src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
   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     for (AlignmentAnnotation aa : alignPanel.getAlignment()
 934             .getAlignmentAnnotation())
 935     {
 936       boolean visible = (aa.sequenceRef == null ? showForAlignment
 937               : showForSequences);
 938       aa.visible = visible;
 939     }
 940     alignPanel.validateAnnotationDimensions(true);
 941     validate();
 942     repaint();
 943   }
 944
 945   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 946   {
 947     this.annotationSortOrder = order;
 948   }
 949
 950   /**
 951    * Set flags on the viewport that control annotation ordering
 952    */
 953   private void setViewportAnnotationOrder()
 954   {
 955     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 956     this.alignPanel.av
 957             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 958   }
 959
 960   private void setShowAutoCalculatedAbove(boolean showAbove)
 961   {
 962     this.showAutoCalculatedAbove = showAbove;
 963   }
 964
 965   private void mouseOverFlag_stateChanged()
 966   {
 967     viewport.setFollowHighlight(followMouseOverFlag.getState());
 968     // TODO: could kick the scrollTo mechanism to reset view for current
 969     // searchresults.
 970   }
 971
 972   private void centreColumnLabelFlag_stateChanged()
 973   {
 974     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 975     this.alignPanel.annotationPanel.repaint();
 976   }
 977
 978   @Override
 979   public void actionPerformed(ActionEvent evt)
 980   {
 981     viewport.applet.currentAlignFrame = this;
 982
 983     Object source = evt.getSource();
 984
 985     if (source == inputText)
 986     {
 987       inputText_actionPerformed();
 988     }
 989     else if (source == loadTree)
 990     {
 991       loadTree_actionPerformed();
 992     }
 993     else if (source == loadApplication)
 994     {
 995       launchFullApplication();
 996     }
 997     else if (source == loadAnnotations)
 998     {
 999       loadAnnotations();
1000     }
1001     else if (source == outputAnnotations)
1002     {
1003       outputAnnotations(true);
1004     }
1005     else if (source == outputFeatures)
1006     {
1007       outputFeatures(true, "Jalview");
1008     }
1009     else if (source == closeMenuItem)
1010     {
1011       closeMenuItem_actionPerformed();
1012     }
1013     else if (source == copy)
1014     {
1015       copy_actionPerformed();
1016     }
1017     else if (source == undoMenuItem)
1018     {
1019       undoMenuItem_actionPerformed();
1020     }
1021     else if (source == redoMenuItem)
1022     {
1023       redoMenuItem_actionPerformed();
1024     }
1025     else if (source == inputText)
1026     {
1027       inputText_actionPerformed();
1028     }
1029     else if (source == closeMenuItem)
1030     {
1031       closeMenuItem_actionPerformed();
1032     }
1033     else if (source == undoMenuItem)
1034     {
1035       undoMenuItem_actionPerformed();
1036     }
1037     else if (source == redoMenuItem)
1038     {
1039       redoMenuItem_actionPerformed();
1040     }
1041     else if (source == copy)
1042     {
1043       copy_actionPerformed();
1044     }
1045     else if (source == pasteNew)
1046     {
1047       pasteNew_actionPerformed();
1048     }
1049     else if (source == pasteThis)
1050     {
1051       pasteThis_actionPerformed();
1052     }
1053     else if (source == cut)
1054     {
1055       cut_actionPerformed();
1056     }
1057     else if (source == delete)
1058     {
1059       delete_actionPerformed();
1060     }
1061     else if (source == grpsFromSelection)
1062     {
1063       makeGrpsFromSelection_actionPerformed();
1064     }
1065     else if (source == deleteGroups)
1066     {
1067       deleteGroups_actionPerformed();
1068     }
1069     else if (source == selectAllSequenceMenuItem)
1070     {
1071       selectAllSequenceMenuItem_actionPerformed();
1072     }
1073     else if (source == deselectAllSequenceMenuItem)
1074     {
1075       deselectAllSequenceMenuItem_actionPerformed();
1076     }
1077     else if (source == invertSequenceMenuItem)
1078     {
1079       invertSequenceMenuItem_actionPerformed();
1080     }
1081     else if (source == invertColSel)
1082     {
1083       viewport.invertColumnSelection();
1084       alignPanel.paintAlignment(true);
1085     }
1086     else if (source == remove2LeftMenuItem)
1087     {
1088       trimAlignment(true);
1089     }
1090     else if (source == remove2RightMenuItem)
1091     {
1092       trimAlignment(false);
1093     }
1094     else if (source == removeGappedColumnMenuItem)
1095     {
1096       removeGappedColumnMenuItem_actionPerformed();
1097     }
1098     else if (source == removeAllGapsMenuItem)
1099     {
1100       removeAllGapsMenuItem_actionPerformed();
1101     }
1102     else if (source == findMenuItem)
1103     {
1104       findMenuItem_actionPerformed();
1105     }
1106     else if (source == font)
1107     {
1108       new FontChooser(alignPanel);
1109     }
1110     else if (source == newView)
1111     {
1112       newView(null);
1113     }
1114     else if (source == showColumns)
1115     {
1116       viewport.showAllHiddenColumns();
1117       alignPanel.paintAlignment(true);
1118     }
1119     else if (source == showSeqs)
1120     {
1121       viewport.showAllHiddenSeqs();
1122       alignPanel.paintAlignment(true);
1123     }
1124     else if (source == hideColumns)
1125     {
1126       viewport.hideSelectedColumns();
1127       alignPanel.paintAlignment(true);
1128     }
1129     else if (source == hideSequences
1130             && viewport.getSelectionGroup() != null)
1131     {
1132       viewport.hideAllSelectedSeqs();
1133       alignPanel.paintAlignment(true);
1134     }
1135     else if (source == hideAllButSelection)
1136     {
1137       toggleHiddenRegions(false, false);
1138       alignPanel.paintAlignment(true);
1139     }
1140     else if (source == hideAllSelection)
1141     {
1142       SequenceGroup sg = viewport.getSelectionGroup();
1143       viewport.expandColSelection(sg, false);
1144       viewport.hideAllSelectedSeqs();
1145       viewport.hideSelectedColumns();
1146       alignPanel.paintAlignment(true);
1147     }
1148     else if (source == showAllHidden)
1149     {
1150       viewport.showAllHiddenColumns();
1151       viewport.showAllHiddenSeqs();
1152       alignPanel.paintAlignment(true);
1153     }
1154     else if (source == showGroupConsensus)
1155     {
1156       showGroupConsensus_actionPerformed();
1157     }
1158     else if (source == showGroupConservation)
1159     {
1160       showGroupConservation_actionPerformed();
1161     }
1162     else if (source == showSequenceLogo)
1163     {
1164       showSequenceLogo_actionPerformed();
1165     }
1166     else if (source == normSequenceLogo)
1167     {
1168       normSequenceLogo_actionPerformed();
1169     }
1170     else if (source == showConsensusHistogram)
1171     {
1172       showConsensusHistogram_actionPerformed();
1173     }
1174     else if (source == applyAutoAnnotationSettings)
1175     {
1176       applyAutoAnnotationSettings_actionPerformed();
1177     }
1178     else if (source == featureSettings)
1179     {
1180       new FeatureSettings(alignPanel);
1181     }
1182     else if (source == alProperties)
1183     {
1184       StringBuffer contents = new jalview.io.AlignmentProperties(
1185               viewport.getAlignment()).formatAsString();
1186       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1187       cap.setText(contents.toString());
1188       Frame frame = new Frame();
1189       frame.add(cap);
1190       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1191               "label.alignment_properties", new String[] { getTitle() }),
1192               400, 250);
1193     }
1194     else if (source == overviewMenuItem)
1195     {
1196       overviewMenuItem_actionPerformed();
1197     }
1198     else if (source == noColourmenuItem)
1199     {
1200       changeColour(null);
1201     }
1202     else if (source == clustalColour)
1203     {
1204       abovePIDThreshold.setState(false);
1205       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1206     }
1207     else if (source == zappoColour)
1208     {
1209       changeColour(new ZappoColourScheme());
1210     }
1211     else if (source == taylorColour)
1212     {
1213       changeColour(new TaylorColourScheme());
1214     }
1215     else if (source == hydrophobicityColour)
1216     {
1217       changeColour(new HydrophobicColourScheme());
1218     }
1219     else if (source == helixColour)
1220     {
1221       changeColour(new HelixColourScheme());
1222     }
1223     else if (source == strandColour)
1224     {
1225       changeColour(new StrandColourScheme());
1226     }
1227     else if (source == turnColour)
1228     {
1229       changeColour(new TurnColourScheme());
1230     }
1231     else if (source == buriedColour)
1232     {
1233       changeColour(new BuriedColourScheme());
1234     }
1235     else if (source == nucleotideColour)
1236     {
1237       changeColour(new NucleotideColourScheme());
1238     }
1239     else if (source == purinePyrimidineColour)
1240     {
1241       changeColour(new PurinePyrimidineColourScheme());
1242     }
1243     // else if (source == RNAInteractionColour)
1244     // {
1245     // changeColour(new RNAInteractionColourScheme());
1246     // }
1247     else if (source == RNAHelixColour)
1248     {
1249       new RNAHelicesColourChooser(viewport, alignPanel);
1250     }
1251     else if (source == modifyPID)
1252     {
1253       modifyPID_actionPerformed();
1254     }
1255     else if (source == modifyConservation)
1256     {
1257       modifyConservation_actionPerformed();
1258     }
1259     else if (source == userDefinedColour)
1260     {
1261       new UserDefinedColours(alignPanel, null);
1262     }
1263     else if (source == PIDColour)
1264     {
1265       changeColour(new PIDColourScheme());
1266     }
1267     else if (source == BLOSUM62Colour)
1268     {
1269       changeColour(new Blosum62ColourScheme());
1270     }
1271     else if (source == tcoffeeColour)
1272     {
1273       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1274     }
1275     else if (source == annotationColour)
1276     {
1277       new AnnotationColourChooser(viewport, alignPanel);
1278     }
1279     else if (source == annotationColumnSelection)
1280     {
1281       new AnnotationColumnChooser(viewport, alignPanel);
1282     }
1283     else if (source == sortPairwiseMenuItem)
1284     {
1285       sortPairwiseMenuItem_actionPerformed();
1286     }
1287     else if (source == sortIDMenuItem)
1288     {
1289       sortIDMenuItem_actionPerformed();
1290     }
1291     else if (source == sortLengthMenuItem)
1292     {
1293       sortLengthMenuItem_actionPerformed();
1294     }
1295     else if (source == sortGroupMenuItem)
1296     {
1297       sortGroupMenuItem_actionPerformed();
1298     }
1299     else if (source == removeRedundancyMenuItem)
1300     {
1301       removeRedundancyMenuItem_actionPerformed();
1302     }
1303     else if (source == pairwiseAlignmentMenuItem)
1304     {
1305       pairwiseAlignmentMenuItem_actionPerformed();
1306     }
1307     else if (source == PCAMenuItem)
1308     {
1309       PCAMenuItem_actionPerformed();
1310     }
1311     else if (source == averageDistanceTreeMenuItem)
1312     {
1313       averageDistanceTreeMenuItem_actionPerformed();
1314     }
1315     else if (source == neighbourTreeMenuItem)
1316     {
1317       neighbourTreeMenuItem_actionPerformed();
1318     }
1319     else if (source == njTreeBlosumMenuItem)
1320     {
1321       njTreeBlosumMenuItem_actionPerformed();
1322     }
1323     else if (source == avDistanceTreeBlosumMenuItem)
1324     {
1325       avTreeBlosumMenuItem_actionPerformed();
1326     }
1327     else if (source == documentation)
1328     {
1329       documentation_actionPerformed();
1330     }
1331     else if (source == about)
1332     {
1333       about_actionPerformed();
1334     }
1335
1336   }
1337
1338   public void inputText_actionPerformed()
1339   {
1340     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1341     Frame frame = new Frame();
1342     frame.add(cap);
1343     jalview.bin.JalviewLite.addFrame(frame,
1344             MessageManager.getString("label.input_cut_paste"), 500, 500);
1345   }
1346
1347   protected void outputText_actionPerformed(ActionEvent e)
1348   {
1349     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1350     Frame frame = new Frame();
1351     frame.add(cap);
1352     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1353             "label.alignment_output_command",
1354             new Object[] { e.getActionCommand() }), 600, 500);
1355
1356     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1357     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1358             e.getActionCommand(), viewport.getAlignment(),
1359             viewport.getShowJVSuffix()));
1360   }
1361
1362   public void loadAnnotations()
1363   {
1364     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1365     cap.setText(MessageManager
1366             .getString("label.paste_features_annotations_Tcoffee_here"));
1367     cap.setAnnotationImport();
1368     Frame frame = new Frame();
1369     frame.add(cap);
1370     jalview.bin.JalviewLite.addFrame(frame,
1371             MessageManager.getString("action.paste_annotations"), 400, 300);
1372
1373   }
1374
1375   public String outputAnnotations(boolean displayTextbox)
1376   {
1377     String annotation = new AnnotationFile()
1378             .printAnnotationsForView(viewport);
1379
1380     if (displayTextbox)
1381     {
1382       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1383       Frame frame = new Frame();
1384       frame.add(cap);
1385       jalview.bin.JalviewLite.addFrame(frame,
1386               MessageManager.getString("label.annotations"), 600, 500);
1387       cap.setText(annotation);
1388     }
1389
1390     return annotation;
1391   }
1392
1393   private Map<String, Object> getDisplayedFeatureCols()
1394   {
1395     if (alignPanel.getFeatureRenderer() != null
1396             && viewport.getFeaturesDisplayed() != null)
1397     {
1398       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1399
1400     }
1401     return null;
1402   }
1403
1404   public String outputFeatures(boolean displayTextbox, String format)
1405   {
1406     String features;
1407     if (format.equalsIgnoreCase("Jalview"))
1408     {
1409       features = new FeaturesFile().printJalviewFormat(viewport
1410               .getAlignment().getSequencesArray(),
1411               getDisplayedFeatureCols());
1412     }
1413     else
1414     {
1415       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1416               .getSequencesArray(), getDisplayedFeatureCols());
1417     }
1418
1419     if (displayTextbox)
1420     {
1421       boolean frimport = false;
1422       if (features == null || features.equals("No Features Visible"))
1423       {
1424         features = "# No features visible - paste some and import them here.";
1425         frimport = true;
1426       }
1427
1428       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1429       if (frimport)
1430       {
1431         cap.setAnnotationImport();
1432       }
1433       Frame frame = new Frame();
1434       frame.add(cap);
1435       jalview.bin.JalviewLite.addFrame(frame,
1436               MessageManager.getString("label.features"), 600, 500);
1437       cap.setText(features);
1438     }
1439     else
1440     {
1441       if (features == null)
1442       {
1443         features = "";
1444       }
1445     }
1446
1447     return features;
1448   }
1449
1450   void launchFullApplication()
1451   {
1452     StringBuffer url = new StringBuffer(jalviewServletURL);
1453
1454     // allow servlet parameters to be passed in applet parameter
1455     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1456             : "?";
1457     url.append(firstSep);
1458
1459     url.append("open="
1460             + appendProtocol(viewport.applet.getParameter("file")));
1461
1462     if (viewport.applet.getParameter("features") != null)
1463     {
1464       url.append("&features=");
1465       url.append(appendProtocol(viewport.applet.getParameter("features")));
1466     }
1467
1468     if (viewport.applet.getParameter("annotations") != null)
1469     {
1470       url.append("&annotations=");
1471       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1472     }
1473
1474     if (viewport.applet.getParameter("jnetfile") != null)
1475     {
1476       url.append("&annotations=");
1477       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1478     }
1479
1480     if (viewport.applet.getParameter("defaultColour") != null)
1481     {
1482       url.append("&colour="
1483               + removeWhiteSpace(viewport.applet
1484                       .getParameter("defaultColour")));
1485     }
1486
1487     if (viewport.applet.getParameter("userDefinedColour") != null)
1488     {
1489       url.append("&colour="
1490               + removeWhiteSpace(viewport.applet
1491                       .getParameter("userDefinedColour")));
1492     }
1493     if (viewport.applet.getParameter("tree") != null)
1494     {
1495       url.append("&tree="
1496               + appendProtocol(viewport.applet.getParameter("tree")));
1497     }
1498     if (viewport.applet.getParameter("treeFile") != null)
1499     {
1500       url.append("&tree="
1501               + appendProtocol(viewport.applet.getParameter("treeFile")));
1502     }
1503
1504     showURL(url.toString(), "FULL_APP");
1505   }
1506
1507   String removeWhiteSpace(String colour)
1508   {
1509     StringBuffer sb = new StringBuffer();
1510     for (int i = 0; i < colour.length(); i++)
1511     {
1512       if (Character.isWhitespace(colour.charAt(i)))
1513       {
1514         sb.append("%20");
1515       }
1516       else
1517       {
1518         sb.append(colour.charAt(i));
1519       }
1520     }
1521
1522     return sb.toString();
1523   }
1524
1525   String appendProtocol(String url)
1526   {
1527     try
1528     {
1529       new URL(url);
1530       url = URLEncoder.encode(url);
1531     }
1532     /*
1533      * When we finally deprecate 1.1 compatibility, we can start to use
1534      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1535      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1536      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1537      * ex.printStackTrace(); }
1538      */
1539     catch (java.net.MalformedURLException ex)
1540     {
1541       url = viewport.applet.getCodeBase() + url;
1542     }
1543     return url;
1544   }
1545
1546   public void closeMenuItem_actionPerformed()
1547   {
1548     PaintRefresher.RemoveComponent(alignPanel);
1549     if (alignPanel.seqPanel != null
1550             && alignPanel.seqPanel.seqCanvas != null)
1551     {
1552       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1553     }
1554     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1555     {
1556       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1557     }
1558
1559     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1560     {
1561       System.exit(0);
1562     }
1563     else
1564     {
1565     }
1566     viewport = null;
1567     alignPanel = null;
1568     this.dispose();
1569   }
1570
1571   /**
1572    * TODO: JAL-1104
1573    */
1574   void updateEditMenuBar()
1575   {
1576
1577     if (viewport.getHistoryList().size() > 0)
1578     {
1579       undoMenuItem.setEnabled(true);
1580       CommandI command = viewport.getHistoryList().peek();
1581       undoMenuItem.setLabel(MessageManager.formatMessage(
1582               "label.undo_command",
1583               new Object[] { command.getDescription() }));
1584     }
1585     else
1586     {
1587       undoMenuItem.setEnabled(false);
1588       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1589     }
1590
1591     if (viewport.getRedoList().size() > 0)
1592     {
1593       redoMenuItem.setEnabled(true);
1594
1595       CommandI command = viewport.getRedoList().peek();
1596       redoMenuItem.setLabel(MessageManager.formatMessage(
1597               "label.redo_command",
1598               new Object[] { command.getDescription() }));
1599     }
1600     else
1601     {
1602       redoMenuItem.setEnabled(false);
1603       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1604     }
1605   }
1606
1607   /**
1608    * TODO: JAL-1104
1609    */
1610   @Override
1611   public void addHistoryItem(CommandI command)
1612   {
1613     if (command.getSize() > 0)
1614     {
1615       viewport.addToHistoryList(command);
1616       viewport.clearRedoList();
1617       updateEditMenuBar();
1618       viewport.updateHiddenColumns();
1619     }
1620   }
1621
1622   /**
1623    * TODO: JAL-1104 DOCUMENT ME!
1624    *
1625    * @param e
1626    *          DOCUMENT ME!
1627    */
1628   protected void undoMenuItem_actionPerformed()
1629   {
1630     if (viewport.getHistoryList().isEmpty())
1631     {
1632       return;
1633     }
1634
1635     CommandI command = viewport.getHistoryList().pop();
1636     viewport.addToRedoList(command);
1637     command.undoCommand(null);
1638
1639     AlignmentViewport originalSource = getOriginatingSource(command);
1640     // JBPNote Test
1641     if (originalSource != viewport)
1642     {
1643       System.err
1644               .println("Warning: Viewport object mismatch whilst undoing");
1645     }
1646     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1647                                           // viewport.getColumnSelection().getHiddenColumns()
1648                                           // != null;
1649     updateEditMenuBar();
1650     originalSource.firePropertyChange("alignment", null, originalSource
1651             .getAlignment().getSequences());
1652   }
1653
1654   /**
1655    * TODO: JAL-1104 DOCUMENT ME!
1656    *
1657    * @param e
1658    *          DOCUMENT ME!
1659    */
1660   protected void redoMenuItem_actionPerformed()
1661   {
1662     if (viewport.getRedoList().isEmpty())
1663     {
1664       return;
1665     }
1666
1667     CommandI command = viewport.getRedoList().pop();
1668     viewport.addToHistoryList(command);
1669     command.doCommand(null);
1670
1671     AlignmentViewport originalSource = getOriginatingSource(command);
1672     // JBPNote Test
1673     if (originalSource != viewport)
1674     {
1675       System.err
1676               .println("Warning: Viewport object mismatch whilst re-doing");
1677     }
1678     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1679                                           // viewport.getColumnSelection().getHiddenColumns()
1680                                           // != null;
1681
1682     updateEditMenuBar();
1683     originalSource.firePropertyChange("alignment", null, originalSource
1684             .getAlignment().getSequences());
1685   }
1686
1687   AlignmentViewport getOriginatingSource(CommandI command)
1688   {
1689     AlignmentViewport originalSource = null;
1690     // For sequence removal and addition, we need to fire
1691     // the property change event FROM the viewport where the
1692     // original alignment was altered
1693     AlignmentI al = null;
1694     if (command instanceof EditCommand)
1695     {
1696       EditCommand editCommand = (EditCommand) command;
1697       al = editCommand.getAlignment();
1698       Vector comps = (Vector) PaintRefresher.components.get(viewport
1699               .getSequenceSetId());
1700       for (int i = 0; i < comps.size(); i++)
1701       {
1702         if (comps.elementAt(i) instanceof AlignmentPanel)
1703         {
1704           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1705           {
1706             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1707             break;
1708           }
1709         }
1710       }
1711     }
1712
1713     if (originalSource == null)
1714     {
1715       // The original view is closed, we must validate
1716       // the current view against the closed view first
1717       if (al != null)
1718       {
1719         PaintRefresher.validateSequences(al, viewport.getAlignment());
1720       }
1721
1722       originalSource = viewport;
1723     }
1724
1725     return originalSource;
1726   }
1727
1728   /**
1729    * Move the currently selected sequences up or down one position in the
1730    * alignment
1731    *
1732    * @param up
1733    */
1734   public void moveSelectedSequences(boolean up)
1735   {
1736     SequenceGroup sg = viewport.getSelectionGroup();
1737     if (sg == null)
1738     {
1739       return;
1740     }
1741     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1742             up ? null : viewport.getHiddenRepSequences(), up);
1743     alignPanel.paintAlignment(true);
1744
1745     /*
1746      * Also move cDNA/protein complement sequences
1747      */
1748     AlignViewportI complement = viewport.getCodingComplement();
1749     if (complement != null)
1750     {
1751       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1752               viewport, complement);
1753       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1754               up ? null : complement.getHiddenRepSequences(), up);
1755       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1756     }
1757   }
1758
1759   synchronized void slideSequences(boolean right, int size)
1760   {
1761     List<SequenceI> sg = new Vector<SequenceI>();
1762     if (viewport.cursorMode)
1763     {
1764       sg.add(viewport.getAlignment().getSequenceAt(
1765               alignPanel.seqPanel.seqCanvas.cursorY));
1766     }
1767     else if (viewport.getSelectionGroup() != null
1768             && viewport.getSelectionGroup().getSize() != viewport
1769                     .getAlignment().getHeight())
1770     {
1771       sg = viewport.getSelectionGroup().getSequences(
1772               viewport.getHiddenRepSequences());
1773     }
1774
1775     if (sg.size() < 1)
1776     {
1777       return;
1778     }
1779
1780     Vector<SequenceI> invertGroup = new Vector();
1781
1782     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1783     {
1784       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1785       {
1786         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1787       }
1788     }
1789
1790     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1791
1792     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1793             .size()]);
1794     for (int i = 0; i < invertGroup.size(); i++)
1795     {
1796       seqs2[i] = invertGroup.elementAt(i);
1797     }
1798
1799     SlideSequencesCommand ssc;
1800     if (right)
1801     {
1802       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1803               size, viewport.getGapCharacter());
1804     }
1805     else
1806     {
1807       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1808               size, viewport.getGapCharacter());
1809     }
1810
1811     int groupAdjustment = 0;
1812     if (ssc.getGapsInsertedBegin() && right)
1813     {
1814       if (viewport.cursorMode)
1815       {
1816         alignPanel.seqPanel.moveCursor(size, 0);
1817       }
1818       else
1819       {
1820         groupAdjustment = size;
1821       }
1822     }
1823     else if (!ssc.getGapsInsertedBegin() && !right)
1824     {
1825       if (viewport.cursorMode)
1826       {
1827         alignPanel.seqPanel.moveCursor(-size, 0);
1828       }
1829       else
1830       {
1831         groupAdjustment = -size;
1832       }
1833     }
1834
1835     if (groupAdjustment != 0)
1836     {
1837       viewport.getSelectionGroup().setStartRes(
1838               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1839       viewport.getSelectionGroup().setEndRes(
1840               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1841     }
1842
1843     boolean appendHistoryItem = false;
1844     Deque<CommandI> historyList = viewport.getHistoryList();
1845     if (historyList != null && historyList.size() > 0
1846             && historyList.peek() instanceof SlideSequencesCommand)
1847     {
1848       appendHistoryItem = ssc
1849               .appendSlideCommand((SlideSequencesCommand) historyList
1850                       .peek());
1851     }
1852
1853     if (!appendHistoryItem)
1854     {
1855       addHistoryItem(ssc);
1856     }
1857
1858     repaint();
1859   }
1860
1861   static StringBuffer copiedSequences;
1862
1863   static Vector copiedHiddenColumns;
1864
1865   protected void copy_actionPerformed()
1866   {
1867     if (viewport.getSelectionGroup() == null)
1868     {
1869       return;
1870     }
1871
1872     SequenceGroup sg = viewport.getSelectionGroup();
1873     copiedSequences = new StringBuffer();
1874     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1875     for (int i = 0; i < sg.getSize(); i++)
1876     {
1877       SequenceI seq = sg.getSequenceAt(i);
1878       int index = viewport.getAlignment().findIndex(seq);
1879       orderedSeqs.put(index, seq);
1880     }
1881
1882     int index = 0, startRes, endRes;
1883     char ch;
1884
1885     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1886     {
1887       copiedHiddenColumns = new Vector();
1888       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1889       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1890       {
1891         copiedHiddenColumns.addElement(new int[] {
1892             region[0] - hiddenOffset, region[1] - hiddenOffset });
1893       }
1894     }
1895     else
1896     {
1897       copiedHiddenColumns = null;
1898     }
1899
1900     for (int i = 0; i < sg.getSize(); i++)
1901     {
1902       SequenceI seq = null;
1903
1904       while (seq == null)
1905       {
1906         if (orderedSeqs.containsKey(index))
1907         {
1908           seq = orderedSeqs.get(index);
1909           index++;
1910           break;
1911         }
1912         else
1913         {
1914           index++;
1915         }
1916       }
1917
1918       // FIND START RES
1919       // Returns residue following index if gap
1920       startRes = seq.findPosition(sg.getStartRes());
1921
1922       // FIND END RES
1923       // Need to find the residue preceeding index if gap
1924       endRes = 0;
1925
1926       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1927       {
1928         ch = seq.getCharAt(j);
1929         if (!jalview.util.Comparison.isGap((ch)))
1930         {
1931           endRes++;
1932         }
1933       }
1934
1935       if (endRes > 0)
1936       {
1937         endRes += seq.getStart() - 1;
1938       }
1939
1940       copiedSequences.append(seq.getName()
1941               + "\t"
1942               + startRes
1943               + "\t"
1944               + endRes
1945               + "\t"
1946               + seq.getSequenceAsString(sg.getStartRes(),
1947                       sg.getEndRes() + 1) + "\n");
1948     }
1949
1950   }
1951
1952   protected void pasteNew_actionPerformed()
1953   {
1954     paste(true);
1955   }
1956
1957   protected void pasteThis_actionPerformed()
1958   {
1959     paste(false);
1960   }
1961
1962   void paste(boolean newAlignment)
1963   {
1964     try
1965     {
1966
1967       if (copiedSequences == null)
1968       {
1969         return;
1970       }
1971
1972       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1973       Vector seqs = new Vector();
1974       while (st.hasMoreElements())
1975       {
1976         String name = st.nextToken();
1977         int start = Integer.parseInt(st.nextToken());
1978         int end = Integer.parseInt(st.nextToken());
1979         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1980       }
1981       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1982       for (int i = 0; i < seqs.size(); i++)
1983       {
1984         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1985       }
1986
1987       if (newAlignment)
1988       {
1989         String newtitle = MessageManager
1990                 .getString("label.copied_sequences");
1991         if (getTitle().startsWith(
1992                 MessageManager.getString("label.copied_sequences")))
1993         {
1994           newtitle = getTitle();
1995         }
1996         else
1997         {
1998           newtitle = newtitle.concat(MessageManager.formatMessage(
1999                   "label.from_msname", new String[] { getTitle() }));
2000         }
2001         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2002                 viewport.applet, newtitle, false);
2003         if (copiedHiddenColumns != null)
2004         {
2005           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2006           {
2007             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2008             af.viewport.hideColumns(region[0], region[1]);
2009           }
2010         }
2011
2012         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2013                 frameHeight);
2014       }
2015       else
2016       {
2017         addSequences(newSeqs);
2018       }
2019
2020     } catch (Exception ex)
2021     {
2022     } // could be anything being pasted in here
2023
2024   }
2025
2026   void addSequences(SequenceI[] seqs)
2027   {
2028     for (int i = 0; i < seqs.length; i++)
2029     {
2030       viewport.getAlignment().addSequence(seqs[i]);
2031     }
2032
2033     // !newAlignment
2034     addHistoryItem(new EditCommand(
2035             MessageManager.getString("label.add_sequences"), Action.PASTE,
2036             seqs, 0, viewport.getAlignment().getWidth(),
2037             viewport.getAlignment()));
2038
2039     viewport.setEndSeq(viewport.getAlignment().getHeight());
2040     viewport.getAlignment().getWidth();
2041     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2042             .getSequences());
2043
2044   }
2045
2046   protected void cut_actionPerformed()
2047   {
2048     copy_actionPerformed();
2049     delete_actionPerformed();
2050   }
2051
2052   protected void delete_actionPerformed()
2053   {
2054
2055     SequenceGroup sg = viewport.getSelectionGroup();
2056     if (sg == null)
2057     {
2058       return;
2059     }
2060
2061     Vector seqs = new Vector();
2062     SequenceI seq;
2063     for (int i = 0; i < sg.getSize(); i++)
2064     {
2065       seq = sg.getSequenceAt(i);
2066       seqs.addElement(seq);
2067     }
2068
2069     /*
2070      * If the cut affects all sequences, warn, remove highlighted columns
2071      */
2072     if (sg.getSize() == viewport.getAlignment().getHeight())
2073     {
2074       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2075               .getAlignment().getWidth()) ? true : false;
2076       if (isEntireAlignWidth)
2077       {
2078         String title = MessageManager.getString("label.delete_all");
2079         Panel infoPanel = new Panel();
2080         infoPanel.setLayout(new FlowLayout());
2081         infoPanel
2082                 .add(new Label(MessageManager.getString("warn.delete_all")));
2083
2084         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2085         dialog.setMainPanel(infoPanel);
2086         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2087         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2088         dialog.setVisible(true);
2089
2090         if (!dialog.accept)
2091         {
2092           return;
2093         }
2094       }
2095       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2096               sg.getEndRes() + 1);
2097     }
2098
2099     SequenceI[] cut = new SequenceI[seqs.size()];
2100     for (int i = 0; i < seqs.size(); i++)
2101     {
2102       cut[i] = (SequenceI) seqs.elementAt(i);
2103     }
2104
2105     /*
2106      * //ADD HISTORY ITEM
2107      */
2108     addHistoryItem(new EditCommand(
2109             MessageManager.getString("label.cut_sequences"), Action.CUT,
2110             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2111             viewport.getAlignment()));
2112
2113     viewport.setSelectionGroup(null);
2114     viewport.getAlignment().deleteGroup(sg);
2115
2116     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2117             .getSequences());
2118
2119     if (viewport.getAlignment().getHeight() < 1)
2120     {
2121       this.setVisible(false);
2122     }
2123     viewport.sendSelection();
2124   }
2125
2126   /**
2127    * group consensus toggled
2128    *
2129    */
2130   protected void showGroupConsensus_actionPerformed()
2131   {
2132     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2133     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2134
2135   }
2136
2137   /**
2138    * group conservation toggled.
2139    */
2140   protected void showGroupConservation_actionPerformed()
2141   {
2142     viewport.setShowGroupConservation(showGroupConservation.getState());
2143     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2144   }
2145
2146   /*
2147    * (non-Javadoc)
2148    *
2149    * @see
2150    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2151    * .event.ActionEvent)
2152    */
2153   protected void showConsensusHistogram_actionPerformed()
2154   {
2155     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2156     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2157   }
2158
2159   /*
2160    * (non-Javadoc)
2161    *
2162    * @see
2163    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2164    * .event.ActionEvent)
2165    */
2166   protected void showSequenceLogo_actionPerformed()
2167   {
2168     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2169     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2170   }
2171
2172   protected void normSequenceLogo_actionPerformed()
2173   {
2174     showSequenceLogo.setState(true);
2175     viewport.setShowSequenceLogo(true);
2176     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2177     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2178   }
2179
2180   protected void applyAutoAnnotationSettings_actionPerformed()
2181   {
2182     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183   }
2184
2185   protected void makeGrpsFromSelection_actionPerformed()
2186   {
2187     if (avc.makeGroupsFromSelection())
2188     {
2189       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2190       alignPanel.updateAnnotation();
2191       alignPanel.paintAlignment(true);
2192     }
2193   }
2194
2195   protected void createGroup_actionPerformed()
2196   {
2197     avc.createGroup();
2198   }
2199
2200   protected void unGroup_actionPerformed()
2201   {
2202     if (avc.unGroup())
2203     {
2204       alignPanel.alignmentChanged();
2205     }
2206   }
2207
2208   protected void deleteGroups_actionPerformed()
2209   {
2210     if (avc.deleteGroups())
2211     {
2212       alignPanel.alignmentChanged();
2213     }
2214   }
2215
2216   public void selectAllSequenceMenuItem_actionPerformed()
2217   {
2218     SequenceGroup sg = new SequenceGroup();
2219     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2220     {
2221       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2222     }
2223     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2224     viewport.setSelectionGroup(sg);
2225     alignPanel.paintAlignment(true);
2226     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2227     viewport.sendSelection();
2228   }
2229
2230   public void deselectAllSequenceMenuItem_actionPerformed()
2231   {
2232     if (viewport.cursorMode)
2233     {
2234       alignPanel.seqPanel.keyboardNo1 = null;
2235       alignPanel.seqPanel.keyboardNo2 = null;
2236     }
2237     viewport.setSelectionGroup(null);
2238     viewport.getColumnSelection().clear();
2239     viewport.setSelectionGroup(null);
2240     alignPanel.idPanel.idCanvas.searchResults = null;
2241     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2242     alignPanel.paintAlignment(true);
2243     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2244     viewport.sendSelection();
2245   }
2246
2247   public void invertSequenceMenuItem_actionPerformed()
2248   {
2249     SequenceGroup sg = viewport.getSelectionGroup();
2250     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2251     {
2252       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2253     }
2254
2255     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2256     viewport.sendSelection();
2257   }
2258
2259   public void invertColSel_actionPerformed()
2260   {
2261     viewport.invertColumnSelection();
2262     alignPanel.paintAlignment(true);
2263     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2264     viewport.sendSelection();
2265   }
2266
2267   void trimAlignment(boolean trimLeft)
2268   {
2269     ColumnSelection colSel = viewport.getColumnSelection();
2270     int column;
2271
2272     if (colSel.size() > 0)
2273     {
2274       if (trimLeft)
2275       {
2276         column = colSel.getMin();
2277       }
2278       else
2279       {
2280         column = colSel.getMax();
2281       }
2282
2283       SequenceI[] seqs;
2284       if (viewport.getSelectionGroup() != null)
2285       {
2286         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2287                 viewport.getHiddenRepSequences());
2288       }
2289       else
2290       {
2291         seqs = viewport.getAlignment().getSequencesArray();
2292       }
2293
2294       TrimRegionCommand trimRegion;
2295       if (trimLeft)
2296       {
2297         trimRegion = new TrimRegionCommand("Remove Left",
2298                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2299                 viewport.getAlignment(), viewport.getColumnSelection(),
2300                 viewport.getSelectionGroup());
2301         viewport.setStartRes(0);
2302       }
2303       else
2304       {
2305         trimRegion = new TrimRegionCommand("Remove Right",
2306                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2307                 viewport.getAlignment(), viewport.getColumnSelection(),
2308                 viewport.getSelectionGroup());
2309       }
2310
2311       statusBar.setText(MessageManager.formatMessage(
2312               "label.removed_columns",
2313               new String[] { Integer.valueOf(trimRegion.getSize())
2314                       .toString() }));
2315       addHistoryItem(trimRegion);
2316
2317       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2318       {
2319         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2320                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2321         {
2322           viewport.getAlignment().deleteGroup(sg);
2323         }
2324       }
2325
2326       viewport.firePropertyChange("alignment", null, viewport
2327               .getAlignment().getSequences());
2328     }
2329   }
2330
2331   public void removeGappedColumnMenuItem_actionPerformed()
2332   {
2333     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2334
2335     SequenceI[] seqs;
2336     if (viewport.getSelectionGroup() != null)
2337     {
2338       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2339               viewport.getHiddenRepSequences());
2340       start = viewport.getSelectionGroup().getStartRes();
2341       end = viewport.getSelectionGroup().getEndRes();
2342     }
2343     else
2344     {
2345       seqs = viewport.getAlignment().getSequencesArray();
2346     }
2347
2348     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2349             "Remove Gapped Columns", seqs, start, end,
2350             viewport.getAlignment());
2351
2352     addHistoryItem(removeGapCols);
2353
2354     statusBar.setText(MessageManager.formatMessage(
2355             "label.removed_empty_columns",
2356             new String[] { Integer.valueOf(removeGapCols.getSize())
2357                     .toString() }));
2358
2359     // This is to maintain viewport position on first residue
2360     // of first sequence
2361     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2362     int startRes = seq.findPosition(viewport.startRes);
2363     // ShiftList shifts;
2364     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2365     // edit.alColumnChanges=shifts.getInverse();
2366     // if (viewport.hasHiddenColumns)
2367     // viewport.getColumnSelection().compensateForEdits(shifts);
2368     viewport.setStartRes(seq.findIndex(startRes) - 1);
2369     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2370             .getSequences());
2371
2372   }
2373
2374   public void removeAllGapsMenuItem_actionPerformed()
2375   {
2376     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2377
2378     SequenceI[] seqs;
2379     if (viewport.getSelectionGroup() != null)
2380     {
2381       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2382               viewport.getHiddenRepSequences());
2383       start = viewport.getSelectionGroup().getStartRes();
2384       end = viewport.getSelectionGroup().getEndRes();
2385     }
2386     else
2387     {
2388       seqs = viewport.getAlignment().getSequencesArray();
2389     }
2390
2391     // This is to maintain viewport position on first residue
2392     // of first sequence
2393     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2394     int startRes = seq.findPosition(viewport.startRes);
2395
2396     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2397             viewport.getAlignment()));
2398
2399     viewport.setStartRes(seq.findIndex(startRes) - 1);
2400
2401     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2402             .getSequences());
2403
2404   }
2405
2406   public void findMenuItem_actionPerformed()
2407   {
2408     new Finder(alignPanel);
2409   }
2410
2411   /**
2412    * create a new view derived from the current view
2413    *
2414    * @param viewtitle
2415    * @return frame for the new view
2416    */
2417   public AlignFrame newView(String viewtitle)
2418   {
2419     AlignmentI newal;
2420     if (viewport.hasHiddenRows())
2421     {
2422       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2423               .getFullAlignment().getSequencesArray());
2424     }
2425     else
2426     {
2427       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2428     }
2429
2430     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2431     {
2432       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2433       {
2434         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2435         {
2436           newal.addAnnotation(viewport.getAlignment()
2437                   .getAlignmentAnnotation()[i]);
2438         }
2439       }
2440     }
2441
2442     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2443
2444     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2445     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2446     PaintRefresher.Register(newaf.alignPanel,
2447             newaf.alignPanel.av.getSequenceSetId());
2448
2449     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2450             newaf.alignPanel.av.getSequenceSetId());
2451     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2452             newaf.alignPanel.av.getSequenceSetId());
2453
2454     Vector comps = (Vector) PaintRefresher.components.get(viewport
2455             .getSequenceSetId());
2456     int viewSize = -1;
2457     for (int i = 0; i < comps.size(); i++)
2458     {
2459       if (comps.elementAt(i) instanceof AlignmentPanel)
2460       {
2461         viewSize++;
2462       }
2463     }
2464
2465     String title = new String(this.getTitle());
2466     if (viewtitle != null)
2467     {
2468       title = viewtitle + " ( " + title + ")";
2469     }
2470     else
2471     {
2472       if (title.indexOf("(View") > -1)
2473       {
2474         title = title.substring(0, title.indexOf("(View"));
2475       }
2476       title += "(View " + viewSize + ")";
2477     }
2478
2479     newaf.setTitle(title.toString());
2480
2481     newaf.viewport.setHistoryList(viewport.getHistoryList());
2482     newaf.viewport.setRedoList(viewport.getRedoList());
2483     return newaf;
2484   }
2485
2486   /**
2487    *
2488    * @return list of feature groups on the view
2489    */
2490   public String[] getFeatureGroups()
2491   {
2492     FeatureRenderer fr = null;
2493     if (alignPanel != null
2494             && (fr = alignPanel.getFeatureRenderer()) != null)
2495     {
2496       List<String> gps = fr.getFeatureGroups();
2497       String[] _gps = gps.toArray(new String[gps.size()]);
2498       return _gps;
2499     }
2500     return null;
2501   }
2502
2503   /**
2504    * get sequence feature groups that are hidden or shown
2505    *
2506    * @param visible
2507    *          true is visible
2508    * @return list
2509    */
2510   public String[] getFeatureGroupsOfState(boolean visible)
2511   {
2512     FeatureRenderer fr = null;
2513     if (alignPanel != null
2514             && (fr = alignPanel.getFeatureRenderer()) != null)
2515     {
2516       List<String> gps = fr.getGroups(visible);
2517       String[] _gps = gps.toArray(new String[gps.size()]);
2518       return _gps;
2519     }
2520     return null;
2521   }
2522
2523   /**
2524    * Change the display state for the given feature groups
2525    *
2526    * @param groups
2527    *          list of group strings
2528    * @param state
2529    *          visible or invisible
2530    */
2531   public void setFeatureGroupState(String[] groups, boolean state)
2532   {
2533     FeatureRenderer fr = null;
2534     this.sequenceFeatures.setState(true);
2535     viewport.setShowSequenceFeatures(true);
2536     if (alignPanel != null
2537             && (fr = alignPanel.getFeatureRenderer()) != null)
2538     {
2539
2540       fr.setGroupVisibility(Arrays.asList(groups), state);
2541       alignPanel.seqPanel.seqCanvas.repaint();
2542       if (alignPanel.overviewPanel != null)
2543       {
2544         alignPanel.overviewPanel.updateOverviewImage();
2545       }
2546     }
2547   }
2548
2549   public void seqLimits_itemStateChanged()
2550   {
2551     viewport.setShowJVSuffix(seqLimits.getState());
2552     alignPanel.fontChanged();
2553     alignPanel.paintAlignment(true);
2554   }
2555
2556   protected void colourTextMenuItem_actionPerformed()
2557   {
2558     viewport.setColourText(colourTextMenuItem.getState());
2559     alignPanel.paintAlignment(true);
2560   }
2561
2562   protected void displayNonconservedMenuItem_actionPerformed()
2563   {
2564     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2565     alignPanel.paintAlignment(true);
2566   }
2567
2568   protected void wrapMenuItem_actionPerformed()
2569   {
2570     viewport.setWrapAlignment(wrapMenuItem.getState());
2571     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2572     scaleAbove.setEnabled(wrapMenuItem.getState());
2573     scaleLeft.setEnabled(wrapMenuItem.getState());
2574     scaleRight.setEnabled(wrapMenuItem.getState());
2575     alignPanel.paintAlignment(true);
2576   }
2577
2578   public void overviewMenuItem_actionPerformed()
2579   {
2580     if (alignPanel.overviewPanel != null)
2581     {
2582       return;
2583     }
2584
2585     Frame frame = new Frame();
2586     OverviewPanel overview = new OverviewPanel(alignPanel);
2587     frame.add(overview);
2588     // +50 must allow for applet frame window
2589     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2590             "label.overview_params", new String[] { this.getTitle() }),
2591             overview.getPreferredSize().width,
2592             overview.getPreferredSize().height + 50);
2593
2594     frame.pack();
2595     final AlignmentPanel ap = alignPanel;
2596     frame.addWindowListener(new WindowAdapter()
2597     {
2598       @Override
2599       public void windowClosing(WindowEvent e)
2600       {
2601         if (ap != null)
2602         {
2603           ap.setOverviewPanel(null);
2604         }
2605       };
2606     });
2607
2608     alignPanel.setOverviewPanel(overview);
2609
2610   }
2611
2612   public void changeColour(ColourSchemeI cs)
2613   {
2614
2615     if (cs != null)
2616     {
2617       if (viewport.getAbovePIDThreshold())
2618       {
2619         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2620                 cs, "Background"));
2621       }
2622
2623       if (viewport.getConservationSelected())
2624       {
2625         cs.setConservationApplied(true);
2626         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2627                 cs, "Background"));
2628       }
2629       else
2630       {
2631         cs.setConservationApplied(false);
2632       }
2633     }
2634     viewport.setGlobalColourScheme(cs);
2635
2636     alignPanel.paintAlignment(true);
2637   }
2638
2639   protected void modifyPID_actionPerformed()
2640   {
2641     if (viewport.getAbovePIDThreshold()
2642             && viewport.getGlobalColourScheme() != null)
2643     {
2644       SliderPanel.setPIDSliderSource(alignPanel,
2645               viewport.getGlobalColourScheme(), "Background");
2646       SliderPanel.showPIDSlider();
2647     }
2648   }
2649
2650   protected void modifyConservation_actionPerformed()
2651   {
2652     if (viewport.getConservationSelected()
2653             && viewport.getGlobalColourScheme() != null)
2654     {
2655       SliderPanel.setConservationSlider(alignPanel,
2656               viewport.getGlobalColourScheme(), "Background");
2657       SliderPanel.showConservationSlider();
2658     }
2659   }
2660
2661   protected void conservationMenuItem_actionPerformed()
2662   {
2663     viewport.setConservationSelected(conservationMenuItem.getState());
2664
2665     viewport.setAbovePIDThreshold(false);
2666     abovePIDThreshold.setState(false);
2667
2668     changeColour(viewport.getGlobalColourScheme());
2669
2670     modifyConservation_actionPerformed();
2671   }
2672
2673   public void abovePIDThreshold_actionPerformed()
2674   {
2675     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2676
2677     conservationMenuItem.setState(false);
2678     viewport.setConservationSelected(false);
2679
2680     changeColour(viewport.getGlobalColourScheme());
2681
2682     modifyPID_actionPerformed();
2683   }
2684
2685   public void sortPairwiseMenuItem_actionPerformed()
2686   {
2687     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2688     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2689             .getAlignment().getSequenceAt(0), null);
2690
2691     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2692             viewport.getAlignment()));
2693     alignPanel.paintAlignment(true);
2694   }
2695
2696   public void sortIDMenuItem_actionPerformed()
2697   {
2698     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2699     AlignmentSorter.sortByID(viewport.getAlignment());
2700     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2701             viewport.getAlignment()));
2702     alignPanel.paintAlignment(true);
2703   }
2704
2705   public void sortLengthMenuItem_actionPerformed()
2706   {
2707     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2708     AlignmentSorter.sortByLength(viewport.getAlignment());
2709     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2710             viewport.getAlignment()));
2711     alignPanel.paintAlignment(true);
2712   }
2713
2714   public void sortGroupMenuItem_actionPerformed()
2715   {
2716     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2717     AlignmentSorter.sortByGroup(viewport.getAlignment());
2718     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2719             viewport.getAlignment()));
2720     alignPanel.paintAlignment(true);
2721
2722   }
2723
2724   public void removeRedundancyMenuItem_actionPerformed()
2725   {
2726     new RedundancyPanel(alignPanel);
2727   }
2728
2729   public void pairwiseAlignmentMenuItem_actionPerformed()
2730   {
2731     if (viewport.getSelectionGroup() != null
2732             && viewport.getSelectionGroup().getSize() > 1)
2733     {
2734       Frame frame = new Frame();
2735       frame.add(new PairwiseAlignPanel(alignPanel));
2736       jalview.bin.JalviewLite.addFrame(frame,
2737               MessageManager.getString("action.pairwise_alignment"), 600,
2738               500);
2739     }
2740   }
2741
2742   public void PCAMenuItem_actionPerformed()
2743   {
2744     // are the sequences aligned?
2745     if (!viewport.getAlignment().isAligned(false))
2746     {
2747       SequenceI current;
2748       int Width = viewport.getAlignment().getWidth();
2749
2750       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2751       {
2752         current = viewport.getAlignment().getSequenceAt(i);
2753
2754         if (current.getLength() < Width)
2755         {
2756           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2757         }
2758       }
2759       alignPanel.paintAlignment(true);
2760     }
2761
2762     if ((viewport.getSelectionGroup() != null
2763             && viewport.getSelectionGroup().getSize() < 4 && viewport
2764             .getSelectionGroup().getSize() > 0)
2765             || viewport.getAlignment().getHeight() < 4)
2766     {
2767       return;
2768     }
2769
2770     try
2771     {
2772       new PCAPanel(viewport);
2773     } catch (java.lang.OutOfMemoryError ex)
2774     {
2775     }
2776
2777   }
2778
2779   public void averageDistanceTreeMenuItem_actionPerformed()
2780   {
2781     NewTreePanel("AV", "PID", "Average distance tree using PID");
2782   }
2783
2784   public void neighbourTreeMenuItem_actionPerformed()
2785   {
2786     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2787   }
2788
2789   protected void njTreeBlosumMenuItem_actionPerformed()
2790   {
2791     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2792   }
2793
2794   protected void avTreeBlosumMenuItem_actionPerformed()
2795   {
2796     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2797   }
2798
2799   void NewTreePanel(String type, String pwType, String title)
2800   {
2801     // are the sequences aligned?
2802     if (!viewport.getAlignment().isAligned(false))
2803     {
2804       SequenceI current;
2805       int Width = viewport.getAlignment().getWidth();
2806
2807       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2808       {
2809         current = viewport.getAlignment().getSequenceAt(i);
2810
2811         if (current.getLength() < Width)
2812         {
2813           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2814         }
2815       }
2816       alignPanel.paintAlignment(true);
2817
2818     }
2819
2820     if ((viewport.getSelectionGroup() != null && viewport
2821             .getSelectionGroup().getSize() > 1)
2822             || (viewport.getAlignment().getHeight() > 1))
2823     {
2824       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2825
2826       addTreeMenuItem(tp, title);
2827
2828       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2829     }
2830   }
2831
2832   void loadTree_actionPerformed()
2833   {
2834     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2835     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2836     cap.setTreeImport();
2837     Frame frame = new Frame();
2838     frame.add(cap);
2839     jalview.bin.JalviewLite.addFrame(frame,
2840             MessageManager.getString("label.paste_newick_file"), 400, 300);
2841   }
2842
2843   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2844   {
2845     TreePanel tp = new TreePanel(alignPanel, treeFile,
2846             MessageManager.getString("label.load_tree_from_file"), tree);
2847     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2848     addTreeMenuItem(tp, treeFile);
2849   }
2850
2851   /**
2852    * sort the alignment using the given treePanel
2853    *
2854    * @param treePanel
2855    *          tree used to sort view
2856    * @param title
2857    *          string used for undo event name
2858    */
2859   public void sortByTree(TreePanel treePanel, String title)
2860   {
2861     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2862     AlignmentSorter
2863             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2864     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2865     // HistoryItem.SORT));
2866     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2867             "label.order_by_params", new String[] { title }), oldOrder,
2868             viewport.getAlignment()));
2869     alignPanel.paintAlignment(true);
2870   }
2871
2872   /**
2873    * Do any automatic reordering of the alignment and add the necessary bits to
2874    * the menu structure for the new tree
2875    *
2876    * @param treePanel
2877    * @param title
2878    */
2879   protected void addTreeMenuItem(final TreePanel treePanel,
2880           final String title)
2881   {
2882     final MenuItem item = new MenuItem(title);
2883     sortByTreeMenu.add(item);
2884     item.addActionListener(new java.awt.event.ActionListener()
2885     {
2886       @Override
2887       public void actionPerformed(ActionEvent evt)
2888       {
2889         sortByTree(treePanel, title); // treePanel.getTitle());
2890       }
2891     });
2892
2893     treePanel.addWindowListener(new WindowAdapter()
2894     {
2895       @Override
2896       public void windowOpened(WindowEvent e)
2897       {
2898         if (viewport.sortByTree)
2899         {
2900           sortByTree(treePanel, title);
2901         }
2902         super.windowOpened(e);
2903       }
2904
2905       @Override
2906       public void windowClosing(WindowEvent e)
2907       {
2908         sortByTreeMenu.remove(item);
2909       };
2910     });
2911   }
2912
2913   public boolean sortBy(AlignmentOrder alorder, String undoname)
2914   {
2915     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2916     if (viewport.applet.debug)
2917     {
2918       System.err.println("Sorting " + alorder.getOrder().size()
2919               + " in alignment '" + getTitle() + "'");
2920     }
2921     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2922     if (undoname != null)
2923     {
2924       addHistoryItem(new OrderCommand(undoname, oldOrder,
2925               viewport.getAlignment()));
2926     }
2927     alignPanel.paintAlignment(true);
2928     return true;
2929   }
2930
2931   protected void documentation_actionPerformed()
2932   {
2933     alignPanel.av.applet.openJalviewHelpUrl();
2934   }
2935
2936   protected void about_actionPerformed()
2937   {
2938
2939     class AboutPanel extends Canvas
2940     {
2941       String version;
2942
2943       String builddate;
2944
2945       public AboutPanel(String version, String builddate)
2946       {
2947         this.version = version;
2948         this.builddate = builddate;
2949       }
2950
2951       @Override
2952       public void paint(Graphics g)
2953       {
2954         g.setColor(Color.white);
2955         g.fillRect(0, 0, getSize().width, getSize().height);
2956         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2957         FontMetrics fm = g.getFontMetrics();
2958         int fh = fm.getHeight();
2959         int y = 5, x = 7;
2960         g.setColor(Color.black);
2961         // TODO: update this text for each release or centrally store it for
2962         // lite and application
2963         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2964         g.drawString(MessageManager.formatMessage(
2965                 "label.jalviewLite_release", new String[] { version }), x,
2966                 y += fh);
2967         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2968         g.drawString(MessageManager.formatMessage(
2969                 "label.jaview_build_date", new String[] { builddate }), x,
2970                 y += fh);
2971         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2972         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2973                 x, y += fh * 1.5);
2974         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2975                 x + 50, y += fh + 8);
2976         g.drawString(
2977                 MessageManager.getString("label.jalview_dev_managers"), x,
2978                 y += fh);
2979         g.drawString(MessageManager
2980                 .getString("label.jalview_distribution_lists"), x, y += fh);
2981         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2982                 x, y += fh + 8);
2983         g.drawString(
2984                 MessageManager.getString("label.jalview_cite_1_authors"),
2985                 x, y += fh);
2986         g.drawString(
2987                 MessageManager.getString("label.jalview_cite_1_title"), x,
2988                 y += fh);
2989         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2990                 x, y += fh);
2991       }
2992     }
2993
2994     Frame frame = new Frame();
2995     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2996             .getBuildDate()));
2997     jalview.bin.JalviewLite.addFrame(frame,
2998             MessageManager.getString("label.jalview"), 580, 220);
2999
3000   }
3001
3002   public void showURL(String url, String target)
3003   {
3004     if (viewport.applet == null)
3005     {
3006       System.out.println("Not running as applet - no browser available.");
3007     }
3008     else
3009     {
3010       viewport.applet.showURL(url, target);
3011     }
3012   }
3013
3014   // ////////////////////////////////////////////////////////////////////////////////
3015   // JBuilder Graphics here
3016
3017   MenuBar alignFrameMenuBar = new MenuBar();
3018
3019   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3020
3021   MenuItem loadApplication = new MenuItem(
3022           MessageManager.getString("label.view_full_application"));
3023
3024   MenuItem loadTree = new MenuItem(
3025           MessageManager.getString("label.load_associated_tree"));
3026
3027   MenuItem loadAnnotations = new MenuItem(
3028           MessageManager.getString("label.load_features_annotations"));
3029
3030   MenuItem outputFeatures = new MenuItem(
3031           MessageManager.getString("label.export_features"));
3032
3033   MenuItem outputAnnotations = new MenuItem(
3034           MessageManager.getString("label.export_annotations"));
3035
3036   MenuItem closeMenuItem = new MenuItem(
3037           MessageManager.getString("action.close"));
3038
3039   MenuItem selectAllSequenceMenuItem = new MenuItem(
3040           MessageManager.getString("action.select_all"));
3041
3042   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3043           MessageManager.getString("action.deselect_all"));
3044
3045   MenuItem invertSequenceMenuItem = new MenuItem(
3046           MessageManager.getString("action.invert_selection"));
3047
3048   MenuItem remove2LeftMenuItem = new MenuItem();
3049
3050   MenuItem remove2RightMenuItem = new MenuItem();
3051
3052   MenuItem removeGappedColumnMenuItem = new MenuItem();
3053
3054   MenuItem removeAllGapsMenuItem = new MenuItem();
3055
3056   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3057
3058   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3059
3060   MenuItem sortPairwiseMenuItem = new MenuItem();
3061
3062   MenuItem sortIDMenuItem = new MenuItem();
3063
3064   MenuItem sortLengthMenuItem = new MenuItem();
3065
3066   MenuItem sortGroupMenuItem = new MenuItem();
3067
3068   MenuItem removeRedundancyMenuItem = new MenuItem();
3069
3070   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3071
3072   MenuItem PCAMenuItem = new MenuItem();
3073
3074   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3075
3076   MenuItem neighbourTreeMenuItem = new MenuItem();
3077
3078   BorderLayout borderLayout1 = new BorderLayout();
3079
3080   public Label statusBar = new Label();
3081
3082   MenuItem clustalColour = new MenuItem();
3083
3084   MenuItem zappoColour = new MenuItem();
3085
3086   MenuItem taylorColour = new MenuItem();
3087
3088   MenuItem hydrophobicityColour = new MenuItem();
3089
3090   MenuItem helixColour = new MenuItem();
3091
3092   MenuItem strandColour = new MenuItem();
3093
3094   MenuItem turnColour = new MenuItem();
3095
3096   MenuItem buriedColour = new MenuItem();
3097
3098   MenuItem purinePyrimidineColour = new MenuItem();
3099
3100   // MenuItem RNAInteractionColour = new MenuItem();
3101
3102   MenuItem RNAHelixColour = new MenuItem();
3103
3104   MenuItem userDefinedColour = new MenuItem();
3105
3106   MenuItem PIDColour = new MenuItem();
3107
3108   MenuItem BLOSUM62Colour = new MenuItem();
3109
3110   MenuItem tcoffeeColour = new MenuItem();
3111
3112   MenuItem njTreeBlosumMenuItem = new MenuItem();
3113
3114   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3115
3116   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3117
3118   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3119
3120   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3121
3122   MenuItem alProperties = new MenuItem(
3123           MessageManager.getString("label.alignment_props"));
3124
3125   MenuItem overviewMenuItem = new MenuItem();
3126
3127   MenuItem undoMenuItem = new MenuItem();
3128
3129   MenuItem redoMenuItem = new MenuItem();
3130
3131   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3132
3133   MenuItem noColourmenuItem = new MenuItem();
3134
3135   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3136
3137   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3138
3139   MenuItem findMenuItem = new MenuItem();
3140
3141   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3142
3143   MenuItem nucleotideColour = new MenuItem();
3144
3145   MenuItem deleteGroups = new MenuItem();
3146
3147   MenuItem grpsFromSelection = new MenuItem();
3148
3149   MenuItem createGroup = new MenuItem();
3150
3151   MenuItem unGroup = new MenuItem();
3152
3153   MenuItem delete = new MenuItem();
3154
3155   MenuItem copy = new MenuItem();
3156
3157   MenuItem cut = new MenuItem();
3158
3159   Menu pasteMenu = new Menu();
3160
3161   MenuItem pasteNew = new MenuItem();
3162
3163   MenuItem pasteThis = new MenuItem();
3164
3165   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3166
3167   MenuItem font = new MenuItem();
3168
3169   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3170
3171   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3174
3175   MenuItem modifyPID = new MenuItem();
3176
3177   MenuItem modifyConservation = new MenuItem();
3178
3179   CheckboxMenuItem autoCalculate = null;
3180
3181   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3182           "Sort Alignment With New Tree", true);
3183
3184   Menu sortByTreeMenu = new Menu();
3185
3186   MenuItem inputText = new MenuItem();
3187
3188   MenuItem documentation = new MenuItem();
3189
3190   MenuItem about = new MenuItem();
3191
3192   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3193
3194   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3195
3196   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3197
3198   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3199
3200   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3201
3202   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3203
3204   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3205
3206   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3209
3210   /**
3211    * Initialise menus and other items
3212    *
3213    * @throws Exception
3214    */
3215   private void jbInit() throws Exception
3216   {
3217     setMenuBar(alignFrameMenuBar);
3218
3219     /*
3220      * Configure File menu items and actions
3221      */
3222     inputText
3223             .setLabel(MessageManager.getString("label.input_from_textbox"));
3224     inputText.addActionListener(this);
3225     Menu outputTextboxMenu = new Menu(
3226             MessageManager.getString("label.out_to_textbox"));
3227     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3228     {
3229
3230       MenuItem item = new MenuItem(
3231               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3232
3233       item.addActionListener(new java.awt.event.ActionListener()
3234       {
3235         @Override
3236         public void actionPerformed(ActionEvent e)
3237         {
3238           outputText_actionPerformed(e);
3239         }
3240       });
3241
3242       outputTextboxMenu.add(item);
3243     }
3244     closeMenuItem.addActionListener(this);
3245     loadApplication.addActionListener(this);
3246     loadTree.addActionListener(this);
3247     loadAnnotations.addActionListener(this);
3248     outputFeatures.addActionListener(this);
3249     outputAnnotations.addActionListener(this);
3250
3251     /*
3252      * Configure Edit menu items and actions
3253      */
3254     undoMenuItem.setEnabled(false);
3255     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3256     undoMenuItem.addActionListener(this);
3257     redoMenuItem.setEnabled(false);
3258     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3259     redoMenuItem.addActionListener(this);
3260     copy.setLabel(MessageManager.getString("action.copy"));
3261     copy.addActionListener(this);
3262     cut.setLabel(MessageManager.getString("action.cut"));
3263     cut.addActionListener(this);
3264     delete.setLabel(MessageManager.getString("action.delete"));
3265     delete.addActionListener(this);
3266     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3267     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3268     pasteNew.addActionListener(this);
3269     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3270     pasteThis.addActionListener(this);
3271     remove2LeftMenuItem.setLabel(MessageManager
3272             .getString("action.remove_left"));
3273     remove2LeftMenuItem.addActionListener(this);
3274     remove2RightMenuItem.setLabel(MessageManager
3275             .getString("action.remove_right"));
3276     remove2RightMenuItem.addActionListener(this);
3277     removeGappedColumnMenuItem.setLabel(MessageManager
3278             .getString("action.remove_empty_columns"));
3279     removeGappedColumnMenuItem.addActionListener(this);
3280     removeAllGapsMenuItem.setLabel(MessageManager
3281             .getString("action.remove_all_gaps"));
3282     removeAllGapsMenuItem.addActionListener(this);
3283     removeRedundancyMenuItem.setLabel(MessageManager
3284             .getString("action.remove_redundancy"));
3285     removeRedundancyMenuItem.addActionListener(this);
3286
3287     /*
3288      * Configure Select menu items and actions
3289      */
3290     findMenuItem.setLabel(MessageManager.getString("action.find"));
3291     findMenuItem.addActionListener(this);
3292     selectAllSequenceMenuItem.addActionListener(this);
3293     deselectAllSequenceMenuItem.addActionListener(this);
3294     invertSequenceMenuItem.setLabel(MessageManager
3295             .getString("action.invert_sequence_selection"));
3296     invertSequenceMenuItem.addActionListener(this);
3297     invertColSel.setLabel(MessageManager
3298             .getString("action.invert_column_selection"));
3299     invertColSel.addActionListener(this);
3300     deleteGroups.setLabel(MessageManager
3301             .getString("action.undefine_groups"));
3302     deleteGroups.addActionListener(this);
3303     grpsFromSelection.setLabel(MessageManager
3304             .getString("action.make_groups_selection"));
3305     grpsFromSelection.addActionListener(this);
3306     createGroup.setLabel(MessageManager.getString("action.create_group"));
3307     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3308     annotationColumnSelection.setLabel(MessageManager
3309             .getString("action.select_by_annotation"));
3310     annotationColumnSelection.addActionListener(this);
3311
3312     /*
3313      * Configure View menu items and actions
3314      */
3315     newView.setLabel(MessageManager.getString("action.new_view"));
3316     newView.addActionListener(this);
3317     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3318     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3319     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3320     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3321     hideColumns
3322             .setLabel(MessageManager.getString("label.selected_columns"));
3323     hideSequences.setLabel(MessageManager
3324             .getString("label.selected_sequences"));
3325     hideAllButSelection.setLabel(MessageManager
3326             .getString("label.all_but_selected_region"));
3327     hideAllSelection.setLabel(MessageManager
3328             .getString("label.selected_region"));
3329     showAllHidden.setLabel(MessageManager
3330             .getString("label.all_sequences_columns"));
3331     showColumns.addActionListener(this);
3332     showSeqs.addActionListener(this);
3333     hideColumns.addActionListener(this);
3334     hideSequences.addActionListener(this);
3335     hideAllButSelection.addActionListener(this);
3336     hideAllSelection.addActionListener(this);
3337     showAllHidden.addActionListener(this);
3338     featureSettings.setLabel(MessageManager
3339             .getString("action.feature_settings"));
3340     featureSettings.addActionListener(this);
3341     sequenceFeatures.setLabel(MessageManager
3342             .getString("label.show_sequence_features"));
3343     sequenceFeatures.addItemListener(this);
3344     sequenceFeatures.setState(false);
3345     followMouseOverFlag.setLabel(MessageManager
3346             .getString("label.automatic_scrolling"));
3347     followMouseOverFlag.addItemListener(this);
3348     alProperties.addActionListener(this);
3349     overviewMenuItem.setLabel(MessageManager
3350             .getString("label.overview_window"));
3351     overviewMenuItem.addActionListener(this);
3352
3353     /*
3354      * Configure Annotations menu items and actions
3355      */
3356     annotationPanelMenuItem.setLabel(MessageManager
3357             .getString("label.show_annotations"));
3358     annotationPanelMenuItem.addItemListener(this);
3359     showGroupConsensus.setLabel(MessageManager
3360             .getString("label.group_consensus"));
3361     showGroupConservation.setLabel(MessageManager
3362             .getString("label.group_conservation"));
3363     showConsensusHistogram.setLabel(MessageManager
3364             .getString("label.show_consensus_histogram"));
3365     showSequenceLogo.setLabel(MessageManager
3366             .getString("label.show_consensus_logo"));
3367     normSequenceLogo.setLabel(MessageManager
3368             .getString("label.norm_consensus_logo"));
3369     applyAutoAnnotationSettings.setLabel(MessageManager
3370             .getString("label.apply_all_groups"));
3371     applyAutoAnnotationSettings.setState(true);
3372     Menu autoAnnMenu = new Menu(
3373             MessageManager.getString("label.autocalculated_annotation"));
3374     showGroupConsensus.addItemListener(this);
3375     showGroupConservation.addItemListener(this);
3376     showConsensusHistogram.addItemListener(this);
3377     showSequenceLogo.addItemListener(this);
3378     normSequenceLogo.addItemListener(this);
3379     applyAutoAnnotationSettings.addItemListener(this);
3380     showAlignmentAnnotations = new CheckboxMenuItem(
3381             MessageManager.getString("label.show_all_al_annotations"));
3382     showSequenceAnnotations = new CheckboxMenuItem(
3383             MessageManager.getString("label.show_all_seq_annotations"));
3384     sortAnnBySequence = new CheckboxMenuItem(
3385             MessageManager.getString("label.sort_annotations_by_sequence"));
3386     sortAnnByLabel = new CheckboxMenuItem(
3387             MessageManager.getString("label.sort_annotations_by_label"));
3388     showAutoFirst = new CheckboxMenuItem(
3389             MessageManager.getString("label.show_first"));
3390     showAutoFirst.setState(false); // pending applet parameter
3391     setShowAutoCalculatedAbove(showAutoFirst.getState());
3392     showAutoLast = new CheckboxMenuItem(
3393             MessageManager.getString("label.show_last"));
3394     showAutoLast.setState(!showAutoFirst.getState());
3395     showAlignmentAnnotations.addItemListener(this);
3396     showSequenceAnnotations.addItemListener(this);
3397     sortAnnBySequence.addItemListener(this);
3398     sortAnnByLabel.addItemListener(this);
3399     showAutoFirst.addItemListener(this);
3400     showAutoLast.addItemListener(this);
3401
3402     /*
3403      * Configure Format menu items and actions
3404      */
3405     font.setLabel(MessageManager.getString("action.font"));
3406     font.addActionListener(this);
3407     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3408     scaleAbove.setState(true);
3409     scaleAbove.setEnabled(false);
3410     scaleAbove.addItemListener(this);
3411     scaleLeft.setEnabled(false);
3412     scaleLeft.setState(true);
3413     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3414     scaleLeft.addItemListener(this);
3415     scaleRight.setEnabled(false);
3416     scaleRight.setState(true);
3417     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3418     scaleRight.addItemListener(this);
3419     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3420     viewBoxesMenuItem.setState(true);
3421     viewBoxesMenuItem.addItemListener(this);
3422     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3423     viewTextMenuItem.setState(true);
3424     viewTextMenuItem.addItemListener(this);
3425     colourTextMenuItem.setLabel(MessageManager
3426             .getString("label.colour_text"));
3427     colourTextMenuItem.addItemListener(this);
3428     displayNonconservedMenuItem.setLabel(MessageManager
3429             .getString("label.show_non_conversed"));
3430     displayNonconservedMenuItem.addItemListener(this);
3431     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3432     wrapMenuItem.addItemListener(this);
3433     renderGapsMenuItem.setLabel(MessageManager
3434             .getString("action.show_gaps"));
3435     renderGapsMenuItem.setState(true);
3436     renderGapsMenuItem.addItemListener(this);
3437     centreColumnLabelFlag.setLabel(MessageManager
3438             .getString("label.centre_column_labels"));
3439     centreColumnLabelFlag.addItemListener(this);
3440     seqLimits.setState(true);
3441     seqLimits.setLabel(MessageManager
3442             .getString("label.show_sequence_limits"));
3443     seqLimits.addItemListener(this);
3444
3445     /*
3446      * Configure Colour menu items and actions
3447      */
3448     applyToAllGroups.setLabel(MessageManager
3449             .getString("label.apply_colour_to_all_groups"));
3450     applyToAllGroups.setState(true);
3451     applyToAllGroups.addItemListener(this);
3452     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3453     clustalColour.addActionListener(this);
3454     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3455     zappoColour.addActionListener(this);
3456     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3457     taylorColour.addActionListener(this);
3458     hydrophobicityColour.setLabel(MessageManager
3459             .getString("label.hydrophobicity"));
3460     hydrophobicityColour.addActionListener(this);
3461     helixColour
3462             .setLabel(MessageManager.getString("label.helix_propensity"));
3463     helixColour.addActionListener(this);
3464     strandColour.setLabel(MessageManager
3465             .getString("label.strand_propensity"));
3466     strandColour.addActionListener(this);
3467     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3468     turnColour.addActionListener(this);
3469     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3470     buriedColour.addActionListener(this);
3471     purinePyrimidineColour.setLabel(MessageManager
3472             .getString("label.purine_pyrimidine"));
3473     purinePyrimidineColour.addActionListener(this);
3474     // RNAInteractionColour.setLabel(MessageManager
3475     // .getString("label.rna_interaction"));
3476     // RNAInteractionColour.addActionListener(this);
3477     RNAHelixColour.setLabel(MessageManager
3478             .getString("action.by_rna_helixes"));
3479     RNAHelixColour.addActionListener(this);
3480     userDefinedColour.setLabel(MessageManager
3481             .getString("action.user_defined"));
3482     userDefinedColour.addActionListener(this);
3483     PIDColour.setLabel(MessageManager
3484             .getString("label.percentage_identity"));
3485     PIDColour.addActionListener(this);
3486     BLOSUM62Colour.setLabel(MessageManager
3487             .getString("label.blosum62_score"));
3488     BLOSUM62Colour.addActionListener(this);
3489     tcoffeeColour
3490             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3491     // it will be enabled only if a score file is provided
3492     tcoffeeColour.setEnabled(false);
3493     tcoffeeColour.addActionListener(this);
3494     conservationMenuItem.setLabel(MessageManager
3495             .getString("action.by_conservation"));
3496     conservationMenuItem.addItemListener(this);
3497     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3498     noColourmenuItem.addActionListener(this);
3499     abovePIDThreshold.setLabel(MessageManager
3500             .getString("label.above_identity_threshold"));
3501     abovePIDThreshold.addItemListener(this);
3502     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3503     nucleotideColour.addActionListener(this);
3504     modifyPID.setLabel(MessageManager
3505             .getString("label.modify_identity_thereshold"));
3506     modifyPID.addActionListener(this);
3507     modifyConservation.setLabel(MessageManager
3508             .getString("label.modify_conservation_thereshold"));
3509     modifyConservation.addActionListener(this);
3510     annotationColour.setLabel(MessageManager
3511             .getString("action.by_annotation"));
3512     annotationColour.addActionListener(this);
3513
3514     /*
3515      * Configure Calculate menu items and actions
3516      */
3517     sortPairwiseMenuItem.setLabel(MessageManager
3518             .getString("action.by_pairwise_id"));
3519     sortPairwiseMenuItem.addActionListener(this);
3520     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3521     sortIDMenuItem.addActionListener(this);
3522     sortLengthMenuItem.setLabel(MessageManager
3523             .getString("action.by_length"));
3524     sortLengthMenuItem.addActionListener(this);
3525     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3526     sortGroupMenuItem.addActionListener(this);
3527     pairwiseAlignmentMenuItem.setLabel(MessageManager
3528             .getString("action.pairwise_alignment"));
3529     pairwiseAlignmentMenuItem.addActionListener(this);
3530     PCAMenuItem.setLabel(MessageManager
3531             .getString("label.principal_component_analysis"));
3532     PCAMenuItem.addActionListener(this);
3533     autoCalculate = new CheckboxMenuItem(
3534             MessageManager.getString("label.autocalculate_consensus"), true);
3535     averageDistanceTreeMenuItem.setLabel(MessageManager
3536             .getString("label.average_distance_identity"));
3537     averageDistanceTreeMenuItem.addActionListener(this);
3538     neighbourTreeMenuItem.setLabel(MessageManager
3539             .getString("label.neighbour_joining_identity"));
3540     neighbourTreeMenuItem.addActionListener(this);
3541     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3542             .getString("label.average_distance_bloslum62"));
3543     avDistanceTreeBlosumMenuItem.addActionListener(this);
3544     njTreeBlosumMenuItem.setLabel(MessageManager
3545             .getString("label.neighbour_blosum62"));
3546     njTreeBlosumMenuItem.addActionListener(this);
3547     sortByTreeMenu.setLabel(MessageManager
3548             .getString("action.by_tree_order"));
3549     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3550     Menu calculateTreeMenu = new Menu(
3551             MessageManager.getString("action.calculate_tree"));
3552     autoCalculate.addItemListener(this);
3553     sortByTree.addItemListener(this);
3554
3555     /*
3556      * Configure Help menu items and actions
3557      */
3558     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3559     documentation.setLabel(MessageManager.getString("label.documentation"));
3560     documentation.addActionListener(this);
3561     about.setLabel(MessageManager.getString("label.about"));
3562     about.addActionListener(this);
3563
3564     /*
3565      * Add top level menus to frame
3566      */
3567     alignFrameMenuBar.add(fileMenu);
3568     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3569     alignFrameMenuBar.add(editMenu);
3570     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3571     alignFrameMenuBar.add(selectMenu);
3572     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3573     alignFrameMenuBar.add(viewMenu);
3574     Menu annotationsMenu = new Menu(
3575             MessageManager.getString("action.annotations"));
3576     alignFrameMenuBar.add(annotationsMenu);
3577     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3578     alignFrameMenuBar.add(formatMenu);
3579     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3580     alignFrameMenuBar.add(colourMenu);
3581     Menu calculateMenu = new Menu(
3582             MessageManager.getString("action.calculate"));
3583     alignFrameMenuBar.add(calculateMenu);
3584     alignFrameMenuBar.add(helpMenu);
3585
3586     /*
3587      * File menu
3588      */
3589     fileMenu.add(inputText);
3590     fileMenu.add(loadTree);
3591     fileMenu.add(loadAnnotations);
3592     fileMenu.addSeparator();
3593     fileMenu.add(outputTextboxMenu);
3594     fileMenu.add(outputFeatures);
3595     fileMenu.add(outputAnnotations);
3596     if (jalviewServletURL != null)
3597     {
3598       fileMenu.add(loadApplication);
3599     }
3600     fileMenu.addSeparator();
3601     fileMenu.add(closeMenuItem);
3602
3603     /*
3604      * Edit menu
3605      */
3606     editMenu.add(undoMenuItem);
3607     editMenu.add(redoMenuItem);
3608     editMenu.add(cut);
3609     editMenu.add(copy);
3610     pasteMenu.add(pasteNew);
3611     pasteMenu.add(pasteThis);
3612     editMenu.add(pasteMenu);
3613     editMenu.add(delete);
3614     editMenu.addSeparator();
3615     editMenu.add(remove2LeftMenuItem);
3616     editMenu.add(remove2RightMenuItem);
3617     editMenu.add(removeGappedColumnMenuItem);
3618     editMenu.add(removeAllGapsMenuItem);
3619     editMenu.add(removeRedundancyMenuItem);
3620
3621     /*
3622      * Select menu
3623      */
3624     selectMenu.add(findMenuItem);
3625     selectMenu.addSeparator();
3626     selectMenu.add(selectAllSequenceMenuItem);
3627     selectMenu.add(deselectAllSequenceMenuItem);
3628     selectMenu.add(invertSequenceMenuItem);
3629     selectMenu.add(invertColSel);
3630     selectMenu.add(createGroup);
3631     selectMenu.add(unGroup);
3632     selectMenu.add(grpsFromSelection);
3633     selectMenu.add(deleteGroups);
3634     selectMenu.add(annotationColumnSelection);
3635
3636     /*
3637      * View menu
3638      */
3639     viewMenu.add(newView);
3640     viewMenu.addSeparator();
3641     showMenu.add(showColumns);
3642     showMenu.add(showSeqs);
3643     showMenu.add(showAllHidden);
3644     viewMenu.add(showMenu);
3645     hideMenu.add(hideColumns);
3646     hideMenu.add(hideSequences);
3647     hideMenu.add(hideAllSelection);
3648     hideMenu.add(hideAllButSelection);
3649     viewMenu.add(hideMenu);
3650     viewMenu.addSeparator();
3651     viewMenu.add(followMouseOverFlag);
3652     viewMenu.addSeparator();
3653     viewMenu.add(sequenceFeatures);
3654     viewMenu.add(featureSettings);
3655     viewMenu.addSeparator();
3656     viewMenu.add(alProperties);
3657     viewMenu.addSeparator();
3658     viewMenu.add(overviewMenuItem);
3659
3660     /*
3661      * Annotations menu
3662      */
3663     annotationsMenu.add(annotationPanelMenuItem);
3664     annotationsMenu.addSeparator();
3665     annotationsMenu.add(showAlignmentAnnotations);
3666     annotationsMenu.add(showSequenceAnnotations);
3667     annotationsMenu.add(sortAnnBySequence);
3668     annotationsMenu.add(sortAnnByLabel);
3669     annotationsMenu.addSeparator();
3670     autoAnnMenu.add(showAutoFirst);
3671     autoAnnMenu.add(showAutoLast);
3672     autoAnnMenu.addSeparator();
3673     autoAnnMenu.add(applyAutoAnnotationSettings);
3674     autoAnnMenu.add(showConsensusHistogram);
3675     autoAnnMenu.add(showSequenceLogo);
3676     autoAnnMenu.add(normSequenceLogo);
3677     autoAnnMenu.addSeparator();
3678     autoAnnMenu.add(showGroupConservation);
3679     autoAnnMenu.add(showGroupConsensus);
3680     annotationsMenu.add(autoAnnMenu);
3681
3682     /*
3683      * Format menu
3684      */
3685     formatMenu.add(font);
3686     formatMenu.add(seqLimits);
3687     formatMenu.add(wrapMenuItem);
3688     formatMenu.add(scaleAbove);
3689     formatMenu.add(scaleLeft);
3690     formatMenu.add(scaleRight);
3691     formatMenu.add(viewBoxesMenuItem);
3692     formatMenu.add(viewTextMenuItem);
3693     formatMenu.add(colourTextMenuItem);
3694     formatMenu.add(displayNonconservedMenuItem);
3695     formatMenu.add(renderGapsMenuItem);
3696     formatMenu.add(centreColumnLabelFlag);
3697
3698     /*
3699      * Colour menu
3700      */
3701     colourMenu.add(applyToAllGroups);
3702     colourMenu.addSeparator();
3703     colourMenu.add(noColourmenuItem);
3704     colourMenu.add(clustalColour);
3705     colourMenu.add(BLOSUM62Colour);
3706     colourMenu.add(PIDColour);
3707     colourMenu.add(zappoColour);
3708     colourMenu.add(taylorColour);
3709     colourMenu.add(hydrophobicityColour);
3710     colourMenu.add(helixColour);
3711     colourMenu.add(strandColour);
3712     colourMenu.add(turnColour);
3713     colourMenu.add(buriedColour);
3714     colourMenu.add(nucleotideColour);
3715     colourMenu.add(purinePyrimidineColour);
3716     // colourMenu.add(RNAInteractionColour);
3717     colourMenu.add(tcoffeeColour);
3718     colourMenu.add(userDefinedColour);
3719     colourMenu.addSeparator();
3720     colourMenu.add(conservationMenuItem);
3721     colourMenu.add(modifyConservation);
3722     colourMenu.add(abovePIDThreshold);
3723     colourMenu.add(modifyPID);
3724     colourMenu.add(annotationColour);
3725     colourMenu.add(RNAHelixColour);
3726
3727     /*
3728      * Calculate menu
3729      */
3730     sortMenu.add(sortIDMenuItem);
3731     sortMenu.add(sortLengthMenuItem);
3732     sortMenu.add(sortByTreeMenu);
3733     sortMenu.add(sortGroupMenuItem);
3734     sortMenu.add(sortPairwiseMenuItem);
3735     calculateMenu.add(sortMenu);
3736     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3737     calculateTreeMenu.add(neighbourTreeMenuItem);
3738     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3739     calculateTreeMenu.add(njTreeBlosumMenuItem);
3740     calculateMenu.add(calculateTreeMenu);
3741     calculateMenu.addSeparator();
3742     calculateMenu.add(pairwiseAlignmentMenuItem);
3743     calculateMenu.add(PCAMenuItem);
3744     calculateMenu.add(autoCalculate);
3745     calculateMenu.add(sortByTree);
3746
3747     /*
3748      * Help menu
3749      */
3750     helpMenu.add(documentation);
3751     helpMenu.add(about);
3752
3753     /*
3754      * Status bar
3755      */
3756     statusBar.setBackground(Color.white);
3757     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3758     statusBar.setText(MessageManager.getString("label.status_bar"));
3759     this.add(statusBar, BorderLayout.SOUTH);
3760   }
3761
3762   public void setStatus(String string)
3763   {
3764     statusBar.setText(string);
3765   };
3766
3767   MenuItem featureSettings = new MenuItem();
3768
3769   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3770
3771   MenuItem annotationColour = new MenuItem();
3772
3773   MenuItem annotationColumnSelection = new MenuItem();
3774
3775   MenuItem invertColSel = new MenuItem();
3776
3777   MenuItem showColumns = new MenuItem();
3778
3779   MenuItem showSeqs = new MenuItem();
3780
3781   MenuItem hideColumns = new MenuItem();
3782
3783   MenuItem hideSequences = new MenuItem();
3784
3785   MenuItem hideAllButSelection = new MenuItem();
3786
3787   MenuItem hideAllSelection = new MenuItem();
3788
3789   MenuItem showAllHidden = new MenuItem();
3790
3791   MenuItem newView = new MenuItem();
3792
3793   private CheckboxMenuItem showAlignmentAnnotations;
3794
3795   private CheckboxMenuItem showSequenceAnnotations;
3796
3797   private CheckboxMenuItem sortAnnBySequence;
3798
3799   private CheckboxMenuItem sortAnnByLabel;
3800
3801   private CheckboxMenuItem showAutoFirst;
3802
3803   private CheckboxMenuItem showAutoLast;
3804
3805   private SplitFrame splitFrame;
3806
3807   /**
3808    * Attach the alignFrame panels after embedding menus, if necessary. This used
3809    * to be called setEmbedded, but is now creates the dropdown menus in a
3810    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3811    *
3812    * @param reallyEmbedded
3813    *          true to attach the view to the applet area on the page rather than
3814    *          in a new window
3815    */
3816   public void createAlignFrameWindow(boolean reallyEmbedded)
3817   {
3818     if (reallyEmbedded)
3819     {
3820       embedAlignFrameInApplet(viewport.applet);
3821     }
3822     else
3823     {
3824       // //////
3825       // test and embed menu bar if necessary.
3826       //
3827       if (embedMenuIfNeeded(alignPanel))
3828       {
3829         /*
3830          * adjust for status bar height too. ? pointless as overridden by layout
3831          * manager
3832          */
3833         alignPanel.setSize(getSize().width,
3834                 getSize().height - statusBar.getHeight());
3835       }
3836       add(statusBar, BorderLayout.SOUTH);
3837       add(alignPanel, BorderLayout.CENTER);
3838       // and register with the applet so it can pass external API calls to us
3839       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3840               frameHeight);
3841     }
3842   }
3843
3844   /**
3845    * Add the components of this AlignFrame to the applet container.
3846    *
3847    * @param theApplet
3848    */
3849   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3850   {
3851     // ////
3852     // Explicitly build the embedded menu panel for the on-page applet
3853     //
3854     // view cannot be closed if its actually on the page
3855     fileMenu.remove(closeMenuItem);
3856     fileMenu.remove(3); // Remove Separator
3857     // construct embedded menu, using default font
3858     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3859     // and actually add the components to the applet area
3860     theApplet.setLayout(new BorderLayout());
3861     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3862     theApplet.add(statusBar, BorderLayout.SOUTH);
3863     // TODO should size be left to the layout manager?
3864     alignPanel.setSize(theApplet.getSize().width,
3865             theApplet.getSize().height - embeddedMenu.getHeight()
3866                     - statusBar.getHeight());
3867     theApplet.add(alignPanel, BorderLayout.CENTER);
3868     final AlignFrame me = this;
3869     theApplet.addFocusListener(new FocusListener()
3870     {
3871
3872       @Override
3873       public void focusLost(FocusEvent e)
3874       {
3875         if (theApplet.currentAlignFrame == me)
3876         {
3877           theApplet.currentAlignFrame = null;
3878         }
3879       }
3880
3881       @Override
3882       public void focusGained(FocusEvent e)
3883       {
3884         theApplet.currentAlignFrame = me;
3885       }
3886     });
3887     theApplet.validate();
3888   }
3889
3890   /**
3891    * create a new binding between structures in an existing jmol viewer instance
3892    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3893    * this does not open a new Jmol window, or modify the display of the
3894    * structures in the original jmol window. Note This method doesn't work
3895    * without an additional javascript library to exchange messages between the
3896    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3897    *
3898    * @param viewer
3899    *          JmolViewer instance
3900    * @param sequenceIds
3901    *          - sequence Ids to search for associations
3902    */
3903   public SequenceStructureBinding addStructureViewInstance(
3904           Object jmolviewer, String[] sequenceIds)
3905   {
3906     Viewer viewer = null;
3907     try
3908     {
3909       viewer = (Viewer) jmolviewer;
3910     } catch (ClassCastException ex)
3911     {
3912       System.err.println("Unsupported viewer object :"
3913               + jmolviewer.getClass());
3914     }
3915     if (viewer == null)
3916     {
3917       System.err.println("Can't use this object as a structure viewer:"
3918               + jmolviewer.getClass());
3919       return null;
3920     }
3921     SequenceI[] seqs = null;
3922     if (sequenceIds == null || sequenceIds.length == 0)
3923     {
3924       seqs = viewport.getAlignment().getSequencesArray();
3925     }
3926     else
3927     {
3928       Vector sqi = new Vector();
3929       AlignmentI al = viewport.getAlignment();
3930       for (int sid = 0; sid < sequenceIds.length; sid++)
3931       {
3932         SequenceI sq = al.findName(sequenceIds[sid]);
3933         if (sq != null)
3934         {
3935           sqi.addElement(sq);
3936         }
3937       }
3938       if (sqi.size() > 0)
3939       {
3940         seqs = new SequenceI[sqi.size()];
3941         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3942         {
3943           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3944         }
3945       }
3946       else
3947       {
3948         return null;
3949       }
3950     }
3951     AAStructureBindingModel jmv = null;
3952     // TODO: search for a jmv that involves viewer
3953     if (jmv == null)
3954     { // create a new viewer/jalview binding.
3955       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3956     }
3957     return jmv;
3958
3959   }
3960
3961   /**
3962    * bind a pdb file to a sequence in the current view
3963    *
3964    * @param sequenceId
3965    *          - sequenceId within the dataset.
3966    * @param pdbEntryString
3967    *          - the short name for the PDB file
3968    * @param pdbFile
3969    *          - pdb file - either a URL or a valid PDB file.
3970    * @return true if binding was as success TODO: consider making an exception
3971    *         structure for indicating when PDB parsing or sequenceId location
3972    *         fails.
3973    */
3974   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3975           String pdbFile)
3976   {
3977     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3978     boolean needtoadd = false;
3979     if (toaddpdb != null)
3980     {
3981       Vector pdbe = toaddpdb.getAllPDBEntries();
3982       PDBEntry pdbentry = null;
3983       if (pdbe != null && pdbe.size() > 0)
3984       {
3985         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3986         {
3987           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3988           if (!pdbentry.getId().equals(pdbEntryString)
3989                   && !pdbentry.getFile().equals(pdbFile))
3990           {
3991             pdbentry = null;
3992           }
3993           else
3994           {
3995             continue;
3996           }
3997         }
3998       }
3999       if (pdbentry == null)
4000       {
4001         pdbentry = new PDBEntry();
4002         pdbentry.setId(pdbEntryString);
4003         pdbentry.setFile(pdbFile);
4004         needtoadd = true; // add this new entry to sequence.
4005       }
4006       // resolve data source
4007       // TODO: this code should be a refactored to an io package
4008       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4009       if (protocol == null)
4010       {
4011         return false;
4012       }
4013       if (needtoadd)
4014       {
4015         // make a note of the access mode and add
4016         if (pdbentry.getProperty() == null)
4017         {
4018           pdbentry.setProperty(new Hashtable());
4019         }
4020         pdbentry.getProperty().put("protocol", protocol);
4021         toaddpdb.addPDBId(pdbentry);
4022         alignPanel.getStructureSelectionManager()
4023                 .registerPDBEntry(pdbentry);
4024       }
4025     }
4026     return true;
4027   }
4028
4029   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4030   {
4031     if (seqs != null)
4032     {
4033       Vector sequences = new Vector();
4034       for (int i = 0; i < seqs.length; i++)
4035       {
4036         if (seqs[i] != null)
4037         {
4038           sequences.addElement(new Object[] { seqs[i],
4039               (chains != null) ? chains[i] : null });
4040         }
4041       }
4042       seqs = new SequenceI[sequences.size()];
4043       chains = new String[sequences.size()];
4044       for (int i = 0, isize = sequences.size(); i < isize; i++)
4045       {
4046         Object[] oj = (Object[]) sequences.elementAt(i);
4047
4048         seqs[i] = (SequenceI) oj[0];
4049         chains[i] = (String) oj[1];
4050       }
4051     }
4052     return new Object[] { seqs, chains };
4053
4054   }
4055
4056   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4057           SequenceI[] seqs, String[] chains, String protocol)
4058   {
4059     // Scrub any null sequences from the array
4060     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4061     seqs = (SequenceI[]) sqch[0];
4062     chains = (String[]) sqch[1];
4063     if (seqs == null || seqs.length == 0)
4064     {
4065       System.err
4066               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4067     }
4068     if (protocol == null || protocol.trim().length() == 0
4069             || protocol.equals("null"))
4070     {
4071       protocol = (String) pdb.getProperty().get("protocol");
4072       if (protocol == null)
4073       {
4074         System.err.println("Couldn't work out protocol to open structure: "
4075                 + pdb.getId());
4076         return;
4077       }
4078     }
4079     if (applet.useXtrnalSviewer)
4080     {
4081       // register the association(s) and quit, don't create any windows.
4082       if (StructureSelectionManager.getStructureSelectionManager(applet)
4083               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4084       {
4085         System.err.println("Failed to map " + pdb.getFile() + " ("
4086                 + protocol + ") to any sequences");
4087       }
4088       return;
4089     }
4090     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4091     {
4092       // can only do alignments with Jmol
4093       // find the last jmol window assigned to this alignment
4094       jalview.appletgui.AppletJmol ajm = null, tajm;
4095       Vector jmols = applet
4096               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4097       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4098       {
4099         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4100         if (tajm.ap.alignFrame == this)
4101         {
4102           ajm = tajm;
4103           break;
4104         }
4105       }
4106       if (ajm != null)
4107       {
4108         System.err
4109                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4110         // try and add the pdb structure
4111         // ajm.addS
4112         ajm = null;
4113       }
4114     }
4115     // otherwise, create a new window
4116     if (applet.jmolAvailable)
4117     {
4118       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4119               protocol);
4120       applet.lastFrameX += 40;
4121       applet.lastFrameY += 40;
4122     }
4123     else
4124     {
4125       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4126     }
4127
4128   }
4129
4130   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4131           SequenceI[][] seqs, String[][] chains, String[] protocols)
4132   {
4133     // TODO Auto-generated method stub
4134     System.err.println("Aligned Structure View: Not yet implemented.");
4135   }
4136
4137   /**
4138    * modify the current selection, providing the user has not made a selection
4139    * already.
4140    *
4141    * @param sel
4142    *          - sequences from this alignment
4143    * @param csel
4144    *          - columns to be selected on the alignment
4145    */
4146   public void select(SequenceGroup sel, ColumnSelection csel)
4147   {
4148     alignPanel.seqPanel.selection(sel, csel, null);
4149   }
4150
4151   public void scrollTo(int row, int column)
4152   {
4153     alignPanel.seqPanel.scrollTo(row, column);
4154   }
4155
4156   public void scrollToRow(int row)
4157   {
4158     alignPanel.seqPanel.scrollToRow(row);
4159   }
4160
4161   public void scrollToColumn(int column)
4162   {
4163     alignPanel.seqPanel.scrollToColumn(column);
4164   }
4165
4166   /**
4167    * @return the alignments unique ID.
4168    */
4169   public String getSequenceSetId()
4170   {
4171     return viewport.getSequenceSetId();
4172   }
4173
4174   /**
4175    * Load the (T-Coffee) score file from the specified url
4176    *
4177    * @param source
4178    *          File/URL/T-COFFEE score file contents
4179    * @throws IOException
4180    * @return true if alignment was annotated with data from source
4181    */
4182   public boolean loadScoreFile(String source) throws IOException
4183   {
4184
4185     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4186             AppletFormatAdapter.checkProtocol(source));
4187     if (!file.isValid())
4188     {
4189       // TODO: raise dialog for gui
4190       System.err.println("Problems parsing T-Coffee scores: "
4191               + file.getWarningMessage());
4192       System.err.println("Origin was:\n" + source);
4193       return false;
4194     }
4195
4196     /*
4197      * check that the score matrix matches the alignment dimensions
4198      */
4199     AlignmentI aln;
4200     if ((aln = viewport.getAlignment()) != null
4201             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4202                     .getWidth()))
4203     {
4204       // TODO: raise a dialog box here rather than bomb out.
4205       System.err
4206               .println("The scores matrix does not match the alignment dimensions");
4207
4208     }
4209
4210     // TODO add parameter to indicate if matching should be done
4211     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4212     {
4213       alignPanel.fontChanged();
4214       tcoffeeColour.setEnabled(true);
4215       // switch to this color
4216       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4217       return true;
4218     }
4219     else
4220     {
4221       System.err.println("Problems resolving T-Coffee scores:");
4222       if (file.getWarningMessage() != null)
4223       {
4224         System.err.println(file.getWarningMessage());
4225       }
4226     }
4227     return false;
4228   }
4229
4230   public SplitFrame getSplitFrame()
4231   {
4232     return this.splitFrame;
4233   }
4234
4235   public void setSplitFrame(SplitFrame sf)
4236   {
4237     this.splitFrame = sf;
4238   }
4239
4240   // may not need this
4241   @Override
4242   public void setShowSeqFeatures(boolean b)
4243   {
4244     // showSeqFeatures.setSelected(b);
4245     viewport.setShowSequenceFeatures(b);
4246
4247   }
4248
4249   @Override
4250   public void setMenusForViewport()
4251   {
4252     // setMenusFromViewport(viewport);
4253
4254   }
4255
4256   @Override
4257   public void refreshFeatureUI(boolean enableIfNecessary)
4258   {
4259     if (enableIfNecessary)
4260     {
4261       sequenceFeatures.setState(true);
4262       alignPanel.av.setShowSequenceFeatures(true);
4263     }
4264   }
4265
4266   @Override
4267   public FeatureSettingsControllerI getFeatureSettingsUI()
4268   {
4269     return alignPanel.av.featureSettings;
4270   }
4271
4272 }