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.RNAHelicesColourChooser;
  69 import jalview.schemes.StrandColourScheme;
  70 import jalview.schemes.TCoffeeColourScheme;
  71 import jalview.schemes.TaylorColourScheme;
  72 import jalview.schemes.TurnColourScheme;
  73 import jalview.schemes.ZappoColourScheme;
  74 import jalview.structure.StructureSelectionManager;
  75 import jalview.structures.models.AAStructureBindingModel;
  76 import jalview.util.MappingUtils;
  77 import jalview.util.MessageManager;
  78 import jalview.viewmodel.AlignmentViewport;
  79
  80 import java.awt.BorderLayout;
  81 import java.awt.Canvas;
  82 import java.awt.CheckboxMenuItem;
  83 import java.awt.Color;
  84 import java.awt.FlowLayout;
  85 import java.awt.Font;
  86 import java.awt.FontMetrics;
  87 import java.awt.Frame;
  88 import java.awt.Graphics;
  89 import java.awt.Label;
  90 import java.awt.Menu;
  91 import java.awt.MenuBar;
  92 import java.awt.MenuItem;
  93 import java.awt.Panel;
  94 import java.awt.event.ActionEvent;
  95 import java.awt.event.ActionListener;
  96 import java.awt.event.FocusEvent;
  97 import java.awt.event.FocusListener;
  98 import java.awt.event.ItemEvent;
  99 import java.awt.event.ItemListener;
 100 import java.awt.event.KeyEvent;
 101 import java.awt.event.KeyListener;
 102 import java.awt.event.WindowAdapter;
 103 import java.awt.event.WindowEvent;
 104 import java.io.IOException;
 105 import java.net.URL;
 106 import java.net.URLEncoder;
 107 import java.util.Arrays;
 108 import java.util.Deque;
 109 import java.util.HashMap;
 110 import java.util.List;
 111 import java.util.Map;
 112 import java.util.StringTokenizer;
 113 import java.util.Vector;
 114
 115 import org.jmol.viewer.Viewer;
 116
 117 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 118         ItemListener, KeyListener, AlignViewControllerGuiI
 119 {
 120   public AlignViewControllerI avc;
 121
 122   public AlignmentPanel alignPanel;
 123
 124   public AlignViewport viewport;
 125
 126   // width and height may be overridden by applet parameters
 127   int frameWidth = 700;
 128
 129   int frameHeight = 500;
 130
 131   String jalviewServletURL;
 132
 133   /*
 134    * Flag for showing autocalculated consensus above or below other consensus
 135    * rows
 136    */
 137   private boolean showAutoCalculatedAbove;
 138
 139   private SequenceAnnotationOrder annotationSortOrder;
 140
 141   /**
 142    * Constructor that creates the frame and adds it to the display.
 143    *
 144    * @param al
 145    * @param applet
 146    * @param title
 147    * @param embedded
 148    */
 149   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 150           boolean embedded)
 151   {
 152     this(al, applet, title, embedded, true);
 153   }
 154
 155   /**
 156    * Constructor that optionally allows the frame to be displayed or only
 157    * created.
 158    *
 159    * @param al
 160    * @param applet
 161    * @param title
 162    * @param embedded
 163    * @param addToDisplay
 164    */
 165   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 166           boolean embedded, boolean addToDisplay)
 167   {
 168     this(al, null, null, applet, title, embedded, addToDisplay);
 169   }
 170
 171   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 172           ColumnSelection columnSelection, JalviewLite applet,
 173           String title, boolean embedded)
 174   {
 175     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 176   }
 177
 178   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 179           ColumnSelection columnSelection, JalviewLite applet,
 180           String title, boolean embedded, boolean addToDisplay)
 181   {
 182     if (applet != null)
 183     {
 184       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 185     }
 186
 187     try
 188     {
 189       jbInit();
 190     } catch (Exception ex)
 191     {
 192       ex.printStackTrace();
 193     }
 194     // need to get window geometry before we calculate alignment layout
 195     if (applet != null)
 196     {
 197       String param;
 198       try
 199       {
 200         param = applet.getParameter("windowWidth");
 201         if (param != null)
 202         {
 203           int width = Integer.parseInt(param);
 204           frameWidth = width;
 205         }
 206         param = applet.getParameter("windowHeight");
 207         if (param != null)
 208         {
 209           int height = Integer.parseInt(param);
 210           frameHeight = height;
 211         }
 212       } catch (Exception ex)
 213       {
 214       }
 215     }
 216     viewport = new AlignViewport(al, applet);
 217
 218     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 219     {
 220       viewport.hideSequence(hiddenSeqs);
 221     }
 222     if (columnSelection != null)
 223     {
 224       viewport.setColumnSelection(columnSelection);
 225     }
 226     viewport.setScaleAboveWrapped(scaleAbove.getState());
 227
 228     alignPanel = new AlignmentPanel(this, viewport);
 229     avc = new jalview.controller.AlignViewController(this, viewport,
 230             alignPanel);
 231     viewport.updateConservation(alignPanel);
 232     viewport.updateConsensus(alignPanel);
 233
 234     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 235     followMouseOverFlag.setState(viewport.isFollowHighlight());
 236     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 237     showGroupConservation.setState(viewport.isShowGroupConservation());
 238     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 239     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 240     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 241     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 242     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 243     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 244     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 245     showAlignmentAnnotations.setState(true);
 246     showSequenceAnnotations.setState(false);
 247
 248     seqLimits.setState(viewport.getShowJVSuffix());
 249
 250     if (applet != null)
 251     {
 252       String param = applet.getParameter("sortBy");
 253       if (param != null)
 254       {
 255         if (param.equalsIgnoreCase("Id"))
 256         {
 257           sortIDMenuItem_actionPerformed();
 258         }
 259         else if (param.equalsIgnoreCase("Pairwise Identity"))
 260         {
 261           sortPairwiseMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Length"))
 264         {
 265           sortLengthMenuItem_actionPerformed();
 266         }
 267       }
 268
 269       param = applet.getParameter("wrap");
 270       if (param != null)
 271       {
 272         if (param.equalsIgnoreCase("true"))
 273         {
 274           wrapMenuItem.setState(true);
 275           wrapMenuItem_actionPerformed();
 276         }
 277       }
 278       param = applet.getParameter("centrecolumnlabels");
 279       if (param != null)
 280       {
 281         centreColumnLabelFlag.setState(true);
 282         centreColumnLabelFlag_stateChanged();
 283       }
 284
 285     }
 286     if (viewport.getAlignment().isNucleotide())
 287     {
 288       viewport.updateStrucConsensus(alignPanel);
 289       if (viewport.getAlignment().hasRNAStructure())
 290       {
 291         RNAHelixColour.setEnabled(true);
 292       }
 293       else
 294       {
 295         RNAHelixColour.setEnabled(false);
 296       }
 297     }
 298     else
 299     {
 300       RNAHelixColour.setEnabled(false);
 301       purinePyrimidineColour.setEnabled(false);
 302       nucleotideColour.setEnabled(false);
 303     }
 304     // Some JVMS send keyevents to Top frame or lowest panel,
 305     // Havent worked out why yet. So add to both this frame and seqCanvas for
 306     // now
 307     this.addKeyListener(this);
 308     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 309     alignPanel.idPanel.idCanvas.addKeyListener(this);
 310     alignPanel.scalePanel.addKeyListener(this);
 311     alignPanel.annotationPanel.addKeyListener(this);
 312     alignPanel.annotationPanelHolder.addKeyListener(this);
 313     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 314     alignPanel.alabels.addKeyListener(this);
 315
 316     setAnnotationsVisibility();
 317
 318     if (addToDisplay)
 319     {
 320       addToDisplay(embedded);
 321     }
 322   }
 323
 324   /**
 325    * @param embedded
 326    */
 327   public void addToDisplay(boolean embedded)
 328   {
 329     createAlignFrameWindow(embedded);
 330     validate();
 331     alignPanel.adjustAnnotationHeight();
 332     alignPanel.paintAlignment(true);
 333   }
 334
 335   public AlignViewport getAlignViewport()
 336   {
 337     return viewport;
 338   }
 339
 340   public SeqCanvas getSeqcanvas()
 341   {
 342     return alignPanel.seqPanel.seqCanvas;
 343   }
 344
 345   /**
 346    * Load a features file onto the alignment
 347    *
 348    * @param file
 349    *          file URL, content, or other resolvable path
 350    * @param type
 351    *          is protocol for accessing data referred to by file
 352    */
 353
 354   public boolean parseFeaturesFile(String file, DataSourceType type)
 355   {
 356     return parseFeaturesFile(file, type, true);
 357   }
 358
 359   /**
 360    * Load a features file onto the alignment
 361    *
 362    * @param file
 363    *          file URL, content, or other resolvable path
 364    * @param sourceType
 365    *          is protocol for accessing data referred to by file
 366    * @param autoenabledisplay
 367    *          when true, display features flag will be automatically enabled if
 368    *          features are loaded
 369    * @return true if data parsed as a features file
 370    */
 371   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 372           boolean autoenabledisplay)
 373   {
 374     boolean featuresFile = false;
 375     try
 376     {
 377       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 378               .getFeatureRenderer().getFeatureColours();
 379       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 380               "relaxedidmatch", false);
 381       featuresFile = new FeaturesFile(file, sourceType).parse(
 382               viewport.getAlignment(), colours, true, relaxedIdMatching);
 383     } catch (Exception ex)
 384     {
 385       ex.printStackTrace();
 386     }
 387
 388     if (featuresFile)
 389     {
 390       if (autoenabledisplay)
 391       {
 392         viewport.setShowSequenceFeatures(true);
 393         sequenceFeatures.setState(true);
 394       }
 395       if (alignPanel.seqPanel.seqCanvas.fr != null)
 396       {
 397         // update the min/max ranges where necessary
 398         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 399       }
 400       if (viewport.featureSettings != null)
 401       {
 402         viewport.featureSettings.refreshTable();
 403       }
 404       alignPanel.paintAlignment(true);
 405       statusBar.setText(MessageManager
 406               .getString("label.successfully_added_features_alignment"));
 407     }
 408     return featuresFile;
 409   }
 410
 411   @Override
 412   public void keyPressed(KeyEvent evt)
 413   {
 414     if (viewport.cursorMode
 415             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 416                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 417                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 418             && Character.isDigit(evt.getKeyChar()))
 419     {
 420       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 421     }
 422
 423     switch (evt.getKeyCode())
 424     {
 425     case 27: // escape key
 426       deselectAllSequenceMenuItem_actionPerformed();
 427
 428       alignPanel.alabels.cancelDrag();
 429       break;
 430     case KeyEvent.VK_X:
 431       if (evt.isControlDown() || evt.isMetaDown())
 432       {
 433         cut_actionPerformed();
 434       }
 435       break;
 436     case KeyEvent.VK_C:
 437       if (viewport.cursorMode && !evt.isControlDown())
 438       {
 439         alignPanel.seqPanel.setCursorColumn();
 440       }
 441       if (evt.isControlDown() || evt.isMetaDown())
 442       {
 443         copy_actionPerformed();
 444       }
 445       break;
 446     case KeyEvent.VK_V:
 447       if (evt.isControlDown())
 448       {
 449         paste(evt.isShiftDown());
 450       }
 451       break;
 452     case KeyEvent.VK_A:
 453       if (evt.isControlDown() || evt.isMetaDown())
 454       {
 455         selectAllSequenceMenuItem_actionPerformed();
 456       }
 457       break;
 458     case KeyEvent.VK_DOWN:
 459       if (viewport.cursorMode)
 460       {
 461         alignPanel.seqPanel.moveCursor(0, 1);
 462       }
 463       else
 464       {
 465         moveSelectedSequences(false);
 466       }
 467       break;
 468
 469     case KeyEvent.VK_UP:
 470       if (viewport.cursorMode)
 471       {
 472         alignPanel.seqPanel.moveCursor(0, -1);
 473       }
 474       else
 475       {
 476         moveSelectedSequences(true);
 477       }
 478       break;
 479
 480     case KeyEvent.VK_LEFT:
 481       if (evt.isAltDown() || !viewport.cursorMode)
 482       {
 483         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 484       }
 485       else
 486       {
 487         alignPanel.seqPanel.moveCursor(-1, 0);
 488       }
 489       break;
 490
 491     case KeyEvent.VK_RIGHT:
 492       if (evt.isAltDown() || !viewport.cursorMode)
 493       {
 494         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 495       }
 496       else
 497       {
 498         alignPanel.seqPanel.moveCursor(1, 0);
 499       }
 500       break;
 501
 502     case KeyEvent.VK_SPACE:
 503       if (viewport.cursorMode)
 504       {
 505         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 506                 || evt.isShiftDown() || evt.isAltDown());
 507       }
 508       break;
 509
 510     case KeyEvent.VK_DELETE:
 511     case KeyEvent.VK_BACK_SPACE:
 512       if (viewport.cursorMode)
 513       {
 514         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 515                 || evt.isShiftDown() || evt.isAltDown());
 516       }
 517       else
 518       {
 519         cut_actionPerformed();
 520         alignPanel.seqPanel.seqCanvas.repaint();
 521       }
 522       break;
 523
 524     case KeyEvent.VK_S:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorRow();
 528       }
 529       break;
 530     case KeyEvent.VK_P:
 531       if (viewport.cursorMode)
 532       {
 533         alignPanel.seqPanel.setCursorPosition();
 534       }
 535       break;
 536
 537     case KeyEvent.VK_ENTER:
 538     case KeyEvent.VK_COMMA:
 539       if (viewport.cursorMode)
 540       {
 541         alignPanel.seqPanel.setCursorRowAndColumn();
 542       }
 543       break;
 544
 545     case KeyEvent.VK_Q:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 549       }
 550       break;
 551     case KeyEvent.VK_M:
 552       if (viewport.cursorMode)
 553       {
 554         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 555       }
 556       break;
 557
 558     case KeyEvent.VK_F2:
 559       viewport.cursorMode = !viewport.cursorMode;
 560       statusBar.setText(MessageManager.formatMessage(
 561               "label.keyboard_editing_mode",
 562               new String[] { (viewport.cursorMode ? "on" : "off") }));
 563       if (viewport.cursorMode)
 564       {
 565         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 566         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 567       }
 568       break;
 569
 570     case KeyEvent.VK_F:
 571       if (evt.isControlDown())
 572       {
 573         findMenuItem_actionPerformed();
 574       }
 575       break;
 576
 577     case KeyEvent.VK_H:
 578     {
 579       boolean toggleSeqs = !evt.isControlDown();
 580       boolean toggleCols = !evt.isShiftDown();
 581       toggleHiddenRegions(toggleSeqs, toggleCols);
 582       break;
 583     }
 584
 585     case KeyEvent.VK_PAGE_UP:
 586       if (viewport.getWrapAlignment())
 587       {
 588         alignPanel.scrollUp(true);
 589       }
 590       else
 591       {
 592         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 593                 - viewport.endSeq + viewport.startSeq);
 594       }
 595       break;
 596
 597     case KeyEvent.VK_PAGE_DOWN:
 598       if (viewport.getWrapAlignment())
 599       {
 600         alignPanel.scrollUp(false);
 601       }
 602       else
 603       {
 604         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 605                 + viewport.endSeq - viewport.startSeq);
 606       }
 607       break;
 608
 609     case KeyEvent.VK_Z:
 610       if (evt.isControlDown())
 611       {
 612         undoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_Y:
 617       if (evt.isControlDown())
 618       {
 619         redoMenuItem_actionPerformed();
 620       }
 621       break;
 622
 623     case KeyEvent.VK_L:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(true);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_R:
 631       if (evt.isControlDown())
 632       {
 633         trimAlignment(false);
 634       }
 635       break;
 636
 637     case KeyEvent.VK_E:
 638       if (evt.isControlDown())
 639       {
 640         if (evt.isShiftDown())
 641         {
 642           this.removeAllGapsMenuItem_actionPerformed();
 643         }
 644         else
 645         {
 646           removeGappedColumnMenuItem_actionPerformed();
 647         }
 648       }
 649       break;
 650     case KeyEvent.VK_I:
 651       if (evt.isControlDown())
 652       {
 653         if (evt.isAltDown())
 654         {
 655           invertColSel_actionPerformed();
 656         }
 657         else
 658         {
 659           invertSequenceMenuItem_actionPerformed();
 660         }
 661       }
 662       break;
 663
 664     case KeyEvent.VK_G:
 665       if (evt.isControlDown())
 666       {
 667         if (evt.isShiftDown())
 668         {
 669           this.unGroup_actionPerformed();
 670         }
 671         else
 672         {
 673           this.createGroup_actionPerformed();
 674         }
 675       }
 676       break;
 677
 678     case KeyEvent.VK_U:
 679       if (evt.isControlDown())
 680       {
 681         this.deleteGroups_actionPerformed();
 682       }
 683       break;
 684
 685     case KeyEvent.VK_T:
 686       if (evt.isControlDown())
 687       {
 688         newView(null);
 689       }
 690       break;
 691
 692     }
 693     alignPanel.paintAlignment(true);
 694   }
 695
 696   /**
 697    * called by key handler and the hide all/show all menu items
 698    *
 699    * @param toggleSeqs
 700    * @param toggleCols
 701    */
 702   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 703   {
 704     boolean hide = false;
 705     SequenceGroup sg = viewport.getSelectionGroup();
 706     if (!toggleSeqs && !toggleCols)
 707     {
 708       // Hide everything by the current selection - this is a hack - we do the
 709       // invert and then hide
 710       // first check that there will be visible columns after the invert.
 711       if (viewport.hasSelectedColumns()
 712               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 713                       .getEndRes()))
 714       {
 715         // now invert the sequence set, if required - empty selection implies
 716         // that no hiding is required.
 717         if (sg != null)
 718         {
 719           invertSequenceMenuItem_actionPerformed();
 720           sg = viewport.getSelectionGroup();
 721           toggleSeqs = true;
 722
 723         }
 724         viewport.expandColSelection(sg, true);
 725         // finally invert the column selection and get the new sequence
 726         // selection and indicate it should be hidden.
 727         invertColSel_actionPerformed();
 728         toggleCols = true;
 729       }
 730     }
 731
 732     if (toggleSeqs)
 733     {
 734       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 735       {
 736         hide = true;
 737         viewport.hideAllSelectedSeqs();
 738       }
 739       else if (!(toggleCols && viewport.hasSelectedColumns()))
 740       {
 741         viewport.showAllHiddenSeqs();
 742       }
 743     }
 744
 745     if (toggleCols)
 746     {
 747       if (viewport.hasSelectedColumns())
 748       {
 749         viewport.hideSelectedColumns();
 750         if (!toggleSeqs)
 751         {
 752           viewport.setSelectionGroup(sg);
 753         }
 754       }
 755       else if (!hide)
 756       {
 757         viewport.showAllHiddenColumns();
 758       }
 759       viewport.sendSelection();
 760     }
 761   }
 762
 763   @Override
 764   public void keyReleased(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void keyTyped(KeyEvent evt)
 770   {
 771   }
 772
 773   @Override
 774   public void itemStateChanged(ItemEvent evt)
 775   {
 776     final Object source = evt.getSource();
 777     if (source == displayNonconservedMenuItem)
 778     {
 779       displayNonconservedMenuItem_actionPerformed();
 780     }
 781     else if (source == colourTextMenuItem)
 782     {
 783       colourTextMenuItem_actionPerformed();
 784     }
 785     else if (source == wrapMenuItem)
 786     {
 787       wrapMenuItem_actionPerformed();
 788     }
 789     else if (source == scaleAbove)
 790     {
 791       viewport.setScaleAboveWrapped(scaleAbove.getState());
 792     }
 793     else if (source == scaleLeft)
 794     {
 795       viewport.setScaleLeftWrapped(scaleLeft.getState());
 796     }
 797     else if (source == scaleRight)
 798     {
 799       viewport.setScaleRightWrapped(scaleRight.getState());
 800     }
 801     else if (source == seqLimits)
 802     {
 803       seqLimits_itemStateChanged();
 804     }
 805     else if (source == viewBoxesMenuItem)
 806     {
 807       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 808     }
 809     else if (source == viewTextMenuItem)
 810     {
 811       viewport.setShowText(viewTextMenuItem.getState());
 812     }
 813     else if (source == renderGapsMenuItem)
 814     {
 815       viewport.setRenderGaps(renderGapsMenuItem.getState());
 816     }
 817     else if (source == annotationPanelMenuItem)
 818     {
 819       boolean showAnnotations = annotationPanelMenuItem.getState();
 820       showAlignmentAnnotations.setEnabled(showAnnotations);
 821       showSequenceAnnotations.setEnabled(showAnnotations);
 822       viewport.setShowAnnotation(showAnnotations);
 823       alignPanel.setAnnotationVisible(showAnnotations);
 824     }
 825     else if (source == sequenceFeatures)
 826     {
 827       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 828       alignPanel.seqPanel.seqCanvas.repaint();
 829     }
 830     else if (source == showAlignmentAnnotations)
 831     {
 832       setAnnotationsVisibility();
 833     }
 834     else if (source == showSequenceAnnotations)
 835     {
 836       setAnnotationsVisibility();
 837     }
 838     else if (source == sortAnnBySequence)
 839     {
 840       boolean newState = sortAnnBySequence.getState();
 841       sortAnnByLabel.setState(false);
 842       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 843               : SequenceAnnotationOrder.NONE);
 844       setViewportAnnotationOrder();
 845     }
 846     else if (source == sortAnnByLabel)
 847     {
 848       boolean newState = sortAnnByLabel.getState();
 849       sortAnnBySequence.setState(false);
 850       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 851               : SequenceAnnotationOrder.NONE);
 852       setViewportAnnotationOrder();
 853     }
 854     else if (source == showAutoFirst)
 855     {
 856       showAutoLast.setState(!showAutoFirst.getState());
 857       setShowAutoCalculatedAbove(showAutoFirst.getState());
 858       setViewportAnnotationOrder();
 859     }
 860     else if (source == showAutoLast)
 861     {
 862       showAutoFirst.setState(!showAutoLast.getState());
 863       setShowAutoCalculatedAbove(showAutoFirst.getState());
 864       setViewportAnnotationOrder();
 865     }
 866     else if (source == conservationMenuItem)
 867     {
 868       conservationMenuItem_actionPerformed();
 869     }
 870     else if (source == abovePIDThreshold)
 871     {
 872       abovePIDThreshold_actionPerformed();
 873     }
 874     else if (source == applyToAllGroups)
 875     {
 876       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 877     }
 878     else if (source == autoCalculate)
 879     {
 880       viewport.autoCalculateConsensus = autoCalculate.getState();
 881     }
 882     else if (source == sortByTree)
 883     {
 884       viewport.sortByTree = sortByTree.getState();
 885     }
 886     else if (source == this.centreColumnLabelFlag)
 887     {
 888       centreColumnLabelFlag_stateChanged();
 889     }
 890     else if (source == this.followMouseOverFlag)
 891     {
 892       mouseOverFlag_stateChanged();
 893     }
 894     else if (source == showGroupConsensus)
 895     {
 896       showGroupConsensus_actionPerformed();
 897     }
 898     else if (source == showGroupConservation)
 899     {
 900       showGroupConservation_actionPerformed();
 901     }
 902     else if (source == showSequenceLogo)
 903     {
 904       showSequenceLogo_actionPerformed();
 905     }
 906     else if (source == normSequenceLogo)
 907     {
 908       normSequenceLogo_actionPerformed();
 909     }
 910     else if (source == showConsensusHistogram)
 911     {
 912       showConsensusHistogram_actionPerformed();
 913     }
 914     else if (source == applyAutoAnnotationSettings)
 915     {
 916       applyAutoAnnotationSettings_actionPerformed();
 917     }
 918     alignPanel.paintAlignment(true);
 919   }
 920
 921   /**
 922    * Set the visibility state of sequence-related and/or alignment-related
 923    * annotations depending on checkbox selections, and repaint.
 924    *
 925    * @param visible
 926    */
 927   private void setAnnotationsVisibility()
 928   {
 929     boolean showForAlignment = showAlignmentAnnotations.getState();
 930     boolean showForSequences = showSequenceAnnotations.getState();
 931     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 932     {
 933       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 934               .getAlignmentAnnotation())
 935       {
 936         boolean visible = (aa.sequenceRef == null ? showForAlignment
 937                 : showForSequences);
 938         aa.visible = visible;
 939       }
 940     }
 941     alignPanel.validateAnnotationDimensions(true);
 942     validate();
 943     repaint();
 944   }
 945
 946   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 947   {
 948     this.annotationSortOrder = order;
 949   }
 950
 951   /**
 952    * Set flags on the viewport that control annotation ordering
 953    */
 954   private void setViewportAnnotationOrder()
 955   {
 956     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 957     this.alignPanel.av
 958             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 959   }
 960
 961   private void setShowAutoCalculatedAbove(boolean showAbove)
 962   {
 963     this.showAutoCalculatedAbove = showAbove;
 964   }
 965
 966   private void mouseOverFlag_stateChanged()
 967   {
 968     viewport.setFollowHighlight(followMouseOverFlag.getState());
 969     // TODO: could kick the scrollTo mechanism to reset view for current
 970     // searchresults.
 971   }
 972
 973   private void centreColumnLabelFlag_stateChanged()
 974   {
 975     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 976     this.alignPanel.annotationPanel.repaint();
 977   }
 978
 979   @Override
 980   public void actionPerformed(ActionEvent evt)
 981   {
 982     viewport.applet.currentAlignFrame = this;
 983
 984     Object source = evt.getSource();
 985
 986     if (source == inputText)
 987     {
 988       inputText_actionPerformed();
 989     }
 990     else if (source == loadTree)
 991     {
 992       loadTree_actionPerformed();
 993     }
 994     else if (source == loadApplication)
 995     {
 996       launchFullApplication();
 997     }
 998     else if (source == loadAnnotations)
 999     {
1000       loadAnnotations();
1001     }
1002     else if (source == outputAnnotations)
1003     {
1004       outputAnnotations(true);
1005     }
1006     else if (source == outputFeatures)
1007     {
1008       outputFeatures(true, "Jalview");
1009     }
1010     else if (source == closeMenuItem)
1011     {
1012       closeMenuItem_actionPerformed();
1013     }
1014     else if (source == copy)
1015     {
1016       copy_actionPerformed();
1017     }
1018     else if (source == undoMenuItem)
1019     {
1020       undoMenuItem_actionPerformed();
1021     }
1022     else if (source == redoMenuItem)
1023     {
1024       redoMenuItem_actionPerformed();
1025     }
1026     else if (source == inputText)
1027     {
1028       inputText_actionPerformed();
1029     }
1030     else if (source == closeMenuItem)
1031     {
1032       closeMenuItem_actionPerformed();
1033     }
1034     else if (source == undoMenuItem)
1035     {
1036       undoMenuItem_actionPerformed();
1037     }
1038     else if (source == redoMenuItem)
1039     {
1040       redoMenuItem_actionPerformed();
1041     }
1042     else if (source == copy)
1043     {
1044       copy_actionPerformed();
1045     }
1046     else if (source == pasteNew)
1047     {
1048       pasteNew_actionPerformed();
1049     }
1050     else if (source == pasteThis)
1051     {
1052       pasteThis_actionPerformed();
1053     }
1054     else if (source == cut)
1055     {
1056       cut_actionPerformed();
1057     }
1058     else if (source == delete)
1059     {
1060       delete_actionPerformed();
1061     }
1062     else if (source == grpsFromSelection)
1063     {
1064       makeGrpsFromSelection_actionPerformed();
1065     }
1066     else if (source == deleteGroups)
1067     {
1068       deleteGroups_actionPerformed();
1069     }
1070     else if (source == selectAllSequenceMenuItem)
1071     {
1072       selectAllSequenceMenuItem_actionPerformed();
1073     }
1074     else if (source == deselectAllSequenceMenuItem)
1075     {
1076       deselectAllSequenceMenuItem_actionPerformed();
1077     }
1078     else if (source == invertSequenceMenuItem)
1079     {
1080       invertSequenceMenuItem_actionPerformed();
1081       // uncomment to slave sequence selections in split frame
1082       // viewport.sendSelection();
1083     }
1084     else if (source == invertColSel)
1085     {
1086       viewport.invertColumnSelection();
1087       alignPanel.paintAlignment(true);
1088       viewport.sendSelection();
1089     }
1090     else if (source == remove2LeftMenuItem)
1091     {
1092       trimAlignment(true);
1093     }
1094     else if (source == remove2RightMenuItem)
1095     {
1096       trimAlignment(false);
1097     }
1098     else if (source == removeGappedColumnMenuItem)
1099     {
1100       removeGappedColumnMenuItem_actionPerformed();
1101     }
1102     else if (source == removeAllGapsMenuItem)
1103     {
1104       removeAllGapsMenuItem_actionPerformed();
1105     }
1106     else if (source == findMenuItem)
1107     {
1108       findMenuItem_actionPerformed();
1109     }
1110     else if (source == font)
1111     {
1112       new FontChooser(alignPanel);
1113     }
1114     else if (source == newView)
1115     {
1116       newView(null);
1117     }
1118     else if (source == showColumns)
1119     {
1120       viewport.showAllHiddenColumns();
1121       alignPanel.paintAlignment(true);
1122       viewport.sendSelection();
1123     }
1124     else if (source == showSeqs)
1125     {
1126       viewport.showAllHiddenSeqs();
1127       alignPanel.paintAlignment(true);
1128       // uncomment if we want to slave sequence selections in split frame
1129       // viewport.sendSelection();
1130     }
1131     else if (source == hideColumns)
1132     {
1133       viewport.hideSelectedColumns();
1134       alignPanel.paintAlignment(true);
1135       viewport.sendSelection();
1136     }
1137     else if (source == hideSequences
1138             && viewport.getSelectionGroup() != null)
1139     {
1140       viewport.hideAllSelectedSeqs();
1141       alignPanel.paintAlignment(true);
1142       // uncomment if we want to slave sequence selections in split frame
1143       // viewport.sendSelection();
1144     }
1145     else if (source == hideAllButSelection)
1146     {
1147       toggleHiddenRegions(false, false);
1148       alignPanel.paintAlignment(true);
1149       viewport.sendSelection();
1150     }
1151     else if (source == hideAllSelection)
1152     {
1153       SequenceGroup sg = viewport.getSelectionGroup();
1154       viewport.expandColSelection(sg, false);
1155       viewport.hideAllSelectedSeqs();
1156       viewport.hideSelectedColumns();
1157       alignPanel.paintAlignment(true);
1158       viewport.sendSelection();
1159     }
1160     else if (source == showAllHidden)
1161     {
1162       viewport.showAllHiddenColumns();
1163       viewport.showAllHiddenSeqs();
1164       alignPanel.paintAlignment(true);
1165       viewport.sendSelection();
1166     }
1167     else if (source == showGroupConsensus)
1168     {
1169       showGroupConsensus_actionPerformed();
1170     }
1171     else if (source == showGroupConservation)
1172     {
1173       showGroupConservation_actionPerformed();
1174     }
1175     else if (source == showSequenceLogo)
1176     {
1177       showSequenceLogo_actionPerformed();
1178     }
1179     else if (source == normSequenceLogo)
1180     {
1181       normSequenceLogo_actionPerformed();
1182     }
1183     else if (source == showConsensusHistogram)
1184     {
1185       showConsensusHistogram_actionPerformed();
1186     }
1187     else if (source == applyAutoAnnotationSettings)
1188     {
1189       applyAutoAnnotationSettings_actionPerformed();
1190     }
1191     else if (source == featureSettings)
1192     {
1193       new FeatureSettings(alignPanel);
1194     }
1195     else if (source == alProperties)
1196     {
1197       StringBuffer contents = new jalview.io.AlignmentProperties(
1198               viewport.getAlignment()).formatAsString();
1199       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1200       cap.setText(contents.toString());
1201       Frame frame = new Frame();
1202       frame.add(cap);
1203       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1204               "label.alignment_properties", new String[] { getTitle() }),
1205               400, 250);
1206     }
1207     else if (source == overviewMenuItem)
1208     {
1209       overviewMenuItem_actionPerformed();
1210     }
1211     else if (source == noColourmenuItem)
1212     {
1213       changeColour(null);
1214     }
1215     else if (source == clustalColour)
1216     {
1217       abovePIDThreshold.setState(false);
1218       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1219     }
1220     else if (source == zappoColour)
1221     {
1222       changeColour(new ZappoColourScheme());
1223     }
1224     else if (source == taylorColour)
1225     {
1226       changeColour(new TaylorColourScheme());
1227     }
1228     else if (source == hydrophobicityColour)
1229     {
1230       changeColour(new HydrophobicColourScheme());
1231     }
1232     else if (source == helixColour)
1233     {
1234       changeColour(new HelixColourScheme());
1235     }
1236     else if (source == strandColour)
1237     {
1238       changeColour(new StrandColourScheme());
1239     }
1240     else if (source == turnColour)
1241     {
1242       changeColour(new TurnColourScheme());
1243     }
1244     else if (source == buriedColour)
1245     {
1246       changeColour(new BuriedColourScheme());
1247     }
1248     else if (source == nucleotideColour)
1249     {
1250       changeColour(new NucleotideColourScheme());
1251     }
1252     else if (source == purinePyrimidineColour)
1253     {
1254       changeColour(new PurinePyrimidineColourScheme());
1255     }
1256     // else if (source == RNAInteractionColour)
1257     // {
1258     // changeColour(new RNAInteractionColourScheme());
1259     // }
1260     else if (source == RNAHelixColour)
1261     {
1262       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1263       // new RNAHelicesColourChooser(viewport, alignPanel);
1264     }
1265     else if (source == modifyPID)
1266     {
1267       modifyPID_actionPerformed();
1268     }
1269     else if (source == modifyConservation)
1270     {
1271       modifyConservation_actionPerformed();
1272     }
1273     else if (source == userDefinedColour)
1274     {
1275       new UserDefinedColours(alignPanel, null);
1276     }
1277     else if (source == PIDColour)
1278     {
1279       changeColour(new PIDColourScheme());
1280     }
1281     else if (source == BLOSUM62Colour)
1282     {
1283       changeColour(new Blosum62ColourScheme());
1284     }
1285     else if (source == tcoffeeColour)
1286     {
1287       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1288     }
1289     else if (source == annotationColour)
1290     {
1291       new AnnotationColourChooser(viewport, alignPanel);
1292     }
1293     else if (source == annotationColumnSelection)
1294     {
1295       new AnnotationColumnChooser(viewport, alignPanel);
1296     }
1297     else if (source == sortPairwiseMenuItem)
1298     {
1299       sortPairwiseMenuItem_actionPerformed();
1300     }
1301     else if (source == sortIDMenuItem)
1302     {
1303       sortIDMenuItem_actionPerformed();
1304     }
1305     else if (source == sortLengthMenuItem)
1306     {
1307       sortLengthMenuItem_actionPerformed();
1308     }
1309     else if (source == sortGroupMenuItem)
1310     {
1311       sortGroupMenuItem_actionPerformed();
1312     }
1313     else if (source == removeRedundancyMenuItem)
1314     {
1315       removeRedundancyMenuItem_actionPerformed();
1316     }
1317     else if (source == pairwiseAlignmentMenuItem)
1318     {
1319       pairwiseAlignmentMenuItem_actionPerformed();
1320     }
1321     else if (source == PCAMenuItem)
1322     {
1323       PCAMenuItem_actionPerformed();
1324     }
1325     else if (source == averageDistanceTreeMenuItem)
1326     {
1327       averageDistanceTreeMenuItem_actionPerformed();
1328     }
1329     else if (source == neighbourTreeMenuItem)
1330     {
1331       neighbourTreeMenuItem_actionPerformed();
1332     }
1333     else if (source == njTreeBlosumMenuItem)
1334     {
1335       njTreeBlosumMenuItem_actionPerformed();
1336     }
1337     else if (source == avDistanceTreeBlosumMenuItem)
1338     {
1339       avTreeBlosumMenuItem_actionPerformed();
1340     }
1341     else if (source == documentation)
1342     {
1343       documentation_actionPerformed();
1344     }
1345     else if (source == about)
1346     {
1347       about_actionPerformed();
1348     }
1349
1350   }
1351
1352   public void inputText_actionPerformed()
1353   {
1354     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1355     Frame frame = new Frame();
1356     frame.add(cap);
1357     jalview.bin.JalviewLite.addFrame(frame,
1358             MessageManager.getString("label.input_cut_paste"), 500, 500);
1359   }
1360
1361   protected void outputText_actionPerformed(ActionEvent e)
1362   {
1363     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1364     Frame frame = new Frame();
1365     frame.add(cap);
1366     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1367             "label.alignment_output_command",
1368             new Object[] { e.getActionCommand() }), 600, 500);
1369
1370     FileFormatI fileFormat = FileFormats.getInstance().forName(
1371             e.getActionCommand());
1372     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1373             fileFormat, viewport.getAlignment(),
1374             viewport.getShowJVSuffix()));
1375   }
1376
1377   public void loadAnnotations()
1378   {
1379     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1380     cap.setText(MessageManager
1381             .getString("label.paste_features_annotations_Tcoffee_here"));
1382     cap.setAnnotationImport();
1383     Frame frame = new Frame();
1384     frame.add(cap);
1385     jalview.bin.JalviewLite.addFrame(frame,
1386             MessageManager.getString("action.paste_annotations"), 400, 300);
1387
1388   }
1389
1390   public String outputAnnotations(boolean displayTextbox)
1391   {
1392     String annotation = new AnnotationFile()
1393             .printAnnotationsForView(viewport);
1394
1395     if (displayTextbox)
1396     {
1397       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1398       Frame frame = new Frame();
1399       frame.add(cap);
1400       jalview.bin.JalviewLite.addFrame(frame,
1401               MessageManager.getString("label.annotations"), 600, 500);
1402       cap.setText(annotation);
1403     }
1404
1405     return annotation;
1406   }
1407
1408   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1409   {
1410     if (alignPanel.getFeatureRenderer() != null
1411             && viewport.getFeaturesDisplayed() != null)
1412     {
1413       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1414
1415     }
1416     return null;
1417   }
1418
1419   public String outputFeatures(boolean displayTextbox, String format)
1420   {
1421     String features;
1422     FeaturesFile formatter = new FeaturesFile();
1423     if (format.equalsIgnoreCase("Jalview"))
1424     {
1425       features = formatter.printJalviewFormat(viewport.getAlignment()
1426               .getSequencesArray(), getDisplayedFeatureCols());
1427     }
1428     else
1429     {
1430       features = formatter.printGffFormat(viewport.getAlignment()
1431               .getSequencesArray(), getDisplayedFeatureCols());
1432     }
1433
1434     if (displayTextbox)
1435     {
1436       boolean frimport = false;
1437       if (features == null || features.equals("No Features Visible"))
1438       {
1439         features = "# No features visible - paste some and import them here.";
1440         frimport = true;
1441       }
1442
1443       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1444       if (frimport)
1445       {
1446         cap.setAnnotationImport();
1447       }
1448       Frame frame = new Frame();
1449       frame.add(cap);
1450       jalview.bin.JalviewLite.addFrame(frame,
1451               MessageManager.getString("label.features"), 600, 500);
1452       cap.setText(features);
1453     }
1454     else
1455     {
1456       if (features == null)
1457       {
1458         features = "";
1459       }
1460     }
1461
1462     return features;
1463   }
1464
1465   void launchFullApplication()
1466   {
1467     StringBuffer url = new StringBuffer(jalviewServletURL);
1468
1469     // allow servlet parameters to be passed in applet parameter
1470     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1471             : "?";
1472     url.append(firstSep);
1473
1474     url.append("open="
1475             + appendProtocol(viewport.applet.getParameter("file")));
1476
1477     if (viewport.applet.getParameter("features") != null)
1478     {
1479       url.append("&features=");
1480       url.append(appendProtocol(viewport.applet.getParameter("features")));
1481     }
1482
1483     if (viewport.applet.getParameter("annotations") != null)
1484     {
1485       url.append("&annotations=");
1486       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1487     }
1488
1489     if (viewport.applet.getParameter("jnetfile") != null
1490             || viewport.applet.getParameter("jpredfile") != null)
1491     {
1492       url.append("&annotations=");
1493       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1494               .getParameter("jnetfile") : viewport.applet
1495               .getParameter("jpredfile")));
1496     }
1497
1498     if (viewport.applet.getParameter("defaultColour") != null)
1499     {
1500       url.append("&colour="
1501               + removeWhiteSpace(viewport.applet
1502                       .getParameter("defaultColour")));
1503     }
1504
1505     if (viewport.applet.getParameter("userDefinedColour") != null)
1506     {
1507       url.append("&colour="
1508               + removeWhiteSpace(viewport.applet
1509                       .getParameter("userDefinedColour")));
1510     }
1511     if (viewport.applet.getParameter("tree") != null)
1512     {
1513       url.append("&tree="
1514               + appendProtocol(viewport.applet.getParameter("tree")));
1515     }
1516     if (viewport.applet.getParameter("treeFile") != null)
1517     {
1518       url.append("&tree="
1519               + appendProtocol(viewport.applet.getParameter("treeFile")));
1520     }
1521
1522     showURL(url.toString(), "FULL_APP");
1523   }
1524
1525   String removeWhiteSpace(String colour)
1526   {
1527     StringBuffer sb = new StringBuffer();
1528     for (int i = 0; i < colour.length(); i++)
1529     {
1530       if (Character.isWhitespace(colour.charAt(i)))
1531       {
1532         sb.append("%20");
1533       }
1534       else
1535       {
1536         sb.append(colour.charAt(i));
1537       }
1538     }
1539
1540     return sb.toString();
1541   }
1542
1543   String appendProtocol(String url)
1544   {
1545     try
1546     {
1547       new URL(url);
1548       url = URLEncoder.encode(url);
1549     }
1550     /*
1551      * When we finally deprecate 1.1 compatibility, we can start to use
1552      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1553      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1554      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1555      * ex.printStackTrace(); }
1556      */
1557     catch (java.net.MalformedURLException ex)
1558     {
1559       url = viewport.applet.getCodeBase() + url;
1560     }
1561     return url;
1562   }
1563
1564   public void closeMenuItem_actionPerformed()
1565   {
1566     PaintRefresher.RemoveComponent(alignPanel);
1567     if (alignPanel.seqPanel != null
1568             && alignPanel.seqPanel.seqCanvas != null)
1569     {
1570       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1571     }
1572     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1573     {
1574       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1575     }
1576
1577     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1578     {
1579       System.exit(0);
1580     }
1581     else
1582     {
1583     }
1584     viewport = null;
1585     alignPanel = null;
1586     this.dispose();
1587   }
1588
1589   /**
1590    * TODO: JAL-1104
1591    */
1592   void updateEditMenuBar()
1593   {
1594
1595     if (viewport.getHistoryList().size() > 0)
1596     {
1597       undoMenuItem.setEnabled(true);
1598       CommandI command = viewport.getHistoryList().peek();
1599       undoMenuItem.setLabel(MessageManager.formatMessage(
1600               "label.undo_command",
1601               new Object[] { command.getDescription() }));
1602     }
1603     else
1604     {
1605       undoMenuItem.setEnabled(false);
1606       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1607     }
1608
1609     if (viewport.getRedoList().size() > 0)
1610     {
1611       redoMenuItem.setEnabled(true);
1612
1613       CommandI command = viewport.getRedoList().peek();
1614       redoMenuItem.setLabel(MessageManager.formatMessage(
1615               "label.redo_command",
1616               new Object[] { command.getDescription() }));
1617     }
1618     else
1619     {
1620       redoMenuItem.setEnabled(false);
1621       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1622     }
1623   }
1624
1625   /**
1626    * TODO: JAL-1104
1627    */
1628   @Override
1629   public void addHistoryItem(CommandI command)
1630   {
1631     if (command.getSize() > 0)
1632     {
1633       viewport.addToHistoryList(command);
1634       viewport.clearRedoList();
1635       updateEditMenuBar();
1636       viewport.updateHiddenColumns();
1637     }
1638   }
1639
1640   /**
1641    * TODO: JAL-1104 DOCUMENT ME!
1642    *
1643    * @param e
1644    *          DOCUMENT ME!
1645    */
1646   protected void undoMenuItem_actionPerformed()
1647   {
1648     if (viewport.getHistoryList().isEmpty())
1649     {
1650       return;
1651     }
1652
1653     CommandI command = viewport.getHistoryList().pop();
1654     viewport.addToRedoList(command);
1655     command.undoCommand(null);
1656
1657     AlignmentViewport originalSource = getOriginatingSource(command);
1658     // JBPNote Test
1659     if (originalSource != viewport)
1660     {
1661       System.err
1662               .println("Warning: Viewport object mismatch whilst undoing");
1663     }
1664     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1665                                           // viewport.getColumnSelection().getHiddenColumns()
1666                                           // != null;
1667     updateEditMenuBar();
1668     originalSource.firePropertyChange("alignment", null, originalSource
1669             .getAlignment().getSequences());
1670   }
1671
1672   /**
1673    * TODO: JAL-1104 DOCUMENT ME!
1674    *
1675    * @param e
1676    *          DOCUMENT ME!
1677    */
1678   protected void redoMenuItem_actionPerformed()
1679   {
1680     if (viewport.getRedoList().isEmpty())
1681     {
1682       return;
1683     }
1684
1685     CommandI command = viewport.getRedoList().pop();
1686     viewport.addToHistoryList(command);
1687     command.doCommand(null);
1688
1689     AlignmentViewport originalSource = getOriginatingSource(command);
1690     // JBPNote Test
1691     if (originalSource != viewport)
1692     {
1693       System.err
1694               .println("Warning: Viewport object mismatch whilst re-doing");
1695     }
1696     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1697                                           // viewport.getColumnSelection().getHiddenColumns()
1698                                           // != null;
1699
1700     updateEditMenuBar();
1701     originalSource.firePropertyChange("alignment", null, originalSource
1702             .getAlignment().getSequences());
1703   }
1704
1705   AlignmentViewport getOriginatingSource(CommandI command)
1706   {
1707     AlignmentViewport originalSource = null;
1708     // For sequence removal and addition, we need to fire
1709     // the property change event FROM the viewport where the
1710     // original alignment was altered
1711     AlignmentI al = null;
1712     if (command instanceof EditCommand)
1713     {
1714       EditCommand editCommand = (EditCommand) command;
1715       al = editCommand.getAlignment();
1716       Vector comps = (Vector) PaintRefresher.components.get(viewport
1717               .getSequenceSetId());
1718       for (int i = 0; i < comps.size(); i++)
1719       {
1720         if (comps.elementAt(i) instanceof AlignmentPanel)
1721         {
1722           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1723           {
1724             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1725             break;
1726           }
1727         }
1728       }
1729     }
1730
1731     if (originalSource == null)
1732     {
1733       // The original view is closed, we must validate
1734       // the current view against the closed view first
1735       if (al != null)
1736       {
1737         PaintRefresher.validateSequences(al, viewport.getAlignment());
1738       }
1739
1740       originalSource = viewport;
1741     }
1742
1743     return originalSource;
1744   }
1745
1746   /**
1747    * Move the currently selected sequences up or down one position in the
1748    * alignment
1749    *
1750    * @param up
1751    */
1752   public void moveSelectedSequences(boolean up)
1753   {
1754     SequenceGroup sg = viewport.getSelectionGroup();
1755     if (sg == null)
1756     {
1757       return;
1758     }
1759     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1760             up ? null : viewport.getHiddenRepSequences(), up);
1761     alignPanel.paintAlignment(true);
1762
1763     /*
1764      * Also move cDNA/protein complement sequences
1765      */
1766     AlignViewportI complement = viewport.getCodingComplement();
1767     if (complement != null)
1768     {
1769       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1770               viewport, complement);
1771       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1772               up ? null : complement.getHiddenRepSequences(), up);
1773       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1774     }
1775   }
1776
1777   synchronized void slideSequences(boolean right, int size)
1778   {
1779     List<SequenceI> sg = new Vector<SequenceI>();
1780     if (viewport.cursorMode)
1781     {
1782       sg.add(viewport.getAlignment().getSequenceAt(
1783               alignPanel.seqPanel.seqCanvas.cursorY));
1784     }
1785     else if (viewport.getSelectionGroup() != null
1786             && viewport.getSelectionGroup().getSize() != viewport
1787                     .getAlignment().getHeight())
1788     {
1789       sg = viewport.getSelectionGroup().getSequences(
1790               viewport.getHiddenRepSequences());
1791     }
1792
1793     if (sg.size() < 1)
1794     {
1795       return;
1796     }
1797
1798     Vector<SequenceI> invertGroup = new Vector();
1799
1800     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1801     {
1802       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1803       {
1804         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1805       }
1806     }
1807
1808     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1809
1810     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1811             .size()]);
1812     for (int i = 0; i < invertGroup.size(); i++)
1813     {
1814       seqs2[i] = invertGroup.elementAt(i);
1815     }
1816
1817     SlideSequencesCommand ssc;
1818     if (right)
1819     {
1820       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1821               size, viewport.getGapCharacter());
1822     }
1823     else
1824     {
1825       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1826               size, viewport.getGapCharacter());
1827     }
1828
1829     int groupAdjustment = 0;
1830     if (ssc.getGapsInsertedBegin() && right)
1831     {
1832       if (viewport.cursorMode)
1833       {
1834         alignPanel.seqPanel.moveCursor(size, 0);
1835       }
1836       else
1837       {
1838         groupAdjustment = size;
1839       }
1840     }
1841     else if (!ssc.getGapsInsertedBegin() && !right)
1842     {
1843       if (viewport.cursorMode)
1844       {
1845         alignPanel.seqPanel.moveCursor(-size, 0);
1846       }
1847       else
1848       {
1849         groupAdjustment = -size;
1850       }
1851     }
1852
1853     if (groupAdjustment != 0)
1854     {
1855       viewport.getSelectionGroup().setStartRes(
1856               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1857       viewport.getSelectionGroup().setEndRes(
1858               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1859     }
1860
1861     boolean appendHistoryItem = false;
1862     Deque<CommandI> historyList = viewport.getHistoryList();
1863     if (historyList != null && historyList.size() > 0
1864             && historyList.peek() instanceof SlideSequencesCommand)
1865     {
1866       appendHistoryItem = ssc
1867               .appendSlideCommand((SlideSequencesCommand) historyList
1868                       .peek());
1869     }
1870
1871     if (!appendHistoryItem)
1872     {
1873       addHistoryItem(ssc);
1874     }
1875
1876     repaint();
1877   }
1878
1879   static StringBuffer copiedSequences;
1880
1881   static Vector copiedHiddenColumns;
1882
1883   protected void copy_actionPerformed()
1884   {
1885     if (viewport.getSelectionGroup() == null)
1886     {
1887       return;
1888     }
1889
1890     SequenceGroup sg = viewport.getSelectionGroup();
1891     copiedSequences = new StringBuffer();
1892     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1893     for (int i = 0; i < sg.getSize(); i++)
1894     {
1895       SequenceI seq = sg.getSequenceAt(i);
1896       int index = viewport.getAlignment().findIndex(seq);
1897       orderedSeqs.put(index, seq);
1898     }
1899
1900     int index = 0, startRes, endRes;
1901     char ch;
1902
1903     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1904     {
1905       copiedHiddenColumns = new Vector();
1906       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1907       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1908       {
1909         copiedHiddenColumns.addElement(new int[] {
1910             region[0] - hiddenOffset, region[1] - hiddenOffset });
1911       }
1912     }
1913     else
1914     {
1915       copiedHiddenColumns = null;
1916     }
1917
1918     for (int i = 0; i < sg.getSize(); i++)
1919     {
1920       SequenceI seq = null;
1921
1922       while (seq == null)
1923       {
1924         if (orderedSeqs.containsKey(index))
1925         {
1926           seq = orderedSeqs.get(index);
1927           index++;
1928           break;
1929         }
1930         else
1931         {
1932           index++;
1933         }
1934       }
1935
1936       // FIND START RES
1937       // Returns residue following index if gap
1938       startRes = seq.findPosition(sg.getStartRes());
1939
1940       // FIND END RES
1941       // Need to find the residue preceeding index if gap
1942       endRes = 0;
1943
1944       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1945       {
1946         ch = seq.getCharAt(j);
1947         if (!jalview.util.Comparison.isGap((ch)))
1948         {
1949           endRes++;
1950         }
1951       }
1952
1953       if (endRes > 0)
1954       {
1955         endRes += seq.getStart() - 1;
1956       }
1957
1958       copiedSequences.append(seq.getName()
1959               + "\t"
1960               + startRes
1961               + "\t"
1962               + endRes
1963               + "\t"
1964               + seq.getSequenceAsString(sg.getStartRes(),
1965                       sg.getEndRes() + 1) + "\n");
1966     }
1967
1968   }
1969
1970   protected void pasteNew_actionPerformed()
1971   {
1972     paste(true);
1973   }
1974
1975   protected void pasteThis_actionPerformed()
1976   {
1977     paste(false);
1978   }
1979
1980   void paste(boolean newAlignment)
1981   {
1982     try
1983     {
1984
1985       if (copiedSequences == null)
1986       {
1987         return;
1988       }
1989
1990       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1991       Vector seqs = new Vector();
1992       while (st.hasMoreElements())
1993       {
1994         String name = st.nextToken();
1995         int start = Integer.parseInt(st.nextToken());
1996         int end = Integer.parseInt(st.nextToken());
1997         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1998       }
1999       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2000       for (int i = 0; i < seqs.size(); i++)
2001       {
2002         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2003       }
2004
2005       if (newAlignment)
2006       {
2007         String newtitle = MessageManager
2008                 .getString("label.copied_sequences");
2009         if (getTitle().startsWith(
2010                 MessageManager.getString("label.copied_sequences")))
2011         {
2012           newtitle = getTitle();
2013         }
2014         else
2015         {
2016           newtitle = newtitle.concat(MessageManager.formatMessage(
2017                   "label.from_msname", new String[] { getTitle() }));
2018         }
2019         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2020                 viewport.applet, newtitle, false);
2021         if (copiedHiddenColumns != null)
2022         {
2023           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2024           {
2025             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2026             af.viewport.hideColumns(region[0], region[1]);
2027           }
2028         }
2029
2030         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2031                 frameHeight);
2032       }
2033       else
2034       {
2035         addSequences(newSeqs);
2036       }
2037
2038     } catch (Exception ex)
2039     {
2040     } // could be anything being pasted in here
2041
2042   }
2043
2044   void addSequences(SequenceI[] seqs)
2045   {
2046     for (int i = 0; i < seqs.length; i++)
2047     {
2048       viewport.getAlignment().addSequence(seqs[i]);
2049     }
2050
2051     // !newAlignment
2052     addHistoryItem(new EditCommand(
2053             MessageManager.getString("label.add_sequences"), Action.PASTE,
2054             seqs, 0, viewport.getAlignment().getWidth(),
2055             viewport.getAlignment()));
2056
2057     viewport.setEndSeq(viewport.getAlignment().getHeight());
2058     viewport.getAlignment().getWidth();
2059     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2060             .getSequences());
2061
2062   }
2063
2064   protected void cut_actionPerformed()
2065   {
2066     copy_actionPerformed();
2067     delete_actionPerformed();
2068   }
2069
2070   protected void delete_actionPerformed()
2071   {
2072
2073     SequenceGroup sg = viewport.getSelectionGroup();
2074     if (sg == null)
2075     {
2076       return;
2077     }
2078
2079     Vector seqs = new Vector();
2080     SequenceI seq;
2081     for (int i = 0; i < sg.getSize(); i++)
2082     {
2083       seq = sg.getSequenceAt(i);
2084       seqs.addElement(seq);
2085     }
2086
2087     /*
2088      * If the cut affects all sequences, warn, remove highlighted columns
2089      */
2090     if (sg.getSize() == viewport.getAlignment().getHeight())
2091     {
2092       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2093               .getAlignment().getWidth()) ? true : false;
2094       if (isEntireAlignWidth)
2095       {
2096         String title = MessageManager.getString("label.delete_all");
2097         Panel infoPanel = new Panel();
2098         infoPanel.setLayout(new FlowLayout());
2099         infoPanel
2100                 .add(new Label(MessageManager.getString("warn.delete_all")));
2101
2102         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2103         dialog.setMainPanel(infoPanel);
2104         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2105         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2106         dialog.setVisible(true);
2107
2108         if (!dialog.accept)
2109         {
2110           return;
2111         }
2112       }
2113       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2114               sg.getEndRes() + 1);
2115     }
2116
2117     SequenceI[] cut = new SequenceI[seqs.size()];
2118     for (int i = 0; i < seqs.size(); i++)
2119     {
2120       cut[i] = (SequenceI) seqs.elementAt(i);
2121     }
2122
2123     /*
2124      * //ADD HISTORY ITEM
2125      */
2126     addHistoryItem(new EditCommand(
2127             MessageManager.getString("label.cut_sequences"), Action.CUT,
2128             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2129             viewport.getAlignment()));
2130
2131     viewport.setSelectionGroup(null);
2132     viewport.getAlignment().deleteGroup(sg);
2133
2134     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2135             .getSequences());
2136
2137     if (viewport.getAlignment().getHeight() < 1)
2138     {
2139       this.setVisible(false);
2140     }
2141     viewport.sendSelection();
2142   }
2143
2144   /**
2145    * group consensus toggled
2146    *
2147    */
2148   protected void showGroupConsensus_actionPerformed()
2149   {
2150     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2151     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2152
2153   }
2154
2155   /**
2156    * group conservation toggled.
2157    */
2158   protected void showGroupConservation_actionPerformed()
2159   {
2160     viewport.setShowGroupConservation(showGroupConservation.getState());
2161     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2162   }
2163
2164   /*
2165    * (non-Javadoc)
2166    *
2167    * @see
2168    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2169    * .event.ActionEvent)
2170    */
2171   protected void showConsensusHistogram_actionPerformed()
2172   {
2173     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2174     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2175   }
2176
2177   /*
2178    * (non-Javadoc)
2179    *
2180    * @see
2181    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2182    * .event.ActionEvent)
2183    */
2184   protected void showSequenceLogo_actionPerformed()
2185   {
2186     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2187     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188   }
2189
2190   protected void normSequenceLogo_actionPerformed()
2191   {
2192     showSequenceLogo.setState(true);
2193     viewport.setShowSequenceLogo(true);
2194     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2195     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2196   }
2197
2198   protected void applyAutoAnnotationSettings_actionPerformed()
2199   {
2200     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2201   }
2202
2203   protected void makeGrpsFromSelection_actionPerformed()
2204   {
2205     if (avc.makeGroupsFromSelection())
2206     {
2207       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2208       alignPanel.updateAnnotation();
2209       alignPanel.paintAlignment(true);
2210     }
2211   }
2212
2213   protected void createGroup_actionPerformed()
2214   {
2215     avc.createGroup();
2216   }
2217
2218   protected void unGroup_actionPerformed()
2219   {
2220     if (avc.unGroup())
2221     {
2222       alignPanel.alignmentChanged();
2223     }
2224   }
2225
2226   protected void deleteGroups_actionPerformed()
2227   {
2228     if (avc.deleteGroups())
2229     {
2230       alignPanel.alignmentChanged();
2231     }
2232   }
2233
2234   public void selectAllSequenceMenuItem_actionPerformed()
2235   {
2236     SequenceGroup sg = new SequenceGroup();
2237     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2238     {
2239       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2240     }
2241     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2242     viewport.setSelectionGroup(sg);
2243     // JAL-2034 - should delegate to
2244     // alignPanel to decide if overview needs
2245     // updating.
2246     alignPanel.paintAlignment(false);
2247     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2248     viewport.sendSelection();
2249   }
2250
2251   public void deselectAllSequenceMenuItem_actionPerformed()
2252   {
2253     if (viewport.cursorMode)
2254     {
2255       alignPanel.seqPanel.keyboardNo1 = null;
2256       alignPanel.seqPanel.keyboardNo2 = null;
2257     }
2258     viewport.setSelectionGroup(null);
2259     viewport.getColumnSelection().clear();
2260     viewport.setSelectionGroup(null);
2261     alignPanel.idPanel.idCanvas.searchResults = null;
2262     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2263     // JAL-2034 - should delegate to
2264     // alignPanel to decide if overview needs
2265     // updating.
2266     alignPanel.paintAlignment(false);
2267     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2268     viewport.sendSelection();
2269   }
2270
2271   public void invertSequenceMenuItem_actionPerformed()
2272   {
2273     SequenceGroup sg = viewport.getSelectionGroup();
2274     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2275     {
2276       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2277     }
2278
2279     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2280     viewport.sendSelection();
2281   }
2282
2283   public void invertColSel_actionPerformed()
2284   {
2285     viewport.invertColumnSelection();
2286     alignPanel.paintAlignment(true);
2287     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2288     viewport.sendSelection();
2289   }
2290
2291   void trimAlignment(boolean trimLeft)
2292   {
2293     ColumnSelection colSel = viewport.getColumnSelection();
2294     int column;
2295
2296     if (!colSel.isEmpty())
2297     {
2298       if (trimLeft)
2299       {
2300         column = colSel.getMin();
2301       }
2302       else
2303       {
2304         column = colSel.getMax();
2305       }
2306
2307       SequenceI[] seqs;
2308       if (viewport.getSelectionGroup() != null)
2309       {
2310         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2311                 viewport.getHiddenRepSequences());
2312       }
2313       else
2314       {
2315         seqs = viewport.getAlignment().getSequencesArray();
2316       }
2317
2318       TrimRegionCommand trimRegion;
2319       if (trimLeft)
2320       {
2321         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2322                 column, viewport.getAlignment());
2323         viewport.setStartRes(0);
2324       }
2325       else
2326       {
2327         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2328                 column, viewport.getAlignment());
2329       }
2330
2331       statusBar.setText(MessageManager.formatMessage(
2332               "label.removed_columns",
2333               new String[] { Integer.valueOf(trimRegion.getSize())
2334                       .toString() }));
2335       addHistoryItem(trimRegion);
2336
2337       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2338       {
2339         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2340                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2341         {
2342           viewport.getAlignment().deleteGroup(sg);
2343         }
2344       }
2345
2346       viewport.firePropertyChange("alignment", null, viewport
2347               .getAlignment().getSequences());
2348     }
2349   }
2350
2351   public void removeGappedColumnMenuItem_actionPerformed()
2352   {
2353     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2354
2355     SequenceI[] seqs;
2356     if (viewport.getSelectionGroup() != null)
2357     {
2358       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2359               viewport.getHiddenRepSequences());
2360       start = viewport.getSelectionGroup().getStartRes();
2361       end = viewport.getSelectionGroup().getEndRes();
2362     }
2363     else
2364     {
2365       seqs = viewport.getAlignment().getSequencesArray();
2366     }
2367
2368     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2369             "Remove Gapped Columns", seqs, start, end,
2370             viewport.getAlignment());
2371
2372     addHistoryItem(removeGapCols);
2373
2374     statusBar.setText(MessageManager.formatMessage(
2375             "label.removed_empty_columns",
2376             new String[] { Integer.valueOf(removeGapCols.getSize())
2377                     .toString() }));
2378
2379     // This is to maintain viewport position on first residue
2380     // of first sequence
2381     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2382     int startRes = seq.findPosition(viewport.startRes);
2383     // ShiftList shifts;
2384     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2385     // edit.alColumnChanges=shifts.getInverse();
2386     // if (viewport.hasHiddenColumns)
2387     // viewport.getColumnSelection().compensateForEdits(shifts);
2388     viewport.setStartRes(seq.findIndex(startRes) - 1);
2389     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2390             .getSequences());
2391
2392   }
2393
2394   public void removeAllGapsMenuItem_actionPerformed()
2395   {
2396     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2397
2398     SequenceI[] seqs;
2399     if (viewport.getSelectionGroup() != null)
2400     {
2401       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2402               viewport.getHiddenRepSequences());
2403       start = viewport.getSelectionGroup().getStartRes();
2404       end = viewport.getSelectionGroup().getEndRes();
2405     }
2406     else
2407     {
2408       seqs = viewport.getAlignment().getSequencesArray();
2409     }
2410
2411     // This is to maintain viewport position on first residue
2412     // of first sequence
2413     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2414     int startRes = seq.findPosition(viewport.startRes);
2415
2416     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2417             viewport.getAlignment()));
2418
2419     viewport.setStartRes(seq.findIndex(startRes) - 1);
2420
2421     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2422             .getSequences());
2423
2424   }
2425
2426   public void findMenuItem_actionPerformed()
2427   {
2428     new Finder(alignPanel);
2429   }
2430
2431   /**
2432    * create a new view derived from the current view
2433    *
2434    * @param viewtitle
2435    * @return frame for the new view
2436    */
2437   public AlignFrame newView(String viewtitle)
2438   {
2439     AlignmentI newal;
2440     if (viewport.hasHiddenRows())
2441     {
2442       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2443               .getFullAlignment().getSequencesArray());
2444     }
2445     else
2446     {
2447       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2448     }
2449
2450     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2451     {
2452       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2453       {
2454         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2455         {
2456           newal.addAnnotation(viewport.getAlignment()
2457                   .getAlignmentAnnotation()[i]);
2458         }
2459       }
2460     }
2461
2462     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2463
2464     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2465     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2466     PaintRefresher.Register(newaf.alignPanel,
2467             newaf.alignPanel.av.getSequenceSetId());
2468
2469     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2470             newaf.alignPanel.av.getSequenceSetId());
2471     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2472             newaf.alignPanel.av.getSequenceSetId());
2473
2474     Vector comps = (Vector) PaintRefresher.components.get(viewport
2475             .getSequenceSetId());
2476     int viewSize = -1;
2477     for (int i = 0; i < comps.size(); i++)
2478     {
2479       if (comps.elementAt(i) instanceof AlignmentPanel)
2480       {
2481         viewSize++;
2482       }
2483     }
2484
2485     String title = new String(this.getTitle());
2486     if (viewtitle != null)
2487     {
2488       title = viewtitle + " ( " + title + ")";
2489     }
2490     else
2491     {
2492       if (title.indexOf("(View") > -1)
2493       {
2494         title = title.substring(0, title.indexOf("(View"));
2495       }
2496       title += "(View " + viewSize + ")";
2497     }
2498
2499     newaf.setTitle(title.toString());
2500
2501     newaf.viewport.setHistoryList(viewport.getHistoryList());
2502     newaf.viewport.setRedoList(viewport.getRedoList());
2503     return newaf;
2504   }
2505
2506   /**
2507    *
2508    * @return list of feature groups on the view
2509    */
2510   public String[] getFeatureGroups()
2511   {
2512     FeatureRenderer fr = null;
2513     if (alignPanel != null
2514             && (fr = alignPanel.getFeatureRenderer()) != null)
2515     {
2516       List<String> gps = fr.getFeatureGroups();
2517       String[] _gps = gps.toArray(new String[gps.size()]);
2518       return _gps;
2519     }
2520     return null;
2521   }
2522
2523   /**
2524    * get sequence feature groups that are hidden or shown
2525    *
2526    * @param visible
2527    *          true is visible
2528    * @return list
2529    */
2530   public String[] getFeatureGroupsOfState(boolean visible)
2531   {
2532     FeatureRenderer fr = null;
2533     if (alignPanel != null
2534             && (fr = alignPanel.getFeatureRenderer()) != null)
2535     {
2536       List<String> gps = fr.getGroups(visible);
2537       String[] _gps = gps.toArray(new String[gps.size()]);
2538       return _gps;
2539     }
2540     return null;
2541   }
2542
2543   /**
2544    * Change the display state for the given feature groups
2545    *
2546    * @param groups
2547    *          list of group strings
2548    * @param state
2549    *          visible or invisible
2550    */
2551   public void setFeatureGroupState(String[] groups, boolean state)
2552   {
2553     FeatureRenderer fr = null;
2554     this.sequenceFeatures.setState(true);
2555     viewport.setShowSequenceFeatures(true);
2556     if (alignPanel != null
2557             && (fr = alignPanel.getFeatureRenderer()) != null)
2558     {
2559
2560       fr.setGroupVisibility(Arrays.asList(groups), state);
2561       alignPanel.seqPanel.seqCanvas.repaint();
2562       if (alignPanel.overviewPanel != null)
2563       {
2564         alignPanel.overviewPanel.updateOverviewImage();
2565       }
2566     }
2567   }
2568
2569   public void seqLimits_itemStateChanged()
2570   {
2571     viewport.setShowJVSuffix(seqLimits.getState());
2572     alignPanel.fontChanged();
2573     alignPanel.paintAlignment(true);
2574   }
2575
2576   protected void colourTextMenuItem_actionPerformed()
2577   {
2578     viewport.setColourText(colourTextMenuItem.getState());
2579     alignPanel.paintAlignment(true);
2580   }
2581
2582   protected void displayNonconservedMenuItem_actionPerformed()
2583   {
2584     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2585     alignPanel.paintAlignment(true);
2586   }
2587
2588   protected void wrapMenuItem_actionPerformed()
2589   {
2590     viewport.setWrapAlignment(wrapMenuItem.getState());
2591     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2592     scaleAbove.setEnabled(wrapMenuItem.getState());
2593     scaleLeft.setEnabled(wrapMenuItem.getState());
2594     scaleRight.setEnabled(wrapMenuItem.getState());
2595     alignPanel.paintAlignment(true);
2596   }
2597
2598   public void overviewMenuItem_actionPerformed()
2599   {
2600     if (alignPanel.overviewPanel != null)
2601     {
2602       return;
2603     }
2604
2605     Frame frame = new Frame();
2606     OverviewPanel overview = new OverviewPanel(alignPanel);
2607     frame.add(overview);
2608     // +50 must allow for applet frame window
2609     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2610             "label.overview_params", new String[] { this.getTitle() }),
2611             overview.getPreferredSize().width,
2612             overview.getPreferredSize().height + 50);
2613
2614     frame.pack();
2615     final AlignmentPanel ap = alignPanel;
2616     frame.addWindowListener(new WindowAdapter()
2617     {
2618       @Override
2619       public void windowClosing(WindowEvent e)
2620       {
2621         if (ap != null)
2622         {
2623           ap.setOverviewPanel(null);
2624         }
2625       };
2626     });
2627
2628     alignPanel.setOverviewPanel(overview);
2629
2630   }
2631
2632   @Override
2633   public void changeColour(ColourSchemeI cs)
2634   {
2635
2636     if (cs != null)
2637     {
2638       if (viewport.getAbovePIDThreshold())
2639       {
2640         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2641                 cs, "Background"));
2642       }
2643
2644       if (viewport.getConservationSelected())
2645       {
2646         cs.setConservationApplied(true);
2647         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2648                 cs, "Background"));
2649       }
2650       else
2651       {
2652         cs.setConservationApplied(false);
2653       }
2654     }
2655     viewport.setGlobalColourScheme(cs);
2656
2657     alignPanel.paintAlignment(true);
2658   }
2659
2660   protected void modifyPID_actionPerformed()
2661   {
2662     if (viewport.getAbovePIDThreshold()
2663             && viewport.getGlobalColourScheme() != null)
2664     {
2665       SliderPanel.setPIDSliderSource(alignPanel,
2666               viewport.getGlobalColourScheme(), "Background");
2667       SliderPanel.showPIDSlider();
2668     }
2669   }
2670
2671   protected void modifyConservation_actionPerformed()
2672   {
2673     if (viewport.getConservationSelected()
2674             && viewport.getGlobalColourScheme() != null)
2675     {
2676       SliderPanel.setConservationSlider(alignPanel,
2677               viewport.getGlobalColourScheme(), "Background");
2678       SliderPanel.showConservationSlider();
2679     }
2680   }
2681
2682   protected void conservationMenuItem_actionPerformed()
2683   {
2684     boolean selected = conservationMenuItem.getState();
2685     modifyConservation.setEnabled(selected);
2686     viewport.setConservationSelected(selected);
2687
2688     // viewport.setAbovePIDThreshold(false);
2689     // abovePIDThreshold.setState(false);
2690
2691     changeColour(viewport.getGlobalColourScheme());
2692
2693     if (selected)
2694     {
2695       modifyConservation_actionPerformed();
2696     }
2697     else
2698     {
2699       SliderPanel.hideConservationSlider();
2700     }
2701   }
2702
2703   public void abovePIDThreshold_actionPerformed()
2704   {
2705     boolean selected = abovePIDThreshold.getState();
2706     modifyPID.setEnabled(selected);
2707     viewport.setAbovePIDThreshold(selected);
2708     // conservationMenuItem.setState(false);
2709     // viewport.setConservationSelected(false);
2710
2711     changeColour(viewport.getGlobalColourScheme());
2712
2713     if (selected)
2714     {
2715       modifyPID_actionPerformed();
2716     }
2717     else
2718     {
2719       SliderPanel.hidePIDSlider();
2720     }
2721   }
2722
2723   public void sortPairwiseMenuItem_actionPerformed()
2724   {
2725     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2726     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2727             .getAlignment().getSequenceAt(0), null);
2728
2729     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2730             viewport.getAlignment()));
2731     alignPanel.paintAlignment(true);
2732   }
2733
2734   public void sortIDMenuItem_actionPerformed()
2735   {
2736     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2737     AlignmentSorter.sortByID(viewport.getAlignment());
2738     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2739             viewport.getAlignment()));
2740     alignPanel.paintAlignment(true);
2741   }
2742
2743   public void sortLengthMenuItem_actionPerformed()
2744   {
2745     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2746     AlignmentSorter.sortByLength(viewport.getAlignment());
2747     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2748             viewport.getAlignment()));
2749     alignPanel.paintAlignment(true);
2750   }
2751
2752   public void sortGroupMenuItem_actionPerformed()
2753   {
2754     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2755     AlignmentSorter.sortByGroup(viewport.getAlignment());
2756     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2757             viewport.getAlignment()));
2758     alignPanel.paintAlignment(true);
2759
2760   }
2761
2762   public void removeRedundancyMenuItem_actionPerformed()
2763   {
2764     new RedundancyPanel(alignPanel);
2765   }
2766
2767   public void pairwiseAlignmentMenuItem_actionPerformed()
2768   {
2769     if (viewport.getSelectionGroup() != null
2770             && viewport.getSelectionGroup().getSize() > 1)
2771     {
2772       Frame frame = new Frame();
2773       frame.add(new PairwiseAlignPanel(alignPanel));
2774       jalview.bin.JalviewLite.addFrame(frame,
2775               MessageManager.getString("action.pairwise_alignment"), 600,
2776               500);
2777     }
2778   }
2779
2780   public void PCAMenuItem_actionPerformed()
2781   {
2782     // are the sequences aligned?
2783     if (!viewport.getAlignment().isAligned(false))
2784     {
2785       SequenceI current;
2786       int Width = viewport.getAlignment().getWidth();
2787
2788       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2789       {
2790         current = viewport.getAlignment().getSequenceAt(i);
2791
2792         if (current.getLength() < Width)
2793         {
2794           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2795         }
2796       }
2797       alignPanel.paintAlignment(true);
2798     }
2799
2800     if ((viewport.getSelectionGroup() != null
2801             && viewport.getSelectionGroup().getSize() < 4 && viewport
2802             .getSelectionGroup().getSize() > 0)
2803             || viewport.getAlignment().getHeight() < 4)
2804     {
2805       return;
2806     }
2807
2808     try
2809     {
2810       new PCAPanel(viewport);
2811     } catch (java.lang.OutOfMemoryError ex)
2812     {
2813     }
2814
2815   }
2816
2817   public void averageDistanceTreeMenuItem_actionPerformed()
2818   {
2819     NewTreePanel("AV", "PID", "Average distance tree using PID");
2820   }
2821
2822   public void neighbourTreeMenuItem_actionPerformed()
2823   {
2824     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2825   }
2826
2827   protected void njTreeBlosumMenuItem_actionPerformed()
2828   {
2829     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2830   }
2831
2832   protected void avTreeBlosumMenuItem_actionPerformed()
2833   {
2834     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2835   }
2836
2837   void NewTreePanel(String type, String pwType, String title)
2838   {
2839     // are the sequences aligned?
2840     if (!viewport.getAlignment().isAligned(false))
2841     {
2842       SequenceI current;
2843       int Width = viewport.getAlignment().getWidth();
2844
2845       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2846       {
2847         current = viewport.getAlignment().getSequenceAt(i);
2848
2849         if (current.getLength() < Width)
2850         {
2851           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2852         }
2853       }
2854       alignPanel.paintAlignment(true);
2855
2856     }
2857
2858     if ((viewport.getSelectionGroup() != null && viewport
2859             .getSelectionGroup().getSize() > 1)
2860             || (viewport.getAlignment().getHeight() > 1))
2861     {
2862       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2863
2864       addTreeMenuItem(tp, title);
2865
2866       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2867     }
2868   }
2869
2870   void loadTree_actionPerformed()
2871   {
2872     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2873     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2874     cap.setTreeImport();
2875     Frame frame = new Frame();
2876     frame.add(cap);
2877     jalview.bin.JalviewLite.addFrame(frame,
2878             MessageManager.getString("label.paste_newick_file"), 400, 300);
2879   }
2880
2881   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2882   {
2883     TreePanel tp = new TreePanel(alignPanel, treeFile,
2884             MessageManager.getString("label.load_tree_from_file"), tree);
2885     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2886     addTreeMenuItem(tp, treeFile);
2887   }
2888
2889   /**
2890    * sort the alignment using the given treePanel
2891    *
2892    * @param treePanel
2893    *          tree used to sort view
2894    * @param title
2895    *          string used for undo event name
2896    */
2897   public void sortByTree(TreePanel treePanel, String title)
2898   {
2899     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2900     AlignmentSorter
2901             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2902     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2903     // HistoryItem.SORT));
2904     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2905             "label.order_by_params", new String[] { title }), oldOrder,
2906             viewport.getAlignment()));
2907     alignPanel.paintAlignment(true);
2908   }
2909
2910   /**
2911    * Do any automatic reordering of the alignment and add the necessary bits to
2912    * the menu structure for the new tree
2913    *
2914    * @param treePanel
2915    * @param title
2916    */
2917   protected void addTreeMenuItem(final TreePanel treePanel,
2918           final String title)
2919   {
2920     final MenuItem item = new MenuItem(title);
2921     sortByTreeMenu.add(item);
2922     item.addActionListener(new java.awt.event.ActionListener()
2923     {
2924       @Override
2925       public void actionPerformed(ActionEvent evt)
2926       {
2927         sortByTree(treePanel, title); // treePanel.getTitle());
2928       }
2929     });
2930
2931     treePanel.addWindowListener(new WindowAdapter()
2932     {
2933       @Override
2934       public void windowOpened(WindowEvent e)
2935       {
2936         if (viewport.sortByTree)
2937         {
2938           sortByTree(treePanel, title);
2939         }
2940         super.windowOpened(e);
2941       }
2942
2943       @Override
2944       public void windowClosing(WindowEvent e)
2945       {
2946         sortByTreeMenu.remove(item);
2947       };
2948     });
2949   }
2950
2951   public boolean sortBy(AlignmentOrder alorder, String undoname)
2952   {
2953     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2954     if (viewport.applet.debug)
2955     {
2956       System.err.println("Sorting " + alorder.getOrder().size()
2957               + " in alignment '" + getTitle() + "'");
2958     }
2959     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2960     if (undoname != null)
2961     {
2962       addHistoryItem(new OrderCommand(undoname, oldOrder,
2963               viewport.getAlignment()));
2964     }
2965     alignPanel.paintAlignment(true);
2966     return true;
2967   }
2968
2969   protected void documentation_actionPerformed()
2970   {
2971     alignPanel.av.applet.openJalviewHelpUrl();
2972   }
2973
2974   protected void about_actionPerformed()
2975   {
2976
2977     class AboutPanel extends Canvas
2978     {
2979       String version;
2980
2981       String builddate;
2982
2983       public AboutPanel(String version, String builddate)
2984       {
2985         this.version = version;
2986         this.builddate = builddate;
2987       }
2988
2989       @Override
2990       public void paint(Graphics g)
2991       {
2992         g.setColor(Color.white);
2993         g.fillRect(0, 0, getSize().width, getSize().height);
2994         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2995         FontMetrics fm = g.getFontMetrics();
2996         int fh = fm.getHeight();
2997         int y = 5, x = 7;
2998         g.setColor(Color.black);
2999         // TODO: update this text for each release or centrally store it for
3000         // lite and application
3001         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3002         g.drawString(MessageManager.formatMessage(
3003                 "label.jalviewLite_release", new String[] { version }), x,
3004                 y += fh);
3005         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3006         g.drawString(MessageManager.formatMessage(
3007                 "label.jaview_build_date", new String[] { builddate }), x,
3008                 y += fh);
3009         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3010         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3011                 x, y += fh * 1.5);
3012         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3013                 x + 50, y += fh + 8);
3014         g.drawString(
3015                 MessageManager.getString("label.jalview_dev_managers"), x,
3016                 y += fh);
3017         g.drawString(MessageManager
3018                 .getString("label.jalview_distribution_lists"), x, y += fh);
3019         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3020                 x, y += fh + 8);
3021         g.drawString(
3022                 MessageManager.getString("label.jalview_cite_1_authors"),
3023                 x, y += fh);
3024         g.drawString(
3025                 MessageManager.getString("label.jalview_cite_1_title"), x,
3026                 y += fh);
3027         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3028                 x, y += fh);
3029       }
3030     }
3031
3032     Frame frame = new Frame();
3033     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3034             .getBuildDate()));
3035     jalview.bin.JalviewLite.addFrame(frame,
3036             MessageManager.getString("label.jalview"), 580, 220);
3037
3038   }
3039
3040   public void showURL(String url, String target)
3041   {
3042     if (viewport.applet == null)
3043     {
3044       System.out.println("Not running as applet - no browser available.");
3045     }
3046     else
3047     {
3048       viewport.applet.showURL(url, target);
3049     }
3050   }
3051
3052   // ////////////////////////////////////////////////////////////////////////////////
3053   // JBuilder Graphics here
3054
3055   MenuBar alignFrameMenuBar = new MenuBar();
3056
3057   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3058
3059   MenuItem loadApplication = new MenuItem(
3060           MessageManager.getString("label.view_full_application"));
3061
3062   MenuItem loadTree = new MenuItem(
3063           MessageManager.getString("label.load_associated_tree"));
3064
3065   MenuItem loadAnnotations = new MenuItem(
3066           MessageManager.getString("label.load_features_annotations"));
3067
3068   MenuItem outputFeatures = new MenuItem(
3069           MessageManager.getString("label.export_features"));
3070
3071   MenuItem outputAnnotations = new MenuItem(
3072           MessageManager.getString("label.export_annotations"));
3073
3074   MenuItem closeMenuItem = new MenuItem(
3075           MessageManager.getString("action.close"));
3076
3077   MenuItem selectAllSequenceMenuItem = new MenuItem(
3078           MessageManager.getString("action.select_all"));
3079
3080   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3081           MessageManager.getString("action.deselect_all"));
3082
3083   MenuItem invertSequenceMenuItem = new MenuItem(
3084           MessageManager.getString("action.invert_selection"));
3085
3086   MenuItem remove2LeftMenuItem = new MenuItem();
3087
3088   MenuItem remove2RightMenuItem = new MenuItem();
3089
3090   MenuItem removeGappedColumnMenuItem = new MenuItem();
3091
3092   MenuItem removeAllGapsMenuItem = new MenuItem();
3093
3094   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3095
3096   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3097
3098   MenuItem sortPairwiseMenuItem = new MenuItem();
3099
3100   MenuItem sortIDMenuItem = new MenuItem();
3101
3102   MenuItem sortLengthMenuItem = new MenuItem();
3103
3104   MenuItem sortGroupMenuItem = new MenuItem();
3105
3106   MenuItem removeRedundancyMenuItem = new MenuItem();
3107
3108   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3109
3110   MenuItem PCAMenuItem = new MenuItem();
3111
3112   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3113
3114   MenuItem neighbourTreeMenuItem = new MenuItem();
3115
3116   BorderLayout borderLayout1 = new BorderLayout();
3117
3118   public Label statusBar = new Label();
3119
3120   MenuItem clustalColour = new MenuItem();
3121
3122   MenuItem zappoColour = new MenuItem();
3123
3124   MenuItem taylorColour = new MenuItem();
3125
3126   MenuItem hydrophobicityColour = new MenuItem();
3127
3128   MenuItem helixColour = new MenuItem();
3129
3130   MenuItem strandColour = new MenuItem();
3131
3132   MenuItem turnColour = new MenuItem();
3133
3134   MenuItem buriedColour = new MenuItem();
3135
3136   MenuItem purinePyrimidineColour = new MenuItem();
3137
3138   // MenuItem RNAInteractionColour = new MenuItem();
3139
3140   MenuItem RNAHelixColour = new MenuItem();
3141
3142   MenuItem userDefinedColour = new MenuItem();
3143
3144   MenuItem PIDColour = new MenuItem();
3145
3146   MenuItem BLOSUM62Colour = new MenuItem();
3147
3148   MenuItem tcoffeeColour = new MenuItem();
3149
3150   MenuItem njTreeBlosumMenuItem = new MenuItem();
3151
3152   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3153
3154   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3155
3156   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3157
3158   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3159
3160   MenuItem alProperties = new MenuItem(
3161           MessageManager.getString("label.alignment_props"));
3162
3163   MenuItem overviewMenuItem = new MenuItem();
3164
3165   MenuItem undoMenuItem = new MenuItem();
3166
3167   MenuItem redoMenuItem = new MenuItem();
3168
3169   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3170
3171   MenuItem noColourmenuItem = new MenuItem();
3172
3173   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3174
3175   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3176
3177   MenuItem findMenuItem = new MenuItem();
3178
3179   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3180
3181   MenuItem nucleotideColour = new MenuItem();
3182
3183   MenuItem deleteGroups = new MenuItem();
3184
3185   MenuItem grpsFromSelection = new MenuItem();
3186
3187   MenuItem createGroup = new MenuItem();
3188
3189   MenuItem unGroup = new MenuItem();
3190
3191   MenuItem delete = new MenuItem();
3192
3193   MenuItem copy = new MenuItem();
3194
3195   MenuItem cut = new MenuItem();
3196
3197   Menu pasteMenu = new Menu();
3198
3199   MenuItem pasteNew = new MenuItem();
3200
3201   MenuItem pasteThis = new MenuItem();
3202
3203   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3204
3205   MenuItem font = new MenuItem();
3206
3207   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3208
3209   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3212
3213   MenuItem modifyPID = new MenuItem();
3214
3215   MenuItem modifyConservation = new MenuItem();
3216
3217   CheckboxMenuItem autoCalculate = null;
3218
3219   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3220           "Sort Alignment With New Tree", true);
3221
3222   Menu sortByTreeMenu = new Menu();
3223
3224   MenuItem inputText = new MenuItem();
3225
3226   MenuItem documentation = new MenuItem();
3227
3228   MenuItem about = new MenuItem();
3229
3230   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3231
3232   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3233
3234   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3235
3236   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3237
3238   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3247
3248   /**
3249    * Initialise menus and other items
3250    *
3251    * @throws Exception
3252    */
3253   private void jbInit() throws Exception
3254   {
3255     setMenuBar(alignFrameMenuBar);
3256
3257     /*
3258      * Configure File menu items and actions
3259      */
3260     inputText
3261             .setLabel(MessageManager.getString("label.input_from_textbox"));
3262     inputText.addActionListener(this);
3263     Menu outputTextboxMenu = new Menu(
3264             MessageManager.getString("label.out_to_textbox"));
3265     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3266     {
3267       MenuItem item = new MenuItem(ff);
3268
3269       item.addActionListener(new java.awt.event.ActionListener()
3270       {
3271         @Override
3272         public void actionPerformed(ActionEvent e)
3273         {
3274           outputText_actionPerformed(e);
3275         }
3276       });
3277
3278       outputTextboxMenu.add(item);
3279     }
3280     closeMenuItem.addActionListener(this);
3281     loadApplication.addActionListener(this);
3282     loadTree.addActionListener(this);
3283     loadAnnotations.addActionListener(this);
3284     outputFeatures.addActionListener(this);
3285     outputAnnotations.addActionListener(this);
3286
3287     /*
3288      * Configure Edit menu items and actions
3289      */
3290     undoMenuItem.setEnabled(false);
3291     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3292     undoMenuItem.addActionListener(this);
3293     redoMenuItem.setEnabled(false);
3294     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3295     redoMenuItem.addActionListener(this);
3296     copy.setLabel(MessageManager.getString("action.copy"));
3297     copy.addActionListener(this);
3298     cut.setLabel(MessageManager.getString("action.cut"));
3299     cut.addActionListener(this);
3300     delete.setLabel(MessageManager.getString("action.delete"));
3301     delete.addActionListener(this);
3302     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3303     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3304     pasteNew.addActionListener(this);
3305     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3306     pasteThis.addActionListener(this);
3307     remove2LeftMenuItem.setLabel(MessageManager
3308             .getString("action.remove_left"));
3309     remove2LeftMenuItem.addActionListener(this);
3310     remove2RightMenuItem.setLabel(MessageManager
3311             .getString("action.remove_right"));
3312     remove2RightMenuItem.addActionListener(this);
3313     removeGappedColumnMenuItem.setLabel(MessageManager
3314             .getString("action.remove_empty_columns"));
3315     removeGappedColumnMenuItem.addActionListener(this);
3316     removeAllGapsMenuItem.setLabel(MessageManager
3317             .getString("action.remove_all_gaps"));
3318     removeAllGapsMenuItem.addActionListener(this);
3319     removeRedundancyMenuItem.setLabel(MessageManager
3320             .getString("action.remove_redundancy"));
3321     removeRedundancyMenuItem.addActionListener(this);
3322
3323     /*
3324      * Configure Select menu items and actions
3325      */
3326     findMenuItem.setLabel(MessageManager.getString("action.find"));
3327     findMenuItem.addActionListener(this);
3328     selectAllSequenceMenuItem.addActionListener(this);
3329     deselectAllSequenceMenuItem.addActionListener(this);
3330     invertSequenceMenuItem.setLabel(MessageManager
3331             .getString("action.invert_sequence_selection"));
3332     invertSequenceMenuItem.addActionListener(this);
3333     invertColSel.setLabel(MessageManager
3334             .getString("action.invert_column_selection"));
3335     invertColSel.addActionListener(this);
3336     deleteGroups.setLabel(MessageManager
3337             .getString("action.undefine_groups"));
3338     deleteGroups.addActionListener(this);
3339     grpsFromSelection.setLabel(MessageManager
3340             .getString("action.make_groups_selection"));
3341     grpsFromSelection.addActionListener(this);
3342     createGroup.setLabel(MessageManager.getString("action.create_group"));
3343     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3344     annotationColumnSelection.setLabel(MessageManager
3345             .getString("action.select_by_annotation"));
3346     annotationColumnSelection.addActionListener(this);
3347
3348     /*
3349      * Configure View menu items and actions
3350      */
3351     newView.setLabel(MessageManager.getString("action.new_view"));
3352     newView.addActionListener(this);
3353     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3354     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3355     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3356     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3357     hideColumns
3358             .setLabel(MessageManager.getString("label.selected_columns"));
3359     hideSequences.setLabel(MessageManager
3360             .getString("label.selected_sequences"));
3361     hideAllButSelection.setLabel(MessageManager
3362             .getString("label.all_but_selected_region"));
3363     hideAllSelection.setLabel(MessageManager
3364             .getString("label.selected_region"));
3365     showAllHidden.setLabel(MessageManager
3366             .getString("label.all_sequences_columns"));
3367     showColumns.addActionListener(this);
3368     showSeqs.addActionListener(this);
3369     hideColumns.addActionListener(this);
3370     hideSequences.addActionListener(this);
3371     hideAllButSelection.addActionListener(this);
3372     hideAllSelection.addActionListener(this);
3373     showAllHidden.addActionListener(this);
3374     featureSettings.setLabel(MessageManager
3375             .getString("action.feature_settings"));
3376     featureSettings.addActionListener(this);
3377     sequenceFeatures.setLabel(MessageManager
3378             .getString("label.show_sequence_features"));
3379     sequenceFeatures.addItemListener(this);
3380     sequenceFeatures.setState(false);
3381     followMouseOverFlag.setLabel(MessageManager
3382             .getString("label.automatic_scrolling"));
3383     followMouseOverFlag.addItemListener(this);
3384     alProperties.addActionListener(this);
3385     overviewMenuItem.setLabel(MessageManager
3386             .getString("label.overview_window"));
3387     overviewMenuItem.addActionListener(this);
3388
3389     /*
3390      * Configure Annotations menu items and actions
3391      */
3392     annotationPanelMenuItem.setLabel(MessageManager
3393             .getString("label.show_annotations"));
3394     annotationPanelMenuItem.addItemListener(this);
3395     showGroupConsensus.setLabel(MessageManager
3396             .getString("label.group_consensus"));
3397     showGroupConservation.setLabel(MessageManager
3398             .getString("label.group_conservation"));
3399     showConsensusHistogram.setLabel(MessageManager
3400             .getString("label.show_consensus_histogram"));
3401     showSequenceLogo.setLabel(MessageManager
3402             .getString("label.show_consensus_logo"));
3403     normSequenceLogo.setLabel(MessageManager
3404             .getString("label.norm_consensus_logo"));
3405     applyAutoAnnotationSettings.setLabel(MessageManager
3406             .getString("label.apply_all_groups"));
3407     applyAutoAnnotationSettings.setState(true);
3408     Menu autoAnnMenu = new Menu(
3409             MessageManager.getString("label.autocalculated_annotation"));
3410     showGroupConsensus.addItemListener(this);
3411     showGroupConservation.addItemListener(this);
3412     showConsensusHistogram.addItemListener(this);
3413     showSequenceLogo.addItemListener(this);
3414     normSequenceLogo.addItemListener(this);
3415     applyAutoAnnotationSettings.addItemListener(this);
3416     showAlignmentAnnotations = new CheckboxMenuItem(
3417             MessageManager.getString("label.show_all_al_annotations"));
3418     showSequenceAnnotations = new CheckboxMenuItem(
3419             MessageManager.getString("label.show_all_seq_annotations"));
3420     sortAnnBySequence = new CheckboxMenuItem(
3421             MessageManager.getString("label.sort_annotations_by_sequence"));
3422     sortAnnByLabel = new CheckboxMenuItem(
3423             MessageManager.getString("label.sort_annotations_by_label"));
3424     showAutoFirst = new CheckboxMenuItem(
3425             MessageManager.getString("label.show_first"));
3426     showAutoFirst.setState(false); // pending applet parameter
3427     setShowAutoCalculatedAbove(showAutoFirst.getState());
3428     showAutoLast = new CheckboxMenuItem(
3429             MessageManager.getString("label.show_last"));
3430     showAutoLast.setState(!showAutoFirst.getState());
3431     showAlignmentAnnotations.addItemListener(this);
3432     showSequenceAnnotations.addItemListener(this);
3433     sortAnnBySequence.addItemListener(this);
3434     sortAnnByLabel.addItemListener(this);
3435     showAutoFirst.addItemListener(this);
3436     showAutoLast.addItemListener(this);
3437
3438     /*
3439      * Configure Format menu items and actions
3440      */
3441     font.setLabel(MessageManager.getString("action.font"));
3442     font.addActionListener(this);
3443     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3444     scaleAbove.setState(true);
3445     scaleAbove.setEnabled(false);
3446     scaleAbove.addItemListener(this);
3447     scaleLeft.setEnabled(false);
3448     scaleLeft.setState(true);
3449     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3450     scaleLeft.addItemListener(this);
3451     scaleRight.setEnabled(false);
3452     scaleRight.setState(true);
3453     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3454     scaleRight.addItemListener(this);
3455     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3456     viewBoxesMenuItem.setState(true);
3457     viewBoxesMenuItem.addItemListener(this);
3458     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3459     viewTextMenuItem.setState(true);
3460     viewTextMenuItem.addItemListener(this);
3461     colourTextMenuItem.setLabel(MessageManager
3462             .getString("label.colour_text"));
3463     colourTextMenuItem.addItemListener(this);
3464     displayNonconservedMenuItem.setLabel(MessageManager
3465             .getString("label.show_non_conserved"));
3466     displayNonconservedMenuItem.addItemListener(this);
3467     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3468     wrapMenuItem.addItemListener(this);
3469     renderGapsMenuItem.setLabel(MessageManager
3470             .getString("action.show_gaps"));
3471     renderGapsMenuItem.setState(true);
3472     renderGapsMenuItem.addItemListener(this);
3473     centreColumnLabelFlag.setLabel(MessageManager
3474             .getString("label.centre_column_labels"));
3475     centreColumnLabelFlag.addItemListener(this);
3476     seqLimits.setState(true);
3477     seqLimits.setLabel(MessageManager
3478             .getString("label.show_sequence_limits"));
3479     seqLimits.addItemListener(this);
3480
3481     /*
3482      * Configure Colour menu items and actions
3483      */
3484     applyToAllGroups.setLabel(MessageManager
3485             .getString("label.apply_colour_to_all_groups"));
3486     applyToAllGroups.setState(true);
3487     applyToAllGroups.addItemListener(this);
3488     clustalColour.setLabel(MessageManager
3489             .getString("label.colourScheme_clustal"));
3490     clustalColour.addActionListener(this);
3491     zappoColour.setLabel(MessageManager
3492             .getString("label.colourScheme_zappo"));
3493     zappoColour.addActionListener(this);
3494     taylorColour.setLabel(MessageManager
3495             .getString("label.colourScheme_taylor"));
3496     taylorColour.addActionListener(this);
3497     hydrophobicityColour.setLabel(MessageManager
3498             .getString("label.colourScheme_hydrophobic"));
3499     hydrophobicityColour.addActionListener(this);
3500     helixColour.setLabel(MessageManager
3501             .getString("label.colourScheme_helix_propensity"));
3502     helixColour.addActionListener(this);
3503     strandColour.setLabel(MessageManager
3504             .getString("label.colourScheme_strand_propensity"));
3505     strandColour.addActionListener(this);
3506     turnColour.setLabel(MessageManager
3507             .getString("label.colourScheme_turn_propensity"));
3508     turnColour.addActionListener(this);
3509     buriedColour.setLabel(MessageManager
3510             .getString("label.colourScheme_buried_index"));
3511     buriedColour.addActionListener(this);
3512     purinePyrimidineColour.setLabel(MessageManager
3513             .getString("label.colourScheme_purine/pyrimidine"));
3514     purinePyrimidineColour.addActionListener(this);
3515     // RNAInteractionColour.setLabel(MessageManager
3516     // .getString("label.rna_interaction"));
3517     // RNAInteractionColour.addActionListener(this);
3518     RNAHelixColour.setLabel(MessageManager
3519             .getString("label.colourScheme_rna_helices"));
3520     RNAHelixColour.addActionListener(this);
3521     userDefinedColour.setLabel(MessageManager
3522             .getString("action.user_defined"));
3523     userDefinedColour.addActionListener(this);
3524     PIDColour.setLabel(MessageManager
3525             .getString("label.colourScheme_%_identity"));
3526     PIDColour.addActionListener(this);
3527     BLOSUM62Colour.setLabel(MessageManager
3528             .getString("label.colourScheme_blosum62"));
3529     BLOSUM62Colour.addActionListener(this);
3530     tcoffeeColour.setLabel(MessageManager
3531             .getString("label.colourScheme_t-coffee_scores"));
3532     // it will be enabled only if a score file is provided
3533     tcoffeeColour.setEnabled(false);
3534     tcoffeeColour.addActionListener(this);
3535     conservationMenuItem.setLabel(MessageManager
3536             .getString("action.by_conservation"));
3537     conservationMenuItem.addItemListener(this);
3538     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3539     noColourmenuItem.addActionListener(this);
3540     abovePIDThreshold.setLabel(MessageManager
3541             .getString("label.above_identity_threshold"));
3542     abovePIDThreshold.addItemListener(this);
3543     nucleotideColour.setLabel(MessageManager
3544             .getString("label.colourScheme_nucleotide"));
3545     nucleotideColour.addActionListener(this);
3546     modifyPID.setLabel(MessageManager
3547             .getString("label.modify_identity_threshold"));
3548     modifyPID.setEnabled(abovePIDThreshold.getState());
3549     modifyPID.addActionListener(this);
3550     modifyConservation.setLabel(MessageManager
3551             .getString("label.modify_conservation_threshold"));
3552     modifyConservation.setEnabled(conservationMenuItem.getState());
3553     modifyConservation.addActionListener(this);
3554     annotationColour.setLabel(MessageManager
3555             .getString("action.by_annotation"));
3556     annotationColour.addActionListener(this);
3557
3558     /*
3559      * Configure Calculate menu items and actions
3560      */
3561     sortPairwiseMenuItem.setLabel(MessageManager
3562             .getString("action.by_pairwise_id"));
3563     sortPairwiseMenuItem.addActionListener(this);
3564     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3565     sortIDMenuItem.addActionListener(this);
3566     sortLengthMenuItem.setLabel(MessageManager
3567             .getString("action.by_length"));
3568     sortLengthMenuItem.addActionListener(this);
3569     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3570     sortGroupMenuItem.addActionListener(this);
3571     pairwiseAlignmentMenuItem.setLabel(MessageManager
3572             .getString("action.pairwise_alignment"));
3573     pairwiseAlignmentMenuItem.addActionListener(this);
3574     PCAMenuItem.setLabel(MessageManager
3575             .getString("label.principal_component_analysis"));
3576     PCAMenuItem.addActionListener(this);
3577     autoCalculate = new CheckboxMenuItem(
3578             MessageManager.getString("label.autocalculate_consensus"), true);
3579     averageDistanceTreeMenuItem.setLabel(MessageManager
3580             .getString("label.average_distance_identity"));
3581     averageDistanceTreeMenuItem.addActionListener(this);
3582     neighbourTreeMenuItem.setLabel(MessageManager
3583             .getString("label.neighbour_joining_identity"));
3584     neighbourTreeMenuItem.addActionListener(this);
3585     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3586             .getString("label.average_distance_blosum62"));
3587     avDistanceTreeBlosumMenuItem.addActionListener(this);
3588     njTreeBlosumMenuItem.setLabel(MessageManager
3589             .getString("label.neighbour_blosum62"));
3590     njTreeBlosumMenuItem.addActionListener(this);
3591     sortByTreeMenu.setLabel(MessageManager
3592             .getString("action.by_tree_order"));
3593     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3594     Menu calculateTreeMenu = new Menu(
3595             MessageManager.getString("action.calculate_tree"));
3596     autoCalculate.addItemListener(this);
3597     sortByTree.addItemListener(this);
3598
3599     /*
3600      * Configure Help menu items and actions
3601      */
3602     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3603     documentation.setLabel(MessageManager.getString("label.documentation"));
3604     documentation.addActionListener(this);
3605     about.setLabel(MessageManager.getString("label.about"));
3606     about.addActionListener(this);
3607
3608     /*
3609      * Add top level menus to frame
3610      */
3611     alignFrameMenuBar.add(fileMenu);
3612     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3613     alignFrameMenuBar.add(editMenu);
3614     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3615     alignFrameMenuBar.add(selectMenu);
3616     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3617     alignFrameMenuBar.add(viewMenu);
3618     Menu annotationsMenu = new Menu(
3619             MessageManager.getString("action.annotations"));
3620     alignFrameMenuBar.add(annotationsMenu);
3621     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3622     alignFrameMenuBar.add(formatMenu);
3623     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3624     alignFrameMenuBar.add(colourMenu);
3625     Menu calculateMenu = new Menu(
3626             MessageManager.getString("action.calculate"));
3627     alignFrameMenuBar.add(calculateMenu);
3628     alignFrameMenuBar.add(helpMenu);
3629
3630     /*
3631      * File menu
3632      */
3633     fileMenu.add(inputText);
3634     fileMenu.add(loadTree);
3635     fileMenu.add(loadAnnotations);
3636     fileMenu.addSeparator();
3637     fileMenu.add(outputTextboxMenu);
3638     fileMenu.add(outputFeatures);
3639     fileMenu.add(outputAnnotations);
3640     if (jalviewServletURL != null)
3641     {
3642       fileMenu.add(loadApplication);
3643     }
3644     fileMenu.addSeparator();
3645     fileMenu.add(closeMenuItem);
3646
3647     /*
3648      * Edit menu
3649      */
3650     editMenu.add(undoMenuItem);
3651     editMenu.add(redoMenuItem);
3652     editMenu.add(cut);
3653     editMenu.add(copy);
3654     pasteMenu.add(pasteNew);
3655     pasteMenu.add(pasteThis);
3656     editMenu.add(pasteMenu);
3657     editMenu.add(delete);
3658     editMenu.addSeparator();
3659     editMenu.add(remove2LeftMenuItem);
3660     editMenu.add(remove2RightMenuItem);
3661     editMenu.add(removeGappedColumnMenuItem);
3662     editMenu.add(removeAllGapsMenuItem);
3663     editMenu.add(removeRedundancyMenuItem);
3664
3665     /*
3666      * Select menu
3667      */
3668     selectMenu.add(findMenuItem);
3669     selectMenu.addSeparator();
3670     selectMenu.add(selectAllSequenceMenuItem);
3671     selectMenu.add(deselectAllSequenceMenuItem);
3672     selectMenu.add(invertSequenceMenuItem);
3673     selectMenu.add(invertColSel);
3674     selectMenu.add(createGroup);
3675     selectMenu.add(unGroup);
3676     selectMenu.add(grpsFromSelection);
3677     selectMenu.add(deleteGroups);
3678     selectMenu.add(annotationColumnSelection);
3679
3680     /*
3681      * View menu
3682      */
3683     viewMenu.add(newView);
3684     viewMenu.addSeparator();
3685     showMenu.add(showColumns);
3686     showMenu.add(showSeqs);
3687     showMenu.add(showAllHidden);
3688     viewMenu.add(showMenu);
3689     hideMenu.add(hideColumns);
3690     hideMenu.add(hideSequences);
3691     hideMenu.add(hideAllSelection);
3692     hideMenu.add(hideAllButSelection);
3693     viewMenu.add(hideMenu);
3694     viewMenu.addSeparator();
3695     viewMenu.add(followMouseOverFlag);
3696     viewMenu.addSeparator();
3697     viewMenu.add(sequenceFeatures);
3698     viewMenu.add(featureSettings);
3699     viewMenu.addSeparator();
3700     viewMenu.add(alProperties);
3701     viewMenu.addSeparator();
3702     viewMenu.add(overviewMenuItem);
3703
3704     /*
3705      * Annotations menu
3706      */
3707     annotationsMenu.add(annotationPanelMenuItem);
3708     annotationsMenu.addSeparator();
3709     annotationsMenu.add(showAlignmentAnnotations);
3710     annotationsMenu.add(showSequenceAnnotations);
3711     annotationsMenu.add(sortAnnBySequence);
3712     annotationsMenu.add(sortAnnByLabel);
3713     annotationsMenu.addSeparator();
3714     autoAnnMenu.add(showAutoFirst);
3715     autoAnnMenu.add(showAutoLast);
3716     autoAnnMenu.addSeparator();
3717     autoAnnMenu.add(applyAutoAnnotationSettings);
3718     autoAnnMenu.add(showConsensusHistogram);
3719     autoAnnMenu.add(showSequenceLogo);
3720     autoAnnMenu.add(normSequenceLogo);
3721     autoAnnMenu.addSeparator();
3722     autoAnnMenu.add(showGroupConservation);
3723     autoAnnMenu.add(showGroupConsensus);
3724     annotationsMenu.add(autoAnnMenu);
3725
3726     /*
3727      * Format menu
3728      */
3729     formatMenu.add(font);
3730     formatMenu.add(seqLimits);
3731     formatMenu.add(wrapMenuItem);
3732     formatMenu.add(scaleAbove);
3733     formatMenu.add(scaleLeft);
3734     formatMenu.add(scaleRight);
3735     formatMenu.add(viewBoxesMenuItem);
3736     formatMenu.add(viewTextMenuItem);
3737     formatMenu.add(colourTextMenuItem);
3738     formatMenu.add(displayNonconservedMenuItem);
3739     formatMenu.add(renderGapsMenuItem);
3740     formatMenu.add(centreColumnLabelFlag);
3741
3742     /*
3743      * Colour menu
3744      */
3745     colourMenu.add(applyToAllGroups);
3746     colourMenu.addSeparator();
3747     colourMenu.add(noColourmenuItem);
3748     colourMenu.add(clustalColour);
3749     colourMenu.add(BLOSUM62Colour);
3750     colourMenu.add(PIDColour);
3751     colourMenu.add(zappoColour);
3752     colourMenu.add(taylorColour);
3753     colourMenu.add(hydrophobicityColour);
3754     colourMenu.add(helixColour);
3755     colourMenu.add(strandColour);
3756     colourMenu.add(turnColour);
3757     colourMenu.add(buriedColour);
3758     colourMenu.add(nucleotideColour);
3759     colourMenu.add(purinePyrimidineColour);
3760     // colourMenu.add(RNAInteractionColour);
3761     colourMenu.add(tcoffeeColour);
3762     colourMenu.add(userDefinedColour);
3763     colourMenu.addSeparator();
3764     colourMenu.add(conservationMenuItem);
3765     colourMenu.add(modifyConservation);
3766     colourMenu.add(abovePIDThreshold);
3767     colourMenu.add(modifyPID);
3768     colourMenu.add(annotationColour);
3769     colourMenu.add(RNAHelixColour);
3770
3771     /*
3772      * Calculate menu
3773      */
3774     sortMenu.add(sortIDMenuItem);
3775     sortMenu.add(sortLengthMenuItem);
3776     sortMenu.add(sortByTreeMenu);
3777     sortMenu.add(sortGroupMenuItem);
3778     sortMenu.add(sortPairwiseMenuItem);
3779     calculateMenu.add(sortMenu);
3780     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3781     calculateTreeMenu.add(neighbourTreeMenuItem);
3782     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3783     calculateTreeMenu.add(njTreeBlosumMenuItem);
3784     calculateMenu.add(calculateTreeMenu);
3785     calculateMenu.addSeparator();
3786     calculateMenu.add(pairwiseAlignmentMenuItem);
3787     calculateMenu.add(PCAMenuItem);
3788     calculateMenu.add(autoCalculate);
3789     calculateMenu.add(sortByTree);
3790
3791     /*
3792      * Help menu
3793      */
3794     helpMenu.add(documentation);
3795     helpMenu.add(about);
3796
3797     /*
3798      * Status bar
3799      */
3800     statusBar.setBackground(Color.white);
3801     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3802     statusBar.setText(MessageManager.getString("label.status_bar"));
3803     this.add(statusBar, BorderLayout.SOUTH);
3804   }
3805
3806   @Override
3807   public void setStatus(String string)
3808   {
3809     statusBar.setText(string);
3810   };
3811
3812   MenuItem featureSettings = new MenuItem();
3813
3814   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3815
3816   MenuItem annotationColour = new MenuItem();
3817
3818   MenuItem annotationColumnSelection = new MenuItem();
3819
3820   MenuItem invertColSel = new MenuItem();
3821
3822   MenuItem showColumns = new MenuItem();
3823
3824   MenuItem showSeqs = new MenuItem();
3825
3826   MenuItem hideColumns = new MenuItem();
3827
3828   MenuItem hideSequences = new MenuItem();
3829
3830   MenuItem hideAllButSelection = new MenuItem();
3831
3832   MenuItem hideAllSelection = new MenuItem();
3833
3834   MenuItem showAllHidden = new MenuItem();
3835
3836   MenuItem newView = new MenuItem();
3837
3838   private CheckboxMenuItem showAlignmentAnnotations;
3839
3840   private CheckboxMenuItem showSequenceAnnotations;
3841
3842   private CheckboxMenuItem sortAnnBySequence;
3843
3844   private CheckboxMenuItem sortAnnByLabel;
3845
3846   private CheckboxMenuItem showAutoFirst;
3847
3848   private CheckboxMenuItem showAutoLast;
3849
3850   private SplitFrame splitFrame;
3851
3852   /**
3853    * Attach the alignFrame panels after embedding menus, if necessary. This used
3854    * to be called setEmbedded, but is now creates the dropdown menus in a
3855    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3856    *
3857    * @param reallyEmbedded
3858    *          true to attach the view to the applet area on the page rather than
3859    *          in a new window
3860    */
3861   public void createAlignFrameWindow(boolean reallyEmbedded)
3862   {
3863     if (reallyEmbedded)
3864     {
3865       embedAlignFrameInApplet(viewport.applet);
3866     }
3867     else
3868     {
3869       // //////
3870       // test and embed menu bar if necessary.
3871       //
3872       if (embedMenuIfNeeded(alignPanel))
3873       {
3874         /*
3875          * adjust for status bar height too. ? pointless as overridden by layout
3876          * manager
3877          */
3878         alignPanel.setSize(getSize().width,
3879                 getSize().height - statusBar.getHeight());
3880       }
3881       add(statusBar, BorderLayout.SOUTH);
3882       add(alignPanel, BorderLayout.CENTER);
3883       // and register with the applet so it can pass external API calls to us
3884       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3885               frameHeight);
3886     }
3887   }
3888
3889   /**
3890    * Add the components of this AlignFrame to the applet container.
3891    *
3892    * @param theApplet
3893    */
3894   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3895   {
3896     // ////
3897     // Explicitly build the embedded menu panel for the on-page applet
3898     //
3899     // view cannot be closed if its actually on the page
3900     fileMenu.remove(closeMenuItem);
3901     fileMenu.remove(3); // Remove Separator
3902     // construct embedded menu, using default font
3903     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3904     // and actually add the components to the applet area
3905     theApplet.setLayout(new BorderLayout());
3906     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3907     theApplet.add(statusBar, BorderLayout.SOUTH);
3908     // TODO should size be left to the layout manager?
3909     alignPanel.setSize(theApplet.getSize().width,
3910             theApplet.getSize().height - embeddedMenu.getHeight()
3911                     - statusBar.getHeight());
3912     theApplet.add(alignPanel, BorderLayout.CENTER);
3913     final AlignFrame me = this;
3914     theApplet.addFocusListener(new FocusListener()
3915     {
3916
3917       @Override
3918       public void focusLost(FocusEvent e)
3919       {
3920         if (theApplet.currentAlignFrame == me)
3921         {
3922           theApplet.currentAlignFrame = null;
3923         }
3924       }
3925
3926       @Override
3927       public void focusGained(FocusEvent e)
3928       {
3929         theApplet.currentAlignFrame = me;
3930       }
3931     });
3932     theApplet.validate();
3933   }
3934
3935   /**
3936    * create a new binding between structures in an existing jmol viewer instance
3937    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3938    * this does not open a new Jmol window, or modify the display of the
3939    * structures in the original jmol window. Note This method doesn't work
3940    * without an additional javascript library to exchange messages between the
3941    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3942    *
3943    * @param viewer
3944    *          JmolViewer instance
3945    * @param sequenceIds
3946    *          - sequence Ids to search for associations
3947    */
3948   public SequenceStructureBinding addStructureViewInstance(
3949           Object jmolviewer, String[] sequenceIds)
3950   {
3951     Viewer viewer = null;
3952     try
3953     {
3954       viewer = (Viewer) jmolviewer;
3955     } catch (ClassCastException ex)
3956     {
3957       System.err.println("Unsupported viewer object :"
3958               + jmolviewer.getClass());
3959     }
3960     if (viewer == null)
3961     {
3962       System.err.println("Can't use this object as a structure viewer:"
3963               + jmolviewer.getClass());
3964       return null;
3965     }
3966     SequenceI[] seqs = null;
3967     if (sequenceIds == null || sequenceIds.length == 0)
3968     {
3969       seqs = viewport.getAlignment().getSequencesArray();
3970     }
3971     else
3972     {
3973       Vector sqi = new Vector();
3974       AlignmentI al = viewport.getAlignment();
3975       for (int sid = 0; sid < sequenceIds.length; sid++)
3976       {
3977         SequenceI sq = al.findName(sequenceIds[sid]);
3978         if (sq != null)
3979         {
3980           sqi.addElement(sq);
3981         }
3982       }
3983       if (sqi.size() > 0)
3984       {
3985         seqs = new SequenceI[sqi.size()];
3986         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3987         {
3988           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3989         }
3990       }
3991       else
3992       {
3993         return null;
3994       }
3995     }
3996     AAStructureBindingModel jmv = null;
3997     // TODO: search for a jmv that involves viewer
3998     if (jmv == null)
3999     { // create a new viewer/jalview binding.
4000       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4001     }
4002     return jmv;
4003
4004   }
4005
4006   /**
4007    * bind a pdb file to a sequence in the current view
4008    *
4009    * @param sequenceId
4010    *          - sequenceId within the dataset.
4011    * @param pdbEntryString
4012    *          - the short name for the PDB file
4013    * @param pdbFile
4014    *          - pdb file - either a URL or a valid PDB file.
4015    * @return true if binding was as success TODO: consider making an exception
4016    *         structure for indicating when PDB parsing or sequenceId location
4017    *         fails.
4018    */
4019   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4020           String pdbFile)
4021   {
4022     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4023     boolean needtoadd = false;
4024     if (toaddpdb != null)
4025     {
4026       Vector pdbe = toaddpdb.getAllPDBEntries();
4027       PDBEntry pdbentry = null;
4028       if (pdbe != null && pdbe.size() > 0)
4029       {
4030         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4031         {
4032           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4033           if (!pdbentry.getId().equals(pdbEntryString)
4034                   && !pdbentry.getFile().equals(pdbFile))
4035           {
4036             pdbentry = null;
4037           }
4038           else
4039           {
4040             continue;
4041           }
4042         }
4043       }
4044       if (pdbentry == null)
4045       {
4046         pdbentry = new PDBEntry();
4047         pdbentry.setId(pdbEntryString);
4048         pdbentry.setFile(pdbFile);
4049         needtoadd = true; // add this new entry to sequence.
4050       }
4051       // resolve data source
4052       // TODO: this code should be a refactored to an io package
4053       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4054               pdbFile, FileFormat.PDB);
4055       if (protocol == null)
4056       {
4057         return false;
4058       }
4059       if (needtoadd)
4060       {
4061         pdbentry.setProperty("protocol", protocol);
4062         toaddpdb.addPDBId(pdbentry);
4063         alignPanel.getStructureSelectionManager()
4064                 .registerPDBEntry(pdbentry);
4065       }
4066     }
4067     return true;
4068   }
4069
4070   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4071   {
4072     if (seqs != null)
4073     {
4074       Vector sequences = new Vector();
4075       for (int i = 0; i < seqs.length; i++)
4076       {
4077         if (seqs[i] != null)
4078         {
4079           sequences.addElement(new Object[] { seqs[i],
4080               (chains != null) ? chains[i] : null });
4081         }
4082       }
4083       seqs = new SequenceI[sequences.size()];
4084       chains = new String[sequences.size()];
4085       for (int i = 0, isize = sequences.size(); i < isize; i++)
4086       {
4087         Object[] oj = (Object[]) sequences.elementAt(i);
4088
4089         seqs[i] = (SequenceI) oj[0];
4090         chains[i] = (String) oj[1];
4091       }
4092     }
4093     return new Object[] { seqs, chains };
4094
4095   }
4096
4097   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4098           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4099   {
4100     // Scrub any null sequences from the array
4101     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4102     seqs = (SequenceI[]) sqch[0];
4103     chains = (String[]) sqch[1];
4104     if (seqs == null || seqs.length == 0)
4105     {
4106       System.err
4107               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4108     }
4109     if (protocol == null)
4110     {
4111       String sourceType = (String) pdb.getProperty("protocol");
4112       try
4113       {
4114         protocol = DataSourceType.valueOf(sourceType);
4115       } catch (IllegalArgumentException e)
4116       {
4117         // ignore
4118       }
4119       if (protocol == null)
4120       {
4121         System.err.println("Couldn't work out protocol to open structure: "
4122                 + pdb.getId());
4123         return;
4124       }
4125     }
4126     if (applet.useXtrnalSviewer)
4127     {
4128       // register the association(s) and quit, don't create any windows.
4129       if (StructureSelectionManager.getStructureSelectionManager(applet)
4130               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4131       {
4132         System.err.println("Failed to map " + pdb.getFile() + " ("
4133                 + protocol + ") to any sequences");
4134       }
4135       return;
4136     }
4137     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4138     {
4139       // can only do alignments with Jmol
4140       // find the last jmol window assigned to this alignment
4141       AppletJmol ajm = null, tajm;
4142       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4143       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4144       {
4145         tajm = (AppletJmol) jmols.elementAt(i);
4146         if (tajm.ap.alignFrame == this)
4147         {
4148           ajm = tajm;
4149           break;
4150         }
4151       }
4152       if (ajm != null)
4153       {
4154         System.err
4155                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4156         // try and add the pdb structure
4157         // ajm.addS
4158         ajm = null;
4159       }
4160     }
4161     // otherwise, create a new window
4162     if (applet.jmolAvailable)
4163     {
4164       new AppletJmol(pdb, seqs, chains, alignPanel,
4165               protocol);
4166       applet.lastFrameX += 40;
4167       applet.lastFrameY += 40;
4168     }
4169     else
4170     {
4171       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4172     }
4173
4174   }
4175
4176   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4177           SequenceI[][] seqs, String[][] chains, String[] protocols)
4178   {
4179     // TODO Auto-generated method stub
4180     System.err.println("Aligned Structure View: Not yet implemented.");
4181   }
4182
4183   /**
4184    * modify the current selection, providing the user has not made a selection
4185    * already.
4186    *
4187    * @param sel
4188    *          - sequences from this alignment
4189    * @param csel
4190    *          - columns to be selected on the alignment
4191    */
4192   public void select(SequenceGroup sel, ColumnSelection csel)
4193   {
4194     alignPanel.seqPanel.selection(sel, csel, null);
4195   }
4196
4197   public void scrollTo(int row, int column)
4198   {
4199     alignPanel.seqPanel.scrollTo(row, column);
4200   }
4201
4202   public void scrollToRow(int row)
4203   {
4204     alignPanel.seqPanel.scrollToRow(row);
4205   }
4206
4207   public void scrollToColumn(int column)
4208   {
4209     alignPanel.seqPanel.scrollToColumn(column);
4210   }
4211
4212   /**
4213    * @return the alignments unique ID.
4214    */
4215   public String getSequenceSetId()
4216   {
4217     return viewport.getSequenceSetId();
4218   }
4219
4220   /**
4221    * Load the (T-Coffee) score file from the specified url
4222    *
4223    * @param source
4224    *          File/URL/T-COFFEE score file contents
4225    * @throws IOException
4226    * @return true if alignment was annotated with data from source
4227    */
4228   public boolean loadScoreFile(String source) throws IOException
4229   {
4230
4231     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4232             AppletFormatAdapter.checkProtocol(source));
4233     if (!file.isValid())
4234     {
4235       // TODO: raise dialog for gui
4236       System.err.println("Problems parsing T-Coffee scores: "
4237               + file.getWarningMessage());
4238       System.err.println("Origin was:\n" + source);
4239       return false;
4240     }
4241
4242     /*
4243      * check that the score matrix matches the alignment dimensions
4244      */
4245     AlignmentI aln;
4246     if ((aln = viewport.getAlignment()) != null
4247             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4248                     .getWidth()))
4249     {
4250       // TODO: raise a dialog box here rather than bomb out.
4251       System.err
4252               .println("The scores matrix does not match the alignment dimensions");
4253
4254     }
4255
4256     // TODO add parameter to indicate if matching should be done
4257     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4258     {
4259       alignPanel.fontChanged();
4260       tcoffeeColour.setEnabled(true);
4261       // switch to this color
4262       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4263       return true;
4264     }
4265     else
4266     {
4267       System.err.println("Problems resolving T-Coffee scores:");
4268       if (file.getWarningMessage() != null)
4269       {
4270         System.err.println(file.getWarningMessage());
4271       }
4272     }
4273     return false;
4274   }
4275
4276   public SplitFrame getSplitFrame()
4277   {
4278     return this.splitFrame;
4279   }
4280
4281   public void setSplitFrame(SplitFrame sf)
4282   {
4283     this.splitFrame = sf;
4284   }
4285
4286   // may not need this
4287   @Override
4288   public void setShowSeqFeatures(boolean b)
4289   {
4290     // showSeqFeatures.setSelected(b);
4291     viewport.setShowSequenceFeatures(b);
4292
4293   }
4294
4295   @Override
4296   public void setMenusForViewport()
4297   {
4298     // setMenusFromViewport(viewport);
4299
4300   }
4301
4302   @Override
4303   public void refreshFeatureUI(boolean enableIfNecessary)
4304   {
4305     if (enableIfNecessary)
4306     {
4307       sequenceFeatures.setState(true);
4308       alignPanel.av.setShowSequenceFeatures(true);
4309     }
4310   }
4311
4312   @Override
4313   public FeatureSettingsControllerI getFeatureSettingsUI()
4314   {
4315     return alignPanel.av.featureSettings;
4316   }
4317
4318 }