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     viewport.setScaleAboveWrapped(scaleAbove.getState());
 223
 224     alignPanel = new AlignmentPanel(this, viewport);
 225     avc = new jalview.controller.AlignViewController(this, viewport,
 226             alignPanel);
 227     viewport.updateConservation(alignPanel);
 228     viewport.updateConsensus(alignPanel);
 229
 230     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 231     followMouseOverFlag.setState(viewport.isFollowHighlight());
 232     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 233     showGroupConservation.setState(viewport.isShowGroupConservation());
 234     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 235     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 236     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 237     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 238     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 239     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 240     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showAlignmentAnnotations.setState(true);
 242     showSequenceAnnotations.setState(false);
 243
 244     seqLimits.setState(viewport.getShowJVSuffix());
 245
 246     if (applet != null)
 247     {
 248       String param = applet.getParameter("sortBy");
 249       if (param != null)
 250       {
 251         if (param.equalsIgnoreCase("Id"))
 252         {
 253           sortIDMenuItem_actionPerformed();
 254         }
 255         else if (param.equalsIgnoreCase("Pairwise Identity"))
 256         {
 257           sortPairwiseMenuItem_actionPerformed();
 258         }
 259         else if (param.equalsIgnoreCase("Length"))
 260         {
 261           sortLengthMenuItem_actionPerformed();
 262         }
 263       }
 264
 265       param = applet.getParameter("wrap");
 266       if (param != null)
 267       {
 268         if (param.equalsIgnoreCase("true"))
 269         {
 270           wrapMenuItem.setState(true);
 271           wrapMenuItem_actionPerformed();
 272         }
 273       }
 274       param = applet.getParameter("centrecolumnlabels");
 275       if (param != null)
 276       {
 277         centreColumnLabelFlag.setState(true);
 278         centreColumnLabelFlag_stateChanged();
 279       }
 280
 281     }
 282     if (viewport.getAlignment().isNucleotide())
 283     {
 284       viewport.updateStrucConsensus(alignPanel);
 285       if (viewport.getAlignment().hasRNAStructure())
 286       {
 287         RNAHelixColour.setEnabled(true);
 288       }
 289       else
 290       {
 291         RNAHelixColour.setEnabled(false);
 292       }
 293     }
 294     else
 295     {
 296       RNAHelixColour.setEnabled(false);
 297       purinePyrimidineColour.setEnabled(false);
 298     }
 299     // Some JVMS send keyevents to Top frame or lowest panel,
 300     // Havent worked out why yet. So add to both this frame and seqCanvas for
 301     // now
 302     this.addKeyListener(this);
 303     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 304     alignPanel.idPanel.idCanvas.addKeyListener(this);
 305     alignPanel.scalePanel.addKeyListener(this);
 306     alignPanel.annotationPanel.addKeyListener(this);
 307     alignPanel.annotationPanelHolder.addKeyListener(this);
 308     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 309     alignPanel.alabels.addKeyListener(this);
 310
 311     setAnnotationsVisibility();
 312
 313     if (addToDisplay)
 314     {
 315       addToDisplay(embedded);
 316     }
 317   }
 318
 319   /**
 320    * @param embedded
 321    */
 322   public void addToDisplay(boolean embedded)
 323   {
 324     createAlignFrameWindow(embedded);
 325     validate();
 326     alignPanel.adjustAnnotationHeight();
 327     alignPanel.paintAlignment(true);
 328   }
 329
 330   public AlignViewport getAlignViewport()
 331   {
 332     return viewport;
 333   }
 334
 335   public SeqCanvas getSeqcanvas()
 336   {
 337     return alignPanel.seqPanel.seqCanvas;
 338   }
 339
 340   /**
 341    * Load a features file onto the alignment
 342    *
 343    * @param file
 344    *          file URL, content, or other resolvable path
 345    * @param type
 346    *          is protocol for accessing data referred to by file
 347    */
 348
 349   public boolean parseFeaturesFile(String file, String type)
 350   {
 351     return parseFeaturesFile(file, type, true);
 352   }
 353
 354   /**
 355    * Load a features file onto the alignment
 356    *
 357    * @param file
 358    *          file URL, content, or other resolvable path
 359    * @param type
 360    *          is protocol for accessing data referred to by file
 361    * @param autoenabledisplay
 362    *          when true, display features flag will be automatically enabled if
 363    *          features are loaded
 364    * @return true if data parsed as a features file
 365    */
 366   public boolean parseFeaturesFile(String file, String type,
 367           boolean autoenabledisplay)
 368   {
 369     boolean featuresFile = false;
 370     try
 371     {
 372       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 373               .getFeatureRenderer().getFeatureColours();
 374       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 375               "relaxedidmatch", false);
 376       featuresFile = new FeaturesFile(file, type).parse(
 377               viewport.getAlignment(), colours, true, relaxedIdMatching);
 378     } catch (Exception ex)
 379     {
 380       ex.printStackTrace();
 381     }
 382
 383     if (featuresFile)
 384     {
 385       if (autoenabledisplay)
 386       {
 387         viewport.setShowSequenceFeatures(true);
 388         sequenceFeatures.setState(true);
 389       }
 390       if (alignPanel.seqPanel.seqCanvas.fr != null)
 391       {
 392         // update the min/max ranges where necessary
 393         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 394       }
 395       if (viewport.featureSettings != null)
 396       {
 397         viewport.featureSettings.refreshTable();
 398       }
 399       alignPanel.paintAlignment(true);
 400       statusBar.setText(MessageManager
 401               .getString("label.successfully_added_features_alignment"));
 402     }
 403     return featuresFile;
 404   }
 405
 406   @Override
 407   public void keyPressed(KeyEvent evt)
 408   {
 409     if (viewport.cursorMode
 410             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 411                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 412                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 413             && Character.isDigit(evt.getKeyChar()))
 414     {
 415       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 416     }
 417
 418     switch (evt.getKeyCode())
 419     {
 420     case 27: // escape key
 421       deselectAllSequenceMenuItem_actionPerformed();
 422
 423       alignPanel.alabels.cancelDrag();
 424       break;
 425     case KeyEvent.VK_X:
 426       if (evt.isControlDown() || evt.isMetaDown())
 427       {
 428         cut_actionPerformed();
 429       }
 430       break;
 431     case KeyEvent.VK_C:
 432       if (viewport.cursorMode && !evt.isControlDown())
 433       {
 434         alignPanel.seqPanel.setCursorColumn();
 435       }
 436       if (evt.isControlDown() || evt.isMetaDown())
 437       {
 438         copy_actionPerformed();
 439       }
 440       break;
 441     case KeyEvent.VK_V:
 442       if (evt.isControlDown())
 443       {
 444         paste(evt.isShiftDown());
 445       }
 446       break;
 447     case KeyEvent.VK_A:
 448       if (evt.isControlDown() || evt.isMetaDown())
 449       {
 450         selectAllSequenceMenuItem_actionPerformed();
 451       }
 452       break;
 453     case KeyEvent.VK_DOWN:
 454       if (viewport.cursorMode)
 455       {
 456         alignPanel.seqPanel.moveCursor(0, 1);
 457       }
 458       else
 459       {
 460         moveSelectedSequences(false);
 461       }
 462       break;
 463
 464     case KeyEvent.VK_UP:
 465       if (viewport.cursorMode)
 466       {
 467         alignPanel.seqPanel.moveCursor(0, -1);
 468       }
 469       else
 470       {
 471         moveSelectedSequences(true);
 472       }
 473       break;
 474
 475     case KeyEvent.VK_LEFT:
 476       if (evt.isAltDown() || !viewport.cursorMode)
 477       {
 478         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 479       }
 480       else
 481       {
 482         alignPanel.seqPanel.moveCursor(-1, 0);
 483       }
 484       break;
 485
 486     case KeyEvent.VK_RIGHT:
 487       if (evt.isAltDown() || !viewport.cursorMode)
 488       {
 489         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 490       }
 491       else
 492       {
 493         alignPanel.seqPanel.moveCursor(1, 0);
 494       }
 495       break;
 496
 497     case KeyEvent.VK_SPACE:
 498       if (viewport.cursorMode)
 499       {
 500         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 501                 || evt.isShiftDown() || evt.isAltDown());
 502       }
 503       break;
 504
 505     case KeyEvent.VK_DELETE:
 506     case KeyEvent.VK_BACK_SPACE:
 507       if (viewport.cursorMode)
 508       {
 509         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 510                 || evt.isShiftDown() || evt.isAltDown());
 511       }
 512       else
 513       {
 514         cut_actionPerformed();
 515         alignPanel.seqPanel.seqCanvas.repaint();
 516       }
 517       break;
 518
 519     case KeyEvent.VK_S:
 520       if (viewport.cursorMode)
 521       {
 522         alignPanel.seqPanel.setCursorRow();
 523       }
 524       break;
 525     case KeyEvent.VK_P:
 526       if (viewport.cursorMode)
 527       {
 528         alignPanel.seqPanel.setCursorPosition();
 529       }
 530       break;
 531
 532     case KeyEvent.VK_ENTER:
 533     case KeyEvent.VK_COMMA:
 534       if (viewport.cursorMode)
 535       {
 536         alignPanel.seqPanel.setCursorRowAndColumn();
 537       }
 538       break;
 539
 540     case KeyEvent.VK_Q:
 541       if (viewport.cursorMode)
 542       {
 543         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 544       }
 545       break;
 546     case KeyEvent.VK_M:
 547       if (viewport.cursorMode)
 548       {
 549         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 550       }
 551       break;
 552
 553     case KeyEvent.VK_F2:
 554       viewport.cursorMode = !viewport.cursorMode;
 555       statusBar.setText(MessageManager.formatMessage(
 556               "label.keyboard_editing_mode",
 557               new String[] { (viewport.cursorMode ? "on" : "off") }));
 558       if (viewport.cursorMode)
 559       {
 560         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 561         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 562       }
 563       break;
 564
 565     case KeyEvent.VK_F:
 566       if (evt.isControlDown())
 567       {
 568         findMenuItem_actionPerformed();
 569       }
 570       break;
 571
 572     case KeyEvent.VK_H:
 573     {
 574       boolean toggleSeqs = !evt.isControlDown();
 575       boolean toggleCols = !evt.isShiftDown();
 576       toggleHiddenRegions(toggleSeqs, toggleCols);
 577       break;
 578     }
 579
 580     case KeyEvent.VK_PAGE_UP:
 581       if (viewport.getWrapAlignment())
 582       {
 583         alignPanel.scrollUp(true);
 584       }
 585       else
 586       {
 587         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 588                 - viewport.endSeq + viewport.startSeq);
 589       }
 590       break;
 591
 592     case KeyEvent.VK_PAGE_DOWN:
 593       if (viewport.getWrapAlignment())
 594       {
 595         alignPanel.scrollUp(false);
 596       }
 597       else
 598       {
 599         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 600                 + viewport.endSeq - viewport.startSeq);
 601       }
 602       break;
 603
 604     case KeyEvent.VK_Z:
 605       if (evt.isControlDown())
 606       {
 607         undoMenuItem_actionPerformed();
 608       }
 609       break;
 610
 611     case KeyEvent.VK_Y:
 612       if (evt.isControlDown())
 613       {
 614         redoMenuItem_actionPerformed();
 615       }
 616       break;
 617
 618     case KeyEvent.VK_L:
 619       if (evt.isControlDown())
 620       {
 621         trimAlignment(true);
 622       }
 623       break;
 624
 625     case KeyEvent.VK_R:
 626       if (evt.isControlDown())
 627       {
 628         trimAlignment(false);
 629       }
 630       break;
 631
 632     case KeyEvent.VK_E:
 633       if (evt.isControlDown())
 634       {
 635         if (evt.isShiftDown())
 636         {
 637           this.removeAllGapsMenuItem_actionPerformed();
 638         }
 639         else
 640         {
 641           removeGappedColumnMenuItem_actionPerformed();
 642         }
 643       }
 644       break;
 645     case KeyEvent.VK_I:
 646       if (evt.isControlDown())
 647       {
 648         if (evt.isAltDown())
 649         {
 650           invertColSel_actionPerformed();
 651         }
 652         else
 653         {
 654           invertSequenceMenuItem_actionPerformed();
 655         }
 656       }
 657       break;
 658
 659     case KeyEvent.VK_G:
 660       if (evt.isControlDown())
 661       {
 662         if (evt.isShiftDown())
 663         {
 664           this.unGroup_actionPerformed();
 665         }
 666         else
 667         {
 668           this.createGroup_actionPerformed();
 669         }
 670       }
 671       break;
 672
 673     case KeyEvent.VK_U:
 674       if (evt.isControlDown())
 675       {
 676         this.deleteGroups_actionPerformed();
 677       }
 678       break;
 679
 680     case KeyEvent.VK_T:
 681       if (evt.isControlDown())
 682       {
 683         newView(null);
 684       }
 685       break;
 686
 687     }
 688     alignPanel.paintAlignment(true);
 689   }
 690
 691   /**
 692    * called by key handler and the hide all/show all menu items
 693    *
 694    * @param toggleSeqs
 695    * @param toggleCols
 696    */
 697   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 698   {
 699     boolean hide = false;
 700     SequenceGroup sg = viewport.getSelectionGroup();
 701     if (!toggleSeqs && !toggleCols)
 702     {
 703       // Hide everything by the current selection - this is a hack - we do the
 704       // invert and then hide
 705       // first check that there will be visible columns after the invert.
 706       if (viewport.hasSelectedColumns()
 707               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 708                       .getEndRes()))
 709       {
 710         // now invert the sequence set, if required - empty selection implies
 711         // that no hiding is required.
 712         if (sg != null)
 713         {
 714           invertSequenceMenuItem_actionPerformed();
 715           sg = viewport.getSelectionGroup();
 716           toggleSeqs = true;
 717
 718         }
 719         viewport.expandColSelection(sg, true);
 720         // finally invert the column selection and get the new sequence
 721         // selection and indicate it should be hidden.
 722         invertColSel_actionPerformed();
 723         toggleCols = true;
 724       }
 725     }
 726
 727     if (toggleSeqs)
 728     {
 729       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 730       {
 731         hide = true;
 732         viewport.hideAllSelectedSeqs();
 733       }
 734       else if (!(toggleCols && viewport.hasSelectedColumns()))
 735       {
 736         viewport.showAllHiddenSeqs();
 737       }
 738     }
 739
 740     if (toggleCols)
 741     {
 742       if (viewport.hasSelectedColumns())
 743       {
 744         viewport.hideSelectedColumns();
 745         if (!toggleSeqs)
 746         {
 747           viewport.setSelectionGroup(sg);
 748         }
 749       }
 750       else if (!hide)
 751       {
 752         viewport.showAllHiddenColumns();
 753       }
 754       viewport.sendSelection();
 755     }
 756   }
 757
 758   @Override
 759   public void keyReleased(KeyEvent evt)
 760   {
 761   }
 762
 763   @Override
 764   public void keyTyped(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void itemStateChanged(ItemEvent evt)
 770   {
 771     final Object source = evt.getSource();
 772     if (source == displayNonconservedMenuItem)
 773     {
 774       displayNonconservedMenuItem_actionPerformed();
 775     }
 776     else if (source == colourTextMenuItem)
 777     {
 778       colourTextMenuItem_actionPerformed();
 779     }
 780     else if (source == wrapMenuItem)
 781     {
 782       wrapMenuItem_actionPerformed();
 783     }
 784     else if (source == scaleAbove)
 785     {
 786       viewport.setScaleAboveWrapped(scaleAbove.getState());
 787     }
 788     else if (source == scaleLeft)
 789     {
 790       viewport.setScaleLeftWrapped(scaleLeft.getState());
 791     }
 792     else if (source == scaleRight)
 793     {
 794       viewport.setScaleRightWrapped(scaleRight.getState());
 795     }
 796     else if (source == seqLimits)
 797     {
 798       seqLimits_itemStateChanged();
 799     }
 800     else if (source == viewBoxesMenuItem)
 801     {
 802       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 803     }
 804     else if (source == viewTextMenuItem)
 805     {
 806       viewport.setShowText(viewTextMenuItem.getState());
 807     }
 808     else if (source == renderGapsMenuItem)
 809     {
 810       viewport.setRenderGaps(renderGapsMenuItem.getState());
 811     }
 812     else if (source == annotationPanelMenuItem)
 813     {
 814       boolean showAnnotations = annotationPanelMenuItem.getState();
 815       showAlignmentAnnotations.setEnabled(showAnnotations);
 816       showSequenceAnnotations.setEnabled(showAnnotations);
 817       viewport.setShowAnnotation(showAnnotations);
 818       alignPanel.setAnnotationVisible(showAnnotations);
 819     }
 820     else if (source == sequenceFeatures)
 821     {
 822       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 823       alignPanel.seqPanel.seqCanvas.repaint();
 824     }
 825     else if (source == showAlignmentAnnotations)
 826     {
 827       setAnnotationsVisibility();
 828     }
 829     else if (source == showSequenceAnnotations)
 830     {
 831       setAnnotationsVisibility();
 832     }
 833     else if (source == sortAnnBySequence)
 834     {
 835       boolean newState = sortAnnBySequence.getState();
 836       sortAnnByLabel.setState(false);
 837       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 838               : SequenceAnnotationOrder.NONE);
 839       setViewportAnnotationOrder();
 840     }
 841     else if (source == sortAnnByLabel)
 842     {
 843       boolean newState = sortAnnByLabel.getState();
 844       sortAnnBySequence.setState(false);
 845       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 846               : SequenceAnnotationOrder.NONE);
 847       setViewportAnnotationOrder();
 848     }
 849     else if (source == showAutoFirst)
 850     {
 851       showAutoLast.setState(!showAutoFirst.getState());
 852       setShowAutoCalculatedAbove(showAutoFirst.getState());
 853       setViewportAnnotationOrder();
 854     }
 855     else if (source == showAutoLast)
 856     {
 857       showAutoFirst.setState(!showAutoLast.getState());
 858       setShowAutoCalculatedAbove(showAutoFirst.getState());
 859       setViewportAnnotationOrder();
 860     }
 861     else if (source == conservationMenuItem)
 862     {
 863       conservationMenuItem_actionPerformed();
 864     }
 865     else if (source == abovePIDThreshold)
 866     {
 867       abovePIDThreshold_actionPerformed();
 868     }
 869     else if (source == applyToAllGroups)
 870     {
 871       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 872     }
 873     else if (source == autoCalculate)
 874     {
 875       viewport.autoCalculateConsensus = autoCalculate.getState();
 876     }
 877     else if (source == sortByTree)
 878     {
 879       viewport.sortByTree = sortByTree.getState();
 880     }
 881     else if (source == this.centreColumnLabelFlag)
 882     {
 883       centreColumnLabelFlag_stateChanged();
 884     }
 885     else if (source == this.followMouseOverFlag)
 886     {
 887       mouseOverFlag_stateChanged();
 888     }
 889     else if (source == showGroupConsensus)
 890     {
 891       showGroupConsensus_actionPerformed();
 892     }
 893     else if (source == showGroupConservation)
 894     {
 895       showGroupConservation_actionPerformed();
 896     }
 897     else if (source == showSequenceLogo)
 898     {
 899       showSequenceLogo_actionPerformed();
 900     }
 901     else if (source == normSequenceLogo)
 902     {
 903       normSequenceLogo_actionPerformed();
 904     }
 905     else if (source == showConsensusHistogram)
 906     {
 907       showConsensusHistogram_actionPerformed();
 908     }
 909     else if (source == applyAutoAnnotationSettings)
 910     {
 911       applyAutoAnnotationSettings_actionPerformed();
 912     }
 913     alignPanel.paintAlignment(true);
 914   }
 915
 916   /**
 917    * Set the visibility state of sequence-related and/or alignment-related
 918    * annotations depending on checkbox selections, and repaint.
 919    *
 920    * @param visible
 921    */
 922   private void setAnnotationsVisibility()
 923   {
 924     boolean showForAlignment = showAlignmentAnnotations.getState();
 925     boolean showForSequences = showSequenceAnnotations.getState();
 926     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 927     {
 928       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 929             .getAlignmentAnnotation())
 930     {
 931       boolean visible = (aa.sequenceRef == null ? showForAlignment
 932               : showForSequences);
 933       aa.visible = visible;
 934       }
 935     }
 936     alignPanel.validateAnnotationDimensions(true);
 937     validate();
 938     repaint();
 939   }
 940
 941   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 942   {
 943     this.annotationSortOrder = order;
 944   }
 945
 946   /**
 947    * Set flags on the viewport that control annotation ordering
 948    */
 949   private void setViewportAnnotationOrder()
 950   {
 951     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 952     this.alignPanel.av
 953             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 954   }
 955
 956   private void setShowAutoCalculatedAbove(boolean showAbove)
 957   {
 958     this.showAutoCalculatedAbove = showAbove;
 959   }
 960
 961   private void mouseOverFlag_stateChanged()
 962   {
 963     viewport.setFollowHighlight(followMouseOverFlag.getState());
 964     // TODO: could kick the scrollTo mechanism to reset view for current
 965     // searchresults.
 966   }
 967
 968   private void centreColumnLabelFlag_stateChanged()
 969   {
 970     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 971     this.alignPanel.annotationPanel.repaint();
 972   }
 973
 974   @Override
 975   public void actionPerformed(ActionEvent evt)
 976   {
 977     viewport.applet.currentAlignFrame = this;
 978
 979     Object source = evt.getSource();
 980
 981     if (source == inputText)
 982     {
 983       inputText_actionPerformed();
 984     }
 985     else if (source == loadTree)
 986     {
 987       loadTree_actionPerformed();
 988     }
 989     else if (source == loadApplication)
 990     {
 991       launchFullApplication();
 992     }
 993     else if (source == loadAnnotations)
 994     {
 995       loadAnnotations();
 996     }
 997     else if (source == outputAnnotations)
 998     {
 999       outputAnnotations(true);
1000     }
1001     else if (source == outputFeatures)
1002     {
1003       outputFeatures(true, "Jalview");
1004     }
1005     else if (source == closeMenuItem)
1006     {
1007       closeMenuItem_actionPerformed();
1008     }
1009     else if (source == copy)
1010     {
1011       copy_actionPerformed();
1012     }
1013     else if (source == undoMenuItem)
1014     {
1015       undoMenuItem_actionPerformed();
1016     }
1017     else if (source == redoMenuItem)
1018     {
1019       redoMenuItem_actionPerformed();
1020     }
1021     else if (source == inputText)
1022     {
1023       inputText_actionPerformed();
1024     }
1025     else if (source == closeMenuItem)
1026     {
1027       closeMenuItem_actionPerformed();
1028     }
1029     else if (source == undoMenuItem)
1030     {
1031       undoMenuItem_actionPerformed();
1032     }
1033     else if (source == redoMenuItem)
1034     {
1035       redoMenuItem_actionPerformed();
1036     }
1037     else if (source == copy)
1038     {
1039       copy_actionPerformed();
1040     }
1041     else if (source == pasteNew)
1042     {
1043       pasteNew_actionPerformed();
1044     }
1045     else if (source == pasteThis)
1046     {
1047       pasteThis_actionPerformed();
1048     }
1049     else if (source == cut)
1050     {
1051       cut_actionPerformed();
1052     }
1053     else if (source == delete)
1054     {
1055       delete_actionPerformed();
1056     }
1057     else if (source == grpsFromSelection)
1058     {
1059       makeGrpsFromSelection_actionPerformed();
1060     }
1061     else if (source == deleteGroups)
1062     {
1063       deleteGroups_actionPerformed();
1064     }
1065     else if (source == selectAllSequenceMenuItem)
1066     {
1067       selectAllSequenceMenuItem_actionPerformed();
1068     }
1069     else if (source == deselectAllSequenceMenuItem)
1070     {
1071       deselectAllSequenceMenuItem_actionPerformed();
1072     }
1073     else if (source == invertSequenceMenuItem)
1074     {
1075       invertSequenceMenuItem_actionPerformed();
1076       // uncomment to slave sequence selections in split frame
1077       // viewport.sendSelection();
1078     }
1079     else if (source == invertColSel)
1080     {
1081       viewport.invertColumnSelection();
1082       alignPanel.paintAlignment(true);
1083       viewport.sendSelection();
1084     }
1085     else if (source == remove2LeftMenuItem)
1086     {
1087       trimAlignment(true);
1088     }
1089     else if (source == remove2RightMenuItem)
1090     {
1091       trimAlignment(false);
1092     }
1093     else if (source == removeGappedColumnMenuItem)
1094     {
1095       removeGappedColumnMenuItem_actionPerformed();
1096     }
1097     else if (source == removeAllGapsMenuItem)
1098     {
1099       removeAllGapsMenuItem_actionPerformed();
1100     }
1101     else if (source == findMenuItem)
1102     {
1103       findMenuItem_actionPerformed();
1104     }
1105     else if (source == font)
1106     {
1107       new FontChooser(alignPanel);
1108     }
1109     else if (source == newView)
1110     {
1111       newView(null);
1112     }
1113     else if (source == showColumns)
1114     {
1115       viewport.showAllHiddenColumns();
1116       alignPanel.paintAlignment(true);
1117       viewport.sendSelection();
1118     }
1119     else if (source == showSeqs)
1120     {
1121       viewport.showAllHiddenSeqs();
1122       alignPanel.paintAlignment(true);
1123       // uncomment if we want to slave sequence selections in split frame
1124       // viewport.sendSelection();
1125     }
1126     else if (source == hideColumns)
1127     {
1128       viewport.hideSelectedColumns();
1129       alignPanel.paintAlignment(true);
1130       viewport.sendSelection();
1131     }
1132     else if (source == hideSequences
1133             && viewport.getSelectionGroup() != null)
1134     {
1135       viewport.hideAllSelectedSeqs();
1136       alignPanel.paintAlignment(true);
1137       // uncomment if we want to slave sequence selections in split frame
1138       // viewport.sendSelection();
1139     }
1140     else if (source == hideAllButSelection)
1141     {
1142       toggleHiddenRegions(false, false);
1143       alignPanel.paintAlignment(true);
1144       viewport.sendSelection();
1145     }
1146     else if (source == hideAllSelection)
1147     {
1148       SequenceGroup sg = viewport.getSelectionGroup();
1149       viewport.expandColSelection(sg, false);
1150       viewport.hideAllSelectedSeqs();
1151       viewport.hideSelectedColumns();
1152       alignPanel.paintAlignment(true);
1153       viewport.sendSelection();
1154     }
1155     else if (source == showAllHidden)
1156     {
1157       viewport.showAllHiddenColumns();
1158       viewport.showAllHiddenSeqs();
1159       alignPanel.paintAlignment(true);
1160       viewport.sendSelection();
1161     }
1162     else if (source == showGroupConsensus)
1163     {
1164       showGroupConsensus_actionPerformed();
1165     }
1166     else if (source == showGroupConservation)
1167     {
1168       showGroupConservation_actionPerformed();
1169     }
1170     else if (source == showSequenceLogo)
1171     {
1172       showSequenceLogo_actionPerformed();
1173     }
1174     else if (source == normSequenceLogo)
1175     {
1176       normSequenceLogo_actionPerformed();
1177     }
1178     else if (source == showConsensusHistogram)
1179     {
1180       showConsensusHistogram_actionPerformed();
1181     }
1182     else if (source == applyAutoAnnotationSettings)
1183     {
1184       applyAutoAnnotationSettings_actionPerformed();
1185     }
1186     else if (source == featureSettings)
1187     {
1188       new FeatureSettings(alignPanel);
1189     }
1190     else if (source == alProperties)
1191     {
1192       StringBuffer contents = new jalview.io.AlignmentProperties(
1193               viewport.getAlignment()).formatAsString();
1194       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1195       cap.setText(contents.toString());
1196       Frame frame = new Frame();
1197       frame.add(cap);
1198       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1199               "label.alignment_properties", new String[] { getTitle() }),
1200               400, 250);
1201     }
1202     else if (source == overviewMenuItem)
1203     {
1204       overviewMenuItem_actionPerformed();
1205     }
1206     else if (source == noColourmenuItem)
1207     {
1208       changeColour(null);
1209     }
1210     else if (source == clustalColour)
1211     {
1212       abovePIDThreshold.setState(false);
1213       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1214     }
1215     else if (source == zappoColour)
1216     {
1217       changeColour(new ZappoColourScheme());
1218     }
1219     else if (source == taylorColour)
1220     {
1221       changeColour(new TaylorColourScheme());
1222     }
1223     else if (source == hydrophobicityColour)
1224     {
1225       changeColour(new HydrophobicColourScheme());
1226     }
1227     else if (source == helixColour)
1228     {
1229       changeColour(new HelixColourScheme());
1230     }
1231     else if (source == strandColour)
1232     {
1233       changeColour(new StrandColourScheme());
1234     }
1235     else if (source == turnColour)
1236     {
1237       changeColour(new TurnColourScheme());
1238     }
1239     else if (source == buriedColour)
1240     {
1241       changeColour(new BuriedColourScheme());
1242     }
1243     else if (source == nucleotideColour)
1244     {
1245       changeColour(new NucleotideColourScheme());
1246     }
1247     else if (source == purinePyrimidineColour)
1248     {
1249       changeColour(new PurinePyrimidineColourScheme());
1250     }
1251     // else if (source == RNAInteractionColour)
1252     // {
1253     // changeColour(new RNAInteractionColourScheme());
1254     // }
1255     else if (source == RNAHelixColour)
1256     {
1257       new RNAHelicesColourChooser(viewport, alignPanel);
1258     }
1259     else if (source == modifyPID)
1260     {
1261       modifyPID_actionPerformed();
1262     }
1263     else if (source == modifyConservation)
1264     {
1265       modifyConservation_actionPerformed();
1266     }
1267     else if (source == userDefinedColour)
1268     {
1269       new UserDefinedColours(alignPanel, null);
1270     }
1271     else if (source == PIDColour)
1272     {
1273       changeColour(new PIDColourScheme());
1274     }
1275     else if (source == BLOSUM62Colour)
1276     {
1277       changeColour(new Blosum62ColourScheme());
1278     }
1279     else if (source == tcoffeeColour)
1280     {
1281       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1282     }
1283     else if (source == annotationColour)
1284     {
1285       new AnnotationColourChooser(viewport, alignPanel);
1286     }
1287     else if (source == annotationColumnSelection)
1288     {
1289       new AnnotationColumnChooser(viewport, alignPanel);
1290     }
1291     else if (source == sortPairwiseMenuItem)
1292     {
1293       sortPairwiseMenuItem_actionPerformed();
1294     }
1295     else if (source == sortIDMenuItem)
1296     {
1297       sortIDMenuItem_actionPerformed();
1298     }
1299     else if (source == sortLengthMenuItem)
1300     {
1301       sortLengthMenuItem_actionPerformed();
1302     }
1303     else if (source == sortGroupMenuItem)
1304     {
1305       sortGroupMenuItem_actionPerformed();
1306     }
1307     else if (source == removeRedundancyMenuItem)
1308     {
1309       removeRedundancyMenuItem_actionPerformed();
1310     }
1311     else if (source == pairwiseAlignmentMenuItem)
1312     {
1313       pairwiseAlignmentMenuItem_actionPerformed();
1314     }
1315     else if (source == PCAMenuItem)
1316     {
1317       PCAMenuItem_actionPerformed();
1318     }
1319     else if (source == averageDistanceTreeMenuItem)
1320     {
1321       averageDistanceTreeMenuItem_actionPerformed();
1322     }
1323     else if (source == neighbourTreeMenuItem)
1324     {
1325       neighbourTreeMenuItem_actionPerformed();
1326     }
1327     else if (source == njTreeBlosumMenuItem)
1328     {
1329       njTreeBlosumMenuItem_actionPerformed();
1330     }
1331     else if (source == avDistanceTreeBlosumMenuItem)
1332     {
1333       avTreeBlosumMenuItem_actionPerformed();
1334     }
1335     else if (source == documentation)
1336     {
1337       documentation_actionPerformed();
1338     }
1339     else if (source == about)
1340     {
1341       about_actionPerformed();
1342     }
1343
1344   }
1345
1346   public void inputText_actionPerformed()
1347   {
1348     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1349     Frame frame = new Frame();
1350     frame.add(cap);
1351     jalview.bin.JalviewLite.addFrame(frame,
1352             MessageManager.getString("label.input_cut_paste"), 500, 500);
1353   }
1354
1355   protected void outputText_actionPerformed(ActionEvent e)
1356   {
1357     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1358     Frame frame = new Frame();
1359     frame.add(cap);
1360     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1361             "label.alignment_output_command",
1362             new Object[] { e.getActionCommand() }), 600, 500);
1363
1364     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1365     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1366             e.getActionCommand(), viewport.getAlignment(),
1367             viewport.getShowJVSuffix()));
1368   }
1369
1370   public void loadAnnotations()
1371   {
1372     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1373     cap.setText(MessageManager
1374             .getString("label.paste_features_annotations_Tcoffee_here"));
1375     cap.setAnnotationImport();
1376     Frame frame = new Frame();
1377     frame.add(cap);
1378     jalview.bin.JalviewLite.addFrame(frame,
1379             MessageManager.getString("action.paste_annotations"), 400, 300);
1380
1381   }
1382
1383   public String outputAnnotations(boolean displayTextbox)
1384   {
1385     String annotation = new AnnotationFile()
1386             .printAnnotationsForView(viewport);
1387
1388     if (displayTextbox)
1389     {
1390       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1391       Frame frame = new Frame();
1392       frame.add(cap);
1393       jalview.bin.JalviewLite.addFrame(frame,
1394               MessageManager.getString("label.annotations"), 600, 500);
1395       cap.setText(annotation);
1396     }
1397
1398     return annotation;
1399   }
1400
1401   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1402   {
1403     if (alignPanel.getFeatureRenderer() != null
1404             && viewport.getFeaturesDisplayed() != null)
1405     {
1406       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1407
1408     }
1409     return null;
1410   }
1411
1412   public String outputFeatures(boolean displayTextbox, String format)
1413   {
1414     String features;
1415     FeaturesFile formatter = new FeaturesFile();
1416     if (format.equalsIgnoreCase("Jalview"))
1417     {
1418       features = formatter.printJalviewFormat(viewport
1419               .getAlignment().getSequencesArray(),
1420               getDisplayedFeatureCols());
1421     }
1422     else
1423     {
1424       features = formatter.printGffFormat(viewport.getAlignment()
1425               .getSequencesArray(), getDisplayedFeatureCols());
1426     }
1427
1428     if (displayTextbox)
1429     {
1430       boolean frimport = false;
1431       if (features == null || features.equals("No Features Visible"))
1432       {
1433         features = "# No features visible - paste some and import them here.";
1434         frimport = true;
1435       }
1436
1437       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1438       if (frimport)
1439       {
1440         cap.setAnnotationImport();
1441       }
1442       Frame frame = new Frame();
1443       frame.add(cap);
1444       jalview.bin.JalviewLite.addFrame(frame,
1445               MessageManager.getString("label.features"), 600, 500);
1446       cap.setText(features);
1447     }
1448     else
1449     {
1450       if (features == null)
1451       {
1452         features = "";
1453       }
1454     }
1455
1456     return features;
1457   }
1458
1459   void launchFullApplication()
1460   {
1461     StringBuffer url = new StringBuffer(jalviewServletURL);
1462
1463     // allow servlet parameters to be passed in applet parameter
1464     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1465             : "?";
1466     url.append(firstSep);
1467
1468     url.append("open="
1469             + appendProtocol(viewport.applet.getParameter("file")));
1470
1471     if (viewport.applet.getParameter("features") != null)
1472     {
1473       url.append("&features=");
1474       url.append(appendProtocol(viewport.applet.getParameter("features")));
1475     }
1476
1477     if (viewport.applet.getParameter("annotations") != null)
1478     {
1479       url.append("&annotations=");
1480       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1481     }
1482
1483     if (viewport.applet.getParameter("jnetfile") != null)
1484     {
1485       url.append("&annotations=");
1486       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1487     }
1488
1489     if (viewport.applet.getParameter("defaultColour") != null)
1490     {
1491       url.append("&colour="
1492               + removeWhiteSpace(viewport.applet
1493                       .getParameter("defaultColour")));
1494     }
1495
1496     if (viewport.applet.getParameter("userDefinedColour") != null)
1497     {
1498       url.append("&colour="
1499               + removeWhiteSpace(viewport.applet
1500                       .getParameter("userDefinedColour")));
1501     }
1502     if (viewport.applet.getParameter("tree") != null)
1503     {
1504       url.append("&tree="
1505               + appendProtocol(viewport.applet.getParameter("tree")));
1506     }
1507     if (viewport.applet.getParameter("treeFile") != null)
1508     {
1509       url.append("&tree="
1510               + appendProtocol(viewport.applet.getParameter("treeFile")));
1511     }
1512
1513     showURL(url.toString(), "FULL_APP");
1514   }
1515
1516   String removeWhiteSpace(String colour)
1517   {
1518     StringBuffer sb = new StringBuffer();
1519     for (int i = 0; i < colour.length(); i++)
1520     {
1521       if (Character.isWhitespace(colour.charAt(i)))
1522       {
1523         sb.append("%20");
1524       }
1525       else
1526       {
1527         sb.append(colour.charAt(i));
1528       }
1529     }
1530
1531     return sb.toString();
1532   }
1533
1534   String appendProtocol(String url)
1535   {
1536     try
1537     {
1538       new URL(url);
1539       url = URLEncoder.encode(url);
1540     }
1541     /*
1542      * When we finally deprecate 1.1 compatibility, we can start to use
1543      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1544      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1545      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1546      * ex.printStackTrace(); }
1547      */
1548     catch (java.net.MalformedURLException ex)
1549     {
1550       url = viewport.applet.getCodeBase() + url;
1551     }
1552     return url;
1553   }
1554
1555   public void closeMenuItem_actionPerformed()
1556   {
1557     PaintRefresher.RemoveComponent(alignPanel);
1558     if (alignPanel.seqPanel != null
1559             && alignPanel.seqPanel.seqCanvas != null)
1560     {
1561       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1562     }
1563     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1564     {
1565       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1566     }
1567
1568     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1569     {
1570       System.exit(0);
1571     }
1572     else
1573     {
1574     }
1575     viewport = null;
1576     alignPanel = null;
1577     this.dispose();
1578   }
1579
1580   /**
1581    * TODO: JAL-1104
1582    */
1583   void updateEditMenuBar()
1584   {
1585
1586     if (viewport.getHistoryList().size() > 0)
1587     {
1588       undoMenuItem.setEnabled(true);
1589       CommandI command = viewport.getHistoryList().peek();
1590       undoMenuItem.setLabel(MessageManager.formatMessage(
1591               "label.undo_command",
1592               new Object[] { command.getDescription() }));
1593     }
1594     else
1595     {
1596       undoMenuItem.setEnabled(false);
1597       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1598     }
1599
1600     if (viewport.getRedoList().size() > 0)
1601     {
1602       redoMenuItem.setEnabled(true);
1603
1604       CommandI command = viewport.getRedoList().peek();
1605       redoMenuItem.setLabel(MessageManager.formatMessage(
1606               "label.redo_command",
1607               new Object[] { command.getDescription() }));
1608     }
1609     else
1610     {
1611       redoMenuItem.setEnabled(false);
1612       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1613     }
1614   }
1615
1616   /**
1617    * TODO: JAL-1104
1618    */
1619   @Override
1620   public void addHistoryItem(CommandI command)
1621   {
1622     if (command.getSize() > 0)
1623     {
1624       viewport.addToHistoryList(command);
1625       viewport.clearRedoList();
1626       updateEditMenuBar();
1627       viewport.updateHiddenColumns();
1628     }
1629   }
1630
1631   /**
1632    * TODO: JAL-1104 DOCUMENT ME!
1633    *
1634    * @param e
1635    *          DOCUMENT ME!
1636    */
1637   protected void undoMenuItem_actionPerformed()
1638   {
1639     if (viewport.getHistoryList().isEmpty())
1640     {
1641       return;
1642     }
1643
1644     CommandI command = viewport.getHistoryList().pop();
1645     viewport.addToRedoList(command);
1646     command.undoCommand(null);
1647
1648     AlignmentViewport originalSource = getOriginatingSource(command);
1649     // JBPNote Test
1650     if (originalSource != viewport)
1651     {
1652       System.err
1653               .println("Warning: Viewport object mismatch whilst undoing");
1654     }
1655     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1656                                           // viewport.getColumnSelection().getHiddenColumns()
1657                                           // != null;
1658     updateEditMenuBar();
1659     originalSource.firePropertyChange("alignment", null, originalSource
1660             .getAlignment().getSequences());
1661   }
1662
1663   /**
1664    * TODO: JAL-1104 DOCUMENT ME!
1665    *
1666    * @param e
1667    *          DOCUMENT ME!
1668    */
1669   protected void redoMenuItem_actionPerformed()
1670   {
1671     if (viewport.getRedoList().isEmpty())
1672     {
1673       return;
1674     }
1675
1676     CommandI command = viewport.getRedoList().pop();
1677     viewport.addToHistoryList(command);
1678     command.doCommand(null);
1679
1680     AlignmentViewport originalSource = getOriginatingSource(command);
1681     // JBPNote Test
1682     if (originalSource != viewport)
1683     {
1684       System.err
1685               .println("Warning: Viewport object mismatch whilst re-doing");
1686     }
1687     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1688                                           // viewport.getColumnSelection().getHiddenColumns()
1689                                           // != null;
1690
1691     updateEditMenuBar();
1692     originalSource.firePropertyChange("alignment", null, originalSource
1693             .getAlignment().getSequences());
1694   }
1695
1696   AlignmentViewport getOriginatingSource(CommandI command)
1697   {
1698     AlignmentViewport originalSource = null;
1699     // For sequence removal and addition, we need to fire
1700     // the property change event FROM the viewport where the
1701     // original alignment was altered
1702     AlignmentI al = null;
1703     if (command instanceof EditCommand)
1704     {
1705       EditCommand editCommand = (EditCommand) command;
1706       al = editCommand.getAlignment();
1707       Vector comps = (Vector) PaintRefresher.components.get(viewport
1708               .getSequenceSetId());
1709       for (int i = 0; i < comps.size(); i++)
1710       {
1711         if (comps.elementAt(i) instanceof AlignmentPanel)
1712         {
1713           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1714           {
1715             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1716             break;
1717           }
1718         }
1719       }
1720     }
1721
1722     if (originalSource == null)
1723     {
1724       // The original view is closed, we must validate
1725       // the current view against the closed view first
1726       if (al != null)
1727       {
1728         PaintRefresher.validateSequences(al, viewport.getAlignment());
1729       }
1730
1731       originalSource = viewport;
1732     }
1733
1734     return originalSource;
1735   }
1736
1737   /**
1738    * Move the currently selected sequences up or down one position in the
1739    * alignment
1740    *
1741    * @param up
1742    */
1743   public void moveSelectedSequences(boolean up)
1744   {
1745     SequenceGroup sg = viewport.getSelectionGroup();
1746     if (sg == null)
1747     {
1748       return;
1749     }
1750     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1751             up ? null : viewport.getHiddenRepSequences(), up);
1752     alignPanel.paintAlignment(true);
1753
1754     /*
1755      * Also move cDNA/protein complement sequences
1756      */
1757     AlignViewportI complement = viewport.getCodingComplement();
1758     if (complement != null)
1759     {
1760       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1761               viewport, complement);
1762       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1763               up ? null : complement.getHiddenRepSequences(), up);
1764       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1765     }
1766   }
1767
1768   synchronized void slideSequences(boolean right, int size)
1769   {
1770     List<SequenceI> sg = new Vector<SequenceI>();
1771     if (viewport.cursorMode)
1772     {
1773       sg.add(viewport.getAlignment().getSequenceAt(
1774               alignPanel.seqPanel.seqCanvas.cursorY));
1775     }
1776     else if (viewport.getSelectionGroup() != null
1777             && viewport.getSelectionGroup().getSize() != viewport
1778                     .getAlignment().getHeight())
1779     {
1780       sg = viewport.getSelectionGroup().getSequences(
1781               viewport.getHiddenRepSequences());
1782     }
1783
1784     if (sg.size() < 1)
1785     {
1786       return;
1787     }
1788
1789     Vector<SequenceI> invertGroup = new Vector();
1790
1791     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1792     {
1793       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1794       {
1795         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1796       }
1797     }
1798
1799     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1800
1801     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1802             .size()]);
1803     for (int i = 0; i < invertGroup.size(); i++)
1804     {
1805       seqs2[i] = invertGroup.elementAt(i);
1806     }
1807
1808     SlideSequencesCommand ssc;
1809     if (right)
1810     {
1811       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1812               size, viewport.getGapCharacter());
1813     }
1814     else
1815     {
1816       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1817               size, viewport.getGapCharacter());
1818     }
1819
1820     int groupAdjustment = 0;
1821     if (ssc.getGapsInsertedBegin() && right)
1822     {
1823       if (viewport.cursorMode)
1824       {
1825         alignPanel.seqPanel.moveCursor(size, 0);
1826       }
1827       else
1828       {
1829         groupAdjustment = size;
1830       }
1831     }
1832     else if (!ssc.getGapsInsertedBegin() && !right)
1833     {
1834       if (viewport.cursorMode)
1835       {
1836         alignPanel.seqPanel.moveCursor(-size, 0);
1837       }
1838       else
1839       {
1840         groupAdjustment = -size;
1841       }
1842     }
1843
1844     if (groupAdjustment != 0)
1845     {
1846       viewport.getSelectionGroup().setStartRes(
1847               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1848       viewport.getSelectionGroup().setEndRes(
1849               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1850     }
1851
1852     boolean appendHistoryItem = false;
1853     Deque<CommandI> historyList = viewport.getHistoryList();
1854     if (historyList != null && historyList.size() > 0
1855             && historyList.peek() instanceof SlideSequencesCommand)
1856     {
1857       appendHistoryItem = ssc
1858               .appendSlideCommand((SlideSequencesCommand) historyList
1859                       .peek());
1860     }
1861
1862     if (!appendHistoryItem)
1863     {
1864       addHistoryItem(ssc);
1865     }
1866
1867     repaint();
1868   }
1869
1870   static StringBuffer copiedSequences;
1871
1872   static Vector copiedHiddenColumns;
1873
1874   protected void copy_actionPerformed()
1875   {
1876     if (viewport.getSelectionGroup() == null)
1877     {
1878       return;
1879     }
1880
1881     SequenceGroup sg = viewport.getSelectionGroup();
1882     copiedSequences = new StringBuffer();
1883     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1884     for (int i = 0; i < sg.getSize(); i++)
1885     {
1886       SequenceI seq = sg.getSequenceAt(i);
1887       int index = viewport.getAlignment().findIndex(seq);
1888       orderedSeqs.put(index, seq);
1889     }
1890
1891     int index = 0, startRes, endRes;
1892     char ch;
1893
1894     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1895     {
1896       copiedHiddenColumns = new Vector();
1897       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1898       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1899       {
1900         copiedHiddenColumns.addElement(new int[] {
1901             region[0] - hiddenOffset, region[1] - hiddenOffset });
1902       }
1903     }
1904     else
1905     {
1906       copiedHiddenColumns = null;
1907     }
1908
1909     for (int i = 0; i < sg.getSize(); i++)
1910     {
1911       SequenceI seq = null;
1912
1913       while (seq == null)
1914       {
1915         if (orderedSeqs.containsKey(index))
1916         {
1917           seq = orderedSeqs.get(index);
1918           index++;
1919           break;
1920         }
1921         else
1922         {
1923           index++;
1924         }
1925       }
1926
1927       // FIND START RES
1928       // Returns residue following index if gap
1929       startRes = seq.findPosition(sg.getStartRes());
1930
1931       // FIND END RES
1932       // Need to find the residue preceeding index if gap
1933       endRes = 0;
1934
1935       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1936       {
1937         ch = seq.getCharAt(j);
1938         if (!jalview.util.Comparison.isGap((ch)))
1939         {
1940           endRes++;
1941         }
1942       }
1943
1944       if (endRes > 0)
1945       {
1946         endRes += seq.getStart() - 1;
1947       }
1948
1949       copiedSequences.append(seq.getName()
1950               + "\t"
1951               + startRes
1952               + "\t"
1953               + endRes
1954               + "\t"
1955               + seq.getSequenceAsString(sg.getStartRes(),
1956                       sg.getEndRes() + 1) + "\n");
1957     }
1958
1959   }
1960
1961   protected void pasteNew_actionPerformed()
1962   {
1963     paste(true);
1964   }
1965
1966   protected void pasteThis_actionPerformed()
1967   {
1968     paste(false);
1969   }
1970
1971   void paste(boolean newAlignment)
1972   {
1973     try
1974     {
1975
1976       if (copiedSequences == null)
1977       {
1978         return;
1979       }
1980
1981       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1982       Vector seqs = new Vector();
1983       while (st.hasMoreElements())
1984       {
1985         String name = st.nextToken();
1986         int start = Integer.parseInt(st.nextToken());
1987         int end = Integer.parseInt(st.nextToken());
1988         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1989       }
1990       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1991       for (int i = 0; i < seqs.size(); i++)
1992       {
1993         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1994       }
1995
1996       if (newAlignment)
1997       {
1998         String newtitle = MessageManager
1999                 .getString("label.copied_sequences");
2000         if (getTitle().startsWith(
2001                 MessageManager.getString("label.copied_sequences")))
2002         {
2003           newtitle = getTitle();
2004         }
2005         else
2006         {
2007           newtitle = newtitle.concat(MessageManager.formatMessage(
2008                   "label.from_msname", new String[] { getTitle() }));
2009         }
2010         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2011                 viewport.applet, newtitle, false);
2012         if (copiedHiddenColumns != null)
2013         {
2014           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2015           {
2016             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2017             af.viewport.hideColumns(region[0], region[1]);
2018           }
2019         }
2020
2021         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2022                 frameHeight);
2023       }
2024       else
2025       {
2026         addSequences(newSeqs);
2027       }
2028
2029     } catch (Exception ex)
2030     {
2031     } // could be anything being pasted in here
2032
2033   }
2034
2035   void addSequences(SequenceI[] seqs)
2036   {
2037     for (int i = 0; i < seqs.length; i++)
2038     {
2039       viewport.getAlignment().addSequence(seqs[i]);
2040     }
2041
2042     // !newAlignment
2043     addHistoryItem(new EditCommand(
2044             MessageManager.getString("label.add_sequences"), Action.PASTE,
2045             seqs, 0, viewport.getAlignment().getWidth(),
2046             viewport.getAlignment()));
2047
2048     viewport.setEndSeq(viewport.getAlignment().getHeight());
2049     viewport.getAlignment().getWidth();
2050     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2051             .getSequences());
2052
2053   }
2054
2055   protected void cut_actionPerformed()
2056   {
2057     copy_actionPerformed();
2058     delete_actionPerformed();
2059   }
2060
2061   protected void delete_actionPerformed()
2062   {
2063
2064     SequenceGroup sg = viewport.getSelectionGroup();
2065     if (sg == null)
2066     {
2067       return;
2068     }
2069
2070     Vector seqs = new Vector();
2071     SequenceI seq;
2072     for (int i = 0; i < sg.getSize(); i++)
2073     {
2074       seq = sg.getSequenceAt(i);
2075       seqs.addElement(seq);
2076     }
2077
2078     /*
2079      * If the cut affects all sequences, warn, remove highlighted columns
2080      */
2081     if (sg.getSize() == viewport.getAlignment().getHeight())
2082     {
2083       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2084               .getAlignment().getWidth()) ? true : false;
2085       if (isEntireAlignWidth)
2086       {
2087         String title = MessageManager.getString("label.delete_all");
2088         Panel infoPanel = new Panel();
2089         infoPanel.setLayout(new FlowLayout());
2090         infoPanel
2091                 .add(new Label(MessageManager.getString("warn.delete_all")));
2092
2093         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2094         dialog.setMainPanel(infoPanel);
2095         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2096         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2097         dialog.setVisible(true);
2098
2099         if (!dialog.accept)
2100         {
2101           return;
2102         }
2103       }
2104       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2105               sg.getEndRes() + 1);
2106     }
2107
2108     SequenceI[] cut = new SequenceI[seqs.size()];
2109     for (int i = 0; i < seqs.size(); i++)
2110     {
2111       cut[i] = (SequenceI) seqs.elementAt(i);
2112     }
2113
2114     /*
2115      * //ADD HISTORY ITEM
2116      */
2117     addHistoryItem(new EditCommand(
2118             MessageManager.getString("label.cut_sequences"), Action.CUT,
2119             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2120             viewport.getAlignment()));
2121
2122     viewport.setSelectionGroup(null);
2123     viewport.getAlignment().deleteGroup(sg);
2124
2125     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2126             .getSequences());
2127
2128     if (viewport.getAlignment().getHeight() < 1)
2129     {
2130       this.setVisible(false);
2131     }
2132     viewport.sendSelection();
2133   }
2134
2135   /**
2136    * group consensus toggled
2137    *
2138    */
2139   protected void showGroupConsensus_actionPerformed()
2140   {
2141     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2142     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2143
2144   }
2145
2146   /**
2147    * group conservation toggled.
2148    */
2149   protected void showGroupConservation_actionPerformed()
2150   {
2151     viewport.setShowGroupConservation(showGroupConservation.getState());
2152     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2153   }
2154
2155   /*
2156    * (non-Javadoc)
2157    *
2158    * @see
2159    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2160    * .event.ActionEvent)
2161    */
2162   protected void showConsensusHistogram_actionPerformed()
2163   {
2164     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2165     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2166   }
2167
2168   /*
2169    * (non-Javadoc)
2170    *
2171    * @see
2172    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2173    * .event.ActionEvent)
2174    */
2175   protected void showSequenceLogo_actionPerformed()
2176   {
2177     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2178     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2179   }
2180
2181   protected void normSequenceLogo_actionPerformed()
2182   {
2183     showSequenceLogo.setState(true);
2184     viewport.setShowSequenceLogo(true);
2185     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2186     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2187   }
2188
2189   protected void applyAutoAnnotationSettings_actionPerformed()
2190   {
2191     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192   }
2193
2194   protected void makeGrpsFromSelection_actionPerformed()
2195   {
2196     if (avc.makeGroupsFromSelection())
2197     {
2198       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2199       alignPanel.updateAnnotation();
2200       alignPanel.paintAlignment(true);
2201     }
2202   }
2203
2204   protected void createGroup_actionPerformed()
2205   {
2206     avc.createGroup();
2207   }
2208
2209   protected void unGroup_actionPerformed()
2210   {
2211     if (avc.unGroup())
2212     {
2213       alignPanel.alignmentChanged();
2214     }
2215   }
2216
2217   protected void deleteGroups_actionPerformed()
2218   {
2219     if (avc.deleteGroups())
2220     {
2221       alignPanel.alignmentChanged();
2222     }
2223   }
2224
2225   public void selectAllSequenceMenuItem_actionPerformed()
2226   {
2227     SequenceGroup sg = new SequenceGroup();
2228     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2229     {
2230       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2231     }
2232     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2233     viewport.setSelectionGroup(sg);
2234     // JAL-2034 - should delegate to
2235     // alignPanel to decide if overview needs
2236     // updating.
2237     alignPanel.paintAlignment(false);
2238     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2239     viewport.sendSelection();
2240   }
2241
2242   public void deselectAllSequenceMenuItem_actionPerformed()
2243   {
2244     if (viewport.cursorMode)
2245     {
2246       alignPanel.seqPanel.keyboardNo1 = null;
2247       alignPanel.seqPanel.keyboardNo2 = null;
2248     }
2249     viewport.setSelectionGroup(null);
2250     viewport.getColumnSelection().clear();
2251     viewport.setSelectionGroup(null);
2252     alignPanel.idPanel.idCanvas.searchResults = null;
2253     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2254     // JAL-2034 - should delegate to
2255     // alignPanel to decide if overview needs
2256     // updating.
2257     alignPanel.paintAlignment(false);
2258     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2259     viewport.sendSelection();
2260   }
2261
2262   public void invertSequenceMenuItem_actionPerformed()
2263   {
2264     SequenceGroup sg = viewport.getSelectionGroup();
2265     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2266     {
2267       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2268     }
2269
2270     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2271     viewport.sendSelection();
2272   }
2273
2274   public void invertColSel_actionPerformed()
2275   {
2276     viewport.invertColumnSelection();
2277     alignPanel.paintAlignment(true);
2278     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2279     viewport.sendSelection();
2280   }
2281
2282   void trimAlignment(boolean trimLeft)
2283   {
2284     ColumnSelection colSel = viewport.getColumnSelection();
2285     int column;
2286
2287     if (!colSel.isEmpty())
2288     {
2289       if (trimLeft)
2290       {
2291         column = colSel.getMin();
2292       }
2293       else
2294       {
2295         column = colSel.getMax();
2296       }
2297
2298       SequenceI[] seqs;
2299       if (viewport.getSelectionGroup() != null)
2300       {
2301         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2302                 viewport.getHiddenRepSequences());
2303       }
2304       else
2305       {
2306         seqs = viewport.getAlignment().getSequencesArray();
2307       }
2308
2309       TrimRegionCommand trimRegion;
2310       if (trimLeft)
2311       {
2312         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2313                 column, viewport.getAlignment());
2314         viewport.setStartRes(0);
2315       }
2316       else
2317       {
2318         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2319                 column, viewport.getAlignment());
2320       }
2321
2322       statusBar.setText(MessageManager.formatMessage(
2323               "label.removed_columns",
2324               new String[] { Integer.valueOf(trimRegion.getSize())
2325                       .toString() }));
2326       addHistoryItem(trimRegion);
2327
2328       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2329       {
2330         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2331                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2332         {
2333           viewport.getAlignment().deleteGroup(sg);
2334         }
2335       }
2336
2337       viewport.firePropertyChange("alignment", null, viewport
2338               .getAlignment().getSequences());
2339     }
2340   }
2341
2342   public void removeGappedColumnMenuItem_actionPerformed()
2343   {
2344     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2345
2346     SequenceI[] seqs;
2347     if (viewport.getSelectionGroup() != null)
2348     {
2349       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2350               viewport.getHiddenRepSequences());
2351       start = viewport.getSelectionGroup().getStartRes();
2352       end = viewport.getSelectionGroup().getEndRes();
2353     }
2354     else
2355     {
2356       seqs = viewport.getAlignment().getSequencesArray();
2357     }
2358
2359     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2360             "Remove Gapped Columns", seqs, start, end,
2361             viewport.getAlignment());
2362
2363     addHistoryItem(removeGapCols);
2364
2365     statusBar.setText(MessageManager.formatMessage(
2366             "label.removed_empty_columns",
2367             new String[] { Integer.valueOf(removeGapCols.getSize())
2368                     .toString() }));
2369
2370     // This is to maintain viewport position on first residue
2371     // of first sequence
2372     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2373     int startRes = seq.findPosition(viewport.startRes);
2374     // ShiftList shifts;
2375     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2376     // edit.alColumnChanges=shifts.getInverse();
2377     // if (viewport.hasHiddenColumns)
2378     // viewport.getColumnSelection().compensateForEdits(shifts);
2379     viewport.setStartRes(seq.findIndex(startRes) - 1);
2380     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2381             .getSequences());
2382
2383   }
2384
2385   public void removeAllGapsMenuItem_actionPerformed()
2386   {
2387     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2388
2389     SequenceI[] seqs;
2390     if (viewport.getSelectionGroup() != null)
2391     {
2392       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2393               viewport.getHiddenRepSequences());
2394       start = viewport.getSelectionGroup().getStartRes();
2395       end = viewport.getSelectionGroup().getEndRes();
2396     }
2397     else
2398     {
2399       seqs = viewport.getAlignment().getSequencesArray();
2400     }
2401
2402     // This is to maintain viewport position on first residue
2403     // of first sequence
2404     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2405     int startRes = seq.findPosition(viewport.startRes);
2406
2407     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2408             viewport.getAlignment()));
2409
2410     viewport.setStartRes(seq.findIndex(startRes) - 1);
2411
2412     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2413             .getSequences());
2414
2415   }
2416
2417   public void findMenuItem_actionPerformed()
2418   {
2419     new Finder(alignPanel);
2420   }
2421
2422   /**
2423    * create a new view derived from the current view
2424    *
2425    * @param viewtitle
2426    * @return frame for the new view
2427    */
2428   public AlignFrame newView(String viewtitle)
2429   {
2430     AlignmentI newal;
2431     if (viewport.hasHiddenRows())
2432     {
2433       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2434               .getFullAlignment().getSequencesArray());
2435     }
2436     else
2437     {
2438       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2439     }
2440
2441     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2442     {
2443       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2444       {
2445         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2446         {
2447           newal.addAnnotation(viewport.getAlignment()
2448                   .getAlignmentAnnotation()[i]);
2449         }
2450       }
2451     }
2452
2453     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2454
2455     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2456     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2457     PaintRefresher.Register(newaf.alignPanel,
2458             newaf.alignPanel.av.getSequenceSetId());
2459
2460     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2461             newaf.alignPanel.av.getSequenceSetId());
2462     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2463             newaf.alignPanel.av.getSequenceSetId());
2464
2465     Vector comps = (Vector) PaintRefresher.components.get(viewport
2466             .getSequenceSetId());
2467     int viewSize = -1;
2468     for (int i = 0; i < comps.size(); i++)
2469     {
2470       if (comps.elementAt(i) instanceof AlignmentPanel)
2471       {
2472         viewSize++;
2473       }
2474     }
2475
2476     String title = new String(this.getTitle());
2477     if (viewtitle != null)
2478     {
2479       title = viewtitle + " ( " + title + ")";
2480     }
2481     else
2482     {
2483       if (title.indexOf("(View") > -1)
2484       {
2485         title = title.substring(0, title.indexOf("(View"));
2486       }
2487       title += "(View " + viewSize + ")";
2488     }
2489
2490     newaf.setTitle(title.toString());
2491
2492     newaf.viewport.setHistoryList(viewport.getHistoryList());
2493     newaf.viewport.setRedoList(viewport.getRedoList());
2494     return newaf;
2495   }
2496
2497   /**
2498    *
2499    * @return list of feature groups on the view
2500    */
2501   public String[] getFeatureGroups()
2502   {
2503     FeatureRenderer fr = null;
2504     if (alignPanel != null
2505             && (fr = alignPanel.getFeatureRenderer()) != null)
2506     {
2507       List<String> gps = fr.getFeatureGroups();
2508       String[] _gps = gps.toArray(new String[gps.size()]);
2509       return _gps;
2510     }
2511     return null;
2512   }
2513
2514   /**
2515    * get sequence feature groups that are hidden or shown
2516    *
2517    * @param visible
2518    *          true is visible
2519    * @return list
2520    */
2521   public String[] getFeatureGroupsOfState(boolean visible)
2522   {
2523     FeatureRenderer fr = null;
2524     if (alignPanel != null
2525             && (fr = alignPanel.getFeatureRenderer()) != null)
2526     {
2527       List<String> gps = fr.getGroups(visible);
2528       String[] _gps = gps.toArray(new String[gps.size()]);
2529       return _gps;
2530     }
2531     return null;
2532   }
2533
2534   /**
2535    * Change the display state for the given feature groups
2536    *
2537    * @param groups
2538    *          list of group strings
2539    * @param state
2540    *          visible or invisible
2541    */
2542   public void setFeatureGroupState(String[] groups, boolean state)
2543   {
2544     FeatureRenderer fr = null;
2545     this.sequenceFeatures.setState(true);
2546     viewport.setShowSequenceFeatures(true);
2547     if (alignPanel != null
2548             && (fr = alignPanel.getFeatureRenderer()) != null)
2549     {
2550
2551       fr.setGroupVisibility(Arrays.asList(groups), state);
2552       alignPanel.seqPanel.seqCanvas.repaint();
2553       if (alignPanel.overviewPanel != null)
2554       {
2555         alignPanel.overviewPanel.updateOverviewImage();
2556       }
2557     }
2558   }
2559
2560   public void seqLimits_itemStateChanged()
2561   {
2562     viewport.setShowJVSuffix(seqLimits.getState());
2563     alignPanel.fontChanged();
2564     alignPanel.paintAlignment(true);
2565   }
2566
2567   protected void colourTextMenuItem_actionPerformed()
2568   {
2569     viewport.setColourText(colourTextMenuItem.getState());
2570     alignPanel.paintAlignment(true);
2571   }
2572
2573   protected void displayNonconservedMenuItem_actionPerformed()
2574   {
2575     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2576     alignPanel.paintAlignment(true);
2577   }
2578
2579   protected void wrapMenuItem_actionPerformed()
2580   {
2581     viewport.setWrapAlignment(wrapMenuItem.getState());
2582     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2583     scaleAbove.setEnabled(wrapMenuItem.getState());
2584     scaleLeft.setEnabled(wrapMenuItem.getState());
2585     scaleRight.setEnabled(wrapMenuItem.getState());
2586     alignPanel.paintAlignment(true);
2587   }
2588
2589   public void overviewMenuItem_actionPerformed()
2590   {
2591     if (alignPanel.overviewPanel != null)
2592     {
2593       return;
2594     }
2595
2596     Frame frame = new Frame();
2597     OverviewPanel overview = new OverviewPanel(alignPanel);
2598     frame.add(overview);
2599     // +50 must allow for applet frame window
2600     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2601             "label.overview_params", new String[] { this.getTitle() }),
2602             overview.getPreferredSize().width,
2603             overview.getPreferredSize().height + 50);
2604
2605     frame.pack();
2606     final AlignmentPanel ap = alignPanel;
2607     frame.addWindowListener(new WindowAdapter()
2608     {
2609       @Override
2610       public void windowClosing(WindowEvent e)
2611       {
2612         if (ap != null)
2613         {
2614           ap.setOverviewPanel(null);
2615         }
2616       };
2617     });
2618
2619     alignPanel.setOverviewPanel(overview);
2620
2621   }
2622
2623   @Override
2624   public void changeColour(ColourSchemeI cs)
2625   {
2626
2627     if (cs != null)
2628     {
2629       if (viewport.getAbovePIDThreshold())
2630       {
2631         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2632                 cs, "Background"));
2633       }
2634
2635       if (viewport.getConservationSelected())
2636       {
2637         cs.setConservationApplied(true);
2638         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2639                 cs, "Background"));
2640       }
2641       else
2642       {
2643         cs.setConservationApplied(false);
2644       }
2645     }
2646     viewport.setGlobalColourScheme(cs);
2647
2648     alignPanel.paintAlignment(true);
2649   }
2650
2651   protected void modifyPID_actionPerformed()
2652   {
2653     if (viewport.getAbovePIDThreshold()
2654             && viewport.getGlobalColourScheme() != null)
2655     {
2656       SliderPanel.setPIDSliderSource(alignPanel,
2657               viewport.getGlobalColourScheme(), "Background");
2658       SliderPanel.showPIDSlider();
2659     }
2660   }
2661
2662   protected void modifyConservation_actionPerformed()
2663   {
2664     if (viewport.getConservationSelected()
2665             && viewport.getGlobalColourScheme() != null)
2666     {
2667       SliderPanel.setConservationSlider(alignPanel,
2668               viewport.getGlobalColourScheme(), "Background");
2669       SliderPanel.showConservationSlider();
2670     }
2671   }
2672
2673   protected void conservationMenuItem_actionPerformed()
2674   {
2675     viewport.setConservationSelected(conservationMenuItem.getState());
2676
2677     viewport.setAbovePIDThreshold(false);
2678     abovePIDThreshold.setState(false);
2679
2680     changeColour(viewport.getGlobalColourScheme());
2681
2682     modifyConservation_actionPerformed();
2683   }
2684
2685   public void abovePIDThreshold_actionPerformed()
2686   {
2687     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2688
2689     conservationMenuItem.setState(false);
2690     viewport.setConservationSelected(false);
2691
2692     changeColour(viewport.getGlobalColourScheme());
2693
2694     modifyPID_actionPerformed();
2695   }
2696
2697   public void sortPairwiseMenuItem_actionPerformed()
2698   {
2699     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2700     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2701             .getAlignment().getSequenceAt(0), null);
2702
2703     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2704             viewport.getAlignment()));
2705     alignPanel.paintAlignment(true);
2706   }
2707
2708   public void sortIDMenuItem_actionPerformed()
2709   {
2710     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2711     AlignmentSorter.sortByID(viewport.getAlignment());
2712     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2713             viewport.getAlignment()));
2714     alignPanel.paintAlignment(true);
2715   }
2716
2717   public void sortLengthMenuItem_actionPerformed()
2718   {
2719     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2720     AlignmentSorter.sortByLength(viewport.getAlignment());
2721     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2722             viewport.getAlignment()));
2723     alignPanel.paintAlignment(true);
2724   }
2725
2726   public void sortGroupMenuItem_actionPerformed()
2727   {
2728     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2729     AlignmentSorter.sortByGroup(viewport.getAlignment());
2730     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2731             viewport.getAlignment()));
2732     alignPanel.paintAlignment(true);
2733
2734   }
2735
2736   public void removeRedundancyMenuItem_actionPerformed()
2737   {
2738     new RedundancyPanel(alignPanel);
2739   }
2740
2741   public void pairwiseAlignmentMenuItem_actionPerformed()
2742   {
2743     if (viewport.getSelectionGroup() != null
2744             && viewport.getSelectionGroup().getSize() > 1)
2745     {
2746       Frame frame = new Frame();
2747       frame.add(new PairwiseAlignPanel(alignPanel));
2748       jalview.bin.JalviewLite.addFrame(frame,
2749               MessageManager.getString("action.pairwise_alignment"), 600,
2750               500);
2751     }
2752   }
2753
2754   public void PCAMenuItem_actionPerformed()
2755   {
2756     // are the sequences aligned?
2757     if (!viewport.getAlignment().isAligned(false))
2758     {
2759       SequenceI current;
2760       int Width = viewport.getAlignment().getWidth();
2761
2762       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2763       {
2764         current = viewport.getAlignment().getSequenceAt(i);
2765
2766         if (current.getLength() < Width)
2767         {
2768           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2769         }
2770       }
2771       alignPanel.paintAlignment(true);
2772     }
2773
2774     if ((viewport.getSelectionGroup() != null
2775             && viewport.getSelectionGroup().getSize() < 4 && viewport
2776             .getSelectionGroup().getSize() > 0)
2777             || viewport.getAlignment().getHeight() < 4)
2778     {
2779       return;
2780     }
2781
2782     try
2783     {
2784       new PCAPanel(viewport);
2785     } catch (java.lang.OutOfMemoryError ex)
2786     {
2787     }
2788
2789   }
2790
2791   public void averageDistanceTreeMenuItem_actionPerformed()
2792   {
2793     NewTreePanel("AV", "PID", "Average distance tree using PID");
2794   }
2795
2796   public void neighbourTreeMenuItem_actionPerformed()
2797   {
2798     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2799   }
2800
2801   protected void njTreeBlosumMenuItem_actionPerformed()
2802   {
2803     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2804   }
2805
2806   protected void avTreeBlosumMenuItem_actionPerformed()
2807   {
2808     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2809   }
2810
2811   void NewTreePanel(String type, String pwType, String title)
2812   {
2813     // are the sequences aligned?
2814     if (!viewport.getAlignment().isAligned(false))
2815     {
2816       SequenceI current;
2817       int Width = viewport.getAlignment().getWidth();
2818
2819       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2820       {
2821         current = viewport.getAlignment().getSequenceAt(i);
2822
2823         if (current.getLength() < Width)
2824         {
2825           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2826         }
2827       }
2828       alignPanel.paintAlignment(true);
2829
2830     }
2831
2832     if ((viewport.getSelectionGroup() != null && viewport
2833             .getSelectionGroup().getSize() > 1)
2834             || (viewport.getAlignment().getHeight() > 1))
2835     {
2836       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2837
2838       addTreeMenuItem(tp, title);
2839
2840       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2841     }
2842   }
2843
2844   void loadTree_actionPerformed()
2845   {
2846     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2847     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2848     cap.setTreeImport();
2849     Frame frame = new Frame();
2850     frame.add(cap);
2851     jalview.bin.JalviewLite.addFrame(frame,
2852             MessageManager.getString("label.paste_newick_file"), 400, 300);
2853   }
2854
2855   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2856   {
2857     TreePanel tp = new TreePanel(alignPanel, treeFile,
2858             MessageManager.getString("label.load_tree_from_file"), tree);
2859     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2860     addTreeMenuItem(tp, treeFile);
2861   }
2862
2863   /**
2864    * sort the alignment using the given treePanel
2865    *
2866    * @param treePanel
2867    *          tree used to sort view
2868    * @param title
2869    *          string used for undo event name
2870    */
2871   public void sortByTree(TreePanel treePanel, String title)
2872   {
2873     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2874     AlignmentSorter
2875             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2876     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2877     // HistoryItem.SORT));
2878     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2879             "label.order_by_params", new String[] { title }), oldOrder,
2880             viewport.getAlignment()));
2881     alignPanel.paintAlignment(true);
2882   }
2883
2884   /**
2885    * Do any automatic reordering of the alignment and add the necessary bits to
2886    * the menu structure for the new tree
2887    *
2888    * @param treePanel
2889    * @param title
2890    */
2891   protected void addTreeMenuItem(final TreePanel treePanel,
2892           final String title)
2893   {
2894     final MenuItem item = new MenuItem(title);
2895     sortByTreeMenu.add(item);
2896     item.addActionListener(new java.awt.event.ActionListener()
2897     {
2898       @Override
2899       public void actionPerformed(ActionEvent evt)
2900       {
2901         sortByTree(treePanel, title); // treePanel.getTitle());
2902       }
2903     });
2904
2905     treePanel.addWindowListener(new WindowAdapter()
2906     {
2907       @Override
2908       public void windowOpened(WindowEvent e)
2909       {
2910         if (viewport.sortByTree)
2911         {
2912           sortByTree(treePanel, title);
2913         }
2914         super.windowOpened(e);
2915       }
2916
2917       @Override
2918       public void windowClosing(WindowEvent e)
2919       {
2920         sortByTreeMenu.remove(item);
2921       };
2922     });
2923   }
2924
2925   public boolean sortBy(AlignmentOrder alorder, String undoname)
2926   {
2927     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2928     if (viewport.applet.debug)
2929     {
2930       System.err.println("Sorting " + alorder.getOrder().size()
2931               + " in alignment '" + getTitle() + "'");
2932     }
2933     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2934     if (undoname != null)
2935     {
2936       addHistoryItem(new OrderCommand(undoname, oldOrder,
2937               viewport.getAlignment()));
2938     }
2939     alignPanel.paintAlignment(true);
2940     return true;
2941   }
2942
2943   protected void documentation_actionPerformed()
2944   {
2945     alignPanel.av.applet.openJalviewHelpUrl();
2946   }
2947
2948   protected void about_actionPerformed()
2949   {
2950
2951     class AboutPanel extends Canvas
2952     {
2953       String version;
2954
2955       String builddate;
2956
2957       public AboutPanel(String version, String builddate)
2958       {
2959         this.version = version;
2960         this.builddate = builddate;
2961       }
2962
2963       @Override
2964       public void paint(Graphics g)
2965       {
2966         g.setColor(Color.white);
2967         g.fillRect(0, 0, getSize().width, getSize().height);
2968         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2969         FontMetrics fm = g.getFontMetrics();
2970         int fh = fm.getHeight();
2971         int y = 5, x = 7;
2972         g.setColor(Color.black);
2973         // TODO: update this text for each release or centrally store it for
2974         // lite and application
2975         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2976         g.drawString(MessageManager.formatMessage(
2977                 "label.jalviewLite_release", new String[] { version }), x,
2978                 y += fh);
2979         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2980         g.drawString(MessageManager.formatMessage(
2981                 "label.jaview_build_date", new String[] { builddate }), x,
2982                 y += fh);
2983         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2984         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2985                 x, y += fh * 1.5);
2986         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2987                 x + 50, y += fh + 8);
2988         g.drawString(
2989                 MessageManager.getString("label.jalview_dev_managers"), x,
2990                 y += fh);
2991         g.drawString(MessageManager
2992                 .getString("label.jalview_distribution_lists"), x, y += fh);
2993         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2994                 x, y += fh + 8);
2995         g.drawString(
2996                 MessageManager.getString("label.jalview_cite_1_authors"),
2997                 x, y += fh);
2998         g.drawString(
2999                 MessageManager.getString("label.jalview_cite_1_title"), x,
3000                 y += fh);
3001         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3002                 x, y += fh);
3003       }
3004     }
3005
3006     Frame frame = new Frame();
3007     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3008             .getBuildDate()));
3009     jalview.bin.JalviewLite.addFrame(frame,
3010             MessageManager.getString("label.jalview"), 580, 220);
3011
3012   }
3013
3014   public void showURL(String url, String target)
3015   {
3016     if (viewport.applet == null)
3017     {
3018       System.out.println("Not running as applet - no browser available.");
3019     }
3020     else
3021     {
3022       viewport.applet.showURL(url, target);
3023     }
3024   }
3025
3026   // ////////////////////////////////////////////////////////////////////////////////
3027   // JBuilder Graphics here
3028
3029   MenuBar alignFrameMenuBar = new MenuBar();
3030
3031   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3032
3033   MenuItem loadApplication = new MenuItem(
3034           MessageManager.getString("label.view_full_application"));
3035
3036   MenuItem loadTree = new MenuItem(
3037           MessageManager.getString("label.load_associated_tree"));
3038
3039   MenuItem loadAnnotations = new MenuItem(
3040           MessageManager.getString("label.load_features_annotations"));
3041
3042   MenuItem outputFeatures = new MenuItem(
3043           MessageManager.getString("label.export_features"));
3044
3045   MenuItem outputAnnotations = new MenuItem(
3046           MessageManager.getString("label.export_annotations"));
3047
3048   MenuItem closeMenuItem = new MenuItem(
3049           MessageManager.getString("action.close"));
3050
3051   MenuItem selectAllSequenceMenuItem = new MenuItem(
3052           MessageManager.getString("action.select_all"));
3053
3054   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3055           MessageManager.getString("action.deselect_all"));
3056
3057   MenuItem invertSequenceMenuItem = new MenuItem(
3058           MessageManager.getString("action.invert_selection"));
3059
3060   MenuItem remove2LeftMenuItem = new MenuItem();
3061
3062   MenuItem remove2RightMenuItem = new MenuItem();
3063
3064   MenuItem removeGappedColumnMenuItem = new MenuItem();
3065
3066   MenuItem removeAllGapsMenuItem = new MenuItem();
3067
3068   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3069
3070   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3071
3072   MenuItem sortPairwiseMenuItem = new MenuItem();
3073
3074   MenuItem sortIDMenuItem = new MenuItem();
3075
3076   MenuItem sortLengthMenuItem = new MenuItem();
3077
3078   MenuItem sortGroupMenuItem = new MenuItem();
3079
3080   MenuItem removeRedundancyMenuItem = new MenuItem();
3081
3082   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3083
3084   MenuItem PCAMenuItem = new MenuItem();
3085
3086   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3087
3088   MenuItem neighbourTreeMenuItem = new MenuItem();
3089
3090   BorderLayout borderLayout1 = new BorderLayout();
3091
3092   public Label statusBar = new Label();
3093
3094   MenuItem clustalColour = new MenuItem();
3095
3096   MenuItem zappoColour = new MenuItem();
3097
3098   MenuItem taylorColour = new MenuItem();
3099
3100   MenuItem hydrophobicityColour = new MenuItem();
3101
3102   MenuItem helixColour = new MenuItem();
3103
3104   MenuItem strandColour = new MenuItem();
3105
3106   MenuItem turnColour = new MenuItem();
3107
3108   MenuItem buriedColour = new MenuItem();
3109
3110   MenuItem purinePyrimidineColour = new MenuItem();
3111
3112   // MenuItem RNAInteractionColour = new MenuItem();
3113
3114   MenuItem RNAHelixColour = new MenuItem();
3115
3116   MenuItem userDefinedColour = new MenuItem();
3117
3118   MenuItem PIDColour = new MenuItem();
3119
3120   MenuItem BLOSUM62Colour = new MenuItem();
3121
3122   MenuItem tcoffeeColour = new MenuItem();
3123
3124   MenuItem njTreeBlosumMenuItem = new MenuItem();
3125
3126   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3127
3128   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3129
3130   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3131
3132   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3133
3134   MenuItem alProperties = new MenuItem(
3135           MessageManager.getString("label.alignment_props"));
3136
3137   MenuItem overviewMenuItem = new MenuItem();
3138
3139   MenuItem undoMenuItem = new MenuItem();
3140
3141   MenuItem redoMenuItem = new MenuItem();
3142
3143   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3144
3145   MenuItem noColourmenuItem = new MenuItem();
3146
3147   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3148
3149   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3150
3151   MenuItem findMenuItem = new MenuItem();
3152
3153   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3154
3155   MenuItem nucleotideColour = new MenuItem();
3156
3157   MenuItem deleteGroups = new MenuItem();
3158
3159   MenuItem grpsFromSelection = new MenuItem();
3160
3161   MenuItem createGroup = new MenuItem();
3162
3163   MenuItem unGroup = new MenuItem();
3164
3165   MenuItem delete = new MenuItem();
3166
3167   MenuItem copy = new MenuItem();
3168
3169   MenuItem cut = new MenuItem();
3170
3171   Menu pasteMenu = new Menu();
3172
3173   MenuItem pasteNew = new MenuItem();
3174
3175   MenuItem pasteThis = new MenuItem();
3176
3177   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3178
3179   MenuItem font = new MenuItem();
3180
3181   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3182
3183   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3184
3185   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3186
3187   MenuItem modifyPID = new MenuItem();
3188
3189   MenuItem modifyConservation = new MenuItem();
3190
3191   CheckboxMenuItem autoCalculate = null;
3192
3193   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3194           "Sort Alignment With New Tree", true);
3195
3196   Menu sortByTreeMenu = new Menu();
3197
3198   MenuItem inputText = new MenuItem();
3199
3200   MenuItem documentation = new MenuItem();
3201
3202   MenuItem about = new MenuItem();
3203
3204   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3205
3206   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3209
3210   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3211
3212   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3213
3214   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3215
3216   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3217
3218   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3219
3220   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3221
3222   /**
3223    * Initialise menus and other items
3224    *
3225    * @throws Exception
3226    */
3227   private void jbInit() throws Exception
3228   {
3229     setMenuBar(alignFrameMenuBar);
3230
3231     /*
3232      * Configure File menu items and actions
3233      */
3234     inputText
3235             .setLabel(MessageManager.getString("label.input_from_textbox"));
3236     inputText.addActionListener(this);
3237     Menu outputTextboxMenu = new Menu(
3238             MessageManager.getString("label.out_to_textbox"));
3239     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3240     {
3241
3242       MenuItem item = new MenuItem(
3243               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3244
3245       item.addActionListener(new java.awt.event.ActionListener()
3246       {
3247         @Override
3248         public void actionPerformed(ActionEvent e)
3249         {
3250           outputText_actionPerformed(e);
3251         }
3252       });
3253
3254       outputTextboxMenu.add(item);
3255     }
3256     closeMenuItem.addActionListener(this);
3257     loadApplication.addActionListener(this);
3258     loadTree.addActionListener(this);
3259     loadAnnotations.addActionListener(this);
3260     outputFeatures.addActionListener(this);
3261     outputAnnotations.addActionListener(this);
3262
3263     /*
3264      * Configure Edit menu items and actions
3265      */
3266     undoMenuItem.setEnabled(false);
3267     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3268     undoMenuItem.addActionListener(this);
3269     redoMenuItem.setEnabled(false);
3270     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3271     redoMenuItem.addActionListener(this);
3272     copy.setLabel(MessageManager.getString("action.copy"));
3273     copy.addActionListener(this);
3274     cut.setLabel(MessageManager.getString("action.cut"));
3275     cut.addActionListener(this);
3276     delete.setLabel(MessageManager.getString("action.delete"));
3277     delete.addActionListener(this);
3278     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3279     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3280     pasteNew.addActionListener(this);
3281     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3282     pasteThis.addActionListener(this);
3283     remove2LeftMenuItem.setLabel(MessageManager
3284             .getString("action.remove_left"));
3285     remove2LeftMenuItem.addActionListener(this);
3286     remove2RightMenuItem.setLabel(MessageManager
3287             .getString("action.remove_right"));
3288     remove2RightMenuItem.addActionListener(this);
3289     removeGappedColumnMenuItem.setLabel(MessageManager
3290             .getString("action.remove_empty_columns"));
3291     removeGappedColumnMenuItem.addActionListener(this);
3292     removeAllGapsMenuItem.setLabel(MessageManager
3293             .getString("action.remove_all_gaps"));
3294     removeAllGapsMenuItem.addActionListener(this);
3295     removeRedundancyMenuItem.setLabel(MessageManager
3296             .getString("action.remove_redundancy"));
3297     removeRedundancyMenuItem.addActionListener(this);
3298
3299     /*
3300      * Configure Select menu items and actions
3301      */
3302     findMenuItem.setLabel(MessageManager.getString("action.find"));
3303     findMenuItem.addActionListener(this);
3304     selectAllSequenceMenuItem.addActionListener(this);
3305     deselectAllSequenceMenuItem.addActionListener(this);
3306     invertSequenceMenuItem.setLabel(MessageManager
3307             .getString("action.invert_sequence_selection"));
3308     invertSequenceMenuItem.addActionListener(this);
3309     invertColSel.setLabel(MessageManager
3310             .getString("action.invert_column_selection"));
3311     invertColSel.addActionListener(this);
3312     deleteGroups.setLabel(MessageManager
3313             .getString("action.undefine_groups"));
3314     deleteGroups.addActionListener(this);
3315     grpsFromSelection.setLabel(MessageManager
3316             .getString("action.make_groups_selection"));
3317     grpsFromSelection.addActionListener(this);
3318     createGroup.setLabel(MessageManager.getString("action.create_group"));
3319     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3320     annotationColumnSelection.setLabel(MessageManager
3321             .getString("action.select_by_annotation"));
3322     annotationColumnSelection.addActionListener(this);
3323
3324     /*
3325      * Configure View menu items and actions
3326      */
3327     newView.setLabel(MessageManager.getString("action.new_view"));
3328     newView.addActionListener(this);
3329     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3330     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3331     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3332     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3333     hideColumns
3334             .setLabel(MessageManager.getString("label.selected_columns"));
3335     hideSequences.setLabel(MessageManager
3336             .getString("label.selected_sequences"));
3337     hideAllButSelection.setLabel(MessageManager
3338             .getString("label.all_but_selected_region"));
3339     hideAllSelection.setLabel(MessageManager
3340             .getString("label.selected_region"));
3341     showAllHidden.setLabel(MessageManager
3342             .getString("label.all_sequences_columns"));
3343     showColumns.addActionListener(this);
3344     showSeqs.addActionListener(this);
3345     hideColumns.addActionListener(this);
3346     hideSequences.addActionListener(this);
3347     hideAllButSelection.addActionListener(this);
3348     hideAllSelection.addActionListener(this);
3349     showAllHidden.addActionListener(this);
3350     featureSettings.setLabel(MessageManager
3351             .getString("action.feature_settings"));
3352     featureSettings.addActionListener(this);
3353     sequenceFeatures.setLabel(MessageManager
3354             .getString("label.show_sequence_features"));
3355     sequenceFeatures.addItemListener(this);
3356     sequenceFeatures.setState(false);
3357     followMouseOverFlag.setLabel(MessageManager
3358             .getString("label.automatic_scrolling"));
3359     followMouseOverFlag.addItemListener(this);
3360     alProperties.addActionListener(this);
3361     overviewMenuItem.setLabel(MessageManager
3362             .getString("label.overview_window"));
3363     overviewMenuItem.addActionListener(this);
3364
3365     /*
3366      * Configure Annotations menu items and actions
3367      */
3368     annotationPanelMenuItem.setLabel(MessageManager
3369             .getString("label.show_annotations"));
3370     annotationPanelMenuItem.addItemListener(this);
3371     showGroupConsensus.setLabel(MessageManager
3372             .getString("label.group_consensus"));
3373     showGroupConservation.setLabel(MessageManager
3374             .getString("label.group_conservation"));
3375     showConsensusHistogram.setLabel(MessageManager
3376             .getString("label.show_consensus_histogram"));
3377     showSequenceLogo.setLabel(MessageManager
3378             .getString("label.show_consensus_logo"));
3379     normSequenceLogo.setLabel(MessageManager
3380             .getString("label.norm_consensus_logo"));
3381     applyAutoAnnotationSettings.setLabel(MessageManager
3382             .getString("label.apply_all_groups"));
3383     applyAutoAnnotationSettings.setState(true);
3384     Menu autoAnnMenu = new Menu(
3385             MessageManager.getString("label.autocalculated_annotation"));
3386     showGroupConsensus.addItemListener(this);
3387     showGroupConservation.addItemListener(this);
3388     showConsensusHistogram.addItemListener(this);
3389     showSequenceLogo.addItemListener(this);
3390     normSequenceLogo.addItemListener(this);
3391     applyAutoAnnotationSettings.addItemListener(this);
3392     showAlignmentAnnotations = new CheckboxMenuItem(
3393             MessageManager.getString("label.show_all_al_annotations"));
3394     showSequenceAnnotations = new CheckboxMenuItem(
3395             MessageManager.getString("label.show_all_seq_annotations"));
3396     sortAnnBySequence = new CheckboxMenuItem(
3397             MessageManager.getString("label.sort_annotations_by_sequence"));
3398     sortAnnByLabel = new CheckboxMenuItem(
3399             MessageManager.getString("label.sort_annotations_by_label"));
3400     showAutoFirst = new CheckboxMenuItem(
3401             MessageManager.getString("label.show_first"));
3402     showAutoFirst.setState(false); // pending applet parameter
3403     setShowAutoCalculatedAbove(showAutoFirst.getState());
3404     showAutoLast = new CheckboxMenuItem(
3405             MessageManager.getString("label.show_last"));
3406     showAutoLast.setState(!showAutoFirst.getState());
3407     showAlignmentAnnotations.addItemListener(this);
3408     showSequenceAnnotations.addItemListener(this);
3409     sortAnnBySequence.addItemListener(this);
3410     sortAnnByLabel.addItemListener(this);
3411     showAutoFirst.addItemListener(this);
3412     showAutoLast.addItemListener(this);
3413
3414     /*
3415      * Configure Format menu items and actions
3416      */
3417     font.setLabel(MessageManager.getString("action.font"));
3418     font.addActionListener(this);
3419     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3420     scaleAbove.setState(true);
3421     scaleAbove.setEnabled(false);
3422     scaleAbove.addItemListener(this);
3423     scaleLeft.setEnabled(false);
3424     scaleLeft.setState(true);
3425     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3426     scaleLeft.addItemListener(this);
3427     scaleRight.setEnabled(false);
3428     scaleRight.setState(true);
3429     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3430     scaleRight.addItemListener(this);
3431     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3432     viewBoxesMenuItem.setState(true);
3433     viewBoxesMenuItem.addItemListener(this);
3434     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3435     viewTextMenuItem.setState(true);
3436     viewTextMenuItem.addItemListener(this);
3437     colourTextMenuItem.setLabel(MessageManager
3438             .getString("label.colour_text"));
3439     colourTextMenuItem.addItemListener(this);
3440     displayNonconservedMenuItem.setLabel(MessageManager
3441             .getString("label.show_non_conversed"));
3442     displayNonconservedMenuItem.addItemListener(this);
3443     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3444     wrapMenuItem.addItemListener(this);
3445     renderGapsMenuItem.setLabel(MessageManager
3446             .getString("action.show_gaps"));
3447     renderGapsMenuItem.setState(true);
3448     renderGapsMenuItem.addItemListener(this);
3449     centreColumnLabelFlag.setLabel(MessageManager
3450             .getString("label.centre_column_labels"));
3451     centreColumnLabelFlag.addItemListener(this);
3452     seqLimits.setState(true);
3453     seqLimits.setLabel(MessageManager
3454             .getString("label.show_sequence_limits"));
3455     seqLimits.addItemListener(this);
3456
3457     /*
3458      * Configure Colour menu items and actions
3459      */
3460     applyToAllGroups.setLabel(MessageManager
3461             .getString("label.apply_colour_to_all_groups"));
3462     applyToAllGroups.setState(true);
3463     applyToAllGroups.addItemListener(this);
3464     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3465     clustalColour.addActionListener(this);
3466     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3467     zappoColour.addActionListener(this);
3468     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3469     taylorColour.addActionListener(this);
3470     hydrophobicityColour.setLabel(MessageManager
3471             .getString("label.hydrophobicity"));
3472     hydrophobicityColour.addActionListener(this);
3473     helixColour
3474             .setLabel(MessageManager.getString("label.helix_propensity"));
3475     helixColour.addActionListener(this);
3476     strandColour.setLabel(MessageManager
3477             .getString("label.strand_propensity"));
3478     strandColour.addActionListener(this);
3479     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3480     turnColour.addActionListener(this);
3481     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3482     buriedColour.addActionListener(this);
3483     purinePyrimidineColour.setLabel(MessageManager
3484             .getString("label.purine_pyrimidine"));
3485     purinePyrimidineColour.addActionListener(this);
3486     // RNAInteractionColour.setLabel(MessageManager
3487     // .getString("label.rna_interaction"));
3488     // RNAInteractionColour.addActionListener(this);
3489     RNAHelixColour.setLabel(MessageManager
3490             .getString("action.by_rna_helixes"));
3491     RNAHelixColour.addActionListener(this);
3492     userDefinedColour.setLabel(MessageManager
3493             .getString("action.user_defined"));
3494     userDefinedColour.addActionListener(this);
3495     PIDColour.setLabel(MessageManager
3496             .getString("label.percentage_identity"));
3497     PIDColour.addActionListener(this);
3498     BLOSUM62Colour.setLabel(MessageManager
3499             .getString("label.blosum62_score"));
3500     BLOSUM62Colour.addActionListener(this);
3501     tcoffeeColour
3502             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3503     // it will be enabled only if a score file is provided
3504     tcoffeeColour.setEnabled(false);
3505     tcoffeeColour.addActionListener(this);
3506     conservationMenuItem.setLabel(MessageManager
3507             .getString("action.by_conservation"));
3508     conservationMenuItem.addItemListener(this);
3509     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3510     noColourmenuItem.addActionListener(this);
3511     abovePIDThreshold.setLabel(MessageManager
3512             .getString("label.above_identity_threshold"));
3513     abovePIDThreshold.addItemListener(this);
3514     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3515     nucleotideColour.addActionListener(this);
3516     modifyPID.setLabel(MessageManager
3517             .getString("label.modify_identity_threshold"));
3518     modifyPID.addActionListener(this);
3519     modifyConservation.setLabel(MessageManager
3520             .getString("label.modify_conservation_threshold"));
3521     modifyConservation.addActionListener(this);
3522     annotationColour.setLabel(MessageManager
3523             .getString("action.by_annotation"));
3524     annotationColour.addActionListener(this);
3525
3526     /*
3527      * Configure Calculate menu items and actions
3528      */
3529     sortPairwiseMenuItem.setLabel(MessageManager
3530             .getString("action.by_pairwise_id"));
3531     sortPairwiseMenuItem.addActionListener(this);
3532     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3533     sortIDMenuItem.addActionListener(this);
3534     sortLengthMenuItem.setLabel(MessageManager
3535             .getString("action.by_length"));
3536     sortLengthMenuItem.addActionListener(this);
3537     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3538     sortGroupMenuItem.addActionListener(this);
3539     pairwiseAlignmentMenuItem.setLabel(MessageManager
3540             .getString("action.pairwise_alignment"));
3541     pairwiseAlignmentMenuItem.addActionListener(this);
3542     PCAMenuItem.setLabel(MessageManager
3543             .getString("label.principal_component_analysis"));
3544     PCAMenuItem.addActionListener(this);
3545     autoCalculate = new CheckboxMenuItem(
3546             MessageManager.getString("label.autocalculate_consensus"), true);
3547     averageDistanceTreeMenuItem.setLabel(MessageManager
3548             .getString("label.average_distance_identity"));
3549     averageDistanceTreeMenuItem.addActionListener(this);
3550     neighbourTreeMenuItem.setLabel(MessageManager
3551             .getString("label.neighbour_joining_identity"));
3552     neighbourTreeMenuItem.addActionListener(this);
3553     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3554             .getString("label.average_distance_bloslum62"));
3555     avDistanceTreeBlosumMenuItem.addActionListener(this);
3556     njTreeBlosumMenuItem.setLabel(MessageManager
3557             .getString("label.neighbour_blosum62"));
3558     njTreeBlosumMenuItem.addActionListener(this);
3559     sortByTreeMenu.setLabel(MessageManager
3560             .getString("action.by_tree_order"));
3561     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3562     Menu calculateTreeMenu = new Menu(
3563             MessageManager.getString("action.calculate_tree"));
3564     autoCalculate.addItemListener(this);
3565     sortByTree.addItemListener(this);
3566
3567     /*
3568      * Configure Help menu items and actions
3569      */
3570     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3571     documentation.setLabel(MessageManager.getString("label.documentation"));
3572     documentation.addActionListener(this);
3573     about.setLabel(MessageManager.getString("label.about"));
3574     about.addActionListener(this);
3575
3576     /*
3577      * Add top level menus to frame
3578      */
3579     alignFrameMenuBar.add(fileMenu);
3580     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3581     alignFrameMenuBar.add(editMenu);
3582     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3583     alignFrameMenuBar.add(selectMenu);
3584     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3585     alignFrameMenuBar.add(viewMenu);
3586     Menu annotationsMenu = new Menu(
3587             MessageManager.getString("action.annotations"));
3588     alignFrameMenuBar.add(annotationsMenu);
3589     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3590     alignFrameMenuBar.add(formatMenu);
3591     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3592     alignFrameMenuBar.add(colourMenu);
3593     Menu calculateMenu = new Menu(
3594             MessageManager.getString("action.calculate"));
3595     alignFrameMenuBar.add(calculateMenu);
3596     alignFrameMenuBar.add(helpMenu);
3597
3598     /*
3599      * File menu
3600      */
3601     fileMenu.add(inputText);
3602     fileMenu.add(loadTree);
3603     fileMenu.add(loadAnnotations);
3604     fileMenu.addSeparator();
3605     fileMenu.add(outputTextboxMenu);
3606     fileMenu.add(outputFeatures);
3607     fileMenu.add(outputAnnotations);
3608     if (jalviewServletURL != null)
3609     {
3610       fileMenu.add(loadApplication);
3611     }
3612     fileMenu.addSeparator();
3613     fileMenu.add(closeMenuItem);
3614
3615     /*
3616      * Edit menu
3617      */
3618     editMenu.add(undoMenuItem);
3619     editMenu.add(redoMenuItem);
3620     editMenu.add(cut);
3621     editMenu.add(copy);
3622     pasteMenu.add(pasteNew);
3623     pasteMenu.add(pasteThis);
3624     editMenu.add(pasteMenu);
3625     editMenu.add(delete);
3626     editMenu.addSeparator();
3627     editMenu.add(remove2LeftMenuItem);
3628     editMenu.add(remove2RightMenuItem);
3629     editMenu.add(removeGappedColumnMenuItem);
3630     editMenu.add(removeAllGapsMenuItem);
3631     editMenu.add(removeRedundancyMenuItem);
3632
3633     /*
3634      * Select menu
3635      */
3636     selectMenu.add(findMenuItem);
3637     selectMenu.addSeparator();
3638     selectMenu.add(selectAllSequenceMenuItem);
3639     selectMenu.add(deselectAllSequenceMenuItem);
3640     selectMenu.add(invertSequenceMenuItem);
3641     selectMenu.add(invertColSel);
3642     selectMenu.add(createGroup);
3643     selectMenu.add(unGroup);
3644     selectMenu.add(grpsFromSelection);
3645     selectMenu.add(deleteGroups);
3646     selectMenu.add(annotationColumnSelection);
3647
3648     /*
3649      * View menu
3650      */
3651     viewMenu.add(newView);
3652     viewMenu.addSeparator();
3653     showMenu.add(showColumns);
3654     showMenu.add(showSeqs);
3655     showMenu.add(showAllHidden);
3656     viewMenu.add(showMenu);
3657     hideMenu.add(hideColumns);
3658     hideMenu.add(hideSequences);
3659     hideMenu.add(hideAllSelection);
3660     hideMenu.add(hideAllButSelection);
3661     viewMenu.add(hideMenu);
3662     viewMenu.addSeparator();
3663     viewMenu.add(followMouseOverFlag);
3664     viewMenu.addSeparator();
3665     viewMenu.add(sequenceFeatures);
3666     viewMenu.add(featureSettings);
3667     viewMenu.addSeparator();
3668     viewMenu.add(alProperties);
3669     viewMenu.addSeparator();
3670     viewMenu.add(overviewMenuItem);
3671
3672     /*
3673      * Annotations menu
3674      */
3675     annotationsMenu.add(annotationPanelMenuItem);
3676     annotationsMenu.addSeparator();
3677     annotationsMenu.add(showAlignmentAnnotations);
3678     annotationsMenu.add(showSequenceAnnotations);
3679     annotationsMenu.add(sortAnnBySequence);
3680     annotationsMenu.add(sortAnnByLabel);
3681     annotationsMenu.addSeparator();
3682     autoAnnMenu.add(showAutoFirst);
3683     autoAnnMenu.add(showAutoLast);
3684     autoAnnMenu.addSeparator();
3685     autoAnnMenu.add(applyAutoAnnotationSettings);
3686     autoAnnMenu.add(showConsensusHistogram);
3687     autoAnnMenu.add(showSequenceLogo);
3688     autoAnnMenu.add(normSequenceLogo);
3689     autoAnnMenu.addSeparator();
3690     autoAnnMenu.add(showGroupConservation);
3691     autoAnnMenu.add(showGroupConsensus);
3692     annotationsMenu.add(autoAnnMenu);
3693
3694     /*
3695      * Format menu
3696      */
3697     formatMenu.add(font);
3698     formatMenu.add(seqLimits);
3699     formatMenu.add(wrapMenuItem);
3700     formatMenu.add(scaleAbove);
3701     formatMenu.add(scaleLeft);
3702     formatMenu.add(scaleRight);
3703     formatMenu.add(viewBoxesMenuItem);
3704     formatMenu.add(viewTextMenuItem);
3705     formatMenu.add(colourTextMenuItem);
3706     formatMenu.add(displayNonconservedMenuItem);
3707     formatMenu.add(renderGapsMenuItem);
3708     formatMenu.add(centreColumnLabelFlag);
3709
3710     /*
3711      * Colour menu
3712      */
3713     colourMenu.add(applyToAllGroups);
3714     colourMenu.addSeparator();
3715     colourMenu.add(noColourmenuItem);
3716     colourMenu.add(clustalColour);
3717     colourMenu.add(BLOSUM62Colour);
3718     colourMenu.add(PIDColour);
3719     colourMenu.add(zappoColour);
3720     colourMenu.add(taylorColour);
3721     colourMenu.add(hydrophobicityColour);
3722     colourMenu.add(helixColour);
3723     colourMenu.add(strandColour);
3724     colourMenu.add(turnColour);
3725     colourMenu.add(buriedColour);
3726     colourMenu.add(nucleotideColour);
3727     colourMenu.add(purinePyrimidineColour);
3728     // colourMenu.add(RNAInteractionColour);
3729     colourMenu.add(tcoffeeColour);
3730     colourMenu.add(userDefinedColour);
3731     colourMenu.addSeparator();
3732     colourMenu.add(conservationMenuItem);
3733     colourMenu.add(modifyConservation);
3734     colourMenu.add(abovePIDThreshold);
3735     colourMenu.add(modifyPID);
3736     colourMenu.add(annotationColour);
3737     colourMenu.add(RNAHelixColour);
3738
3739     /*
3740      * Calculate menu
3741      */
3742     sortMenu.add(sortIDMenuItem);
3743     sortMenu.add(sortLengthMenuItem);
3744     sortMenu.add(sortByTreeMenu);
3745     sortMenu.add(sortGroupMenuItem);
3746     sortMenu.add(sortPairwiseMenuItem);
3747     calculateMenu.add(sortMenu);
3748     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3749     calculateTreeMenu.add(neighbourTreeMenuItem);
3750     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3751     calculateTreeMenu.add(njTreeBlosumMenuItem);
3752     calculateMenu.add(calculateTreeMenu);
3753     calculateMenu.addSeparator();
3754     calculateMenu.add(pairwiseAlignmentMenuItem);
3755     calculateMenu.add(PCAMenuItem);
3756     calculateMenu.add(autoCalculate);
3757     calculateMenu.add(sortByTree);
3758
3759     /*
3760      * Help menu
3761      */
3762     helpMenu.add(documentation);
3763     helpMenu.add(about);
3764
3765     /*
3766      * Status bar
3767      */
3768     statusBar.setBackground(Color.white);
3769     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3770     statusBar.setText(MessageManager.getString("label.status_bar"));
3771     this.add(statusBar, BorderLayout.SOUTH);
3772   }
3773
3774   @Override
3775   public void setStatus(String string)
3776   {
3777     statusBar.setText(string);
3778   };
3779
3780   MenuItem featureSettings = new MenuItem();
3781
3782   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3783
3784   MenuItem annotationColour = new MenuItem();
3785
3786   MenuItem annotationColumnSelection = new MenuItem();
3787
3788   MenuItem invertColSel = new MenuItem();
3789
3790   MenuItem showColumns = new MenuItem();
3791
3792   MenuItem showSeqs = new MenuItem();
3793
3794   MenuItem hideColumns = new MenuItem();
3795
3796   MenuItem hideSequences = new MenuItem();
3797
3798   MenuItem hideAllButSelection = new MenuItem();
3799
3800   MenuItem hideAllSelection = new MenuItem();
3801
3802   MenuItem showAllHidden = new MenuItem();
3803
3804   MenuItem newView = new MenuItem();
3805
3806   private CheckboxMenuItem showAlignmentAnnotations;
3807
3808   private CheckboxMenuItem showSequenceAnnotations;
3809
3810   private CheckboxMenuItem sortAnnBySequence;
3811
3812   private CheckboxMenuItem sortAnnByLabel;
3813
3814   private CheckboxMenuItem showAutoFirst;
3815
3816   private CheckboxMenuItem showAutoLast;
3817
3818   private SplitFrame splitFrame;
3819
3820   /**
3821    * Attach the alignFrame panels after embedding menus, if necessary. This used
3822    * to be called setEmbedded, but is now creates the dropdown menus in a
3823    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3824    *
3825    * @param reallyEmbedded
3826    *          true to attach the view to the applet area on the page rather than
3827    *          in a new window
3828    */
3829   public void createAlignFrameWindow(boolean reallyEmbedded)
3830   {
3831     if (reallyEmbedded)
3832     {
3833       embedAlignFrameInApplet(viewport.applet);
3834     }
3835     else
3836     {
3837       // //////
3838       // test and embed menu bar if necessary.
3839       //
3840       if (embedMenuIfNeeded(alignPanel))
3841       {
3842         /*
3843          * adjust for status bar height too. ? pointless as overridden by layout
3844          * manager
3845          */
3846         alignPanel.setSize(getSize().width,
3847                 getSize().height - statusBar.getHeight());
3848       }
3849       add(statusBar, BorderLayout.SOUTH);
3850       add(alignPanel, BorderLayout.CENTER);
3851       // and register with the applet so it can pass external API calls to us
3852       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3853               frameHeight);
3854     }
3855   }
3856
3857   /**
3858    * Add the components of this AlignFrame to the applet container.
3859    *
3860    * @param theApplet
3861    */
3862   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3863   {
3864     // ////
3865     // Explicitly build the embedded menu panel for the on-page applet
3866     //
3867     // view cannot be closed if its actually on the page
3868     fileMenu.remove(closeMenuItem);
3869     fileMenu.remove(3); // Remove Separator
3870     // construct embedded menu, using default font
3871     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3872     // and actually add the components to the applet area
3873     theApplet.setLayout(new BorderLayout());
3874     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3875     theApplet.add(statusBar, BorderLayout.SOUTH);
3876     // TODO should size be left to the layout manager?
3877     alignPanel.setSize(theApplet.getSize().width,
3878             theApplet.getSize().height - embeddedMenu.getHeight()
3879                     - statusBar.getHeight());
3880     theApplet.add(alignPanel, BorderLayout.CENTER);
3881     final AlignFrame me = this;
3882     theApplet.addFocusListener(new FocusListener()
3883     {
3884
3885       @Override
3886       public void focusLost(FocusEvent e)
3887       {
3888         if (theApplet.currentAlignFrame == me)
3889         {
3890           theApplet.currentAlignFrame = null;
3891         }
3892       }
3893
3894       @Override
3895       public void focusGained(FocusEvent e)
3896       {
3897         theApplet.currentAlignFrame = me;
3898       }
3899     });
3900     theApplet.validate();
3901   }
3902
3903   /**
3904    * create a new binding between structures in an existing jmol viewer instance
3905    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3906    * this does not open a new Jmol window, or modify the display of the
3907    * structures in the original jmol window. Note This method doesn't work
3908    * without an additional javascript library to exchange messages between the
3909    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3910    *
3911    * @param viewer
3912    *          JmolViewer instance
3913    * @param sequenceIds
3914    *          - sequence Ids to search for associations
3915    */
3916   public SequenceStructureBinding addStructureViewInstance(
3917           Object jmolviewer, String[] sequenceIds)
3918   {
3919     Viewer viewer = null;
3920     try
3921     {
3922       viewer = (Viewer) jmolviewer;
3923     } catch (ClassCastException ex)
3924     {
3925       System.err.println("Unsupported viewer object :"
3926               + jmolviewer.getClass());
3927     }
3928     if (viewer == null)
3929     {
3930       System.err.println("Can't use this object as a structure viewer:"
3931               + jmolviewer.getClass());
3932       return null;
3933     }
3934     SequenceI[] seqs = null;
3935     if (sequenceIds == null || sequenceIds.length == 0)
3936     {
3937       seqs = viewport.getAlignment().getSequencesArray();
3938     }
3939     else
3940     {
3941       Vector sqi = new Vector();
3942       AlignmentI al = viewport.getAlignment();
3943       for (int sid = 0; sid < sequenceIds.length; sid++)
3944       {
3945         SequenceI sq = al.findName(sequenceIds[sid]);
3946         if (sq != null)
3947         {
3948           sqi.addElement(sq);
3949         }
3950       }
3951       if (sqi.size() > 0)
3952       {
3953         seqs = new SequenceI[sqi.size()];
3954         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3955         {
3956           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3957         }
3958       }
3959       else
3960       {
3961         return null;
3962       }
3963     }
3964     AAStructureBindingModel jmv = null;
3965     // TODO: search for a jmv that involves viewer
3966     if (jmv == null)
3967     { // create a new viewer/jalview binding.
3968       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3969     }
3970     return jmv;
3971
3972   }
3973
3974   /**
3975    * bind a pdb file to a sequence in the current view
3976    *
3977    * @param sequenceId
3978    *          - sequenceId within the dataset.
3979    * @param pdbEntryString
3980    *          - the short name for the PDB file
3981    * @param pdbFile
3982    *          - pdb file - either a URL or a valid PDB file.
3983    * @return true if binding was as success TODO: consider making an exception
3984    *         structure for indicating when PDB parsing or sequenceId location
3985    *         fails.
3986    */
3987   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3988           String pdbFile)
3989   {
3990     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3991     boolean needtoadd = false;
3992     if (toaddpdb != null)
3993     {
3994       Vector pdbe = toaddpdb.getAllPDBEntries();
3995       PDBEntry pdbentry = null;
3996       if (pdbe != null && pdbe.size() > 0)
3997       {
3998         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3999         {
4000           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4001           if (!pdbentry.getId().equals(pdbEntryString)
4002                   && !pdbentry.getFile().equals(pdbFile))
4003           {
4004             pdbentry = null;
4005           }
4006           else
4007           {
4008             continue;
4009           }
4010         }
4011       }
4012       if (pdbentry == null)
4013       {
4014         pdbentry = new PDBEntry();
4015         pdbentry.setId(pdbEntryString);
4016         pdbentry.setFile(pdbFile);
4017         needtoadd = true; // add this new entry to sequence.
4018       }
4019       // resolve data source
4020       // TODO: this code should be a refactored to an io package
4021       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4022       if (protocol == null)
4023       {
4024         return false;
4025       }
4026       if (needtoadd)
4027       {
4028         // make a note of the access mode and add
4029         if (pdbentry.getProperty() == null)
4030         {
4031           pdbentry.setProperty(new Hashtable());
4032         }
4033         pdbentry.getProperty().put("protocol", protocol);
4034         toaddpdb.addPDBId(pdbentry);
4035         alignPanel.getStructureSelectionManager()
4036                 .registerPDBEntry(pdbentry);
4037       }
4038     }
4039     return true;
4040   }
4041
4042   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4043   {
4044     if (seqs != null)
4045     {
4046       Vector sequences = new Vector();
4047       for (int i = 0; i < seqs.length; i++)
4048       {
4049         if (seqs[i] != null)
4050         {
4051           sequences.addElement(new Object[] { seqs[i],
4052               (chains != null) ? chains[i] : null });
4053         }
4054       }
4055       seqs = new SequenceI[sequences.size()];
4056       chains = new String[sequences.size()];
4057       for (int i = 0, isize = sequences.size(); i < isize; i++)
4058       {
4059         Object[] oj = (Object[]) sequences.elementAt(i);
4060
4061         seqs[i] = (SequenceI) oj[0];
4062         chains[i] = (String) oj[1];
4063       }
4064     }
4065     return new Object[] { seqs, chains };
4066
4067   }
4068
4069   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4070           SequenceI[] seqs, String[] chains, String protocol)
4071   {
4072     // Scrub any null sequences from the array
4073     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4074     seqs = (SequenceI[]) sqch[0];
4075     chains = (String[]) sqch[1];
4076     if (seqs == null || seqs.length == 0)
4077     {
4078       System.err
4079               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4080     }
4081     if (protocol == null || protocol.trim().length() == 0
4082             || protocol.equals("null"))
4083     {
4084       protocol = (String) pdb.getProperty().get("protocol");
4085       if (protocol == null)
4086       {
4087         System.err.println("Couldn't work out protocol to open structure: "
4088                 + pdb.getId());
4089         return;
4090       }
4091     }
4092     if (applet.useXtrnalSviewer)
4093     {
4094       // register the association(s) and quit, don't create any windows.
4095       if (StructureSelectionManager.getStructureSelectionManager(applet)
4096               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4097       {
4098         System.err.println("Failed to map " + pdb.getFile() + " ("
4099                 + protocol + ") to any sequences");
4100       }
4101       return;
4102     }
4103     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4104     {
4105       // can only do alignments with Jmol
4106       // find the last jmol window assigned to this alignment
4107       jalview.appletgui.AppletJmol ajm = null, tajm;
4108       Vector jmols = applet
4109               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4110       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4111       {
4112         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4113         if (tajm.ap.alignFrame == this)
4114         {
4115           ajm = tajm;
4116           break;
4117         }
4118       }
4119       if (ajm != null)
4120       {
4121         System.err
4122                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4123         // try and add the pdb structure
4124         // ajm.addS
4125         ajm = null;
4126       }
4127     }
4128     // otherwise, create a new window
4129     if (applet.jmolAvailable)
4130     {
4131       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4132               protocol);
4133       applet.lastFrameX += 40;
4134       applet.lastFrameY += 40;
4135     }
4136     else
4137     {
4138       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4139     }
4140
4141   }
4142
4143   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4144           SequenceI[][] seqs, String[][] chains, String[] protocols)
4145   {
4146     // TODO Auto-generated method stub
4147     System.err.println("Aligned Structure View: Not yet implemented.");
4148   }
4149
4150   /**
4151    * modify the current selection, providing the user has not made a selection
4152    * already.
4153    *
4154    * @param sel
4155    *          - sequences from this alignment
4156    * @param csel
4157    *          - columns to be selected on the alignment
4158    */
4159   public void select(SequenceGroup sel, ColumnSelection csel)
4160   {
4161     alignPanel.seqPanel.selection(sel, csel, null);
4162   }
4163
4164   public void scrollTo(int row, int column)
4165   {
4166     alignPanel.seqPanel.scrollTo(row, column);
4167   }
4168
4169   public void scrollToRow(int row)
4170   {
4171     alignPanel.seqPanel.scrollToRow(row);
4172   }
4173
4174   public void scrollToColumn(int column)
4175   {
4176     alignPanel.seqPanel.scrollToColumn(column);
4177   }
4178
4179   /**
4180    * @return the alignments unique ID.
4181    */
4182   public String getSequenceSetId()
4183   {
4184     return viewport.getSequenceSetId();
4185   }
4186
4187   /**
4188    * Load the (T-Coffee) score file from the specified url
4189    *
4190    * @param source
4191    *          File/URL/T-COFFEE score file contents
4192    * @throws IOException
4193    * @return true if alignment was annotated with data from source
4194    */
4195   public boolean loadScoreFile(String source) throws IOException
4196   {
4197
4198     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4199             AppletFormatAdapter.checkProtocol(source));
4200     if (!file.isValid())
4201     {
4202       // TODO: raise dialog for gui
4203       System.err.println("Problems parsing T-Coffee scores: "
4204               + file.getWarningMessage());
4205       System.err.println("Origin was:\n" + source);
4206       return false;
4207     }
4208
4209     /*
4210      * check that the score matrix matches the alignment dimensions
4211      */
4212     AlignmentI aln;
4213     if ((aln = viewport.getAlignment()) != null
4214             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4215                     .getWidth()))
4216     {
4217       // TODO: raise a dialog box here rather than bomb out.
4218       System.err
4219               .println("The scores matrix does not match the alignment dimensions");
4220
4221     }
4222
4223     // TODO add parameter to indicate if matching should be done
4224     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4225     {
4226       alignPanel.fontChanged();
4227       tcoffeeColour.setEnabled(true);
4228       // switch to this color
4229       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4230       return true;
4231     }
4232     else
4233     {
4234       System.err.println("Problems resolving T-Coffee scores:");
4235       if (file.getWarningMessage() != null)
4236       {
4237         System.err.println(file.getWarningMessage());
4238       }
4239     }
4240     return false;
4241   }
4242
4243   public SplitFrame getSplitFrame()
4244   {
4245     return this.splitFrame;
4246   }
4247
4248   public void setSplitFrame(SplitFrame sf)
4249   {
4250     this.splitFrame = sf;
4251   }
4252
4253   // may not need this
4254   @Override
4255   public void setShowSeqFeatures(boolean b)
4256   {
4257     // showSeqFeatures.setSelected(b);
4258     viewport.setShowSequenceFeatures(b);
4259
4260   }
4261
4262   @Override
4263   public void setMenusForViewport()
4264   {
4265     // setMenusFromViewport(viewport);
4266
4267   }
4268
4269   @Override
4270   public void refreshFeatureUI(boolean enableIfNecessary)
4271   {
4272     if (enableIfNecessary)
4273     {
4274       sequenceFeatures.setState(true);
4275       alignPanel.av.setShowSequenceFeatures(true);
4276     }
4277   }
4278
4279   @Override
4280   public FeatureSettingsControllerI getFeatureSettingsUI()
4281   {
4282     return alignPanel.av.featureSettings;
4283   }
4284
4285 }