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