src/jalview/appletgui/AlignFrame.java

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