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.List;
 106 import java.util.Map;
 107 import java.util.StringTokenizer;
 108 import java.util.Vector;
 109
 110 import org.jmol.viewer.Viewer;
 111
 112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 113         ItemListener, KeyListener, AlignViewControllerGuiI
 114 {
 115   public AlignViewControllerI avc;
 116
 117   public AlignmentPanel alignPanel;
 118
 119   public AlignViewport viewport;
 120
 121   // width and height may be overridden by applet parameters
 122   int frameWidth = 700;
 123
 124   int frameHeight = 500;
 125
 126   String jalviewServletURL;
 127
 128   /*
 129    * Flag for showing autocalculated consensus above or below other consensus
 130    * rows
 131    */
 132   private boolean showAutoCalculatedAbove;
 133
 134   private SequenceAnnotationOrder annotationSortOrder;
 135
 136   /**
 137    * Constructor that creates the frame and adds it to the display.
 138    *
 139    * @param al
 140    * @param applet
 141    * @param title
 142    * @param embedded
 143    */
 144   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 145           boolean embedded)
 146   {
 147     this(al, applet, title, embedded, true);
 148   }
 149
 150   /**
 151    * Constructor that optionally allows the frame to be displayed or only
 152    * created.
 153    *
 154    * @param al
 155    * @param applet
 156    * @param title
 157    * @param embedded
 158    * @param addToDisplay
 159    */
 160   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 161           boolean embedded, boolean addToDisplay)
 162   {
 163     this(al, null, null, applet, title, embedded, addToDisplay);
 164   }
 165
 166   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 167           ColumnSelection columnSelection, JalviewLite applet,
 168           String title, boolean embedded)
 169   {
 170     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 171   }
 172
 173   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 174           ColumnSelection columnSelection, JalviewLite applet,
 175           String title, boolean embedded, boolean addToDisplay)
 176   {
 177     if (applet != null)
 178     {
 179       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 180     }
 181
 182     try
 183     {
 184       jbInit();
 185     } catch (Exception ex)
 186     {
 187       ex.printStackTrace();
 188     }
 189     // need to get window geometry before we calculate alignment layout
 190     if (applet != null)
 191     {
 192       String param;
 193       try
 194       {
 195         param = applet.getParameter("windowWidth");
 196         if (param != null)
 197         {
 198           int width = Integer.parseInt(param);
 199           frameWidth = width;
 200         }
 201         param = applet.getParameter("windowHeight");
 202         if (param != null)
 203         {
 204           int height = Integer.parseInt(param);
 205           frameHeight = height;
 206         }
 207       } catch (Exception ex)
 208       {
 209       }
 210     }
 211     viewport = new AlignViewport(al, applet);
 212
 213     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 214     {
 215       viewport.hideSequence(hiddenSeqs);
 216     }
 217     if (columnSelection != null)
 218     {
 219       viewport.setColumnSelection(columnSelection);
 220     }
 221     viewport.setScaleAboveWrapped(scaleAbove.getState());
 222
 223     alignPanel = new AlignmentPanel(this, viewport);
 224     avc = new jalview.controller.AlignViewController(this, viewport,
 225             alignPanel);
 226     viewport.updateConservation(alignPanel);
 227     viewport.updateConsensus(alignPanel);
 228
 229     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 230     followMouseOverFlag.setState(viewport.isFollowHighlight());
 231     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 232     showGroupConservation.setState(viewport.isShowGroupConservation());
 233     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 234     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 235     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 236     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 237     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 238     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 239     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 240     showAlignmentAnnotations.setState(true);
 241     showSequenceAnnotations.setState(false);
 242
 243     seqLimits.setState(viewport.getShowJVSuffix());
 244
 245     if (applet != null)
 246     {
 247       String param = applet.getParameter("sortBy");
 248       if (param != null)
 249       {
 250         if (param.equalsIgnoreCase("Id"))
 251         {
 252           sortIDMenuItem_actionPerformed();
 253         }
 254         else if (param.equalsIgnoreCase("Pairwise Identity"))
 255         {
 256           sortPairwiseMenuItem_actionPerformed();
 257         }
 258         else if (param.equalsIgnoreCase("Length"))
 259         {
 260           sortLengthMenuItem_actionPerformed();
 261         }
 262       }
 263
 264       param = applet.getParameter("wrap");
 265       if (param != null)
 266       {
 267         if (param.equalsIgnoreCase("true"))
 268         {
 269           wrapMenuItem.setState(true);
 270           wrapMenuItem_actionPerformed();
 271         }
 272       }
 273       param = applet.getParameter("centrecolumnlabels");
 274       if (param != null)
 275       {
 276         centreColumnLabelFlag.setState(true);
 277         centreColumnLabelFlag_stateChanged();
 278       }
 279
 280     }
 281     if (viewport.getAlignment().isNucleotide())
 282     {
 283       viewport.updateStrucConsensus(alignPanel);
 284       if (viewport.getAlignment().hasRNAStructure())
 285       {
 286         RNAHelixColour.setEnabled(true);
 287       }
 288       else
 289       {
 290         RNAHelixColour.setEnabled(false);
 291       }
 292     }
 293     else
 294     {
 295       RNAHelixColour.setEnabled(false);
 296       purinePyrimidineColour.setEnabled(false);
 297     }
 298     // Some JVMS send keyevents to Top frame or lowest panel,
 299     // Havent worked out why yet. So add to both this frame and seqCanvas for
 300     // now
 301     this.addKeyListener(this);
 302     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 303     alignPanel.idPanel.idCanvas.addKeyListener(this);
 304     alignPanel.scalePanel.addKeyListener(this);
 305     alignPanel.annotationPanel.addKeyListener(this);
 306     alignPanel.annotationPanelHolder.addKeyListener(this);
 307     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 308     alignPanel.alabels.addKeyListener(this);
 309
 310     setAnnotationsVisibility();
 311
 312     if (addToDisplay)
 313     {
 314       addToDisplay(embedded);
 315     }
 316   }
 317
 318   /**
 319    * @param embedded
 320    */
 321   public void addToDisplay(boolean embedded)
 322   {
 323     createAlignFrameWindow(embedded);
 324     validate();
 325     alignPanel.adjustAnnotationHeight();
 326     alignPanel.paintAlignment(true);
 327   }
 328
 329   public AlignViewport getAlignViewport()
 330   {
 331     return viewport;
 332   }
 333
 334   public SeqCanvas getSeqcanvas()
 335   {
 336     return alignPanel.seqPanel.seqCanvas;
 337   }
 338
 339   /**
 340    * Load a features file onto the alignment
 341    *
 342    * @param file
 343    *          file URL, content, or other resolvable path
 344    * @param type
 345    *          is protocol for accessing data referred to by file
 346    */
 347
 348   public boolean parseFeaturesFile(String file, String type)
 349   {
 350     return parseFeaturesFile(file, type, true);
 351   }
 352
 353   /**
 354    * Load a features file onto the alignment
 355    *
 356    * @param file
 357    *          file URL, content, or other resolvable path
 358    * @param type
 359    *          is protocol for accessing data referred to by file
 360    * @param autoenabledisplay
 361    *          when true, display features flag will be automatically enabled if
 362    *          features are loaded
 363    * @return true if data parsed as a features file
 364    */
 365   public boolean parseFeaturesFile(String file, String type,
 366           boolean autoenabledisplay)
 367   {
 368     boolean featuresFile = false;
 369     try
 370     {
 371       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 372               .getFeatureRenderer().getFeatureColours();
 373       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 374               "relaxedidmatch", false);
 375       featuresFile = new FeaturesFile(file, type).parse(
 376               viewport.getAlignment(), colours, true, relaxedIdMatching);
 377     } catch (Exception ex)
 378     {
 379       ex.printStackTrace();
 380     }
 381
 382     if (featuresFile)
 383     {
 384       if (autoenabledisplay)
 385       {
 386         viewport.setShowSequenceFeatures(true);
 387         sequenceFeatures.setState(true);
 388       }
 389       if (alignPanel.seqPanel.seqCanvas.fr != null)
 390       {
 391         // update the min/max ranges where necessary
 392         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 393       }
 394       if (viewport.featureSettings != null)
 395       {
 396         viewport.featureSettings.refreshTable();
 397       }
 398       alignPanel.paintAlignment(true);
 399       statusBar.setText(MessageManager
 400               .getString("label.successfully_added_features_alignment"));
 401     }
 402     return featuresFile;
 403   }
 404
 405   @Override
 406   public void keyPressed(KeyEvent evt)
 407   {
 408     if (viewport.cursorMode
 409             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 410                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 411                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 412             && Character.isDigit(evt.getKeyChar()))
 413     {
 414       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 415     }
 416
 417     switch (evt.getKeyCode())
 418     {
 419     case 27: // escape key
 420       deselectAllSequenceMenuItem_actionPerformed();
 421
 422       alignPanel.alabels.cancelDrag();
 423       break;
 424     case KeyEvent.VK_X:
 425       if (evt.isControlDown() || evt.isMetaDown())
 426       {
 427         cut_actionPerformed();
 428       }
 429       break;
 430     case KeyEvent.VK_C:
 431       if (viewport.cursorMode && !evt.isControlDown())
 432       {
 433         alignPanel.seqPanel.setCursorColumn();
 434       }
 435       if (evt.isControlDown() || evt.isMetaDown())
 436       {
 437         copy_actionPerformed();
 438       }
 439       break;
 440     case KeyEvent.VK_V:
 441       if (evt.isControlDown())
 442       {
 443         paste(evt.isShiftDown());
 444       }
 445       break;
 446     case KeyEvent.VK_A:
 447       if (evt.isControlDown() || evt.isMetaDown())
 448       {
 449         selectAllSequenceMenuItem_actionPerformed();
 450       }
 451       break;
 452     case KeyEvent.VK_DOWN:
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.moveCursor(0, 1);
 456       }
 457       else
 458       {
 459         moveSelectedSequences(false);
 460       }
 461       break;
 462
 463     case KeyEvent.VK_UP:
 464       if (viewport.cursorMode)
 465       {
 466         alignPanel.seqPanel.moveCursor(0, -1);
 467       }
 468       else
 469       {
 470         moveSelectedSequences(true);
 471       }
 472       break;
 473
 474     case KeyEvent.VK_LEFT:
 475       if (evt.isAltDown() || !viewport.cursorMode)
 476       {
 477         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 478       }
 479       else
 480       {
 481         alignPanel.seqPanel.moveCursor(-1, 0);
 482       }
 483       break;
 484
 485     case KeyEvent.VK_RIGHT:
 486       if (evt.isAltDown() || !viewport.cursorMode)
 487       {
 488         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 489       }
 490       else
 491       {
 492         alignPanel.seqPanel.moveCursor(1, 0);
 493       }
 494       break;
 495
 496     case KeyEvent.VK_SPACE:
 497       if (viewport.cursorMode)
 498       {
 499         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 500                 || evt.isShiftDown() || evt.isAltDown());
 501       }
 502       break;
 503
 504     case KeyEvent.VK_DELETE:
 505     case KeyEvent.VK_BACK_SPACE:
 506       if (viewport.cursorMode)
 507       {
 508         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 509                 || evt.isShiftDown() || evt.isAltDown());
 510       }
 511       else
 512       {
 513         cut_actionPerformed();
 514         alignPanel.seqPanel.seqCanvas.repaint();
 515       }
 516       break;
 517
 518     case KeyEvent.VK_S:
 519       if (viewport.cursorMode)
 520       {
 521         alignPanel.seqPanel.setCursorRow();
 522       }
 523       break;
 524     case KeyEvent.VK_P:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorPosition();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_ENTER:
 532     case KeyEvent.VK_COMMA:
 533       if (viewport.cursorMode)
 534       {
 535         alignPanel.seqPanel.setCursorRowAndColumn();
 536       }
 537       break;
 538
 539     case KeyEvent.VK_Q:
 540       if (viewport.cursorMode)
 541       {
 542         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 543       }
 544       break;
 545     case KeyEvent.VK_M:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_F2:
 553       viewport.cursorMode = !viewport.cursorMode;
 554       statusBar.setText(MessageManager.formatMessage(
 555               "label.keyboard_editing_mode",
 556               new String[] { (viewport.cursorMode ? "on" : "off") }));
 557       if (viewport.cursorMode)
 558       {
 559         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 560         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 561       }
 562       break;
 563
 564     case KeyEvent.VK_F:
 565       if (evt.isControlDown())
 566       {
 567         findMenuItem_actionPerformed();
 568       }
 569       break;
 570
 571     case KeyEvent.VK_H:
 572     {
 573       boolean toggleSeqs = !evt.isControlDown();
 574       boolean toggleCols = !evt.isShiftDown();
 575       toggleHiddenRegions(toggleSeqs, toggleCols);
 576       break;
 577     }
 578
 579     case KeyEvent.VK_PAGE_UP:
 580       if (viewport.getWrapAlignment())
 581       {
 582         alignPanel.scrollUp(true);
 583       }
 584       else
 585       {
 586         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 587                 - viewport.endSeq + viewport.startSeq);
 588       }
 589       break;
 590
 591     case KeyEvent.VK_PAGE_DOWN:
 592       if (viewport.getWrapAlignment())
 593       {
 594         alignPanel.scrollUp(false);
 595       }
 596       else
 597       {
 598         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 599                 + viewport.endSeq - viewport.startSeq);
 600       }
 601       break;
 602
 603     case KeyEvent.VK_Z:
 604       if (evt.isControlDown())
 605       {
 606         undoMenuItem_actionPerformed();
 607       }
 608       break;
 609
 610     case KeyEvent.VK_Y:
 611       if (evt.isControlDown())
 612       {
 613         redoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_L:
 618       if (evt.isControlDown())
 619       {
 620         trimAlignment(true);
 621       }
 622       break;
 623
 624     case KeyEvent.VK_R:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(false);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_E:
 632       if (evt.isControlDown())
 633       {
 634         if (evt.isShiftDown())
 635         {
 636           this.removeAllGapsMenuItem_actionPerformed();
 637         }
 638         else
 639         {
 640           removeGappedColumnMenuItem_actionPerformed();
 641         }
 642       }
 643       break;
 644     case KeyEvent.VK_I:
 645       if (evt.isControlDown())
 646       {
 647         if (evt.isAltDown())
 648         {
 649           invertColSel_actionPerformed();
 650         }
 651         else
 652         {
 653           invertSequenceMenuItem_actionPerformed();
 654         }
 655       }
 656       break;
 657
 658     case KeyEvent.VK_G:
 659       if (evt.isControlDown())
 660       {
 661         if (evt.isShiftDown())
 662         {
 663           this.unGroup_actionPerformed();
 664         }
 665         else
 666         {
 667           this.createGroup_actionPerformed();
 668         }
 669       }
 670       break;
 671
 672     case KeyEvent.VK_U:
 673       if (evt.isControlDown())
 674       {
 675         this.deleteGroups_actionPerformed();
 676       }
 677       break;
 678
 679     case KeyEvent.VK_T:
 680       if (evt.isControlDown())
 681       {
 682         newView(null);
 683       }
 684       break;
 685
 686     }
 687     alignPanel.paintAlignment(true);
 688   }
 689
 690   /**
 691    * called by key handler and the hide all/show all menu items
 692    *
 693    * @param toggleSeqs
 694    * @param toggleCols
 695    */
 696   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 697   {
 698     boolean hide = false;
 699     SequenceGroup sg = viewport.getSelectionGroup();
 700     if (!toggleSeqs && !toggleCols)
 701     {
 702       // Hide everything by the current selection - this is a hack - we do the
 703       // invert and then hide
 704       // first check that there will be visible columns after the invert.
 705       if ((viewport.getColumnSelection() != null
 706               && viewport.getColumnSelection().getSelected() != null && viewport
 707               .getColumnSelection().getSelected().size() > 0)
 708               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 709                       .getEndRes()))
 710       {
 711         // now invert the sequence set, if required - empty selection implies
 712         // that no hiding is required.
 713         if (sg != null)
 714         {
 715           invertSequenceMenuItem_actionPerformed();
 716           sg = viewport.getSelectionGroup();
 717           toggleSeqs = true;
 718
 719         }
 720         viewport.expandColSelection(sg, true);
 721         // finally invert the column selection and get the new sequence
 722         // selection and indicate it should be hidden.
 723         invertColSel_actionPerformed();
 724         toggleCols = true;
 725       }
 726     }
 727
 728     if (toggleSeqs)
 729     {
 730       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 731       {
 732         hide = true;
 733         viewport.hideAllSelectedSeqs();
 734       }
 735       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 736               .size() > 0))
 737       {
 738         viewport.showAllHiddenSeqs();
 739       }
 740     }
 741
 742     if (toggleCols)
 743     {
 744       if (viewport.getColumnSelection().getSelected().size() > 0)
 745       {
 746         viewport.hideSelectedColumns();
 747         if (!toggleSeqs)
 748         {
 749           viewport.setSelectionGroup(sg);
 750         }
 751       }
 752       else if (!hide)
 753       {
 754         viewport.showAllHiddenColumns();
 755       }
 756       viewport.sendSelection();
 757     }
 758   }
 759
 760   @Override
 761   public void keyReleased(KeyEvent evt)
 762   {
 763   }
 764
 765   @Override
 766   public void keyTyped(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void itemStateChanged(ItemEvent evt)
 772   {
 773     final Object source = evt.getSource();
 774     if (source == displayNonconservedMenuItem)
 775     {
 776       displayNonconservedMenuItem_actionPerformed();
 777     }
 778     else if (source == colourTextMenuItem)
 779     {
 780       colourTextMenuItem_actionPerformed();
 781     }
 782     else if (source == wrapMenuItem)
 783     {
 784       wrapMenuItem_actionPerformed();
 785     }
 786     else if (source == scaleAbove)
 787     {
 788       viewport.setScaleAboveWrapped(scaleAbove.getState());
 789     }
 790     else if (source == scaleLeft)
 791     {
 792       viewport.setScaleLeftWrapped(scaleLeft.getState());
 793     }
 794     else if (source == scaleRight)
 795     {
 796       viewport.setScaleRightWrapped(scaleRight.getState());
 797     }
 798     else if (source == seqLimits)
 799     {
 800       seqLimits_itemStateChanged();
 801     }
 802     else if (source == viewBoxesMenuItem)
 803     {
 804       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 805     }
 806     else if (source == viewTextMenuItem)
 807     {
 808       viewport.setShowText(viewTextMenuItem.getState());
 809     }
 810     else if (source == renderGapsMenuItem)
 811     {
 812       viewport.setRenderGaps(renderGapsMenuItem.getState());
 813     }
 814     else if (source == annotationPanelMenuItem)
 815     {
 816       boolean showAnnotations = annotationPanelMenuItem.getState();
 817       showAlignmentAnnotations.setEnabled(showAnnotations);
 818       showSequenceAnnotations.setEnabled(showAnnotations);
 819       viewport.setShowAnnotation(showAnnotations);
 820       alignPanel.setAnnotationVisible(showAnnotations);
 821     }
 822     else if (source == sequenceFeatures)
 823     {
 824       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 825       alignPanel.seqPanel.seqCanvas.repaint();
 826     }
 827     else if (source == showAlignmentAnnotations)
 828     {
 829       setAnnotationsVisibility();
 830     }
 831     else if (source == showSequenceAnnotations)
 832     {
 833       setAnnotationsVisibility();
 834     }
 835     else if (source == sortAnnBySequence)
 836     {
 837       boolean newState = sortAnnBySequence.getState();
 838       sortAnnByLabel.setState(false);
 839       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 840               : SequenceAnnotationOrder.NONE);
 841       setViewportAnnotationOrder();
 842     }
 843     else if (source == sortAnnByLabel)
 844     {
 845       boolean newState = sortAnnByLabel.getState();
 846       sortAnnBySequence.setState(false);
 847       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 848               : SequenceAnnotationOrder.NONE);
 849       setViewportAnnotationOrder();
 850     }
 851     else if (source == showAutoFirst)
 852     {
 853       showAutoLast.setState(!showAutoFirst.getState());
 854       setShowAutoCalculatedAbove(showAutoFirst.getState());
 855       setViewportAnnotationOrder();
 856     }
 857     else if (source == showAutoLast)
 858     {
 859       showAutoFirst.setState(!showAutoLast.getState());
 860       setShowAutoCalculatedAbove(showAutoFirst.getState());
 861       setViewportAnnotationOrder();
 862     }
 863     else if (source == conservationMenuItem)
 864     {
 865       conservationMenuItem_actionPerformed();
 866     }
 867     else if (source == abovePIDThreshold)
 868     {
 869       abovePIDThreshold_actionPerformed();
 870     }
 871     else if (source == applyToAllGroups)
 872     {
 873       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 874     }
 875     else if (source == autoCalculate)
 876     {
 877       viewport.autoCalculateConsensus = autoCalculate.getState();
 878     }
 879     else if (source == sortByTree)
 880     {
 881       viewport.sortByTree = sortByTree.getState();
 882     }
 883     else if (source == this.centreColumnLabelFlag)
 884     {
 885       centreColumnLabelFlag_stateChanged();
 886     }
 887     else if (source == this.followMouseOverFlag)
 888     {
 889       mouseOverFlag_stateChanged();
 890     }
 891     else if (source == showGroupConsensus)
 892     {
 893       showGroupConsensus_actionPerformed();
 894     }
 895     else if (source == showGroupConservation)
 896     {
 897       showGroupConservation_actionPerformed();
 898     }
 899     else if (source == showSequenceLogo)
 900     {
 901       showSequenceLogo_actionPerformed();
 902     }
 903     else if (source == normSequenceLogo)
 904     {
 905       normSequenceLogo_actionPerformed();
 906     }
 907     else if (source == showConsensusHistogram)
 908     {
 909       showConsensusHistogram_actionPerformed();
 910     }
 911     else if (source == applyAutoAnnotationSettings)
 912     {
 913       applyAutoAnnotationSettings_actionPerformed();
 914     }
 915     alignPanel.paintAlignment(true);
 916   }
 917
 918   /**
 919    * Set the visibility state of sequence-related and/or alignment-related
 920    * annotations depending on checkbox selections, and repaint.
 921    *
 922    * @param visible
 923    */
 924   private void setAnnotationsVisibility()
 925   {
 926     boolean showForAlignment = showAlignmentAnnotations.getState();
 927     boolean showForSequences = showSequenceAnnotations.getState();
 928     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 929     {
 930       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 931             .getAlignmentAnnotation())
 932     {
 933       boolean visible = (aa.sequenceRef == null ? showForAlignment
 934               : showForSequences);
 935       aa.visible = visible;
 936       }
 937     }
 938     alignPanel.validateAnnotationDimensions(true);
 939     validate();
 940     repaint();
 941   }
 942
 943   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 944   {
 945     this.annotationSortOrder = order;
 946   }
 947
 948   /**
 949    * Set flags on the viewport that control annotation ordering
 950    */
 951   private void setViewportAnnotationOrder()
 952   {
 953     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 954     this.alignPanel.av
 955             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 956   }
 957
 958   private void setShowAutoCalculatedAbove(boolean showAbove)
 959   {
 960     this.showAutoCalculatedAbove = showAbove;
 961   }
 962
 963   private void mouseOverFlag_stateChanged()
 964   {
 965     viewport.setFollowHighlight(followMouseOverFlag.getState());
 966     // TODO: could kick the scrollTo mechanism to reset view for current
 967     // searchresults.
 968   }
 969
 970   private void centreColumnLabelFlag_stateChanged()
 971   {
 972     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 973     this.alignPanel.annotationPanel.repaint();
 974   }
 975
 976   @Override
 977   public void actionPerformed(ActionEvent evt)
 978   {
 979     viewport.applet.currentAlignFrame = this;
 980
 981     Object source = evt.getSource();
 982
 983     if (source == inputText)
 984     {
 985       inputText_actionPerformed();
 986     }
 987     else if (source == loadTree)
 988     {
 989       loadTree_actionPerformed();
 990     }
 991     else if (source == loadApplication)
 992     {
 993       launchFullApplication();
 994     }
 995     else if (source == loadAnnotations)
 996     {
 997       loadAnnotations();
 998     }
 999     else if (source == outputAnnotations)
1000     {
1001       outputAnnotations(true);
1002     }
1003     else if (source == outputFeatures)
1004     {
1005       outputFeatures(true, "Jalview");
1006     }
1007     else if (source == closeMenuItem)
1008     {
1009       closeMenuItem_actionPerformed();
1010     }
1011     else if (source == copy)
1012     {
1013       copy_actionPerformed();
1014     }
1015     else if (source == undoMenuItem)
1016     {
1017       undoMenuItem_actionPerformed();
1018     }
1019     else if (source == redoMenuItem)
1020     {
1021       redoMenuItem_actionPerformed();
1022     }
1023     else if (source == inputText)
1024     {
1025       inputText_actionPerformed();
1026     }
1027     else if (source == closeMenuItem)
1028     {
1029       closeMenuItem_actionPerformed();
1030     }
1031     else if (source == undoMenuItem)
1032     {
1033       undoMenuItem_actionPerformed();
1034     }
1035     else if (source == redoMenuItem)
1036     {
1037       redoMenuItem_actionPerformed();
1038     }
1039     else if (source == copy)
1040     {
1041       copy_actionPerformed();
1042     }
1043     else if (source == pasteNew)
1044     {
1045       pasteNew_actionPerformed();
1046     }
1047     else if (source == pasteThis)
1048     {
1049       pasteThis_actionPerformed();
1050     }
1051     else if (source == cut)
1052     {
1053       cut_actionPerformed();
1054     }
1055     else if (source == delete)
1056     {
1057       delete_actionPerformed();
1058     }
1059     else if (source == grpsFromSelection)
1060     {
1061       makeGrpsFromSelection_actionPerformed();
1062     }
1063     else if (source == deleteGroups)
1064     {
1065       deleteGroups_actionPerformed();
1066     }
1067     else if (source == selectAllSequenceMenuItem)
1068     {
1069       selectAllSequenceMenuItem_actionPerformed();
1070     }
1071     else if (source == deselectAllSequenceMenuItem)
1072     {
1073       deselectAllSequenceMenuItem_actionPerformed();
1074     }
1075     else if (source == invertSequenceMenuItem)
1076     {
1077       invertSequenceMenuItem_actionPerformed();
1078       // uncomment to slave sequence selections in split frame
1079       // viewport.sendSelection();
1080     }
1081     else if (source == invertColSel)
1082     {
1083       viewport.invertColumnSelection();
1084       alignPanel.paintAlignment(true);
1085       viewport.sendSelection();
1086     }
1087     else if (source == remove2LeftMenuItem)
1088     {
1089       trimAlignment(true);
1090     }
1091     else if (source == remove2RightMenuItem)
1092     {
1093       trimAlignment(false);
1094     }
1095     else if (source == removeGappedColumnMenuItem)
1096     {
1097       removeGappedColumnMenuItem_actionPerformed();
1098     }
1099     else if (source == removeAllGapsMenuItem)
1100     {
1101       removeAllGapsMenuItem_actionPerformed();
1102     }
1103     else if (source == findMenuItem)
1104     {
1105       findMenuItem_actionPerformed();
1106     }
1107     else if (source == font)
1108     {
1109       new FontChooser(alignPanel);
1110     }
1111     else if (source == newView)
1112     {
1113       newView(null);
1114     }
1115     else if (source == showColumns)
1116     {
1117       viewport.showAllHiddenColumns();
1118       alignPanel.paintAlignment(true);
1119       viewport.sendSelection();
1120     }
1121     else if (source == showSeqs)
1122     {
1123       viewport.showAllHiddenSeqs();
1124       alignPanel.paintAlignment(true);
1125       // uncomment if we want to slave sequence selections in split frame
1126       // viewport.sendSelection();
1127     }
1128     else if (source == hideColumns)
1129     {
1130       viewport.hideSelectedColumns();
1131       alignPanel.paintAlignment(true);
1132       viewport.sendSelection();
1133     }
1134     else if (source == hideSequences
1135             && viewport.getSelectionGroup() != null)
1136     {
1137       viewport.hideAllSelectedSeqs();
1138       alignPanel.paintAlignment(true);
1139       // uncomment if we want to slave sequence selections in split frame
1140       // viewport.sendSelection();
1141     }
1142     else if (source == hideAllButSelection)
1143     {
1144       toggleHiddenRegions(false, false);
1145       alignPanel.paintAlignment(true);
1146       viewport.sendSelection();
1147     }
1148     else if (source == hideAllSelection)
1149     {
1150       SequenceGroup sg = viewport.getSelectionGroup();
1151       viewport.expandColSelection(sg, false);
1152       viewport.hideAllSelectedSeqs();
1153       viewport.hideSelectedColumns();
1154       alignPanel.paintAlignment(true);
1155       viewport.sendSelection();
1156     }
1157     else if (source == showAllHidden)
1158     {
1159       viewport.showAllHiddenColumns();
1160       viewport.showAllHiddenSeqs();
1161       alignPanel.paintAlignment(true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == showGroupConsensus)
1165     {
1166       showGroupConsensus_actionPerformed();
1167     }
1168     else if (source == showGroupConservation)
1169     {
1170       showGroupConservation_actionPerformed();
1171     }
1172     else if (source == showSequenceLogo)
1173     {
1174       showSequenceLogo_actionPerformed();
1175     }
1176     else if (source == normSequenceLogo)
1177     {
1178       normSequenceLogo_actionPerformed();
1179     }
1180     else if (source == showConsensusHistogram)
1181     {
1182       showConsensusHistogram_actionPerformed();
1183     }
1184     else if (source == applyAutoAnnotationSettings)
1185     {
1186       applyAutoAnnotationSettings_actionPerformed();
1187     }
1188     else if (source == featureSettings)
1189     {
1190       new FeatureSettings(alignPanel);
1191     }
1192     else if (source == alProperties)
1193     {
1194       StringBuffer contents = new jalview.io.AlignmentProperties(
1195               viewport.getAlignment()).formatAsString();
1196       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1197       cap.setText(contents.toString());
1198       Frame frame = new Frame();
1199       frame.add(cap);
1200       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1201               "label.alignment_properties", new String[] { getTitle() }),
1202               400, 250);
1203     }
1204     else if (source == overviewMenuItem)
1205     {
1206       overviewMenuItem_actionPerformed();
1207     }
1208     else if (source == noColourmenuItem)
1209     {
1210       changeColour(null);
1211     }
1212     else if (source == clustalColour)
1213     {
1214       abovePIDThreshold.setState(false);
1215       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1216     }
1217     else if (source == zappoColour)
1218     {
1219       changeColour(new ZappoColourScheme());
1220     }
1221     else if (source == taylorColour)
1222     {
1223       changeColour(new TaylorColourScheme());
1224     }
1225     else if (source == hydrophobicityColour)
1226     {
1227       changeColour(new HydrophobicColourScheme());
1228     }
1229     else if (source == helixColour)
1230     {
1231       changeColour(new HelixColourScheme());
1232     }
1233     else if (source == strandColour)
1234     {
1235       changeColour(new StrandColourScheme());
1236     }
1237     else if (source == turnColour)
1238     {
1239       changeColour(new TurnColourScheme());
1240     }
1241     else if (source == buriedColour)
1242     {
1243       changeColour(new BuriedColourScheme());
1244     }
1245     else if (source == nucleotideColour)
1246     {
1247       changeColour(new NucleotideColourScheme());
1248     }
1249     else if (source == purinePyrimidineColour)
1250     {
1251       changeColour(new PurinePyrimidineColourScheme());
1252     }
1253     // else if (source == RNAInteractionColour)
1254     // {
1255     // changeColour(new RNAInteractionColourScheme());
1256     // }
1257     else if (source == RNAHelixColour)
1258     {
1259       new RNAHelicesColourChooser(viewport, alignPanel);
1260     }
1261     else if (source == modifyPID)
1262     {
1263       modifyPID_actionPerformed();
1264     }
1265     else if (source == modifyConservation)
1266     {
1267       modifyConservation_actionPerformed();
1268     }
1269     else if (source == userDefinedColour)
1270     {
1271       new UserDefinedColours(alignPanel, null);
1272     }
1273     else if (source == PIDColour)
1274     {
1275       changeColour(new PIDColourScheme());
1276     }
1277     else if (source == BLOSUM62Colour)
1278     {
1279       changeColour(new Blosum62ColourScheme());
1280     }
1281     else if (source == tcoffeeColour)
1282     {
1283       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1284     }
1285     else if (source == annotationColour)
1286     {
1287       new AnnotationColourChooser(viewport, alignPanel);
1288     }
1289     else if (source == annotationColumnSelection)
1290     {
1291       new AnnotationColumnChooser(viewport, alignPanel);
1292     }
1293     else if (source == sortPairwiseMenuItem)
1294     {
1295       sortPairwiseMenuItem_actionPerformed();
1296     }
1297     else if (source == sortIDMenuItem)
1298     {
1299       sortIDMenuItem_actionPerformed();
1300     }
1301     else if (source == sortLengthMenuItem)
1302     {
1303       sortLengthMenuItem_actionPerformed();
1304     }
1305     else if (source == sortGroupMenuItem)
1306     {
1307       sortGroupMenuItem_actionPerformed();
1308     }
1309     else if (source == removeRedundancyMenuItem)
1310     {
1311       removeRedundancyMenuItem_actionPerformed();
1312     }
1313     else if (source == pairwiseAlignmentMenuItem)
1314     {
1315       pairwiseAlignmentMenuItem_actionPerformed();
1316     }
1317     else if (source == PCAMenuItem)
1318     {
1319       PCAMenuItem_actionPerformed();
1320     }
1321     else if (source == averageDistanceTreeMenuItem)
1322     {
1323       averageDistanceTreeMenuItem_actionPerformed();
1324     }
1325     else if (source == neighbourTreeMenuItem)
1326     {
1327       neighbourTreeMenuItem_actionPerformed();
1328     }
1329     else if (source == njTreeBlosumMenuItem)
1330     {
1331       njTreeBlosumMenuItem_actionPerformed();
1332     }
1333     else if (source == avDistanceTreeBlosumMenuItem)
1334     {
1335       avTreeBlosumMenuItem_actionPerformed();
1336     }
1337     else if (source == documentation)
1338     {
1339       documentation_actionPerformed();
1340     }
1341     else if (source == about)
1342     {
1343       about_actionPerformed();
1344     }
1345
1346   }
1347
1348   public void inputText_actionPerformed()
1349   {
1350     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1351     Frame frame = new Frame();
1352     frame.add(cap);
1353     jalview.bin.JalviewLite.addFrame(frame,
1354             MessageManager.getString("label.input_cut_paste"), 500, 500);
1355   }
1356
1357   protected void outputText_actionPerformed(ActionEvent e)
1358   {
1359     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1360     Frame frame = new Frame();
1361     frame.add(cap);
1362     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1363             "label.alignment_output_command",
1364             new Object[] { e.getActionCommand() }), 600, 500);
1365
1366     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1367     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1368             e.getActionCommand(), viewport.getAlignment(),
1369             viewport.getShowJVSuffix()));
1370   }
1371
1372   public void loadAnnotations()
1373   {
1374     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1375     cap.setText(MessageManager
1376             .getString("label.paste_features_annotations_Tcoffee_here"));
1377     cap.setAnnotationImport();
1378     Frame frame = new Frame();
1379     frame.add(cap);
1380     jalview.bin.JalviewLite.addFrame(frame,
1381             MessageManager.getString("action.paste_annotations"), 400, 300);
1382
1383   }
1384
1385   public String outputAnnotations(boolean displayTextbox)
1386   {
1387     String annotation = new AnnotationFile()
1388             .printAnnotationsForView(viewport);
1389
1390     if (displayTextbox)
1391     {
1392       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1393       Frame frame = new Frame();
1394       frame.add(cap);
1395       jalview.bin.JalviewLite.addFrame(frame,
1396               MessageManager.getString("label.annotations"), 600, 500);
1397       cap.setText(annotation);
1398     }
1399
1400     return annotation;
1401   }
1402
1403   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1404   {
1405     if (alignPanel.getFeatureRenderer() != null
1406             && viewport.getFeaturesDisplayed() != null)
1407     {
1408       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1409
1410     }
1411     return null;
1412   }
1413
1414   public String outputFeatures(boolean displayTextbox, String format)
1415   {
1416     String features;
1417     FeaturesFile formatter = new FeaturesFile();
1418     if (format.equalsIgnoreCase("Jalview"))
1419     {
1420       features = formatter.printJalviewFormat(viewport
1421               .getAlignment().getSequencesArray(),
1422               getDisplayedFeatureCols());
1423     }
1424     else
1425     {
1426       features = formatter.printGffFormat(viewport.getAlignment()
1427               .getSequencesArray(), getDisplayedFeatureCols());
1428     }
1429
1430     if (displayTextbox)
1431     {
1432       boolean frimport = false;
1433       if (features == null || features.equals("No Features Visible"))
1434       {
1435         features = "# No features visible - paste some and import them here.";
1436         frimport = true;
1437       }
1438
1439       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1440       if (frimport)
1441       {
1442         cap.setAnnotationImport();
1443       }
1444       Frame frame = new Frame();
1445       frame.add(cap);
1446       jalview.bin.JalviewLite.addFrame(frame,
1447               MessageManager.getString("label.features"), 600, 500);
1448       cap.setText(features);
1449     }
1450     else
1451     {
1452       if (features == null)
1453       {
1454         features = "";
1455       }
1456     }
1457
1458     return features;
1459   }
1460
1461   void launchFullApplication()
1462   {
1463     StringBuffer url = new StringBuffer(jalviewServletURL);
1464
1465     // allow servlet parameters to be passed in applet parameter
1466     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1467             : "?";
1468     url.append(firstSep);
1469
1470     url.append("open="
1471             + appendProtocol(viewport.applet.getParameter("file")));
1472
1473     if (viewport.applet.getParameter("features") != null)
1474     {
1475       url.append("&features=");
1476       url.append(appendProtocol(viewport.applet.getParameter("features")));
1477     }
1478
1479     if (viewport.applet.getParameter("annotations") != null)
1480     {
1481       url.append("&annotations=");
1482       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1483     }
1484
1485     if (viewport.applet.getParameter("jnetfile") != null)
1486     {
1487       url.append("&annotations=");
1488       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1489     }
1490
1491     if (viewport.applet.getParameter("defaultColour") != null)
1492     {
1493       url.append("&colour="
1494               + removeWhiteSpace(viewport.applet
1495                       .getParameter("defaultColour")));
1496     }
1497
1498     if (viewport.applet.getParameter("userDefinedColour") != null)
1499     {
1500       url.append("&colour="
1501               + removeWhiteSpace(viewport.applet
1502                       .getParameter("userDefinedColour")));
1503     }
1504     if (viewport.applet.getParameter("tree") != null)
1505     {
1506       url.append("&tree="
1507               + appendProtocol(viewport.applet.getParameter("tree")));
1508     }
1509     if (viewport.applet.getParameter("treeFile") != null)
1510     {
1511       url.append("&tree="
1512               + appendProtocol(viewport.applet.getParameter("treeFile")));
1513     }
1514
1515     showURL(url.toString(), "FULL_APP");
1516   }
1517
1518   String removeWhiteSpace(String colour)
1519   {
1520     StringBuffer sb = new StringBuffer();
1521     for (int i = 0; i < colour.length(); i++)
1522     {
1523       if (Character.isWhitespace(colour.charAt(i)))
1524       {
1525         sb.append("%20");
1526       }
1527       else
1528       {
1529         sb.append(colour.charAt(i));
1530       }
1531     }
1532
1533     return sb.toString();
1534   }
1535
1536   String appendProtocol(String url)
1537   {
1538     try
1539     {
1540       new URL(url);
1541       url = URLEncoder.encode(url);
1542     }
1543     /*
1544      * When we finally deprecate 1.1 compatibility, we can start to use
1545      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1546      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1547      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1548      * ex.printStackTrace(); }
1549      */
1550     catch (java.net.MalformedURLException ex)
1551     {
1552       url = viewport.applet.getCodeBase() + url;
1553     }
1554     return url;
1555   }
1556
1557   public void closeMenuItem_actionPerformed()
1558   {
1559     PaintRefresher.RemoveComponent(alignPanel);
1560     if (alignPanel.seqPanel != null
1561             && alignPanel.seqPanel.seqCanvas != null)
1562     {
1563       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1564     }
1565     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1566     {
1567       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1568     }
1569
1570     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1571     {
1572       System.exit(0);
1573     }
1574     else
1575     {
1576     }
1577     viewport = null;
1578     alignPanel = null;
1579     this.dispose();
1580   }
1581
1582   /**
1583    * TODO: JAL-1104
1584    */
1585   void updateEditMenuBar()
1586   {
1587
1588     if (viewport.getHistoryList().size() > 0)
1589     {
1590       undoMenuItem.setEnabled(true);
1591       CommandI command = viewport.getHistoryList().peek();
1592       undoMenuItem.setLabel(MessageManager.formatMessage(
1593               "label.undo_command",
1594               new Object[] { command.getDescription() }));
1595     }
1596     else
1597     {
1598       undoMenuItem.setEnabled(false);
1599       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1600     }
1601
1602     if (viewport.getRedoList().size() > 0)
1603     {
1604       redoMenuItem.setEnabled(true);
1605
1606       CommandI command = viewport.getRedoList().peek();
1607       redoMenuItem.setLabel(MessageManager.formatMessage(
1608               "label.redo_command",
1609               new Object[] { command.getDescription() }));
1610     }
1611     else
1612     {
1613       redoMenuItem.setEnabled(false);
1614       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1615     }
1616   }
1617
1618   /**
1619    * TODO: JAL-1104
1620    */
1621   @Override
1622   public void addHistoryItem(CommandI command)
1623   {
1624     if (command.getSize() > 0)
1625     {
1626       viewport.addToHistoryList(command);
1627       viewport.clearRedoList();
1628       updateEditMenuBar();
1629       viewport.updateHiddenColumns();
1630     }
1631   }
1632
1633   /**
1634    * TODO: JAL-1104 DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   protected void undoMenuItem_actionPerformed()
1640   {
1641     if (viewport.getHistoryList().isEmpty())
1642     {
1643       return;
1644     }
1645
1646     CommandI command = viewport.getHistoryList().pop();
1647     viewport.addToRedoList(command);
1648     command.undoCommand(null);
1649
1650     AlignmentViewport originalSource = getOriginatingSource(command);
1651     // JBPNote Test
1652     if (originalSource != viewport)
1653     {
1654       System.err
1655               .println("Warning: Viewport object mismatch whilst undoing");
1656     }
1657     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1658                                           // viewport.getColumnSelection().getHiddenColumns()
1659                                           // != null;
1660     updateEditMenuBar();
1661     originalSource.firePropertyChange("alignment", null, originalSource
1662             .getAlignment().getSequences());
1663   }
1664
1665   /**
1666    * TODO: JAL-1104 DOCUMENT ME!
1667    *
1668    * @param e
1669    *          DOCUMENT ME!
1670    */
1671   protected void redoMenuItem_actionPerformed()
1672   {
1673     if (viewport.getRedoList().isEmpty())
1674     {
1675       return;
1676     }
1677
1678     CommandI command = viewport.getRedoList().pop();
1679     viewport.addToHistoryList(command);
1680     command.doCommand(null);
1681
1682     AlignmentViewport originalSource = getOriginatingSource(command);
1683     // JBPNote Test
1684     if (originalSource != viewport)
1685     {
1686       System.err
1687               .println("Warning: Viewport object mismatch whilst re-doing");
1688     }
1689     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1690                                           // viewport.getColumnSelection().getHiddenColumns()
1691                                           // != null;
1692
1693     updateEditMenuBar();
1694     originalSource.firePropertyChange("alignment", null, originalSource
1695             .getAlignment().getSequences());
1696   }
1697
1698   AlignmentViewport getOriginatingSource(CommandI command)
1699   {
1700     AlignmentViewport originalSource = null;
1701     // For sequence removal and addition, we need to fire
1702     // the property change event FROM the viewport where the
1703     // original alignment was altered
1704     AlignmentI al = null;
1705     if (command instanceof EditCommand)
1706     {
1707       EditCommand editCommand = (EditCommand) command;
1708       al = editCommand.getAlignment();
1709       Vector comps = (Vector) PaintRefresher.components.get(viewport
1710               .getSequenceSetId());
1711       for (int i = 0; i < comps.size(); i++)
1712       {
1713         if (comps.elementAt(i) instanceof AlignmentPanel)
1714         {
1715           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1716           {
1717             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1718             break;
1719           }
1720         }
1721       }
1722     }
1723
1724     if (originalSource == null)
1725     {
1726       // The original view is closed, we must validate
1727       // the current view against the closed view first
1728       if (al != null)
1729       {
1730         PaintRefresher.validateSequences(al, viewport.getAlignment());
1731       }
1732
1733       originalSource = viewport;
1734     }
1735
1736     return originalSource;
1737   }
1738
1739   /**
1740    * Move the currently selected sequences up or down one position in the
1741    * alignment
1742    *
1743    * @param up
1744    */
1745   public void moveSelectedSequences(boolean up)
1746   {
1747     SequenceGroup sg = viewport.getSelectionGroup();
1748     if (sg == null)
1749     {
1750       return;
1751     }
1752     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753             up ? null : viewport.getHiddenRepSequences(), up);
1754     alignPanel.paintAlignment(true);
1755
1756     /*
1757      * Also move cDNA/protein complement sequences
1758      */
1759     AlignViewportI complement = viewport.getCodingComplement();
1760     if (complement != null)
1761     {
1762       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1763               viewport, complement);
1764       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1765               up ? null : complement.getHiddenRepSequences(), up);
1766       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1767     }
1768   }
1769
1770   synchronized void slideSequences(boolean right, int size)
1771   {
1772     List<SequenceI> sg = new Vector<SequenceI>();
1773     if (viewport.cursorMode)
1774     {
1775       sg.add(viewport.getAlignment().getSequenceAt(
1776               alignPanel.seqPanel.seqCanvas.cursorY));
1777     }
1778     else if (viewport.getSelectionGroup() != null
1779             && viewport.getSelectionGroup().getSize() != viewport
1780                     .getAlignment().getHeight())
1781     {
1782       sg = viewport.getSelectionGroup().getSequences(
1783               viewport.getHiddenRepSequences());
1784     }
1785
1786     if (sg.size() < 1)
1787     {
1788       return;
1789     }
1790
1791     Vector<SequenceI> invertGroup = new Vector();
1792
1793     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1794     {
1795       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1796       {
1797         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1798       }
1799     }
1800
1801     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1802
1803     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1804             .size()]);
1805     for (int i = 0; i < invertGroup.size(); i++)
1806     {
1807       seqs2[i] = invertGroup.elementAt(i);
1808     }
1809
1810     SlideSequencesCommand ssc;
1811     if (right)
1812     {
1813       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1814               size, viewport.getGapCharacter());
1815     }
1816     else
1817     {
1818       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1819               size, viewport.getGapCharacter());
1820     }
1821
1822     int groupAdjustment = 0;
1823     if (ssc.getGapsInsertedBegin() && right)
1824     {
1825       if (viewport.cursorMode)
1826       {
1827         alignPanel.seqPanel.moveCursor(size, 0);
1828       }
1829       else
1830       {
1831         groupAdjustment = size;
1832       }
1833     }
1834     else if (!ssc.getGapsInsertedBegin() && !right)
1835     {
1836       if (viewport.cursorMode)
1837       {
1838         alignPanel.seqPanel.moveCursor(-size, 0);
1839       }
1840       else
1841       {
1842         groupAdjustment = -size;
1843       }
1844     }
1845
1846     if (groupAdjustment != 0)
1847     {
1848       viewport.getSelectionGroup().setStartRes(
1849               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1850       viewport.getSelectionGroup().setEndRes(
1851               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1852     }
1853
1854     boolean appendHistoryItem = false;
1855     Deque<CommandI> historyList = viewport.getHistoryList();
1856     if (historyList != null && historyList.size() > 0
1857             && historyList.peek() instanceof SlideSequencesCommand)
1858     {
1859       appendHistoryItem = ssc
1860               .appendSlideCommand((SlideSequencesCommand) historyList
1861                       .peek());
1862     }
1863
1864     if (!appendHistoryItem)
1865     {
1866       addHistoryItem(ssc);
1867     }
1868
1869     repaint();
1870   }
1871
1872   static StringBuffer copiedSequences;
1873
1874   static Vector copiedHiddenColumns;
1875
1876   protected void copy_actionPerformed()
1877   {
1878     if (viewport.getSelectionGroup() == null)
1879     {
1880       return;
1881     }
1882
1883     SequenceGroup sg = viewport.getSelectionGroup();
1884     copiedSequences = new StringBuffer();
1885     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1886     for (int i = 0; i < sg.getSize(); i++)
1887     {
1888       SequenceI seq = sg.getSequenceAt(i);
1889       int index = viewport.getAlignment().findIndex(seq);
1890       orderedSeqs.put(index, seq);
1891     }
1892
1893     int index = 0, startRes, endRes;
1894     char ch;
1895
1896     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1897     {
1898       copiedHiddenColumns = new Vector();
1899       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1900       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1901       {
1902         copiedHiddenColumns.addElement(new int[] {
1903             region[0] - hiddenOffset, region[1] - hiddenOffset });
1904       }
1905     }
1906     else
1907     {
1908       copiedHiddenColumns = null;
1909     }
1910
1911     for (int i = 0; i < sg.getSize(); i++)
1912     {
1913       SequenceI seq = null;
1914
1915       while (seq == null)
1916       {
1917         if (orderedSeqs.containsKey(index))
1918         {
1919           seq = orderedSeqs.get(index);
1920           index++;
1921           break;
1922         }
1923         else
1924         {
1925           index++;
1926         }
1927       }
1928
1929       // FIND START RES
1930       // Returns residue following index if gap
1931       startRes = seq.findPosition(sg.getStartRes());
1932
1933       // FIND END RES
1934       // Need to find the residue preceeding index if gap
1935       endRes = 0;
1936
1937       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1938       {
1939         ch = seq.getCharAt(j);
1940         if (!jalview.util.Comparison.isGap((ch)))
1941         {
1942           endRes++;
1943         }
1944       }
1945
1946       if (endRes > 0)
1947       {
1948         endRes += seq.getStart() - 1;
1949       }
1950
1951       copiedSequences.append(seq.getName()
1952               + "\t"
1953               + startRes
1954               + "\t"
1955               + endRes
1956               + "\t"
1957               + seq.getSequenceAsString(sg.getStartRes(),
1958                       sg.getEndRes() + 1) + "\n");
1959     }
1960
1961   }
1962
1963   protected void pasteNew_actionPerformed()
1964   {
1965     paste(true);
1966   }
1967
1968   protected void pasteThis_actionPerformed()
1969   {
1970     paste(false);
1971   }
1972
1973   void paste(boolean newAlignment)
1974   {
1975     try
1976     {
1977
1978       if (copiedSequences == null)
1979       {
1980         return;
1981       }
1982
1983       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1984       Vector seqs = new Vector();
1985       while (st.hasMoreElements())
1986       {
1987         String name = st.nextToken();
1988         int start = Integer.parseInt(st.nextToken());
1989         int end = Integer.parseInt(st.nextToken());
1990         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1991       }
1992       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1993       for (int i = 0; i < seqs.size(); i++)
1994       {
1995         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1996       }
1997
1998       if (newAlignment)
1999       {
2000         String newtitle = MessageManager
2001                 .getString("label.copied_sequences");
2002         if (getTitle().startsWith(
2003                 MessageManager.getString("label.copied_sequences")))
2004         {
2005           newtitle = getTitle();
2006         }
2007         else
2008         {
2009           newtitle = newtitle.concat(MessageManager.formatMessage(
2010                   "label.from_msname", new String[] { getTitle() }));
2011         }
2012         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2013                 viewport.applet, newtitle, false);
2014         if (copiedHiddenColumns != null)
2015         {
2016           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2017           {
2018             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2019             af.viewport.hideColumns(region[0], region[1]);
2020           }
2021         }
2022
2023         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2024                 frameHeight);
2025       }
2026       else
2027       {
2028         addSequences(newSeqs);
2029       }
2030
2031     } catch (Exception ex)
2032     {
2033     } // could be anything being pasted in here
2034
2035   }
2036
2037   void addSequences(SequenceI[] seqs)
2038   {
2039     for (int i = 0; i < seqs.length; i++)
2040     {
2041       viewport.getAlignment().addSequence(seqs[i]);
2042     }
2043
2044     // !newAlignment
2045     addHistoryItem(new EditCommand(
2046             MessageManager.getString("label.add_sequences"), Action.PASTE,
2047             seqs, 0, viewport.getAlignment().getWidth(),
2048             viewport.getAlignment()));
2049
2050     viewport.setEndSeq(viewport.getAlignment().getHeight());
2051     viewport.getAlignment().getWidth();
2052     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2053             .getSequences());
2054
2055   }
2056
2057   protected void cut_actionPerformed()
2058   {
2059     copy_actionPerformed();
2060     delete_actionPerformed();
2061   }
2062
2063   protected void delete_actionPerformed()
2064   {
2065
2066     SequenceGroup sg = viewport.getSelectionGroup();
2067     if (sg == null)
2068     {
2069       return;
2070     }
2071
2072     Vector seqs = new Vector();
2073     SequenceI seq;
2074     for (int i = 0; i < sg.getSize(); i++)
2075     {
2076       seq = sg.getSequenceAt(i);
2077       seqs.addElement(seq);
2078     }
2079
2080     /*
2081      * If the cut affects all sequences, warn, remove highlighted columns
2082      */
2083     if (sg.getSize() == viewport.getAlignment().getHeight())
2084     {
2085       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2086               .getAlignment().getWidth()) ? true : false;
2087       if (isEntireAlignWidth)
2088       {
2089         String title = MessageManager.getString("label.delete_all");
2090         Panel infoPanel = new Panel();
2091         infoPanel.setLayout(new FlowLayout());
2092         infoPanel
2093                 .add(new Label(MessageManager.getString("warn.delete_all")));
2094
2095         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2096         dialog.setMainPanel(infoPanel);
2097         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2098         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2099         dialog.setVisible(true);
2100
2101         if (!dialog.accept)
2102         {
2103           return;
2104         }
2105       }
2106       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2107               sg.getEndRes() + 1);
2108     }
2109
2110     SequenceI[] cut = new SequenceI[seqs.size()];
2111     for (int i = 0; i < seqs.size(); i++)
2112     {
2113       cut[i] = (SequenceI) seqs.elementAt(i);
2114     }
2115
2116     /*
2117      * //ADD HISTORY ITEM
2118      */
2119     addHistoryItem(new EditCommand(
2120             MessageManager.getString("label.cut_sequences"), Action.CUT,
2121             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2122             viewport.getAlignment()));
2123
2124     viewport.setSelectionGroup(null);
2125     viewport.getAlignment().deleteGroup(sg);
2126
2127     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2128             .getSequences());
2129
2130     if (viewport.getAlignment().getHeight() < 1)
2131     {
2132       this.setVisible(false);
2133     }
2134     viewport.sendSelection();
2135   }
2136
2137   /**
2138    * group consensus toggled
2139    *
2140    */
2141   protected void showGroupConsensus_actionPerformed()
2142   {
2143     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2144     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145
2146   }
2147
2148   /**
2149    * group conservation toggled.
2150    */
2151   protected void showGroupConservation_actionPerformed()
2152   {
2153     viewport.setShowGroupConservation(showGroupConservation.getState());
2154     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2155   }
2156
2157   /*
2158    * (non-Javadoc)
2159    *
2160    * @see
2161    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2162    * .event.ActionEvent)
2163    */
2164   protected void showConsensusHistogram_actionPerformed()
2165   {
2166     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2167     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2168   }
2169
2170   /*
2171    * (non-Javadoc)
2172    *
2173    * @see
2174    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2175    * .event.ActionEvent)
2176    */
2177   protected void showSequenceLogo_actionPerformed()
2178   {
2179     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2180     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181   }
2182
2183   protected void normSequenceLogo_actionPerformed()
2184   {
2185     showSequenceLogo.setState(true);
2186     viewport.setShowSequenceLogo(true);
2187     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2188     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2189   }
2190
2191   protected void applyAutoAnnotationSettings_actionPerformed()
2192   {
2193     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2194   }
2195
2196   protected void makeGrpsFromSelection_actionPerformed()
2197   {
2198     if (avc.makeGroupsFromSelection())
2199     {
2200       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2201       alignPanel.updateAnnotation();
2202       alignPanel.paintAlignment(true);
2203     }
2204   }
2205
2206   protected void createGroup_actionPerformed()
2207   {
2208     avc.createGroup();
2209   }
2210
2211   protected void unGroup_actionPerformed()
2212   {
2213     if (avc.unGroup())
2214     {
2215       alignPanel.alignmentChanged();
2216     }
2217   }
2218
2219   protected void deleteGroups_actionPerformed()
2220   {
2221     if (avc.deleteGroups())
2222     {
2223       alignPanel.alignmentChanged();
2224     }
2225   }
2226
2227   public void selectAllSequenceMenuItem_actionPerformed()
2228   {
2229     SequenceGroup sg = new SequenceGroup();
2230     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2231     {
2232       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2233     }
2234     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2235     viewport.setSelectionGroup(sg);
2236     // JAL-2034 - should delegate to
2237     // alignPanel to decide if overview needs
2238     // updating.
2239     alignPanel.paintAlignment(false);
2240     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2241     viewport.sendSelection();
2242   }
2243
2244   public void deselectAllSequenceMenuItem_actionPerformed()
2245   {
2246     if (viewport.cursorMode)
2247     {
2248       alignPanel.seqPanel.keyboardNo1 = null;
2249       alignPanel.seqPanel.keyboardNo2 = null;
2250     }
2251     viewport.setSelectionGroup(null);
2252     viewport.getColumnSelection().clear();
2253     viewport.setSelectionGroup(null);
2254     alignPanel.idPanel.idCanvas.searchResults = null;
2255     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2256     // JAL-2034 - should delegate to
2257     // alignPanel to decide if overview needs
2258     // updating.
2259     alignPanel.paintAlignment(false);
2260     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2261     viewport.sendSelection();
2262   }
2263
2264   public void invertSequenceMenuItem_actionPerformed()
2265   {
2266     SequenceGroup sg = viewport.getSelectionGroup();
2267     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2268     {
2269       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2270     }
2271
2272     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273     viewport.sendSelection();
2274   }
2275
2276   public void invertColSel_actionPerformed()
2277   {
2278     viewport.invertColumnSelection();
2279     alignPanel.paintAlignment(true);
2280     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281     viewport.sendSelection();
2282   }
2283
2284   void trimAlignment(boolean trimLeft)
2285   {
2286     ColumnSelection colSel = viewport.getColumnSelection();
2287     int column;
2288
2289     if (!colSel.isEmpty())
2290     {
2291       if (trimLeft)
2292       {
2293         column = colSel.getMin();
2294       }
2295       else
2296       {
2297         column = colSel.getMax();
2298       }
2299
2300       SequenceI[] seqs;
2301       if (viewport.getSelectionGroup() != null)
2302       {
2303         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2304                 viewport.getHiddenRepSequences());
2305       }
2306       else
2307       {
2308         seqs = viewport.getAlignment().getSequencesArray();
2309       }
2310
2311       TrimRegionCommand trimRegion;
2312       if (trimLeft)
2313       {
2314         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2315                 column, viewport.getAlignment());
2316         viewport.setStartRes(0);
2317       }
2318       else
2319       {
2320         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2321                 column, viewport.getAlignment());
2322       }
2323
2324       statusBar.setText(MessageManager.formatMessage(
2325               "label.removed_columns",
2326               new String[] { Integer.valueOf(trimRegion.getSize())
2327                       .toString() }));
2328       addHistoryItem(trimRegion);
2329
2330       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2331       {
2332         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2333                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2334         {
2335           viewport.getAlignment().deleteGroup(sg);
2336         }
2337       }
2338
2339       viewport.firePropertyChange("alignment", null, viewport
2340               .getAlignment().getSequences());
2341     }
2342   }
2343
2344   public void removeGappedColumnMenuItem_actionPerformed()
2345   {
2346     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2347
2348     SequenceI[] seqs;
2349     if (viewport.getSelectionGroup() != null)
2350     {
2351       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2352               viewport.getHiddenRepSequences());
2353       start = viewport.getSelectionGroup().getStartRes();
2354       end = viewport.getSelectionGroup().getEndRes();
2355     }
2356     else
2357     {
2358       seqs = viewport.getAlignment().getSequencesArray();
2359     }
2360
2361     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2362             "Remove Gapped Columns", seqs, start, end,
2363             viewport.getAlignment());
2364
2365     addHistoryItem(removeGapCols);
2366
2367     statusBar.setText(MessageManager.formatMessage(
2368             "label.removed_empty_columns",
2369             new String[] { Integer.valueOf(removeGapCols.getSize())
2370                     .toString() }));
2371
2372     // This is to maintain viewport position on first residue
2373     // of first sequence
2374     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2375     int startRes = seq.findPosition(viewport.startRes);
2376     // ShiftList shifts;
2377     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2378     // edit.alColumnChanges=shifts.getInverse();
2379     // if (viewport.hasHiddenColumns)
2380     // viewport.getColumnSelection().compensateForEdits(shifts);
2381     viewport.setStartRes(seq.findIndex(startRes) - 1);
2382     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2383             .getSequences());
2384
2385   }
2386
2387   public void removeAllGapsMenuItem_actionPerformed()
2388   {
2389     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2390
2391     SequenceI[] seqs;
2392     if (viewport.getSelectionGroup() != null)
2393     {
2394       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2395               viewport.getHiddenRepSequences());
2396       start = viewport.getSelectionGroup().getStartRes();
2397       end = viewport.getSelectionGroup().getEndRes();
2398     }
2399     else
2400     {
2401       seqs = viewport.getAlignment().getSequencesArray();
2402     }
2403
2404     // This is to maintain viewport position on first residue
2405     // of first sequence
2406     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2407     int startRes = seq.findPosition(viewport.startRes);
2408
2409     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2410             viewport.getAlignment()));
2411
2412     viewport.setStartRes(seq.findIndex(startRes) - 1);
2413
2414     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2415             .getSequences());
2416
2417   }
2418
2419   public void findMenuItem_actionPerformed()
2420   {
2421     new Finder(alignPanel);
2422   }
2423
2424   /**
2425    * create a new view derived from the current view
2426    *
2427    * @param viewtitle
2428    * @return frame for the new view
2429    */
2430   public AlignFrame newView(String viewtitle)
2431   {
2432     AlignmentI newal;
2433     if (viewport.hasHiddenRows())
2434     {
2435       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2436               .getFullAlignment().getSequencesArray());
2437     }
2438     else
2439     {
2440       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2441     }
2442
2443     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2444     {
2445       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2446       {
2447         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2448         {
2449           newal.addAnnotation(viewport.getAlignment()
2450                   .getAlignmentAnnotation()[i]);
2451         }
2452       }
2453     }
2454
2455     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2456
2457     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2458     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2459     PaintRefresher.Register(newaf.alignPanel,
2460             newaf.alignPanel.av.getSequenceSetId());
2461
2462     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2463             newaf.alignPanel.av.getSequenceSetId());
2464     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2465             newaf.alignPanel.av.getSequenceSetId());
2466
2467     Vector comps = (Vector) PaintRefresher.components.get(viewport
2468             .getSequenceSetId());
2469     int viewSize = -1;
2470     for (int i = 0; i < comps.size(); i++)
2471     {
2472       if (comps.elementAt(i) instanceof AlignmentPanel)
2473       {
2474         viewSize++;
2475       }
2476     }
2477
2478     String title = new String(this.getTitle());
2479     if (viewtitle != null)
2480     {
2481       title = viewtitle + " ( " + title + ")";
2482     }
2483     else
2484     {
2485       if (title.indexOf("(View") > -1)
2486       {
2487         title = title.substring(0, title.indexOf("(View"));
2488       }
2489       title += "(View " + viewSize + ")";
2490     }
2491
2492     newaf.setTitle(title.toString());
2493
2494     newaf.viewport.setHistoryList(viewport.getHistoryList());
2495     newaf.viewport.setRedoList(viewport.getRedoList());
2496     return newaf;
2497   }
2498
2499   /**
2500    *
2501    * @return list of feature groups on the view
2502    */
2503   public String[] getFeatureGroups()
2504   {
2505     FeatureRenderer fr = null;
2506     if (alignPanel != null
2507             && (fr = alignPanel.getFeatureRenderer()) != null)
2508     {
2509       List<String> gps = fr.getFeatureGroups();
2510       String[] _gps = gps.toArray(new String[gps.size()]);
2511       return _gps;
2512     }
2513     return null;
2514   }
2515
2516   /**
2517    * get sequence feature groups that are hidden or shown
2518    *
2519    * @param visible
2520    *          true is visible
2521    * @return list
2522    */
2523   public String[] getFeatureGroupsOfState(boolean visible)
2524   {
2525     FeatureRenderer fr = null;
2526     if (alignPanel != null
2527             && (fr = alignPanel.getFeatureRenderer()) != null)
2528     {
2529       List<String> gps = fr.getGroups(visible);
2530       String[] _gps = gps.toArray(new String[gps.size()]);
2531       return _gps;
2532     }
2533     return null;
2534   }
2535
2536   /**
2537    * Change the display state for the given feature groups
2538    *
2539    * @param groups
2540    *          list of group strings
2541    * @param state
2542    *          visible or invisible
2543    */
2544   public void setFeatureGroupState(String[] groups, boolean state)
2545   {
2546     FeatureRenderer fr = null;
2547     this.sequenceFeatures.setState(true);
2548     viewport.setShowSequenceFeatures(true);
2549     if (alignPanel != null
2550             && (fr = alignPanel.getFeatureRenderer()) != null)
2551     {
2552
2553       fr.setGroupVisibility(Arrays.asList(groups), state);
2554       alignPanel.seqPanel.seqCanvas.repaint();
2555       if (alignPanel.overviewPanel != null)
2556       {
2557         alignPanel.overviewPanel.updateOverviewImage();
2558       }
2559     }
2560   }
2561
2562   public void seqLimits_itemStateChanged()
2563   {
2564     viewport.setShowJVSuffix(seqLimits.getState());
2565     alignPanel.fontChanged();
2566     alignPanel.paintAlignment(true);
2567   }
2568
2569   protected void colourTextMenuItem_actionPerformed()
2570   {
2571     viewport.setColourText(colourTextMenuItem.getState());
2572     alignPanel.paintAlignment(true);
2573   }
2574
2575   protected void displayNonconservedMenuItem_actionPerformed()
2576   {
2577     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2578     alignPanel.paintAlignment(true);
2579   }
2580
2581   protected void wrapMenuItem_actionPerformed()
2582   {
2583     viewport.setWrapAlignment(wrapMenuItem.getState());
2584     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2585     scaleAbove.setEnabled(wrapMenuItem.getState());
2586     scaleLeft.setEnabled(wrapMenuItem.getState());
2587     scaleRight.setEnabled(wrapMenuItem.getState());
2588     alignPanel.paintAlignment(true);
2589   }
2590
2591   public void overviewMenuItem_actionPerformed()
2592   {
2593     if (alignPanel.overviewPanel != null)
2594     {
2595       return;
2596     }
2597
2598     Frame frame = new Frame();
2599     OverviewPanel overview = new OverviewPanel(alignPanel);
2600     frame.add(overview);
2601     // +50 must allow for applet frame window
2602     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2603             "label.overview_params", new String[] { this.getTitle() }),
2604             overview.getPreferredSize().width,
2605             overview.getPreferredSize().height + 50);
2606
2607     frame.pack();
2608     final AlignmentPanel ap = alignPanel;
2609     frame.addWindowListener(new WindowAdapter()
2610     {
2611       @Override
2612       public void windowClosing(WindowEvent e)
2613       {
2614         if (ap != null)
2615         {
2616           ap.setOverviewPanel(null);
2617         }
2618       };
2619     });
2620
2621     alignPanel.setOverviewPanel(overview);
2622
2623   }
2624
2625   @Override
2626   public void changeColour(ColourSchemeI cs)
2627   {
2628
2629     if (cs != null)
2630     {
2631       if (viewport.getAbovePIDThreshold())
2632       {
2633         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2634                 cs, "Background"));
2635       }
2636
2637       if (viewport.getConservationSelected())
2638       {
2639         cs.setConservationApplied(true);
2640         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2641                 cs, "Background"));
2642       }
2643       else
2644       {
2645         cs.setConservationApplied(false);
2646       }
2647     }
2648     viewport.setGlobalColourScheme(cs);
2649
2650     alignPanel.paintAlignment(true);
2651   }
2652
2653   protected void modifyPID_actionPerformed()
2654   {
2655     if (viewport.getAbovePIDThreshold()
2656             && viewport.getGlobalColourScheme() != null)
2657     {
2658       SliderPanel.setPIDSliderSource(alignPanel,
2659               viewport.getGlobalColourScheme(), "Background");
2660       SliderPanel.showPIDSlider();
2661     }
2662   }
2663
2664   protected void modifyConservation_actionPerformed()
2665   {
2666     if (viewport.getConservationSelected()
2667             && viewport.getGlobalColourScheme() != null)
2668     {
2669       SliderPanel.setConservationSlider(alignPanel,
2670               viewport.getGlobalColourScheme(), "Background");
2671       SliderPanel.showConservationSlider();
2672     }
2673   }
2674
2675   protected void conservationMenuItem_actionPerformed()
2676   {
2677     viewport.setConservationSelected(conservationMenuItem.getState());
2678
2679     viewport.setAbovePIDThreshold(false);
2680     abovePIDThreshold.setState(false);
2681
2682     changeColour(viewport.getGlobalColourScheme());
2683
2684     modifyConservation_actionPerformed();
2685   }
2686
2687   public void abovePIDThreshold_actionPerformed()
2688   {
2689     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2690
2691     conservationMenuItem.setState(false);
2692     viewport.setConservationSelected(false);
2693
2694     changeColour(viewport.getGlobalColourScheme());
2695
2696     modifyPID_actionPerformed();
2697   }
2698
2699   public void sortPairwiseMenuItem_actionPerformed()
2700   {
2701     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2702     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2703             .getAlignment().getSequenceAt(0), null);
2704
2705     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2706             viewport.getAlignment()));
2707     alignPanel.paintAlignment(true);
2708   }
2709
2710   public void sortIDMenuItem_actionPerformed()
2711   {
2712     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2713     AlignmentSorter.sortByID(viewport.getAlignment());
2714     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2715             viewport.getAlignment()));
2716     alignPanel.paintAlignment(true);
2717   }
2718
2719   public void sortLengthMenuItem_actionPerformed()
2720   {
2721     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2722     AlignmentSorter.sortByLength(viewport.getAlignment());
2723     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2724             viewport.getAlignment()));
2725     alignPanel.paintAlignment(true);
2726   }
2727
2728   public void sortGroupMenuItem_actionPerformed()
2729   {
2730     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2731     AlignmentSorter.sortByGroup(viewport.getAlignment());
2732     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2733             viewport.getAlignment()));
2734     alignPanel.paintAlignment(true);
2735
2736   }
2737
2738   public void removeRedundancyMenuItem_actionPerformed()
2739   {
2740     new RedundancyPanel(alignPanel);
2741   }
2742
2743   public void pairwiseAlignmentMenuItem_actionPerformed()
2744   {
2745     if (viewport.getSelectionGroup() != null
2746             && viewport.getSelectionGroup().getSize() > 1)
2747     {
2748       Frame frame = new Frame();
2749       frame.add(new PairwiseAlignPanel(alignPanel));
2750       jalview.bin.JalviewLite.addFrame(frame,
2751               MessageManager.getString("action.pairwise_alignment"), 600,
2752               500);
2753     }
2754   }
2755
2756   public void PCAMenuItem_actionPerformed()
2757   {
2758     // are the sequences aligned?
2759     if (!viewport.getAlignment().isAligned(false))
2760     {
2761       SequenceI current;
2762       int Width = viewport.getAlignment().getWidth();
2763
2764       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2765       {
2766         current = viewport.getAlignment().getSequenceAt(i);
2767
2768         if (current.getLength() < Width)
2769         {
2770           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2771         }
2772       }
2773       alignPanel.paintAlignment(true);
2774     }
2775
2776     if ((viewport.getSelectionGroup() != null
2777             && viewport.getSelectionGroup().getSize() < 4 && viewport
2778             .getSelectionGroup().getSize() > 0)
2779             || viewport.getAlignment().getHeight() < 4)
2780     {
2781       return;
2782     }
2783
2784     try
2785     {
2786       new PCAPanel(viewport);
2787     } catch (java.lang.OutOfMemoryError ex)
2788     {
2789     }
2790
2791   }
2792
2793   public void averageDistanceTreeMenuItem_actionPerformed()
2794   {
2795     NewTreePanel("AV", "PID", "Average distance tree using PID");
2796   }
2797
2798   public void neighbourTreeMenuItem_actionPerformed()
2799   {
2800     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2801   }
2802
2803   protected void njTreeBlosumMenuItem_actionPerformed()
2804   {
2805     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2806   }
2807
2808   protected void avTreeBlosumMenuItem_actionPerformed()
2809   {
2810     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2811   }
2812
2813   void NewTreePanel(String type, String pwType, String title)
2814   {
2815     // are the sequences aligned?
2816     if (!viewport.getAlignment().isAligned(false))
2817     {
2818       SequenceI current;
2819       int Width = viewport.getAlignment().getWidth();
2820
2821       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2822       {
2823         current = viewport.getAlignment().getSequenceAt(i);
2824
2825         if (current.getLength() < Width)
2826         {
2827           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2828         }
2829       }
2830       alignPanel.paintAlignment(true);
2831
2832     }
2833
2834     if ((viewport.getSelectionGroup() != null && viewport
2835             .getSelectionGroup().getSize() > 1)
2836             || (viewport.getAlignment().getHeight() > 1))
2837     {
2838       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2839
2840       addTreeMenuItem(tp, title);
2841
2842       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2843     }
2844   }
2845
2846   void loadTree_actionPerformed()
2847   {
2848     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2849     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2850     cap.setTreeImport();
2851     Frame frame = new Frame();
2852     frame.add(cap);
2853     jalview.bin.JalviewLite.addFrame(frame,
2854             MessageManager.getString("label.paste_newick_file"), 400, 300);
2855   }
2856
2857   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2858   {
2859     TreePanel tp = new TreePanel(alignPanel, treeFile,
2860             MessageManager.getString("label.load_tree_from_file"), tree);
2861     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2862     addTreeMenuItem(tp, treeFile);
2863   }
2864
2865   /**
2866    * sort the alignment using the given treePanel
2867    *
2868    * @param treePanel
2869    *          tree used to sort view
2870    * @param title
2871    *          string used for undo event name
2872    */
2873   public void sortByTree(TreePanel treePanel, String title)
2874   {
2875     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2876     AlignmentSorter
2877             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2878     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2879     // HistoryItem.SORT));
2880     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2881             "label.order_by_params", new String[] { title }), oldOrder,
2882             viewport.getAlignment()));
2883     alignPanel.paintAlignment(true);
2884   }
2885
2886   /**
2887    * Do any automatic reordering of the alignment and add the necessary bits to
2888    * the menu structure for the new tree
2889    *
2890    * @param treePanel
2891    * @param title
2892    */
2893   protected void addTreeMenuItem(final TreePanel treePanel,
2894           final String title)
2895   {
2896     final MenuItem item = new MenuItem(title);
2897     sortByTreeMenu.add(item);
2898     item.addActionListener(new java.awt.event.ActionListener()
2899     {
2900       @Override
2901       public void actionPerformed(ActionEvent evt)
2902       {
2903         sortByTree(treePanel, title); // treePanel.getTitle());
2904       }
2905     });
2906
2907     treePanel.addWindowListener(new WindowAdapter()
2908     {
2909       @Override
2910       public void windowOpened(WindowEvent e)
2911       {
2912         if (viewport.sortByTree)
2913         {
2914           sortByTree(treePanel, title);
2915         }
2916         super.windowOpened(e);
2917       }
2918
2919       @Override
2920       public void windowClosing(WindowEvent e)
2921       {
2922         sortByTreeMenu.remove(item);
2923       };
2924     });
2925   }
2926
2927   public boolean sortBy(AlignmentOrder alorder, String undoname)
2928   {
2929     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2930     if (viewport.applet.debug)
2931     {
2932       System.err.println("Sorting " + alorder.getOrder().size()
2933               + " in alignment '" + getTitle() + "'");
2934     }
2935     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2936     if (undoname != null)
2937     {
2938       addHistoryItem(new OrderCommand(undoname, oldOrder,
2939               viewport.getAlignment()));
2940     }
2941     alignPanel.paintAlignment(true);
2942     return true;
2943   }
2944
2945   protected void documentation_actionPerformed()
2946   {
2947     alignPanel.av.applet.openJalviewHelpUrl();
2948   }
2949
2950   protected void about_actionPerformed()
2951   {
2952
2953     class AboutPanel extends Canvas
2954     {
2955       String version;
2956
2957       String builddate;
2958
2959       public AboutPanel(String version, String builddate)
2960       {
2961         this.version = version;
2962         this.builddate = builddate;
2963       }
2964
2965       @Override
2966       public void paint(Graphics g)
2967       {
2968         g.setColor(Color.white);
2969         g.fillRect(0, 0, getSize().width, getSize().height);
2970         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2971         FontMetrics fm = g.getFontMetrics();
2972         int fh = fm.getHeight();
2973         int y = 5, x = 7;
2974         g.setColor(Color.black);
2975         // TODO: update this text for each release or centrally store it for
2976         // lite and application
2977         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2978         g.drawString(MessageManager.formatMessage(
2979                 "label.jalviewLite_release", new String[] { version }), x,
2980                 y += fh);
2981         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2982         g.drawString(MessageManager.formatMessage(
2983                 "label.jaview_build_date", new String[] { builddate }), x,
2984                 y += fh);
2985         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2986         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2987                 x, y += fh * 1.5);
2988         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2989                 x + 50, y += fh + 8);
2990         g.drawString(
2991                 MessageManager.getString("label.jalview_dev_managers"), x,
2992                 y += fh);
2993         g.drawString(MessageManager
2994                 .getString("label.jalview_distribution_lists"), x, y += fh);
2995         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2996                 x, y += fh + 8);
2997         g.drawString(
2998                 MessageManager.getString("label.jalview_cite_1_authors"),
2999                 x, y += fh);
3000         g.drawString(
3001                 MessageManager.getString("label.jalview_cite_1_title"), x,
3002                 y += fh);
3003         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3004                 x, y += fh);
3005       }
3006     }
3007
3008     Frame frame = new Frame();
3009     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3010             .getBuildDate()));
3011     jalview.bin.JalviewLite.addFrame(frame,
3012             MessageManager.getString("label.jalview"), 580, 220);
3013
3014   }
3015
3016   public void showURL(String url, String target)
3017   {
3018     if (viewport.applet == null)
3019     {
3020       System.out.println("Not running as applet - no browser available.");
3021     }
3022     else
3023     {
3024       viewport.applet.showURL(url, target);
3025     }
3026   }
3027
3028   // ////////////////////////////////////////////////////////////////////////////////
3029   // JBuilder Graphics here
3030
3031   MenuBar alignFrameMenuBar = new MenuBar();
3032
3033   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3034
3035   MenuItem loadApplication = new MenuItem(
3036           MessageManager.getString("label.view_full_application"));
3037
3038   MenuItem loadTree = new MenuItem(
3039           MessageManager.getString("label.load_associated_tree"));
3040
3041   MenuItem loadAnnotations = new MenuItem(
3042           MessageManager.getString("label.load_features_annotations"));
3043
3044   MenuItem outputFeatures = new MenuItem(
3045           MessageManager.getString("label.export_features"));
3046
3047   MenuItem outputAnnotations = new MenuItem(
3048           MessageManager.getString("label.export_annotations"));
3049
3050   MenuItem closeMenuItem = new MenuItem(
3051           MessageManager.getString("action.close"));
3052
3053   MenuItem selectAllSequenceMenuItem = new MenuItem(
3054           MessageManager.getString("action.select_all"));
3055
3056   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3057           MessageManager.getString("action.deselect_all"));
3058
3059   MenuItem invertSequenceMenuItem = new MenuItem(
3060           MessageManager.getString("action.invert_selection"));
3061
3062   MenuItem remove2LeftMenuItem = new MenuItem();
3063
3064   MenuItem remove2RightMenuItem = new MenuItem();
3065
3066   MenuItem removeGappedColumnMenuItem = new MenuItem();
3067
3068   MenuItem removeAllGapsMenuItem = new MenuItem();
3069
3070   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3071
3072   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3073
3074   MenuItem sortPairwiseMenuItem = new MenuItem();
3075
3076   MenuItem sortIDMenuItem = new MenuItem();
3077
3078   MenuItem sortLengthMenuItem = new MenuItem();
3079
3080   MenuItem sortGroupMenuItem = new MenuItem();
3081
3082   MenuItem removeRedundancyMenuItem = new MenuItem();
3083
3084   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3085
3086   MenuItem PCAMenuItem = new MenuItem();
3087
3088   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3089
3090   MenuItem neighbourTreeMenuItem = new MenuItem();
3091
3092   BorderLayout borderLayout1 = new BorderLayout();
3093
3094   public Label statusBar = new Label();
3095
3096   MenuItem clustalColour = new MenuItem();
3097
3098   MenuItem zappoColour = new MenuItem();
3099
3100   MenuItem taylorColour = new MenuItem();
3101
3102   MenuItem hydrophobicityColour = new MenuItem();
3103
3104   MenuItem helixColour = new MenuItem();
3105
3106   MenuItem strandColour = new MenuItem();
3107
3108   MenuItem turnColour = new MenuItem();
3109
3110   MenuItem buriedColour = new MenuItem();
3111
3112   MenuItem purinePyrimidineColour = new MenuItem();
3113
3114   // MenuItem RNAInteractionColour = new MenuItem();
3115
3116   MenuItem RNAHelixColour = new MenuItem();
3117
3118   MenuItem userDefinedColour = new MenuItem();
3119
3120   MenuItem PIDColour = new MenuItem();
3121
3122   MenuItem BLOSUM62Colour = new MenuItem();
3123
3124   MenuItem tcoffeeColour = new MenuItem();
3125
3126   MenuItem njTreeBlosumMenuItem = new MenuItem();
3127
3128   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3129
3130   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3131
3132   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3133
3134   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3135
3136   MenuItem alProperties = new MenuItem(
3137           MessageManager.getString("label.alignment_props"));
3138
3139   MenuItem overviewMenuItem = new MenuItem();
3140
3141   MenuItem undoMenuItem = new MenuItem();
3142
3143   MenuItem redoMenuItem = new MenuItem();
3144
3145   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3146
3147   MenuItem noColourmenuItem = new MenuItem();
3148
3149   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3150
3151   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3152
3153   MenuItem findMenuItem = new MenuItem();
3154
3155   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3156
3157   MenuItem nucleotideColour = new MenuItem();
3158
3159   MenuItem deleteGroups = new MenuItem();
3160
3161   MenuItem grpsFromSelection = new MenuItem();
3162
3163   MenuItem createGroup = new MenuItem();
3164
3165   MenuItem unGroup = new MenuItem();
3166
3167   MenuItem delete = new MenuItem();
3168
3169   MenuItem copy = new MenuItem();
3170
3171   MenuItem cut = new MenuItem();
3172
3173   Menu pasteMenu = new Menu();
3174
3175   MenuItem pasteNew = new MenuItem();
3176
3177   MenuItem pasteThis = new MenuItem();
3178
3179   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3180
3181   MenuItem font = new MenuItem();
3182
3183   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3184
3185   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3186
3187   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3188
3189   MenuItem modifyPID = new MenuItem();
3190
3191   MenuItem modifyConservation = new MenuItem();
3192
3193   CheckboxMenuItem autoCalculate = null;
3194
3195   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3196           "Sort Alignment With New Tree", true);
3197
3198   Menu sortByTreeMenu = new Menu();
3199
3200   MenuItem inputText = new MenuItem();
3201
3202   MenuItem documentation = new MenuItem();
3203
3204   MenuItem about = new MenuItem();
3205
3206   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3209
3210   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3211
3212   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3213
3214   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3215
3216   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3217
3218   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3219
3220   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3221
3222   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3223
3224   /**
3225    * Initialise menus and other items
3226    *
3227    * @throws Exception
3228    */
3229   private void jbInit() throws Exception
3230   {
3231     setMenuBar(alignFrameMenuBar);
3232
3233     /*
3234      * Configure File menu items and actions
3235      */
3236     inputText
3237             .setLabel(MessageManager.getString("label.input_from_textbox"));
3238     inputText.addActionListener(this);
3239     Menu outputTextboxMenu = new Menu(
3240             MessageManager.getString("label.out_to_textbox"));
3241     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3242     {
3243
3244       MenuItem item = new MenuItem(
3245               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3246
3247       item.addActionListener(new java.awt.event.ActionListener()
3248       {
3249         @Override
3250         public void actionPerformed(ActionEvent e)
3251         {
3252           outputText_actionPerformed(e);
3253         }
3254       });
3255
3256       outputTextboxMenu.add(item);
3257     }
3258     closeMenuItem.addActionListener(this);
3259     loadApplication.addActionListener(this);
3260     loadTree.addActionListener(this);
3261     loadAnnotations.addActionListener(this);
3262     outputFeatures.addActionListener(this);
3263     outputAnnotations.addActionListener(this);
3264
3265     /*
3266      * Configure Edit menu items and actions
3267      */
3268     undoMenuItem.setEnabled(false);
3269     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3270     undoMenuItem.addActionListener(this);
3271     redoMenuItem.setEnabled(false);
3272     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3273     redoMenuItem.addActionListener(this);
3274     copy.setLabel(MessageManager.getString("action.copy"));
3275     copy.addActionListener(this);
3276     cut.setLabel(MessageManager.getString("action.cut"));
3277     cut.addActionListener(this);
3278     delete.setLabel(MessageManager.getString("action.delete"));
3279     delete.addActionListener(this);
3280     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3281     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3282     pasteNew.addActionListener(this);
3283     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3284     pasteThis.addActionListener(this);
3285     remove2LeftMenuItem.setLabel(MessageManager
3286             .getString("action.remove_left"));
3287     remove2LeftMenuItem.addActionListener(this);
3288     remove2RightMenuItem.setLabel(MessageManager
3289             .getString("action.remove_right"));
3290     remove2RightMenuItem.addActionListener(this);
3291     removeGappedColumnMenuItem.setLabel(MessageManager
3292             .getString("action.remove_empty_columns"));
3293     removeGappedColumnMenuItem.addActionListener(this);
3294     removeAllGapsMenuItem.setLabel(MessageManager
3295             .getString("action.remove_all_gaps"));
3296     removeAllGapsMenuItem.addActionListener(this);
3297     removeRedundancyMenuItem.setLabel(MessageManager
3298             .getString("action.remove_redundancy"));
3299     removeRedundancyMenuItem.addActionListener(this);
3300
3301     /*
3302      * Configure Select menu items and actions
3303      */
3304     findMenuItem.setLabel(MessageManager.getString("action.find"));
3305     findMenuItem.addActionListener(this);
3306     selectAllSequenceMenuItem.addActionListener(this);
3307     deselectAllSequenceMenuItem.addActionListener(this);
3308     invertSequenceMenuItem.setLabel(MessageManager
3309             .getString("action.invert_sequence_selection"));
3310     invertSequenceMenuItem.addActionListener(this);
3311     invertColSel.setLabel(MessageManager
3312             .getString("action.invert_column_selection"));
3313     invertColSel.addActionListener(this);
3314     deleteGroups.setLabel(MessageManager
3315             .getString("action.undefine_groups"));
3316     deleteGroups.addActionListener(this);
3317     grpsFromSelection.setLabel(MessageManager
3318             .getString("action.make_groups_selection"));
3319     grpsFromSelection.addActionListener(this);
3320     createGroup.setLabel(MessageManager.getString("action.create_group"));
3321     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3322     annotationColumnSelection.setLabel(MessageManager
3323             .getString("action.select_by_annotation"));
3324     annotationColumnSelection.addActionListener(this);
3325
3326     /*
3327      * Configure View menu items and actions
3328      */
3329     newView.setLabel(MessageManager.getString("action.new_view"));
3330     newView.addActionListener(this);
3331     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3332     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3333     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3334     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3335     hideColumns
3336             .setLabel(MessageManager.getString("label.selected_columns"));
3337     hideSequences.setLabel(MessageManager
3338             .getString("label.selected_sequences"));
3339     hideAllButSelection.setLabel(MessageManager
3340             .getString("label.all_but_selected_region"));
3341     hideAllSelection.setLabel(MessageManager
3342             .getString("label.selected_region"));
3343     showAllHidden.setLabel(MessageManager
3344             .getString("label.all_sequences_columns"));
3345     showColumns.addActionListener(this);
3346     showSeqs.addActionListener(this);
3347     hideColumns.addActionListener(this);
3348     hideSequences.addActionListener(this);
3349     hideAllButSelection.addActionListener(this);
3350     hideAllSelection.addActionListener(this);
3351     showAllHidden.addActionListener(this);
3352     featureSettings.setLabel(MessageManager
3353             .getString("action.feature_settings"));
3354     featureSettings.addActionListener(this);
3355     sequenceFeatures.setLabel(MessageManager
3356             .getString("label.show_sequence_features"));
3357     sequenceFeatures.addItemListener(this);
3358     sequenceFeatures.setState(false);
3359     followMouseOverFlag.setLabel(MessageManager
3360             .getString("label.automatic_scrolling"));
3361     followMouseOverFlag.addItemListener(this);
3362     alProperties.addActionListener(this);
3363     overviewMenuItem.setLabel(MessageManager
3364             .getString("label.overview_window"));
3365     overviewMenuItem.addActionListener(this);
3366
3367     /*
3368      * Configure Annotations menu items and actions
3369      */
3370     annotationPanelMenuItem.setLabel(MessageManager
3371             .getString("label.show_annotations"));
3372     annotationPanelMenuItem.addItemListener(this);
3373     showGroupConsensus.setLabel(MessageManager
3374             .getString("label.group_consensus"));
3375     showGroupConservation.setLabel(MessageManager
3376             .getString("label.group_conservation"));
3377     showConsensusHistogram.setLabel(MessageManager
3378             .getString("label.show_consensus_histogram"));
3379     showSequenceLogo.setLabel(MessageManager
3380             .getString("label.show_consensus_logo"));
3381     normSequenceLogo.setLabel(MessageManager
3382             .getString("label.norm_consensus_logo"));
3383     applyAutoAnnotationSettings.setLabel(MessageManager
3384             .getString("label.apply_all_groups"));
3385     applyAutoAnnotationSettings.setState(true);
3386     Menu autoAnnMenu = new Menu(
3387             MessageManager.getString("label.autocalculated_annotation"));
3388     showGroupConsensus.addItemListener(this);
3389     showGroupConservation.addItemListener(this);
3390     showConsensusHistogram.addItemListener(this);
3391     showSequenceLogo.addItemListener(this);
3392     normSequenceLogo.addItemListener(this);
3393     applyAutoAnnotationSettings.addItemListener(this);
3394     showAlignmentAnnotations = new CheckboxMenuItem(
3395             MessageManager.getString("label.show_all_al_annotations"));
3396     showSequenceAnnotations = new CheckboxMenuItem(
3397             MessageManager.getString("label.show_all_seq_annotations"));
3398     sortAnnBySequence = new CheckboxMenuItem(
3399             MessageManager.getString("label.sort_annotations_by_sequence"));
3400     sortAnnByLabel = new CheckboxMenuItem(
3401             MessageManager.getString("label.sort_annotations_by_label"));
3402     showAutoFirst = new CheckboxMenuItem(
3403             MessageManager.getString("label.show_first"));
3404     showAutoFirst.setState(false); // pending applet parameter
3405     setShowAutoCalculatedAbove(showAutoFirst.getState());
3406     showAutoLast = new CheckboxMenuItem(
3407             MessageManager.getString("label.show_last"));
3408     showAutoLast.setState(!showAutoFirst.getState());
3409     showAlignmentAnnotations.addItemListener(this);
3410     showSequenceAnnotations.addItemListener(this);
3411     sortAnnBySequence.addItemListener(this);
3412     sortAnnByLabel.addItemListener(this);
3413     showAutoFirst.addItemListener(this);
3414     showAutoLast.addItemListener(this);
3415
3416     /*
3417      * Configure Format menu items and actions
3418      */
3419     font.setLabel(MessageManager.getString("action.font"));
3420     font.addActionListener(this);
3421     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3422     scaleAbove.setState(true);
3423     scaleAbove.setEnabled(false);
3424     scaleAbove.addItemListener(this);
3425     scaleLeft.setEnabled(false);
3426     scaleLeft.setState(true);
3427     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3428     scaleLeft.addItemListener(this);
3429     scaleRight.setEnabled(false);
3430     scaleRight.setState(true);
3431     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3432     scaleRight.addItemListener(this);
3433     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3434     viewBoxesMenuItem.setState(true);
3435     viewBoxesMenuItem.addItemListener(this);
3436     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3437     viewTextMenuItem.setState(true);
3438     viewTextMenuItem.addItemListener(this);
3439     colourTextMenuItem.setLabel(MessageManager
3440             .getString("label.colour_text"));
3441     colourTextMenuItem.addItemListener(this);
3442     displayNonconservedMenuItem.setLabel(MessageManager
3443             .getString("label.show_non_conversed"));
3444     displayNonconservedMenuItem.addItemListener(this);
3445     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3446     wrapMenuItem.addItemListener(this);
3447     renderGapsMenuItem.setLabel(MessageManager
3448             .getString("action.show_gaps"));
3449     renderGapsMenuItem.setState(true);
3450     renderGapsMenuItem.addItemListener(this);
3451     centreColumnLabelFlag.setLabel(MessageManager
3452             .getString("label.centre_column_labels"));
3453     centreColumnLabelFlag.addItemListener(this);
3454     seqLimits.setState(true);
3455     seqLimits.setLabel(MessageManager
3456             .getString("label.show_sequence_limits"));
3457     seqLimits.addItemListener(this);
3458
3459     /*
3460      * Configure Colour menu items and actions
3461      */
3462     applyToAllGroups.setLabel(MessageManager
3463             .getString("label.apply_colour_to_all_groups"));
3464     applyToAllGroups.setState(true);
3465     applyToAllGroups.addItemListener(this);
3466     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3467     clustalColour.addActionListener(this);
3468     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3469     zappoColour.addActionListener(this);
3470     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3471     taylorColour.addActionListener(this);
3472     hydrophobicityColour.setLabel(MessageManager
3473             .getString("label.hydrophobicity"));
3474     hydrophobicityColour.addActionListener(this);
3475     helixColour
3476             .setLabel(MessageManager.getString("label.helix_propensity"));
3477     helixColour.addActionListener(this);
3478     strandColour.setLabel(MessageManager
3479             .getString("label.strand_propensity"));
3480     strandColour.addActionListener(this);
3481     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3482     turnColour.addActionListener(this);
3483     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3484     buriedColour.addActionListener(this);
3485     purinePyrimidineColour.setLabel(MessageManager
3486             .getString("label.purine_pyrimidine"));
3487     purinePyrimidineColour.addActionListener(this);
3488     // RNAInteractionColour.setLabel(MessageManager
3489     // .getString("label.rna_interaction"));
3490     // RNAInteractionColour.addActionListener(this);
3491     RNAHelixColour.setLabel(MessageManager
3492             .getString("action.by_rna_helixes"));
3493     RNAHelixColour.addActionListener(this);
3494     userDefinedColour.setLabel(MessageManager
3495             .getString("action.user_defined"));
3496     userDefinedColour.addActionListener(this);
3497     PIDColour.setLabel(MessageManager
3498             .getString("label.percentage_identity"));
3499     PIDColour.addActionListener(this);
3500     BLOSUM62Colour.setLabel(MessageManager
3501             .getString("label.blosum62_score"));
3502     BLOSUM62Colour.addActionListener(this);
3503     tcoffeeColour
3504             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3505     // it will be enabled only if a score file is provided
3506     tcoffeeColour.setEnabled(false);
3507     tcoffeeColour.addActionListener(this);
3508     conservationMenuItem.setLabel(MessageManager
3509             .getString("action.by_conservation"));
3510     conservationMenuItem.addItemListener(this);
3511     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3512     noColourmenuItem.addActionListener(this);
3513     abovePIDThreshold.setLabel(MessageManager
3514             .getString("label.above_identity_threshold"));
3515     abovePIDThreshold.addItemListener(this);
3516     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3517     nucleotideColour.addActionListener(this);
3518     modifyPID.setLabel(MessageManager
3519             .getString("label.modify_identity_threshold"));
3520     modifyPID.addActionListener(this);
3521     modifyConservation.setLabel(MessageManager
3522             .getString("label.modify_conservation_threshold"));
3523     modifyConservation.addActionListener(this);
3524     annotationColour.setLabel(MessageManager
3525             .getString("action.by_annotation"));
3526     annotationColour.addActionListener(this);
3527
3528     /*
3529      * Configure Calculate menu items and actions
3530      */
3531     sortPairwiseMenuItem.setLabel(MessageManager
3532             .getString("action.by_pairwise_id"));
3533     sortPairwiseMenuItem.addActionListener(this);
3534     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3535     sortIDMenuItem.addActionListener(this);
3536     sortLengthMenuItem.setLabel(MessageManager
3537             .getString("action.by_length"));
3538     sortLengthMenuItem.addActionListener(this);
3539     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3540     sortGroupMenuItem.addActionListener(this);
3541     pairwiseAlignmentMenuItem.setLabel(MessageManager
3542             .getString("action.pairwise_alignment"));
3543     pairwiseAlignmentMenuItem.addActionListener(this);
3544     PCAMenuItem.setLabel(MessageManager
3545             .getString("label.principal_component_analysis"));
3546     PCAMenuItem.addActionListener(this);
3547     autoCalculate = new CheckboxMenuItem(
3548             MessageManager.getString("label.autocalculate_consensus"), true);
3549     averageDistanceTreeMenuItem.setLabel(MessageManager
3550             .getString("label.average_distance_identity"));
3551     averageDistanceTreeMenuItem.addActionListener(this);
3552     neighbourTreeMenuItem.setLabel(MessageManager
3553             .getString("label.neighbour_joining_identity"));
3554     neighbourTreeMenuItem.addActionListener(this);
3555     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3556             .getString("label.average_distance_bloslum62"));
3557     avDistanceTreeBlosumMenuItem.addActionListener(this);
3558     njTreeBlosumMenuItem.setLabel(MessageManager
3559             .getString("label.neighbour_blosum62"));
3560     njTreeBlosumMenuItem.addActionListener(this);
3561     sortByTreeMenu.setLabel(MessageManager
3562             .getString("action.by_tree_order"));
3563     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3564     Menu calculateTreeMenu = new Menu(
3565             MessageManager.getString("action.calculate_tree"));
3566     autoCalculate.addItemListener(this);
3567     sortByTree.addItemListener(this);
3568
3569     /*
3570      * Configure Help menu items and actions
3571      */
3572     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3573     documentation.setLabel(MessageManager.getString("label.documentation"));
3574     documentation.addActionListener(this);
3575     about.setLabel(MessageManager.getString("label.about"));
3576     about.addActionListener(this);
3577
3578     /*
3579      * Add top level menus to frame
3580      */
3581     alignFrameMenuBar.add(fileMenu);
3582     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3583     alignFrameMenuBar.add(editMenu);
3584     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3585     alignFrameMenuBar.add(selectMenu);
3586     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3587     alignFrameMenuBar.add(viewMenu);
3588     Menu annotationsMenu = new Menu(
3589             MessageManager.getString("action.annotations"));
3590     alignFrameMenuBar.add(annotationsMenu);
3591     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3592     alignFrameMenuBar.add(formatMenu);
3593     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3594     alignFrameMenuBar.add(colourMenu);
3595     Menu calculateMenu = new Menu(
3596             MessageManager.getString("action.calculate"));
3597     alignFrameMenuBar.add(calculateMenu);
3598     alignFrameMenuBar.add(helpMenu);
3599
3600     /*
3601      * File menu
3602      */
3603     fileMenu.add(inputText);
3604     fileMenu.add(loadTree);
3605     fileMenu.add(loadAnnotations);
3606     fileMenu.addSeparator();
3607     fileMenu.add(outputTextboxMenu);
3608     fileMenu.add(outputFeatures);
3609     fileMenu.add(outputAnnotations);
3610     if (jalviewServletURL != null)
3611     {
3612       fileMenu.add(loadApplication);
3613     }
3614     fileMenu.addSeparator();
3615     fileMenu.add(closeMenuItem);
3616
3617     /*
3618      * Edit menu
3619      */
3620     editMenu.add(undoMenuItem);
3621     editMenu.add(redoMenuItem);
3622     editMenu.add(cut);
3623     editMenu.add(copy);
3624     pasteMenu.add(pasteNew);
3625     pasteMenu.add(pasteThis);
3626     editMenu.add(pasteMenu);
3627     editMenu.add(delete);
3628     editMenu.addSeparator();
3629     editMenu.add(remove2LeftMenuItem);
3630     editMenu.add(remove2RightMenuItem);
3631     editMenu.add(removeGappedColumnMenuItem);
3632     editMenu.add(removeAllGapsMenuItem);
3633     editMenu.add(removeRedundancyMenuItem);
3634
3635     /*
3636      * Select menu
3637      */
3638     selectMenu.add(findMenuItem);
3639     selectMenu.addSeparator();
3640     selectMenu.add(selectAllSequenceMenuItem);
3641     selectMenu.add(deselectAllSequenceMenuItem);
3642     selectMenu.add(invertSequenceMenuItem);
3643     selectMenu.add(invertColSel);
3644     selectMenu.add(createGroup);
3645     selectMenu.add(unGroup);
3646     selectMenu.add(grpsFromSelection);
3647     selectMenu.add(deleteGroups);
3648     selectMenu.add(annotationColumnSelection);
3649
3650     /*
3651      * View menu
3652      */
3653     viewMenu.add(newView);
3654     viewMenu.addSeparator();
3655     showMenu.add(showColumns);
3656     showMenu.add(showSeqs);
3657     showMenu.add(showAllHidden);
3658     viewMenu.add(showMenu);
3659     hideMenu.add(hideColumns);
3660     hideMenu.add(hideSequences);
3661     hideMenu.add(hideAllSelection);
3662     hideMenu.add(hideAllButSelection);
3663     viewMenu.add(hideMenu);
3664     viewMenu.addSeparator();
3665     viewMenu.add(followMouseOverFlag);
3666     viewMenu.addSeparator();
3667     viewMenu.add(sequenceFeatures);
3668     viewMenu.add(featureSettings);
3669     viewMenu.addSeparator();
3670     viewMenu.add(alProperties);
3671     viewMenu.addSeparator();
3672     viewMenu.add(overviewMenuItem);
3673
3674     /*
3675      * Annotations menu
3676      */
3677     annotationsMenu.add(annotationPanelMenuItem);
3678     annotationsMenu.addSeparator();
3679     annotationsMenu.add(showAlignmentAnnotations);
3680     annotationsMenu.add(showSequenceAnnotations);
3681     annotationsMenu.add(sortAnnBySequence);
3682     annotationsMenu.add(sortAnnByLabel);
3683     annotationsMenu.addSeparator();
3684     autoAnnMenu.add(showAutoFirst);
3685     autoAnnMenu.add(showAutoLast);
3686     autoAnnMenu.addSeparator();
3687     autoAnnMenu.add(applyAutoAnnotationSettings);
3688     autoAnnMenu.add(showConsensusHistogram);
3689     autoAnnMenu.add(showSequenceLogo);
3690     autoAnnMenu.add(normSequenceLogo);
3691     autoAnnMenu.addSeparator();
3692     autoAnnMenu.add(showGroupConservation);
3693     autoAnnMenu.add(showGroupConsensus);
3694     annotationsMenu.add(autoAnnMenu);
3695
3696     /*
3697      * Format menu
3698      */
3699     formatMenu.add(font);
3700     formatMenu.add(seqLimits);
3701     formatMenu.add(wrapMenuItem);
3702     formatMenu.add(scaleAbove);
3703     formatMenu.add(scaleLeft);
3704     formatMenu.add(scaleRight);
3705     formatMenu.add(viewBoxesMenuItem);
3706     formatMenu.add(viewTextMenuItem);
3707     formatMenu.add(colourTextMenuItem);
3708     formatMenu.add(displayNonconservedMenuItem);
3709     formatMenu.add(renderGapsMenuItem);
3710     formatMenu.add(centreColumnLabelFlag);
3711
3712     /*
3713      * Colour menu
3714      */
3715     colourMenu.add(applyToAllGroups);
3716     colourMenu.addSeparator();
3717     colourMenu.add(noColourmenuItem);
3718     colourMenu.add(clustalColour);
3719     colourMenu.add(BLOSUM62Colour);
3720     colourMenu.add(PIDColour);
3721     colourMenu.add(zappoColour);
3722     colourMenu.add(taylorColour);
3723     colourMenu.add(hydrophobicityColour);
3724     colourMenu.add(helixColour);
3725     colourMenu.add(strandColour);
3726     colourMenu.add(turnColour);
3727     colourMenu.add(buriedColour);
3728     colourMenu.add(nucleotideColour);
3729     colourMenu.add(purinePyrimidineColour);
3730     // colourMenu.add(RNAInteractionColour);
3731     colourMenu.add(tcoffeeColour);
3732     colourMenu.add(userDefinedColour);
3733     colourMenu.addSeparator();
3734     colourMenu.add(conservationMenuItem);
3735     colourMenu.add(modifyConservation);
3736     colourMenu.add(abovePIDThreshold);
3737     colourMenu.add(modifyPID);
3738     colourMenu.add(annotationColour);
3739     colourMenu.add(RNAHelixColour);
3740
3741     /*
3742      * Calculate menu
3743      */
3744     sortMenu.add(sortIDMenuItem);
3745     sortMenu.add(sortLengthMenuItem);
3746     sortMenu.add(sortByTreeMenu);
3747     sortMenu.add(sortGroupMenuItem);
3748     sortMenu.add(sortPairwiseMenuItem);
3749     calculateMenu.add(sortMenu);
3750     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3751     calculateTreeMenu.add(neighbourTreeMenuItem);
3752     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3753     calculateTreeMenu.add(njTreeBlosumMenuItem);
3754     calculateMenu.add(calculateTreeMenu);
3755     calculateMenu.addSeparator();
3756     calculateMenu.add(pairwiseAlignmentMenuItem);
3757     calculateMenu.add(PCAMenuItem);
3758     calculateMenu.add(autoCalculate);
3759     calculateMenu.add(sortByTree);
3760
3761     /*
3762      * Help menu
3763      */
3764     helpMenu.add(documentation);
3765     helpMenu.add(about);
3766
3767     /*
3768      * Status bar
3769      */
3770     statusBar.setBackground(Color.white);
3771     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3772     statusBar.setText(MessageManager.getString("label.status_bar"));
3773     this.add(statusBar, BorderLayout.SOUTH);
3774   }
3775
3776   @Override
3777   public void setStatus(String string)
3778   {
3779     statusBar.setText(string);
3780   };
3781
3782   MenuItem featureSettings = new MenuItem();
3783
3784   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3785
3786   MenuItem annotationColour = new MenuItem();
3787
3788   MenuItem annotationColumnSelection = new MenuItem();
3789
3790   MenuItem invertColSel = new MenuItem();
3791
3792   MenuItem showColumns = new MenuItem();
3793
3794   MenuItem showSeqs = new MenuItem();
3795
3796   MenuItem hideColumns = new MenuItem();
3797
3798   MenuItem hideSequences = new MenuItem();
3799
3800   MenuItem hideAllButSelection = new MenuItem();
3801
3802   MenuItem hideAllSelection = new MenuItem();
3803
3804   MenuItem showAllHidden = new MenuItem();
3805
3806   MenuItem newView = new MenuItem();
3807
3808   private CheckboxMenuItem showAlignmentAnnotations;
3809
3810   private CheckboxMenuItem showSequenceAnnotations;
3811
3812   private CheckboxMenuItem sortAnnBySequence;
3813
3814   private CheckboxMenuItem sortAnnByLabel;
3815
3816   private CheckboxMenuItem showAutoFirst;
3817
3818   private CheckboxMenuItem showAutoLast;
3819
3820   private SplitFrame splitFrame;
3821
3822   /**
3823    * Attach the alignFrame panels after embedding menus, if necessary. This used
3824    * to be called setEmbedded, but is now creates the dropdown menus in a
3825    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3826    *
3827    * @param reallyEmbedded
3828    *          true to attach the view to the applet area on the page rather than
3829    *          in a new window
3830    */
3831   public void createAlignFrameWindow(boolean reallyEmbedded)
3832   {
3833     if (reallyEmbedded)
3834     {
3835       embedAlignFrameInApplet(viewport.applet);
3836     }
3837     else
3838     {
3839       // //////
3840       // test and embed menu bar if necessary.
3841       //
3842       if (embedMenuIfNeeded(alignPanel))
3843       {
3844         /*
3845          * adjust for status bar height too. ? pointless as overridden by layout
3846          * manager
3847          */
3848         alignPanel.setSize(getSize().width,
3849                 getSize().height - statusBar.getHeight());
3850       }
3851       add(statusBar, BorderLayout.SOUTH);
3852       add(alignPanel, BorderLayout.CENTER);
3853       // and register with the applet so it can pass external API calls to us
3854       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3855               frameHeight);
3856     }
3857   }
3858
3859   /**
3860    * Add the components of this AlignFrame to the applet container.
3861    *
3862    * @param theApplet
3863    */
3864   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3865   {
3866     // ////
3867     // Explicitly build the embedded menu panel for the on-page applet
3868     //
3869     // view cannot be closed if its actually on the page
3870     fileMenu.remove(closeMenuItem);
3871     fileMenu.remove(3); // Remove Separator
3872     // construct embedded menu, using default font
3873     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3874     // and actually add the components to the applet area
3875     theApplet.setLayout(new BorderLayout());
3876     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3877     theApplet.add(statusBar, BorderLayout.SOUTH);
3878     // TODO should size be left to the layout manager?
3879     alignPanel.setSize(theApplet.getSize().width,
3880             theApplet.getSize().height - embeddedMenu.getHeight()
3881                     - statusBar.getHeight());
3882     theApplet.add(alignPanel, BorderLayout.CENTER);
3883     final AlignFrame me = this;
3884     theApplet.addFocusListener(new FocusListener()
3885     {
3886
3887       @Override
3888       public void focusLost(FocusEvent e)
3889       {
3890         if (theApplet.currentAlignFrame == me)
3891         {
3892           theApplet.currentAlignFrame = null;
3893         }
3894       }
3895
3896       @Override
3897       public void focusGained(FocusEvent e)
3898       {
3899         theApplet.currentAlignFrame = me;
3900       }
3901     });
3902     theApplet.validate();
3903   }
3904
3905   /**
3906    * create a new binding between structures in an existing jmol viewer instance
3907    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3908    * this does not open a new Jmol window, or modify the display of the
3909    * structures in the original jmol window. Note This method doesn't work
3910    * without an additional javascript library to exchange messages between the
3911    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3912    *
3913    * @param viewer
3914    *          JmolViewer instance
3915    * @param sequenceIds
3916    *          - sequence Ids to search for associations
3917    */
3918   public SequenceStructureBinding addStructureViewInstance(
3919           Object jmolviewer, String[] sequenceIds)
3920   {
3921     Viewer viewer = null;
3922     try
3923     {
3924       viewer = (Viewer) jmolviewer;
3925     } catch (ClassCastException ex)
3926     {
3927       System.err.println("Unsupported viewer object :"
3928               + jmolviewer.getClass());
3929     }
3930     if (viewer == null)
3931     {
3932       System.err.println("Can't use this object as a structure viewer:"
3933               + jmolviewer.getClass());
3934       return null;
3935     }
3936     SequenceI[] seqs = null;
3937     if (sequenceIds == null || sequenceIds.length == 0)
3938     {
3939       seqs = viewport.getAlignment().getSequencesArray();
3940     }
3941     else
3942     {
3943       Vector sqi = new Vector();
3944       AlignmentI al = viewport.getAlignment();
3945       for (int sid = 0; sid < sequenceIds.length; sid++)
3946       {
3947         SequenceI sq = al.findName(sequenceIds[sid]);
3948         if (sq != null)
3949         {
3950           sqi.addElement(sq);
3951         }
3952       }
3953       if (sqi.size() > 0)
3954       {
3955         seqs = new SequenceI[sqi.size()];
3956         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3957         {
3958           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3959         }
3960       }
3961       else
3962       {
3963         return null;
3964       }
3965     }
3966     AAStructureBindingModel jmv = null;
3967     // TODO: search for a jmv that involves viewer
3968     if (jmv == null)
3969     { // create a new viewer/jalview binding.
3970       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3971     }
3972     return jmv;
3973
3974   }
3975
3976   /**
3977    * bind a pdb file to a sequence in the current view
3978    *
3979    * @param sequenceId
3980    *          - sequenceId within the dataset.
3981    * @param pdbEntryString
3982    *          - the short name for the PDB file
3983    * @param pdbFile
3984    *          - pdb file - either a URL or a valid PDB file.
3985    * @return true if binding was as success TODO: consider making an exception
3986    *         structure for indicating when PDB parsing or sequenceId location
3987    *         fails.
3988    */
3989   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3990           String pdbFile)
3991   {
3992     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3993     boolean needtoadd = false;
3994     if (toaddpdb != null)
3995     {
3996       Vector pdbe = toaddpdb.getAllPDBEntries();
3997       PDBEntry pdbentry = null;
3998       if (pdbe != null && pdbe.size() > 0)
3999       {
4000         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4001         {
4002           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4003           if (!pdbentry.getId().equals(pdbEntryString)
4004                   && !pdbentry.getFile().equals(pdbFile))
4005           {
4006             pdbentry = null;
4007           }
4008           else
4009           {
4010             continue;
4011           }
4012         }
4013       }
4014       if (pdbentry == null)
4015       {
4016         pdbentry = new PDBEntry();
4017         pdbentry.setId(pdbEntryString);
4018         pdbentry.setFile(pdbFile);
4019         needtoadd = true; // add this new entry to sequence.
4020       }
4021       // resolve data source
4022       // TODO: this code should be a refactored to an io package
4023       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4024       if (protocol == null)
4025       {
4026         return false;
4027       }
4028       if (needtoadd)
4029       {
4030         pdbentry.setProperty("protocol", protocol);
4031         toaddpdb.addPDBId(pdbentry);
4032         alignPanel.getStructureSelectionManager()
4033                 .registerPDBEntry(pdbentry);
4034       }
4035     }
4036     return true;
4037   }
4038
4039   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4040   {
4041     if (seqs != null)
4042     {
4043       Vector sequences = new Vector();
4044       for (int i = 0; i < seqs.length; i++)
4045       {
4046         if (seqs[i] != null)
4047         {
4048           sequences.addElement(new Object[] { seqs[i],
4049               (chains != null) ? chains[i] : null });
4050         }
4051       }
4052       seqs = new SequenceI[sequences.size()];
4053       chains = new String[sequences.size()];
4054       for (int i = 0, isize = sequences.size(); i < isize; i++)
4055       {
4056         Object[] oj = (Object[]) sequences.elementAt(i);
4057
4058         seqs[i] = (SequenceI) oj[0];
4059         chains[i] = (String) oj[1];
4060       }
4061     }
4062     return new Object[] { seqs, chains };
4063
4064   }
4065
4066   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4067           SequenceI[] seqs, String[] chains, String protocol)
4068   {
4069     // Scrub any null sequences from the array
4070     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4071     seqs = (SequenceI[]) sqch[0];
4072     chains = (String[]) sqch[1];
4073     if (seqs == null || seqs.length == 0)
4074     {
4075       System.err
4076               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4077     }
4078     if (protocol == null || protocol.trim().length() == 0
4079             || protocol.equals("null"))
4080     {
4081       protocol = (String) pdb.getProperty("protocol");
4082       if (protocol == null)
4083       {
4084         System.err.println("Couldn't work out protocol to open structure: "
4085                 + pdb.getId());
4086         return;
4087       }
4088     }
4089     if (applet.useXtrnalSviewer)
4090     {
4091       // register the association(s) and quit, don't create any windows.
4092       if (StructureSelectionManager.getStructureSelectionManager(applet)
4093               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4094       {
4095         System.err.println("Failed to map " + pdb.getFile() + " ("
4096                 + protocol + ") to any sequences");
4097       }
4098       return;
4099     }
4100     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4101     {
4102       // can only do alignments with Jmol
4103       // find the last jmol window assigned to this alignment
4104       jalview.appletgui.AppletJmol ajm = null, tajm;
4105       Vector jmols = applet
4106               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4107       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4108       {
4109         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4110         if (tajm.ap.alignFrame == this)
4111         {
4112           ajm = tajm;
4113           break;
4114         }
4115       }
4116       if (ajm != null)
4117       {
4118         System.err
4119                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4120         // try and add the pdb structure
4121         // ajm.addS
4122         ajm = null;
4123       }
4124     }
4125     // otherwise, create a new window
4126     if (applet.jmolAvailable)
4127     {
4128       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4129               protocol);
4130       applet.lastFrameX += 40;
4131       applet.lastFrameY += 40;
4132     }
4133     else
4134     {
4135       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4136     }
4137
4138   }
4139
4140   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4141           SequenceI[][] seqs, String[][] chains, String[] protocols)
4142   {
4143     // TODO Auto-generated method stub
4144     System.err.println("Aligned Structure View: Not yet implemented.");
4145   }
4146
4147   /**
4148    * modify the current selection, providing the user has not made a selection
4149    * already.
4150    *
4151    * @param sel
4152    *          - sequences from this alignment
4153    * @param csel
4154    *          - columns to be selected on the alignment
4155    */
4156   public void select(SequenceGroup sel, ColumnSelection csel)
4157   {
4158     alignPanel.seqPanel.selection(sel, csel, null);
4159   }
4160
4161   public void scrollTo(int row, int column)
4162   {
4163     alignPanel.seqPanel.scrollTo(row, column);
4164   }
4165
4166   public void scrollToRow(int row)
4167   {
4168     alignPanel.seqPanel.scrollToRow(row);
4169   }
4170
4171   public void scrollToColumn(int column)
4172   {
4173     alignPanel.seqPanel.scrollToColumn(column);
4174   }
4175
4176   /**
4177    * @return the alignments unique ID.
4178    */
4179   public String getSequenceSetId()
4180   {
4181     return viewport.getSequenceSetId();
4182   }
4183
4184   /**
4185    * Load the (T-Coffee) score file from the specified url
4186    *
4187    * @param source
4188    *          File/URL/T-COFFEE score file contents
4189    * @throws IOException
4190    * @return true if alignment was annotated with data from source
4191    */
4192   public boolean loadScoreFile(String source) throws IOException
4193   {
4194
4195     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4196             AppletFormatAdapter.checkProtocol(source));
4197     if (!file.isValid())
4198     {
4199       // TODO: raise dialog for gui
4200       System.err.println("Problems parsing T-Coffee scores: "
4201               + file.getWarningMessage());
4202       System.err.println("Origin was:\n" + source);
4203       return false;
4204     }
4205
4206     /*
4207      * check that the score matrix matches the alignment dimensions
4208      */
4209     AlignmentI aln;
4210     if ((aln = viewport.getAlignment()) != null
4211             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4212                     .getWidth()))
4213     {
4214       // TODO: raise a dialog box here rather than bomb out.
4215       System.err
4216               .println("The scores matrix does not match the alignment dimensions");
4217
4218     }
4219
4220     // TODO add parameter to indicate if matching should be done
4221     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4222     {
4223       alignPanel.fontChanged();
4224       tcoffeeColour.setEnabled(true);
4225       // switch to this color
4226       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4227       return true;
4228     }
4229     else
4230     {
4231       System.err.println("Problems resolving T-Coffee scores:");
4232       if (file.getWarningMessage() != null)
4233       {
4234         System.err.println(file.getWarningMessage());
4235       }
4236     }
4237     return false;
4238   }
4239
4240   public SplitFrame getSplitFrame()
4241   {
4242     return this.splitFrame;
4243   }
4244
4245   public void setSplitFrame(SplitFrame sf)
4246   {
4247     this.splitFrame = sf;
4248   }
4249
4250   // may not need this
4251   @Override
4252   public void setShowSeqFeatures(boolean b)
4253   {
4254     // showSeqFeatures.setSelected(b);
4255     viewport.setShowSequenceFeatures(b);
4256
4257   }
4258
4259   @Override
4260   public void setMenusForViewport()
4261   {
4262     // setMenusFromViewport(viewport);
4263
4264   }
4265
4266   @Override
4267   public void refreshFeatureUI(boolean enableIfNecessary)
4268   {
4269     if (enableIfNecessary)
4270     {
4271       sequenceFeatures.setState(true);
4272       alignPanel.av.setShowSequenceFeatures(true);
4273     }
4274   }
4275
4276   @Override
4277   public FeatureSettingsControllerI getFeatureSettingsUI()
4278   {
4279     return alignPanel.av.featureSettings;
4280   }
4281
4282 }