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.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.FileFormatI;
  56 import jalview.io.FileFormats;
  57 import jalview.io.TCoffeeScoreFile;
  58 import jalview.schemes.Blosum62ColourScheme;
  59 import jalview.schemes.BuriedColourScheme;
  60 import jalview.schemes.ClustalxColourScheme;
  61 import jalview.schemes.ColourSchemeI;
  62 import jalview.schemes.HelixColourScheme;
  63 import jalview.schemes.HydrophobicColourScheme;
  64 import jalview.schemes.NucleotideColourScheme;
  65 import jalview.schemes.PIDColourScheme;
  66 import jalview.schemes.PurinePyrimidineColourScheme;
  67 import jalview.schemes.RNAHelicesColour;
  68 import jalview.schemes.StrandColourScheme;
  69 import jalview.schemes.TCoffeeColourScheme;
  70 import jalview.schemes.TaylorColourScheme;
  71 import jalview.schemes.TurnColourScheme;
  72 import jalview.schemes.ZappoColourScheme;
  73 import jalview.structure.StructureSelectionManager;
  74 import jalview.structures.models.AAStructureBindingModel;
  75 import jalview.util.MappingUtils;
  76 import jalview.util.MessageManager;
  77 import jalview.viewmodel.AlignmentViewport;
  78
  79 import java.awt.BorderLayout;
  80 import java.awt.Canvas;
  81 import java.awt.CheckboxMenuItem;
  82 import java.awt.Color;
  83 import java.awt.FlowLayout;
  84 import java.awt.Font;
  85 import java.awt.FontMetrics;
  86 import java.awt.Frame;
  87 import java.awt.Graphics;
  88 import java.awt.Label;
  89 import java.awt.Menu;
  90 import java.awt.MenuBar;
  91 import java.awt.MenuItem;
  92 import java.awt.Panel;
  93 import java.awt.event.ActionEvent;
  94 import java.awt.event.ActionListener;
  95 import java.awt.event.FocusEvent;
  96 import java.awt.event.FocusListener;
  97 import java.awt.event.ItemEvent;
  98 import java.awt.event.ItemListener;
  99 import java.awt.event.KeyEvent;
 100 import java.awt.event.KeyListener;
 101 import java.awt.event.WindowAdapter;
 102 import java.awt.event.WindowEvent;
 103 import java.io.IOException;
 104 import java.net.URL;
 105 import java.net.URLEncoder;
 106 import java.util.Arrays;
 107 import java.util.Deque;
 108 import java.util.HashMap;
 109 import java.util.List;
 110 import java.util.Map;
 111 import java.util.StringTokenizer;
 112 import java.util.Vector;
 113
 114 import org.jmol.viewer.Viewer;
 115
 116 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 117         ItemListener, KeyListener, AlignViewControllerGuiI
 118 {
 119   public AlignViewControllerI avc;
 120
 121   public AlignmentPanel alignPanel;
 122
 123   public AlignViewport viewport;
 124
 125   // width and height may be overridden by applet parameters
 126   int frameWidth = 700;
 127
 128   int frameHeight = 500;
 129
 130   String jalviewServletURL;
 131
 132   /*
 133    * Flag for showing autocalculated consensus above or below other consensus
 134    * rows
 135    */
 136   private boolean showAutoCalculatedAbove;
 137
 138   private SequenceAnnotationOrder annotationSortOrder;
 139
 140   /**
 141    * Constructor that creates the frame and adds it to the display.
 142    *
 143    * @param al
 144    * @param applet
 145    * @param title
 146    * @param embedded
 147    */
 148   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 149           boolean embedded)
 150   {
 151     this(al, applet, title, embedded, true);
 152   }
 153
 154   /**
 155    * Constructor that optionally allows the frame to be displayed or only
 156    * created.
 157    *
 158    * @param al
 159    * @param applet
 160    * @param title
 161    * @param embedded
 162    * @param addToDisplay
 163    */
 164   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 165           boolean embedded, boolean addToDisplay)
 166   {
 167     this(al, null, null, applet, title, embedded, addToDisplay);
 168   }
 169
 170   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 171           ColumnSelection columnSelection, JalviewLite applet,
 172           String title, boolean embedded)
 173   {
 174     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 175   }
 176
 177   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 178           ColumnSelection columnSelection, JalviewLite applet,
 179           String title, boolean embedded, boolean addToDisplay)
 180   {
 181     if (applet != null)
 182     {
 183       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 184     }
 185
 186     try
 187     {
 188       jbInit();
 189     } catch (Exception ex)
 190     {
 191       ex.printStackTrace();
 192     }
 193     // need to get window geometry before we calculate alignment layout
 194     if (applet != null)
 195     {
 196       String param;
 197       try
 198       {
 199         param = applet.getParameter("windowWidth");
 200         if (param != null)
 201         {
 202           int width = Integer.parseInt(param);
 203           frameWidth = width;
 204         }
 205         param = applet.getParameter("windowHeight");
 206         if (param != null)
 207         {
 208           int height = Integer.parseInt(param);
 209           frameHeight = height;
 210         }
 211       } catch (Exception ex)
 212       {
 213       }
 214     }
 215     viewport = new AlignViewport(al, applet);
 216
 217     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 218     {
 219       viewport.hideSequence(hiddenSeqs);
 220     }
 221     if (columnSelection != null)
 222     {
 223       viewport.setColumnSelection(columnSelection);
 224     }
 225     viewport.setScaleAboveWrapped(scaleAbove.getState());
 226
 227     alignPanel = new AlignmentPanel(this, viewport);
 228     avc = new jalview.controller.AlignViewController(this, viewport,
 229             alignPanel);
 230     viewport.updateConservation(alignPanel);
 231     viewport.updateConsensus(alignPanel);
 232
 233     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 234     followMouseOverFlag.setState(viewport.isFollowHighlight());
 235     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 236     showGroupConservation.setState(viewport.isShowGroupConservation());
 237     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 238     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 239     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 240     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 241     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 242     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 243     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 244     showAlignmentAnnotations.setState(true);
 245     showSequenceAnnotations.setState(false);
 246
 247     seqLimits.setState(viewport.getShowJVSuffix());
 248
 249     if (applet != null)
 250     {
 251       String param = applet.getParameter("sortBy");
 252       if (param != null)
 253       {
 254         if (param.equalsIgnoreCase("Id"))
 255         {
 256           sortIDMenuItem_actionPerformed();
 257         }
 258         else if (param.equalsIgnoreCase("Pairwise Identity"))
 259         {
 260           sortPairwiseMenuItem_actionPerformed();
 261         }
 262         else if (param.equalsIgnoreCase("Length"))
 263         {
 264           sortLengthMenuItem_actionPerformed();
 265         }
 266       }
 267
 268       param = applet.getParameter("wrap");
 269       if (param != null)
 270       {
 271         if (param.equalsIgnoreCase("true"))
 272         {
 273           wrapMenuItem.setState(true);
 274           wrapMenuItem_actionPerformed();
 275         }
 276       }
 277       param = applet.getParameter("centrecolumnlabels");
 278       if (param != null)
 279       {
 280         centreColumnLabelFlag.setState(true);
 281         centreColumnLabelFlag_stateChanged();
 282       }
 283
 284     }
 285     if (viewport.getAlignment().isNucleotide())
 286     {
 287       viewport.updateStrucConsensus(alignPanel);
 288       if (viewport.getAlignment().hasRNAStructure())
 289       {
 290         RNAHelixColour.setEnabled(true);
 291       }
 292       else
 293       {
 294         RNAHelixColour.setEnabled(false);
 295       }
 296     }
 297     else
 298     {
 299       RNAHelixColour.setEnabled(false);
 300       purinePyrimidineColour.setEnabled(false);
 301       nucleotideColour.setEnabled(false);
 302     }
 303     // Some JVMS send keyevents to Top frame or lowest panel,
 304     // Havent worked out why yet. So add to both this frame and seqCanvas for
 305     // now
 306     this.addKeyListener(this);
 307     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 308     alignPanel.idPanel.idCanvas.addKeyListener(this);
 309     alignPanel.scalePanel.addKeyListener(this);
 310     alignPanel.annotationPanel.addKeyListener(this);
 311     alignPanel.annotationPanelHolder.addKeyListener(this);
 312     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 313     alignPanel.alabels.addKeyListener(this);
 314
 315     setAnnotationsVisibility();
 316
 317     if (addToDisplay)
 318     {
 319       addToDisplay(embedded);
 320     }
 321   }
 322
 323   /**
 324    * @param embedded
 325    */
 326   public void addToDisplay(boolean embedded)
 327   {
 328     createAlignFrameWindow(embedded);
 329     validate();
 330     alignPanel.adjustAnnotationHeight();
 331     alignPanel.paintAlignment(true);
 332   }
 333
 334   public AlignViewport getAlignViewport()
 335   {
 336     return viewport;
 337   }
 338
 339   public SeqCanvas getSeqcanvas()
 340   {
 341     return alignPanel.seqPanel.seqCanvas;
 342   }
 343
 344   /**
 345    * Load a features file onto the alignment
 346    *
 347    * @param file
 348    *          file URL, content, or other resolvable path
 349    * @param type
 350    *          is protocol for accessing data referred to by file
 351    */
 352
 353   public boolean parseFeaturesFile(String file, DataSourceType type)
 354   {
 355     return parseFeaturesFile(file, type, true);
 356   }
 357
 358   /**
 359    * Load a features file onto the alignment
 360    *
 361    * @param file
 362    *          file URL, content, or other resolvable path
 363    * @param sourceType
 364    *          is protocol for accessing data referred to by file
 365    * @param autoenabledisplay
 366    *          when true, display features flag will be automatically enabled if
 367    *          features are loaded
 368    * @return true if data parsed as a features file
 369    */
 370   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 371           boolean autoenabledisplay)
 372   {
 373     boolean featuresFile = false;
 374     try
 375     {
 376       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 377               .getFeatureRenderer().getFeatureColours();
 378       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 379               "relaxedidmatch", false);
 380       featuresFile = new FeaturesFile(file, sourceType).parse(
 381               viewport.getAlignment(), colours, true, relaxedIdMatching);
 382     } catch (Exception ex)
 383     {
 384       ex.printStackTrace();
 385     }
 386
 387     if (featuresFile)
 388     {
 389       if (autoenabledisplay)
 390       {
 391         viewport.setShowSequenceFeatures(true);
 392         sequenceFeatures.setState(true);
 393       }
 394       if (alignPanel.seqPanel.seqCanvas.fr != null)
 395       {
 396         // update the min/max ranges where necessary
 397         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 398       }
 399       if (viewport.featureSettings != null)
 400       {
 401         viewport.featureSettings.refreshTable();
 402       }
 403       alignPanel.paintAlignment(true);
 404       statusBar.setText(MessageManager
 405               .getString("label.successfully_added_features_alignment"));
 406     }
 407     return featuresFile;
 408   }
 409
 410   @Override
 411   public void keyPressed(KeyEvent evt)
 412   {
 413     if (viewport.cursorMode
 414             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 415                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 416                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 417             && Character.isDigit(evt.getKeyChar()))
 418     {
 419       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 420     }
 421
 422     switch (evt.getKeyCode())
 423     {
 424     case 27: // escape key
 425       deselectAllSequenceMenuItem_actionPerformed();
 426
 427       alignPanel.alabels.cancelDrag();
 428       break;
 429     case KeyEvent.VK_X:
 430       if (evt.isControlDown() || evt.isMetaDown())
 431       {
 432         cut_actionPerformed();
 433       }
 434       break;
 435     case KeyEvent.VK_C:
 436       if (viewport.cursorMode && !evt.isControlDown())
 437       {
 438         alignPanel.seqPanel.setCursorColumn();
 439       }
 440       if (evt.isControlDown() || evt.isMetaDown())
 441       {
 442         copy_actionPerformed();
 443       }
 444       break;
 445     case KeyEvent.VK_V:
 446       if (evt.isControlDown())
 447       {
 448         paste(evt.isShiftDown());
 449       }
 450       break;
 451     case KeyEvent.VK_A:
 452       if (evt.isControlDown() || evt.isMetaDown())
 453       {
 454         selectAllSequenceMenuItem_actionPerformed();
 455       }
 456       break;
 457     case KeyEvent.VK_DOWN:
 458       if (viewport.cursorMode)
 459       {
 460         alignPanel.seqPanel.moveCursor(0, 1);
 461       }
 462       else
 463       {
 464         moveSelectedSequences(false);
 465       }
 466       break;
 467
 468     case KeyEvent.VK_UP:
 469       if (viewport.cursorMode)
 470       {
 471         alignPanel.seqPanel.moveCursor(0, -1);
 472       }
 473       else
 474       {
 475         moveSelectedSequences(true);
 476       }
 477       break;
 478
 479     case KeyEvent.VK_LEFT:
 480       if (evt.isAltDown() || !viewport.cursorMode)
 481       {
 482         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 483       }
 484       else
 485       {
 486         alignPanel.seqPanel.moveCursor(-1, 0);
 487       }
 488       break;
 489
 490     case KeyEvent.VK_RIGHT:
 491       if (evt.isAltDown() || !viewport.cursorMode)
 492       {
 493         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 494       }
 495       else
 496       {
 497         alignPanel.seqPanel.moveCursor(1, 0);
 498       }
 499       break;
 500
 501     case KeyEvent.VK_SPACE:
 502       if (viewport.cursorMode)
 503       {
 504         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 505                 || evt.isShiftDown() || evt.isAltDown());
 506       }
 507       break;
 508
 509     case KeyEvent.VK_DELETE:
 510     case KeyEvent.VK_BACK_SPACE:
 511       if (viewport.cursorMode)
 512       {
 513         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 514                 || evt.isShiftDown() || evt.isAltDown());
 515       }
 516       else
 517       {
 518         cut_actionPerformed();
 519         alignPanel.seqPanel.seqCanvas.repaint();
 520       }
 521       break;
 522
 523     case KeyEvent.VK_S:
 524       if (viewport.cursorMode)
 525       {
 526         alignPanel.seqPanel.setCursorRow();
 527       }
 528       break;
 529     case KeyEvent.VK_P:
 530       if (viewport.cursorMode)
 531       {
 532         alignPanel.seqPanel.setCursorPosition();
 533       }
 534       break;
 535
 536     case KeyEvent.VK_ENTER:
 537     case KeyEvent.VK_COMMA:
 538       if (viewport.cursorMode)
 539       {
 540         alignPanel.seqPanel.setCursorRowAndColumn();
 541       }
 542       break;
 543
 544     case KeyEvent.VK_Q:
 545       if (viewport.cursorMode)
 546       {
 547         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 548       }
 549       break;
 550     case KeyEvent.VK_M:
 551       if (viewport.cursorMode)
 552       {
 553         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 554       }
 555       break;
 556
 557     case KeyEvent.VK_F2:
 558       viewport.cursorMode = !viewport.cursorMode;
 559       statusBar.setText(MessageManager.formatMessage(
 560               "label.keyboard_editing_mode",
 561               new String[] { (viewport.cursorMode ? "on" : "off") }));
 562       if (viewport.cursorMode)
 563       {
 564         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 565         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 566       }
 567       break;
 568
 569     case KeyEvent.VK_F:
 570       if (evt.isControlDown())
 571       {
 572         findMenuItem_actionPerformed();
 573       }
 574       break;
 575
 576     case KeyEvent.VK_H:
 577     {
 578       boolean toggleSeqs = !evt.isControlDown();
 579       boolean toggleCols = !evt.isShiftDown();
 580       toggleHiddenRegions(toggleSeqs, toggleCols);
 581       break;
 582     }
 583
 584     case KeyEvent.VK_PAGE_UP:
 585       if (viewport.getWrapAlignment())
 586       {
 587         alignPanel.scrollUp(true);
 588       }
 589       else
 590       {
 591         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 592                 - viewport.endSeq + viewport.startSeq);
 593       }
 594       break;
 595
 596     case KeyEvent.VK_PAGE_DOWN:
 597       if (viewport.getWrapAlignment())
 598       {
 599         alignPanel.scrollUp(false);
 600       }
 601       else
 602       {
 603         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 604                 + viewport.endSeq - viewport.startSeq);
 605       }
 606       break;
 607
 608     case KeyEvent.VK_Z:
 609       if (evt.isControlDown())
 610       {
 611         undoMenuItem_actionPerformed();
 612       }
 613       break;
 614
 615     case KeyEvent.VK_Y:
 616       if (evt.isControlDown())
 617       {
 618         redoMenuItem_actionPerformed();
 619       }
 620       break;
 621
 622     case KeyEvent.VK_L:
 623       if (evt.isControlDown())
 624       {
 625         trimAlignment(true);
 626       }
 627       break;
 628
 629     case KeyEvent.VK_R:
 630       if (evt.isControlDown())
 631       {
 632         trimAlignment(false);
 633       }
 634       break;
 635
 636     case KeyEvent.VK_E:
 637       if (evt.isControlDown())
 638       {
 639         if (evt.isShiftDown())
 640         {
 641           this.removeAllGapsMenuItem_actionPerformed();
 642         }
 643         else
 644         {
 645           removeGappedColumnMenuItem_actionPerformed();
 646         }
 647       }
 648       break;
 649     case KeyEvent.VK_I:
 650       if (evt.isControlDown())
 651       {
 652         if (evt.isAltDown())
 653         {
 654           invertColSel_actionPerformed();
 655         }
 656         else
 657         {
 658           invertSequenceMenuItem_actionPerformed();
 659         }
 660       }
 661       break;
 662
 663     case KeyEvent.VK_G:
 664       if (evt.isControlDown())
 665       {
 666         if (evt.isShiftDown())
 667         {
 668           this.unGroup_actionPerformed();
 669         }
 670         else
 671         {
 672           this.createGroup_actionPerformed();
 673         }
 674       }
 675       break;
 676
 677     case KeyEvent.VK_U:
 678       if (evt.isControlDown())
 679       {
 680         this.deleteGroups_actionPerformed();
 681       }
 682       break;
 683
 684     case KeyEvent.VK_T:
 685       if (evt.isControlDown())
 686       {
 687         newView(null);
 688       }
 689       break;
 690
 691     }
 692     alignPanel.paintAlignment(true);
 693   }
 694
 695   /**
 696    * called by key handler and the hide all/show all menu items
 697    *
 698    * @param toggleSeqs
 699    * @param toggleCols
 700    */
 701   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 702   {
 703     boolean hide = false;
 704     SequenceGroup sg = viewport.getSelectionGroup();
 705     if (!toggleSeqs && !toggleCols)
 706     {
 707       // Hide everything by the current selection - this is a hack - we do the
 708       // invert and then hide
 709       // first check that there will be visible columns after the invert.
 710       if (viewport.hasSelectedColumns()
 711               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 712                       .getEndRes()))
 713       {
 714         // now invert the sequence set, if required - empty selection implies
 715         // that no hiding is required.
 716         if (sg != null)
 717         {
 718           invertSequenceMenuItem_actionPerformed();
 719           sg = viewport.getSelectionGroup();
 720           toggleSeqs = true;
 721
 722         }
 723         viewport.expandColSelection(sg, true);
 724         // finally invert the column selection and get the new sequence
 725         // selection and indicate it should be hidden.
 726         invertColSel_actionPerformed();
 727         toggleCols = true;
 728       }
 729     }
 730
 731     if (toggleSeqs)
 732     {
 733       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 734       {
 735         hide = true;
 736         viewport.hideAllSelectedSeqs();
 737       }
 738       else if (!(toggleCols && viewport.hasSelectedColumns()))
 739       {
 740         viewport.showAllHiddenSeqs();
 741       }
 742     }
 743
 744     if (toggleCols)
 745     {
 746       if (viewport.hasSelectedColumns())
 747       {
 748         viewport.hideSelectedColumns();
 749         if (!toggleSeqs)
 750         {
 751           viewport.setSelectionGroup(sg);
 752         }
 753       }
 754       else if (!hide)
 755       {
 756         viewport.showAllHiddenColumns();
 757       }
 758       viewport.sendSelection();
 759     }
 760   }
 761
 762   @Override
 763   public void keyReleased(KeyEvent evt)
 764   {
 765   }
 766
 767   @Override
 768   public void keyTyped(KeyEvent evt)
 769   {
 770   }
 771
 772   @Override
 773   public void itemStateChanged(ItemEvent evt)
 774   {
 775     final Object source = evt.getSource();
 776     if (source == displayNonconservedMenuItem)
 777     {
 778       displayNonconservedMenuItem_actionPerformed();
 779     }
 780     else if (source == colourTextMenuItem)
 781     {
 782       colourTextMenuItem_actionPerformed();
 783     }
 784     else if (source == wrapMenuItem)
 785     {
 786       wrapMenuItem_actionPerformed();
 787     }
 788     else if (source == scaleAbove)
 789     {
 790       viewport.setScaleAboveWrapped(scaleAbove.getState());
 791     }
 792     else if (source == scaleLeft)
 793     {
 794       viewport.setScaleLeftWrapped(scaleLeft.getState());
 795     }
 796     else if (source == scaleRight)
 797     {
 798       viewport.setScaleRightWrapped(scaleRight.getState());
 799     }
 800     else if (source == seqLimits)
 801     {
 802       seqLimits_itemStateChanged();
 803     }
 804     else if (source == viewBoxesMenuItem)
 805     {
 806       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 807     }
 808     else if (source == viewTextMenuItem)
 809     {
 810       viewport.setShowText(viewTextMenuItem.getState());
 811     }
 812     else if (source == renderGapsMenuItem)
 813     {
 814       viewport.setRenderGaps(renderGapsMenuItem.getState());
 815     }
 816     else if (source == annotationPanelMenuItem)
 817     {
 818       boolean showAnnotations = annotationPanelMenuItem.getState();
 819       showAlignmentAnnotations.setEnabled(showAnnotations);
 820       showSequenceAnnotations.setEnabled(showAnnotations);
 821       viewport.setShowAnnotation(showAnnotations);
 822       alignPanel.setAnnotationVisible(showAnnotations);
 823     }
 824     else if (source == sequenceFeatures)
 825     {
 826       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 827       alignPanel.seqPanel.seqCanvas.repaint();
 828     }
 829     else if (source == showAlignmentAnnotations)
 830     {
 831       setAnnotationsVisibility();
 832     }
 833     else if (source == showSequenceAnnotations)
 834     {
 835       setAnnotationsVisibility();
 836     }
 837     else if (source == sortAnnBySequence)
 838     {
 839       boolean newState = sortAnnBySequence.getState();
 840       sortAnnByLabel.setState(false);
 841       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 842               : SequenceAnnotationOrder.NONE);
 843       setViewportAnnotationOrder();
 844     }
 845     else if (source == sortAnnByLabel)
 846     {
 847       boolean newState = sortAnnByLabel.getState();
 848       sortAnnBySequence.setState(false);
 849       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 850               : SequenceAnnotationOrder.NONE);
 851       setViewportAnnotationOrder();
 852     }
 853     else if (source == showAutoFirst)
 854     {
 855       showAutoLast.setState(!showAutoFirst.getState());
 856       setShowAutoCalculatedAbove(showAutoFirst.getState());
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == showAutoLast)
 860     {
 861       showAutoFirst.setState(!showAutoLast.getState());
 862       setShowAutoCalculatedAbove(showAutoFirst.getState());
 863       setViewportAnnotationOrder();
 864     }
 865     else if (source == conservationMenuItem)
 866     {
 867       conservationMenuItem_actionPerformed();
 868     }
 869     else if (source == abovePIDThreshold)
 870     {
 871       abovePIDThreshold_actionPerformed();
 872     }
 873     else if (source == applyToAllGroups)
 874     {
 875       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 876     }
 877     else if (source == autoCalculate)
 878     {
 879       viewport.autoCalculateConsensus = autoCalculate.getState();
 880     }
 881     else if (source == sortByTree)
 882     {
 883       viewport.sortByTree = sortByTree.getState();
 884     }
 885     else if (source == this.centreColumnLabelFlag)
 886     {
 887       centreColumnLabelFlag_stateChanged();
 888     }
 889     else if (source == this.followMouseOverFlag)
 890     {
 891       mouseOverFlag_stateChanged();
 892     }
 893     else if (source == showGroupConsensus)
 894     {
 895       showGroupConsensus_actionPerformed();
 896     }
 897     else if (source == showGroupConservation)
 898     {
 899       showGroupConservation_actionPerformed();
 900     }
 901     else if (source == showSequenceLogo)
 902     {
 903       showSequenceLogo_actionPerformed();
 904     }
 905     else if (source == normSequenceLogo)
 906     {
 907       normSequenceLogo_actionPerformed();
 908     }
 909     else if (source == showConsensusHistogram)
 910     {
 911       showConsensusHistogram_actionPerformed();
 912     }
 913     else if (source == applyAutoAnnotationSettings)
 914     {
 915       applyAutoAnnotationSettings_actionPerformed();
 916     }
 917     alignPanel.paintAlignment(true);
 918   }
 919
 920   /**
 921    * Set the visibility state of sequence-related and/or alignment-related
 922    * annotations depending on checkbox selections, and repaint.
 923    *
 924    * @param visible
 925    */
 926   private void setAnnotationsVisibility()
 927   {
 928     boolean showForAlignment = showAlignmentAnnotations.getState();
 929     boolean showForSequences = showSequenceAnnotations.getState();
 930     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 931     {
 932       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 933               .getAlignmentAnnotation())
 934       {
 935         boolean visible = (aa.sequenceRef == null ? showForAlignment
 936                 : showForSequences);
 937         aa.visible = visible;
 938       }
 939     }
 940     alignPanel.validateAnnotationDimensions(true);
 941     validate();
 942     repaint();
 943   }
 944
 945   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 946   {
 947     this.annotationSortOrder = order;
 948   }
 949
 950   /**
 951    * Set flags on the viewport that control annotation ordering
 952    */
 953   private void setViewportAnnotationOrder()
 954   {
 955     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 956     this.alignPanel.av
 957             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 958   }
 959
 960   private void setShowAutoCalculatedAbove(boolean showAbove)
 961   {
 962     this.showAutoCalculatedAbove = showAbove;
 963   }
 964
 965   private void mouseOverFlag_stateChanged()
 966   {
 967     viewport.setFollowHighlight(followMouseOverFlag.getState());
 968     // TODO: could kick the scrollTo mechanism to reset view for current
 969     // searchresults.
 970   }
 971
 972   private void centreColumnLabelFlag_stateChanged()
 973   {
 974     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 975     this.alignPanel.annotationPanel.repaint();
 976   }
 977
 978   @Override
 979   public void actionPerformed(ActionEvent evt)
 980   {
 981     viewport.applet.currentAlignFrame = this;
 982
 983     Object source = evt.getSource();
 984
 985     if (source == inputText)
 986     {
 987       inputText_actionPerformed();
 988     }
 989     else if (source == loadTree)
 990     {
 991       loadTree_actionPerformed();
 992     }
 993     else if (source == loadApplication)
 994     {
 995       launchFullApplication();
 996     }
 997     else if (source == loadAnnotations)
 998     {
 999       loadAnnotations();
1000     }
1001     else if (source == outputAnnotations)
1002     {
1003       outputAnnotations(true);
1004     }
1005     else if (source == outputFeatures)
1006     {
1007       outputFeatures(true, "Jalview");
1008     }
1009     else if (source == closeMenuItem)
1010     {
1011       closeMenuItem_actionPerformed();
1012     }
1013     else if (source == copy)
1014     {
1015       copy_actionPerformed();
1016     }
1017     else if (source == undoMenuItem)
1018     {
1019       undoMenuItem_actionPerformed();
1020     }
1021     else if (source == redoMenuItem)
1022     {
1023       redoMenuItem_actionPerformed();
1024     }
1025     else if (source == inputText)
1026     {
1027       inputText_actionPerformed();
1028     }
1029     else if (source == closeMenuItem)
1030     {
1031       closeMenuItem_actionPerformed();
1032     }
1033     else if (source == undoMenuItem)
1034     {
1035       undoMenuItem_actionPerformed();
1036     }
1037     else if (source == redoMenuItem)
1038     {
1039       redoMenuItem_actionPerformed();
1040     }
1041     else if (source == copy)
1042     {
1043       copy_actionPerformed();
1044     }
1045     else if (source == pasteNew)
1046     {
1047       pasteNew_actionPerformed();
1048     }
1049     else if (source == pasteThis)
1050     {
1051       pasteThis_actionPerformed();
1052     }
1053     else if (source == cut)
1054     {
1055       cut_actionPerformed();
1056     }
1057     else if (source == delete)
1058     {
1059       delete_actionPerformed();
1060     }
1061     else if (source == grpsFromSelection)
1062     {
1063       makeGrpsFromSelection_actionPerformed();
1064     }
1065     else if (source == deleteGroups)
1066     {
1067       deleteGroups_actionPerformed();
1068     }
1069     else if (source == selectAllSequenceMenuItem)
1070     {
1071       selectAllSequenceMenuItem_actionPerformed();
1072     }
1073     else if (source == deselectAllSequenceMenuItem)
1074     {
1075       deselectAllSequenceMenuItem_actionPerformed();
1076     }
1077     else if (source == invertSequenceMenuItem)
1078     {
1079       invertSequenceMenuItem_actionPerformed();
1080       // uncomment to slave sequence selections in split frame
1081       // viewport.sendSelection();
1082     }
1083     else if (source == invertColSel)
1084     {
1085       viewport.invertColumnSelection();
1086       alignPanel.paintAlignment(true);
1087       viewport.sendSelection();
1088     }
1089     else if (source == remove2LeftMenuItem)
1090     {
1091       trimAlignment(true);
1092     }
1093     else if (source == remove2RightMenuItem)
1094     {
1095       trimAlignment(false);
1096     }
1097     else if (source == removeGappedColumnMenuItem)
1098     {
1099       removeGappedColumnMenuItem_actionPerformed();
1100     }
1101     else if (source == removeAllGapsMenuItem)
1102     {
1103       removeAllGapsMenuItem_actionPerformed();
1104     }
1105     else if (source == findMenuItem)
1106     {
1107       findMenuItem_actionPerformed();
1108     }
1109     else if (source == font)
1110     {
1111       new FontChooser(alignPanel);
1112     }
1113     else if (source == newView)
1114     {
1115       newView(null);
1116     }
1117     else if (source == showColumns)
1118     {
1119       viewport.showAllHiddenColumns();
1120       alignPanel.paintAlignment(true);
1121       viewport.sendSelection();
1122     }
1123     else if (source == showSeqs)
1124     {
1125       viewport.showAllHiddenSeqs();
1126       alignPanel.paintAlignment(true);
1127       // uncomment if we want to slave sequence selections in split frame
1128       // viewport.sendSelection();
1129     }
1130     else if (source == hideColumns)
1131     {
1132       viewport.hideSelectedColumns();
1133       alignPanel.paintAlignment(true);
1134       viewport.sendSelection();
1135     }
1136     else if (source == hideSequences
1137             && viewport.getSelectionGroup() != null)
1138     {
1139       viewport.hideAllSelectedSeqs();
1140       alignPanel.paintAlignment(true);
1141       // uncomment if we want to slave sequence selections in split frame
1142       // viewport.sendSelection();
1143     }
1144     else if (source == hideAllButSelection)
1145     {
1146       toggleHiddenRegions(false, false);
1147       alignPanel.paintAlignment(true);
1148       viewport.sendSelection();
1149     }
1150     else if (source == hideAllSelection)
1151     {
1152       SequenceGroup sg = viewport.getSelectionGroup();
1153       viewport.expandColSelection(sg, false);
1154       viewport.hideAllSelectedSeqs();
1155       viewport.hideSelectedColumns();
1156       alignPanel.paintAlignment(true);
1157       viewport.sendSelection();
1158     }
1159     else if (source == showAllHidden)
1160     {
1161       viewport.showAllHiddenColumns();
1162       viewport.showAllHiddenSeqs();
1163       alignPanel.paintAlignment(true);
1164       viewport.sendSelection();
1165     }
1166     else if (source == showGroupConsensus)
1167     {
1168       showGroupConsensus_actionPerformed();
1169     }
1170     else if (source == showGroupConservation)
1171     {
1172       showGroupConservation_actionPerformed();
1173     }
1174     else if (source == showSequenceLogo)
1175     {
1176       showSequenceLogo_actionPerformed();
1177     }
1178     else if (source == normSequenceLogo)
1179     {
1180       normSequenceLogo_actionPerformed();
1181     }
1182     else if (source == showConsensusHistogram)
1183     {
1184       showConsensusHistogram_actionPerformed();
1185     }
1186     else if (source == applyAutoAnnotationSettings)
1187     {
1188       applyAutoAnnotationSettings_actionPerformed();
1189     }
1190     else if (source == featureSettings)
1191     {
1192       new FeatureSettings(alignPanel);
1193     }
1194     else if (source == alProperties)
1195     {
1196       StringBuffer contents = new jalview.io.AlignmentProperties(
1197               viewport.getAlignment()).formatAsString();
1198       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1199       cap.setText(contents.toString());
1200       Frame frame = new Frame();
1201       frame.add(cap);
1202       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1203               "label.alignment_properties", new String[] { getTitle() }),
1204               400, 250);
1205     }
1206     else if (source == overviewMenuItem)
1207     {
1208       overviewMenuItem_actionPerformed();
1209     }
1210     else if (source == noColourmenuItem)
1211     {
1212       changeColour(null);
1213     }
1214     else if (source == clustalColour)
1215     {
1216       abovePIDThreshold.setState(false);
1217       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1218     }
1219     else if (source == zappoColour)
1220     {
1221       changeColour(new ZappoColourScheme());
1222     }
1223     else if (source == taylorColour)
1224     {
1225       changeColour(new TaylorColourScheme());
1226     }
1227     else if (source == hydrophobicityColour)
1228     {
1229       changeColour(new HydrophobicColourScheme());
1230     }
1231     else if (source == helixColour)
1232     {
1233       changeColour(new HelixColourScheme());
1234     }
1235     else if (source == strandColour)
1236     {
1237       changeColour(new StrandColourScheme());
1238     }
1239     else if (source == turnColour)
1240     {
1241       changeColour(new TurnColourScheme());
1242     }
1243     else if (source == buriedColour)
1244     {
1245       changeColour(new BuriedColourScheme());
1246     }
1247     else if (source == nucleotideColour)
1248     {
1249       changeColour(new NucleotideColourScheme());
1250     }
1251     else if (source == purinePyrimidineColour)
1252     {
1253       changeColour(new PurinePyrimidineColourScheme());
1254     }
1255     // else if (source == RNAInteractionColour)
1256     // {
1257     // changeColour(new RNAInteractionColourScheme());
1258     // }
1259     else if (source == RNAHelixColour)
1260     {
1261       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1262       // new RNAHelicesColourChooser(viewport, alignPanel);
1263     }
1264     else if (source == modifyPID)
1265     {
1266       modifyPID_actionPerformed();
1267     }
1268     else if (source == modifyConservation)
1269     {
1270       modifyConservation_actionPerformed();
1271     }
1272     else if (source == userDefinedColour)
1273     {
1274       new UserDefinedColours(alignPanel, null);
1275     }
1276     else if (source == PIDColour)
1277     {
1278       changeColour(new PIDColourScheme());
1279     }
1280     else if (source == BLOSUM62Colour)
1281     {
1282       changeColour(new Blosum62ColourScheme());
1283     }
1284     else if (source == tcoffeeColour)
1285     {
1286       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1287     }
1288     else if (source == annotationColour)
1289     {
1290       new AnnotationColourChooser(viewport, alignPanel);
1291     }
1292     else if (source == annotationColumnSelection)
1293     {
1294       new AnnotationColumnChooser(viewport, alignPanel);
1295     }
1296     else if (source == sortPairwiseMenuItem)
1297     {
1298       sortPairwiseMenuItem_actionPerformed();
1299     }
1300     else if (source == sortIDMenuItem)
1301     {
1302       sortIDMenuItem_actionPerformed();
1303     }
1304     else if (source == sortLengthMenuItem)
1305     {
1306       sortLengthMenuItem_actionPerformed();
1307     }
1308     else if (source == sortGroupMenuItem)
1309     {
1310       sortGroupMenuItem_actionPerformed();
1311     }
1312     else if (source == removeRedundancyMenuItem)
1313     {
1314       removeRedundancyMenuItem_actionPerformed();
1315     }
1316     else if (source == pairwiseAlignmentMenuItem)
1317     {
1318       pairwiseAlignmentMenuItem_actionPerformed();
1319     }
1320     else if (source == PCAMenuItem)
1321     {
1322       PCAMenuItem_actionPerformed();
1323     }
1324     else if (source == averageDistanceTreeMenuItem)
1325     {
1326       averageDistanceTreeMenuItem_actionPerformed();
1327     }
1328     else if (source == neighbourTreeMenuItem)
1329     {
1330       neighbourTreeMenuItem_actionPerformed();
1331     }
1332     else if (source == njTreeBlosumMenuItem)
1333     {
1334       njTreeBlosumMenuItem_actionPerformed();
1335     }
1336     else if (source == avDistanceTreeBlosumMenuItem)
1337     {
1338       avTreeBlosumMenuItem_actionPerformed();
1339     }
1340     else if (source == documentation)
1341     {
1342       documentation_actionPerformed();
1343     }
1344     else if (source == about)
1345     {
1346       about_actionPerformed();
1347     }
1348
1349   }
1350
1351   public void inputText_actionPerformed()
1352   {
1353     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1354     Frame frame = new Frame();
1355     frame.add(cap);
1356     jalview.bin.JalviewLite.addFrame(frame,
1357             MessageManager.getString("label.input_cut_paste"), 500, 500);
1358   }
1359
1360   protected void outputText_actionPerformed(ActionEvent e)
1361   {
1362     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1363     Frame frame = new Frame();
1364     frame.add(cap);
1365     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1366             "label.alignment_output_command",
1367             new Object[] { e.getActionCommand() }), 600, 500);
1368
1369     FileFormatI fileFormat = FileFormats.getInstance().forName(
1370             e.getActionCommand());
1371     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1372             fileFormat, viewport.getAlignment(),
1373             viewport.getShowJVSuffix()));
1374   }
1375
1376   public void loadAnnotations()
1377   {
1378     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1379     cap.setText(MessageManager
1380             .getString("label.paste_features_annotations_Tcoffee_here"));
1381     cap.setAnnotationImport();
1382     Frame frame = new Frame();
1383     frame.add(cap);
1384     jalview.bin.JalviewLite.addFrame(frame,
1385             MessageManager.getString("action.paste_annotations"), 400, 300);
1386
1387   }
1388
1389   public String outputAnnotations(boolean displayTextbox)
1390   {
1391     String annotation = new AnnotationFile()
1392             .printAnnotationsForView(viewport);
1393
1394     if (displayTextbox)
1395     {
1396       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1397       Frame frame = new Frame();
1398       frame.add(cap);
1399       jalview.bin.JalviewLite.addFrame(frame,
1400               MessageManager.getString("label.annotations"), 600, 500);
1401       cap.setText(annotation);
1402     }
1403
1404     return annotation;
1405   }
1406
1407   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1408   {
1409     if (alignPanel.getFeatureRenderer() != null
1410             && viewport.getFeaturesDisplayed() != null)
1411     {
1412       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1413
1414     }
1415     return null;
1416   }
1417
1418   public String outputFeatures(boolean displayTextbox, String format)
1419   {
1420     String features;
1421     FeaturesFile formatter = new FeaturesFile();
1422     if (format.equalsIgnoreCase("Jalview"))
1423     {
1424       features = formatter.printJalviewFormat(viewport.getAlignment()
1425               .getSequencesArray(), getDisplayedFeatureCols());
1426     }
1427     else
1428     {
1429       features = formatter.printGffFormat(viewport.getAlignment()
1430               .getSequencesArray(), getDisplayedFeatureCols());
1431     }
1432
1433     if (displayTextbox)
1434     {
1435       boolean frimport = false;
1436       if (features == null || features.equals("No Features Visible"))
1437       {
1438         features = "# No features visible - paste some and import them here.";
1439         frimport = true;
1440       }
1441
1442       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1443       if (frimport)
1444       {
1445         cap.setAnnotationImport();
1446       }
1447       Frame frame = new Frame();
1448       frame.add(cap);
1449       jalview.bin.JalviewLite.addFrame(frame,
1450               MessageManager.getString("label.features"), 600, 500);
1451       cap.setText(features);
1452     }
1453     else
1454     {
1455       if (features == null)
1456       {
1457         features = "";
1458       }
1459     }
1460
1461     return features;
1462   }
1463
1464   void launchFullApplication()
1465   {
1466     StringBuffer url = new StringBuffer(jalviewServletURL);
1467
1468     // allow servlet parameters to be passed in applet parameter
1469     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1470             : "?";
1471     url.append(firstSep);
1472
1473     url.append("open="
1474             + appendProtocol(viewport.applet.getParameter("file")));
1475
1476     if (viewport.applet.getParameter("features") != null)
1477     {
1478       url.append("&features=");
1479       url.append(appendProtocol(viewport.applet.getParameter("features")));
1480     }
1481
1482     if (viewport.applet.getParameter("annotations") != null)
1483     {
1484       url.append("&annotations=");
1485       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1486     }
1487
1488     if (viewport.applet.getParameter("jnetfile") != null
1489             || viewport.applet.getParameter("jpredfile") != null)
1490     {
1491       url.append("&annotations=");
1492       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1493               .getParameter("jnetfile") : viewport.applet
1494               .getParameter("jpredfile")));
1495     }
1496
1497     if (viewport.applet.getParameter("defaultColour") != null)
1498     {
1499       url.append("&colour="
1500               + removeWhiteSpace(viewport.applet
1501                       .getParameter("defaultColour")));
1502     }
1503
1504     if (viewport.applet.getParameter("userDefinedColour") != null)
1505     {
1506       url.append("&colour="
1507               + removeWhiteSpace(viewport.applet
1508                       .getParameter("userDefinedColour")));
1509     }
1510     if (viewport.applet.getParameter("tree") != null)
1511     {
1512       url.append("&tree="
1513               + appendProtocol(viewport.applet.getParameter("tree")));
1514     }
1515     if (viewport.applet.getParameter("treeFile") != null)
1516     {
1517       url.append("&tree="
1518               + appendProtocol(viewport.applet.getParameter("treeFile")));
1519     }
1520
1521     showURL(url.toString(), "FULL_APP");
1522   }
1523
1524   String removeWhiteSpace(String colour)
1525   {
1526     StringBuffer sb = new StringBuffer();
1527     for (int i = 0; i < colour.length(); i++)
1528     {
1529       if (Character.isWhitespace(colour.charAt(i)))
1530       {
1531         sb.append("%20");
1532       }
1533       else
1534       {
1535         sb.append(colour.charAt(i));
1536       }
1537     }
1538
1539     return sb.toString();
1540   }
1541
1542   String appendProtocol(String url)
1543   {
1544     try
1545     {
1546       new URL(url);
1547       url = URLEncoder.encode(url);
1548     }
1549     /*
1550      * When we finally deprecate 1.1 compatibility, we can start to use
1551      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1552      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1553      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1554      * ex.printStackTrace(); }
1555      */
1556     catch (java.net.MalformedURLException ex)
1557     {
1558       url = viewport.applet.getCodeBase() + url;
1559     }
1560     return url;
1561   }
1562
1563   public void closeMenuItem_actionPerformed()
1564   {
1565     PaintRefresher.RemoveComponent(alignPanel);
1566     if (alignPanel.seqPanel != null
1567             && alignPanel.seqPanel.seqCanvas != null)
1568     {
1569       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1570     }
1571     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1572     {
1573       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1574     }
1575
1576     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1577     {
1578       System.exit(0);
1579     }
1580     else
1581     {
1582     }
1583     viewport = null;
1584     alignPanel = null;
1585     this.dispose();
1586   }
1587
1588   /**
1589    * TODO: JAL-1104
1590    */
1591   void updateEditMenuBar()
1592   {
1593
1594     if (viewport.getHistoryList().size() > 0)
1595     {
1596       undoMenuItem.setEnabled(true);
1597       CommandI command = viewport.getHistoryList().peek();
1598       undoMenuItem.setLabel(MessageManager.formatMessage(
1599               "label.undo_command",
1600               new Object[] { command.getDescription() }));
1601     }
1602     else
1603     {
1604       undoMenuItem.setEnabled(false);
1605       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1606     }
1607
1608     if (viewport.getRedoList().size() > 0)
1609     {
1610       redoMenuItem.setEnabled(true);
1611
1612       CommandI command = viewport.getRedoList().peek();
1613       redoMenuItem.setLabel(MessageManager.formatMessage(
1614               "label.redo_command",
1615               new Object[] { command.getDescription() }));
1616     }
1617     else
1618     {
1619       redoMenuItem.setEnabled(false);
1620       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1621     }
1622   }
1623
1624   /**
1625    * TODO: JAL-1104
1626    */
1627   @Override
1628   public void addHistoryItem(CommandI command)
1629   {
1630     if (command.getSize() > 0)
1631     {
1632       viewport.addToHistoryList(command);
1633       viewport.clearRedoList();
1634       updateEditMenuBar();
1635       viewport.updateHiddenColumns();
1636     }
1637   }
1638
1639   /**
1640    * TODO: JAL-1104 DOCUMENT ME!
1641    *
1642    * @param e
1643    *          DOCUMENT ME!
1644    */
1645   protected void undoMenuItem_actionPerformed()
1646   {
1647     if (viewport.getHistoryList().isEmpty())
1648     {
1649       return;
1650     }
1651
1652     CommandI command = viewport.getHistoryList().pop();
1653     viewport.addToRedoList(command);
1654     command.undoCommand(null);
1655
1656     AlignmentViewport originalSource = getOriginatingSource(command);
1657     // JBPNote Test
1658     if (originalSource != viewport)
1659     {
1660       System.err
1661               .println("Warning: Viewport object mismatch whilst undoing");
1662     }
1663     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1664                                           // viewport.getColumnSelection().getHiddenColumns()
1665                                           // != null;
1666     updateEditMenuBar();
1667     originalSource.firePropertyChange("alignment", null, originalSource
1668             .getAlignment().getSequences());
1669   }
1670
1671   /**
1672    * TODO: JAL-1104 DOCUMENT ME!
1673    *
1674    * @param e
1675    *          DOCUMENT ME!
1676    */
1677   protected void redoMenuItem_actionPerformed()
1678   {
1679     if (viewport.getRedoList().isEmpty())
1680     {
1681       return;
1682     }
1683
1684     CommandI command = viewport.getRedoList().pop();
1685     viewport.addToHistoryList(command);
1686     command.doCommand(null);
1687
1688     AlignmentViewport originalSource = getOriginatingSource(command);
1689     // JBPNote Test
1690     if (originalSource != viewport)
1691     {
1692       System.err
1693               .println("Warning: Viewport object mismatch whilst re-doing");
1694     }
1695     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1696                                           // viewport.getColumnSelection().getHiddenColumns()
1697                                           // != null;
1698
1699     updateEditMenuBar();
1700     originalSource.firePropertyChange("alignment", null, originalSource
1701             .getAlignment().getSequences());
1702   }
1703
1704   AlignmentViewport getOriginatingSource(CommandI command)
1705   {
1706     AlignmentViewport originalSource = null;
1707     // For sequence removal and addition, we need to fire
1708     // the property change event FROM the viewport where the
1709     // original alignment was altered
1710     AlignmentI al = null;
1711     if (command instanceof EditCommand)
1712     {
1713       EditCommand editCommand = (EditCommand) command;
1714       al = editCommand.getAlignment();
1715       Vector comps = (Vector) PaintRefresher.components.get(viewport
1716               .getSequenceSetId());
1717       for (int i = 0; i < comps.size(); i++)
1718       {
1719         if (comps.elementAt(i) instanceof AlignmentPanel)
1720         {
1721           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1722           {
1723             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1724             break;
1725           }
1726         }
1727       }
1728     }
1729
1730     if (originalSource == null)
1731     {
1732       // The original view is closed, we must validate
1733       // the current view against the closed view first
1734       if (al != null)
1735       {
1736         PaintRefresher.validateSequences(al, viewport.getAlignment());
1737       }
1738
1739       originalSource = viewport;
1740     }
1741
1742     return originalSource;
1743   }
1744
1745   /**
1746    * Move the currently selected sequences up or down one position in the
1747    * alignment
1748    *
1749    * @param up
1750    */
1751   public void moveSelectedSequences(boolean up)
1752   {
1753     SequenceGroup sg = viewport.getSelectionGroup();
1754     if (sg == null)
1755     {
1756       return;
1757     }
1758     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1759             up ? null : viewport.getHiddenRepSequences(), up);
1760     alignPanel.paintAlignment(true);
1761
1762     /*
1763      * Also move cDNA/protein complement sequences
1764      */
1765     AlignViewportI complement = viewport.getCodingComplement();
1766     if (complement != null)
1767     {
1768       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1769               viewport, complement);
1770       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1771               up ? null : complement.getHiddenRepSequences(), up);
1772       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1773     }
1774   }
1775
1776   synchronized void slideSequences(boolean right, int size)
1777   {
1778     List<SequenceI> sg = new Vector<SequenceI>();
1779     if (viewport.cursorMode)
1780     {
1781       sg.add(viewport.getAlignment().getSequenceAt(
1782               alignPanel.seqPanel.seqCanvas.cursorY));
1783     }
1784     else if (viewport.getSelectionGroup() != null
1785             && viewport.getSelectionGroup().getSize() != viewport
1786                     .getAlignment().getHeight())
1787     {
1788       sg = viewport.getSelectionGroup().getSequences(
1789               viewport.getHiddenRepSequences());
1790     }
1791
1792     if (sg.size() < 1)
1793     {
1794       return;
1795     }
1796
1797     Vector<SequenceI> invertGroup = new Vector();
1798
1799     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1800     {
1801       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1802       {
1803         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1804       }
1805     }
1806
1807     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1808
1809     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1810             .size()]);
1811     for (int i = 0; i < invertGroup.size(); i++)
1812     {
1813       seqs2[i] = invertGroup.elementAt(i);
1814     }
1815
1816     SlideSequencesCommand ssc;
1817     if (right)
1818     {
1819       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1820               size, viewport.getGapCharacter());
1821     }
1822     else
1823     {
1824       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1825               size, viewport.getGapCharacter());
1826     }
1827
1828     int groupAdjustment = 0;
1829     if (ssc.getGapsInsertedBegin() && right)
1830     {
1831       if (viewport.cursorMode)
1832       {
1833         alignPanel.seqPanel.moveCursor(size, 0);
1834       }
1835       else
1836       {
1837         groupAdjustment = size;
1838       }
1839     }
1840     else if (!ssc.getGapsInsertedBegin() && !right)
1841     {
1842       if (viewport.cursorMode)
1843       {
1844         alignPanel.seqPanel.moveCursor(-size, 0);
1845       }
1846       else
1847       {
1848         groupAdjustment = -size;
1849       }
1850     }
1851
1852     if (groupAdjustment != 0)
1853     {
1854       viewport.getSelectionGroup().setStartRes(
1855               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1856       viewport.getSelectionGroup().setEndRes(
1857               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1858     }
1859
1860     boolean appendHistoryItem = false;
1861     Deque<CommandI> historyList = viewport.getHistoryList();
1862     if (historyList != null && historyList.size() > 0
1863             && historyList.peek() instanceof SlideSequencesCommand)
1864     {
1865       appendHistoryItem = ssc
1866               .appendSlideCommand((SlideSequencesCommand) historyList
1867                       .peek());
1868     }
1869
1870     if (!appendHistoryItem)
1871     {
1872       addHistoryItem(ssc);
1873     }
1874
1875     repaint();
1876   }
1877
1878   static StringBuffer copiedSequences;
1879
1880   static Vector copiedHiddenColumns;
1881
1882   protected void copy_actionPerformed()
1883   {
1884     if (viewport.getSelectionGroup() == null)
1885     {
1886       return;
1887     }
1888
1889     SequenceGroup sg = viewport.getSelectionGroup();
1890     copiedSequences = new StringBuffer();
1891     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1892     for (int i = 0; i < sg.getSize(); i++)
1893     {
1894       SequenceI seq = sg.getSequenceAt(i);
1895       int index = viewport.getAlignment().findIndex(seq);
1896       orderedSeqs.put(index, seq);
1897     }
1898
1899     int index = 0, startRes, endRes;
1900     char ch;
1901
1902     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1903     {
1904       copiedHiddenColumns = new Vector();
1905       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1906       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1907       {
1908         copiedHiddenColumns.addElement(new int[] {
1909             region[0] - hiddenOffset, region[1] - hiddenOffset });
1910       }
1911     }
1912     else
1913     {
1914       copiedHiddenColumns = null;
1915     }
1916
1917     for (int i = 0; i < sg.getSize(); i++)
1918     {
1919       SequenceI seq = null;
1920
1921       while (seq == null)
1922       {
1923         if (orderedSeqs.containsKey(index))
1924         {
1925           seq = orderedSeqs.get(index);
1926           index++;
1927           break;
1928         }
1929         else
1930         {
1931           index++;
1932         }
1933       }
1934
1935       // FIND START RES
1936       // Returns residue following index if gap
1937       startRes = seq.findPosition(sg.getStartRes());
1938
1939       // FIND END RES
1940       // Need to find the residue preceeding index if gap
1941       endRes = 0;
1942
1943       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1944       {
1945         ch = seq.getCharAt(j);
1946         if (!jalview.util.Comparison.isGap((ch)))
1947         {
1948           endRes++;
1949         }
1950       }
1951
1952       if (endRes > 0)
1953       {
1954         endRes += seq.getStart() - 1;
1955       }
1956
1957       copiedSequences.append(seq.getName()
1958               + "\t"
1959               + startRes
1960               + "\t"
1961               + endRes
1962               + "\t"
1963               + seq.getSequenceAsString(sg.getStartRes(),
1964                       sg.getEndRes() + 1) + "\n");
1965     }
1966
1967   }
1968
1969   protected void pasteNew_actionPerformed()
1970   {
1971     paste(true);
1972   }
1973
1974   protected void pasteThis_actionPerformed()
1975   {
1976     paste(false);
1977   }
1978
1979   void paste(boolean newAlignment)
1980   {
1981     try
1982     {
1983
1984       if (copiedSequences == null)
1985       {
1986         return;
1987       }
1988
1989       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1990       Vector seqs = new Vector();
1991       while (st.hasMoreElements())
1992       {
1993         String name = st.nextToken();
1994         int start = Integer.parseInt(st.nextToken());
1995         int end = Integer.parseInt(st.nextToken());
1996         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1997       }
1998       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1999       for (int i = 0; i < seqs.size(); i++)
2000       {
2001         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2002       }
2003
2004       if (newAlignment)
2005       {
2006         String newtitle = MessageManager
2007                 .getString("label.copied_sequences");
2008         if (getTitle().startsWith(
2009                 MessageManager.getString("label.copied_sequences")))
2010         {
2011           newtitle = getTitle();
2012         }
2013         else
2014         {
2015           newtitle = newtitle.concat(MessageManager.formatMessage(
2016                   "label.from_msname", new String[] { getTitle() }));
2017         }
2018         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2019                 viewport.applet, newtitle, false);
2020         if (copiedHiddenColumns != null)
2021         {
2022           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2023           {
2024             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2025             af.viewport.hideColumns(region[0], region[1]);
2026           }
2027         }
2028
2029         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2030                 frameHeight);
2031       }
2032       else
2033       {
2034         addSequences(newSeqs);
2035       }
2036
2037     } catch (Exception ex)
2038     {
2039     } // could be anything being pasted in here
2040
2041   }
2042
2043   void addSequences(SequenceI[] seqs)
2044   {
2045     for (int i = 0; i < seqs.length; i++)
2046     {
2047       viewport.getAlignment().addSequence(seqs[i]);
2048     }
2049
2050     // !newAlignment
2051     addHistoryItem(new EditCommand(
2052             MessageManager.getString("label.add_sequences"), Action.PASTE,
2053             seqs, 0, viewport.getAlignment().getWidth(),
2054             viewport.getAlignment()));
2055
2056     viewport.setEndSeq(viewport.getAlignment().getHeight());
2057     viewport.getAlignment().getWidth();
2058     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2059             .getSequences());
2060
2061   }
2062
2063   protected void cut_actionPerformed()
2064   {
2065     copy_actionPerformed();
2066     delete_actionPerformed();
2067   }
2068
2069   protected void delete_actionPerformed()
2070   {
2071
2072     SequenceGroup sg = viewport.getSelectionGroup();
2073     if (sg == null)
2074     {
2075       return;
2076     }
2077
2078     Vector seqs = new Vector();
2079     SequenceI seq;
2080     for (int i = 0; i < sg.getSize(); i++)
2081     {
2082       seq = sg.getSequenceAt(i);
2083       seqs.addElement(seq);
2084     }
2085
2086     /*
2087      * If the cut affects all sequences, warn, remove highlighted columns
2088      */
2089     if (sg.getSize() == viewport.getAlignment().getHeight())
2090     {
2091       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2092               .getAlignment().getWidth()) ? true : false;
2093       if (isEntireAlignWidth)
2094       {
2095         String title = MessageManager.getString("label.delete_all");
2096         Panel infoPanel = new Panel();
2097         infoPanel.setLayout(new FlowLayout());
2098         infoPanel
2099                 .add(new Label(MessageManager.getString("warn.delete_all")));
2100
2101         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2102         dialog.setMainPanel(infoPanel);
2103         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2104         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2105         dialog.setVisible(true);
2106
2107         if (!dialog.accept)
2108         {
2109           return;
2110         }
2111       }
2112       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2113               sg.getEndRes() + 1);
2114     }
2115
2116     SequenceI[] cut = new SequenceI[seqs.size()];
2117     for (int i = 0; i < seqs.size(); i++)
2118     {
2119       cut[i] = (SequenceI) seqs.elementAt(i);
2120     }
2121
2122     /*
2123      * //ADD HISTORY ITEM
2124      */
2125     addHistoryItem(new EditCommand(
2126             MessageManager.getString("label.cut_sequences"), Action.CUT,
2127             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2128             viewport.getAlignment()));
2129
2130     viewport.setSelectionGroup(null);
2131     viewport.getAlignment().deleteGroup(sg);
2132
2133     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2134             .getSequences());
2135
2136     if (viewport.getAlignment().getHeight() < 1)
2137     {
2138       this.setVisible(false);
2139     }
2140     viewport.sendSelection();
2141   }
2142
2143   /**
2144    * group consensus toggled
2145    *
2146    */
2147   protected void showGroupConsensus_actionPerformed()
2148   {
2149     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2150     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2151
2152   }
2153
2154   /**
2155    * group conservation toggled.
2156    */
2157   protected void showGroupConservation_actionPerformed()
2158   {
2159     viewport.setShowGroupConservation(showGroupConservation.getState());
2160     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2161   }
2162
2163   /*
2164    * (non-Javadoc)
2165    *
2166    * @see
2167    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2168    * .event.ActionEvent)
2169    */
2170   protected void showConsensusHistogram_actionPerformed()
2171   {
2172     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2173     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174   }
2175
2176   /*
2177    * (non-Javadoc)
2178    *
2179    * @see
2180    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2181    * .event.ActionEvent)
2182    */
2183   protected void showSequenceLogo_actionPerformed()
2184   {
2185     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2186     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2187   }
2188
2189   protected void normSequenceLogo_actionPerformed()
2190   {
2191     showSequenceLogo.setState(true);
2192     viewport.setShowSequenceLogo(true);
2193     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195   }
2196
2197   protected void applyAutoAnnotationSettings_actionPerformed()
2198   {
2199     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2200   }
2201
2202   protected void makeGrpsFromSelection_actionPerformed()
2203   {
2204     if (avc.makeGroupsFromSelection())
2205     {
2206       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2207       alignPanel.updateAnnotation();
2208       alignPanel.paintAlignment(true);
2209     }
2210   }
2211
2212   protected void createGroup_actionPerformed()
2213   {
2214     avc.createGroup();
2215   }
2216
2217   protected void unGroup_actionPerformed()
2218   {
2219     if (avc.unGroup())
2220     {
2221       alignPanel.alignmentChanged();
2222     }
2223   }
2224
2225   protected void deleteGroups_actionPerformed()
2226   {
2227     if (avc.deleteGroups())
2228     {
2229       alignPanel.alignmentChanged();
2230     }
2231   }
2232
2233   public void selectAllSequenceMenuItem_actionPerformed()
2234   {
2235     SequenceGroup sg = new SequenceGroup();
2236     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2237     {
2238       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2239     }
2240     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2241     viewport.setSelectionGroup(sg);
2242     // JAL-2034 - should delegate to
2243     // alignPanel to decide if overview needs
2244     // updating.
2245     alignPanel.paintAlignment(false);
2246     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2247     viewport.sendSelection();
2248   }
2249
2250   public void deselectAllSequenceMenuItem_actionPerformed()
2251   {
2252     if (viewport.cursorMode)
2253     {
2254       alignPanel.seqPanel.keyboardNo1 = null;
2255       alignPanel.seqPanel.keyboardNo2 = null;
2256     }
2257     viewport.setSelectionGroup(null);
2258     viewport.getColumnSelection().clear();
2259     viewport.setSelectionGroup(null);
2260     alignPanel.idPanel.idCanvas.searchResults = null;
2261     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2262     // JAL-2034 - should delegate to
2263     // alignPanel to decide if overview needs
2264     // updating.
2265     alignPanel.paintAlignment(false);
2266     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2267     viewport.sendSelection();
2268   }
2269
2270   public void invertSequenceMenuItem_actionPerformed()
2271   {
2272     SequenceGroup sg = viewport.getSelectionGroup();
2273     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2274     {
2275       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2276     }
2277
2278     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2279     viewport.sendSelection();
2280   }
2281
2282   public void invertColSel_actionPerformed()
2283   {
2284     viewport.invertColumnSelection();
2285     alignPanel.paintAlignment(true);
2286     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2287     viewport.sendSelection();
2288   }
2289
2290   void trimAlignment(boolean trimLeft)
2291   {
2292     ColumnSelection colSel = viewport.getColumnSelection();
2293     int column;
2294
2295     if (!colSel.isEmpty())
2296     {
2297       if (trimLeft)
2298       {
2299         column = colSel.getMin();
2300       }
2301       else
2302       {
2303         column = colSel.getMax();
2304       }
2305
2306       SequenceI[] seqs;
2307       if (viewport.getSelectionGroup() != null)
2308       {
2309         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2310                 viewport.getHiddenRepSequences());
2311       }
2312       else
2313       {
2314         seqs = viewport.getAlignment().getSequencesArray();
2315       }
2316
2317       TrimRegionCommand trimRegion;
2318       if (trimLeft)
2319       {
2320         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2321                 column, viewport.getAlignment());
2322         viewport.setStartRes(0);
2323       }
2324       else
2325       {
2326         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2327                 column, viewport.getAlignment());
2328       }
2329
2330       statusBar.setText(MessageManager.formatMessage(
2331               "label.removed_columns",
2332               new String[] { Integer.valueOf(trimRegion.getSize())
2333                       .toString() }));
2334       addHistoryItem(trimRegion);
2335
2336       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2337       {
2338         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2339                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2340         {
2341           viewport.getAlignment().deleteGroup(sg);
2342         }
2343       }
2344
2345       viewport.firePropertyChange("alignment", null, viewport
2346               .getAlignment().getSequences());
2347     }
2348   }
2349
2350   public void removeGappedColumnMenuItem_actionPerformed()
2351   {
2352     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2353
2354     SequenceI[] seqs;
2355     if (viewport.getSelectionGroup() != null)
2356     {
2357       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2358               viewport.getHiddenRepSequences());
2359       start = viewport.getSelectionGroup().getStartRes();
2360       end = viewport.getSelectionGroup().getEndRes();
2361     }
2362     else
2363     {
2364       seqs = viewport.getAlignment().getSequencesArray();
2365     }
2366
2367     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2368             "Remove Gapped Columns", seqs, start, end,
2369             viewport.getAlignment());
2370
2371     addHistoryItem(removeGapCols);
2372
2373     statusBar.setText(MessageManager.formatMessage(
2374             "label.removed_empty_columns",
2375             new String[] { Integer.valueOf(removeGapCols.getSize())
2376                     .toString() }));
2377
2378     // This is to maintain viewport position on first residue
2379     // of first sequence
2380     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2381     int startRes = seq.findPosition(viewport.startRes);
2382     // ShiftList shifts;
2383     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2384     // edit.alColumnChanges=shifts.getInverse();
2385     // if (viewport.hasHiddenColumns)
2386     // viewport.getColumnSelection().compensateForEdits(shifts);
2387     viewport.setStartRes(seq.findIndex(startRes) - 1);
2388     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2389             .getSequences());
2390
2391   }
2392
2393   public void removeAllGapsMenuItem_actionPerformed()
2394   {
2395     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2396
2397     SequenceI[] seqs;
2398     if (viewport.getSelectionGroup() != null)
2399     {
2400       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2401               viewport.getHiddenRepSequences());
2402       start = viewport.getSelectionGroup().getStartRes();
2403       end = viewport.getSelectionGroup().getEndRes();
2404     }
2405     else
2406     {
2407       seqs = viewport.getAlignment().getSequencesArray();
2408     }
2409
2410     // This is to maintain viewport position on first residue
2411     // of first sequence
2412     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2413     int startRes = seq.findPosition(viewport.startRes);
2414
2415     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2416             viewport.getAlignment()));
2417
2418     viewport.setStartRes(seq.findIndex(startRes) - 1);
2419
2420     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2421             .getSequences());
2422
2423   }
2424
2425   public void findMenuItem_actionPerformed()
2426   {
2427     new Finder(alignPanel);
2428   }
2429
2430   /**
2431    * create a new view derived from the current view
2432    *
2433    * @param viewtitle
2434    * @return frame for the new view
2435    */
2436   public AlignFrame newView(String viewtitle)
2437   {
2438     AlignmentI newal;
2439     if (viewport.hasHiddenRows())
2440     {
2441       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2442               .getFullAlignment().getSequencesArray());
2443     }
2444     else
2445     {
2446       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2447     }
2448
2449     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2450     {
2451       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2452       {
2453         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2454         {
2455           newal.addAnnotation(viewport.getAlignment()
2456                   .getAlignmentAnnotation()[i]);
2457         }
2458       }
2459     }
2460
2461     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2462
2463     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2464     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2465     PaintRefresher.Register(newaf.alignPanel,
2466             newaf.alignPanel.av.getSequenceSetId());
2467
2468     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2469             newaf.alignPanel.av.getSequenceSetId());
2470     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2471             newaf.alignPanel.av.getSequenceSetId());
2472
2473     Vector comps = (Vector) PaintRefresher.components.get(viewport
2474             .getSequenceSetId());
2475     int viewSize = -1;
2476     for (int i = 0; i < comps.size(); i++)
2477     {
2478       if (comps.elementAt(i) instanceof AlignmentPanel)
2479       {
2480         viewSize++;
2481       }
2482     }
2483
2484     String title = new String(this.getTitle());
2485     if (viewtitle != null)
2486     {
2487       title = viewtitle + " ( " + title + ")";
2488     }
2489     else
2490     {
2491       if (title.indexOf("(View") > -1)
2492       {
2493         title = title.substring(0, title.indexOf("(View"));
2494       }
2495       title += "(View " + viewSize + ")";
2496     }
2497
2498     newaf.setTitle(title.toString());
2499
2500     newaf.viewport.setHistoryList(viewport.getHistoryList());
2501     newaf.viewport.setRedoList(viewport.getRedoList());
2502     return newaf;
2503   }
2504
2505   /**
2506    *
2507    * @return list of feature groups on the view
2508    */
2509   public String[] getFeatureGroups()
2510   {
2511     FeatureRenderer fr = null;
2512     if (alignPanel != null
2513             && (fr = alignPanel.getFeatureRenderer()) != null)
2514     {
2515       List<String> gps = fr.getFeatureGroups();
2516       String[] _gps = gps.toArray(new String[gps.size()]);
2517       return _gps;
2518     }
2519     return null;
2520   }
2521
2522   /**
2523    * get sequence feature groups that are hidden or shown
2524    *
2525    * @param visible
2526    *          true is visible
2527    * @return list
2528    */
2529   public String[] getFeatureGroupsOfState(boolean visible)
2530   {
2531     FeatureRenderer fr = null;
2532     if (alignPanel != null
2533             && (fr = alignPanel.getFeatureRenderer()) != null)
2534     {
2535       List<String> gps = fr.getGroups(visible);
2536       String[] _gps = gps.toArray(new String[gps.size()]);
2537       return _gps;
2538     }
2539     return null;
2540   }
2541
2542   /**
2543    * Change the display state for the given feature groups
2544    *
2545    * @param groups
2546    *          list of group strings
2547    * @param state
2548    *          visible or invisible
2549    */
2550   public void setFeatureGroupState(String[] groups, boolean state)
2551   {
2552     FeatureRenderer fr = null;
2553     this.sequenceFeatures.setState(true);
2554     viewport.setShowSequenceFeatures(true);
2555     if (alignPanel != null
2556             && (fr = alignPanel.getFeatureRenderer()) != null)
2557     {
2558
2559       fr.setGroupVisibility(Arrays.asList(groups), state);
2560       alignPanel.seqPanel.seqCanvas.repaint();
2561       if (alignPanel.overviewPanel != null)
2562       {
2563         alignPanel.overviewPanel.updateOverviewImage();
2564       }
2565     }
2566   }
2567
2568   public void seqLimits_itemStateChanged()
2569   {
2570     viewport.setShowJVSuffix(seqLimits.getState());
2571     alignPanel.fontChanged();
2572     alignPanel.paintAlignment(true);
2573   }
2574
2575   protected void colourTextMenuItem_actionPerformed()
2576   {
2577     viewport.setColourText(colourTextMenuItem.getState());
2578     alignPanel.paintAlignment(true);
2579   }
2580
2581   protected void displayNonconservedMenuItem_actionPerformed()
2582   {
2583     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2584     alignPanel.paintAlignment(true);
2585   }
2586
2587   protected void wrapMenuItem_actionPerformed()
2588   {
2589     viewport.setWrapAlignment(wrapMenuItem.getState());
2590     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2591     scaleAbove.setEnabled(wrapMenuItem.getState());
2592     scaleLeft.setEnabled(wrapMenuItem.getState());
2593     scaleRight.setEnabled(wrapMenuItem.getState());
2594     alignPanel.paintAlignment(true);
2595   }
2596
2597   public void overviewMenuItem_actionPerformed()
2598   {
2599     if (alignPanel.overviewPanel != null)
2600     {
2601       return;
2602     }
2603
2604     Frame frame = new Frame();
2605     OverviewPanel overview = new OverviewPanel(alignPanel);
2606     frame.add(overview);
2607     // +50 must allow for applet frame window
2608     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2609             "label.overview_params", new String[] { this.getTitle() }),
2610             overview.getPreferredSize().width,
2611             overview.getPreferredSize().height + 50);
2612
2613     frame.pack();
2614     final AlignmentPanel ap = alignPanel;
2615     frame.addWindowListener(new WindowAdapter()
2616     {
2617       @Override
2618       public void windowClosing(WindowEvent e)
2619       {
2620         if (ap != null)
2621         {
2622           ap.setOverviewPanel(null);
2623         }
2624       };
2625     });
2626
2627     alignPanel.setOverviewPanel(overview);
2628
2629   }
2630
2631   @Override
2632   public void changeColour(ColourSchemeI cs)
2633   {
2634     // FIXME threshold, conservation, increment belong inside
2635     // AlignmentColourScheme and/or ViewStyleI, not ColourSchemeI
2636     if (cs != null)
2637     {
2638       if (viewport.getAbovePIDThreshold())
2639       {
2640         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2641                 viewport.getViewportColourScheme(), "Background"));
2642       }
2643
2644       if (viewport.getConservationSelected())
2645       {
2646         // cs.setConservationApplied(true);
2647         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2648                 viewport.getViewportColourScheme(), "Background"));
2649       }
2650       // else
2651       // {
2652       // cs.setConservationApplied(false);
2653       // }
2654     }
2655     viewport.setGlobalColourScheme(cs);
2656     viewport.getViewportColourScheme().setConservationApplied(
2657             viewport.getConservationSelected());
2658
2659     alignPanel.paintAlignment(true);
2660   }
2661
2662   protected void modifyPID_actionPerformed()
2663   {
2664     if (viewport.getAbovePIDThreshold()
2665             && viewport.getGlobalColourScheme() != null)
2666     {
2667       SliderPanel.setPIDSliderSource(alignPanel,
2668               viewport.getViewportColourScheme(), "Background");
2669       SliderPanel.showPIDSlider();
2670     }
2671   }
2672
2673   protected void modifyConservation_actionPerformed()
2674   {
2675     if (viewport.getConservationSelected()
2676             && viewport.getGlobalColourScheme() != null)
2677     {
2678       SliderPanel.setConservationSlider(alignPanel,
2679               viewport.getViewportColourScheme(), "Background");
2680       SliderPanel.showConservationSlider();
2681     }
2682   }
2683
2684   protected void conservationMenuItem_actionPerformed()
2685   {
2686     viewport.setConservationSelected(conservationMenuItem.getState());
2687
2688     viewport.setAbovePIDThreshold(false);
2689     abovePIDThreshold.setState(false);
2690
2691     changeColour(viewport.getGlobalColourScheme());
2692
2693     modifyConservation_actionPerformed();
2694   }
2695
2696   public void abovePIDThreshold_actionPerformed()
2697   {
2698     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2699
2700     conservationMenuItem.setState(false);
2701     viewport.setConservationSelected(false);
2702
2703     changeColour(viewport.getGlobalColourScheme());
2704
2705     modifyPID_actionPerformed();
2706   }
2707
2708   public void sortPairwiseMenuItem_actionPerformed()
2709   {
2710     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2711     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2712             .getAlignment().getSequenceAt(0), null);
2713
2714     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2715             viewport.getAlignment()));
2716     alignPanel.paintAlignment(true);
2717   }
2718
2719   public void sortIDMenuItem_actionPerformed()
2720   {
2721     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2722     AlignmentSorter.sortByID(viewport.getAlignment());
2723     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2724             viewport.getAlignment()));
2725     alignPanel.paintAlignment(true);
2726   }
2727
2728   public void sortLengthMenuItem_actionPerformed()
2729   {
2730     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2731     AlignmentSorter.sortByLength(viewport.getAlignment());
2732     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2733             viewport.getAlignment()));
2734     alignPanel.paintAlignment(true);
2735   }
2736
2737   public void sortGroupMenuItem_actionPerformed()
2738   {
2739     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2740     AlignmentSorter.sortByGroup(viewport.getAlignment());
2741     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2742             viewport.getAlignment()));
2743     alignPanel.paintAlignment(true);
2744
2745   }
2746
2747   public void removeRedundancyMenuItem_actionPerformed()
2748   {
2749     new RedundancyPanel(alignPanel);
2750   }
2751
2752   public void pairwiseAlignmentMenuItem_actionPerformed()
2753   {
2754     if (viewport.getSelectionGroup() != null
2755             && viewport.getSelectionGroup().getSize() > 1)
2756     {
2757       Frame frame = new Frame();
2758       frame.add(new PairwiseAlignPanel(alignPanel));
2759       jalview.bin.JalviewLite.addFrame(frame,
2760               MessageManager.getString("action.pairwise_alignment"), 600,
2761               500);
2762     }
2763   }
2764
2765   public void PCAMenuItem_actionPerformed()
2766   {
2767     // are the sequences aligned?
2768     if (!viewport.getAlignment().isAligned(false))
2769     {
2770       SequenceI current;
2771       int Width = viewport.getAlignment().getWidth();
2772
2773       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2774       {
2775         current = viewport.getAlignment().getSequenceAt(i);
2776
2777         if (current.getLength() < Width)
2778         {
2779           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2780         }
2781       }
2782       alignPanel.paintAlignment(true);
2783     }
2784
2785     if ((viewport.getSelectionGroup() != null
2786             && viewport.getSelectionGroup().getSize() < 4 && viewport
2787             .getSelectionGroup().getSize() > 0)
2788             || viewport.getAlignment().getHeight() < 4)
2789     {
2790       return;
2791     }
2792
2793     try
2794     {
2795       new PCAPanel(viewport);
2796     } catch (java.lang.OutOfMemoryError ex)
2797     {
2798     }
2799
2800   }
2801
2802   public void averageDistanceTreeMenuItem_actionPerformed()
2803   {
2804     NewTreePanel("AV", "PID", "Average distance tree using PID");
2805   }
2806
2807   public void neighbourTreeMenuItem_actionPerformed()
2808   {
2809     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2810   }
2811
2812   protected void njTreeBlosumMenuItem_actionPerformed()
2813   {
2814     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2815   }
2816
2817   protected void avTreeBlosumMenuItem_actionPerformed()
2818   {
2819     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2820   }
2821
2822   void NewTreePanel(String type, String pwType, String title)
2823   {
2824     // are the sequences aligned?
2825     if (!viewport.getAlignment().isAligned(false))
2826     {
2827       SequenceI current;
2828       int Width = viewport.getAlignment().getWidth();
2829
2830       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2831       {
2832         current = viewport.getAlignment().getSequenceAt(i);
2833
2834         if (current.getLength() < Width)
2835         {
2836           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2837         }
2838       }
2839       alignPanel.paintAlignment(true);
2840
2841     }
2842
2843     if ((viewport.getSelectionGroup() != null && viewport
2844             .getSelectionGroup().getSize() > 1)
2845             || (viewport.getAlignment().getHeight() > 1))
2846     {
2847       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2848
2849       addTreeMenuItem(tp, title);
2850
2851       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2852     }
2853   }
2854
2855   void loadTree_actionPerformed()
2856   {
2857     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2858     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2859     cap.setTreeImport();
2860     Frame frame = new Frame();
2861     frame.add(cap);
2862     jalview.bin.JalviewLite.addFrame(frame,
2863             MessageManager.getString("label.paste_newick_file"), 400, 300);
2864   }
2865
2866   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2867   {
2868     TreePanel tp = new TreePanel(alignPanel, treeFile,
2869             MessageManager.getString("label.load_tree_from_file"), tree);
2870     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2871     addTreeMenuItem(tp, treeFile);
2872   }
2873
2874   /**
2875    * sort the alignment using the given treePanel
2876    *
2877    * @param treePanel
2878    *          tree used to sort view
2879    * @param title
2880    *          string used for undo event name
2881    */
2882   public void sortByTree(TreePanel treePanel, String title)
2883   {
2884     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2885     AlignmentSorter
2886             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2887     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2888     // HistoryItem.SORT));
2889     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2890             "label.order_by_params", new String[] { title }), oldOrder,
2891             viewport.getAlignment()));
2892     alignPanel.paintAlignment(true);
2893   }
2894
2895   /**
2896    * Do any automatic reordering of the alignment and add the necessary bits to
2897    * the menu structure for the new tree
2898    *
2899    * @param treePanel
2900    * @param title
2901    */
2902   protected void addTreeMenuItem(final TreePanel treePanel,
2903           final String title)
2904   {
2905     final MenuItem item = new MenuItem(title);
2906     sortByTreeMenu.add(item);
2907     item.addActionListener(new java.awt.event.ActionListener()
2908     {
2909       @Override
2910       public void actionPerformed(ActionEvent evt)
2911       {
2912         sortByTree(treePanel, title); // treePanel.getTitle());
2913       }
2914     });
2915
2916     treePanel.addWindowListener(new WindowAdapter()
2917     {
2918       @Override
2919       public void windowOpened(WindowEvent e)
2920       {
2921         if (viewport.sortByTree)
2922         {
2923           sortByTree(treePanel, title);
2924         }
2925         super.windowOpened(e);
2926       }
2927
2928       @Override
2929       public void windowClosing(WindowEvent e)
2930       {
2931         sortByTreeMenu.remove(item);
2932       };
2933     });
2934   }
2935
2936   public boolean sortBy(AlignmentOrder alorder, String undoname)
2937   {
2938     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2939     if (viewport.applet.debug)
2940     {
2941       System.err.println("Sorting " + alorder.getOrder().size()
2942               + " in alignment '" + getTitle() + "'");
2943     }
2944     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2945     if (undoname != null)
2946     {
2947       addHistoryItem(new OrderCommand(undoname, oldOrder,
2948               viewport.getAlignment()));
2949     }
2950     alignPanel.paintAlignment(true);
2951     return true;
2952   }
2953
2954   protected void documentation_actionPerformed()
2955   {
2956     alignPanel.av.applet.openJalviewHelpUrl();
2957   }
2958
2959   protected void about_actionPerformed()
2960   {
2961
2962     class AboutPanel extends Canvas
2963     {
2964       String version;
2965
2966       String builddate;
2967
2968       public AboutPanel(String version, String builddate)
2969       {
2970         this.version = version;
2971         this.builddate = builddate;
2972       }
2973
2974       @Override
2975       public void paint(Graphics g)
2976       {
2977         g.setColor(Color.white);
2978         g.fillRect(0, 0, getSize().width, getSize().height);
2979         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2980         FontMetrics fm = g.getFontMetrics();
2981         int fh = fm.getHeight();
2982         int y = 5, x = 7;
2983         g.setColor(Color.black);
2984         // TODO: update this text for each release or centrally store it for
2985         // lite and application
2986         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2987         g.drawString(MessageManager.formatMessage(
2988                 "label.jalviewLite_release", new String[] { version }), x,
2989                 y += fh);
2990         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2991         g.drawString(MessageManager.formatMessage(
2992                 "label.jaview_build_date", new String[] { builddate }), x,
2993                 y += fh);
2994         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2995         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2996                 x, y += fh * 1.5);
2997         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2998                 x + 50, y += fh + 8);
2999         g.drawString(
3000                 MessageManager.getString("label.jalview_dev_managers"), x,
3001                 y += fh);
3002         g.drawString(MessageManager
3003                 .getString("label.jalview_distribution_lists"), x, y += fh);
3004         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3005                 x, y += fh + 8);
3006         g.drawString(
3007                 MessageManager.getString("label.jalview_cite_1_authors"),
3008                 x, y += fh);
3009         g.drawString(
3010                 MessageManager.getString("label.jalview_cite_1_title"), x,
3011                 y += fh);
3012         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3013                 x, y += fh);
3014       }
3015     }
3016
3017     Frame frame = new Frame();
3018     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3019             .getBuildDate()));
3020     jalview.bin.JalviewLite.addFrame(frame,
3021             MessageManager.getString("label.jalview"), 580, 220);
3022
3023   }
3024
3025   public void showURL(String url, String target)
3026   {
3027     if (viewport.applet == null)
3028     {
3029       System.out.println("Not running as applet - no browser available.");
3030     }
3031     else
3032     {
3033       viewport.applet.showURL(url, target);
3034     }
3035   }
3036
3037   // ////////////////////////////////////////////////////////////////////////////////
3038   // JBuilder Graphics here
3039
3040   MenuBar alignFrameMenuBar = new MenuBar();
3041
3042   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3043
3044   MenuItem loadApplication = new MenuItem(
3045           MessageManager.getString("label.view_full_application"));
3046
3047   MenuItem loadTree = new MenuItem(
3048           MessageManager.getString("label.load_associated_tree"));
3049
3050   MenuItem loadAnnotations = new MenuItem(
3051           MessageManager.getString("label.load_features_annotations"));
3052
3053   MenuItem outputFeatures = new MenuItem(
3054           MessageManager.getString("label.export_features"));
3055
3056   MenuItem outputAnnotations = new MenuItem(
3057           MessageManager.getString("label.export_annotations"));
3058
3059   MenuItem closeMenuItem = new MenuItem(
3060           MessageManager.getString("action.close"));
3061
3062   MenuItem selectAllSequenceMenuItem = new MenuItem(
3063           MessageManager.getString("action.select_all"));
3064
3065   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3066           MessageManager.getString("action.deselect_all"));
3067
3068   MenuItem invertSequenceMenuItem = new MenuItem(
3069           MessageManager.getString("action.invert_selection"));
3070
3071   MenuItem remove2LeftMenuItem = new MenuItem();
3072
3073   MenuItem remove2RightMenuItem = new MenuItem();
3074
3075   MenuItem removeGappedColumnMenuItem = new MenuItem();
3076
3077   MenuItem removeAllGapsMenuItem = new MenuItem();
3078
3079   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3080
3081   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3082
3083   MenuItem sortPairwiseMenuItem = new MenuItem();
3084
3085   MenuItem sortIDMenuItem = new MenuItem();
3086
3087   MenuItem sortLengthMenuItem = new MenuItem();
3088
3089   MenuItem sortGroupMenuItem = new MenuItem();
3090
3091   MenuItem removeRedundancyMenuItem = new MenuItem();
3092
3093   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3094
3095   MenuItem PCAMenuItem = new MenuItem();
3096
3097   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3098
3099   MenuItem neighbourTreeMenuItem = new MenuItem();
3100
3101   BorderLayout borderLayout1 = new BorderLayout();
3102
3103   public Label statusBar = new Label();
3104
3105   MenuItem clustalColour = new MenuItem();
3106
3107   MenuItem zappoColour = new MenuItem();
3108
3109   MenuItem taylorColour = new MenuItem();
3110
3111   MenuItem hydrophobicityColour = new MenuItem();
3112
3113   MenuItem helixColour = new MenuItem();
3114
3115   MenuItem strandColour = new MenuItem();
3116
3117   MenuItem turnColour = new MenuItem();
3118
3119   MenuItem buriedColour = new MenuItem();
3120
3121   MenuItem purinePyrimidineColour = new MenuItem();
3122
3123   // MenuItem RNAInteractionColour = new MenuItem();
3124
3125   MenuItem RNAHelixColour = new MenuItem();
3126
3127   MenuItem userDefinedColour = new MenuItem();
3128
3129   MenuItem PIDColour = new MenuItem();
3130
3131   MenuItem BLOSUM62Colour = new MenuItem();
3132
3133   MenuItem tcoffeeColour = new MenuItem();
3134
3135   MenuItem njTreeBlosumMenuItem = new MenuItem();
3136
3137   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3138
3139   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3140
3141   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3142
3143   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3144
3145   MenuItem alProperties = new MenuItem(
3146           MessageManager.getString("label.alignment_props"));
3147
3148   MenuItem overviewMenuItem = new MenuItem();
3149
3150   MenuItem undoMenuItem = new MenuItem();
3151
3152   MenuItem redoMenuItem = new MenuItem();
3153
3154   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3155
3156   MenuItem noColourmenuItem = new MenuItem();
3157
3158   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3159
3160   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3161
3162   MenuItem findMenuItem = new MenuItem();
3163
3164   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3165
3166   MenuItem nucleotideColour = new MenuItem();
3167
3168   MenuItem deleteGroups = new MenuItem();
3169
3170   MenuItem grpsFromSelection = new MenuItem();
3171
3172   MenuItem createGroup = new MenuItem();
3173
3174   MenuItem unGroup = new MenuItem();
3175
3176   MenuItem delete = new MenuItem();
3177
3178   MenuItem copy = new MenuItem();
3179
3180   MenuItem cut = new MenuItem();
3181
3182   Menu pasteMenu = new Menu();
3183
3184   MenuItem pasteNew = new MenuItem();
3185
3186   MenuItem pasteThis = new MenuItem();
3187
3188   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3189
3190   MenuItem font = new MenuItem();
3191
3192   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3193
3194   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3195
3196   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3197
3198   MenuItem modifyPID = new MenuItem();
3199
3200   MenuItem modifyConservation = new MenuItem();
3201
3202   CheckboxMenuItem autoCalculate = null;
3203
3204   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3205           "Sort Alignment With New Tree", true);
3206
3207   Menu sortByTreeMenu = new Menu();
3208
3209   MenuItem inputText = new MenuItem();
3210
3211   MenuItem documentation = new MenuItem();
3212
3213   MenuItem about = new MenuItem();
3214
3215   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3222
3223   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3224
3225   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3226
3227   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3228
3229   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3230
3231   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3232
3233   /**
3234    * Initialise menus and other items
3235    *
3236    * @throws Exception
3237    */
3238   private void jbInit() throws Exception
3239   {
3240     setMenuBar(alignFrameMenuBar);
3241
3242     /*
3243      * Configure File menu items and actions
3244      */
3245     inputText
3246             .setLabel(MessageManager.getString("label.input_from_textbox"));
3247     inputText.addActionListener(this);
3248     Menu outputTextboxMenu = new Menu(
3249             MessageManager.getString("label.out_to_textbox"));
3250     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3251     {
3252       MenuItem item = new MenuItem(ff);
3253
3254       item.addActionListener(new java.awt.event.ActionListener()
3255       {
3256         @Override
3257         public void actionPerformed(ActionEvent e)
3258         {
3259           outputText_actionPerformed(e);
3260         }
3261       });
3262
3263       outputTextboxMenu.add(item);
3264     }
3265     closeMenuItem.addActionListener(this);
3266     loadApplication.addActionListener(this);
3267     loadTree.addActionListener(this);
3268     loadAnnotations.addActionListener(this);
3269     outputFeatures.addActionListener(this);
3270     outputAnnotations.addActionListener(this);
3271
3272     /*
3273      * Configure Edit menu items and actions
3274      */
3275     undoMenuItem.setEnabled(false);
3276     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3277     undoMenuItem.addActionListener(this);
3278     redoMenuItem.setEnabled(false);
3279     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3280     redoMenuItem.addActionListener(this);
3281     copy.setLabel(MessageManager.getString("action.copy"));
3282     copy.addActionListener(this);
3283     cut.setLabel(MessageManager.getString("action.cut"));
3284     cut.addActionListener(this);
3285     delete.setLabel(MessageManager.getString("action.delete"));
3286     delete.addActionListener(this);
3287     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3288     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3289     pasteNew.addActionListener(this);
3290     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3291     pasteThis.addActionListener(this);
3292     remove2LeftMenuItem.setLabel(MessageManager
3293             .getString("action.remove_left"));
3294     remove2LeftMenuItem.addActionListener(this);
3295     remove2RightMenuItem.setLabel(MessageManager
3296             .getString("action.remove_right"));
3297     remove2RightMenuItem.addActionListener(this);
3298     removeGappedColumnMenuItem.setLabel(MessageManager
3299             .getString("action.remove_empty_columns"));
3300     removeGappedColumnMenuItem.addActionListener(this);
3301     removeAllGapsMenuItem.setLabel(MessageManager
3302             .getString("action.remove_all_gaps"));
3303     removeAllGapsMenuItem.addActionListener(this);
3304     removeRedundancyMenuItem.setLabel(MessageManager
3305             .getString("action.remove_redundancy"));
3306     removeRedundancyMenuItem.addActionListener(this);
3307
3308     /*
3309      * Configure Select menu items and actions
3310      */
3311     findMenuItem.setLabel(MessageManager.getString("action.find"));
3312     findMenuItem.addActionListener(this);
3313     selectAllSequenceMenuItem.addActionListener(this);
3314     deselectAllSequenceMenuItem.addActionListener(this);
3315     invertSequenceMenuItem.setLabel(MessageManager
3316             .getString("action.invert_sequence_selection"));
3317     invertSequenceMenuItem.addActionListener(this);
3318     invertColSel.setLabel(MessageManager
3319             .getString("action.invert_column_selection"));
3320     invertColSel.addActionListener(this);
3321     deleteGroups.setLabel(MessageManager
3322             .getString("action.undefine_groups"));
3323     deleteGroups.addActionListener(this);
3324     grpsFromSelection.setLabel(MessageManager
3325             .getString("action.make_groups_selection"));
3326     grpsFromSelection.addActionListener(this);
3327     createGroup.setLabel(MessageManager.getString("action.create_group"));
3328     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3329     annotationColumnSelection.setLabel(MessageManager
3330             .getString("action.select_by_annotation"));
3331     annotationColumnSelection.addActionListener(this);
3332
3333     /*
3334      * Configure View menu items and actions
3335      */
3336     newView.setLabel(MessageManager.getString("action.new_view"));
3337     newView.addActionListener(this);
3338     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3339     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3340     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3341     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3342     hideColumns
3343             .setLabel(MessageManager.getString("label.selected_columns"));
3344     hideSequences.setLabel(MessageManager
3345             .getString("label.selected_sequences"));
3346     hideAllButSelection.setLabel(MessageManager
3347             .getString("label.all_but_selected_region"));
3348     hideAllSelection.setLabel(MessageManager
3349             .getString("label.selected_region"));
3350     showAllHidden.setLabel(MessageManager
3351             .getString("label.all_sequences_columns"));
3352     showColumns.addActionListener(this);
3353     showSeqs.addActionListener(this);
3354     hideColumns.addActionListener(this);
3355     hideSequences.addActionListener(this);
3356     hideAllButSelection.addActionListener(this);
3357     hideAllSelection.addActionListener(this);
3358     showAllHidden.addActionListener(this);
3359     featureSettings.setLabel(MessageManager
3360             .getString("action.feature_settings"));
3361     featureSettings.addActionListener(this);
3362     sequenceFeatures.setLabel(MessageManager
3363             .getString("label.show_sequence_features"));
3364     sequenceFeatures.addItemListener(this);
3365     sequenceFeatures.setState(false);
3366     followMouseOverFlag.setLabel(MessageManager
3367             .getString("label.automatic_scrolling"));
3368     followMouseOverFlag.addItemListener(this);
3369     alProperties.addActionListener(this);
3370     overviewMenuItem.setLabel(MessageManager
3371             .getString("label.overview_window"));
3372     overviewMenuItem.addActionListener(this);
3373
3374     /*
3375      * Configure Annotations menu items and actions
3376      */
3377     annotationPanelMenuItem.setLabel(MessageManager
3378             .getString("label.show_annotations"));
3379     annotationPanelMenuItem.addItemListener(this);
3380     showGroupConsensus.setLabel(MessageManager
3381             .getString("label.group_consensus"));
3382     showGroupConservation.setLabel(MessageManager
3383             .getString("label.group_conservation"));
3384     showConsensusHistogram.setLabel(MessageManager
3385             .getString("label.show_consensus_histogram"));
3386     showSequenceLogo.setLabel(MessageManager
3387             .getString("label.show_consensus_logo"));
3388     normSequenceLogo.setLabel(MessageManager
3389             .getString("label.norm_consensus_logo"));
3390     applyAutoAnnotationSettings.setLabel(MessageManager
3391             .getString("label.apply_all_groups"));
3392     applyAutoAnnotationSettings.setState(true);
3393     Menu autoAnnMenu = new Menu(
3394             MessageManager.getString("label.autocalculated_annotation"));
3395     showGroupConsensus.addItemListener(this);
3396     showGroupConservation.addItemListener(this);
3397     showConsensusHistogram.addItemListener(this);
3398     showSequenceLogo.addItemListener(this);
3399     normSequenceLogo.addItemListener(this);
3400     applyAutoAnnotationSettings.addItemListener(this);
3401     showAlignmentAnnotations = new CheckboxMenuItem(
3402             MessageManager.getString("label.show_all_al_annotations"));
3403     showSequenceAnnotations = new CheckboxMenuItem(
3404             MessageManager.getString("label.show_all_seq_annotations"));
3405     sortAnnBySequence = new CheckboxMenuItem(
3406             MessageManager.getString("label.sort_annotations_by_sequence"));
3407     sortAnnByLabel = new CheckboxMenuItem(
3408             MessageManager.getString("label.sort_annotations_by_label"));
3409     showAutoFirst = new CheckboxMenuItem(
3410             MessageManager.getString("label.show_first"));
3411     showAutoFirst.setState(false); // pending applet parameter
3412     setShowAutoCalculatedAbove(showAutoFirst.getState());
3413     showAutoLast = new CheckboxMenuItem(
3414             MessageManager.getString("label.show_last"));
3415     showAutoLast.setState(!showAutoFirst.getState());
3416     showAlignmentAnnotations.addItemListener(this);
3417     showSequenceAnnotations.addItemListener(this);
3418     sortAnnBySequence.addItemListener(this);
3419     sortAnnByLabel.addItemListener(this);
3420     showAutoFirst.addItemListener(this);
3421     showAutoLast.addItemListener(this);
3422
3423     /*
3424      * Configure Format menu items and actions
3425      */
3426     font.setLabel(MessageManager.getString("action.font"));
3427     font.addActionListener(this);
3428     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3429     scaleAbove.setState(true);
3430     scaleAbove.setEnabled(false);
3431     scaleAbove.addItemListener(this);
3432     scaleLeft.setEnabled(false);
3433     scaleLeft.setState(true);
3434     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3435     scaleLeft.addItemListener(this);
3436     scaleRight.setEnabled(false);
3437     scaleRight.setState(true);
3438     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3439     scaleRight.addItemListener(this);
3440     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3441     viewBoxesMenuItem.setState(true);
3442     viewBoxesMenuItem.addItemListener(this);
3443     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3444     viewTextMenuItem.setState(true);
3445     viewTextMenuItem.addItemListener(this);
3446     colourTextMenuItem.setLabel(MessageManager
3447             .getString("label.colour_text"));
3448     colourTextMenuItem.addItemListener(this);
3449     displayNonconservedMenuItem.setLabel(MessageManager
3450             .getString("label.show_non_conserved"));
3451     displayNonconservedMenuItem.addItemListener(this);
3452     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3453     wrapMenuItem.addItemListener(this);
3454     renderGapsMenuItem.setLabel(MessageManager
3455             .getString("action.show_gaps"));
3456     renderGapsMenuItem.setState(true);
3457     renderGapsMenuItem.addItemListener(this);
3458     centreColumnLabelFlag.setLabel(MessageManager
3459             .getString("label.centre_column_labels"));
3460     centreColumnLabelFlag.addItemListener(this);
3461     seqLimits.setState(true);
3462     seqLimits.setLabel(MessageManager
3463             .getString("label.show_sequence_limits"));
3464     seqLimits.addItemListener(this);
3465
3466     /*
3467      * Configure Colour menu items and actions
3468      */
3469     applyToAllGroups.setLabel(MessageManager
3470             .getString("label.apply_colour_to_all_groups"));
3471     applyToAllGroups.setState(true);
3472     applyToAllGroups.addItemListener(this);
3473     clustalColour.setLabel(MessageManager
3474             .getString("label.colourScheme_clustal"));
3475     clustalColour.addActionListener(this);
3476     zappoColour.setLabel(MessageManager
3477             .getString("label.colourScheme_zappo"));
3478     zappoColour.addActionListener(this);
3479     taylorColour.setLabel(MessageManager
3480             .getString("label.colourScheme_taylor"));
3481     taylorColour.addActionListener(this);
3482     hydrophobicityColour.setLabel(MessageManager
3483             .getString("label.colourScheme_hydrophobic"));
3484     hydrophobicityColour.addActionListener(this);
3485     helixColour.setLabel(MessageManager
3486             .getString("label.colourScheme_helix_propensity"));
3487     helixColour.addActionListener(this);
3488     strandColour.setLabel(MessageManager
3489             .getString("label.colourScheme_strand_propensity"));
3490     strandColour.addActionListener(this);
3491     turnColour.setLabel(MessageManager
3492             .getString("label.colourScheme_turn_propensity"));
3493     turnColour.addActionListener(this);
3494     buriedColour.setLabel(MessageManager
3495             .getString("label.colourScheme_buried_index"));
3496     buriedColour.addActionListener(this);
3497     purinePyrimidineColour.setLabel(MessageManager
3498             .getString("label.colourScheme_purine/pyrimidine"));
3499     purinePyrimidineColour.addActionListener(this);
3500     // RNAInteractionColour.setLabel(MessageManager
3501     // .getString("label.rna_interaction"));
3502     // RNAInteractionColour.addActionListener(this);
3503     RNAHelixColour.setLabel(MessageManager
3504             .getString("label.colourScheme_rna_helices"));
3505     RNAHelixColour.addActionListener(this);
3506     userDefinedColour.setLabel(MessageManager
3507             .getString("action.user_defined"));
3508     userDefinedColour.addActionListener(this);
3509     PIDColour.setLabel(MessageManager
3510             .getString("label.colourScheme_%_identity"));
3511     PIDColour.addActionListener(this);
3512     BLOSUM62Colour.setLabel(MessageManager
3513             .getString("label.colourScheme_blosum62"));
3514     BLOSUM62Colour.addActionListener(this);
3515     tcoffeeColour.setLabel(MessageManager
3516             .getString("label.colourScheme_t-coffee_scores"));
3517     // it will be enabled only if a score file is provided
3518     tcoffeeColour.setEnabled(false);
3519     tcoffeeColour.addActionListener(this);
3520     conservationMenuItem.setLabel(MessageManager
3521             .getString("action.by_conservation"));
3522     conservationMenuItem.addItemListener(this);
3523     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3524     noColourmenuItem.addActionListener(this);
3525     abovePIDThreshold.setLabel(MessageManager
3526             .getString("label.above_identity_threshold"));
3527     abovePIDThreshold.addItemListener(this);
3528     nucleotideColour.setLabel(MessageManager
3529             .getString("label.colourScheme_nucleotide"));
3530     nucleotideColour.addActionListener(this);
3531     modifyPID.setLabel(MessageManager
3532             .getString("label.modify_identity_threshold"));
3533     modifyPID.addActionListener(this);
3534     modifyConservation.setLabel(MessageManager
3535             .getString("label.modify_conservation_threshold"));
3536     modifyConservation.addActionListener(this);
3537     annotationColour.setLabel(MessageManager
3538             .getString("action.by_annotation"));
3539     annotationColour.addActionListener(this);
3540
3541     /*
3542      * Configure Calculate menu items and actions
3543      */
3544     sortPairwiseMenuItem.setLabel(MessageManager
3545             .getString("action.by_pairwise_id"));
3546     sortPairwiseMenuItem.addActionListener(this);
3547     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3548     sortIDMenuItem.addActionListener(this);
3549     sortLengthMenuItem.setLabel(MessageManager
3550             .getString("action.by_length"));
3551     sortLengthMenuItem.addActionListener(this);
3552     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3553     sortGroupMenuItem.addActionListener(this);
3554     pairwiseAlignmentMenuItem.setLabel(MessageManager
3555             .getString("action.pairwise_alignment"));
3556     pairwiseAlignmentMenuItem.addActionListener(this);
3557     PCAMenuItem.setLabel(MessageManager
3558             .getString("label.principal_component_analysis"));
3559     PCAMenuItem.addActionListener(this);
3560     autoCalculate = new CheckboxMenuItem(
3561             MessageManager.getString("label.autocalculate_consensus"), true);
3562     averageDistanceTreeMenuItem.setLabel(MessageManager
3563             .getString("label.average_distance_identity"));
3564     averageDistanceTreeMenuItem.addActionListener(this);
3565     neighbourTreeMenuItem.setLabel(MessageManager
3566             .getString("label.neighbour_joining_identity"));
3567     neighbourTreeMenuItem.addActionListener(this);
3568     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3569             .getString("label.average_distance_blosum62"));
3570     avDistanceTreeBlosumMenuItem.addActionListener(this);
3571     njTreeBlosumMenuItem.setLabel(MessageManager
3572             .getString("label.neighbour_blosum62"));
3573     njTreeBlosumMenuItem.addActionListener(this);
3574     sortByTreeMenu.setLabel(MessageManager
3575             .getString("action.by_tree_order"));
3576     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3577     Menu calculateTreeMenu = new Menu(
3578             MessageManager.getString("action.calculate_tree"));
3579     autoCalculate.addItemListener(this);
3580     sortByTree.addItemListener(this);
3581
3582     /*
3583      * Configure Help menu items and actions
3584      */
3585     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3586     documentation.setLabel(MessageManager.getString("label.documentation"));
3587     documentation.addActionListener(this);
3588     about.setLabel(MessageManager.getString("label.about"));
3589     about.addActionListener(this);
3590
3591     /*
3592      * Add top level menus to frame
3593      */
3594     alignFrameMenuBar.add(fileMenu);
3595     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3596     alignFrameMenuBar.add(editMenu);
3597     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3598     alignFrameMenuBar.add(selectMenu);
3599     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3600     alignFrameMenuBar.add(viewMenu);
3601     Menu annotationsMenu = new Menu(
3602             MessageManager.getString("action.annotations"));
3603     alignFrameMenuBar.add(annotationsMenu);
3604     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3605     alignFrameMenuBar.add(formatMenu);
3606     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3607     alignFrameMenuBar.add(colourMenu);
3608     Menu calculateMenu = new Menu(
3609             MessageManager.getString("action.calculate"));
3610     alignFrameMenuBar.add(calculateMenu);
3611     alignFrameMenuBar.add(helpMenu);
3612
3613     /*
3614      * File menu
3615      */
3616     fileMenu.add(inputText);
3617     fileMenu.add(loadTree);
3618     fileMenu.add(loadAnnotations);
3619     fileMenu.addSeparator();
3620     fileMenu.add(outputTextboxMenu);
3621     fileMenu.add(outputFeatures);
3622     fileMenu.add(outputAnnotations);
3623     if (jalviewServletURL != null)
3624     {
3625       fileMenu.add(loadApplication);
3626     }
3627     fileMenu.addSeparator();
3628     fileMenu.add(closeMenuItem);
3629
3630     /*
3631      * Edit menu
3632      */
3633     editMenu.add(undoMenuItem);
3634     editMenu.add(redoMenuItem);
3635     editMenu.add(cut);
3636     editMenu.add(copy);
3637     pasteMenu.add(pasteNew);
3638     pasteMenu.add(pasteThis);
3639     editMenu.add(pasteMenu);
3640     editMenu.add(delete);
3641     editMenu.addSeparator();
3642     editMenu.add(remove2LeftMenuItem);
3643     editMenu.add(remove2RightMenuItem);
3644     editMenu.add(removeGappedColumnMenuItem);
3645     editMenu.add(removeAllGapsMenuItem);
3646     editMenu.add(removeRedundancyMenuItem);
3647
3648     /*
3649      * Select menu
3650      */
3651     selectMenu.add(findMenuItem);
3652     selectMenu.addSeparator();
3653     selectMenu.add(selectAllSequenceMenuItem);
3654     selectMenu.add(deselectAllSequenceMenuItem);
3655     selectMenu.add(invertSequenceMenuItem);
3656     selectMenu.add(invertColSel);
3657     selectMenu.add(createGroup);
3658     selectMenu.add(unGroup);
3659     selectMenu.add(grpsFromSelection);
3660     selectMenu.add(deleteGroups);
3661     selectMenu.add(annotationColumnSelection);
3662
3663     /*
3664      * View menu
3665      */
3666     viewMenu.add(newView);
3667     viewMenu.addSeparator();
3668     showMenu.add(showColumns);
3669     showMenu.add(showSeqs);
3670     showMenu.add(showAllHidden);
3671     viewMenu.add(showMenu);
3672     hideMenu.add(hideColumns);
3673     hideMenu.add(hideSequences);
3674     hideMenu.add(hideAllSelection);
3675     hideMenu.add(hideAllButSelection);
3676     viewMenu.add(hideMenu);
3677     viewMenu.addSeparator();
3678     viewMenu.add(followMouseOverFlag);
3679     viewMenu.addSeparator();
3680     viewMenu.add(sequenceFeatures);
3681     viewMenu.add(featureSettings);
3682     viewMenu.addSeparator();
3683     viewMenu.add(alProperties);
3684     viewMenu.addSeparator();
3685     viewMenu.add(overviewMenuItem);
3686
3687     /*
3688      * Annotations menu
3689      */
3690     annotationsMenu.add(annotationPanelMenuItem);
3691     annotationsMenu.addSeparator();
3692     annotationsMenu.add(showAlignmentAnnotations);
3693     annotationsMenu.add(showSequenceAnnotations);
3694     annotationsMenu.add(sortAnnBySequence);
3695     annotationsMenu.add(sortAnnByLabel);
3696     annotationsMenu.addSeparator();
3697     autoAnnMenu.add(showAutoFirst);
3698     autoAnnMenu.add(showAutoLast);
3699     autoAnnMenu.addSeparator();
3700     autoAnnMenu.add(applyAutoAnnotationSettings);
3701     autoAnnMenu.add(showConsensusHistogram);
3702     autoAnnMenu.add(showSequenceLogo);
3703     autoAnnMenu.add(normSequenceLogo);
3704     autoAnnMenu.addSeparator();
3705     autoAnnMenu.add(showGroupConservation);
3706     autoAnnMenu.add(showGroupConsensus);
3707     annotationsMenu.add(autoAnnMenu);
3708
3709     /*
3710      * Format menu
3711      */
3712     formatMenu.add(font);
3713     formatMenu.add(seqLimits);
3714     formatMenu.add(wrapMenuItem);
3715     formatMenu.add(scaleAbove);
3716     formatMenu.add(scaleLeft);
3717     formatMenu.add(scaleRight);
3718     formatMenu.add(viewBoxesMenuItem);
3719     formatMenu.add(viewTextMenuItem);
3720     formatMenu.add(colourTextMenuItem);
3721     formatMenu.add(displayNonconservedMenuItem);
3722     formatMenu.add(renderGapsMenuItem);
3723     formatMenu.add(centreColumnLabelFlag);
3724
3725     /*
3726      * Colour menu
3727      */
3728     colourMenu.add(applyToAllGroups);
3729     colourMenu.addSeparator();
3730     colourMenu.add(noColourmenuItem);
3731     colourMenu.add(clustalColour);
3732     colourMenu.add(BLOSUM62Colour);
3733     colourMenu.add(PIDColour);
3734     colourMenu.add(zappoColour);
3735     colourMenu.add(taylorColour);
3736     colourMenu.add(hydrophobicityColour);
3737     colourMenu.add(helixColour);
3738     colourMenu.add(strandColour);
3739     colourMenu.add(turnColour);
3740     colourMenu.add(buriedColour);
3741     colourMenu.add(nucleotideColour);
3742     colourMenu.add(purinePyrimidineColour);
3743     // colourMenu.add(RNAInteractionColour);
3744     colourMenu.add(tcoffeeColour);
3745     colourMenu.add(userDefinedColour);
3746     colourMenu.addSeparator();
3747     colourMenu.add(conservationMenuItem);
3748     colourMenu.add(modifyConservation);
3749     colourMenu.add(abovePIDThreshold);
3750     colourMenu.add(modifyPID);
3751     colourMenu.add(annotationColour);
3752     colourMenu.add(RNAHelixColour);
3753
3754     /*
3755      * Calculate menu
3756      */
3757     sortMenu.add(sortIDMenuItem);
3758     sortMenu.add(sortLengthMenuItem);
3759     sortMenu.add(sortByTreeMenu);
3760     sortMenu.add(sortGroupMenuItem);
3761     sortMenu.add(sortPairwiseMenuItem);
3762     calculateMenu.add(sortMenu);
3763     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3764     calculateTreeMenu.add(neighbourTreeMenuItem);
3765     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3766     calculateTreeMenu.add(njTreeBlosumMenuItem);
3767     calculateMenu.add(calculateTreeMenu);
3768     calculateMenu.addSeparator();
3769     calculateMenu.add(pairwiseAlignmentMenuItem);
3770     calculateMenu.add(PCAMenuItem);
3771     calculateMenu.add(autoCalculate);
3772     calculateMenu.add(sortByTree);
3773
3774     /*
3775      * Help menu
3776      */
3777     helpMenu.add(documentation);
3778     helpMenu.add(about);
3779
3780     /*
3781      * Status bar
3782      */
3783     statusBar.setBackground(Color.white);
3784     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3785     statusBar.setText(MessageManager.getString("label.status_bar"));
3786     this.add(statusBar, BorderLayout.SOUTH);
3787   }
3788
3789   @Override
3790   public void setStatus(String string)
3791   {
3792     statusBar.setText(string);
3793   };
3794
3795   MenuItem featureSettings = new MenuItem();
3796
3797   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3798
3799   MenuItem annotationColour = new MenuItem();
3800
3801   MenuItem annotationColumnSelection = new MenuItem();
3802
3803   MenuItem invertColSel = new MenuItem();
3804
3805   MenuItem showColumns = new MenuItem();
3806
3807   MenuItem showSeqs = new MenuItem();
3808
3809   MenuItem hideColumns = new MenuItem();
3810
3811   MenuItem hideSequences = new MenuItem();
3812
3813   MenuItem hideAllButSelection = new MenuItem();
3814
3815   MenuItem hideAllSelection = new MenuItem();
3816
3817   MenuItem showAllHidden = new MenuItem();
3818
3819   MenuItem newView = new MenuItem();
3820
3821   private CheckboxMenuItem showAlignmentAnnotations;
3822
3823   private CheckboxMenuItem showSequenceAnnotations;
3824
3825   private CheckboxMenuItem sortAnnBySequence;
3826
3827   private CheckboxMenuItem sortAnnByLabel;
3828
3829   private CheckboxMenuItem showAutoFirst;
3830
3831   private CheckboxMenuItem showAutoLast;
3832
3833   private SplitFrame splitFrame;
3834
3835   /**
3836    * Attach the alignFrame panels after embedding menus, if necessary. This used
3837    * to be called setEmbedded, but is now creates the dropdown menus in a
3838    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3839    *
3840    * @param reallyEmbedded
3841    *          true to attach the view to the applet area on the page rather than
3842    *          in a new window
3843    */
3844   public void createAlignFrameWindow(boolean reallyEmbedded)
3845   {
3846     if (reallyEmbedded)
3847     {
3848       embedAlignFrameInApplet(viewport.applet);
3849     }
3850     else
3851     {
3852       // //////
3853       // test and embed menu bar if necessary.
3854       //
3855       if (embedMenuIfNeeded(alignPanel))
3856       {
3857         /*
3858          * adjust for status bar height too. ? pointless as overridden by layout
3859          * manager
3860          */
3861         alignPanel.setSize(getSize().width,
3862                 getSize().height - statusBar.getHeight());
3863       }
3864       add(statusBar, BorderLayout.SOUTH);
3865       add(alignPanel, BorderLayout.CENTER);
3866       // and register with the applet so it can pass external API calls to us
3867       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3868               frameHeight);
3869     }
3870   }
3871
3872   /**
3873    * Add the components of this AlignFrame to the applet container.
3874    *
3875    * @param theApplet
3876    */
3877   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3878   {
3879     // ////
3880     // Explicitly build the embedded menu panel for the on-page applet
3881     //
3882     // view cannot be closed if its actually on the page
3883     fileMenu.remove(closeMenuItem);
3884     fileMenu.remove(3); // Remove Separator
3885     // construct embedded menu, using default font
3886     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3887     // and actually add the components to the applet area
3888     theApplet.setLayout(new BorderLayout());
3889     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3890     theApplet.add(statusBar, BorderLayout.SOUTH);
3891     // TODO should size be left to the layout manager?
3892     alignPanel.setSize(theApplet.getSize().width,
3893             theApplet.getSize().height - embeddedMenu.getHeight()
3894                     - statusBar.getHeight());
3895     theApplet.add(alignPanel, BorderLayout.CENTER);
3896     final AlignFrame me = this;
3897     theApplet.addFocusListener(new FocusListener()
3898     {
3899
3900       @Override
3901       public void focusLost(FocusEvent e)
3902       {
3903         if (theApplet.currentAlignFrame == me)
3904         {
3905           theApplet.currentAlignFrame = null;
3906         }
3907       }
3908
3909       @Override
3910       public void focusGained(FocusEvent e)
3911       {
3912         theApplet.currentAlignFrame = me;
3913       }
3914     });
3915     theApplet.validate();
3916   }
3917
3918   /**
3919    * create a new binding between structures in an existing jmol viewer instance
3920    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3921    * this does not open a new Jmol window, or modify the display of the
3922    * structures in the original jmol window. Note This method doesn't work
3923    * without an additional javascript library to exchange messages between the
3924    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3925    *
3926    * @param viewer
3927    *          JmolViewer instance
3928    * @param sequenceIds
3929    *          - sequence Ids to search for associations
3930    */
3931   public SequenceStructureBinding addStructureViewInstance(
3932           Object jmolviewer, String[] sequenceIds)
3933   {
3934     Viewer viewer = null;
3935     try
3936     {
3937       viewer = (Viewer) jmolviewer;
3938     } catch (ClassCastException ex)
3939     {
3940       System.err.println("Unsupported viewer object :"
3941               + jmolviewer.getClass());
3942     }
3943     if (viewer == null)
3944     {
3945       System.err.println("Can't use this object as a structure viewer:"
3946               + jmolviewer.getClass());
3947       return null;
3948     }
3949     SequenceI[] seqs = null;
3950     if (sequenceIds == null || sequenceIds.length == 0)
3951     {
3952       seqs = viewport.getAlignment().getSequencesArray();
3953     }
3954     else
3955     {
3956       Vector sqi = new Vector();
3957       AlignmentI al = viewport.getAlignment();
3958       for (int sid = 0; sid < sequenceIds.length; sid++)
3959       {
3960         SequenceI sq = al.findName(sequenceIds[sid]);
3961         if (sq != null)
3962         {
3963           sqi.addElement(sq);
3964         }
3965       }
3966       if (sqi.size() > 0)
3967       {
3968         seqs = new SequenceI[sqi.size()];
3969         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3970         {
3971           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3972         }
3973       }
3974       else
3975       {
3976         return null;
3977       }
3978     }
3979     AAStructureBindingModel jmv = null;
3980     // TODO: search for a jmv that involves viewer
3981     if (jmv == null)
3982     { // create a new viewer/jalview binding.
3983       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3984     }
3985     return jmv;
3986
3987   }
3988
3989   /**
3990    * bind a pdb file to a sequence in the current view
3991    *
3992    * @param sequenceId
3993    *          - sequenceId within the dataset.
3994    * @param pdbEntryString
3995    *          - the short name for the PDB file
3996    * @param pdbFile
3997    *          - pdb file - either a URL or a valid PDB file.
3998    * @return true if binding was as success TODO: consider making an exception
3999    *         structure for indicating when PDB parsing or sequenceId location
4000    *         fails.
4001    */
4002   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4003           String pdbFile)
4004   {
4005     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4006     boolean needtoadd = false;
4007     if (toaddpdb != null)
4008     {
4009       Vector pdbe = toaddpdb.getAllPDBEntries();
4010       PDBEntry pdbentry = null;
4011       if (pdbe != null && pdbe.size() > 0)
4012       {
4013         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4014         {
4015           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4016           if (!pdbentry.getId().equals(pdbEntryString)
4017                   && !pdbentry.getFile().equals(pdbFile))
4018           {
4019             pdbentry = null;
4020           }
4021           else
4022           {
4023             continue;
4024           }
4025         }
4026       }
4027       if (pdbentry == null)
4028       {
4029         pdbentry = new PDBEntry();
4030         pdbentry.setId(pdbEntryString);
4031         pdbentry.setFile(pdbFile);
4032         needtoadd = true; // add this new entry to sequence.
4033       }
4034       // resolve data source
4035       // TODO: this code should be a refactored to an io package
4036       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4037               pdbFile, FileFormat.PDB);
4038       if (protocol == null)
4039       {
4040         return false;
4041       }
4042       if (needtoadd)
4043       {
4044         pdbentry.setProperty("protocol", protocol);
4045         toaddpdb.addPDBId(pdbentry);
4046         alignPanel.getStructureSelectionManager()
4047                 .registerPDBEntry(pdbentry);
4048       }
4049     }
4050     return true;
4051   }
4052
4053   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4054   {
4055     if (seqs != null)
4056     {
4057       Vector sequences = new Vector();
4058       for (int i = 0; i < seqs.length; i++)
4059       {
4060         if (seqs[i] != null)
4061         {
4062           sequences.addElement(new Object[] { seqs[i],
4063               (chains != null) ? chains[i] : null });
4064         }
4065       }
4066       seqs = new SequenceI[sequences.size()];
4067       chains = new String[sequences.size()];
4068       for (int i = 0, isize = sequences.size(); i < isize; i++)
4069       {
4070         Object[] oj = (Object[]) sequences.elementAt(i);
4071
4072         seqs[i] = (SequenceI) oj[0];
4073         chains[i] = (String) oj[1];
4074       }
4075     }
4076     return new Object[] { seqs, chains };
4077
4078   }
4079
4080   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4081           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4082   {
4083     // Scrub any null sequences from the array
4084     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4085     seqs = (SequenceI[]) sqch[0];
4086     chains = (String[]) sqch[1];
4087     if (seqs == null || seqs.length == 0)
4088     {
4089       System.err
4090               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4091     }
4092     if (protocol == null)
4093     {
4094       String sourceType = (String) pdb.getProperty("protocol");
4095       try
4096       {
4097         protocol = DataSourceType.valueOf(sourceType);
4098       } catch (IllegalArgumentException e)
4099       {
4100         // ignore
4101       }
4102       if (protocol == null)
4103       {
4104         System.err.println("Couldn't work out protocol to open structure: "
4105                 + pdb.getId());
4106         return;
4107       }
4108     }
4109     if (applet.useXtrnalSviewer)
4110     {
4111       // register the association(s) and quit, don't create any windows.
4112       if (StructureSelectionManager.getStructureSelectionManager(applet)
4113               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4114       {
4115         System.err.println("Failed to map " + pdb.getFile() + " ("
4116                 + protocol + ") to any sequences");
4117       }
4118       return;
4119     }
4120     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4121     {
4122       // can only do alignments with Jmol
4123       // find the last jmol window assigned to this alignment
4124       AppletJmol ajm = null, tajm;
4125       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4126       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4127       {
4128         tajm = (AppletJmol) jmols.elementAt(i);
4129         if (tajm.ap.alignFrame == this)
4130         {
4131           ajm = tajm;
4132           break;
4133         }
4134       }
4135       if (ajm != null)
4136       {
4137         System.err
4138                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4139         // try and add the pdb structure
4140         // ajm.addS
4141         ajm = null;
4142       }
4143     }
4144     // otherwise, create a new window
4145     if (applet.jmolAvailable)
4146     {
4147       new AppletJmol(pdb, seqs, chains, alignPanel,
4148               protocol);
4149       applet.lastFrameX += 40;
4150       applet.lastFrameY += 40;
4151     }
4152     else
4153     {
4154       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4155     }
4156
4157   }
4158
4159   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4160           SequenceI[][] seqs, String[][] chains, String[] protocols)
4161   {
4162     // TODO Auto-generated method stub
4163     System.err.println("Aligned Structure View: Not yet implemented.");
4164   }
4165
4166   /**
4167    * modify the current selection, providing the user has not made a selection
4168    * already.
4169    *
4170    * @param sel
4171    *          - sequences from this alignment
4172    * @param csel
4173    *          - columns to be selected on the alignment
4174    */
4175   public void select(SequenceGroup sel, ColumnSelection csel)
4176   {
4177     alignPanel.seqPanel.selection(sel, csel, null);
4178   }
4179
4180   public void scrollTo(int row, int column)
4181   {
4182     alignPanel.seqPanel.scrollTo(row, column);
4183   }
4184
4185   public void scrollToRow(int row)
4186   {
4187     alignPanel.seqPanel.scrollToRow(row);
4188   }
4189
4190   public void scrollToColumn(int column)
4191   {
4192     alignPanel.seqPanel.scrollToColumn(column);
4193   }
4194
4195   /**
4196    * @return the alignments unique ID.
4197    */
4198   public String getSequenceSetId()
4199   {
4200     return viewport.getSequenceSetId();
4201   }
4202
4203   /**
4204    * Load the (T-Coffee) score file from the specified url
4205    *
4206    * @param source
4207    *          File/URL/T-COFFEE score file contents
4208    * @throws IOException
4209    * @return true if alignment was annotated with data from source
4210    */
4211   public boolean loadScoreFile(String source) throws IOException
4212   {
4213
4214     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4215             AppletFormatAdapter.checkProtocol(source));
4216     if (!file.isValid())
4217     {
4218       // TODO: raise dialog for gui
4219       System.err.println("Problems parsing T-Coffee scores: "
4220               + file.getWarningMessage());
4221       System.err.println("Origin was:\n" + source);
4222       return false;
4223     }
4224
4225     /*
4226      * check that the score matrix matches the alignment dimensions
4227      */
4228     AlignmentI aln;
4229     if ((aln = viewport.getAlignment()) != null
4230             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4231                     .getWidth()))
4232     {
4233       // TODO: raise a dialog box here rather than bomb out.
4234       System.err
4235               .println("The scores matrix does not match the alignment dimensions");
4236
4237     }
4238
4239     // TODO add parameter to indicate if matching should be done
4240     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4241     {
4242       alignPanel.fontChanged();
4243       tcoffeeColour.setEnabled(true);
4244       // switch to this color
4245       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4246       return true;
4247     }
4248     else
4249     {
4250       System.err.println("Problems resolving T-Coffee scores:");
4251       if (file.getWarningMessage() != null)
4252       {
4253         System.err.println(file.getWarningMessage());
4254       }
4255     }
4256     return false;
4257   }
4258
4259   public SplitFrame getSplitFrame()
4260   {
4261     return this.splitFrame;
4262   }
4263
4264   public void setSplitFrame(SplitFrame sf)
4265   {
4266     this.splitFrame = sf;
4267   }
4268
4269   // may not need this
4270   @Override
4271   public void setShowSeqFeatures(boolean b)
4272   {
4273     // showSeqFeatures.setSelected(b);
4274     viewport.setShowSequenceFeatures(b);
4275
4276   }
4277
4278   @Override
4279   public void setMenusForViewport()
4280   {
4281     // setMenusFromViewport(viewport);
4282
4283   }
4284
4285   @Override
4286   public void refreshFeatureUI(boolean enableIfNecessary)
4287   {
4288     if (enableIfNecessary)
4289     {
4290       sequenceFeatures.setState(true);
4291       alignPanel.av.setShowSequenceFeatures(true);
4292     }
4293   }
4294
4295   @Override
4296   public FeatureSettingsControllerI getFeatureSettingsUI()
4297   {
4298     return alignPanel.av.featureSettings;
4299   }
4300
4301 }