && historyList.size() > 0
1849             && historyList.peek() instanceof SlideSequencesCommand)
1850     {
1851       appendHistoryItem = ssc
1852               .appendSlideCommand((SlideSequencesCommand) historyList
1853                       .peek());
1854     }
1855
1856     if (!appendHistoryItem)
1857     {
1858       addHistoryItem(ssc);
1859     }
1860
1861     repaint();
1862   }
1863
1864   static StringBuffer copiedSequences;
1865
1866   static Vector copiedHiddenColumns;
1867
1868   protected void copy_actionPerformed()
1869   {
1870     if (viewport.getSelectionGroup() == null)
1871     {
1872       return;
1873     }
1874
1875     SequenceGroup sg = viewport.getSelectionGroup();
1876     copiedSequences = new StringBuffer();
1877     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1878     for (int i = 0; i < sg.getSize(); i++)
1879     {
1880       SequenceI seq = sg.getSequenceAt(i);
1881       int index = viewport.getAlignment().findIndex(seq);
1882       orderedSeqs.put(index, seq);
1883     }
1884
1885     int index = 0, startRes, endRes;
1886     char ch;
1887
1888     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1889     {
1890       copiedHiddenColumns = new Vector();
1891       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1892       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1893       {
1894         copiedHiddenColumns.addElement(new int[] {
1895             region[0] - hiddenOffset, region[1] - hiddenOffset });
1896       }
1897     }
1898     else
1899     {
1900       copiedHiddenColumns = null;
1901     }
1902
1903     for (int i = 0; i < sg.getSize(); i++)
1904     {
1905       SequenceI seq = null;
1906
1907       while (seq == null)
1908       {
1909         if (orderedSeqs.containsKey(index))
1910         {
1911           seq = orderedSeqs.get(index);
1912           index++;
1913           break;
1914         }
1915         else
1916         {
1917           index++;
1918         }
1919       }
1920
1921       // FIND START RES
1922       // Returns residue following index if gap
1923       startRes = seq.findPosition(sg.getStartRes());
1924
1925       // FIND END RES
1926       // Need to find the residue preceeding index if gap
1927       endRes = 0;
1928
1929       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1930       {
1931         ch = seq.getCharAt(j);
1932         if (!jalview.util.Comparison.isGap((ch)))
1933         {
1934           endRes++;
1935         }
1936       }
1937
1938       if (endRes > 0)
1939       {
1940         endRes += seq.getStart() - 1;
1941       }
1942
1943       copiedSequences.append(seq.getName()
1944               + "\t"
1945               + startRes
1946               + "\t"
1947               + endRes
1948               + "\t"
1949               + seq.getSequenceAsString(sg.getStartRes(),
1950                       sg.getEndRes() + 1) + "\n");
1951     }
1952
1953   }
1954
1955   protected void pasteNew_actionPerformed()
1956   {
1957     paste(true);
1958   }
1959
1960   protected void pasteThis_actionPerformed()
1961   {
1962     paste(false);
1963   }
1964
1965   void paste(boolean newAlignment)
1966   {
1967     try
1968     {
1969
1970       if (copiedSequences == null)
1971       {
1972         return;
1973       }
1974
1975       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1976       Vector seqs = new Vector();
1977       while (st.hasMoreElements())
1978       {
1979         String name = st.nextToken();
1980         int start = Integer.parseInt(st.nextToken());
1981         int end = Integer.parseInt(st.nextToken());
1982         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1983       }
1984       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1985       for (int i = 0; i < seqs.size(); i++)
1986       {
1987         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1988       }
1989
1990       if (newAlignment)
1991       {
1992         String newtitle = MessageManager
1993                 .getString("label.copied_sequences");
1994         if (getTitle().startsWith(
1995                 MessageManager.getString("label.copied_sequences")))
1996         {
1997           newtitle = getTitle();
1998         }
1999         else
2000         {
2001           newtitle = newtitle.concat(MessageManager.formatMessage(
2002                   "label.from_msname", new String[] { getTitle() }));
2003         }
2004         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2005                 viewport.applet, newtitle, false);
2006         if (copiedHiddenColumns != null)
2007         {
2008           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2009           {
2010             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2011             af.viewport.hideColumns(region[0], region[1]);
2012           }
2013         }
2014
2015         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2016                 frameHeight);
2017       }
2018       else
2019       {
2020         addSequences(newSeqs);
2021       }
2022
2023     } catch (Exception ex)
2024     {
2025     } // could be anything being pasted in here
2026
2027   }
2028
2029   void addSequences(SequenceI[] seqs)
2030   {
2031     for (int i = 0; i < seqs.length; i++)
2032     {
2033       viewport.getAlignment().addSequence(seqs[i]);
2034     }
2035
2036     // !newAlignment
2037     addHistoryItem(new EditCommand(
2038             MessageManager.getString("label.add_sequences"), Action.PASTE,
2039             seqs, 0, viewport.getAlignment().getWidth(),
2040             viewport.getAlignment()));
2041
2042     viewport.setEndSeq(viewport.getAlignment().getHeight());
2043     viewport.getAlignment().getWidth();
2044     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2045             .getSequences());
2046
2047   }
2048
2049   protected void cut_actionPerformed()
2050   {
2051     copy_actionPerformed();
2052     delete_actionPerformed();
2053   }
2054
2055   protected void delete_actionPerformed()
2056   {
2057
2058     SequenceGroup sg = viewport.getSelectionGroup();
2059     if (sg == null)
2060     {
2061       return;
2062     }
2063
2064     Vector seqs = new Vector();
2065     SequenceI seq;
2066     for (int i = 0; i < sg.getSize(); i++)
2067     {
2068       seq = sg.getSequenceAt(i);
2069       seqs.addElement(seq);
2070     }
2071
2072     /*
2073      * If the cut affects all sequences, warn, remove highlighted columns
2074      */
2075     if (sg.getSize() == viewport.getAlignment().getHeight())
2076     {
2077       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2078               .getAlignment().getWidth()) ? true : false;
2079       if (isEntireAlignWidth)
2080       {
2081         String title = MessageManager.getString("label.delete_all");
2082         Panel infoPanel = new Panel();
2083         infoPanel.setLayout(new FlowLayout());
2084         infoPanel
2085                 .add(new Label(MessageManager.getString("warn.delete_all")));
2086
2087         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2088         dialog.setMainPanel(infoPanel);
2089         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2090         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2091         dialog.setVisible(true);
2092
2093         if (!dialog.accept)
2094         {
2095           return;
2096         }
2097       }
2098       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2099               sg.getEndRes() + 1);
2100     }
2101
2102     SequenceI[] cut = new SequenceI[seqs.size()];
2103     for (int i = 0; i < seqs.size(); i++)
2104     {
2105       cut[i] = (SequenceI) seqs.elementAt(i);
2106     }
2107
2108     /*
2109      * //ADD HISTORY ITEM
2110      */
2111     addHistoryItem(new EditCommand(
2112             MessageManager.getString("label.cut_sequences"), Action.CUT,
2113             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2114             viewport.getAlignment()));
2115
2116     viewport.setSelectionGroup(null);
2117     viewport.getAlignment().deleteGroup(sg);
2118
2119     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2120             .getSequences());
2121
2122     if (viewport.getAlignment().getHeight() < 1)
2123     {
2124       this.setVisible(false);
2125     }
2126     viewport.sendSelection();
2127   }
2128
2129   /**
2130    * group consensus toggled
2131    *
2132    */
2133   protected void showGroupConsensus_actionPerformed()
2134   {
2135     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2136     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2137
2138   }
2139
2140   /**
2141    * group conservation toggled.
2142    */
2143   protected void showGroupConservation_actionPerformed()
2144   {
2145     viewport.setShowGroupConservation(showGroupConservation.getState());
2146     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2147   }
2148
2149   /*
2150    * (non-Javadoc)
2151    *
2152    * @see
2153    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2154    * .event.ActionEvent)
2155    */
2156   protected void showConsensusHistogram_actionPerformed()
2157   {
2158     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2159     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2160   }
2161
2162   /*
2163    * (non-Javadoc)
2164    *
2165    * @see
2166    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2167    * .event.ActionEvent)
2168    */
2169   protected void showSequenceLogo_actionPerformed()
2170   {
2171     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2172     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2173   }
2174
2175   protected void normSequenceLogo_actionPerformed()
2176   {
2177     showSequenceLogo.setState(true);
2178     viewport.setShowSequenceLogo(true);
2179     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2180     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181   }
2182
2183   protected void applyAutoAnnotationSettings_actionPerformed()
2184   {
2185     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2186   }
2187
2188   protected void makeGrpsFromSelection_actionPerformed()
2189   {
2190     if (avc.makeGroupsFromSelection())
2191     {
2192       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2193       alignPanel.updateAnnotation();
2194       alignPanel.paintAlignment(true);
2195     }
2196   }
2197
2198   protected void createGroup_actionPerformed()
2199   {
2200     avc.createGroup();
2201   }
2202
2203   protected void unGroup_actionPerformed()
2204   {
2205     if (avc.unGroup())
2206     {
2207       alignPanel.alignmentChanged();
2208     }
2209   }
2210
2211   protected void deleteGroups_actionPerformed()
2212   {
2213     if (avc.deleteGroups())
2214     {
2215       alignPanel.alignmentChanged();
2216     }
2217   }
2218
2219   public void selectAllSequenceMenuItem_actionPerformed()
2220   {
2221     SequenceGroup sg = new SequenceGroup();
2222     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2223     {
2224       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2225     }
2226     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2227     viewport.setSelectionGroup(sg);
2228     alignPanel.paintAlignment(true);
2229     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2230     viewport.sendSelection();
2231   }
2232
2233   public void deselectAllSequenceMenuItem_actionPerformed()
2234   {
2235     if (viewport.cursorMode)
2236     {
2237       alignPanel.seqPanel.keyboardNo1 = null;
2238       alignPanel.seqPanel.keyboardNo2 = null;
2239     }
2240     viewport.setSelectionGroup(null);
2241     viewport.getColumnSelection().clear();
2242     viewport.setSelectionGroup(null);
2243     alignPanel.idPanel.idCanvas.searchResults = null;
2244     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2245     alignPanel.paintAlignment(true);
2246     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2247     viewport.sendSelection();
2248   }
2249
2250   public void invertSequenceMenuItem_actionPerformed()
2251   {
2252     SequenceGroup sg = viewport.getSelectionGroup();
2253     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2254     {
2255       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2256     }
2257
2258     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2259     viewport.sendSelection();
2260   }
2261
2262   public void invertColSel_actionPerformed()
2263   {
2264     viewport.invertColumnSelection();
2265     alignPanel.paintAlignment(true);
2266     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2267     viewport.sendSelection();
2268   }
2269
2270   void trimAlignment(boolean trimLeft)
2271   {
2272     ColumnSelection colSel = viewport.getColumnSelection();
2273     int column;
2274
2275     if (colSel.size() > 0)
2276     {
2277       if (trimLeft)
2278       {
2279         column = colSel.getMin();
2280       }
2281       else
2282       {
2283         column = colSel.getMax();
2284       }
2285
2286       SequenceI[] seqs;
2287       if (viewport.getSelectionGroup() != null)
2288       {
2289         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2290                 viewport.getHiddenRepSequences());
2291       }
2292       else
2293       {
2294         seqs = viewport.getAlignment().getSequencesArray();
2295       }
2296
2297       TrimRegionCommand trimRegion;
2298       if (trimLeft)
2299       {
2300         trimRegion = new TrimRegionCommand("Remove Left",
2301                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2302                 viewport.getAlignment(), viewport.getColumnSelection(),
2303                 viewport.getSelectionGroup());
2304         viewport.setStartRes(0);
2305       }
2306       else
2307       {
2308         trimRegion = new TrimRegionCommand("Remove Right",
2309                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2310                 viewport.getAlignment(), viewport.getColumnSelection(),
2311                 viewport.getSelectionGroup());
2312       }
2313
2314       statusBar.setText(MessageManager.formatMessage(
2315               "label.removed_columns",
2316               new String[] { Integer.valueOf(trimRegion.getSize())
2317                       .toString() }));
2318       addHistoryItem(trimRegion);
2319
2320       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2321       {
2322         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2323                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2324         {
2325           viewport.getAlignment().deleteGroup(sg);
2326         }
2327       }
2328
2329       viewport.firePropertyChange("alignment", null, viewport
2330               .getAlignment().getSequences());
2331     }
2332   }
2333
2334   public void removeGappedColumnMenuItem_actionPerformed()
2335   {
2336     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2337
2338     SequenceI[] seqs;
2339     if (viewport.getSelectionGroup() != null)
2340     {
2341       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2342               viewport.getHiddenRepSequences());
2343       start = viewport.getSelectionGroup().getStartRes();
2344       end = viewport.getSelectionGroup().getEndRes();
2345     }
2346     else
2347     {
2348       seqs = viewport.getAlignment().getSequencesArray();
2349     }
2350
2351     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2352             "Remove Gapped Columns", seqs, start, end,
2353             viewport.getAlignment());
2354
2355     addHistoryItem(removeGapCols);
2356
2357     statusBar.setText(MessageManager.formatMessage(
2358             "label.removed_empty_columns",
2359             new String[] { Integer.valueOf(removeGapCols.getSize())
2360                     .toString() }));
2361
2362     // This is to maintain viewport position on first residue
2363     // of first sequence
2364     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2365     int startRes = seq.findPosition(viewport.startRes);
2366     // ShiftList shifts;
2367     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2368     // edit.alColumnChanges=shifts.getInverse();
2369     // if (viewport.hasHiddenColumns)
2370     // viewport.getColumnSelection().compensateForEdits(shifts);
2371     viewport.setStartRes(seq.findIndex(startRes) - 1);
2372     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2373             .getSequences());
2374
2375   }
2376
2377   public void removeAllGapsMenuItem_actionPerformed()
2378   {
2379     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2380
2381     SequenceI[] seqs;
2382     if (viewport.getSelectionGroup() != null)
2383     {
2384       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2385               viewport.getHiddenRepSequences());
2386       start = viewport.getSelectionGroup().getStartRes();
2387       end = viewport.getSelectionGroup().getEndRes();
2388     }
2389     else
2390     {
2391       seqs = viewport.getAlignment().getSequencesArray();
2392     }
2393
2394     // This is to maintain viewport position on first residue
2395     // of first sequence
2396     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2397     int startRes = seq.findPosition(viewport.startRes);
2398
2399     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2400             viewport.getAlignment()));
2401
2402     viewport.setStartRes(seq.findIndex(startRes) - 1);
2403
2404     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2405             .getSequences());
2406
2407   }
2408
2409   public void findMenuItem_actionPerformed()
2410   {
2411     new Finder(alignPanel);
2412   }
2413
2414   /**
2415    * create a new view derived from the current view
2416    *
2417    * @param viewtitle
2418    * @return frame for the new view
2419    */
2420   public AlignFrame newView(String viewtitle)
2421   {
2422     AlignmentI newal;
2423     if (viewport.hasHiddenRows())
2424     {
2425       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2426               .getFullAlignment().getSequencesArray());
2427     }
2428     else
2429     {
2430       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2431     }
2432
2433     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2434     {
2435       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2436       {
2437         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2438         {
2439           newal.addAnnotation(viewport.getAlignment()
2440                   .getAlignmentAnnotation()[i]);
2441         }
2442       }
2443     }
2444
2445     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2446
2447     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2448     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2449     PaintRefresher.Register(newaf.alignPanel,
2450             newaf.alignPanel.av.getSequenceSetId());
2451
2452     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2453             newaf.alignPanel.av.getSequenceSetId());
2454     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2455             newaf.alignPanel.av.getSequenceSetId());
2456
2457     Vector comps = (Vector) PaintRefresher.components.get(viewport
2458             .getSequenceSetId());
2459     int viewSize = -1;
2460     for (int i = 0; i < comps.size(); i++)
2461     {
2462       if (comps.elementAt(i) instanceof AlignmentPanel)
2463       {
2464         viewSize++;
2465       }
2466     }
2467
2468     String title = new String(this.getTitle());
2469     if (viewtitle != null)
2470     {
2471       title = viewtitle + " ( " + title + ")";
2472     }
2473     else
2474     {
2475       if (title.indexOf("(View") > -1)
2476       {
2477         title = title.substring(0, title.indexOf("(View"));
2478       }
2479       title += "(View " + viewSize + ")";
2480     }
2481
2482     newaf.setTitle(title.toString());
2483
2484     newaf.viewport.setHistoryList(viewport.getHistoryList());
2485     newaf.viewport.setRedoList(viewport.getRedoList());
2486     return newaf;
2487   }
2488
2489   /**
2490    *
2491    * @return list of feature groups on the view
2492    */
2493   public String[] getFeatureGroups()
2494   {
2495     FeatureRenderer fr = null;
2496     if (alignPanel != null
2497             && (fr = alignPanel.getFeatureRenderer()) != null)
2498     {
2499       List<String> gps = fr.getFeatureGroups();
2500       String[] _gps = gps.toArray(new String[gps.size()]);
2501       return _gps;
2502     }
2503     return null;
2504   }
2505
2506   /**
2507    * get sequence feature groups that are hidden or shown
2508    *
2509    * @param visible
2510    *          true is visible
2511    * @return list
2512    */
2513   public String[] getFeatureGroupsOfState(boolean visible)
2514   {
2515     FeatureRenderer fr = null;
2516     if (alignPanel != null
2517             && (fr = alignPanel.getFeatureRenderer()) != null)
2518     {
2519       List<String> gps = fr.getGroups(visible);
2520       String[] _gps = gps.toArray(new String[gps.size()]);
2521       return _gps;
2522     }
2523     return null;
2524   }
2525
2526   /**
2527    * Change the display state for the given feature groups
2528    *
2529    * @param groups
2530    *          list of group strings
2531    * @param state
2532    *          visible or invisible
2533    */
2534   public void setFeatureGroupState(String[] groups, boolean state)
2535   {
2536     FeatureRenderer fr = null;
2537     this.sequenceFeatures.setState(true);
2538     viewport.setShowSequenceFeatures(true);
2539     if (alignPanel != null
2540             && (fr = alignPanel.getFeatureRenderer()) != null)
2541     {
2542
2543       fr.setGroupVisibility(Arrays.asList(groups), state);
2544       alignPanel.seqPanel.seqCanvas.repaint();
2545       if (alignPanel.overviewPanel != null)
2546       {
2547         alignPanel.overviewPanel.updateOverviewImage();
2548       }
2549     }
2550   }
2551
2552   public void seqLimits_itemStateChanged()
2553   {
2554     viewport.setShowJVSuffix(seqLimits.getState());
2555     alignPanel.fontChanged();
2556     alignPanel.paintAlignment(true);
2557   }
2558
2559   protected void colourTextMenuItem_actionPerformed()
2560   {
2561     viewport.setColourText(colourTextMenuItem.getState());
2562     alignPanel.paintAlignment(true);
2563   }
2564
2565   protected void displayNonconservedMenuItem_actionPerformed()
2566   {
2567     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2568     alignPanel.paintAlignment(true);
2569   }
2570
2571   protected void wrapMenuItem_actionPerformed()
2572   {
2573     viewport.setWrapAlignment(wrapMenuItem.getState());
2574     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2575     scaleAbove.setEnabled(wrapMenuItem.getState());
2576     scaleLeft.setEnabled(wrapMenuItem.getState());
2577     scaleRight.setEnabled(wrapMenuItem.getState());
2578     alignPanel.paintAlignment(true);
2579   }
2580
2581   public void overviewMenuItem_actionPerformed()
2582   {
2583     if (alignPanel.overviewPanel != null)
2584     {
2585       return;
2586     }
2587
2588     Frame frame = new Frame();
2589     OverviewPanel overview = new OverviewPanel(alignPanel);
2590     frame.add(overview);
2591     // +50 must allow for applet frame window
2592     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2593             "label.overview_params", new String[] { this.getTitle() }),
2594             overview.getPreferredSize().width,
2595             overview.getPreferredSize().height + 50);
2596
2597     frame.pack();
2598     final AlignmentPanel ap = alignPanel;
2599     frame.addWindowListener(new WindowAdapter()
2600     {
2601       @Override
2602       public void windowClosing(WindowEvent e)
2603       {
2604         if (ap != null)
2605         {
2606           ap.setOverviewPanel(null);
2607         }
2608       };
2609     });
2610
2611     alignPanel.setOverviewPanel(overview);
2612
2613   }
2614
2615   @Override
2616   public void changeColour(ColourSchemeI cs)
2617   {
2618
2619     if (cs != null)
2620     {
2621       if (viewport.getAbovePIDThreshold())
2622       {
2623         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2624                 cs, "Background"));
2625       }
2626
2627       if (viewport.getConservationSelected())
2628       {
2629         cs.setConservationApplied(true);
2630         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2631                 cs, "Background"));
2632       }
2633       else
2634       {
2635         cs.setConservationApplied(false);
2636       }
2637     }
2638     viewport.setGlobalColourScheme(cs);
2639
2640     alignPanel.paintAlignment(true);
2641   }
2642
2643   protected void modifyPID_actionPerformed()
2644   {
2645     if (viewport.getAbovePIDThreshold()
2646             && viewport.getGlobalColourScheme() != null)
2647     {
2648       SliderPanel.setPIDSliderSource(alignPanel,
2649               viewport.getGlobalColourScheme(), "Background");
2650       SliderPanel.showPIDSlider();
2651     }
2652   }
2653
2654   protected void modifyConservation_actionPerformed()
2655   {
2656     if (viewport.getConservationSelected()
2657             && viewport.getGlobalColourScheme() != null)
2658     {
2659       SliderPanel.setConservationSlider(alignPanel,
2660               viewport.getGlobalColourScheme(), "Background");
2661       SliderPanel.showConservationSlider();
2662     }
2663   }
2664
2665   protected void conservationMenuItem_actionPerformed()
2666   {
2667     viewport.setConservationSelected(conservationMenuItem.getState());
2668
2669     viewport.setAbovePIDThreshold(false);
2670     abovePIDThreshold.setState(false);
2671
2672     changeColour(viewport.getGlobalColourScheme());
2673
2674     modifyConservation_actionPerformed();
2675   }
2676
2677   public void abovePIDThreshold_actionPerformed()
2678   {
2679     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2680
2681     conservationMenuItem.setState(false);
2682     viewport.setConservationSelected(false);
2683
2684     changeColour(viewport.getGlobalColourScheme());
2685
2686     modifyPID_actionPerformed();
2687   }
2688
2689   public void sortPairwiseMenuItem_actionPerformed()
2690   {
2691     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2692     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2693             .getAlignment().getSequenceAt(0), null);
2694
2695     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2696             viewport.getAlignment()));
2697     alignPanel.paintAlignment(true);
2698   }
2699
2700   public void sortIDMenuItem_actionPerformed()
2701   {
2702     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2703     AlignmentSorter.sortByID(viewport.getAlignment());
2704     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2705             viewport.getAlignment()));
2706     alignPanel.paintAlignment(true);
2707   }
2708
2709   public void sortLengthMenuItem_actionPerformed()
2710   {
2711     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2712     AlignmentSorter.sortByLength(viewport.getAlignment());
2713     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2714             viewport.getAlignment()));
2715     alignPanel.paintAlignment(true);
2716   }
2717
2718   public void sortGroupMenuItem_actionPerformed()
2719   {
2720     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2721     AlignmentSorter.sortByGroup(viewport.getAlignment());
2722     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2723             viewport.getAlignment()));
2724     alignPanel.paintAlignment(true);
2725
2726   }
2727
2728   public void removeRedundancyMenuItem_actionPerformed()
2729   {
2730     new RedundancyPanel(alignPanel);
2731   }
2732
2733   public void pairwiseAlignmentMenuItem_actionPerformed()
2734   {
2735     if (viewport.getSelectionGroup() != null
2736             && viewport.getSelectionGroup().getSize() > 1)
2737     {
2738       Frame frame = new Frame();
2739       frame.add(new PairwiseAlignPanel(alignPanel));
2740       jalview.bin.JalviewLite.addFrame(frame,
2741               MessageManager.getString("action.pairwise_alignment"), 600,
2742               500);
2743     }
2744   }
2745
2746   public void PCAMenuItem_actionPerformed()
2747   {
2748     // are the sequences aligned?
2749     if (!viewport.getAlignment().isAligned(false))
2750     {
2751       SequenceI current;
2752       int Width = viewport.getAlignment().getWidth();
2753
2754       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2755       {
2756         current = viewport.getAlignment().getSequenceAt(i);
2757
2758         if (current.getLength() < Width)
2759         {
2760           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2761         }
2762       }
2763       alignPanel.paintAlignment(true);
2764     }
2765
2766     if ((viewport.getSelectionGroup() != null
2767             && viewport.getSelectionGroup().getSize() < 4 && viewport
2768             .getSelectionGroup().getSize() > 0)
2769             || viewport.getAlignment().getHeight() < 4)
2770     {
2771       return;
2772     }
2773
2774     try
2775     {
2776       new PCAPanel(viewport);
2777     } catch (java.lang.OutOfMemoryError ex)
2778     {
2779     }
2780
2781   }
2782
2783   public void averageDistanceTreeMenuItem_actionPerformed()
2784   {
2785     NewTreePanel("AV", "PID", "Average distance tree using PID");
2786   }
2787
2788   public void neighbourTreeMenuItem_actionPerformed()
2789   {
2790     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2791   }
2792
2793   protected void njTreeBlosumMenuItem_actionPerformed()
2794   {
2795     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2796   }
2797
2798   protected void avTreeBlosumMenuItem_actionPerformed()
2799   {
2800     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2801   }
2802
2803   void NewTreePanel(String type, String pwType, String title)
2804   {
2805     // are the sequences aligned?
2806     if (!viewport.getAlignment().isAligned(false))
2807     {
2808       SequenceI current;
2809       int Width = viewport.getAlignment().getWidth();
2810
2811       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2812       {
2813         current = viewport.getAlignment().getSequenceAt(i);
2814
2815         if (current.getLength() < Width)
2816         {
2817           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2818         }
2819       }
2820       alignPanel.paintAlignment(true);
2821
2822     }
2823
2824     if ((viewport.getSelectionGroup() != null && viewport
2825             .getSelectionGroup().getSize() > 1)
2826             || (viewport.getAlignment().getHeight() > 1))
2827     {
2828       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2829
2830       addTreeMenuItem(tp, title);
2831
2832       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2833     }
2834   }
2835
2836   void loadTree_actionPerformed()
2837   {
2838     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2839     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2840     cap.setTreeImport();
2841     Frame frame = new Frame();
2842     frame.add(cap);
2843     jalview.bin.JalviewLite.addFrame(frame,
2844             MessageManager.getString("label.paste_newick_file"), 400, 300);
2845   }
2846
2847   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2848   {
2849     TreePanel tp = new TreePanel(alignPanel, treeFile,
2850             MessageManager.getString("label.load_tree_from_file"), tree);
2851     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2852     addTreeMenuItem(tp, treeFile);
2853   }
2854
2855   /**
2856    * sort the alignment using the given treePanel
2857    *
2858    * @param treePanel
2859    *          tree used to sort view
2860    * @param title
2861    *          string used for undo event name
2862    */
2863   public void sortByTree(TreePanel treePanel, String title)
2864   {
2865     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2866     AlignmentSorter
2867             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2868     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2869     // HistoryItem.SORT));
2870     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2871             "label.order_by_params", new String[] { title }), oldOrder,
2872             viewport.getAlignment()));
2873     alignPanel.paintAlignment(true);
2874   }
2875
2876   /**
2877    * Do any automatic reordering of the alignment and add the necessary bits to
2878    * the menu structure for the new tree
2879    *
2880    * @param treePanel
2881    * @param title
2882    */
2883   protected void addTreeMenuItem(final TreePanel treePanel,
2884           final String title)
2885   {
2886     final MenuItem item = new MenuItem(title);
2887     sortByTreeMenu.add(item);
2888     item.addActionListener(new java.awt.event.ActionListener()
2889     {
2890       @Override
2891       public void actionPerformed(ActionEvent evt)
2892       {
2893         sortByTree(treePanel, title); // treePanel.getTitle());
2894       }
2895     });
2896
2897     treePanel.addWindowListener(new WindowAdapter()
2898     {
2899       @Override
2900       public void windowOpened(WindowEvent e)
2901       {
2902         if (viewport.sortByTree)
2903         {
2904           sortByTree(treePanel, title);
2905         }
2906         super.windowOpened(e);
2907       }
2908
2909       @Override
2910       public void windowClosing(WindowEvent e)
2911       {
2912         sortByTreeMenu.remove(item);
2913       };
2914     });
2915   }
2916
2917   public boolean sortBy(AlignmentOrder alorder, String undoname)
2918   {
2919     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2920     if (viewport.applet.debug)
2921     {
2922       System.err.println("Sorting " + alorder.getOrder().size()
2923               + " in alignment '" + getTitle() + "'");
2924     }
2925     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2926     if (undoname != null)
2927     {
2928       addHistoryItem(new OrderCommand(undoname, oldOrder,
2929               viewport.getAlignment()));
2930     }
2931     alignPanel.paintAlignment(true);
2932     return true;
2933   }
2934
2935   protected void documentation_actionPerformed()
2936   {
2937     alignPanel.av.applet.openJalviewHelpUrl();
2938   }
2939
2940   protected void about_actionPerformed()
2941   {
2942
2943     class AboutPanel extends Canvas
2944     {
2945       String version;
2946
2947       String builddate;
2948
2949       public AboutPanel(String version, String builddate)
2950       {
2951         this.version = version;
2952         this.builddate = builddate;
2953       }
2954
2955       @Override
2956       public void paint(Graphics g)
2957       {
2958         g.setColor(Color.white);
2959         g.fillRect(0, 0, getSize().width, getSize().height);
2960         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2961         FontMetrics fm = g.getFontMetrics();
2962         int fh = fm.getHeight();
2963         int y = 5, x = 7;
2964         g.setColor(Color.black);
2965         // TODO: update this text for each release or centrally store it for
2966         // lite and application
2967         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2968         g.drawString(MessageManager.formatMessage(
2969                 "label.jalviewLite_release", new String[] { version }), x,
2970                 y += fh);
2971         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2972         g.drawString(MessageManager.formatMessage(
2973                 "label.jaview_build_date", new String[] { builddate }), x,
2974                 y += fh);
2975         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2976         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2977                 x, y += fh * 1.5);
2978         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2979                 x + 50, y += fh + 8);
2980         g.drawString(
2981                 MessageManager.getString("label.jalview_dev_managers"), x,
2982                 y += fh);
2983         g.drawString(MessageManager
2984                 .getString("label.jalview_distribution_lists"), x, y += fh);
2985         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2986                 x, y += fh + 8);
2987         g.drawString(
2988                 MessageManager.getString("label.jalview_cite_1_authors"),
2989                 x, y += fh);
2990         g.drawString(
2991                 MessageManager.getString("label.jalview_cite_1_title"), x,
2992                 y += fh);
2993         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2994                 x, y += fh);
2995       }
2996     }
2997
2998     Frame frame = new Frame();
2999     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3000             .getBuildDate()));
3001     jalview.bin.JalviewLite.addFrame(frame,
3002             MessageManager.getString("label.jalview"), 580, 220);
3003
3004   }
3005
3006   public void showURL(String url, String target)
3007   {
3008     if (viewport.applet == null)
3009     {
3010       System.out.println("Not running as applet - no browser available.");
3011     }
3012     else
3013     {
3014       viewport.applet.showURL(url, target);
3015     }
3016   }
3017
3018   // ////////////////////////////////////////////////////////////////////////////////
3019   // JBuilder Graphics here
3020
3021   MenuBar alignFrameMenuBar = new MenuBar();
3022
3023   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3024
3025   MenuItem loadApplication = new MenuItem(
3026           MessageManager.getString("label.view_full_application"));
3027
3028   MenuItem loadTree = new MenuItem(
3029           MessageManager.getString("label.load_associated_tree"));
3030
3031   MenuItem loadAnnotations = new MenuItem(
3032           MessageManager.getString("label.load_features_annotations"));
3033
3034   MenuItem outputFeatures = new MenuItem(
3035           MessageManager.getString("label.export_features"));
3036
3037   MenuItem outputAnnotations = new MenuItem(
3038           MessageManager.getString("label.export_annotations"));
3039
3040   MenuItem closeMenuItem = new MenuItem(
3041           MessageManager.getString("action.close"));
3042
3043   MenuItem selectAllSequenceMenuItem = new MenuItem(
3044           MessageManager.getString("action.select_all"));
3045
3046   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3047           MessageManager.getString("action.deselect_all"));
3048
3049   MenuItem invertSequenceMenuItem = new MenuItem(
3050           MessageManager.getString("action.invert_selection"));
3051
3052   MenuItem remove2LeftMenuItem = new MenuItem();
3053
3054   MenuItem remove2RightMenuItem = new MenuItem();
3055
3056   MenuItem removeGappedColumnMenuItem = new MenuItem();
3057
3058   MenuItem removeAllGapsMenuItem = new MenuItem();
3059
3060   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3061
3062   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3063
3064   MenuItem sortPairwiseMenuItem = new MenuItem();
3065
3066   MenuItem sortIDMenuItem = new MenuItem();
3067
3068   MenuItem sortLengthMenuItem = new MenuItem();
3069
3070   MenuItem sortGroupMenuItem = new MenuItem();
3071
3072   MenuItem removeRedundancyMenuItem = new MenuItem();
3073
3074   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3075
3076   MenuItem PCAMenuItem = new MenuItem();
3077
3078   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3079
3080   MenuItem neighbourTreeMenuItem = new MenuItem();
3081
3082   BorderLayout borderLayout1 = new BorderLayout();
3083
3084   public Label statusBar = new Label();
3085
3086   MenuItem clustalColour = new MenuItem();
3087
3088   MenuItem zappoColour = new MenuItem();
3089
3090   MenuItem taylorColour = new MenuItem();
3091
3092   MenuItem hydrophobicityColour = new MenuItem();
3093
3094   MenuItem helixColour = new MenuItem();
3095
3096   MenuItem strandColour = new MenuItem();
3097
3098   MenuItem turnColour = new MenuItem();
3099
3100   MenuItem buriedColour = new MenuItem();
3101
3102   MenuItem purinePyrimidineColour = new MenuItem();
3103
3104   // MenuItem RNAInteractionColour = new MenuItem();
3105
3106   MenuItem RNAHelixColour = new MenuItem();
3107
3108   MenuItem userDefinedColour = new MenuItem();
3109
3110   MenuItem PIDColour = new MenuItem();
3111
3112   MenuItem BLOSUM62Colour = new MenuItem();
3113
3114   MenuItem tcoffeeColour = new MenuItem();
3115
3116   MenuItem njTreeBlosumMenuItem = new MenuItem();
3117
3118   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3119
3120   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3121
3122   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3123
3124   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3125
3126   MenuItem alProperties = new MenuItem(
3127           MessageManager.getString("label.alignment_props"));
3128
3129   MenuItem overviewMenuItem = new MenuItem();
3130
3131   MenuItem undoMenuItem = new MenuItem();
3132
3133   MenuItem redoMenuItem = new MenuItem();
3134
3135   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3136
3137   MenuItem noColourmenuItem = new MenuItem();
3138
3139   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3140
3141   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3142
3143   MenuItem findMenuItem = new MenuItem();
3144
3145   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3146
3147   MenuItem nucleotideColour = new MenuItem();
3148
3149   MenuItem deleteGroups = new MenuItem();
3150
3151   MenuItem grpsFromSelection = new MenuItem();
3152
3153   MenuItem createGroup = new MenuItem();
3154
3155   MenuItem unGroup = new MenuItem();
3156
3157   MenuItem delete = new MenuItem();
3158
3159   MenuItem copy = new MenuItem();
3160
3161   MenuItem cut = new MenuItem();
3162
3163   Menu pasteMenu = new Menu();
3164
3165   MenuItem pasteNew = new MenuItem();
3166
3167   MenuItem pasteThis = new MenuItem();
3168
3169   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3170
3171   MenuItem font = new MenuItem();
3172
3173   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3174
3175   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3176
3177   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3178
3179   MenuItem modifyPID = new MenuItem();
3180
3181   MenuItem modifyConservation = new MenuItem();
3182
3183   CheckboxMenuItem autoCalculate = null;
3184
3185   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3186           "Sort Alignment With New Tree", true);
3187
3188   Menu sortByTreeMenu = new Menu();
3189
3190   MenuItem inputText = new MenuItem();
3191
3192   MenuItem documentation = new MenuItem();
3193
3194   MenuItem about = new MenuItem();
3195
3196   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3197
3198   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3199
3200   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3201
3202   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3203
3204   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3205
3206   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3209
3210   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3211
3212   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3213
3214   /**
3215    * Initialise menus and other items
3216    *
3217    * @throws Exception
3218    */
3219   private void jbInit() throws Exception
3220   {
3221     setMenuBar(alignFrameMenuBar);
3222
3223     /*
3224      * Configure File menu items and actions
3225      */
3226     inputText
3227             .setLabel(MessageManager.getString("label.input_from_textbox"));
3228     inputText.addActionListener(this);
3229     Menu outputTextboxMenu = new Menu(
3230             MessageManager.getString("label.out_to_textbox"));
3231     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3232     {
3233
3234       MenuItem item = new MenuItem(
3235               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3236
3237       item.addActionListener(new java.awt.event.ActionListener()
3238       {
3239         @Override
3240         public void actionPerformed(ActionEvent e)
3241         {
3242           outputText_actionPerformed(e);
3243         }
3244       });
3245
3246       outputTextboxMenu.add(item);
3247     }
3248     closeMenuItem.addActionListener(this);
3249     loadApplication.addActionListener(this);
3250     loadTree.addActionListener(this);
3251     loadAnnotations.addActionListener(this);
3252     outputFeatures.addActionListener(this);
3253     outputAnnotations.addActionListener(this);
3254
3255     /*
3256      * Configure Edit menu items and actions
3257      */
3258     undoMenuItem.setEnabled(false);
3259     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3260     undoMenuItem.addActionListener(this);
3261     redoMenuItem.setEnabled(false);
3262     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3263     redoMenuItem.addActionListener(this);
3264     copy.setLabel(MessageManager.getString("action.copy"));
3265     copy.addActionListener(this);
3266     cut.setLabel(MessageManager.getString("action.cut"));
3267     cut.addActionListener(this);
3268     delete.setLabel(MessageManager.getString("action.delete"));
3269     delete.addActionListener(this);
3270     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3271     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3272     pasteNew.addActionListener(this);
3273     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3274     pasteThis.addActionListener(this);
3275     remove2LeftMenuItem.setLabel(MessageManager
3276             .getString("action.remove_left"));
3277     remove2LeftMenuItem.addActionListener(this);
3278     remove2RightMenuItem.setLabel(MessageManager
3279             .getString("action.remove_right"));
3280     remove2RightMenuItem.addActionListener(this);
3281     removeGappedColumnMenuItem.setLabel(MessageManager
3282             .getString("action.remove_empty_columns"));
3283     removeGappedColumnMenuItem.addActionListener(this);
3284     removeAllGapsMenuItem.setLabel(MessageManager
3285             .getString("action.remove_all_gaps"));
3286     removeAllGapsMenuItem.addActionListener(this);
3287     removeRedundancyMenuItem.setLabel(MessageManager
3288             .getString("action.remove_redundancy"));
3289     removeRedundancyMenuItem.addActionListener(this);
3290
3291     /*
3292      * Configure Select menu items and actions
3293      */
3294     findMenuItem.setLabel(MessageManager.getString("action.find"));
3295     findMenuItem.addActionListener(this);
3296     selectAllSequenceMenuItem.addActionListener(this);
3297     deselectAllSequenceMenuItem.addActionListener(this);
3298     invertSequenceMenuItem.setLabel(MessageManager
3299             .getString("action.invert_sequence_selection"));
3300     invertSequenceMenuItem.addActionListener(this);
3301     invertColSel.setLabel(MessageManager
3302             .getString("action.invert_column_selection"));
3303     invertColSel.addActionListener(this);
3304     deleteGroups.setLabel(MessageManager
3305             .getString("action.undefine_groups"));
3306     deleteGroups.addActionListener(this);
3307     grpsFromSelection.setLabel(MessageManager
3308             .getString("action.make_groups_selection"));
3309     grpsFromSelection.addActionListener(this);
3310     createGroup.setLabel(MessageManager.getString("action.create_group"));
3311     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3312     annotationColumnSelection.setLabel(MessageManager
3313             .getString("action.select_by_annotation"));
3314     annotationColumnSelection.addActionListener(this);
3315
3316     /*
3317      * Configure View menu items and actions
3318      */
3319     newView.setLabel(MessageManager.getString("action.new_view"));
3320     newView.addActionListener(this);
3321     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3322     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3323     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3324     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3325     hideColumns
3326             .setLabel(MessageManager.getString("label.selected_columns"));
3327     hideSequences.setLabel(MessageManager
3328             .getString("label.selected_sequences"));
3329     hideAllButSelection.setLabel(MessageManager
3330             .getString("label.all_but_selected_region"));
3331     hideAllSelection.setLabel(MessageManager
3332             .getString("label.selected_region"));
3333     showAllHidden.setLabel(MessageManager
3334             .getString("label.all_sequences_columns"));
3335     showColumns.addActionListener(this);
3336     showSeqs.addActionListener(this);
3337     hideColumns.addActionListener(this);
3338     hideSequences.addActionListener(this);
3339     hideAllButSelection.addActionListener(this);
3340     hideAllSelection.addActionListener(this);
3341     showAllHidden.addActionListener(this);
3342     featureSettings.setLabel(MessageManager
3343             .getString("action.feature_settings"));
3344     featureSettings.addActionListener(this);
3345     sequenceFeatures.setLabel(MessageManager
3346             .getString("label.show_sequence_features"));
3347     sequenceFeatures.addItemListener(this);
3348     sequenceFeatures.setState(false);
3349     followMouseOverFlag.setLabel(MessageManager
3350             .getString("label.automatic_scrolling"));
3351     followMouseOverFlag.addItemListener(this);
3352     alProperties.addActionListener(this);
3353     overviewMenuItem.setLabel(MessageManager
3354             .getString("label.overview_window"));
3355     overviewMenuItem.addActionListener(this);
3356
3357     /*
3358      * Configure Annotations menu items and actions
3359      */
3360     annotationPanelMenuItem.setLabel(MessageManager
3361             .getString("label.show_annotations"));
3362     annotationPanelMenuItem.addItemListener(this);
3363     showGroupConsensus.setLabel(MessageManager
3364             .getString("label.group_consensus"));
3365     showGroupConservation.setLabel(MessageManager
3366             .getString("label.group_conservation"));
3367     showConsensusHistogram.setLabel(MessageManager
3368             .getString("label.show_consensus_histogram"));
3369     showSequenceLogo.setLabel(MessageManager
3370             .getString("label.show_consensus_logo"));
3371     normSequenceLogo.setLabel(MessageManager
3372             .getString("label.norm_consensus_logo"));
3373     applyAutoAnnotationSettings.setLabel(MessageManager
3374             .getString("label.apply_all_groups"));
3375     applyAutoAnnotationSettings.setState(true);
3376     Menu autoAnnMenu = new Menu(
3377             MessageManager.getString("label.autocalculated_annotation"));
3378     showGroupConsensus.addItemListener(this);
3379     showGroupConservation.addItemListener(this);
3380     showConsensusHistogram.addItemListener(this);
3381     showSequenceLogo.addItemListener(this);
3382     normSequenceLogo.addItemListener(this);
3383     applyAutoAnnotationSettings.addItemListener(this);
3384     showAlignmentAnnotations = new CheckboxMenuItem(
3385             MessageManager.getString("label.show_all_al_annotations"));
3386     showSequenceAnnotations = new CheckboxMenuItem(
3387             MessageManager.getString("label.show_all_seq_annotations"));
3388     sortAnnBySequence = new CheckboxMenuItem(
3389             MessageManager.getString("label.sort_annotations_by_sequence"));
3390     sortAnnByLabel = new CheckboxMenuItem(
3391             MessageManager.getString("label.sort_annotations_by_label"));
3392     showAutoFirst = new CheckboxMenuItem(
3393             MessageManager.getString("label.show_first"));
3394     showAutoFirst.setState(false); // pending applet parameter
3395     setShowAutoCalculatedAbove(showAutoFirst.getState());
3396     showAutoLast = new CheckboxMenuItem(
3397             MessageManager.getString("label.show_last"));
3398     showAutoLast.setState(!showAutoFirst.getState());
3399     showAlignmentAnnotations.addItemListener(this);
3400     showSequenceAnnotations.addItemListener(this);
3401     sortAnnBySequence.addItemListener(this);
3402     sortAnnByLabel.addItemListener(this);
3403     showAutoFirst.addItemListener(this);
3404     showAutoLast.addItemListener(this);
3405
3406     /*
3407      * Configure Format menu items and actions
3408      */
3409     font.setLabel(MessageManager.getString("action.font"));
3410     font.addActionListener(this);
3411     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3412     scaleAbove.setState(true);
3413     scaleAbove.setEnabled(false);
3414     scaleAbove.addItemListener(this);
3415     scaleLeft.setEnabled(false);
3416     scaleLeft.setState(true);
3417     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3418     scaleLeft.addItemListener(this);
3419     scaleRight.setEnabled(false);
3420     scaleRight.setState(true);
3421     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3422     scaleRight.addItemListener(this);
3423     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3424     viewBoxesMenuItem.setState(true);
3425     viewBoxesMenuItem.addItemListener(this);
3426     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3427     viewTextMenuItem.setState(true);
3428     viewTextMenuItem.addItemListener(this);
3429     colourTextMenuItem.setLabel(MessageManager
3430             .getString("label.colour_text"));
3431     colourTextMenuItem.addItemListener(this);
3432     displayNonconservedMenuItem.setLabel(MessageManager
3433             .getString("label.show_non_conversed"));
3434     displayNonconservedMenuItem.addItemListener(this);
3435     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3436     wrapMenuItem.addItemListener(this);
3437     renderGapsMenuItem.setLabel(MessageManager
3438             .getString("action.show_gaps"));
3439     renderGapsMenuItem.setState(true);
3440     renderGapsMenuItem.addItemListener(this);
3441     centreColumnLabelFlag.setLabel(MessageManager
3442             .getString("label.centre_column_labels"));
3443     centreColumnLabelFlag.addItemListener(this);
3444     seqLimits.setState(true);
3445     seqLimits.setLabel(MessageManager
3446             .getString("label.show_sequence_limits"));
3447     seqLimits.addItemListener(this);
3448
3449     /*
3450      * Configure Colour menu items and actions
3451      */
3452     applyToAllGroups.setLabel(MessageManager
3453             .getString("label.apply_colour_to_all_groups"));
3454     applyToAllGroups.setState(true);
3455     applyToAllGroups.addItemListener(this);
3456     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3457     clustalColour.addActionListener(this);
3458     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3459     zappoColour.addActionListener(this);
3460     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3461     taylorColour.addActionListener(this);
3462     hydrophobicityColour.setLabel(MessageManager
3463             .getString("label.hydrophobicity"));
3464     hydrophobicityColour.addActionListener(this);
3465     helixColour
3466             .setLabel(MessageManager.getString("label.helix_propensity"));
3467     helixColour.addActionListener(this);
3468     strandColour.setLabel(MessageManager
3469             .getString("label.strand_propensity"));
3470     strandColour.addActionListener(this);
3471     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3472     turnColour.addActionListener(this);
3473     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3474     buriedColour.addActionListener(this);
3475     purinePyrimidineColour.setLabel(MessageManager
3476             .getString("label.purine_pyrimidine"));
3477     purinePyrimidineColour.addActionListener(this);
3478     // RNAInteractionColour.setLabel(MessageManager
3479     // .getString("label.rna_interaction"));
3480     // RNAInteractionColour.addActionListener(this);
3481     RNAHelixColour.setLabel(MessageManager
3482             .getString("action.by_rna_helixes"));
3483     RNAHelixColour.addActionListener(this);
3484     userDefinedColour.setLabel(MessageManager
3485             .getString("action.user_defined"));
3486     userDefinedColour.addActionListener(this);
3487     PIDColour.setLabel(MessageManager
3488             .getString("label.percentage_identity"));
3489     PIDColour.addActionListener(this);
3490     BLOSUM62Colour.setLabel(MessageManager
3491             .getString("label.blosum62_score"));
3492     BLOSUM62Colour.addActionListener(this);
3493     tcoffeeColour
3494             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3495     // it will be enabled only if a score file is provided
3496     tcoffeeColour.setEnabled(false);
3497     tcoffeeColour.addActionListener(this);
3498     conservationMenuItem.setLabel(MessageManager
3499             .getString("action.by_conservation"));
3500     conservationMenuItem.addItemListener(this);
3501     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3502     noColourmenuItem.addActionListener(this);
3503     abovePIDThreshold.setLabel(MessageManager
3504             .getString("label.above_identity_threshold"));
3505     abovePIDThreshold.addItemListener(this);
3506     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3507     nucleotideColour.addActionListener(this);
3508     modifyPID.setLabel(MessageManager
3509             .getString("label.modify_identity_thereshold"));
3510     modifyPID.addActionListener(this);
3511     modifyConservation.setLabel(MessageManager
3512             .getString("label.modify_conservation_thereshold"));
3513     modifyConservation.addActionListener(this);
3514     annotationColour.setLabel(MessageManager
3515             .getString("action.by_annotation"));
3516     annotationColour.addActionListener(this);
3517
3518     /*
3519      * Configure Calculate menu items and actions
3520      */
3521     sortPairwiseMenuItem.setLabel(MessageManager
3522             .getString("action.by_pairwise_id"));
3523     sortPairwiseMenuItem.addActionListener(this);
3524     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3525     sortIDMenuItem.addActionListener(this);
3526     sortLengthMenuItem.setLabel(MessageManager
3527             .getString("action.by_length"));
3528     sortLengthMenuItem.addActionListener(this);
3529     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3530     sortGroupMenuItem.addActionListener(this);
3531     pairwiseAlignmentMenuItem.setLabel(MessageManager
3532             .getString("action.pairwise_alignment"));
3533     pairwiseAlignmentMenuItem.addActionListener(this);
3534     PCAMenuItem.setLabel(MessageManager
3535             .getString("label.principal_component_analysis"));
3536     PCAMenuItem.addActionListener(this);
3537     autoCalculate = new CheckboxMenuItem(
3538             MessageManager.getString("label.autocalculate_consensus"), true);
3539     averageDistanceTreeMenuItem.setLabel(MessageManager
3540             .getString("label.average_distance_identity"));
3541     averageDistanceTreeMenuItem.addActionListener(this);
3542     neighbourTreeMenuItem.setLabel(MessageManager
3543             .getString("label.neighbour_joining_identity"));
3544     neighbourTreeMenuItem.addActionListener(this);
3545     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3546             .getString("label.average_distance_bloslum62"));
3547     avDistanceTreeBlosumMenuItem.addActionListener(this);
3548     njTreeBlosumMenuItem.setLabel(MessageManager
3549             .getString("label.neighbour_blosum62"));
3550     njTreeBlosumMenuItem.addActionListener(this);
3551     sortByTreeMenu.setLabel(MessageManager
3552             .getString("action.by_tree_order"));
3553     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3554     Menu calculateTreeMenu = new Menu(
3555             MessageManager.getString("action.calculate_tree"));
3556     autoCalculate.addItemListener(this);
3557     sortByTree.addItemListener(this);
3558
3559     /*
3560      * Configure Help menu items and actions
3561      */
3562     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3563     documentation.setLabel(MessageManager.getString("label.documentation"));
3564     documentation.addActionListener(this);
3565     about.setLabel(MessageManager.getString("label.about"));
3566     about.addActionListener(this);
3567
3568     /*
3569      * Add top level menus to frame
3570      */
3571     alignFrameMenuBar.add(fileMenu);
3572     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3573     alignFrameMenuBar.add(editMenu);
3574     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3575     alignFrameMenuBar.add(selectMenu);
3576     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3577     alignFrameMenuBar.add(viewMenu);
3578     Menu annotationsMenu = new Menu(
3579             MessageManager.getString("action.annotations"));
3580     alignFrameMenuBar.add(annotationsMenu);
3581     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3582     alignFrameMenuBar.add(formatMenu);
3583     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3584     alignFrameMenuBar.add(colourMenu);
3585     Menu calculateMenu = new Menu(
3586             MessageManager.getString("action.calculate"));
3587     alignFrameMenuBar.add(calculateMenu);
3588     alignFrameMenuBar.add(helpMenu);
3589
3590     /*
3591      * File menu
3592      */
3593     fileMenu.add(inputText);
3594     fileMenu.add(loadTree);
3595     fileMenu.add(loadAnnotations);
3596     fileMenu.addSeparator();
3597     fileMenu.add(outputTextboxMenu);
3598     fileMenu.add(outputFeatures);
3599     fileMenu.add(outputAnnotations);
3600     if (jalviewServletURL != null)
3601     {
3602       fileMenu.add(loadApplication);
3603     }
3604     fileMenu.addSeparator();
3605     fileMenu.add(closeMenuItem);
3606
3607     /*
3608      * Edit menu
3609      */
3610     editMenu.add(undoMenuItem);
3611     editMenu.add(redoMenuItem);
3612     editMenu.add(cut);
3613     editMenu.add(copy);
3614     pasteMenu.add(pasteNew);
3615     pasteMenu.add(pasteThis);
3616     editMenu.add(pasteMenu);
3617     editMenu.add(delete);
3618     editMenu.addSeparator();
3619     editMenu.add(remove2LeftMenuItem);
3620     editMenu.add(remove2RightMenuItem);
3621     editMenu.add(removeGappedColumnMenuItem);
3622     editMenu.add(removeAllGapsMenuItem);
3623     editMenu.add(removeRedundancyMenuItem);
3624
3625     /*
3626      * Select menu
3627      */
3628     selectMenu.add(findMenuItem);
3629     selectMenu.addSeparator();
3630     selectMenu.add(selectAllSequenceMenuItem);
3631     selectMenu.add(deselectAllSequenceMenuItem);
3632     selectMenu.add(invertSequenceMenuItem);
3633     selectMenu.add(invertColSel);
3634     selectMenu.add(createGroup);
3635     selectMenu.add(unGroup);
3636     selectMenu.add(grpsFromSelection);
3637     selectMenu.add(deleteGroups);
3638     selectMenu.add(annotationColumnSelection);
3639
3640     /*
3641      * View menu
3642      */
3643     viewMenu.add(newView);
3644     viewMenu.addSeparator();
3645     showMenu.add(showColumns);
3646     showMenu.add(showSeqs);
3647     showMenu.add(showAllHidden);
3648     viewMenu.add(showMenu);
3649     hideMenu.add(hideColumns);
3650     hideMenu.add(hideSequences);
3651     hideMenu.add(hideAllSelection);
3652     hideMenu.add(hideAllButSelection);
3653     viewMenu.add(hideMenu);
3654     viewMenu.addSeparator();
3655     viewMenu.add(followMouseOverFlag);
3656     viewMenu.addSeparator();
3657     viewMenu.add(sequenceFeatures);
3658     viewMenu.add(featureSettings);
3659     viewMenu.addSeparator();
3660     viewMenu.add(alProperties);
3661     viewMenu.addSeparator();
3662     viewMenu.add(overviewMenuItem);
3663
3664     /*
3665      * Annotations menu
3666      */
3667     annotationsMenu.add(annotationPanelMenuItem);
3668     annotationsMenu.addSeparator();
3669     annotationsMenu.add(showAlignmentAnnotations);
3670     annotationsMenu.add(showSequenceAnnotations);
3671     annotationsMenu.add(sortAnnBySequence);
3672     annotationsMenu.add(sortAnnByLabel);
3673     annotationsMenu.addSeparator();
3674     autoAnnMenu.add(showAutoFirst);
3675     autoAnnMenu.add(showAutoLast);
3676     autoAnnMenu.addSeparator();
3677     autoAnnMenu.add(applyAutoAnnotationSettings);
3678     autoAnnMenu.add(showConsensusHistogram);
3679     autoAnnMenu.add(showSequenceLogo);
3680     autoAnnMenu.add(normSequenceLogo);
3681     autoAnnMenu.addSeparator();
3682     autoAnnMenu.add(showGroupConservation);
3683     autoAnnMenu.add(showGroupConsensus);
3684     annotationsMenu.add(autoAnnMenu);
3685
3686     /*
3687      * Format menu
3688      */
3689     formatMenu.add(font);
3690     formatMenu.add(seqLimits);
3691     formatMenu.add(wrapMenuItem);
3692     formatMenu.add(scaleAbove);
3693     formatMenu.add(scaleLeft);
3694     formatMenu.add(scaleRight);
3695     formatMenu.add(viewBoxesMenuItem);
3696     formatMenu.add(viewTextMenuItem);
3697     formatMenu.add(colourTextMenuItem);
3698     formatMenu.add(displayNonconservedMenuItem);
3699     formatMenu.add(renderGapsMenuItem);
3700     formatMenu.add(centreColumnLabelFlag);
3701
3702     /*
3703      * Colour menu
3704      */
3705     colourMenu.add(applyToAllGroups);
3706     colourMenu.addSeparator();
3707     colourMenu.add(noColourmenuItem);
3708     colourMenu.add(clustalColour);
3709     colourMenu.add(BLOSUM62Colour);
3710     colourMenu.add(PIDColour);
3711     colourMenu.add(zappoColour);
3712     colourMenu.add(taylorColour);
3713     colourMenu.add(hydrophobicityColour);
3714     colourMenu.add(helixColour);
3715     colourMenu.add(strandColour);
3716     colourMenu.add(turnColour);
3717     colourMenu.add(buriedColour);
3718     colourMenu.add(nucleotideColour);
3719     colourMenu.add(purinePyrimidineColour);
3720     // colourMenu.add(RNAInteractionColour);
3721     colourMenu.add(tcoffeeColour);
3722     colourMenu.add(userDefinedColour);
3723     colourMenu.addSeparator();
3724     colourMenu.add(conservationMenuItem);
3725     colourMenu.add(modifyConservation);
3726     colourMenu.add(abovePIDThreshold);
3727     colourMenu.add(modifyPID);
3728     colourMenu.add(annotationColour);
3729     colourMenu.add(RNAHelixColour);
3730
3731     /*
3732      * Calculate menu
3733      */
3734     sortMenu.add(sortIDMenuItem);
3735     sortMenu.add(sortLengthMenuItem);
3736     sortMenu.add(sortByTreeMenu);
3737     sortMenu.add(sortGroupMenuItem);
3738     sortMenu.add(sortPairwiseMenuItem);
3739     calculateMenu.add(sortMenu);
3740     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3741     calculateTreeMenu.add(neighbourTreeMenuItem);
3742     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3743     calculateTreeMenu.add(njTreeBlosumMenuItem);
3744     calculateMenu.add(calculateTreeMenu);
3745     calculateMenu.addSeparator();
3746     calculateMenu.add(pairwiseAlignmentMenuItem);
3747     calculateMenu.add(PCAMenuItem);
3748     calculateMenu.add(autoCalculate);
3749     calculateMenu.add(sortByTree);
3750
3751     /*
3752      * Help menu
3753      */
3754     helpMenu.add(documentation);
3755     helpMenu.add(about);
3756
3757     /*
3758      * Status bar
3759      */
3760     statusBar.setBackground(Color.white);
3761     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3762     statusBar.setText(MessageManager.getString("label.status_bar"));
3763     this.add(statusBar, BorderLayout.SOUTH);
3764   }
3765
3766   @Override
3767   public void setStatus(String string)
3768   {
3769     statusBar.setText(string);
3770   };
3771
3772   MenuItem featureSettings = new MenuItem();
3773
3774   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3775
3776   MenuItem annotationColour = new MenuItem();
3777
3778   MenuItem annotationColumnSelection = new MenuItem();
3779
3780   MenuItem invertColSel = new MenuItem();
3781
3782   MenuItem showColumns = new MenuItem();
3783
3784   MenuItem showSeqs = new MenuItem();
3785
3786   MenuItem hideColumns = new MenuItem();
3787
3788   MenuItem hideSequences = new MenuItem();
3789
3790   MenuItem hideAllButSelection = new MenuItem();
3791
3792   MenuItem hideAllSelection = new MenuItem();
3793
3794   MenuItem showAllHidden = new MenuItem();
3795
3796   MenuItem newView = new MenuItem();
3797
3798   private CheckboxMenuItem showAlignmentAnnotations;
3799
3800   private CheckboxMenuItem showSequenceAnnotations;
3801
3802   private CheckboxMenuItem sortAnnBySequence;
3803
3804   private CheckboxMenuItem sortAnnByLabel;
3805
3806   private CheckboxMenuItem showAutoFirst;
3807
3808   private CheckboxMenuItem showAutoLast;
3809
3810   private SplitFrame splitFrame;
3811
3812   /**
3813    * Attach the alignFrame panels after embedding menus, if necessary. This used
3814    * to be called setEmbedded, but is now creates the dropdown menus in a
3815    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3816    *
3817    * @param reallyEmbedded
3818    *          true to attach the view to the applet area on the page rather than
3819    *          in a new window
3820    */
3821   public void createAlignFrameWindow(boolean reallyEmbedded)
3822   {
3823     if (reallyEmbedded)
3824     {
3825       embedAlignFrameInApplet(viewport.applet);
3826     }
3827     else
3828     {
3829       // //////
3830       // test and embed menu bar if necessary.
3831       //
3832       if (embedMenuIfNeeded(alignPanel))
3833       {
3834         /*
3835          * adjust for status bar height too. ? pointless as overridden by layout
3836          * manager
3837          */
3838         alignPanel.setSize(getSize().width,
3839                 getSize().height - statusBar.getHeight());
3840       }
3841       add(statusBar, BorderLayout.SOUTH);
3842       add(alignPanel, BorderLayout.CENTER);
3843       // and register with the applet so it can pass external API calls to us
3844       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3845               frameHeight);
3846     }
3847   }
3848
3849   /**
3850    * Add the components of this AlignFrame to the applet container.
3851    *
3852    * @param theApplet
3853    */
3854   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3855   {
3856     // ////
3857     // Explicitly build the embedded menu panel for the on-page applet
3858     //
3859     // view cannot be closed if its actually on the page
3860     fileMenu.remove(closeMenuItem);
3861     fileMenu.remove(3); // Remove Separator
3862     // construct embedded menu, using default font
3863     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3864     // and actually add the components to the applet area
3865     theApplet.setLayout(new BorderLayout());
3866     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3867     theApplet.add(statusBar, BorderLayout.SOUTH);
3868     // TODO should size be left to the layout manager?
3869     alignPanel.setSize(theApplet.getSize().width,
3870             theApplet.getSize().height - embeddedMenu.getHeight()
3871                     - statusBar.getHeight());
3872     theApplet.add(alignPanel, BorderLayout.CENTER);
3873     final AlignFrame me = this;
3874     theApplet.addFocusListener(new FocusListener()
3875     {
3876
3877       @Override
3878       public void focusLost(FocusEvent e)
3879       {
3880         if (theApplet.currentAlignFrame == me)
3881         {
3882           theApplet.currentAlignFrame = null;
3883         }
3884       }
3885
3886       @Override
3887       public void focusGained(FocusEvent e)
3888       {
3889         theApplet.currentAlignFrame = me;
3890       }
3891     });
3892     theApplet.validate();
3893   }
3894
3895   /**
3896    * create a new binding between structures in an existing jmol viewer instance
3897    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3898    * this does not open a new Jmol window, or modify the display of the
3899    * structures in the original jmol window. Note This method doesn't work
3900    * without an additional javascript library to exchange messages between the
3901    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3902    *
3903    * @param viewer
3904    *          JmolViewer instance
3905    * @param sequenceIds
3906    *          - sequence Ids to search for associations
3907    */
3908   public SequenceStructureBinding addStructureViewInstance(
3909           Object jmolviewer, String[] sequenceIds)
3910   {
3911     Viewer viewer = null;
3912     try
3913     {
3914       viewer = (Viewer) jmolviewer;
3915     } catch (ClassCastException ex)
3916     {
3917       System.err.println("Unsupported viewer object :"
3918               + jmolviewer.getClass());
3919     }
3920     if (viewer == null)
3921     {
3922       System.err.println("Can't use this object as a structure viewer:"
3923               + jmolviewer.getClass());
3924       return null;
3925     }
3926     SequenceI[] seqs = null;
3927     if (sequenceIds == null || sequenceIds.length == 0)
3928     {
3929       seqs = viewport.getAlignment().getSequencesArray();
3930     }
3931     else
3932     {
3933       Vector sqi = new Vector();
3934       AlignmentI al = viewport.getAlignment();
3935       for (int sid = 0; sid < sequenceIds.length; sid++)
3936       {
3937         SequenceI sq = al.findName(sequenceIds[sid]);
3938         if (sq != null)
3939         {
3940           sqi.addElement(sq);
3941         }
3942       }
3943       if (sqi.size() > 0)
3944       {
3945         seqs = new SequenceI[sqi.size()];
3946         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3947         {
3948           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3949         }
3950       }
3951       else
3952       {
3953         return null;
3954       }
3955     }
3956     AAStructureBindingModel jmv = null;
3957     // TODO: search for a jmv that involves viewer
3958     if (jmv == null)
3959     { // create a new viewer/jalview binding.
3960       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3961     }
3962     return jmv;
3963
3964   }
3965
3966   /**
3967    * bind a pdb file to a sequence in the current view
3968    *
3969    * @param sequenceId
3970    *          - sequenceId within the dataset.
3971    * @param pdbEntryString
3972    *          - the short name for the PDB file
3973    * @param pdbFile
3974    *          - pdb file - either a URL or a valid PDB file.
3975    * @return true if binding was as success TODO: consider making an exception
3976    *         structure for indicating when PDB parsing or sequenceId location
3977    *         fails.
3978    */
3979   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3980           String pdbFile)
3981   {
3982     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3983     boolean needtoadd = false;
3984     if (toaddpdb != null)
3985     {
3986       Vector pdbe = toaddpdb.getAllPDBEntries();
3987       PDBEntry pdbentry = null;
3988       if (pdbe != null && pdbe.size() > 0)
3989       {
3990         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3991         {
3992           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3993           if (!pdbentry.getId().equals(pdbEntryString)
3994                   && !pdbentry.getFile().equals(pdbFile))
3995           {
3996             pdbentry = null;
3997           }
3998           else
3999           {
4000             continue;
4001           }
4002         }
4003       }
4004       if (pdbentry == null)
4005       {
4006         pdbentry = new PDBEntry();
4007         pdbentry.setId(pdbEntryString);
4008         pdbentry.setFile(pdbFile);
4009         needtoadd = true; // add this new entry to sequence.
4010       }
4011       // resolve data source
4012       // TODO: this code should be a refactored to an io package
4013       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4014       if (protocol == null)
4015       {
4016         return false;
4017       }
4018       if (needtoadd)
4019       {
4020         // make a note of the access mode and add
4021         if (pdbentry.getProperty() == null)
4022         {
4023           pdbentry.setProperty(new Hashtable());
4024         }
4025         pdbentry.getProperty().put("protocol", protocol);
4026         toaddpdb.addPDBId(pdbentry);
4027         alignPanel.getStructureSelectionManager()
4028                 .registerPDBEntry(pdbentry);
4029       }
4030     }
4031     return true;
4032   }
4033
4034   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4035   {
4036     if (seqs != null)
4037     {
4038       Vector sequences = new Vector();
4039       for (int i = 0; i < seqs.length; i++)
4040       {
4041         if (seqs[i] != null)
4042         {
4043           sequences.addElement(new Object[] { seqs[i],
4044               (chains != null) ? chains[i] : null });
4045         }
4046       }
4047       seqs = new SequenceI[sequences.size()];
4048       chains = new String[sequences.size()];
4049       for (int i = 0, isize = sequences.size(); i < isize; i++)
4050       {
4051         Object[] oj = (Object[]) sequences.elementAt(i);
4052
4053         seqs[i] = (SequenceI) oj[0];
4054         chains[i] = (String) oj[1];
4055       }
4056     }
4057     return new Object[] { seqs, chains };
4058
4059   }
4060
4061   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4062           SequenceI[] seqs, String[] chains, String protocol)
4063   {
4064     // Scrub any null sequences from the array
4065     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4066     seqs = (SequenceI[]) sqch[0];
4067     chains = (String[]) sqch[1];
4068     if (seqs == null || seqs.length == 0)
4069     {
4070       System.err
4071               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4072     }
4073     if (protocol == null || protocol.trim().length() == 0
4074             || protocol.equals("null"))
4075     {
4076       protocol = (String) pdb.getProperty().get("protocol");
4077       if (protocol == null)
4078       {
4079         System.err.println("Couldn't work out protocol to open structure: "
4080                 + pdb.getId());
4081         return;
4082       }
4083     }
4084     if (applet.useXtrnalSviewer)
4085     {
4086       // register the association(s) and quit, don't create any windows.
4087       if (StructureSelectionManager.getStructureSelectionManager(applet)
4088               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4089       {
4090         System.err.println("Failed to map " + pdb.getFile() + " ("
4091                 + protocol + ") to any sequences");
4092       }
4093       return;
4094     }
4095     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4096     {
4097       // can only do alignments with Jmol
4098       // find the last jmol window assigned to this alignment
4099       jalview.appletgui.AppletJmol ajm = null, tajm;
4100       Vector jmols = applet
4101               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4102       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4103       {
4104         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4105         if (tajm.ap.alignFrame == this)
4106         {
4107           ajm = tajm;
4108           break;
4109         }
4110       }
4111       if (ajm != null)
4112       {
4113         System.err
4114                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4115         // try and add the pdb structure
4116         // ajm.addS
4117         ajm = null;
4118       }
4119     }
4120     // otherwise, create a new window
4121     if (applet.jmolAvailable)
4122     {
4123       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4124               protocol);
4125       applet.lastFrameX += 40;
4126       applet.lastFrameY += 40;
4127     }
4128     else
4129     {
4130       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4131     }
4132
4133   }
4134
4135   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4136           SequenceI[][] seqs, String[][] chains, String[] protocols)
4137   {
4138     // TODO Auto-generated method stub
4139     System.err.println("Aligned Structure View: Not yet implemented.");
4140   }
4141
4142   /**
4143    * modify the current selection, providing the user has not made a selection
4144    * already.
4145    *
4146    * @param sel
4147    *          - sequences from this alignment
4148    * @param csel
4149    *          - columns to be selected on the alignment
4150    */
4151   public void select(SequenceGroup sel, ColumnSelection csel)
4152   {
4153     alignPanel.seqPanel.selection(sel, csel, null);
4154   }
4155
4156   public void scrollTo(int row, int column)
4157   {
4158     alignPanel.seqPanel.scrollTo(row, column);
4159   }
4160
4161   public void scrollToRow(int row)
4162   {
4163     alignPanel.seqPanel.scrollToRow(row);
4164   }
4165
4166   public void scrollToColumn(int column)
4167   {
4168     alignPanel.seqPanel.scrollToColumn(column);
4169   }
4170
4171   /**
4172    * @return the alignments unique ID.
4173    */
4174   public String getSequenceSetId()
4175   {
4176     return viewport.getSequenceSetId();
4177   }
4178
4179   /**
4180    * Load the (T-Coffee) score file from the specified url
4181    *
4182    * @param source
4183    *          File/URL/T-COFFEE score file contents
4184    * @throws IOException
4185    * @return true if alignment was annotated with data from source
4186    */
4187   public boolean loadScoreFile(String source) throws IOException
4188   {
4189
4190     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4191             AppletFormatAdapter.checkProtocol(source));
4192     if (!file.isValid())
4193     {
4194       // TODO: raise dialog for gui
4195       System.err.println("Problems parsing T-Coffee scores: "
4196               + file.getWarningMessage());
4197       System.err.println("Origin was:\n" + source);
4198       return false;
4199     }
4200
4201     /*
4202      * check that the score matrix matches the alignment dimensions
4203      */
4204     AlignmentI aln;
4205     if ((aln = viewport.getAlignment()) != null
4206             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4207                     .getWidth()))
4208     {
4209       // TODO: raise a dialog box here rather than bomb out.
4210       System.err
4211               .println("The scores matrix does not match the alignment dimensions");
4212
4213     }
4214
4215     // TODO add parameter to indicate if matching should be done
4216     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4217     {
4218       alignPanel.fontChanged();
4219       tcoffeeColour.setEnabled(true);
4220       // switch to this color
4221       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4222       return true;
4223     }
4224     else
4225     {
4226       System.err.println("Problems resolving T-Coffee scores:");
4227       if (file.getWarningMessage() != null)
4228       {
4229         System.err.println(file.getWarningMessage());
4230       }
4231     }
4232     return false;
4233   }
4234
4235   public SplitFrame getSplitFrame()
4236   {
4237     return this.splitFrame;
4238   }
4239
4240   public void setSplitFrame(SplitFrame sf)
4241   {
4242     this.splitFrame = sf;
4243   }
4244
4245   // may not need this
4246   @Override
4247   public void setShowSeqFeatures(boolean b)
4248   {
4249     // showSeqFeatures.setSelected(b);
4250     viewport.setShowSequenceFeatures(b);
4251
4252   }
4253
4254   @Override
4255   public void setMenusForViewport()
4256   {
4257     // setMenusFromViewport(viewport);
4258
4259   }
4260
4261   @Override
4262   public void refreshFeatureUI(boolean enableIfNecessary)
4263   {
4264     if (enableIfNecessary)
4265     {
4266       sequenceFeatures.setState(true);
4267       alignPanel.av.setShowSequenceFeatures(true);
4268     }
4269   }
4270
4271   @Override
4272   public FeatureSettingsControllerI getFeatureSettingsUI()
4273   {
4274     return alignPanel.av.featureSettings;
4275   }
4276
4277 }