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