src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.FeaturesFile;
  53 import jalview.io.TCoffeeScoreFile;
  54 import jalview.schemes.Blosum62ColourScheme;
  55 import jalview.schemes.BuriedColourScheme;
  56 import jalview.schemes.ClustalxColourScheme;
  57 import jalview.schemes.ColourSchemeI;
  58 import jalview.schemes.HelixColourScheme;
  59 import jalview.schemes.HydrophobicColourScheme;
  60 import jalview.schemes.NucleotideColourScheme;
  61 import jalview.schemes.PIDColourScheme;
  62 import jalview.schemes.PurinePyrimidineColourScheme;
  63 import jalview.schemes.RNAHelicesColourChooser;
  64 import jalview.schemes.StrandColourScheme;
  65 import jalview.schemes.TCoffeeColourScheme;
  66 import jalview.schemes.TaylorColourScheme;
  67 import jalview.schemes.TurnColourScheme;
  68 import jalview.schemes.ZappoColourScheme;
  69 import jalview.structure.StructureSelectionManager;
  70 import jalview.structures.models.AAStructureBindingModel;
  71 import jalview.util.MappingUtils;
  72 import jalview.util.MessageManager;
  73 import jalview.viewmodel.AlignmentViewport;
  74
  75 import java.awt.BorderLayout;
  76 import java.awt.Canvas;
  77 import java.awt.CheckboxMenuItem;
  78 import java.awt.Color;
  79 import java.awt.FlowLayout;
  80 import java.awt.Font;
  81 import java.awt.FontMetrics;
  82 import java.awt.Frame;
  83 import java.awt.Graphics;
  84 import java.awt.Label;
  85 import java.awt.Menu;
  86 import java.awt.MenuBar;
  87 import java.awt.MenuItem;
  88 import java.awt.Panel;
  89 import java.awt.event.ActionEvent;
  90 import java.awt.event.ActionListener;
  91 import java.awt.event.FocusEvent;
  92 import java.awt.event.FocusListener;
  93 import java.awt.event.ItemEvent;
  94 import java.awt.event.ItemListener;
  95 import java.awt.event.KeyEvent;
  96 import java.awt.event.KeyListener;
  97 import java.awt.event.WindowAdapter;
  98 import java.awt.event.WindowEvent;
  99 import java.io.IOException;
 100 import java.net.URL;
 101 import java.net.URLEncoder;
 102 import java.util.Arrays;
 103 import java.util.Deque;
 104 import java.util.HashMap;
 105 import java.util.Hashtable;
 106 import java.util.List;
 107 import java.util.Map;
 108 import java.util.StringTokenizer;
 109 import java.util.Vector;
 110
 111 import org.jmol.viewer.Viewer;
 112
 113 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 114         ItemListener, KeyListener, AlignViewControllerGuiI
 115 {
 116   public AlignViewControllerI avc;
 117
 118   public AlignmentPanel alignPanel;
 119
 120   public AlignViewport viewport;
 121
 122   // width and height may be overridden by applet parameters
 123   int frameWidth = 700;
 124
 125   int frameHeight = 500;
 126
 127   String jalviewServletURL;
 128
 129   /*
 130    * Flag for showing autocalculated consensus above or below other consensus
 131    * rows
 132    */
 133   private boolean showAutoCalculatedAbove;
 134
 135   private SequenceAnnotationOrder annotationSortOrder;
 136
 137   /**
 138    * Constructor that creates the frame and adds it to the display.
 139    *
 140    * @param al
 141    * @param applet
 142    * @param title
 143    * @param embedded
 144    */
 145   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 146           boolean embedded)
 147   {
 148     this(al, applet, title, embedded, true);
 149   }
 150
 151   /**
 152    * Constructor that optionally allows the frame to be displayed or only
 153    * created.
 154    *
 155    * @param al
 156    * @param applet
 157    * @param title
 158    * @param embedded
 159    * @param addToDisplay
 160    */
 161   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 162           boolean embedded, boolean addToDisplay)
 163   {
 164     this(al, null, null, applet, title, embedded, addToDisplay);
 165   }
 166
 167   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 168           ColumnSelection columnSelection, JalviewLite applet,
 169           String title, boolean embedded)
 170   {
 171     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 172   }
 173
 174   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 175           ColumnSelection columnSelection, JalviewLite applet,
 176           String title, boolean embedded, boolean addToDisplay)
 177   {
 178     if (applet != null)
 179     {
 180       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 181     }
 182
 183     try
 184     {
 185       jbInit();
 186     } catch (Exception ex)
 187     {
 188       ex.printStackTrace();
 189     }
 190     // need to get window geometry before we calculate alignment layout
 191     if (applet != null)
 192     {
 193       String param;
 194       try
 195       {
 196         param = applet.getParameter("windowWidth");
 197         if (param != null)
 198         {
 199           int width = Integer.parseInt(param);
 200           frameWidth = width;
 201         }
 202         param = applet.getParameter("windowHeight");
 203         if (param != null)
 204         {
 205           int height = Integer.parseInt(param);
 206           frameHeight = height;
 207         }
 208       } catch (Exception ex)
 209       {
 210       }
 211     }
 212     viewport = new AlignViewport(al, applet);
 213
 214     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 215     {
 216       viewport.hideSequence(hiddenSeqs);
 217     }
 218     if (columnSelection != null)
 219     {
 220       viewport.setColumnSelection(columnSelection);
 221     }
 222
 223     alignPanel = new AlignmentPanel(this, viewport);
 224     avc = new jalview.controller.AlignViewController(this, viewport,
 225             alignPanel);
 226     viewport.updateConservation(alignPanel);
 227     viewport.updateConsensus(alignPanel);
 228
 229     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 230     followMouseOverFlag.setState(viewport.isFollowHighlight());
 231     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 232     showGroupConservation.setState(viewport.isShowGroupConservation());
 233     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 234     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 235     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 236     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 237     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 238     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 239     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 240     showAlignmentAnnotations.setState(true);
 241     showSequenceAnnotations.setState(false);
 242
 243     seqLimits.setState(viewport.getShowJVSuffix());
 244
 245     if (applet != null)
 246     {
 247       String param = applet.getParameter("sortBy");
 248       if (param != null)
 249       {
 250         if (param.equalsIgnoreCase("Id"))
 251         {
 252           sortIDMenuItem_actionPerformed();
 253         }
 254         else if (param.equalsIgnoreCase("Pairwise Identity"))
 255         {
 256           sortPairwiseMenuItem_actionPerformed();
 257         }
 258         else if (param.equalsIgnoreCase("Length"))
 259         {
 260           sortLengthMenuItem_actionPerformed();
 261         }
 262       }
 263
 264       param = applet.getParameter("wrap");
 265       if (param != null)
 266       {
 267         if (param.equalsIgnoreCase("true"))
 268         {
 269           wrapMenuItem.setState(true);
 270           wrapMenuItem_actionPerformed();
 271         }
 272       }
 273       param = applet.getParameter("centrecolumnlabels");
 274       if (param != null)
 275       {
 276         centreColumnLabelFlag.setState(true);
 277         centreColumnLabelFlag_stateChanged();
 278       }
 279
 280     }
 281     if (viewport.getAlignment().isNucleotide())
 282     {
 283       viewport.updateStrucConsensus(alignPanel);
 284       if (viewport.getAlignment().hasRNAStructure())
 285       {
 286         RNAHelixColour.setEnabled(true);
 287       }
 288       else
 289       {
 290         RNAHelixColour.setEnabled(false);
 291       }
 292     }
 293     else
 294     {
 295       RNAHelixColour.setEnabled(false);
 296       purinePyrimidineColour.setEnabled(false);
 297     }
 298     // Some JVMS send keyevents to Top frame or lowest panel,
 299     // Havent worked out why yet. So add to both this frame and seqCanvas for
 300     // now
 301     this.addKeyListener(this);
 302     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 303     alignPanel.idPanel.idCanvas.addKeyListener(this);
 304     alignPanel.scalePanel.addKeyListener(this);
 305     alignPanel.annotationPanel.addKeyListener(this);
 306     alignPanel.annotationPanelHolder.addKeyListener(this);
 307     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 308     alignPanel.alabels.addKeyListener(this);
 309
 310     setAnnotationsVisibility();
 311
 312     if (addToDisplay)
 313     {
 314       addToDisplay(embedded);
 315     }
 316   }
 317
 318   /**
 319    * @param embedded
 320    */
 321   public void addToDisplay(boolean embedded)
 322   {
 323     createAlignFrameWindow(embedded);
 324     validate();
 325     alignPanel.adjustAnnotationHeight();
 326     alignPanel.paintAlignment(true);
 327   }
 328
 329   public AlignViewport getAlignViewport()
 330   {
 331     return viewport;
 332   }
 333
 334   public SeqCanvas getSeqcanvas()
 335   {
 336     return alignPanel.seqPanel.seqCanvas;
 337   }
 338
 339   /**
 340    * Load a features file onto the alignment
 341    *
 342    * @param file
 343    *          file URL, content, or other resolvable path
 344    * @param type
 345    *          is protocol for accessing data referred to by file
 346    */
 347
 348   public boolean parseFeaturesFile(String file, String type)
 349   {
 350     return parseFeaturesFile(file, type, true);
 351   }
 352
 353   /**
 354    * Load a features file onto the alignment
 355    *
 356    * @param file
 357    *          file URL, content, or other resolvable path
 358    * @param type
 359    *          is protocol for accessing data referred to by file
 360    * @param autoenabledisplay
 361    *          when true, display features flag will be automatically enabled if
 362    *          features are loaded
 363    * @return true if data parsed as a features file
 364    */
 365   public boolean parseFeaturesFile(String file, String type,
 366           boolean autoenabledisplay)
 367   {
 368     // TODO: test if importing a features file onto an alignment which already
 369     // has features with links overwrites the original links.
 370
 371     Hashtable featureLinks = new Hashtable();
 372     boolean featuresFile = false;
 373     try
 374     {
 375       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
 376               .getAlignment(), alignPanel.seqPanel.seqCanvas
 377               .getFeatureRenderer().getFeatureColours(), featureLinks,
 378               true, viewport.applet.getDefaultParameter("relaxedidmatch",
 379                       false));
 380     } catch (Exception ex)
 381     {
 382       ex.printStackTrace();
 383     }
 384
 385     if (featuresFile)
 386     {
 387       if (featureLinks.size() > 0)
 388       {
 389         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 390       }
 391       if (autoenabledisplay)
 392       {
 393         viewport.setShowSequenceFeatures(true);
 394         sequenceFeatures.setState(true);
 395       }
 396       if (alignPanel.seqPanel.seqCanvas.fr != null)
 397       {
 398         // update the min/max ranges where necessary
 399         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 400       }
 401       if (viewport.featureSettings != null)
 402       {
 403         viewport.featureSettings.refreshTable();
 404       }
 405       alignPanel.paintAlignment(true);
 406       statusBar.setText(MessageManager
 407               .getString("label.successfully_added_features_alignment"));
 408     }
 409     return featuresFile;
 410   }
 411
 412   @Override
 413   public void keyPressed(KeyEvent evt)
 414   {
 415     if (viewport.cursorMode
 416             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 417                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 418                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 419             && Character.isDigit(evt.getKeyChar()))
 420     {
 421       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 422     }
 423
 424     switch (evt.getKeyCode())
 425     {
 426     case 27: // escape key
 427       deselectAllSequenceMenuItem_actionPerformed();
 428
 429       alignPanel.alabels.cancelDrag();
 430       break;
 431     case KeyEvent.VK_X:
 432       if (evt.isControlDown() || evt.isMetaDown())
 433       {
 434         cut_actionPerformed();
 435       }
 436       break;
 437     case KeyEvent.VK_C:
 438       if (viewport.cursorMode && !evt.isControlDown())
 439       {
 440         alignPanel.seqPanel.setCursorColumn();
 441       }
 442       if (evt.isControlDown() || evt.isMetaDown())
 443       {
 444         copy_actionPerformed();
 445       }
 446       break;
 447     case KeyEvent.VK_V:
 448       if (evt.isControlDown())
 449       {
 450         paste(evt.isShiftDown());
 451       }
 452       break;
 453     case KeyEvent.VK_A:
 454       if (evt.isControlDown() || evt.isMetaDown())
 455       {
 456         selectAllSequenceMenuItem_actionPerformed();
 457       }
 458       break;
 459     case KeyEvent.VK_DOWN:
 460       if (viewport.cursorMode)
 461       {
 462         alignPanel.seqPanel.moveCursor(0, 1);
 463       }
 464       else
 465       {
 466         moveSelectedSequences(false);
 467       }
 468       break;
 469
 470     case KeyEvent.VK_UP:
 471       if (viewport.cursorMode)
 472       {
 473         alignPanel.seqPanel.moveCursor(0, -1);
 474       }
 475       else
 476       {
 477         moveSelectedSequences(true);
 478       }
 479       break;
 480
 481     case KeyEvent.VK_LEFT:
 482       if (evt.isAltDown() || !viewport.cursorMode)
 483       {
 484         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 485       }
 486       else
 487       {
 488         alignPanel.seqPanel.moveCursor(-1, 0);
 489       }
 490       break;
 491
 492     case KeyEvent.VK_RIGHT:
 493       if (evt.isAltDown() || !viewport.cursorMode)
 494       {
 495         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 496       }
 497       else
 498       {
 499         alignPanel.seqPanel.moveCursor(1, 0);
 500       }
 501       break;
 502
 503     case KeyEvent.VK_SPACE:
 504       if (viewport.cursorMode)
 505       {
 506         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 507                 || evt.isShiftDown() || evt.isAltDown());
 508       }
 509       break;
 510
 511     case KeyEvent.VK_DELETE:
 512     case KeyEvent.VK_BACK_SPACE:
 513       if (viewport.cursorMode)
 514       {
 515         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 516                 || evt.isShiftDown() || evt.isAltDown());
 517       }
 518       else
 519       {
 520         cut_actionPerformed();
 521         alignPanel.seqPanel.seqCanvas.repaint();
 522       }
 523       break;
 524
 525     case KeyEvent.VK_S:
 526       if (viewport.cursorMode)
 527       {
 528         alignPanel.seqPanel.setCursorRow();
 529       }
 530       break;
 531     case KeyEvent.VK_P:
 532       if (viewport.cursorMode)
 533       {
 534         alignPanel.seqPanel.setCursorPosition();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_ENTER:
 539     case KeyEvent.VK_COMMA:
 540       if (viewport.cursorMode)
 541       {
 542         alignPanel.seqPanel.setCursorRowAndColumn();
 543       }
 544       break;
 545
 546     case KeyEvent.VK_Q:
 547       if (viewport.cursorMode)
 548       {
 549         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 550       }
 551       break;
 552     case KeyEvent.VK_M:
 553       if (viewport.cursorMode)
 554       {
 555         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 556       }
 557       break;
 558
 559     case KeyEvent.VK_F2:
 560       viewport.cursorMode = !viewport.cursorMode;
 561       statusBar.setText(MessageManager.formatMessage(
 562               "label.keyboard_editing_mode",
 563               new String[] { (viewport.cursorMode ? "on" : "off") }));
 564       if (viewport.cursorMode)
 565       {
 566         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 567         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 568       }
 569       break;
 570
 571     case KeyEvent.VK_F:
 572       if (evt.isControlDown())
 573       {
 574         findMenuItem_actionPerformed();
 575       }
 576       break;
 577
 578     case KeyEvent.VK_H:
 579     {
 580       boolean toggleSeqs = !evt.isControlDown();
 581       boolean toggleCols = !evt.isShiftDown();
 582       toggleHiddenRegions(toggleSeqs, toggleCols);
 583       break;
 584     }
 585
 586     case KeyEvent.VK_PAGE_UP:
 587       if (viewport.getWrapAlignment())
 588       {
 589         alignPanel.scrollUp(true);
 590       }
 591       else
 592       {
 593         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 594                 - viewport.endSeq + viewport.startSeq);
 595       }
 596       break;
 597
 598     case KeyEvent.VK_PAGE_DOWN:
 599       if (viewport.getWrapAlignment())
 600       {
 601         alignPanel.scrollUp(false);
 602       }
 603       else
 604       {
 605         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 606                 + viewport.endSeq - viewport.startSeq);
 607       }
 608       break;
 609
 610     case KeyEvent.VK_Z:
 611       if (evt.isControlDown())
 612       {
 613         undoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_Y:
 618       if (evt.isControlDown())
 619       {
 620         redoMenuItem_actionPerformed();
 621       }
 622       break;
 623
 624     case KeyEvent.VK_L:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(true);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_R:
 632       if (evt.isControlDown())
 633       {
 634         trimAlignment(false);
 635       }
 636       break;
 637
 638     case KeyEvent.VK_E:
 639       if (evt.isControlDown())
 640       {
 641         if (evt.isShiftDown())
 642         {
 643           this.removeAllGapsMenuItem_actionPerformed();
 644         }
 645         else
 646         {
 647           removeGappedColumnMenuItem_actionPerformed();
 648         }
 649       }
 650       break;
 651     case KeyEvent.VK_I:
 652       if (evt.isControlDown())
 653       {
 654         if (evt.isAltDown())
 655         {
 656           invertColSel_actionPerformed();
 657         }
 658         else
 659         {
 660           invertSequenceMenuItem_actionPerformed();
 661         }
 662       }
 663       break;
 664
 665     case KeyEvent.VK_G:
 666       if (evt.isControlDown())
 667       {
 668         if (evt.isShiftDown())
 669         {
 670           this.unGroup_actionPerformed();
 671         }
 672         else
 673         {
 674           this.createGroup_actionPerformed();
 675         }
 676       }
 677       break;
 678
 679     case KeyEvent.VK_U:
 680       if (evt.isControlDown())
 681       {
 682         this.deleteGroups_actionPerformed();
 683       }
 684       break;
 685
 686     case KeyEvent.VK_T:
 687       if (evt.isControlDown())
 688       {
 689         newView(null);
 690       }
 691       break;
 692
 693     }
 694     alignPanel.paintAlignment(true);
 695   }
 696
 697   /**
 698    * called by key handler and the hide all/show all menu items
 699    *
 700    * @param toggleSeqs
 701    * @param toggleCols
 702    */
 703   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 704   {
 705     boolean hide = false;
 706     SequenceGroup sg = viewport.getSelectionGroup();
 707     if (!toggleSeqs && !toggleCols)
 708     {
 709       // Hide everything by the current selection - this is a hack - we do the
 710       // invert and then hide
 711       // first check that there will be visible columns after the invert.
 712       if ((viewport.getColumnSelection() != null
 713               && viewport.getColumnSelection().getSelected() != null && viewport
 714               .getColumnSelection().getSelected().size() > 0)
 715               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 716                       .getEndRes()))
 717       {
 718         // now invert the sequence set, if required - empty selection implies
 719         // that no hiding is required.
 720         if (sg != null)
 721         {
 722           invertSequenceMenuItem_actionPerformed();
 723           sg = viewport.getSelectionGroup();
 724           toggleSeqs = true;
 725
 726         }
 727         viewport.expandColSelection(sg, true);
 728         // finally invert the column selection and get the new sequence
 729         // selection and indicate it should be hidden.
 730         invertColSel_actionPerformed();
 731         toggleCols = true;
 732       }
 733     }
 734
 735     if (toggleSeqs)
 736     {
 737       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 738       {
 739         hide = true;
 740         viewport.hideAllSelectedSeqs();
 741       }
 742       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 743               .size() > 0))
 744       {
 745         viewport.showAllHiddenSeqs();
 746       }
 747     }
 748
 749     if (toggleCols)
 750     {
 751       if (viewport.getColumnSelection().getSelected().size() > 0)
 752       {
 753         viewport.hideSelectedColumns();
 754         if (!toggleSeqs)
 755         {
 756           viewport.setSelectionGroup(sg);
 757         }
 758       }
 759       else if (!hide)
 760       {
 761         viewport.showAllHiddenColumns();
 762       }
 763       viewport.sendSelection();
 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       boolean showAnnotations = annotationPanelMenuItem.getState();
 824       showAlignmentAnnotations.setEnabled(showAnnotations);
 825       showSequenceAnnotations.setEnabled(showAnnotations);
 826       viewport.setShowAnnotation(showAnnotations);
 827       alignPanel.setAnnotationVisible(showAnnotations);
 828     }
 829     else if (source == sequenceFeatures)
 830     {
 831       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 832       alignPanel.seqPanel.seqCanvas.repaint();
 833     }
 834     else if (source == showAlignmentAnnotations)
 835     {
 836       setAnnotationsVisibility();
 837     }
 838     else if (source == showSequenceAnnotations)
 839     {
 840       setAnnotationsVisibility();
 841     }
 842     else if (source == sortAnnBySequence)
 843     {
 844       boolean newState = sortAnnBySequence.getState();
 845       sortAnnByLabel.setState(false);
 846       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 847               : SequenceAnnotationOrder.NONE);
 848       setViewportAnnotationOrder();
 849     }
 850     else if (source == sortAnnByLabel)
 851     {
 852       boolean newState = sortAnnByLabel.getState();
 853       sortAnnBySequence.setState(false);
 854       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 855               : SequenceAnnotationOrder.NONE);
 856       setViewportAnnotationOrder();
 857     }
 858     else if (source == showAutoFirst)
 859     {
 860       showAutoLast.setState(!showAutoFirst.getState());
 861       setShowAutoCalculatedAbove(showAutoFirst.getState());
 862       setViewportAnnotationOrder();
 863     }
 864     else if (source == showAutoLast)
 865     {
 866       showAutoFirst.setState(!showAutoLast.getState());
 867       setShowAutoCalculatedAbove(showAutoFirst.getState());
 868       setViewportAnnotationOrder();
 869     }
 870     else if (source == conservationMenuItem)
 871     {
 872       conservationMenuItem_actionPerformed();
 873     }
 874     else if (source == abovePIDThreshold)
 875     {
 876       abovePIDThreshold_actionPerformed();
 877     }
 878     else if (source == applyToAllGroups)
 879     {
 880       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 881     }
 882     else if (source == autoCalculate)
 883     {
 884       viewport.autoCalculateConsensus = autoCalculate.getState();
 885     }
 886     else if (source == sortByTree)
 887     {
 888       viewport.sortByTree = sortByTree.getState();
 889     }
 890     else if (source == this.centreColumnLabelFlag)
 891     {
 892       centreColumnLabelFlag_stateChanged();
 893     }
 894     else if (source == this.followMouseOverFlag)
 895     {
 896       mouseOverFlag_stateChanged();
 897     }
 898     else if (source == showGroupConsensus)
 899     {
 900       showGroupConsensus_actionPerformed();
 901     }
 902     else if (source == showGroupConservation)
 903     {
 904       showGroupConservation_actionPerformed();
 905     }
 906     else if (source == showSequenceLogo)
 907     {
 908       showSequenceLogo_actionPerformed();
 909     }
 910     else if (source == normSequenceLogo)
 911     {
 912       normSequenceLogo_actionPerformed();
 913     }
 914     else if (source == showConsensusHistogram)
 915     {
 916       showConsensusHistogram_actionPerformed();
 917     }
 918     else if (source == applyAutoAnnotationSettings)
 919     {
 920       applyAutoAnnotationSettings_actionPerformed();
 921     }
 922     alignPanel.paintAlignment(true);
 923   }
 924
 925   /**
 926    * Set the visibility state of sequence-related and/or alignment-related
 927    * annotations depending on checkbox selections, and repaint.
 928    *
 929    * @param visible
 930    */
 931   private void setAnnotationsVisibility()
 932   {
 933     boolean showForAlignment = showAlignmentAnnotations.getState();
 934     boolean showForSequences = showSequenceAnnotations.getState();
 935     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 936     {
 937       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 938             .getAlignmentAnnotation())
 939     {
 940       boolean visible = (aa.sequenceRef == null ? showForAlignment
 941               : showForSequences);
 942       aa.visible = visible;
 943       }
 944     }
 945     alignPanel.validateAnnotationDimensions(true);
 946     validate();
 947     repaint();
 948   }
 949
 950   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 951   {
 952     this.annotationSortOrder = order;
 953   }
 954
 955   /**
 956    * Set flags on the viewport that control annotation ordering
 957    */
 958   private void setViewportAnnotationOrder()
 959   {
 960     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 961     this.alignPanel.av
 962             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 963   }
 964
 965   private void setShowAutoCalculatedAbove(boolean showAbove)
 966   {
 967     this.showAutoCalculatedAbove = showAbove;
 968   }
 969
 970   private void mouseOverFlag_stateChanged()
 971   {
 972     viewport.setFollowHighlight(followMouseOverFlag.getState());
 973     // TODO: could kick the scrollTo mechanism to reset view for current
 974     // searchresults.
 975   }
 976
 977   private void centreColumnLabelFlag_stateChanged()
 978   {
 979     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 980     this.alignPanel.annotationPanel.repaint();
 981   }
 982
 983   @Override
 984   public void actionPerformed(ActionEvent evt)
 985   {
 986     viewport.applet.currentAlignFrame = this;
 987
 988     Object source = evt.getSource();
 989
 990     if (source == inputText)
 991     {
 992       inputText_actionPerformed();
 993     }
 994     else if (source == loadTree)
 995     {
 996       loadTree_actionPerformed();
 997     }
 998     else if (source == loadApplication)
 999     {
1000       launchFullApplication();
1001     }
1002     else if (source == loadAnnotations)
1003     {
1004       loadAnnotations();
1005     }
1006     else if (source == outputAnnotations)
1007     {
1008       outputAnnotations(true);
1009     }
1010     else if (source == outputFeatures)
1011     {
1012       outputFeatures(true, "Jalview");
1013     }
1014     else if (source == closeMenuItem)
1015     {
1016       closeMenuItem_actionPerformed();
1017     }
1018     else if (source == copy)
1019     {
1020       copy_actionPerformed();
1021     }
1022     else if (source == undoMenuItem)
1023     {
1024       undoMenuItem_actionPerformed();
1025     }
1026     else if (source == redoMenuItem)
1027     {
1028       redoMenuItem_actionPerformed();
1029     }
1030     else if (source == inputText)
1031     {
1032       inputText_actionPerformed();
1033     }
1034     else if (source == closeMenuItem)
1035     {
1036       closeMenuItem_actionPerformed();
1037     }
1038     else if (source == undoMenuItem)
1039     {
1040       undoMenuItem_actionPerformed();
1041     }
1042     else if (source == redoMenuItem)
1043     {
1044       redoMenuItem_actionPerformed();
1045     }
1046     else if (source == copy)
1047     {
1048       copy_actionPerformed();
1049     }
1050     else if (source == pasteNew)
1051     {
1052       pasteNew_actionPerformed();
1053     }
1054     else if (source == pasteThis)
1055     {
1056       pasteThis_actionPerformed();
1057     }
1058     else if (source == cut)
1059     {
1060       cut_actionPerformed();
1061     }
1062     else if (source == delete)
1063     {
1064       delete_actionPerformed();
1065     }
1066     else if (source == grpsFromSelection)
1067     {
1068       makeGrpsFromSelection_actionPerformed();
1069     }
1070     else if (source == deleteGroups)
1071     {
1072       deleteGroups_actionPerformed();
1073     }
1074     else if (source == selectAllSequenceMenuItem)
1075     {
1076       selectAllSequenceMenuItem_actionPerformed();
1077     }
1078     else if (source == deselectAllSequenceMenuItem)
1079     {
1080       deselectAllSequenceMenuItem_actionPerformed();
1081     }
1082     else if (source == invertSequenceMenuItem)
1083     {
1084       invertSequenceMenuItem_actionPerformed();
1085       // uncomment to slave sequence selections in split frame
1086       // viewport.sendSelection();
1087     }
1088     else if (source == invertColSel)
1089     {
1090       viewport.invertColumnSelection();
1091       alignPanel.paintAlignment(true);
1092       viewport.sendSelection();
1093     }
1094     else if (source == remove2LeftMenuItem)
1095     {
1096       trimAlignment(true);
1097     }
1098     else if (source == remove2RightMenuItem)
1099     {
1100       trimAlignment(false);
1101     }
1102     else if (source == removeGappedColumnMenuItem)
1103     {
1104       removeGappedColumnMenuItem_actionPerformed();
1105     }
1106     else if (source == removeAllGapsMenuItem)
1107     {
1108       removeAllGapsMenuItem_actionPerformed();
1109     }
1110     else if (source == findMenuItem)
1111     {
1112       findMenuItem_actionPerformed();
1113     }
1114     else if (source == font)
1115     {
1116       new FontChooser(alignPanel);
1117     }
1118     else if (source == newView)
1119     {
1120       newView(null);
1121     }
1122     else if (source == showColumns)
1123     {
1124       viewport.showAllHiddenColumns();
1125       alignPanel.paintAlignment(true);
1126       viewport.sendSelection();
1127     }
1128     else if (source == showSeqs)
1129     {
1130       viewport.showAllHiddenSeqs();
1131       alignPanel.paintAlignment(true);
1132       // uncomment if we want to slave sequence selections in split frame
1133       // viewport.sendSelection();
1134     }
1135     else if (source == hideColumns)
1136     {
1137       viewport.hideSelectedColumns();
1138       alignPanel.paintAlignment(true);
1139       viewport.sendSelection();
1140     }
1141     else if (source == hideSequences
1142             && viewport.getSelectionGroup() != null)
1143     {
1144       viewport.hideAllSelectedSeqs();
1145       alignPanel.paintAlignment(true);
1146       // uncomment if we want to slave sequence selections in split frame
1147       // viewport.sendSelection();
1148     }
1149     else if (source == hideAllButSelection)
1150     {
1151       toggleHiddenRegions(false, false);
1152       alignPanel.paintAlignment(true);
1153       viewport.sendSelection();
1154     }
1155     else if (source == hideAllSelection)
1156     {
1157       SequenceGroup sg = viewport.getSelectionGroup();
1158       viewport.expandColSelection(sg, false);
1159       viewport.hideAllSelectedSeqs();
1160       viewport.hideSelectedColumns();
1161       alignPanel.paintAlignment(true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == showAllHidden)
1165     {
1166       viewport.showAllHiddenColumns();
1167       viewport.showAllHiddenSeqs();
1168       alignPanel.paintAlignment(true);
1169       viewport.sendSelection();
1170     }
1171     else if (source == showGroupConsensus)
1172     {
1173       showGroupConsensus_actionPerformed();
1174     }
1175     else if (source == showGroupConservation)
1176     {
1177       showGroupConservation_actionPerformed();
1178     }
1179     else if (source == showSequenceLogo)
1180     {
1181       showSequenceLogo_actionPerformed();
1182     }
1183     else if (source == normSequenceLogo)
1184     {
1185       normSequenceLogo_actionPerformed();
1186     }
1187     else if (source == showConsensusHistogram)
1188     {
1189       showConsensusHistogram_actionPerformed();
1190     }
1191     else if (source == applyAutoAnnotationSettings)
1192     {
1193       applyAutoAnnotationSettings_actionPerformed();
1194     }
1195     else if (source == featureSettings)
1196     {
1197       new FeatureSettings(alignPanel);
1198     }
1199     else if (source == alProperties)
1200     {
1201       StringBuffer contents = new jalview.io.AlignmentProperties(
1202               viewport.getAlignment()).formatAsString();
1203       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1204       cap.setText(contents.toString());
1205       Frame frame = new Frame();
1206       frame.add(cap);
1207       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1208               "label.alignment_properties", new String[] { getTitle() }),
1209               400, 250);
1210     }
1211     else if (source == overviewMenuItem)
1212     {
1213       overviewMenuItem_actionPerformed();
1214     }
1215     else if (source == noColourmenuItem)
1216     {
1217       changeColour(null);
1218     }
1219     else if (source == clustalColour)
1220     {
1221       abovePIDThreshold.setState(false);
1222       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1223     }
1224     else if (source == zappoColour)
1225     {
1226       changeColour(new ZappoColourScheme());
1227     }
1228     else if (source == taylorColour)
1229     {
1230       changeColour(new TaylorColourScheme());
1231     }
1232     else if (source == hydrophobicityColour)
1233     {
1234       changeColour(new HydrophobicColourScheme());
1235     }
1236     else if (source == helixColour)
1237     {
1238       changeColour(new HelixColourScheme());
1239     }
1240     else if (source == strandColour)
1241     {
1242       changeColour(new StrandColourScheme());
1243     }
1244     else if (source == turnColour)
1245     {
1246       changeColour(new TurnColourScheme());
1247     }
1248     else if (source == buriedColour)
1249     {
1250       changeColour(new BuriedColourScheme());
1251     }
1252     else if (source == nucleotideColour)
1253     {
1254       changeColour(new NucleotideColourScheme());
1255     }
1256     else if (source == purinePyrimidineColour)
1257     {
1258       changeColour(new PurinePyrimidineColourScheme());
1259     }
1260     // else if (source == RNAInteractionColour)
1261     // {
1262     // changeColour(new RNAInteractionColourScheme());
1263     // }
1264     else if (source == RNAHelixColour)
1265     {
1266       new RNAHelicesColourChooser(viewport, alignPanel);
1267     }
1268     else if (source == modifyPID)
1269     {
1270       modifyPID_actionPerformed();
1271     }
1272     else if (source == modifyConservation)
1273     {
1274       modifyConservation_actionPerformed();
1275     }
1276     else if (source == userDefinedColour)
1277     {
1278       new UserDefinedColours(alignPanel, null);
1279     }
1280     else if (source == PIDColour)
1281     {
1282       changeColour(new PIDColourScheme());
1283     }
1284     else if (source == BLOSUM62Colour)
1285     {
1286       changeColour(new Blosum62ColourScheme());
1287     }
1288     else if (source == tcoffeeColour)
1289     {
1290       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1291     }
1292     else if (source == annotationColour)
1293     {
1294       new AnnotationColourChooser(viewport, alignPanel);
1295     }
1296     else if (source == annotationColumnSelection)
1297     {
1298       new AnnotationColumnChooser(viewport, alignPanel);
1299     }
1300     else if (source == sortPairwiseMenuItem)
1301     {
1302       sortPairwiseMenuItem_actionPerformed();
1303     }
1304     else if (source == sortIDMenuItem)
1305     {
1306       sortIDMenuItem_actionPerformed();
1307     }
1308     else if (source == sortLengthMenuItem)
1309     {
1310       sortLengthMenuItem_actionPerformed();
1311     }
1312     else if (source == sortGroupMenuItem)
1313     {
1314       sortGroupMenuItem_actionPerformed();
1315     }
1316     else if (source == removeRedundancyMenuItem)
1317     {
1318       removeRedundancyMenuItem_actionPerformed();
1319     }
1320     else if (source == pairwiseAlignmentMenuItem)
1321     {
1322       pairwiseAlignmentMenuItem_actionPerformed();
1323     }
1324     else if (source == PCAMenuItem)
1325     {
1326       PCAMenuItem_actionPerformed();
1327     }
1328     else if (source == averageDistanceTreeMenuItem)
1329     {
1330       averageDistanceTreeMenuItem_actionPerformed();
1331     }
1332     else if (source == neighbourTreeMenuItem)
1333     {
1334       neighbourTreeMenuItem_actionPerformed();
1335     }
1336     else if (source == njTreeBlosumMenuItem)
1337     {
1338       njTreeBlosumMenuItem_actionPerformed();
1339     }
1340     else if (source == avDistanceTreeBlosumMenuItem)
1341     {
1342       avTreeBlosumMenuItem_actionPerformed();
1343     }
1344     else if (source == documentation)
1345     {
1346       documentation_actionPerformed();
1347     }
1348     else if (source == about)
1349     {
1350       about_actionPerformed();
1351     }
1352
1353   }
1354
1355   public void inputText_actionPerformed()
1356   {
1357     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1358     Frame frame = new Frame();
1359     frame.add(cap);
1360     jalview.bin.JalviewLite.addFrame(frame,
1361             MessageManager.getString("label.input_cut_paste"), 500, 500);
1362   }
1363
1364   protected void outputText_actionPerformed(ActionEvent e)
1365   {
1366     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1367     Frame frame = new Frame();
1368     frame.add(cap);
1369     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1370             "label.alignment_output_command",
1371             new Object[] { e.getActionCommand() }), 600, 500);
1372
1373     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1374     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1375             e.getActionCommand(), viewport.getAlignment(),
1376             viewport.getShowJVSuffix()));
1377   }
1378
1379   public void loadAnnotations()
1380   {
1381     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1382     cap.setText(MessageManager
1383             .getString("label.paste_features_annotations_Tcoffee_here"));
1384     cap.setAnnotationImport();
1385     Frame frame = new Frame();
1386     frame.add(cap);
1387     jalview.bin.JalviewLite.addFrame(frame,
1388             MessageManager.getString("action.paste_annotations"), 400, 300);
1389
1390   }
1391
1392   public String outputAnnotations(boolean displayTextbox)
1393   {
1394     String annotation = new AnnotationFile()
1395             .printAnnotationsForView(viewport);
1396
1397     if (displayTextbox)
1398     {
1399       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1400       Frame frame = new Frame();
1401       frame.add(cap);
1402       jalview.bin.JalviewLite.addFrame(frame,
1403               MessageManager.getString("label.annotations"), 600, 500);
1404       cap.setText(annotation);
1405     }
1406
1407     return annotation;
1408   }
1409
1410   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1411   {
1412     if (alignPanel.getFeatureRenderer() != null
1413             && viewport.getFeaturesDisplayed() != null)
1414     {
1415       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1416
1417     }
1418     return null;
1419   }
1420
1421   public String outputFeatures(boolean displayTextbox, String format)
1422   {
1423     String features;
1424     if (format.equalsIgnoreCase("Jalview"))
1425     {
1426       features = new FeaturesFile().printJalviewFormat(viewport
1427               .getAlignment().getSequencesArray(),
1428               getDisplayedFeatureCols());
1429     }
1430     else
1431     {
1432       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1433               .getSequencesArray(), getDisplayedFeatureCols());
1434     }
1435
1436     if (displayTextbox)
1437     {
1438       boolean frimport = false;
1439       if (features == null || features.equals("No Features Visible"))
1440       {
1441         features = "# No features visible - paste some and import them here.";
1442         frimport = true;
1443       }
1444
1445       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1446       if (frimport)
1447       {
1448         cap.setAnnotationImport();
1449       }
1450       Frame frame = new Frame();
1451       frame.add(cap);
1452       jalview.bin.JalviewLite.addFrame(frame,
1453               MessageManager.getString("label.features"), 600, 500);
1454       cap.setText(features);
1455     }
1456     else
1457     {
1458       if (features == null)
1459       {
1460         features = "";
1461       }
1462     }
1463
1464     return features;
1465   }
1466
1467   void launchFullApplication()
1468   {
1469     StringBuffer url = new StringBuffer(jalviewServletURL);
1470
1471     // allow servlet parameters to be passed in applet parameter
1472     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1473             : "?";
1474     url.append(firstSep);
1475
1476     url.append("open="
1477             + appendProtocol(viewport.applet.getParameter("file")));
1478
1479     if (viewport.applet.getParameter("features") != null)
1480     {
1481       url.append("&features=");
1482       url.append(appendProtocol(viewport.applet.getParameter("features")));
1483     }
1484
1485     if (viewport.applet.getParameter("annotations") != null)
1486     {
1487       url.append("&annotations=");
1488       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1489     }
1490
1491     if (viewport.applet.getParameter("jnetfile") != null)
1492     {
1493       url.append("&annotations=");
1494       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1495     }
1496
1497     if (viewport.applet.getParameter("defaultColour") != null)
1498     {
1499       url.append("&colour="
1500               + removeWhiteSpace(viewport.applet
1501                       .getParameter("defaultColour")));
1502     }
1503
1504     if (viewport.applet.getParameter("userDefinedColour") != null)
1505     {
1506       url.append("&colour="
1507               + removeWhiteSpace(viewport.applet
1508                       .getParameter("userDefinedColour")));
1509     }
1510     if (viewport.applet.getParameter("tree") != null)
1511     {
1512       url.append("&tree="
1513               + appendProtocol(viewport.applet.getParameter("tree")));
1514     }
1515     if (viewport.applet.getParameter("treeFile") != null)
1516     {
1517       url.append("&tree="
1518               + appendProtocol(viewport.applet.getParameter("treeFile")));
1519     }
1520
1521     showURL(url.toString(), "FULL_APP");
1522   }
1523
1524   String removeWhiteSpace(String colour)
1525   {
1526     StringBuffer sb = new StringBuffer();
1527     for (int i = 0; i < colour.length(); i++)
1528     {
1529       if (Character.isWhitespace(colour.charAt(i)))
1530       {
1531         sb.append("%20");
1532       }
1533       else
1534       {
1535         sb.append(colour.charAt(i));
1536       }
1537     }
1538
1539     return sb.toString();
1540   }
1541
1542   String appendProtocol(String url)
1543   {
1544     try
1545     {
1546       new URL(url);
1547       url = URLEncoder.encode(url);
1548     }
1549     /*
1550      * When we finally deprecate 1.1 compatibility, we can start to use
1551      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1552      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1553      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1554      * ex.printStackTrace(); }
1555      */
1556     catch (java.net.MalformedURLException ex)
1557     {
1558       url = viewport.applet.getCodeBase() + url;
1559     }
1560     return url;
1561   }
1562
1563   public void closeMenuItem_actionPerformed()
1564   {
1565     PaintRefresher.RemoveComponent(alignPanel);
1566     if (alignPanel.seqPanel != null
1567             && alignPanel.seqPanel.seqCanvas != null)
1568     {
1569       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1570     }
1571     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1572     {
1573       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1574     }
1575
1576     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1577     {
1578       System.exit(0);
1579     }
1580     else
1581     {
1582     }
1583     viewport = null;
1584     alignPanel = null;
1585     this.dispose();
1586   }
1587
1588   /**
1589    * TODO: JAL-1104
1590    */
1591   void updateEditMenuBar()
1592   {
1593
1594     if (viewport.getHistoryList().size() > 0)
1595     {
1596       undoMenuItem.setEnabled(true);
1597       CommandI command = viewport.getHistoryList().peek();
1598       undoMenuItem.setLabel(MessageManager.formatMessage(
1599               "label.undo_command",
1600               new Object[] { command.getDescription() }));
1601     }
1602     else
1603     {
1604       undoMenuItem.setEnabled(false);
1605       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1606     }
1607
1608     if (viewport.getRedoList().size() > 0)
1609     {
1610       redoMenuItem.setEnabled(true);
1611
1612       CommandI command = viewport.getRedoList().peek();
1613       redoMenuItem.setLabel(MessageManager.formatMessage(
1614               "label.redo_command",
1615               new Object[] { command.getDescription() }));
1616     }
1617     else
1618     {
1619       redoMenuItem.setEnabled(false);
1620       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1621     }
1622   }
1623
1624   /**
1625    * TODO: JAL-1104
1626    */
1627   @Override
1628   public void addHistoryItem(CommandI command)
1629   {
1630     if (command.getSize() > 0)
1631     {
1632       viewport.addToHistoryList(command);
1633       viewport.clearRedoList();
1634       updateEditMenuBar();
1635       viewport.updateHiddenColumns();
1636     }
1637   }
1638
1639   /**
1640    * TODO: JAL-1104 DOCUMENT ME!
1641    *
1642    * @param e
1643    *          DOCUMENT ME!
1644    */
1645   protected void undoMenuItem_actionPerformed()
1646   {
1647     if (viewport.getHistoryList().isEmpty())
1648     {
1649       return;
1650     }
1651
1652     CommandI command = viewport.getHistoryList().pop();
1653     viewport.addToRedoList(command);
1654     command.undoCommand(null);
1655
1656     AlignmentViewport originalSource = getOriginatingSource(command);
1657     // JBPNote Test
1658     if (originalSource != viewport)
1659     {
1660       System.err
1661               .println("Warning: Viewport object mismatch whilst undoing");
1662     }
1663     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1664                                           // viewport.getColumnSelection().getHiddenColumns()
1665                                           // != null;
1666     updateEditMenuBar();
1667     originalSource.firePropertyChange("alignment", null, originalSource
1668             .getAlignment().getSequences());
1669   }
1670
1671   /**
1672    * TODO: JAL-1104 DOCUMENT ME!
1673    *
1674    * @param e
1675    *          DOCUMENT ME!
1676    */
1677   protected void redoMenuItem_actionPerformed()
1678   {
1679     if (viewport.getRedoList().isEmpty())
1680     {
1681       return;
1682     }
1683
1684     CommandI command = viewport.getRedoList().pop();
1685     viewport.addToHistoryList(command);
1686     command.doCommand(null);
1687
1688     AlignmentViewport originalSource = getOriginatingSource(command);
1689     // JBPNote Test
1690     if (originalSource != viewport)
1691     {
1692       System.err
1693               .println("Warning: Viewport object mismatch whilst re-doing");
1694     }
1695     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1696                                           // viewport.getColumnSelection().getHiddenColumns()
1697                                           // != null;
1698
1699     updateEditMenuBar();
1700     originalSource.firePropertyChange("alignment", null, originalSource
1701             .getAlignment().getSequences());
1702   }
1703
1704   AlignmentViewport getOriginatingSource(CommandI command)
1705   {
1706     AlignmentViewport originalSource = null;
1707     // For sequence removal and addition, we need to fire
1708     // the property change event FROM the viewport where the
1709     // original alignment was altered
1710     AlignmentI al = null;
1711     if (command instanceof EditCommand)
1712     {
1713       EditCommand editCommand = (EditCommand) command;
1714       al = editCommand.getAlignment();
1715       Vector comps = (Vector) PaintRefresher.components.get(viewport
1716               .getSequenceSetId());
1717       for (int i = 0; i < comps.size(); i++)
1718       {
1719         if (comps.elementAt(i) instanceof AlignmentPanel)
1720         {
1721           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1722           {
1723             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1724             break;
1725           }
1726         }
1727       }
1728     }
1729
1730     if (originalSource == null)
1731     {
1732       // The original view is closed, we must validate
1733       // the current view against the closed view first
1734       if (al != null)
1735       {
1736         PaintRefresher.validateSequences(al, viewport.getAlignment());
1737       }
1738
1739       originalSource = viewport;
1740     }
1741
1742     return originalSource;
1743   }
1744
1745   /**
1746    * Move the currently selected sequences up or down one position in the
1747    * alignment
1748    *
1749    * @param up
1750    */
1751   public void moveSelectedSequences(boolean up)
1752   {
1753     SequenceGroup sg = viewport.getSelectionGroup();
1754     if (sg == null)
1755     {
1756       return;
1757     }
1758     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1759             up ? null : viewport.getHiddenRepSequences(), up);
1760     alignPanel.paintAlignment(true);
1761
1762     /*
1763      * Also move cDNA/protein complement sequences
1764      */
1765     AlignViewportI complement = viewport.getCodingComplement();
1766     if (complement != null)
1767     {
1768       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1769               viewport, complement);
1770       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1771               up ? null : complement.getHiddenRepSequences(), up);
1772       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1773     }
1774   }
1775
1776   synchronized void slideSequences(boolean right, int size)
1777   {
1778     List<SequenceI> sg = new Vector<SequenceI>();
1779     if (viewport.cursorMode)
1780     {
1781       sg.add(viewport.getAlignment().getSequenceAt(
1782               alignPanel.seqPanel.seqCanvas.cursorY));
1783     }
1784     else if (viewport.getSelectionGroup() != null
1785             && viewport.getSelectionGroup().getSize() != viewport
1786                     .getAlignment().getHeight())
1787     {
1788       sg = viewport.getSelectionGroup().getSequences(
1789               viewport.getHiddenRepSequences());
1790     }
1791
1792     if (sg.size() < 1)
1793     {
1794       return;
1795     }
1796
1797     Vector<SequenceI> invertGroup = new Vector();
1798
1799     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1800     {
1801       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1802       {
1803         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1804       }
1805     }
1806
1807     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1808
1809     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1810             .size()]);
1811     for (int i = 0; i < invertGroup.size(); i++)
1812     {
1813       seqs2[i] = invertGroup.elementAt(i);
1814     }
1815
1816     SlideSequencesCommand ssc;
1817     if (right)
1818     {
1819       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1820               size, viewport.getGapCharacter());
1821     }
1822     else
1823     {
1824       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1825               size, viewport.getGapCharacter());
1826     }
1827
1828     int groupAdjustment = 0;
1829     if (ssc.getGapsInsertedBegin() && right)
1830     {
1831       if (viewport.cursorMode)
1832       {
1833         alignPanel.seqPanel.moveCursor(size, 0);
1834       }
1835       else
1836       {
1837         groupAdjustment = size;
1838       }
1839     }
1840     else if (!ssc.getGapsInsertedBegin() && !right)
1841     {
1842       if (viewport.cursorMode)
1843       {
1844         alignPanel.seqPanel.moveCursor(-size, 0);
1845       }
1846       else
1847       {
1848         groupAdjustment = -size;
1849       }
1850     }
1851
1852     if (groupAdjustment != 0)
1853     {
1854       viewport.getSelectionGroup().setStartRes(
1855               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1856       viewport.getSelectionGroup().setEndRes(
1857               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1858     }
1859
1860     boolean appendHistoryItem = false;
1861     Deque<CommandI> historyList = viewport.getHistoryList();
1862     if (historyList != null && historyList.size() > 0
1863             && historyList.peek() instanceof SlideSequencesCommand)
1864     {
1865       appendHistoryItem = ssc
1866               .appendSlideCommand((SlideSequencesCommand) historyList
1867                       .peek());
1868     }
1869
1870     if (!appendHistoryItem)
1871     {
1872       addHistoryItem(ssc);
1873     }
1874
1875     repaint();
1876   }
1877
1878   static StringBuffer copiedSequences;
1879
1880   static Vector copiedHiddenColumns;
1881
1882   protected void copy_actionPerformed()
1883   {
1884     if (viewport.getSelectionGroup() == null)
1885     {
1886       return;
1887     }
1888
1889     SequenceGroup sg = viewport.getSelectionGroup();
1890     copiedSequences = new StringBuffer();
1891     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1892     for (int i = 0; i < sg.getSize(); i++)
1893     {
1894       SequenceI seq = sg.getSequenceAt(i);
1895       int index = viewport.getAlignment().findIndex(seq);
1896       orderedSeqs.put(index, seq);
1897     }
1898
1899     int index = 0, startRes, endRes;
1900     char ch;
1901
1902     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1903     {
1904       copiedHiddenColumns = new Vector();
1905       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1906       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1907       {
1908         copiedHiddenColumns.addElement(new int[] {
1909             region[0] - hiddenOffset, region[1] - hiddenOffset });
1910       }
1911     }
1912     else
1913     {
1914       copiedHiddenColumns = null;
1915     }
1916
1917     for (int i = 0; i < sg.getSize(); i++)
1918     {
1919       SequenceI seq = null;
1920
1921       while (seq == null)
1922       {
1923         if (orderedSeqs.containsKey(index))
1924         {
1925           seq = orderedSeqs.get(index);
1926           index++;
1927           break;
1928         }
1929         else
1930         {
1931           index++;
1932         }
1933       }
1934
1935       // FIND START RES
1936       // Returns residue following index if gap
1937       startRes = seq.findPosition(sg.getStartRes());
1938
1939       // FIND END RES
1940       // Need to find the residue preceeding index if gap
1941       endRes = 0;
1942
1943       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1944       {
1945         ch = seq.getCharAt(j);
1946         if (!jalview.util.Comparison.isGap((ch)))
1947         {
1948           endRes++;
1949         }
1950       }
1951
1952       if (endRes > 0)
1953       {
1954         endRes += seq.getStart() - 1;
1955       }
1956
1957       copiedSequences.append(seq.getName()
1958               + "\t"
1959               + startRes
1960               + "\t"
1961               + endRes
1962               + "\t"
1963               + seq.getSequenceAsString(sg.getStartRes(),
1964                       sg.getEndRes() + 1) + "\n");
1965     }
1966
1967   }
1968
1969   protected void pasteNew_actionPerformed()
1970   {
1971     paste(true);
1972   }
1973
1974   protected void pasteThis_actionPerformed()
1975   {
1976     paste(false);
1977   }
1978
1979   void paste(boolean newAlignment)
1980   {
1981     try
1982     {
1983
1984       if (copiedSequences == null)
1985       {
1986         return;
1987       }
1988
1989       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1990       Vector seqs = new Vector();
1991       while (st.hasMoreElements())
1992       {
1993         String name = st.nextToken();
1994         int start = Integer.parseInt(st.nextToken());
1995         int end = Integer.parseInt(st.nextToken());
1996         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1997       }
1998       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1999       for (int i = 0; i < seqs.size(); i++)
2000       {
2001         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2002       }
2003
2004       if (newAlignment)
2005       {
2006         String newtitle = MessageManager
2007                 .getString("label.copied_sequences");
2008         if (getTitle().startsWith(
2009                 MessageManager.getString("label.copied_sequences")))
2010         {
2011           newtitle = getTitle();
2012         }
2013         else
2014         {
2015           newtitle = newtitle.concat(MessageManager.formatMessage(
2016                   "label.from_msname", new String[] { getTitle() }));
2017         }
2018         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2019                 viewport.applet, newtitle, false);
2020         if (copiedHiddenColumns != null)
2021         {
2022           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2023           {
2024             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2025             af.viewport.hideColumns(region[0], region[1]);
2026           }
2027         }
2028
2029         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2030                 frameHeight);
2031       }
2032       else
2033       {
2034         addSequences(newSeqs);
2035       }
2036
2037     } catch (Exception ex)
2038     {
2039     } // could be anything being pasted in here
2040
2041   }
2042
2043   void addSequences(SequenceI[] seqs)
2044   {
2045     for (int i = 0; i < seqs.length; i++)
2046     {
2047       viewport.getAlignment().addSequence(seqs[i]);
2048     }
2049
2050     // !newAlignment
2051     addHistoryItem(new EditCommand(
2052             MessageManager.getString("label.add_sequences"), Action.PASTE,
2053             seqs, 0, viewport.getAlignment().getWidth(),
2054             viewport.getAlignment()));
2055
2056     viewport.setEndSeq(viewport.getAlignment().getHeight());
2057     viewport.getAlignment().getWidth();
2058     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2059             .getSequences());
2060
2061   }
2062
2063   protected void cut_actionPerformed()
2064   {
2065     copy_actionPerformed();
2066     delete_actionPerformed();
2067   }
2068
2069   protected void delete_actionPerformed()
2070   {
2071
2072     SequenceGroup sg = viewport.getSelectionGroup();
2073     if (sg == null)
2074     {
2075       return;
2076     }
2077
2078     Vector seqs = new Vector();
2079     SequenceI seq;
2080     for (int i = 0; i < sg.getSize(); i++)
2081     {
2082       seq = sg.getSequenceAt(i);
2083       seqs.addElement(seq);
2084     }
2085
2086     /*
2087      * If the cut affects all sequences, warn, remove highlighted columns
2088      */
2089     if (sg.getSize() == viewport.getAlignment().getHeight())
2090     {
2091       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2092               .getAlignment().getWidth()) ? true : false;
2093       if (isEntireAlignWidth)
2094       {
2095         String title = MessageManager.getString("label.delete_all");
2096         Panel infoPanel = new Panel();
2097         infoPanel.setLayout(new FlowLayout());
2098         infoPanel
2099                 .add(new Label(MessageManager.getString("warn.delete_all")));
2100
2101         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2102         dialog.setMainPanel(infoPanel);
2103         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2104         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2105         dialog.setVisible(true);
2106
2107         if (!dialog.accept)
2108         {
2109           return;
2110         }
2111       }
2112       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2113               sg.getEndRes() + 1);
2114     }
2115
2116     SequenceI[] cut = new SequenceI[seqs.size()];
2117     for (int i = 0; i < seqs.size(); i++)
2118     {
2119       cut[i] = (SequenceI) seqs.elementAt(i);
2120     }
2121
2122     /*
2123      * //ADD HISTORY ITEM
2124      */
2125     addHistoryItem(new EditCommand(
2126             MessageManager.getString("label.cut_sequences"), Action.CUT,
2127             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2128             viewport.getAlignment()));
2129
2130     viewport.setSelectionGroup(null);
2131     viewport.getAlignment().deleteGroup(sg);
2132
2133     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2134             .getSequences());
2135
2136     if (viewport.getAlignment().getHeight() < 1)
2137     {
2138       this.setVisible(false);
2139     }
2140     viewport.sendSelection();
2141   }
2142
2143   /**
2144    * group consensus toggled
2145    *
2146    */
2147   protected void showGroupConsensus_actionPerformed()
2148   {
2149     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2150     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2151
2152   }
2153
2154   /**
2155    * group conservation toggled.
2156    */
2157   protected void showGroupConservation_actionPerformed()
2158   {
2159     viewport.setShowGroupConservation(showGroupConservation.getState());
2160     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2161   }
2162
2163   /*
2164    * (non-Javadoc)
2165    *
2166    * @see
2167    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2168    * .event.ActionEvent)
2169    */
2170   protected void showConsensusHistogram_actionPerformed()
2171   {
2172     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2173     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174   }
2175
2176   /*
2177    * (non-Javadoc)
2178    *
2179    * @see
2180    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2181    * .event.ActionEvent)
2182    */
2183   protected void showSequenceLogo_actionPerformed()
2184   {
2185     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2186     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2187   }
2188
2189   protected void normSequenceLogo_actionPerformed()
2190   {
2191     showSequenceLogo.setState(true);
2192     viewport.setShowSequenceLogo(true);
2193     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195   }
2196
2197   protected void applyAutoAnnotationSettings_actionPerformed()
2198   {
2199     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2200   }
2201
2202   protected void makeGrpsFromSelection_actionPerformed()
2203   {
2204     if (avc.makeGroupsFromSelection())
2205     {
2206       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2207       alignPanel.updateAnnotation();
2208       alignPanel.paintAlignment(true);
2209     }
2210   }
2211
2212   protected void createGroup_actionPerformed()
2213   {
2214     avc.createGroup();
2215   }
2216
2217   protected void unGroup_actionPerformed()
2218   {
2219     if (avc.unGroup())
2220     {
2221       alignPanel.alignmentChanged();
2222     }
2223   }
2224
2225   protected void deleteGroups_actionPerformed()
2226   {
2227     if (avc.deleteGroups())
2228     {
2229       alignPanel.alignmentChanged();
2230     }
2231   }
2232
2233   public void selectAllSequenceMenuItem_actionPerformed()
2234   {
2235     SequenceGroup sg = new SequenceGroup();
2236     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2237     {
2238       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2239     }
2240     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2241     viewport.setSelectionGroup(sg);
2242     alignPanel.paintAlignment(true);
2243     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2244     viewport.sendSelection();
2245   }
2246
2247   public void deselectAllSequenceMenuItem_actionPerformed()
2248   {
2249     if (viewport.cursorMode)
2250     {
2251       alignPanel.seqPanel.keyboardNo1 = null;
2252       alignPanel.seqPanel.keyboardNo2 = null;
2253     }
2254     viewport.setSelectionGroup(null);
2255     viewport.getColumnSelection().clear();
2256     viewport.setSelectionGroup(null);
2257     alignPanel.idPanel.idCanvas.searchResults = null;
2258     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2259     alignPanel.paintAlignment(true);
2260     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2261     viewport.sendSelection();
2262   }
2263
2264   public void invertSequenceMenuItem_actionPerformed()
2265   {
2266     SequenceGroup sg = viewport.getSelectionGroup();
2267     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2268     {
2269       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2270     }
2271
2272     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273     viewport.sendSelection();
2274   }
2275
2276   public void invertColSel_actionPerformed()
2277   {
2278     viewport.invertColumnSelection();
2279     alignPanel.paintAlignment(true);
2280     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281     viewport.sendSelection();
2282   }
2283
2284   void trimAlignment(boolean trimLeft)
2285   {
2286     ColumnSelection colSel = viewport.getColumnSelection();
2287     int column;
2288
2289     if (!colSel.isEmpty())
2290     {
2291       if (trimLeft)
2292       {
2293         column = colSel.getMin();
2294       }
2295       else
2296       {
2297         column = colSel.getMax();
2298       }
2299
2300       SequenceI[] seqs;
2301       if (viewport.getSelectionGroup() != null)
2302       {
2303         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2304                 viewport.getHiddenRepSequences());
2305       }
2306       else
2307       {
2308         seqs = viewport.getAlignment().getSequencesArray();
2309       }
2310
2311       TrimRegionCommand trimRegion;
2312       if (trimLeft)
2313       {
2314         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2315                 column, viewport.getAlignment());
2316         viewport.setStartRes(0);
2317       }
2318       else
2319       {
2320         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2321                 column, viewport.getAlignment());
2322       }
2323
2324       statusBar.setText(MessageManager.formatMessage(
2325               "label.removed_columns",
2326               new String[] { Integer.valueOf(trimRegion.getSize())
2327                       .toString() }));
2328       addHistoryItem(trimRegion);
2329
2330       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2331       {
2332         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2333                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2334         {
2335           viewport.getAlignment().deleteGroup(sg);
2336         }
2337       }
2338
2339       viewport.firePropertyChange("alignment", null, viewport
2340               .getAlignment().getSequences());
2341     }
2342   }
2343
2344   public void removeGappedColumnMenuItem_actionPerformed()
2345   {
2346     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2347
2348     SequenceI[] seqs;
2349     if (viewport.getSelectionGroup() != null)
2350     {
2351       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2352               viewport.getHiddenRepSequences());
2353       start = viewport.getSelectionGroup().getStartRes();
2354       end = viewport.getSelectionGroup().getEndRes();
2355     }
2356     else
2357     {
2358       seqs = viewport.getAlignment().getSequencesArray();
2359     }
2360
2361     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2362             "Remove Gapped Columns", seqs, start, end,
2363             viewport.getAlignment());
2364
2365     addHistoryItem(removeGapCols);
2366
2367     statusBar.setText(MessageManager.formatMessage(
2368             "label.removed_empty_columns",
2369             new String[] { Integer.valueOf(removeGapCols.getSize())
2370                     .toString() }));
2371
2372     // This is to maintain viewport position on first residue
2373     // of first sequence
2374     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2375     int startRes = seq.findPosition(viewport.startRes);
2376     // ShiftList shifts;
2377     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2378     // edit.alColumnChanges=shifts.getInverse();
2379     // if (viewport.hasHiddenColumns)
2380     // viewport.getColumnSelection().compensateForEdits(shifts);
2381     viewport.setStartRes(seq.findIndex(startRes) - 1);
2382     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2383             .getSequences());
2384
2385   }
2386
2387   public void removeAllGapsMenuItem_actionPerformed()
2388   {
2389     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2390
2391     SequenceI[] seqs;
2392     if (viewport.getSelectionGroup() != null)
2393     {
2394       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2395               viewport.getHiddenRepSequences());
2396       start = viewport.getSelectionGroup().getStartRes();
2397       end = viewport.getSelectionGroup().getEndRes();
2398     }
2399     else
2400     {
2401       seqs = viewport.getAlignment().getSequencesArray();
2402     }
2403
2404     // This is to maintain viewport position on first residue
2405     // of first sequence
2406     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2407     int startRes = seq.findPosition(viewport.startRes);
2408
2409     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2410             viewport.getAlignment()));
2411
2412     viewport.setStartRes(seq.findIndex(startRes) - 1);
2413
2414     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2415             .getSequences());
2416
2417   }
2418
2419   public void findMenuItem_actionPerformed()
2420   {
2421     new Finder(alignPanel);
2422   }
2423
2424   /**
2425    * create a new view derived from the current view
2426    *
2427    * @param viewtitle
2428    * @return frame for the new view
2429    */
2430   public AlignFrame newView(String viewtitle)
2431   {
2432     AlignmentI newal;
2433     if (viewport.hasHiddenRows())
2434     {
2435       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2436               .getFullAlignment().getSequencesArray());
2437     }
2438     else
2439     {
2440       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2441     }
2442
2443     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2444     {
2445       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2446       {
2447         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2448         {
2449           newal.addAnnotation(viewport.getAlignment()
2450                   .getAlignmentAnnotation()[i]);
2451         }
2452       }
2453     }
2454
2455     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2456
2457     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2458     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2459     PaintRefresher.Register(newaf.alignPanel,
2460             newaf.alignPanel.av.getSequenceSetId());
2461
2462     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2463             newaf.alignPanel.av.getSequenceSetId());
2464     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2465             newaf.alignPanel.av.getSequenceSetId());
2466
2467     Vector comps = (Vector) PaintRefresher.components.get(viewport
2468             .getSequenceSetId());
2469     int viewSize = -1;
2470     for (int i = 0; i < comps.size(); i++)
2471     {
2472       if (comps.elementAt(i) instanceof AlignmentPanel)
2473       {
2474         viewSize++;
2475       }
2476     }
2477
2478     String title = new String(this.getTitle());
2479     if (viewtitle != null)
2480     {
2481       title = viewtitle + " ( " + title + ")";
2482     }
2483     else
2484     {
2485       if (title.indexOf("(View") > -1)
2486       {
2487         title = title.substring(0, title.indexOf("(View"));
2488       }
2489       title += "(View " + viewSize + ")";
2490     }
2491
2492     newaf.setTitle(title.toString());
2493
2494     newaf.viewport.setHistoryList(viewport.getHistoryList());
2495     newaf.viewport.setRedoList(viewport.getRedoList());
2496     return newaf;
2497   }
2498
2499   /**
2500    *
2501    * @return list of feature groups on the view
2502    */
2503   public String[] getFeatureGroups()
2504   {
2505     FeatureRenderer fr = null;
2506     if (alignPanel != null
2507             && (fr = alignPanel.getFeatureRenderer()) != null)
2508     {
2509       List<String> gps = fr.getFeatureGroups();
2510       String[] _gps = gps.toArray(new String[gps.size()]);
2511       return _gps;
2512     }
2513     return null;
2514   }
2515
2516   /**
2517    * get sequence feature groups that are hidden or shown
2518    *
2519    * @param visible
2520    *          true is visible
2521    * @return list
2522    */
2523   public String[] getFeatureGroupsOfState(boolean visible)
2524   {
2525     FeatureRenderer fr = null;
2526     if (alignPanel != null
2527             && (fr = alignPanel.getFeatureRenderer()) != null)
2528     {
2529       List<String> gps = fr.getGroups(visible);
2530       String[] _gps = gps.toArray(new String[gps.size()]);
2531       return _gps;
2532     }
2533     return null;
2534   }
2535
2536   /**
2537    * Change the display state for the given feature groups
2538    *
2539    * @param groups
2540    *          list of group strings
2541    * @param state
2542    *          visible or invisible
2543    */
2544   public void setFeatureGroupState(String[] groups, boolean state)
2545   {
2546     FeatureRenderer fr = null;
2547     this.sequenceFeatures.setState(true);
2548     viewport.setShowSequenceFeatures(true);
2549     if (alignPanel != null
2550             && (fr = alignPanel.getFeatureRenderer()) != null)
2551     {
2552
2553       fr.setGroupVisibility(Arrays.asList(groups), state);
2554       alignPanel.seqPanel.seqCanvas.repaint();
2555       if (alignPanel.overviewPanel != null)
2556       {
2557         alignPanel.overviewPanel.updateOverviewImage();
2558       }
2559     }
2560   }
2561
2562   public void seqLimits_itemStateChanged()
2563   {
2564     viewport.setShowJVSuffix(seqLimits.getState());
2565     alignPanel.fontChanged();
2566     alignPanel.paintAlignment(true);
2567   }
2568
2569   protected void colourTextMenuItem_actionPerformed()
2570   {
2571     viewport.setColourText(colourTextMenuItem.getState());
2572     alignPanel.paintAlignment(true);
2573   }
2574
2575   protected void displayNonconservedMenuItem_actionPerformed()
2576   {
2577     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2578     alignPanel.paintAlignment(true);
2579   }
2580
2581   protected void wrapMenuItem_actionPerformed()
2582   {
2583     viewport.setWrapAlignment(wrapMenuItem.getState());
2584     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2585     scaleAbove.setEnabled(wrapMenuItem.getState());
2586     scaleLeft.setEnabled(wrapMenuItem.getState());
2587     scaleRight.setEnabled(wrapMenuItem.getState());
2588     alignPanel.paintAlignment(true);
2589   }
2590
2591   public void overviewMenuItem_actionPerformed()
2592   {
2593     if (alignPanel.overviewPanel != null)
2594     {
2595       return;
2596     }
2597
2598     Frame frame = new Frame();
2599     OverviewPanel overview = new OverviewPanel(alignPanel);
2600     frame.add(overview);
2601     // +50 must allow for applet frame window
2602     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2603             "label.overview_params", new String[] { this.getTitle() }),
2604             overview.getPreferredSize().width,
2605             overview.getPreferredSize().height + 50);
2606
2607     frame.pack();
2608     final AlignmentPanel ap = alignPanel;
2609     frame.addWindowListener(new WindowAdapter()
2610     {
2611       @Override
2612       public void windowClosing(WindowEvent e)
2613       {
2614         if (ap != null)
2615         {
2616           ap.setOverviewPanel(null);
2617         }
2618       };
2619     });
2620
2621     alignPanel.setOverviewPanel(overview);
2622
2623   }
2624
2625   @Override
2626   public void changeColour(ColourSchemeI cs)
2627   {
2628
2629     if (cs != null)
2630     {
2631       if (viewport.getAbovePIDThreshold())
2632       {
2633         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2634                 cs, "Background"));
2635       }
2636
2637       if (viewport.getConservationSelected())
2638       {
2639         cs.setConservationApplied(true);
2640         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2641                 cs, "Background"));
2642       }
2643       else
2644       {
2645         cs.setConservationApplied(false);
2646       }
2647     }
2648     viewport.setGlobalColourScheme(cs);
2649
2650     alignPanel.paintAlignment(true);
2651   }
2652
2653   protected void modifyPID_actionPerformed()
2654   {
2655     if (viewport.getAbovePIDThreshold()
2656             && viewport.getGlobalColourScheme() != null)
2657     {
2658       SliderPanel.setPIDSliderSource(alignPanel,
2659               viewport.getGlobalColourScheme(), "Background");
2660       SliderPanel.showPIDSlider();
2661     }
2662   }
2663
2664   protected void modifyConservation_actionPerformed()
2665   {
2666     if (viewport.getConservationSelected()
2667             && viewport.getGlobalColourScheme() != null)
2668     {
2669       SliderPanel.setConservationSlider(alignPanel,
2670               viewport.getGlobalColourScheme(), "Background");
2671       SliderPanel.showConservationSlider();
2672     }
2673   }
2674
2675   protected void conservationMenuItem_actionPerformed()
2676   {
2677     viewport.setConservationSelected(conservationMenuItem.getState());
2678
2679     viewport.setAbovePIDThreshold(false);
2680     abovePIDThreshold.setState(false);
2681
2682     changeColour(viewport.getGlobalColourScheme());
2683
2684     modifyConservation_actionPerformed();
2685   }
2686
2687   public void abovePIDThreshold_actionPerformed()
2688   {
2689     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2690
2691     conservationMenuItem.setState(false);
2692     viewport.setConservationSelected(false);
2693
2694     changeColour(viewport.getGlobalColourScheme());
2695
2696     modifyPID_actionPerformed();
2697   }
2698
2699   public void sortPairwiseMenuItem_actionPerformed()
2700   {
2701     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2702     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2703             .getAlignment().getSequenceAt(0), null);
2704
2705     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2706             viewport.getAlignment()));
2707     alignPanel.paintAlignment(true);
2708   }
2709
2710   public void sortIDMenuItem_actionPerformed()
2711   {
2712     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2713     AlignmentSorter.sortByID(viewport.getAlignment());
2714     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2715             viewport.getAlignment()));
2716     alignPanel.paintAlignment(true);
2717   }
2718
2719   public void sortLengthMenuItem_actionPerformed()
2720   {
2721     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2722     AlignmentSorter.sortByLength(viewport.getAlignment());
2723     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2724             viewport.getAlignment()));
2725     alignPanel.paintAlignment(true);
2726   }
2727
2728   public void sortGroupMenuItem_actionPerformed()
2729   {
2730     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2731     AlignmentSorter.sortByGroup(viewport.getAlignment());
2732     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2733             viewport.getAlignment()));
2734     alignPanel.paintAlignment(true);
2735
2736   }
2737
2738   public void removeRedundancyMenuItem_actionPerformed()
2739   {
2740     new RedundancyPanel(alignPanel);
2741   }
2742
2743   public void pairwiseAlignmentMenuItem_actionPerformed()
2744   {
2745     if (viewport.getSelectionGroup() != null
2746             && viewport.getSelectionGroup().getSize() > 1)
2747     {
2748       Frame frame = new Frame();
2749       frame.add(new PairwiseAlignPanel(alignPanel));
2750       jalview.bin.JalviewLite.addFrame(frame,
2751               MessageManager.getString("action.pairwise_alignment"), 600,
2752               500);
2753     }
2754   }
2755
2756   public void PCAMenuItem_actionPerformed()
2757   {
2758     // are the sequences aligned?
2759     if (!viewport.getAlignment().isAligned(false))
2760     {
2761       SequenceI current;
2762       int Width = viewport.getAlignment().getWidth();
2763
2764       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2765       {
2766         current = viewport.getAlignment().getSequenceAt(i);
2767
2768         if (current.getLength() < Width)
2769         {
2770           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2771         }
2772       }
2773       alignPanel.paintAlignment(true);
2774     }
2775
2776     if ((viewport.getSelectionGroup() != null
2777             && viewport.getSelectionGroup().getSize() < 4 && viewport
2778             .getSelectionGroup().getSize() > 0)
2779             || viewport.getAlignment().getHeight() < 4)
2780     {
2781       return;
2782     }
2783
2784     try
2785     {
2786       new PCAPanel(viewport);
2787     } catch (java.lang.OutOfMemoryError ex)
2788     {
2789     }
2790
2791   }
2792
2793   public void averageDistanceTreeMenuItem_actionPerformed()
2794   {
2795     NewTreePanel("AV", "PID", "Average distance tree using PID");
2796   }
2797
2798   public void neighbourTreeMenuItem_actionPerformed()
2799   {
2800     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2801   }
2802
2803   protected void njTreeBlosumMenuItem_actionPerformed()
2804   {
2805     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2806   }
2807
2808   protected void avTreeBlosumMenuItem_actionPerformed()
2809   {
2810     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2811   }
2812
2813   void NewTreePanel(String type, String pwType, String title)
2814   {
2815     // are the sequences aligned?
2816     if (!viewport.getAlignment().isAligned(false))
2817     {
2818       SequenceI current;
2819       int Width = viewport.getAlignment().getWidth();
2820
2821       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2822       {
2823         current = viewport.getAlignment().getSequenceAt(i);
2824
2825         if (current.getLength() < Width)
2826         {
2827           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2828         }
2829       }
2830       alignPanel.paintAlignment(true);
2831
2832     }
2833
2834     if ((viewport.getSelectionGroup() != null && viewport
2835             .getSelectionGroup().getSize() > 1)
2836             || (viewport.getAlignment().getHeight() > 1))
2837     {
2838       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2839
2840       addTreeMenuItem(tp, title);
2841
2842       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2843     }
2844   }
2845
2846   void loadTree_actionPerformed()
2847   {
2848     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2849     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2850     cap.setTreeImport();
2851     Frame frame = new Frame();
2852     frame.add(cap);
2853     jalview.bin.JalviewLite.addFrame(frame,
2854             MessageManager.getString("label.paste_newick_file"), 400, 300);
2855   }
2856
2857   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2858   {
2859     TreePanel tp = new TreePanel(alignPanel, treeFile,
2860             MessageManager.getString("label.load_tree_from_file"), tree);
2861     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2862     addTreeMenuItem(tp, treeFile);
2863   }
2864
2865   /**
2866    * sort the alignment using the given treePanel
2867    *
2868    * @param treePanel
2869    *          tree used to sort view
2870    * @param title
2871    *          string used for undo event name
2872    */
2873   public void sortByTree(TreePanel treePanel, String title)
2874   {
2875     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2876     AlignmentSorter
2877             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2878     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2879     // HistoryItem.SORT));
2880     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2881             "label.order_by_params", new String[] { title }), oldOrder,
2882             viewport.getAlignment()));
2883     alignPanel.paintAlignment(true);
2884   }
2885
2886   /**
2887    * Do any automatic reordering of the alignment and add the necessary bits to
2888    * the menu structure for the new tree
2889    *
2890    * @param treePanel
2891    * @param title
2892    */
2893   protected void addTreeMenuItem(final TreePanel treePanel,
2894           final String title)
2895   {
2896     final MenuItem item = new MenuItem(title);
2897     sortByTreeMenu.add(item);
2898     item.addActionListener(new java.awt.event.ActionListener()
2899     {
2900       @Override
2901       public void actionPerformed(ActionEvent evt)
2902       {
2903         sortByTree(treePanel, title); // treePanel.getTitle());
2904       }
2905     });
2906
2907     treePanel.addWindowListener(new WindowAdapter()
2908     {
2909       @Override
2910       public void windowOpened(WindowEvent e)
2911       {
2912         if (viewport.sortByTree)
2913         {
2914           sortByTree(treePanel, title);
2915         }
2916         super.windowOpened(e);
2917       }
2918
2919       @Override
2920       public void windowClosing(WindowEvent e)
2921       {
2922         sortByTreeMenu.remove(item);
2923       };
2924     });
2925   }
2926
2927   public boolean sortBy(AlignmentOrder alorder, String undoname)
2928   {
2929     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2930     if (viewport.applet.debug)
2931     {
2932       System.err.println("Sorting " + alorder.getOrder().size()
2933               + " in alignment '" + getTitle() + "'");
2934     }
2935     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2936     if (undoname != null)
2937     {
2938       addHistoryItem(new OrderCommand(undoname, oldOrder,
2939               viewport.getAlignment()));
2940     }
2941     alignPanel.paintAlignment(true);
2942     return true;
2943   }
2944
2945   protected void documentation_actionPerformed()
2946   {
2947     alignPanel.av.applet.openJalviewHelpUrl();
2948   }
2949
2950   protected void about_actionPerformed()
2951   {
2952
2953     class AboutPanel extends Canvas
2954     {
2955       String version;
2956
2957       String builddate;
2958
2959       public AboutPanel(String version, String builddate)
2960       {
2961         this.version = version;
2962         this.builddate = builddate;
2963       }
2964
2965       @Override
2966       public void paint(Graphics g)
2967       {
2968         g.setColor(Color.white);
2969         g.fillRect(0, 0, getSize().width, getSize().height);
2970         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2971         FontMetrics fm = g.getFontMetrics();
2972         int fh = fm.getHeight();
2973         int y = 5, x = 7;
2974         g.setColor(Color.black);
2975         // TODO: update this text for each release or centrally store it for
2976         // lite and application
2977         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2978         g.drawString(MessageManager.formatMessage(
2979                 "label.jalviewLite_release", new String[] { version }), x,
2980                 y += fh);
2981         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2982         g.drawString(MessageManager.formatMessage(
2983                 "label.jaview_build_date", new String[] { builddate }), x,
2984                 y += fh);
2985         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2986         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2987                 x, y += fh * 1.5);
2988         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2989                 x + 50, y += fh + 8);
2990         g.drawString(
2991                 MessageManager.getString("label.jalview_dev_managers"), x,
2992                 y += fh);
2993         g.drawString(MessageManager
2994                 .getString("label.jalview_distribution_lists"), x, y += fh);
2995         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2996                 x, y += fh + 8);
2997         g.drawString(
2998                 MessageManager.getString("label.jalview_cite_1_authors"),
2999                 x, y += fh);
3000         g.drawString(
3001                 MessageManager.getString("label.jalview_cite_1_title"), x,
3002                 y += fh);
3003         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3004                 x, y += fh);
3005       }
3006     }
3007
3008     Frame frame = new Frame();
3009     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3010             .getBuildDate()));
3011     jalview.bin.JalviewLite.addFrame(frame,
3012             MessageManager.getString("label.jalview"), 580, 220);
3013
3014   }
3015
3016   public void showURL(String url, String target)
3017   {
3018     if (viewport.applet == null)
3019     {
3020       System.out.println("Not running as applet - no browser available.");
3021     }
3022     else
3023     {
3024       viewport.applet.showURL(url, target);
3025     }
3026   }
3027
3028   // ////////////////////////////////////////////////////////////////////////////////
3029   // JBuilder Graphics here
3030
3031   MenuBar alignFrameMenuBar = new MenuBar();
3032
3033   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3034
3035   MenuItem loadApplication = new MenuItem(
3036           MessageManager.getString("label.view_full_application"));
3037
3038   MenuItem loadTree = new MenuItem(
3039           MessageManager.getString("label.load_associated_tree"));
3040
3041   MenuItem loadAnnotations = new MenuItem(
3042           MessageManager.getString("label.load_features_annotations"));
3043
3044   MenuItem outputFeatures = new MenuItem(
3045           MessageManager.getString("label.export_features"));
3046
3047   MenuItem outputAnnotations = new MenuItem(
3048           MessageManager.getString("label.export_annotations"));
3049
3050   MenuItem closeMenuItem = new MenuItem(
3051           MessageManager.getString("action.close"));
3052
3053   MenuItem selectAllSequenceMenuItem = new MenuItem(
3054           MessageManager.getString("action.select_all"));
3055
3056   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3057           MessageManager.getString("action.deselect_all"));
3058
3059   MenuItem invertSequenceMenuItem = new MenuItem(
3060           MessageManager.getString("action.invert_selection"));
3061
3062   MenuItem remove2LeftMenuItem = new MenuItem();
3063
3064   MenuItem remove2RightMenuItem = new MenuItem();
3065
3066   MenuItem removeGappedColumnMenuItem = new MenuItem();
3067
3068   MenuItem removeAllGapsMenuItem = new MenuItem();
3069
3070   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3071
3072   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3073
3074   MenuItem sortPairwiseMenuItem = new MenuItem();
3075
3076   MenuItem sortIDMenuItem = new MenuItem();
3077
3078   MenuItem sortLengthMenuItem = new MenuItem();
3079
3080   MenuItem sortGroupMenuItem = new MenuItem();
3081
3082   MenuItem removeRedundancyMenuItem = new MenuItem();
3083
3084   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3085
3086   MenuItem PCAMenuItem = new MenuItem();
3087
3088   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3089
3090   MenuItem neighbourTreeMenuItem = new MenuItem();
3091
3092   BorderLayout borderLayout1 = new BorderLayout();
3093
3094   public Label statusBar = new Label();
3095
3096   MenuItem clustalColour = new MenuItem();
3097
3098   MenuItem zappoColour = new MenuItem();
3099
3100   MenuItem taylorColour = new MenuItem();
3101
3102   MenuItem hydrophobicityColour = new MenuItem();
3103
3104   MenuItem helixColour = new MenuItem();
3105
3106   MenuItem strandColour = new MenuItem();
3107
3108   MenuItem turnColour = new MenuItem();
3109
3110   MenuItem buriedColour = new MenuItem();
3111
3112   MenuItem purinePyrimidineColour = new MenuItem();
3113
3114   // MenuItem RNAInteractionColour = new MenuItem();
3115
3116   MenuItem RNAHelixColour = new MenuItem();
3117
3118   MenuItem userDefinedColour = new MenuItem();
3119
3120   MenuItem PIDColour = new MenuItem();
3121
3122   MenuItem BLOSUM62Colour = new MenuItem();
3123
3124   MenuItem tcoffeeColour = new MenuItem();
3125
3126   MenuItem njTreeBlosumMenuItem = new MenuItem();
3127
3128   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3129
3130   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3131
3132   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3133
3134   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3135
3136   MenuItem alProperties = new MenuItem(
3137           MessageManager.getString("label.alignment_props"));
3138
3139   MenuItem overviewMenuItem = new MenuItem();
3140
3141   MenuItem undoMenuItem = new MenuItem();
3142
3143   MenuItem redoMenuItem = new MenuItem();
3144
3145   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3146
3147   MenuItem noColourmenuItem = new MenuItem();
3148
3149   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3150
3151   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3152
3153   MenuItem findMenuItem = new MenuItem();
3154
3155   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3156
3157   MenuItem nucleotideColour = new MenuItem();
3158
3159   MenuItem deleteGroups = new MenuItem();
3160
3161   MenuItem grpsFromSelection = new MenuItem();
3162
3163   MenuItem createGroup = new MenuItem();
3164
3165   MenuItem unGroup = new MenuItem();
3166
3167   MenuItem delete = new MenuItem();
3168
3169   MenuItem copy = new MenuItem();
3170
3171   MenuItem cut = new MenuItem();
3172
3173   Menu pasteMenu = new Menu();
3174
3175   MenuItem pasteNew = new MenuItem();
3176
3177   MenuItem pasteThis = new MenuItem();
3178
3179   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3180
3181   MenuItem font = new MenuItem();
3182
3183   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3184
3185   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3186
3187   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3188
3189   MenuItem modifyPID = new MenuItem();
3190
3191   MenuItem modifyConservation = new MenuItem();
3192
3193   CheckboxMenuItem autoCalculate = null;
3194
3195   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3196           "Sort Alignment With New Tree", true);
3197
3198   Menu sortByTreeMenu = new Menu();
3199
3200   MenuItem inputText = new MenuItem();
3201
3202   MenuItem documentation = new MenuItem();
3203
3204   MenuItem about = new MenuItem();
3205
3206   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3209
3210   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3211
3212   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3213
3214   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3215
3216   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3217
3218   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3219
3220   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3221
3222   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3223
3224   /**
3225    * Initialise menus and other items
3226    *
3227    * @throws Exception
3228    */
3229   private void jbInit() throws Exception
3230   {
3231     setMenuBar(alignFrameMenuBar);
3232
3233     /*
3234      * Configure File menu items and actions
3235      */
3236     inputText
3237             .setLabel(MessageManager.getString("label.input_from_textbox"));
3238     inputText.addActionListener(this);
3239     Menu outputTextboxMenu = new Menu(
3240             MessageManager.getString("label.out_to_textbox"));
3241     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3242     {
3243
3244       MenuItem item = new MenuItem(
3245               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3246
3247       item.addActionListener(new java.awt.event.ActionListener()
3248       {
3249         @Override
3250         public void actionPerformed(ActionEvent e)
3251         {
3252           outputText_actionPerformed(e);
3253         }
3254       });
3255
3256       outputTextboxMenu.add(item);
3257     }
3258     closeMenuItem.addActionListener(this);
3259     loadApplication.addActionListener(this);
3260     loadTree.addActionListener(this);
3261     loadAnnotations.addActionListener(this);
3262     outputFeatures.addActionListener(this);
3263     outputAnnotations.addActionListener(this);
3264
3265     /*
3266      * Configure Edit menu items and actions
3267      */
3268     undoMenuItem.setEnabled(false);
3269     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3270     undoMenuItem.addActionListener(this);
3271     redoMenuItem.setEnabled(false);
3272     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3273     redoMenuItem.addActionListener(this);
3274     copy.setLabel(MessageManager.getString("action.copy"));
3275     copy.addActionListener(this);
3276     cut.setLabel(MessageManager.getString("action.cut"));
3277     cut.addActionListener(this);
3278     delete.setLabel(MessageManager.getString("action.delete"));
3279     delete.addActionListener(this);
3280     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3281     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3282     pasteNew.addActionListener(this);
3283     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3284     pasteThis.addActionListener(this);
3285     remove2LeftMenuItem.setLabel(MessageManager
3286             .getString("action.remove_left"));
3287     remove2LeftMenuItem.addActionListener(this);
3288     remove2RightMenuItem.setLabel(MessageManager
3289             .getString("action.remove_right"));
3290     remove2RightMenuItem.addActionListener(this);
3291     removeGappedColumnMenuItem.setLabel(MessageManager
3292             .getString("action.remove_empty_columns"));
3293     removeGappedColumnMenuItem.addActionListener(this);
3294     removeAllGapsMenuItem.setLabel(MessageManager
3295             .getString("action.remove_all_gaps"));
3296     removeAllGapsMenuItem.addActionListener(this);
3297     removeRedundancyMenuItem.setLabel(MessageManager
3298             .getString("action.remove_redundancy"));
3299     removeRedundancyMenuItem.addActionListener(this);
3300
3301     /*
3302      * Configure Select menu items and actions
3303      */
3304     findMenuItem.setLabel(MessageManager.getString("action.find"));
3305     findMenuItem.addActionListener(this);
3306     selectAllSequenceMenuItem.addActionListener(this);
3307     deselectAllSequenceMenuItem.addActionListener(this);
3308     invertSequenceMenuItem.setLabel(MessageManager
3309             .getString("action.invert_sequence_selection"));
3310     invertSequenceMenuItem.addActionListener(this);
3311     invertColSel.setLabel(MessageManager
3312             .getString("action.invert_column_selection"));
3313     invertColSel.addActionListener(this);
3314     deleteGroups.setLabel(MessageManager
3315             .getString("action.undefine_groups"));
3316     deleteGroups.addActionListener(this);
3317     grpsFromSelection.setLabel(MessageManager
3318             .getString("action.make_groups_selection"));
3319     grpsFromSelection.addActionListener(this);
3320     createGroup.setLabel(MessageManager.getString("action.create_group"));
3321     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3322     annotationColumnSelection.setLabel(MessageManager
3323             .getString("action.select_by_annotation"));
3324     annotationColumnSelection.addActionListener(this);
3325
3326     /*
3327      * Configure View menu items and actions
3328      */
3329     newView.setLabel(MessageManager.getString("action.new_view"));
3330     newView.addActionListener(this);
3331     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3332     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3333     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3334     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3335     hideColumns
3336             .setLabel(MessageManager.getString("label.selected_columns"));
3337     hideSequences.setLabel(MessageManager
3338             .getString("label.selected_sequences"));
3339     hideAllButSelection.setLabel(MessageManager
3340             .getString("label.all_but_selected_region"));
3341     hideAllSelection.setLabel(MessageManager
3342             .getString("label.selected_region"));
3343     showAllHidden.setLabel(MessageManager
3344             .getString("label.all_sequences_columns"));
3345     showColumns.addActionListener(this);
3346     showSeqs.addActionListener(this);
3347     hideColumns.addActionListener(this);
3348     hideSequences.addActionListener(this);
3349     hideAllButSelection.addActionListener(this);
3350     hideAllSelection.addActionListener(this);
3351     showAllHidden.addActionListener(this);
3352     featureSettings.setLabel(MessageManager
3353             .getString("action.feature_settings"));
3354     featureSettings.addActionListener(this);
3355     sequenceFeatures.setLabel(MessageManager
3356             .getString("label.show_sequence_features"));
3357     sequenceFeatures.addItemListener(this);
3358     sequenceFeatures.setState(false);
3359     followMouseOverFlag.setLabel(MessageManager
3360             .getString("label.automatic_scrolling"));
3361     followMouseOverFlag.addItemListener(this);
3362     alProperties.addActionListener(this);
3363     overviewMenuItem.setLabel(MessageManager
3364             .getString("label.overview_window"));
3365     overviewMenuItem.addActionListener(this);
3366
3367     /*
3368      * Configure Annotations menu items and actions
3369      */
3370     annotationPanelMenuItem.setLabel(MessageManager
3371             .getString("label.show_annotations"));
3372     annotationPanelMenuItem.addItemListener(this);
3373     showGroupConsensus.setLabel(MessageManager
3374             .getString("label.group_consensus"));
3375     showGroupConservation.setLabel(MessageManager
3376             .getString("label.group_conservation"));
3377     showConsensusHistogram.setLabel(MessageManager
3378             .getString("label.show_consensus_histogram"));
3379     showSequenceLogo.setLabel(MessageManager
3380             .getString("label.show_consensus_logo"));
3381     normSequenceLogo.setLabel(MessageManager
3382             .getString("label.norm_consensus_logo"));
3383     applyAutoAnnotationSettings.setLabel(MessageManager
3384             .getString("label.apply_all_groups"));
3385     applyAutoAnnotationSettings.setState(true);
3386     Menu autoAnnMenu = new Menu(
3387             MessageManager.getString("label.autocalculated_annotation"));
3388     showGroupConsensus.addItemListener(this);
3389     showGroupConservation.addItemListener(this);
3390     showConsensusHistogram.addItemListener(this);
3391     showSequenceLogo.addItemListener(this);
3392     normSequenceLogo.addItemListener(this);
3393     applyAutoAnnotationSettings.addItemListener(this);
3394     showAlignmentAnnotations = new CheckboxMenuItem(
3395             MessageManager.getString("label.show_all_al_annotations"));
3396     showSequenceAnnotations = new CheckboxMenuItem(
3397             MessageManager.getString("label.show_all_seq_annotations"));
3398     sortAnnBySequence = new CheckboxMenuItem(
3399             MessageManager.getString("label.sort_annotations_by_sequence"));
3400     sortAnnByLabel = new CheckboxMenuItem(
3401             MessageManager.getString("label.sort_annotations_by_label"));
3402     showAutoFirst = new CheckboxMenuItem(
3403             MessageManager.getString("label.show_first"));
3404     showAutoFirst.setState(false); // pending applet parameter
3405     setShowAutoCalculatedAbove(showAutoFirst.getState());
3406     showAutoLast = new CheckboxMenuItem(
3407             MessageManager.getString("label.show_last"));
3408     showAutoLast.setState(!showAutoFirst.getState());
3409     showAlignmentAnnotations.addItemListener(this);
3410     showSequenceAnnotations.addItemListener(this);
3411     sortAnnBySequence.addItemListener(this);
3412     sortAnnByLabel.addItemListener(this);
3413     showAutoFirst.addItemListener(this);
3414     showAutoLast.addItemListener(this);
3415
3416     /*
3417      * Configure Format menu items and actions
3418      */
3419     font.setLabel(MessageManager.getString("action.font"));
3420     font.addActionListener(this);
3421     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3422     scaleAbove.setState(true);
3423     scaleAbove.setEnabled(false);
3424     scaleAbove.addItemListener(this);
3425     scaleLeft.setEnabled(false);
3426     scaleLeft.setState(true);
3427     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3428     scaleLeft.addItemListener(this);
3429     scaleRight.setEnabled(false);
3430     scaleRight.setState(true);
3431     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3432     scaleRight.addItemListener(this);
3433     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3434     viewBoxesMenuItem.setState(true);
3435     viewBoxesMenuItem.addItemListener(this);
3436     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3437     viewTextMenuItem.setState(true);
3438     viewTextMenuItem.addItemListener(this);
3439     colourTextMenuItem.setLabel(MessageManager
3440             .getString("label.colour_text"));
3441     colourTextMenuItem.addItemListener(this);
3442     displayNonconservedMenuItem.setLabel(MessageManager
3443             .getString("label.show_non_conversed"));
3444     displayNonconservedMenuItem.addItemListener(this);
3445     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3446     wrapMenuItem.addItemListener(this);
3447     renderGapsMenuItem.setLabel(MessageManager
3448             .getString("action.show_gaps"));
3449     renderGapsMenuItem.setState(true);
3450     renderGapsMenuItem.addItemListener(this);
3451     centreColumnLabelFlag.setLabel(MessageManager
3452             .getString("label.centre_column_labels"));
3453     centreColumnLabelFlag.addItemListener(this);
3454     seqLimits.setState(true);
3455     seqLimits.setLabel(MessageManager
3456             .getString("label.show_sequence_limits"));
3457     seqLimits.addItemListener(this);
3458
3459     /*
3460      * Configure Colour menu items and actions
3461      */
3462     applyToAllGroups.setLabel(MessageManager
3463             .getString("label.apply_colour_to_all_groups"));
3464     applyToAllGroups.setState(true);
3465     applyToAllGroups.addItemListener(this);
3466     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3467     clustalColour.addActionListener(this);
3468     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3469     zappoColour.addActionListener(this);
3470     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3471     taylorColour.addActionListener(this);
3472     hydrophobicityColour.setLabel(MessageManager
3473             .getString("label.hydrophobicity"));
3474     hydrophobicityColour.addActionListener(this);
3475     helixColour
3476             .setLabel(MessageManager.getString("label.helix_propensity"));
3477     helixColour.addActionListener(this);
3478     strandColour.setLabel(MessageManager
3479             .getString("label.strand_propensity"));
3480     strandColour.addActionListener(this);
3481     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3482     turnColour.addActionListener(this);
3483     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3484     buriedColour.addActionListener(this);
3485     purinePyrimidineColour.setLabel(MessageManager
3486             .getString("label.purine_pyrimidine"));
3487     purinePyrimidineColour.addActionListener(this);
3488     // RNAInteractionColour.setLabel(MessageManager
3489     // .getString("label.rna_interaction"));
3490     // RNAInteractionColour.addActionListener(this);
3491     RNAHelixColour.setLabel(MessageManager
3492             .getString("action.by_rna_helixes"));
3493     RNAHelixColour.addActionListener(this);
3494     userDefinedColour.setLabel(MessageManager
3495             .getString("action.user_defined"));
3496     userDefinedColour.addActionListener(this);
3497     PIDColour.setLabel(MessageManager
3498             .getString("label.percentage_identity"));
3499     PIDColour.addActionListener(this);
3500     BLOSUM62Colour.setLabel(MessageManager
3501             .getString("label.blosum62_score"));
3502     BLOSUM62Colour.addActionListener(this);
3503     tcoffeeColour
3504             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3505     // it will be enabled only if a score file is provided
3506     tcoffeeColour.setEnabled(false);
3507     tcoffeeColour.addActionListener(this);
3508     conservationMenuItem.setLabel(MessageManager
3509             .getString("action.by_conservation"));
3510     conservationMenuItem.addItemListener(this);
3511     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3512     noColourmenuItem.addActionListener(this);
3513     abovePIDThreshold.setLabel(MessageManager
3514             .getString("label.above_identity_threshold"));
3515     abovePIDThreshold.addItemListener(this);
3516     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3517     nucleotideColour.addActionListener(this);
3518     modifyPID.setLabel(MessageManager
3519             .getString("label.modify_identity_thereshold"));
3520     modifyPID.addActionListener(this);
3521     modifyConservation.setLabel(MessageManager
3522             .getString("label.modify_conservation_thereshold"));
3523     modifyConservation.addActionListener(this);
3524     annotationColour.setLabel(MessageManager
3525             .getString("action.by_annotation"));
3526     annotationColour.addActionListener(this);
3527
3528     /*
3529      * Configure Calculate menu items and actions
3530      */
3531     sortPairwiseMenuItem.setLabel(MessageManager
3532             .getString("action.by_pairwise_id"));
3533     sortPairwiseMenuItem.addActionListener(this);
3534     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3535     sortIDMenuItem.addActionListener(this);
3536     sortLengthMenuItem.setLabel(MessageManager
3537             .getString("action.by_length"));
3538     sortLengthMenuItem.addActionListener(this);
3539     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3540     sortGroupMenuItem.addActionListener(this);
3541     pairwiseAlignmentMenuItem.setLabel(MessageManager
3542             .getString("action.pairwise_alignment"));
3543     pairwiseAlignmentMenuItem.addActionListener(this);
3544     PCAMenuItem.setLabel(MessageManager
3545             .getString("label.principal_component_analysis"));
3546     PCAMenuItem.addActionListener(this);
3547     autoCalculate = new CheckboxMenuItem(
3548             MessageManager.getString("label.autocalculate_consensus"), true);
3549     averageDistanceTreeMenuItem.setLabel(MessageManager
3550             .getString("label.average_distance_identity"));
3551     averageDistanceTreeMenuItem.addActionListener(this);
3552     neighbourTreeMenuItem.setLabel(MessageManager
3553             .getString("label.neighbour_joining_identity"));
3554     neighbourTreeMenuItem.addActionListener(this);
3555     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3556             .getString("label.average_distance_bloslum62"));
3557     avDistanceTreeBlosumMenuItem.addActionListener(this);
3558     njTreeBlosumMenuItem.setLabel(MessageManager
3559             .getString("label.neighbour_blosum62"));
3560     njTreeBlosumMenuItem.addActionListener(this);
3561     sortByTreeMenu.setLabel(MessageManager
3562             .getString("action.by_tree_order"));
3563     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3564     Menu calculateTreeMenu = new Menu(
3565             MessageManager.getString("action.calculate_tree"));
3566     autoCalculate.addItemListener(this);
3567     sortByTree.addItemListener(this);
3568
3569     /*
3570      * Configure Help menu items and actions
3571      */
3572     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3573     documentation.setLabel(MessageManager.getString("label.documentation"));
3574     documentation.addActionListener(this);
3575     about.setLabel(MessageManager.getString("label.about"));
3576     about.addActionListener(this);
3577
3578     /*
3579      * Add top level menus to frame
3580      */
3581     alignFrameMenuBar.add(fileMenu);
3582     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3583     alignFrameMenuBar.add(editMenu);
3584     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3585     alignFrameMenuBar.add(selectMenu);
3586     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3587     alignFrameMenuBar.add(viewMenu);
3588     Menu annotationsMenu = new Menu(
3589             MessageManager.getString("action.annotations"));
3590     alignFrameMenuBar.add(annotationsMenu);
3591     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3592     alignFrameMenuBar.add(formatMenu);
3593     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3594     alignFrameMenuBar.add(colourMenu);
3595     Menu calculateMenu = new Menu(
3596             MessageManager.getString("action.calculate"));
3597     alignFrameMenuBar.add(calculateMenu);
3598     alignFrameMenuBar.add(helpMenu);
3599
3600     /*
3601      * File menu
3602      */
3603     fileMenu.add(inputText);
3604     fileMenu.add(loadTree);
3605     fileMenu.add(loadAnnotations);
3606     fileMenu.addSeparator();
3607     fileMenu.add(outputTextboxMenu);
3608     fileMenu.add(outputFeatures);
3609     fileMenu.add(outputAnnotations);
3610     if (jalviewServletURL != null)
3611     {
3612       fileMenu.add(loadApplication);
3613     }
3614     fileMenu.addSeparator();
3615     fileMenu.add(closeMenuItem);
3616
3617     /*
3618      * Edit menu
3619      */
3620     editMenu.add(undoMenuItem);
3621     editMenu.add(redoMenuItem);
3622     editMenu.add(cut);
3623     editMenu.add(copy);
3624     pasteMenu.add(pasteNew);
3625     pasteMenu.add(pasteThis);
3626     editMenu.add(pasteMenu);
3627     editMenu.add(delete);
3628     editMenu.addSeparator();
3629     editMenu.add(remove2LeftMenuItem);
3630     editMenu.add(remove2RightMenuItem);
3631     editMenu.add(removeGappedColumnMenuItem);
3632     editMenu.add(removeAllGapsMenuItem);
3633     editMenu.add(removeRedundancyMenuItem);
3634
3635     /*
3636      * Select menu
3637      */
3638     selectMenu.add(findMenuItem);
3639     selectMenu.addSeparator();
3640     selectMenu.add(selectAllSequenceMenuItem);
3641     selectMenu.add(deselectAllSequenceMenuItem);
3642     selectMenu.add(invertSequenceMenuItem);
3643     selectMenu.add(invertColSel);
3644     selectMenu.add(createGroup);
3645     selectMenu.add(unGroup);
3646     selectMenu.add(grpsFromSelection);
3647     selectMenu.add(deleteGroups);
3648     selectMenu.add(annotationColumnSelection);
3649
3650     /*
3651      * View menu
3652      */
3653     viewMenu.add(newView);
3654     viewMenu.addSeparator();
3655     showMenu.add(showColumns);
3656     showMenu.add(showSeqs);
3657     showMenu.add(showAllHidden);
3658     viewMenu.add(showMenu);
3659     hideMenu.add(hideColumns);
3660     hideMenu.add(hideSequences);
3661     hideMenu.add(hideAllSelection);
3662     hideMenu.add(hideAllButSelection);
3663     viewMenu.add(hideMenu);
3664     viewMenu.addSeparator();
3665     viewMenu.add(followMouseOverFlag);
3666     viewMenu.addSeparator();
3667     viewMenu.add(sequenceFeatures);
3668     viewMenu.add(featureSettings);
3669     viewMenu.addSeparator();
3670     viewMenu.add(alProperties);
3671     viewMenu.addSeparator();
3672     viewMenu.add(overviewMenuItem);
3673
3674     /*
3675      * Annotations menu
3676      */
3677     annotationsMenu.add(annotationPanelMenuItem);
3678     annotationsMenu.addSeparator();
3679     annotationsMenu.add(showAlignmentAnnotations);
3680     annotationsMenu.add(showSequenceAnnotations);
3681     annotationsMenu.add(sortAnnBySequence);
3682     annotationsMenu.add(sortAnnByLabel);
3683     annotationsMenu.addSeparator();
3684     autoAnnMenu.add(showAutoFirst);
3685     autoAnnMenu.add(showAutoLast);
3686     autoAnnMenu.addSeparator();
3687     autoAnnMenu.add(applyAutoAnnotationSettings);
3688     autoAnnMenu.add(showConsensusHistogram);
3689     autoAnnMenu.add(showSequenceLogo);
3690     autoAnnMenu.add(normSequenceLogo);
3691     autoAnnMenu.addSeparator();
3692     autoAnnMenu.add(showGroupConservation);
3693     autoAnnMenu.add(showGroupConsensus);
3694     annotationsMenu.add(autoAnnMenu);
3695
3696     /*
3697      * Format menu
3698      */
3699     formatMenu.add(font);
3700     formatMenu.add(seqLimits);
3701     formatMenu.add(wrapMenuItem);
3702     formatMenu.add(scaleAbove);
3703     formatMenu.add(scaleLeft);
3704     formatMenu.add(scaleRight);
3705     formatMenu.add(viewBoxesMenuItem);
3706     formatMenu.add(viewTextMenuItem);
3707     formatMenu.add(colourTextMenuItem);
3708     formatMenu.add(displayNonconservedMenuItem);
3709     formatMenu.add(renderGapsMenuItem);
3710     formatMenu.add(centreColumnLabelFlag);
3711
3712     /*
3713      * Colour menu
3714      */
3715     colourMenu.add(applyToAllGroups);
3716     colourMenu.addSeparator();
3717     colourMenu.add(noColourmenuItem);
3718     colourMenu.add(clustalColour);
3719     colourMenu.add(BLOSUM62Colour);
3720     colourMenu.add(PIDColour);
3721     colourMenu.add(zappoColour);
3722     colourMenu.add(taylorColour);
3723     colourMenu.add(hydrophobicityColour);
3724     colourMenu.add(helixColour);
3725     colourMenu.add(strandColour);
3726     colourMenu.add(turnColour);
3727     colourMenu.add(buriedColour);
3728     colourMenu.add(nucleotideColour);
3729     colourMenu.add(purinePyrimidineColour);
3730     // colourMenu.add(RNAInteractionColour);
3731     colourMenu.add(tcoffeeColour);
3732     colourMenu.add(userDefinedColour);
3733     colourMenu.addSeparator();
3734     colourMenu.add(conservationMenuItem);
3735     colourMenu.add(modifyConservation);
3736     colourMenu.add(abovePIDThreshold);
3737     colourMenu.add(modifyPID);
3738     colourMenu.add(annotationColour);
3739     colourMenu.add(RNAHelixColour);
3740
3741     /*
3742      * Calculate menu
3743      */
3744     sortMenu.add(sortIDMenuItem);
3745     sortMenu.add(sortLengthMenuItem);
3746     sortMenu.add(sortByTreeMenu);
3747     sortMenu.add(sortGroupMenuItem);
3748     sortMenu.add(sortPairwiseMenuItem);
3749     calculateMenu.add(sortMenu);
3750     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3751     calculateTreeMenu.add(neighbourTreeMenuItem);
3752     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3753     calculateTreeMenu.add(njTreeBlosumMenuItem);
3754     calculateMenu.add(calculateTreeMenu);
3755     calculateMenu.addSeparator();
3756     calculateMenu.add(pairwiseAlignmentMenuItem);
3757     calculateMenu.add(PCAMenuItem);
3758     calculateMenu.add(autoCalculate);
3759     calculateMenu.add(sortByTree);
3760
3761     /*
3762      * Help menu
3763      */
3764     helpMenu.add(documentation);
3765     helpMenu.add(about);
3766
3767     /*
3768      * Status bar
3769      */
3770     statusBar.setBackground(Color.white);
3771     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3772     statusBar.setText(MessageManager.getString("label.status_bar"));
3773     this.add(statusBar, BorderLayout.SOUTH);
3774   }
3775
3776   @Override
3777   public void setStatus(String string)
3778   {
3779     statusBar.setText(string);
3780   };
3781
3782   MenuItem featureSettings = new MenuItem();
3783
3784   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3785
3786   MenuItem annotationColour = new MenuItem();
3787
3788   MenuItem annotationColumnSelection = new MenuItem();
3789
3790   MenuItem invertColSel = new MenuItem();
3791
3792   MenuItem showColumns = new MenuItem();
3793
3794   MenuItem showSeqs = new MenuItem();
3795
3796   MenuItem hideColumns = new MenuItem();
3797
3798   MenuItem hideSequences = new MenuItem();
3799
3800   MenuItem hideAllButSelection = new MenuItem();
3801
3802   MenuItem hideAllSelection = new MenuItem();
3803
3804   MenuItem showAllHidden = new MenuItem();
3805
3806   MenuItem newView = new MenuItem();
3807
3808   private CheckboxMenuItem showAlignmentAnnotations;
3809
3810   private CheckboxMenuItem showSequenceAnnotations;
3811
3812   private CheckboxMenuItem sortAnnBySequence;
3813
3814   private CheckboxMenuItem sortAnnByLabel;
3815
3816   private CheckboxMenuItem showAutoFirst;
3817
3818   private CheckboxMenuItem showAutoLast;
3819
3820   private SplitFrame splitFrame;
3821
3822   /**
3823    * Attach the alignFrame panels after embedding menus, if necessary. This used
3824    * to be called setEmbedded, but is now creates the dropdown menus in a
3825    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3826    *
3827    * @param reallyEmbedded
3828    *          true to attach the view to the applet area on the page rather than
3829    *          in a new window
3830    */
3831   public void createAlignFrameWindow(boolean reallyEmbedded)
3832   {
3833     if (reallyEmbedded)
3834     {
3835       embedAlignFrameInApplet(viewport.applet);
3836     }
3837     else
3838     {
3839       // //////
3840       // test and embed menu bar if necessary.
3841       //
3842       if (embedMenuIfNeeded(alignPanel))
3843       {
3844         /*
3845          * adjust for status bar height too. ? pointless as overridden by layout
3846          * manager
3847          */
3848         alignPanel.setSize(getSize().width,
3849                 getSize().height - statusBar.getHeight());
3850       }
3851       add(statusBar, BorderLayout.SOUTH);
3852       add(alignPanel, BorderLayout.CENTER);
3853       // and register with the applet so it can pass external API calls to us
3854       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3855               frameHeight);
3856     }
3857   }
3858
3859   /**
3860    * Add the components of this AlignFrame to the applet container.
3861    *
3862    * @param theApplet
3863    */
3864   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3865   {
3866     // ////
3867     // Explicitly build the embedded menu panel for the on-page applet
3868     //
3869     // view cannot be closed if its actually on the page
3870     fileMenu.remove(closeMenuItem);
3871     fileMenu.remove(3); // Remove Separator
3872     // construct embedded menu, using default font
3873     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3874     // and actually add the components to the applet area
3875     theApplet.setLayout(new BorderLayout());
3876     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3877     theApplet.add(statusBar, BorderLayout.SOUTH);
3878     // TODO should size be left to the layout manager?
3879     alignPanel.setSize(theApplet.getSize().width,
3880             theApplet.getSize().height - embeddedMenu.getHeight()
3881                     - statusBar.getHeight());
3882     theApplet.add(alignPanel, BorderLayout.CENTER);
3883     final AlignFrame me = this;
3884     theApplet.addFocusListener(new FocusListener()
3885     {
3886
3887       @Override
3888       public void focusLost(FocusEvent e)
3889       {
3890         if (theApplet.currentAlignFrame == me)
3891         {
3892           theApplet.currentAlignFrame = null;
3893         }
3894       }
3895
3896       @Override
3897       public void focusGained(FocusEvent e)
3898       {
3899         theApplet.currentAlignFrame = me;
3900       }
3901     });
3902     theApplet.validate();
3903   }
3904
3905   /**
3906    * create a new binding between structures in an existing jmol viewer instance
3907    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3908    * this does not open a new Jmol window, or modify the display of the
3909    * structures in the original jmol window. Note This method doesn't work
3910    * without an additional javascript library to exchange messages between the
3911    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3912    *
3913    * @param viewer
3914    *          JmolViewer instance
3915    * @param sequenceIds
3916    *          - sequence Ids to search for associations
3917    */
3918   public SequenceStructureBinding addStructureViewInstance(
3919           Object jmolviewer, String[] sequenceIds)
3920   {
3921     Viewer viewer = null;
3922     try
3923     {
3924       viewer = (Viewer) jmolviewer;
3925     } catch (ClassCastException ex)
3926     {
3927       System.err.println("Unsupported viewer object :"
3928               + jmolviewer.getClass());
3929     }
3930     if (viewer == null)
3931     {
3932       System.err.println("Can't use this object as a structure viewer:"
3933               + jmolviewer.getClass());
3934       return null;
3935     }
3936     SequenceI[] seqs = null;
3937     if (sequenceIds == null || sequenceIds.length == 0)
3938     {
3939       seqs = viewport.getAlignment().getSequencesArray();
3940     }
3941     else
3942     {
3943       Vector sqi = new Vector();
3944       AlignmentI al = viewport.getAlignment();
3945       for (int sid = 0; sid < sequenceIds.length; sid++)
3946       {
3947         SequenceI sq = al.findName(sequenceIds[sid]);
3948         if (sq != null)
3949         {
3950           sqi.addElement(sq);
3951         }
3952       }
3953       if (sqi.size() > 0)
3954       {
3955         seqs = new SequenceI[sqi.size()];
3956         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3957         {
3958           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3959         }
3960       }
3961       else
3962       {
3963         return null;
3964       }
3965     }
3966     AAStructureBindingModel jmv = null;
3967     // TODO: search for a jmv that involves viewer
3968     if (jmv == null)
3969     { // create a new viewer/jalview binding.
3970       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3971     }
3972     return jmv;
3973
3974   }
3975
3976   /**
3977    * bind a pdb file to a sequence in the current view
3978    *
3979    * @param sequenceId
3980    *          - sequenceId within the dataset.
3981    * @param pdbEntryString
3982    *          - the short name for the PDB file
3983    * @param pdbFile
3984    *          - pdb file - either a URL or a valid PDB file.
3985    * @return true if binding was as success TODO: consider making an exception
3986    *         structure for indicating when PDB parsing or sequenceId location
3987    *         fails.
3988    */
3989   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3990           String pdbFile)
3991   {
3992     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3993     boolean needtoadd = false;
3994     if (toaddpdb != null)
3995     {
3996       Vector pdbe = toaddpdb.getAllPDBEntries();
3997       PDBEntry pdbentry = null;
3998       if (pdbe != null && pdbe.size() > 0)
3999       {
4000         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4001         {
4002           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4003           if (!pdbentry.getId().equals(pdbEntryString)
4004                   && !pdbentry.getFile().equals(pdbFile))
4005           {
4006             pdbentry = null;
4007           }
4008           else
4009           {
4010             continue;
4011           }
4012         }
4013       }
4014       if (pdbentry == null)
4015       {
4016         pdbentry = new PDBEntry();
4017         pdbentry.setId(pdbEntryString);
4018         pdbentry.setFile(pdbFile);
4019         needtoadd = true; // add this new entry to sequence.
4020       }
4021       // resolve data source
4022       // TODO: this code should be a refactored to an io package
4023       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4024       if (protocol == null)
4025       {
4026         return false;
4027       }
4028       if (needtoadd)
4029       {
4030         // make a note of the access mode and add
4031         if (pdbentry.getProperty() == null)
4032         {
4033           pdbentry.setProperty(new Hashtable());
4034         }
4035         pdbentry.getProperty().put("protocol", protocol);
4036         toaddpdb.addPDBId(pdbentry);
4037         alignPanel.getStructureSelectionManager()
4038                 .registerPDBEntry(pdbentry);
4039       }
4040     }
4041     return true;
4042   }
4043
4044   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4045   {
4046     if (seqs != null)
4047     {
4048       Vector sequences = new Vector();
4049       for (int i = 0; i < seqs.length; i++)
4050       {
4051         if (seqs[i] != null)
4052         {
4053           sequences.addElement(new Object[] { seqs[i],
4054               (chains != null) ? chains[i] : null });
4055         }
4056       }
4057       seqs = new SequenceI[sequences.size()];
4058       chains = new String[sequences.size()];
4059       for (int i = 0, isize = sequences.size(); i < isize; i++)
4060       {
4061         Object[] oj = (Object[]) sequences.elementAt(i);
4062
4063         seqs[i] = (SequenceI) oj[0];
4064         chains[i] = (String) oj[1];
4065       }
4066     }
4067     return new Object[] { seqs, chains };
4068
4069   }
4070
4071   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4072           SequenceI[] seqs, String[] chains, String protocol)
4073   {
4074     // Scrub any null sequences from the array
4075     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4076     seqs = (SequenceI[]) sqch[0];
4077     chains = (String[]) sqch[1];
4078     if (seqs == null || seqs.length == 0)
4079     {
4080       System.err
4081               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4082     }
4083     if (protocol == null || protocol.trim().length() == 0
4084             || protocol.equals("null"))
4085     {
4086       protocol = (String) pdb.getProperty().get("protocol");
4087       if (protocol == null)
4088       {
4089         System.err.println("Couldn't work out protocol to open structure: "
4090                 + pdb.getId());
4091         return;
4092       }
4093     }
4094     if (applet.useXtrnalSviewer)
4095     {
4096       // register the association(s) and quit, don't create any windows.
4097       if (StructureSelectionManager.getStructureSelectionManager(applet)
4098               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4099       {
4100         System.err.println("Failed to map " + pdb.getFile() + " ("
4101                 + protocol + ") to any sequences");
4102       }
4103       return;
4104     }
4105     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4106     {
4107       // can only do alignments with Jmol
4108       // find the last jmol window assigned to this alignment
4109       jalview.appletgui.AppletJmol ajm = null, tajm;
4110       Vector jmols = applet
4111               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4112       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4113       {
4114         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4115         if (tajm.ap.alignFrame == this)
4116         {
4117           ajm = tajm;
4118           break;
4119         }
4120       }
4121       if (ajm != null)
4122       {
4123         System.err
4124                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4125         // try and add the pdb structure
4126         // ajm.addS
4127         ajm = null;
4128       }
4129     }
4130     // otherwise, create a new window
4131     if (applet.jmolAvailable)
4132     {
4133       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4134               protocol);
4135       applet.lastFrameX += 40;
4136       applet.lastFrameY += 40;
4137     }
4138     else
4139     {
4140       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4141     }
4142
4143   }
4144
4145   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4146           SequenceI[][] seqs, String[][] chains, String[] protocols)
4147   {
4148     // TODO Auto-generated method stub
4149     System.err.println("Aligned Structure View: Not yet implemented.");
4150   }
4151
4152   /**
4153    * modify the current selection, providing the user has not made a selection
4154    * already.
4155    *
4156    * @param sel
4157    *          - sequences from this alignment
4158    * @param csel
4159    *          - columns to be selected on the alignment
4160    */
4161   public void select(SequenceGroup sel, ColumnSelection csel)
4162   {
4163     alignPanel.seqPanel.selection(sel, csel, null);
4164   }
4165
4166   public void scrollTo(int row, int column)
4167   {
4168     alignPanel.seqPanel.scrollTo(row, column);
4169   }
4170
4171   public void scrollToRow(int row)
4172   {
4173     alignPanel.seqPanel.scrollToRow(row);
4174   }
4175
4176   public void scrollToColumn(int column)
4177   {
4178     alignPanel.seqPanel.scrollToColumn(column);
4179   }
4180
4181   /**
4182    * @return the alignments unique ID.
4183    */
4184   public String getSequenceSetId()
4185   {
4186     return viewport.getSequenceSetId();
4187   }
4188
4189   /**
4190    * Load the (T-Coffee) score file from the specified url
4191    *
4192    * @param source
4193    *          File/URL/T-COFFEE score file contents
4194    * @throws IOException
4195    * @return true if alignment was annotated with data from source
4196    */
4197   public boolean loadScoreFile(String source) throws IOException
4198   {
4199
4200     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4201             AppletFormatAdapter.checkProtocol(source));
4202     if (!file.isValid())
4203     {
4204       // TODO: raise dialog for gui
4205       System.err.println("Problems parsing T-Coffee scores: "
4206               + file.getWarningMessage());
4207       System.err.println("Origin was:\n" + source);
4208       return false;
4209     }
4210
4211     /*
4212      * check that the score matrix matches the alignment dimensions
4213      */
4214     AlignmentI aln;
4215     if ((aln = viewport.getAlignment()) != null
4216             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4217                     .getWidth()))
4218     {
4219       // TODO: raise a dialog box here rather than bomb out.
4220       System.err
4221               .println("The scores matrix does not match the alignment dimensions");
4222
4223     }
4224
4225     // TODO add parameter to indicate if matching should be done
4226     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4227     {
4228       alignPanel.fontChanged();
4229       tcoffeeColour.setEnabled(true);
4230       // switch to this color
4231       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4232       return true;
4233     }
4234     else
4235     {
4236       System.err.println("Problems resolving T-Coffee scores:");
4237       if (file.getWarningMessage() != null)
4238       {
4239         System.err.println(file.getWarningMessage());
4240       }
4241     }
4242     return false;
4243   }
4244
4245   public SplitFrame getSplitFrame()
4246   {
4247     return this.splitFrame;
4248   }
4249
4250   public void setSplitFrame(SplitFrame sf)
4251   {
4252     this.splitFrame = sf;
4253   }
4254
4255   // may not need this
4256   @Override
4257   public void setShowSeqFeatures(boolean b)
4258   {
4259     // showSeqFeatures.setSelected(b);
4260     viewport.setShowSequenceFeatures(b);
4261
4262   }
4263
4264   @Override
4265   public void setMenusForViewport()
4266   {
4267     // setMenusFromViewport(viewport);
4268
4269   }
4270
4271   @Override
4272   public void refreshFeatureUI(boolean enableIfNecessary)
4273   {
4274     if (enableIfNecessary)
4275     {
4276       sequenceFeatures.setState(true);
4277       alignPanel.av.setShowSequenceFeatures(true);
4278     }
4279   }
4280
4281   @Override
4282   public FeatureSettingsControllerI getFeatureSettingsUI()
4283   {
4284     return alignPanel.av.featureSettings;
4285   }
4286
4287 }