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.analysis.TreeBuilder;
  26 import jalview.analysis.scoremodels.PIDModel;
  27 import jalview.analysis.scoremodels.ScoreModels;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.FeatureColourI;
  32 import jalview.api.FeatureRenderer;
  33 import jalview.api.FeatureSettingsControllerI;
  34 import jalview.api.SequenceStructureBinding;
  35 import jalview.bin.JalviewLite;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentAnnotation;
  46 import jalview.datamodel.AlignmentI;
  47 import jalview.datamodel.AlignmentOrder;
  48 import jalview.datamodel.ColumnSelection;
  49 import jalview.datamodel.HiddenColumns;
  50 import jalview.datamodel.PDBEntry;
  51 import jalview.datamodel.Sequence;
  52 import jalview.datamodel.SequenceGroup;
  53 import jalview.datamodel.SequenceI;
  54 import jalview.io.AnnotationFile;
  55 import jalview.io.AppletFormatAdapter;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FeaturesFile;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileFormatI;
  60 import jalview.io.FileFormats;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColour;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.ZappoColourScheme;
  77 import jalview.structure.StructureSelectionManager;
  78 import jalview.structures.models.AAStructureBindingModel;
  79 import jalview.util.MappingUtils;
  80 import jalview.util.MessageManager;
  81 import jalview.viewmodel.AlignmentViewport;
  82 import jalview.viewmodel.ViewportRanges;
  83
  84 import java.awt.BorderLayout;
  85 import java.awt.Canvas;
  86 import java.awt.CheckboxMenuItem;
  87 import java.awt.Color;
  88 import java.awt.FlowLayout;
  89 import java.awt.Font;
  90 import java.awt.FontMetrics;
  91 import java.awt.Frame;
  92 import java.awt.Graphics;
  93 import java.awt.Label;
  94 import java.awt.Menu;
  95 import java.awt.MenuBar;
  96 import java.awt.MenuItem;
  97 import java.awt.Panel;
  98 import java.awt.event.ActionEvent;
  99 import java.awt.event.ActionListener;
 100 import java.awt.event.FocusEvent;
 101 import java.awt.event.FocusListener;
 102 import java.awt.event.ItemEvent;
 103 import java.awt.event.ItemListener;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.KeyListener;
 106 import java.awt.event.WindowAdapter;
 107 import java.awt.event.WindowEvent;
 108 import java.io.IOException;
 109 import java.net.URL;
 110 import java.net.URLEncoder;
 111 import java.util.Arrays;
 112 import java.util.Deque;
 113 import java.util.HashMap;
 114 import java.util.List;
 115 import java.util.Map;
 116 import java.util.StringTokenizer;
 117 import java.util.Vector;
 118
 119 import org.jmol.viewer.Viewer;
 120
 121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 122         ItemListener, KeyListener, AlignViewControllerGuiI
 123 {
 124   public AlignViewControllerI avc;
 125
 126   public AlignmentPanel alignPanel;
 127
 128   public AlignViewport viewport;
 129
 130   // width and height may be overridden by applet parameters
 131   int frameWidth = 700;
 132
 133   int frameHeight = 500;
 134
 135   String jalviewServletURL;
 136
 137   /*
 138    * Flag for showing autocalculated consensus above or below other consensus
 139    * rows
 140    */
 141   private boolean showAutoCalculatedAbove;
 142
 143   private SequenceAnnotationOrder annotationSortOrder;
 144
 145   /**
 146    * Constructor that creates the frame and adds it to the display.
 147    *
 148    * @param al
 149    * @param applet
 150    * @param title
 151    * @param embedded
 152    */
 153   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 154           boolean embedded)
 155   {
 156     this(al, applet, title, embedded, true);
 157   }
 158
 159   /**
 160    * Constructor that optionally allows the frame to be displayed or only
 161    * created.
 162    *
 163    * @param al
 164    * @param applet
 165    * @param title
 166    * @param embedded
 167    * @param addToDisplay
 168    */
 169   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 170           boolean embedded, boolean addToDisplay)
 171   {
 172     this(al, null, null, applet, title, embedded, addToDisplay);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           HiddenColumns hidden, JalviewLite applet, String title,
 177           boolean embedded)
 178   {
 179     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 180   }
 181
 182   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 183           HiddenColumns hidden, JalviewLite applet, String title,
 184           boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237
 238     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 239     followMouseOverFlag.setState(viewport.isFollowHighlight());
 240     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 241     showGroupConservation.setState(viewport.isShowGroupConservation());
 242     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 243     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 244     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 245     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 246     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 247     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 248     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showAlignmentAnnotations.setState(true);
 250     showSequenceAnnotations.setState(false);
 251
 252     seqLimits.setState(viewport.getShowJVSuffix());
 253
 254     if (applet != null)
 255     {
 256       String param = applet.getParameter("sortBy");
 257       if (param != null)
 258       {
 259         if (param.equalsIgnoreCase("Id"))
 260         {
 261           sortIDMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Pairwise Identity"))
 264         {
 265           sortPairwiseMenuItem_actionPerformed();
 266         }
 267         else if (param.equalsIgnoreCase("Length"))
 268         {
 269           sortLengthMenuItem_actionPerformed();
 270         }
 271       }
 272
 273       param = applet.getParameter("wrap");
 274       if (param != null)
 275       {
 276         if (param.equalsIgnoreCase("true"))
 277         {
 278           wrapMenuItem.setState(true);
 279           wrapMenuItem_actionPerformed();
 280         }
 281       }
 282       param = applet.getParameter("centrecolumnlabels");
 283       if (param != null)
 284       {
 285         centreColumnLabelFlag.setState(true);
 286         centreColumnLabelFlag_stateChanged();
 287       }
 288
 289     }
 290     if (viewport.getAlignment().isNucleotide())
 291     {
 292       conservationMenuItem.setEnabled(false);
 293       clustalColour.setEnabled(false);
 294       BLOSUM62Colour.setEnabled(false);
 295       zappoColour.setEnabled(false);
 296       taylorColour.setEnabled(false);
 297       hydrophobicityColour.setEnabled(false);
 298       helixColour.setEnabled(false);
 299       strandColour.setEnabled(false);
 300       turnColour.setEnabled(false);
 301       buriedColour.setEnabled(false);
 302       viewport.updateStrucConsensus(alignPanel);
 303       if (viewport.getAlignment().hasRNAStructure())
 304       {
 305         RNAHelixColour.setEnabled(true);
 306       }
 307       else
 308       {
 309         RNAHelixColour.setEnabled(false);
 310       }
 311     }
 312     else
 313     {
 314       RNAHelixColour.setEnabled(false);
 315       purinePyrimidineColour.setEnabled(false);
 316       nucleotideColour.setEnabled(false);
 317     }
 318     // Some JVMS send keyevents to Top frame or lowest panel,
 319     // Havent worked out why yet. So add to both this frame and seqCanvas for
 320     // now
 321     this.addKeyListener(this);
 322     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 323     alignPanel.idPanel.idCanvas.addKeyListener(this);
 324     alignPanel.scalePanel.addKeyListener(this);
 325     alignPanel.annotationPanel.addKeyListener(this);
 326     alignPanel.annotationPanelHolder.addKeyListener(this);
 327     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 328     alignPanel.alabels.addKeyListener(this);
 329
 330     setAnnotationsVisibility();
 331
 332     if (addToDisplay)
 333     {
 334       addToDisplay(embedded);
 335     }
 336   }
 337
 338   /**
 339    * @param embedded
 340    */
 341   public void addToDisplay(boolean embedded)
 342   {
 343     createAlignFrameWindow(embedded);
 344     validate();
 345     alignPanel.adjustAnnotationHeight();
 346     alignPanel.paintAlignment(true);
 347   }
 348
 349   public AlignViewport getAlignViewport()
 350   {
 351     return viewport;
 352   }
 353
 354   public SeqCanvas getSeqcanvas()
 355   {
 356     return alignPanel.seqPanel.seqCanvas;
 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 type
 365    *          is protocol for accessing data referred to by file
 366    */
 367
 368   public boolean parseFeaturesFile(String file, DataSourceType type)
 369   {
 370     return parseFeaturesFile(file, type, true);
 371   }
 372
 373   /**
 374    * Load a features file onto the alignment
 375    *
 376    * @param file
 377    *          file URL, content, or other resolvable path
 378    * @param sourceType
 379    *          is protocol for accessing data referred to by file
 380    * @param autoenabledisplay
 381    *          when true, display features flag will be automatically enabled if
 382    *          features are loaded
 383    * @return true if data parsed as a features file
 384    */
 385   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 386           boolean autoenabledisplay)
 387   {
 388     boolean featuresFile = false;
 389     try
 390     {
 391       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 392               .getFeatureRenderer().getFeatureColours();
 393       boolean relaxedIdMatching = viewport.applet
 394               .getDefaultParameter("relaxedidmatch", false);
 395       featuresFile = new FeaturesFile(file, sourceType).parse(
 396               viewport.getAlignment(), colours, true, relaxedIdMatching);
 397     } catch (Exception ex)
 398     {
 399       ex.printStackTrace();
 400     }
 401
 402     if (featuresFile)
 403     {
 404       if (autoenabledisplay)
 405       {
 406         viewport.setShowSequenceFeatures(true);
 407         sequenceFeatures.setState(true);
 408       }
 409       if (alignPanel.seqPanel.seqCanvas.fr != null)
 410       {
 411         // update the min/max ranges where necessary
 412         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 413       }
 414       if (viewport.featureSettings != null)
 415       {
 416         viewport.featureSettings.refreshTable();
 417       }
 418       alignPanel.paintAlignment(true);
 419       statusBar.setText(MessageManager
 420               .getString("label.successfully_added_features_alignment"));
 421     }
 422     return featuresFile;
 423   }
 424
 425   @Override
 426   public void keyPressed(KeyEvent evt)
 427   {
 428     ViewportRanges ranges = viewport.getRanges();
 429
 430     if (viewport.cursorMode
 431             && ((evt.getKeyCode() >= KeyEvent.VK_0
 432                     && evt.getKeyCode() <= KeyEvent.VK_9)
 433                     || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 434                             && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 435             && Character.isDigit(evt.getKeyChar()))
 436     {
 437       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 438     }
 439
 440     switch (evt.getKeyCode())
 441     {
 442     case 27: // escape key
 443       deselectAllSequenceMenuItem_actionPerformed();
 444
 445       alignPanel.alabels.cancelDrag();
 446       break;
 447     case KeyEvent.VK_X:
 448       if (evt.isControlDown() || evt.isMetaDown())
 449       {
 450         cut_actionPerformed();
 451       }
 452       break;
 453     case KeyEvent.VK_C:
 454       if (viewport.cursorMode && !evt.isControlDown())
 455       {
 456         alignPanel.seqPanel.setCursorColumn();
 457       }
 458       if (evt.isControlDown() || evt.isMetaDown())
 459       {
 460         copy_actionPerformed();
 461       }
 462       break;
 463     case KeyEvent.VK_V:
 464       if (evt.isControlDown())
 465       {
 466         paste(evt.isShiftDown());
 467       }
 468       break;
 469     case KeyEvent.VK_A:
 470       if (evt.isControlDown() || evt.isMetaDown())
 471       {
 472         selectAllSequenceMenuItem_actionPerformed();
 473       }
 474       break;
 475     case KeyEvent.VK_DOWN:
 476       if (viewport.cursorMode)
 477       {
 478         alignPanel.seqPanel.moveCursor(0, 1);
 479       }
 480       else
 481       {
 482         moveSelectedSequences(false);
 483       }
 484       break;
 485
 486     case KeyEvent.VK_UP:
 487       if (viewport.cursorMode)
 488       {
 489         alignPanel.seqPanel.moveCursor(0, -1);
 490       }
 491       else
 492       {
 493         moveSelectedSequences(true);
 494       }
 495       break;
 496
 497     case KeyEvent.VK_LEFT:
 498       if (evt.isAltDown() || !viewport.cursorMode)
 499       {
 500         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 501       }
 502       else
 503       {
 504         alignPanel.seqPanel.moveCursor(-1, 0);
 505       }
 506       break;
 507
 508     case KeyEvent.VK_RIGHT:
 509       if (evt.isAltDown() || !viewport.cursorMode)
 510       {
 511         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 512       }
 513       else
 514       {
 515         alignPanel.seqPanel.moveCursor(1, 0);
 516       }
 517       break;
 518
 519     case KeyEvent.VK_SPACE:
 520       if (viewport.cursorMode)
 521       {
 522         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 523                 || evt.isShiftDown() || evt.isAltDown());
 524       }
 525       break;
 526
 527     case KeyEvent.VK_DELETE:
 528     case KeyEvent.VK_BACK_SPACE:
 529       if (viewport.cursorMode)
 530       {
 531         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 532                 || evt.isShiftDown() || evt.isAltDown());
 533       }
 534       else
 535       {
 536         cut_actionPerformed();
 537         alignPanel.seqPanel.seqCanvas.repaint();
 538       }
 539       break;
 540
 541     case KeyEvent.VK_S:
 542       if (viewport.cursorMode)
 543       {
 544         alignPanel.seqPanel.setCursorRow();
 545       }
 546       break;
 547     case KeyEvent.VK_P:
 548       if (viewport.cursorMode)
 549       {
 550         alignPanel.seqPanel.setCursorPosition();
 551       }
 552       break;
 553
 554     case KeyEvent.VK_ENTER:
 555     case KeyEvent.VK_COMMA:
 556       if (viewport.cursorMode)
 557       {
 558         alignPanel.seqPanel.setCursorRowAndColumn();
 559       }
 560       break;
 561
 562     case KeyEvent.VK_Q:
 563       if (viewport.cursorMode)
 564       {
 565         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 566       }
 567       break;
 568     case KeyEvent.VK_M:
 569       if (viewport.cursorMode)
 570       {
 571         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 572       }
 573       break;
 574
 575     case KeyEvent.VK_F2:
 576       viewport.cursorMode = !viewport.cursorMode;
 577       statusBar.setText(MessageManager
 578               .formatMessage("label.keyboard_editing_mode", new String[]
 579               { (viewport.cursorMode ? "on" : "off") }));
 580       if (viewport.cursorMode)
 581       {
 582         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 583         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 584       }
 585       break;
 586
 587     case KeyEvent.VK_F:
 588       if (evt.isControlDown())
 589       {
 590         findMenuItem_actionPerformed();
 591       }
 592       break;
 593
 594     case KeyEvent.VK_H:
 595     {
 596       boolean toggleSeqs = !evt.isControlDown();
 597       boolean toggleCols = !evt.isShiftDown();
 598       toggleHiddenRegions(toggleSeqs, toggleCols);
 599       break;
 600     }
 601
 602     case KeyEvent.VK_PAGE_UP:
 603       ranges.pageUp();
 604       break;
 605
 606     case KeyEvent.VK_PAGE_DOWN:
 607       ranges.pageDown();
 608       break;
 609
 610     case KeyEvent.VK_Z:
 611       if (evt.isControlDown())
 612       {
 613         undoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_Y:
 618       if (evt.isControlDown())
 619       {
 620         redoMenuItem_actionPerformed();
 621       }
 622       break;
 623
 624     case KeyEvent.VK_L:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(true);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_R:
 632       if (evt.isControlDown())
 633       {
 634         trimAlignment(false);
 635       }
 636       break;
 637
 638     case KeyEvent.VK_E:
 639       if (evt.isControlDown())
 640       {
 641         if (evt.isShiftDown())
 642         {
 643           this.removeAllGapsMenuItem_actionPerformed();
 644         }
 645         else
 646         {
 647           removeGappedColumnMenuItem_actionPerformed();
 648         }
 649       }
 650       break;
 651     case KeyEvent.VK_I:
 652       if (evt.isControlDown())
 653       {
 654         if (evt.isAltDown())
 655         {
 656           invertColSel_actionPerformed();
 657         }
 658         else
 659         {
 660           invertSequenceMenuItem_actionPerformed();
 661         }
 662       }
 663       break;
 664
 665     case KeyEvent.VK_G:
 666       if (evt.isControlDown())
 667       {
 668         if (evt.isShiftDown())
 669         {
 670           this.unGroup_actionPerformed();
 671         }
 672         else
 673         {
 674           this.createGroup_actionPerformed();
 675         }
 676       }
 677       break;
 678
 679     case KeyEvent.VK_U:
 680       if (evt.isControlDown())
 681       {
 682         this.deleteGroups_actionPerformed();
 683       }
 684       break;
 685
 686     case KeyEvent.VK_T:
 687       if (evt.isControlDown())
 688       {
 689         newView(null);
 690       }
 691       break;
 692
 693     }
 694     alignPanel.paintAlignment(true);
 695   }
 696
 697   /**
 698    * called by key handler and the hide all/show all menu items
 699    *
 700    * @param toggleSeqs
 701    * @param toggleCols
 702    */
 703   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 704   {
 705     boolean hide = false;
 706     SequenceGroup sg = viewport.getSelectionGroup();
 707     if (!toggleSeqs && !toggleCols)
 708     {
 709       // Hide everything by the current selection - this is a hack - we do the
 710       // invert and then hide
 711       // first check that there will be visible columns after the invert.
 712       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 713               && sg.getStartRes() <= sg.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(
 843               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 844                       : SequenceAnnotationOrder.NONE);
 845       setViewportAnnotationOrder();
 846     }
 847     else if (source == sortAnnByLabel)
 848     {
 849       boolean newState = sortAnnByLabel.getState();
 850       sortAnnBySequence.setState(false);
 851       setAnnotationSortOrder(
 852               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 853                       : SequenceAnnotationOrder.NONE);
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == showAutoFirst)
 857     {
 858       showAutoLast.setState(!showAutoFirst.getState());
 859       setShowAutoCalculatedAbove(showAutoFirst.getState());
 860       setViewportAnnotationOrder();
 861     }
 862     else if (source == showAutoLast)
 863     {
 864       showAutoFirst.setState(!showAutoLast.getState());
 865       setShowAutoCalculatedAbove(showAutoFirst.getState());
 866       setViewportAnnotationOrder();
 867     }
 868     else if (source == conservationMenuItem)
 869     {
 870       conservationMenuItem_actionPerformed();
 871     }
 872     else if (source == abovePIDThreshold)
 873     {
 874       abovePIDThreshold_actionPerformed();
 875     }
 876     else if (source == applyToAllGroups)
 877     {
 878       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 879     }
 880     else if (source == autoCalculate)
 881     {
 882       viewport.autoCalculateConsensus = autoCalculate.getState();
 883     }
 884     else if (source == sortByTree)
 885     {
 886       viewport.sortByTree = sortByTree.getState();
 887     }
 888     else if (source == this.centreColumnLabelFlag)
 889     {
 890       centreColumnLabelFlag_stateChanged();
 891     }
 892     else if (source == this.followMouseOverFlag)
 893     {
 894       mouseOverFlag_stateChanged();
 895     }
 896     else if (source == showGroupConsensus)
 897     {
 898       showGroupConsensus_actionPerformed();
 899     }
 900     else if (source == showGroupConservation)
 901     {
 902       showGroupConservation_actionPerformed();
 903     }
 904     else if (source == showSequenceLogo)
 905     {
 906       showSequenceLogo_actionPerformed();
 907     }
 908     else if (source == normSequenceLogo)
 909     {
 910       normSequenceLogo_actionPerformed();
 911     }
 912     else if (source == showConsensusHistogram)
 913     {
 914       showConsensusHistogram_actionPerformed();
 915     }
 916     else if (source == applyAutoAnnotationSettings)
 917     {
 918       applyAutoAnnotationSettings_actionPerformed();
 919     }
 920     alignPanel.paintAlignment(true);
 921   }
 922
 923   /**
 924    * Set the visibility state of sequence-related and/or alignment-related
 925    * annotations depending on checkbox selections, and repaint.
 926    *
 927    * @param visible
 928    */
 929   private void setAnnotationsVisibility()
 930   {
 931     boolean showForAlignment = showAlignmentAnnotations.getState();
 932     boolean showForSequences = showSequenceAnnotations.getState();
 933     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 934     {
 935       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 936               .getAlignmentAnnotation())
 937       {
 938         boolean visible = (aa.sequenceRef == null ? showForAlignment
 939                 : showForSequences);
 940         aa.visible = visible;
 941       }
 942     }
 943     alignPanel.validateAnnotationDimensions(true);
 944     validate();
 945     repaint();
 946   }
 947
 948   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 949   {
 950     this.annotationSortOrder = order;
 951   }
 952
 953   /**
 954    * Set flags on the viewport that control annotation ordering
 955    */
 956   private void setViewportAnnotationOrder()
 957   {
 958     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 959     this.alignPanel.av
 960             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 961   }
 962
 963   private void setShowAutoCalculatedAbove(boolean showAbove)
 964   {
 965     this.showAutoCalculatedAbove = showAbove;
 966   }
 967
 968   private void mouseOverFlag_stateChanged()
 969   {
 970     viewport.setFollowHighlight(followMouseOverFlag.getState());
 971     // TODO: could kick the scrollTo mechanism to reset view for current
 972     // searchresults.
 973   }
 974
 975   private void centreColumnLabelFlag_stateChanged()
 976   {
 977     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 978     this.alignPanel.annotationPanel.repaint();
 979   }
 980
 981   @Override
 982   public void actionPerformed(ActionEvent evt)
 983   {
 984     viewport.applet.currentAlignFrame = this;
 985
 986     Object source = evt.getSource();
 987
 988     if (source == inputText)
 989     {
 990       inputText_actionPerformed();
 991     }
 992     else if (source == loadTree)
 993     {
 994       loadTree_actionPerformed();
 995     }
 996     else if (source == loadApplication)
 997     {
 998       launchFullApplication();
 999     }
1000     else if (source == loadAnnotations)
1001     {
1002       loadAnnotations();
1003     }
1004     else if (source == outputAnnotations)
1005     {
1006       outputAnnotations(true);
1007     }
1008     else if (source == outputFeatures)
1009     {
1010       outputFeatures(true, "Jalview");
1011     }
1012     else if (source == closeMenuItem)
1013     {
1014       closeMenuItem_actionPerformed();
1015     }
1016     else if (source == copy)
1017     {
1018       copy_actionPerformed();
1019     }
1020     else if (source == undoMenuItem)
1021     {
1022       undoMenuItem_actionPerformed();
1023     }
1024     else if (source == redoMenuItem)
1025     {
1026       redoMenuItem_actionPerformed();
1027     }
1028     else if (source == inputText)
1029     {
1030       inputText_actionPerformed();
1031     }
1032     else if (source == closeMenuItem)
1033     {
1034       closeMenuItem_actionPerformed();
1035     }
1036     else if (source == undoMenuItem)
1037     {
1038       undoMenuItem_actionPerformed();
1039     }
1040     else if (source == redoMenuItem)
1041     {
1042       redoMenuItem_actionPerformed();
1043     }
1044     else if (source == copy)
1045     {
1046       copy_actionPerformed();
1047     }
1048     else if (source == pasteNew)
1049     {
1050       pasteNew_actionPerformed();
1051     }
1052     else if (source == pasteThis)
1053     {
1054       pasteThis_actionPerformed();
1055     }
1056     else if (source == cut)
1057     {
1058       cut_actionPerformed();
1059     }
1060     else if (source == delete)
1061     {
1062       delete_actionPerformed();
1063     }
1064     else if (source == createGroup)
1065     {
1066       createGroup_actionPerformed();
1067     }
1068     else if (source == unGroup)
1069     {
1070       unGroup_actionPerformed();
1071     }
1072     else if (source == grpsFromSelection)
1073     {
1074       makeGrpsFromSelection_actionPerformed();
1075     }
1076     else if (source == deleteGroups)
1077     {
1078       deleteGroups_actionPerformed();
1079     }
1080     else if (source == selectAllSequenceMenuItem)
1081     {
1082       selectAllSequenceMenuItem_actionPerformed();
1083     }
1084     else if (source == deselectAllSequenceMenuItem)
1085     {
1086       deselectAllSequenceMenuItem_actionPerformed();
1087     }
1088     else if (source == invertSequenceMenuItem)
1089     {
1090       invertSequenceMenuItem_actionPerformed();
1091       // uncomment to slave sequence selections in split frame
1092       // viewport.sendSelection();
1093     }
1094     else if (source == invertColSel)
1095     {
1096       viewport.invertColumnSelection();
1097       alignPanel.paintAlignment(true);
1098       viewport.sendSelection();
1099     }
1100     else if (source == remove2LeftMenuItem)
1101     {
1102       trimAlignment(true);
1103     }
1104     else if (source == remove2RightMenuItem)
1105     {
1106       trimAlignment(false);
1107     }
1108     else if (source == removeGappedColumnMenuItem)
1109     {
1110       removeGappedColumnMenuItem_actionPerformed();
1111     }
1112     else if (source == removeAllGapsMenuItem)
1113     {
1114       removeAllGapsMenuItem_actionPerformed();
1115     }
1116     else if (source == findMenuItem)
1117     {
1118       findMenuItem_actionPerformed();
1119     }
1120     else if (source == font)
1121     {
1122       new FontChooser(alignPanel);
1123     }
1124     else if (source == newView)
1125     {
1126       newView(null);
1127     }
1128     else if (source == showColumns)
1129     {
1130       viewport.showAllHiddenColumns();
1131       alignPanel.paintAlignment(true);
1132       viewport.sendSelection();
1133     }
1134     else if (source == showSeqs)
1135     {
1136       viewport.showAllHiddenSeqs();
1137       alignPanel.paintAlignment(true);
1138       // uncomment if we want to slave sequence selections in split frame
1139       // viewport.sendSelection();
1140     }
1141     else if (source == hideColumns)
1142     {
1143       viewport.hideSelectedColumns();
1144       alignPanel.paintAlignment(true);
1145       viewport.sendSelection();
1146     }
1147     else if (source == hideSequences
1148             && viewport.getSelectionGroup() != null)
1149     {
1150       viewport.hideAllSelectedSeqs();
1151       alignPanel.paintAlignment(true);
1152       // uncomment if we want to slave sequence selections in split frame
1153       // viewport.sendSelection();
1154     }
1155     else if (source == hideAllButSelection)
1156     {
1157       toggleHiddenRegions(false, false);
1158       alignPanel.paintAlignment(true);
1159       viewport.sendSelection();
1160     }
1161     else if (source == hideAllSelection)
1162     {
1163       SequenceGroup sg = viewport.getSelectionGroup();
1164       viewport.expandColSelection(sg, false);
1165       viewport.hideAllSelectedSeqs();
1166       viewport.hideSelectedColumns();
1167       alignPanel.paintAlignment(true);
1168       viewport.sendSelection();
1169     }
1170     else if (source == showAllHidden)
1171     {
1172       viewport.showAllHiddenColumns();
1173       viewport.showAllHiddenSeqs();
1174       alignPanel.paintAlignment(true);
1175       viewport.sendSelection();
1176     }
1177     else if (source == showGroupConsensus)
1178     {
1179       showGroupConsensus_actionPerformed();
1180     }
1181     else if (source == showGroupConservation)
1182     {
1183       showGroupConservation_actionPerformed();
1184     }
1185     else if (source == showSequenceLogo)
1186     {
1187       showSequenceLogo_actionPerformed();
1188     }
1189     else if (source == normSequenceLogo)
1190     {
1191       normSequenceLogo_actionPerformed();
1192     }
1193     else if (source == showConsensusHistogram)
1194     {
1195       showConsensusHistogram_actionPerformed();
1196     }
1197     else if (source == applyAutoAnnotationSettings)
1198     {
1199       applyAutoAnnotationSettings_actionPerformed();
1200     }
1201     else if (source == featureSettings)
1202     {
1203       new FeatureSettings(alignPanel);
1204     }
1205     else if (source == alProperties)
1206     {
1207       StringBuffer contents = new jalview.io.AlignmentProperties(
1208               viewport.getAlignment()).formatAsString();
1209       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1210       cap.setText(contents.toString());
1211       Frame frame = new Frame();
1212       frame.add(cap);
1213       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1214               .formatMessage("label.alignment_properties", new String[]
1215               { getTitle() }), 400, 250);
1216     }
1217     else if (source == overviewMenuItem)
1218     {
1219       overviewMenuItem_actionPerformed();
1220     }
1221     else if (source == noColourmenuItem)
1222     {
1223       changeColour(null);
1224     }
1225     else if (source == clustalColour)
1226     {
1227       abovePIDThreshold.setState(false);
1228       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1229     }
1230     else if (source == zappoColour)
1231     {
1232       changeColour(new ZappoColourScheme());
1233     }
1234     else if (source == taylorColour)
1235     {
1236       changeColour(new TaylorColourScheme());
1237     }
1238     else if (source == hydrophobicityColour)
1239     {
1240       changeColour(new HydrophobicColourScheme());
1241     }
1242     else if (source == helixColour)
1243     {
1244       changeColour(new HelixColourScheme());
1245     }
1246     else if (source == strandColour)
1247     {
1248       changeColour(new StrandColourScheme());
1249     }
1250     else if (source == turnColour)
1251     {
1252       changeColour(new TurnColourScheme());
1253     }
1254     else if (source == buriedColour)
1255     {
1256       changeColour(new BuriedColourScheme());
1257     }
1258     else if (source == nucleotideColour)
1259     {
1260       changeColour(new NucleotideColourScheme());
1261     }
1262     else if (source == purinePyrimidineColour)
1263     {
1264       changeColour(new PurinePyrimidineColourScheme());
1265     }
1266     // else if (source == RNAInteractionColour)
1267     // {
1268     // changeColour(new RNAInteractionColourScheme());
1269     // }
1270     else if (source == RNAHelixColour)
1271     {
1272       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1273       // new RNAHelicesColourChooser(viewport, alignPanel);
1274     }
1275     else if (source == modifyPID)
1276     {
1277       modifyPID_actionPerformed();
1278     }
1279     else if (source == modifyConservation)
1280     {
1281       modifyConservation_actionPerformed();
1282     }
1283     else if (source == userDefinedColour)
1284     {
1285       new UserDefinedColours(alignPanel, null);
1286     }
1287     else if (source == PIDColour)
1288     {
1289       changeColour(new PIDColourScheme());
1290     }
1291     else if (source == BLOSUM62Colour)
1292     {
1293       changeColour(new Blosum62ColourScheme());
1294     }
1295     else if (source == tcoffeeColour)
1296     {
1297       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1298     }
1299     else if (source == annotationColour)
1300     {
1301       new AnnotationColourChooser(viewport, alignPanel);
1302     }
1303     else if (source == annotationColumnSelection)
1304     {
1305       new AnnotationColumnChooser(viewport, alignPanel);
1306     }
1307     else if (source == sortPairwiseMenuItem)
1308     {
1309       sortPairwiseMenuItem_actionPerformed();
1310     }
1311     else if (source == sortIDMenuItem)
1312     {
1313       sortIDMenuItem_actionPerformed();
1314     }
1315     else if (source == sortLengthMenuItem)
1316     {
1317       sortLengthMenuItem_actionPerformed();
1318     }
1319     else if (source == sortGroupMenuItem)
1320     {
1321       sortGroupMenuItem_actionPerformed();
1322     }
1323     else if (source == removeRedundancyMenuItem)
1324     {
1325       removeRedundancyMenuItem_actionPerformed();
1326     }
1327     else if (source == pairwiseAlignmentMenuItem)
1328     {
1329       pairwiseAlignmentMenuItem_actionPerformed();
1330     }
1331     else if (source == PCAMenuItem)
1332     {
1333       PCAMenuItem_actionPerformed();
1334     }
1335     else if (source == averageDistanceTreeMenuItem)
1336     {
1337       averageDistanceTreeMenuItem_actionPerformed();
1338     }
1339     else if (source == neighbourTreeMenuItem)
1340     {
1341       neighbourTreeMenuItem_actionPerformed();
1342     }
1343     else if (source == njTreeBlosumMenuItem)
1344     {
1345       njTreeBlosumMenuItem_actionPerformed();
1346     }
1347     else if (source == avDistanceTreeBlosumMenuItem)
1348     {
1349       avTreeBlosumMenuItem_actionPerformed();
1350     }
1351     else if (source == documentation)
1352     {
1353       documentation_actionPerformed();
1354     }
1355     else if (source == about)
1356     {
1357       about_actionPerformed();
1358     }
1359
1360   }
1361
1362   public void inputText_actionPerformed()
1363   {
1364     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1365     Frame frame = new Frame();
1366     frame.add(cap);
1367     jalview.bin.JalviewLite.addFrame(frame,
1368             MessageManager.getString("label.input_cut_paste"), 500, 500);
1369   }
1370
1371   protected void outputText_actionPerformed(ActionEvent e)
1372   {
1373     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1374     Frame frame = new Frame();
1375     frame.add(cap);
1376     JalviewLite.addFrame(frame, MessageManager
1377             .formatMessage("label.alignment_output_command", new Object[]
1378             { e.getActionCommand() }), 600, 500);
1379
1380     FileFormatI fileFormat = FileFormats.getInstance()
1381             .forName(e.getActionCommand());
1382     cap.setText(
1383             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1384                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1385   }
1386
1387   public void loadAnnotations()
1388   {
1389     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1390     cap.setText(MessageManager
1391             .getString("label.paste_features_annotations_Tcoffee_here"));
1392     cap.setAnnotationImport();
1393     Frame frame = new Frame();
1394     frame.add(cap);
1395     jalview.bin.JalviewLite.addFrame(frame,
1396             MessageManager.getString("action.paste_annotations"), 400, 300);
1397
1398   }
1399
1400   public String outputAnnotations(boolean displayTextbox)
1401   {
1402     String annotation = new AnnotationFile()
1403             .printAnnotationsForView(viewport);
1404
1405     if (displayTextbox)
1406     {
1407       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1408       Frame frame = new Frame();
1409       frame.add(cap);
1410       jalview.bin.JalviewLite.addFrame(frame,
1411               MessageManager.getString("label.annotations"), 600, 500);
1412       cap.setText(annotation);
1413     }
1414
1415     return annotation;
1416   }
1417
1418   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1419   {
1420     if (alignPanel.getFeatureRenderer() != null
1421             && viewport.getFeaturesDisplayed() != null)
1422     {
1423       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1424
1425     }
1426     return null;
1427   }
1428
1429   private List<String> getDisplayedFeatureGroups()
1430   {
1431     if (alignPanel.getFeatureRenderer() != null
1432             && viewport.getFeaturesDisplayed() != null)
1433     {
1434       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1435
1436     }
1437     return null;
1438   }
1439
1440   public String outputFeatures(boolean displayTextbox, String format)
1441   {
1442     String features;
1443     FeaturesFile formatter = new FeaturesFile();
1444     if (format.equalsIgnoreCase("Jalview"))
1445     {
1446       features = formatter.printJalviewFormat(viewport.getAlignment()
1447               .getSequencesArray(), getDisplayedFeatureCols(),
1448               getDisplayedFeatureGroups(), true);
1449     }
1450     else
1451     {
1452       features = formatter.printGffFormat(viewport.getAlignment()
1453               .getSequencesArray(), getDisplayedFeatureCols(),
1454               getDisplayedFeatureGroups(), true);
1455     }
1456
1457     if (displayTextbox)
1458     {
1459       boolean frimport = false;
1460       if (features == null || features.equals("No Features Visible"))
1461       {
1462         features = "# No features visible - paste some and import them here.";
1463         frimport = true;
1464       }
1465
1466       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1467       if (frimport)
1468       {
1469         cap.setAnnotationImport();
1470       }
1471       Frame frame = new Frame();
1472       frame.add(cap);
1473       jalview.bin.JalviewLite.addFrame(frame,
1474               MessageManager.getString("label.features"), 600, 500);
1475       cap.setText(features);
1476     }
1477     else
1478     {
1479       if (features == null)
1480       {
1481         features = "";
1482       }
1483     }
1484
1485     return features;
1486   }
1487
1488   void launchFullApplication()
1489   {
1490     StringBuffer url = new StringBuffer(jalviewServletURL);
1491
1492     // allow servlet parameters to be passed in applet parameter
1493     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1494             : "?";
1495     url.append(firstSep);
1496
1497     url.append(
1498             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1499
1500     if (viewport.applet.getParameter("features") != null)
1501     {
1502       url.append("&features=");
1503       url.append(appendProtocol(viewport.applet.getParameter("features")));
1504     }
1505
1506     if (viewport.applet.getParameter("annotations") != null)
1507     {
1508       url.append("&annotations=");
1509       url.append(
1510               appendProtocol(viewport.applet.getParameter("annotations")));
1511     }
1512
1513     if (viewport.applet.getParameter("jnetfile") != null
1514             || viewport.applet.getParameter("jpredfile") != null)
1515     {
1516       url.append("&annotations=");
1517       url.append(appendProtocol(
1518               viewport.applet.getParameter("jnetfile") != null
1519                       ? viewport.applet.getParameter("jnetfile")
1520                       : viewport.applet.getParameter("jpredfile")));
1521     }
1522
1523     if (viewport.applet.getParameter("defaultColour") != null)
1524     {
1525       url.append("&colour=" + removeWhiteSpace(
1526               viewport.applet.getParameter("defaultColour")));
1527     }
1528
1529     if (viewport.applet.getParameter("userDefinedColour") != null)
1530     {
1531       url.append("&colour=" + removeWhiteSpace(
1532               viewport.applet.getParameter("userDefinedColour")));
1533     }
1534     if (viewport.applet.getParameter("tree") != null)
1535     {
1536       url.append("&tree="
1537               + appendProtocol(viewport.applet.getParameter("tree")));
1538     }
1539     if (viewport.applet.getParameter("treeFile") != null)
1540     {
1541       url.append("&tree="
1542               + appendProtocol(viewport.applet.getParameter("treeFile")));
1543     }
1544
1545     showURL(url.toString(), "FULL_APP");
1546   }
1547
1548   String removeWhiteSpace(String colour)
1549   {
1550     StringBuffer sb = new StringBuffer();
1551     for (int i = 0; i < colour.length(); i++)
1552     {
1553       if (Character.isWhitespace(colour.charAt(i)))
1554       {
1555         sb.append("%20");
1556       }
1557       else
1558       {
1559         sb.append(colour.charAt(i));
1560       }
1561     }
1562
1563     return sb.toString();
1564   }
1565
1566   String appendProtocol(String url)
1567   {
1568     try
1569     {
1570       new URL(url);
1571       url = URLEncoder.encode(url);
1572     }
1573     /*
1574      * When we finally deprecate 1.1 compatibility, we can start to use
1575      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1576      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1577      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1578      * ex.printStackTrace(); }
1579      */
1580     catch (java.net.MalformedURLException ex)
1581     {
1582       url = viewport.applet.getCodeBase() + url;
1583     }
1584     return url;
1585   }
1586
1587   public void closeMenuItem_actionPerformed()
1588   {
1589     PaintRefresher.RemoveComponent(alignPanel);
1590     if (alignPanel.seqPanel != null
1591             && alignPanel.seqPanel.seqCanvas != null)
1592     {
1593       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1594     }
1595     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1596     {
1597       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1598     }
1599
1600     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1601     {
1602       System.exit(0);
1603     }
1604     else
1605     {
1606     }
1607     viewport = null;
1608     alignPanel = null;
1609     this.dispose();
1610   }
1611
1612   /**
1613    * TODO: JAL-1104
1614    */
1615   void updateEditMenuBar()
1616   {
1617
1618     if (viewport.getHistoryList().size() > 0)
1619     {
1620       undoMenuItem.setEnabled(true);
1621       CommandI command = viewport.getHistoryList().peek();
1622       undoMenuItem.setLabel(MessageManager
1623               .formatMessage("label.undo_command", new Object[]
1624               { command.getDescription() }));
1625     }
1626     else
1627     {
1628       undoMenuItem.setEnabled(false);
1629       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1630     }
1631
1632     if (viewport.getRedoList().size() > 0)
1633     {
1634       redoMenuItem.setEnabled(true);
1635
1636       CommandI command = viewport.getRedoList().peek();
1637       redoMenuItem.setLabel(MessageManager
1638               .formatMessage("label.redo_command", new Object[]
1639               { command.getDescription() }));
1640     }
1641     else
1642     {
1643       redoMenuItem.setEnabled(false);
1644       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1645     }
1646   }
1647
1648   /**
1649    * TODO: JAL-1104
1650    */
1651   @Override
1652   public void addHistoryItem(CommandI command)
1653   {
1654     if (command.getSize() > 0)
1655     {
1656       viewport.addToHistoryList(command);
1657       viewport.clearRedoList();
1658       updateEditMenuBar();
1659       viewport.updateHiddenColumns();
1660     }
1661   }
1662
1663   /**
1664    * TODO: JAL-1104 DOCUMENT ME!
1665    *
1666    * @param e
1667    *          DOCUMENT ME!
1668    */
1669   protected void undoMenuItem_actionPerformed()
1670   {
1671     if (viewport.getHistoryList().isEmpty())
1672     {
1673       return;
1674     }
1675
1676     CommandI command = viewport.getHistoryList().pop();
1677     viewport.addToRedoList(command);
1678     command.undoCommand(null);
1679
1680     AlignmentViewport originalSource = getOriginatingSource(command);
1681     // JBPNote Test
1682     if (originalSource != viewport)
1683     {
1684       System.err
1685               .println("Warning: Viewport object mismatch whilst undoing");
1686     }
1687     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1688                                           // viewport.getColumnSelection().getHiddenColumns()
1689                                           // != null;
1690     updateEditMenuBar();
1691     originalSource.firePropertyChange("alignment", null,
1692             originalSource.getAlignment().getSequences());
1693   }
1694
1695   /**
1696    * TODO: JAL-1104 DOCUMENT ME!
1697    *
1698    * @param e
1699    *          DOCUMENT ME!
1700    */
1701   protected void redoMenuItem_actionPerformed()
1702   {
1703     if (viewport.getRedoList().isEmpty())
1704     {
1705       return;
1706     }
1707
1708     CommandI command = viewport.getRedoList().pop();
1709     viewport.addToHistoryList(command);
1710     command.doCommand(null);
1711
1712     AlignmentViewport originalSource = getOriginatingSource(command);
1713     // JBPNote Test
1714     if (originalSource != viewport)
1715     {
1716       System.err
1717               .println("Warning: Viewport object mismatch whilst re-doing");
1718     }
1719     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1720                                           // viewport.getColumnSelection().getHiddenColumns()
1721                                           // != null;
1722
1723     updateEditMenuBar();
1724     originalSource.firePropertyChange("alignment", null,
1725             originalSource.getAlignment().getSequences());
1726   }
1727
1728   AlignmentViewport getOriginatingSource(CommandI command)
1729   {
1730     AlignmentViewport originalSource = null;
1731     // For sequence removal and addition, we need to fire
1732     // the property change event FROM the viewport where the
1733     // original alignment was altered
1734     AlignmentI al = null;
1735     if (command instanceof EditCommand)
1736     {
1737       EditCommand editCommand = (EditCommand) command;
1738       al = editCommand.getAlignment();
1739       Vector comps = PaintRefresher.components
1740               .get(viewport.getSequenceSetId());
1741       for (int i = 0; i < comps.size(); i++)
1742       {
1743         if (comps.elementAt(i) instanceof AlignmentPanel)
1744         {
1745           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1746           {
1747             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1748             break;
1749           }
1750         }
1751       }
1752     }
1753
1754     if (originalSource == null)
1755     {
1756       // The original view is closed, we must validate
1757       // the current view against the closed view first
1758       if (al != null)
1759       {
1760         PaintRefresher.validateSequences(al, viewport.getAlignment());
1761       }
1762
1763       originalSource = viewport;
1764     }
1765
1766     return originalSource;
1767   }
1768
1769   /**
1770    * Move the currently selected sequences up or down one position in the
1771    * alignment
1772    *
1773    * @param up
1774    */
1775   public void moveSelectedSequences(boolean up)
1776   {
1777     SequenceGroup sg = viewport.getSelectionGroup();
1778     if (sg == null)
1779     {
1780       return;
1781     }
1782     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1783             up ? null : viewport.getHiddenRepSequences(), up);
1784     alignPanel.paintAlignment(true);
1785
1786     /*
1787      * Also move cDNA/protein complement sequences
1788      */
1789     AlignViewportI complement = viewport.getCodingComplement();
1790     if (complement != null)
1791     {
1792       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1793               viewport, complement);
1794       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1795               up ? null : complement.getHiddenRepSequences(), up);
1796       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1797     }
1798   }
1799
1800   synchronized void slideSequences(boolean right, int size)
1801   {
1802     List<SequenceI> sg = new Vector<>();
1803     if (viewport.cursorMode)
1804     {
1805       sg.add(viewport.getAlignment()
1806               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1807     }
1808     else if (viewport.getSelectionGroup() != null
1809             && viewport.getSelectionGroup().getSize() != viewport
1810                     .getAlignment().getHeight())
1811     {
1812       sg = viewport.getSelectionGroup()
1813               .getSequences(viewport.getHiddenRepSequences());
1814     }
1815
1816     if (sg.size() < 1)
1817     {
1818       return;
1819     }
1820
1821     Vector<SequenceI> invertGroup = new Vector();
1822
1823     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1824     {
1825       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1826       {
1827         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1828       }
1829     }
1830
1831     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1832
1833     SequenceI[] seqs2 = invertGroup
1834             .toArray(new SequenceI[invertGroup.size()]);
1835     for (int i = 0; i < invertGroup.size(); i++)
1836     {
1837       seqs2[i] = invertGroup.elementAt(i);
1838     }
1839
1840     SlideSequencesCommand ssc;
1841     if (right)
1842     {
1843       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1844               viewport.getGapCharacter());
1845     }
1846     else
1847     {
1848       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1849               viewport.getGapCharacter());
1850     }
1851
1852     int groupAdjustment = 0;
1853     if (ssc.getGapsInsertedBegin() && right)
1854     {
1855       if (viewport.cursorMode)
1856       {
1857         alignPanel.seqPanel.moveCursor(size, 0);
1858       }
1859       else
1860       {
1861         groupAdjustment = size;
1862       }
1863     }
1864     else if (!ssc.getGapsInsertedBegin() && !right)
1865     {
1866       if (viewport.cursorMode)
1867       {
1868         alignPanel.seqPanel.moveCursor(-size, 0);
1869       }
1870       else
1871       {
1872         groupAdjustment = -size;
1873       }
1874     }
1875
1876     if (groupAdjustment != 0)
1877     {
1878       viewport.getSelectionGroup().setStartRes(
1879               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1880       viewport.getSelectionGroup().setEndRes(
1881               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1882     }
1883
1884     boolean appendHistoryItem = false;
1885     Deque<CommandI> historyList = viewport.getHistoryList();
1886     if (historyList != null && historyList.size() > 0
1887             && historyList.peek() instanceof SlideSequencesCommand)
1888     {
1889       appendHistoryItem = ssc.appendSlideCommand(
1890               (SlideSequencesCommand) historyList.peek());
1891     }
1892
1893     if (!appendHistoryItem)
1894     {
1895       addHistoryItem(ssc);
1896     }
1897
1898     repaint();
1899   }
1900
1901   static StringBuffer copiedSequences;
1902
1903   static HiddenColumns copiedHiddenColumns;
1904
1905   protected void copy_actionPerformed()
1906   {
1907     if (viewport.getSelectionGroup() == null)
1908     {
1909       return;
1910     }
1911
1912     SequenceGroup sg = viewport.getSelectionGroup();
1913     copiedSequences = new StringBuffer();
1914     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1915     for (int i = 0; i < sg.getSize(); i++)
1916     {
1917       SequenceI seq = sg.getSequenceAt(i);
1918       int index = viewport.getAlignment().findIndex(seq);
1919       orderedSeqs.put(index, seq);
1920     }
1921
1922     int index = 0, startRes, endRes;
1923     char ch;
1924
1925     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1926     {
1927       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1928       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1929
1930       // create new HiddenColumns object with copy of hidden regions
1931       // between startRes and endRes, offset by startRes
1932       copiedHiddenColumns = new HiddenColumns(
1933               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1934               hiddenCutoff, hiddenOffset);
1935     }
1936     else
1937     {
1938       copiedHiddenColumns = null;
1939     }
1940
1941     for (int i = 0; i < sg.getSize(); i++)
1942     {
1943       SequenceI seq = null;
1944
1945       while (seq == null)
1946       {
1947         if (orderedSeqs.containsKey(index))
1948         {
1949           seq = orderedSeqs.get(index);
1950           index++;
1951           break;
1952         }
1953         else
1954         {
1955           index++;
1956         }
1957       }
1958
1959       // FIND START RES
1960       // Returns residue following index if gap
1961       startRes = seq.findPosition(sg.getStartRes());
1962
1963       // FIND END RES
1964       // Need to find the residue preceeding index if gap
1965       endRes = 0;
1966
1967       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1968       {
1969         ch = seq.getCharAt(j);
1970         if (!jalview.util.Comparison.isGap((ch)))
1971         {
1972           endRes++;
1973         }
1974       }
1975
1976       if (endRes > 0)
1977       {
1978         endRes += seq.getStart() - 1;
1979       }
1980
1981       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1982               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1983                       sg.getEndRes() + 1)
1984               + "\n");
1985     }
1986
1987   }
1988
1989   protected void pasteNew_actionPerformed()
1990   {
1991     paste(true);
1992   }
1993
1994   protected void pasteThis_actionPerformed()
1995   {
1996     paste(false);
1997   }
1998
1999   void paste(boolean newAlignment)
2000   {
2001     try
2002     {
2003
2004       if (copiedSequences == null)
2005       {
2006         return;
2007       }
2008
2009       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2010       Vector seqs = new Vector();
2011       while (st.hasMoreElements())
2012       {
2013         String name = st.nextToken();
2014         int start = Integer.parseInt(st.nextToken());
2015         int end = Integer.parseInt(st.nextToken());
2016         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2017       }
2018       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2019       for (int i = 0; i < seqs.size(); i++)
2020       {
2021         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2022       }
2023
2024       if (newAlignment)
2025       {
2026         String newtitle = MessageManager
2027                 .getString("label.copied_sequences");
2028         if (getTitle().startsWith(
2029                 MessageManager.getString("label.copied_sequences")))
2030         {
2031           newtitle = getTitle();
2032         }
2033         else
2034         {
2035           newtitle = newtitle.concat(MessageManager
2036                   .formatMessage("label.from_msname", new String[]
2037                   { getTitle() }));
2038         }
2039         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2040                 viewport.applet, newtitle, false);
2041         af.viewport.setHiddenColumns(copiedHiddenColumns);
2042
2043         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2044                 frameHeight);
2045       }
2046       else
2047       {
2048         addSequences(newSeqs);
2049       }
2050
2051     } catch (Exception ex)
2052     {
2053     } // could be anything being pasted in here
2054
2055   }
2056
2057   void addSequences(SequenceI[] seqs)
2058   {
2059     for (int i = 0; i < seqs.length; i++)
2060     {
2061       viewport.getAlignment().addSequence(seqs[i]);
2062     }
2063
2064     // !newAlignment
2065     addHistoryItem(new EditCommand(
2066             MessageManager.getString("label.add_sequences"), Action.PASTE,
2067             seqs, 0, viewport.getAlignment().getWidth(),
2068             viewport.getAlignment()));
2069
2070     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2071     viewport.getAlignment().getWidth();
2072     viewport.firePropertyChange("alignment", null,
2073             viewport.getAlignment().getSequences());
2074
2075   }
2076
2077   protected void cut_actionPerformed()
2078   {
2079     copy_actionPerformed();
2080     delete_actionPerformed();
2081   }
2082
2083   protected void delete_actionPerformed()
2084   {
2085
2086     SequenceGroup sg = viewport.getSelectionGroup();
2087     if (sg == null)
2088     {
2089       return;
2090     }
2091
2092     Vector seqs = new Vector();
2093     SequenceI seq;
2094     for (int i = 0; i < sg.getSize(); i++)
2095     {
2096       seq = sg.getSequenceAt(i);
2097       seqs.addElement(seq);
2098     }
2099
2100     /*
2101      * If the cut affects all sequences, warn, remove highlighted columns
2102      */
2103     if (sg.getSize() == viewport.getAlignment().getHeight())
2104     {
2105       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2106               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2107       if (isEntireAlignWidth)
2108       {
2109         String title = MessageManager.getString("label.delete_all");
2110         Panel infoPanel = new Panel();
2111         infoPanel.setLayout(new FlowLayout());
2112         infoPanel.add(
2113                 new Label(MessageManager.getString("warn.delete_all")));
2114
2115         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2116         dialog.setMainPanel(infoPanel);
2117         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2118         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2119         dialog.setVisible(true);
2120
2121         if (!dialog.accept)
2122         {
2123           return;
2124         }
2125       }
2126       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2127               sg.getEndRes() + 1);
2128     }
2129
2130     SequenceI[] cut = new SequenceI[seqs.size()];
2131     for (int i = 0; i < seqs.size(); i++)
2132     {
2133       cut[i] = (SequenceI) seqs.elementAt(i);
2134     }
2135
2136     /*
2137      * //ADD HISTORY ITEM
2138      */
2139     addHistoryItem(new EditCommand(
2140             MessageManager.getString("label.cut_sequences"), Action.CUT,
2141             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2142             viewport.getAlignment()));
2143
2144     viewport.setSelectionGroup(null);
2145     viewport.getAlignment().deleteGroup(sg);
2146
2147     viewport.firePropertyChange("alignment", null,
2148             viewport.getAlignment().getSequences());
2149
2150     if (viewport.getAlignment().getHeight() < 1)
2151     {
2152       this.setVisible(false);
2153     }
2154     viewport.sendSelection();
2155   }
2156
2157   /**
2158    * group consensus toggled
2159    *
2160    */
2161   protected void showGroupConsensus_actionPerformed()
2162   {
2163     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2164     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2165
2166   }
2167
2168   /**
2169    * group conservation toggled.
2170    */
2171   protected void showGroupConservation_actionPerformed()
2172   {
2173     viewport.setShowGroupConservation(showGroupConservation.getState());
2174     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2175   }
2176
2177   /*
2178    * (non-Javadoc)
2179    *
2180    * @see
2181    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2182    * .event.ActionEvent)
2183    */
2184   protected void showConsensusHistogram_actionPerformed()
2185   {
2186     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2187     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188   }
2189
2190   /*
2191    * (non-Javadoc)
2192    *
2193    * @see
2194    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2195    * .event.ActionEvent)
2196    */
2197   protected void showSequenceLogo_actionPerformed()
2198   {
2199     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2200     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2201   }
2202
2203   protected void normSequenceLogo_actionPerformed()
2204   {
2205     showSequenceLogo.setState(true);
2206     viewport.setShowSequenceLogo(true);
2207     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2208     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2209   }
2210
2211   protected void applyAutoAnnotationSettings_actionPerformed()
2212   {
2213     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2214   }
2215
2216   protected void makeGrpsFromSelection_actionPerformed()
2217   {
2218     if (avc.makeGroupsFromSelection())
2219     {
2220       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2221       alignPanel.updateAnnotation();
2222       alignPanel.paintAlignment(true);
2223     }
2224   }
2225
2226   protected void createGroup_actionPerformed()
2227   {
2228     avc.createGroup();
2229   }
2230
2231   protected void unGroup_actionPerformed()
2232   {
2233     if (avc.unGroup())
2234     {
2235       alignPanel.alignmentChanged();
2236     }
2237   }
2238
2239   protected void deleteGroups_actionPerformed()
2240   {
2241     if (avc.deleteGroups())
2242     {
2243       alignPanel.alignmentChanged();
2244     }
2245   }
2246
2247   public void selectAllSequenceMenuItem_actionPerformed()
2248   {
2249     SequenceGroup sg = new SequenceGroup();
2250     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2251     {
2252       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2253     }
2254     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2255     viewport.setSelectionGroup(sg);
2256     // JAL-2034 - should delegate to
2257     // alignPanel to decide if overview needs
2258     // updating.
2259     alignPanel.paintAlignment(false);
2260     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2261     viewport.sendSelection();
2262   }
2263
2264   public void deselectAllSequenceMenuItem_actionPerformed()
2265   {
2266     if (viewport.cursorMode)
2267     {
2268       alignPanel.seqPanel.keyboardNo1 = null;
2269       alignPanel.seqPanel.keyboardNo2 = null;
2270     }
2271     viewport.setSelectionGroup(null);
2272     viewport.getColumnSelection().clear();
2273     viewport.setSelectionGroup(null);
2274     alignPanel.idPanel.idCanvas.searchResults = null;
2275     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2276     // JAL-2034 - should delegate to
2277     // alignPanel to decide if overview needs
2278     // updating.
2279     alignPanel.paintAlignment(false);
2280     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281     viewport.sendSelection();
2282   }
2283
2284   public void invertSequenceMenuItem_actionPerformed()
2285   {
2286     SequenceGroup sg = viewport.getSelectionGroup();
2287     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2288     {
2289       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2290     }
2291
2292     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2293     viewport.sendSelection();
2294   }
2295
2296   public void invertColSel_actionPerformed()
2297   {
2298     viewport.invertColumnSelection();
2299     alignPanel.paintAlignment(true);
2300     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2301     viewport.sendSelection();
2302   }
2303
2304   void trimAlignment(boolean trimLeft)
2305   {
2306     AlignmentI al = viewport.getAlignment();
2307     ViewportRanges ranges = viewport.getRanges();
2308     ColumnSelection colSel = viewport.getColumnSelection();
2309     int column;
2310
2311     if (!colSel.isEmpty())
2312     {
2313       if (trimLeft)
2314       {
2315         column = colSel.getMin();
2316       }
2317       else
2318       {
2319         column = colSel.getMax();
2320       }
2321
2322       SequenceI[] seqs;
2323       if (viewport.getSelectionGroup() != null)
2324       {
2325         seqs = viewport.getSelectionGroup()
2326                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2327       }
2328       else
2329       {
2330         seqs = al.getSequencesArray();
2331       }
2332
2333       TrimRegionCommand trimRegion;
2334       if (trimLeft)
2335       {
2336         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2337                 column, al);
2338         ranges.setStartRes(0);
2339       }
2340       else
2341       {
2342         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2343                 column, al);
2344       }
2345
2346       statusBar.setText(MessageManager
2347               .formatMessage("label.removed_columns", new String[]
2348               { Integer.valueOf(trimRegion.getSize()).toString() }));
2349       addHistoryItem(trimRegion);
2350
2351       for (SequenceGroup sg : al.getGroups())
2352       {
2353         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2354                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2355         {
2356           al.deleteGroup(sg);
2357         }
2358       }
2359
2360       viewport.firePropertyChange("alignment", null, al.getSequences());
2361     }
2362   }
2363
2364   public void removeGappedColumnMenuItem_actionPerformed()
2365   {
2366     AlignmentI al = viewport.getAlignment();
2367     ViewportRanges ranges = viewport.getRanges();
2368     int start = 0;
2369     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2370
2371     SequenceI[] seqs;
2372     if (viewport.getSelectionGroup() != null)
2373     {
2374       seqs = viewport.getSelectionGroup()
2375               .getSequencesAsArray(viewport.getHiddenRepSequences());
2376       start = viewport.getSelectionGroup().getStartRes();
2377       end = viewport.getSelectionGroup().getEndRes();
2378     }
2379     else
2380     {
2381       seqs = viewport.getAlignment().getSequencesArray();
2382     }
2383
2384     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2385             "Remove Gapped Columns", seqs, start, end,
2386             viewport.getAlignment());
2387
2388     addHistoryItem(removeGapCols);
2389
2390     statusBar.setText(MessageManager
2391             .formatMessage("label.removed_empty_columns", new String[]
2392             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2393
2394     // This is to maintain viewport position on first residue
2395     // of first sequence
2396     SequenceI seq = al.getSequenceAt(0);
2397     int startRes = seq.findPosition(ranges.getStartRes());
2398     // ShiftList shifts;
2399     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2400     // edit.alColumnChanges=shifts.getInverse();
2401     // if (viewport.hasHiddenColumns)
2402     // viewport.getColumnSelection().compensateForEdits(shifts);
2403     ranges.setStartRes(seq.findIndex(startRes) - 1);
2404     viewport.firePropertyChange("alignment", null, al.getSequences());
2405
2406   }
2407
2408   public void removeAllGapsMenuItem_actionPerformed()
2409   {
2410     AlignmentI al = viewport.getAlignment();
2411     ViewportRanges ranges = viewport.getRanges();
2412     int start = 0;
2413     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2414
2415     SequenceI[] seqs;
2416     if (viewport.getSelectionGroup() != null)
2417     {
2418       seqs = viewport.getSelectionGroup()
2419               .getSequencesAsArray(viewport.getHiddenRepSequences());
2420       start = viewport.getSelectionGroup().getStartRes();
2421       end = viewport.getSelectionGroup().getEndRes();
2422     }
2423     else
2424     {
2425       seqs = viewport.getAlignment().getSequencesArray();
2426     }
2427
2428     // This is to maintain viewport position on first residue
2429     // of first sequence
2430     SequenceI seq = al.getSequenceAt(0);
2431     int startRes = seq.findPosition(ranges.getStartRes());
2432
2433     addHistoryItem(
2434             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2435
2436     ranges.setStartRes(seq.findIndex(startRes) - 1);
2437
2438     viewport.firePropertyChange("alignment", null, al.getSequences());
2439
2440   }
2441
2442   public void findMenuItem_actionPerformed()
2443   {
2444     new Finder(alignPanel);
2445   }
2446
2447   /**
2448    * create a new view derived from the current view
2449    *
2450    * @param viewtitle
2451    * @return frame for the new view
2452    */
2453   public AlignFrame newView(String viewtitle)
2454   {
2455     AlignmentI newal;
2456     if (viewport.hasHiddenRows())
2457     {
2458       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2459               .getFullAlignment().getSequencesArray());
2460     }
2461     else
2462     {
2463       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2464     }
2465
2466     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2467     {
2468       for (int i = 0; i < viewport.getAlignment()
2469               .getAlignmentAnnotation().length; i++)
2470       {
2471         if (!viewport.getAlignment()
2472                 .getAlignmentAnnotation()[i].autoCalculated)
2473         {
2474           newal.addAnnotation(
2475                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2476         }
2477       }
2478     }
2479
2480     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2481
2482     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2483     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2484     PaintRefresher.Register(newaf.alignPanel,
2485             newaf.alignPanel.av.getSequenceSetId());
2486
2487     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2488             newaf.alignPanel.av.getSequenceSetId());
2489     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2490             newaf.alignPanel.av.getSequenceSetId());
2491
2492     Vector comps = PaintRefresher.components
2493             .get(viewport.getSequenceSetId());
2494     int viewSize = -1;
2495     for (int i = 0; i < comps.size(); i++)
2496     {
2497       if (comps.elementAt(i) instanceof AlignmentPanel)
2498       {
2499         viewSize++;
2500       }
2501     }
2502
2503     String title = new String(this.getTitle());
2504     if (viewtitle != null)
2505     {
2506       title = viewtitle + " ( " + title + ")";
2507     }
2508     else
2509     {
2510       if (title.indexOf("(View") > -1)
2511       {
2512         title = title.substring(0, title.indexOf("(View"));
2513       }
2514       title += "(View " + viewSize + ")";
2515     }
2516
2517     newaf.setTitle(title.toString());
2518
2519     newaf.viewport.setHistoryList(viewport.getHistoryList());
2520     newaf.viewport.setRedoList(viewport.getRedoList());
2521     return newaf;
2522   }
2523
2524   /**
2525    *
2526    * @return list of feature groups on the view
2527    */
2528   public String[] getFeatureGroups()
2529   {
2530     FeatureRenderer fr = null;
2531     if (alignPanel != null
2532             && (fr = alignPanel.getFeatureRenderer()) != null)
2533     {
2534       List<String> gps = fr.getFeatureGroups();
2535       String[] _gps = gps.toArray(new String[gps.size()]);
2536       return _gps;
2537     }
2538     return null;
2539   }
2540
2541   /**
2542    * get sequence feature groups that are hidden or shown
2543    *
2544    * @param visible
2545    *          true is visible
2546    * @return list
2547    */
2548   public String[] getFeatureGroupsOfState(boolean visible)
2549   {
2550     FeatureRenderer fr = null;
2551     if (alignPanel != null
2552             && (fr = alignPanel.getFeatureRenderer()) != null)
2553     {
2554       List<String> gps = fr.getGroups(visible);
2555       String[] _gps = gps.toArray(new String[gps.size()]);
2556       return _gps;
2557     }
2558     return null;
2559   }
2560
2561   /**
2562    * Change the display state for the given feature groups
2563    *
2564    * @param groups
2565    *          list of group strings
2566    * @param state
2567    *          visible or invisible
2568    */
2569   public void setFeatureGroupState(String[] groups, boolean state)
2570   {
2571     FeatureRenderer fr = null;
2572     this.sequenceFeatures.setState(true);
2573     viewport.setShowSequenceFeatures(true);
2574     if (alignPanel != null
2575             && (fr = alignPanel.getFeatureRenderer()) != null)
2576     {
2577
2578       fr.setGroupVisibility(Arrays.asList(groups), state);
2579       alignPanel.seqPanel.seqCanvas.repaint();
2580       if (alignPanel.overviewPanel != null)
2581       {
2582         alignPanel.overviewPanel.updateOverviewImage();
2583       }
2584     }
2585   }
2586
2587   public void seqLimits_itemStateChanged()
2588   {
2589     viewport.setShowJVSuffix(seqLimits.getState());
2590     alignPanel.fontChanged();
2591     alignPanel.paintAlignment(true);
2592   }
2593
2594   protected void colourTextMenuItem_actionPerformed()
2595   {
2596     viewport.setColourText(colourTextMenuItem.getState());
2597     alignPanel.paintAlignment(true);
2598   }
2599
2600   protected void displayNonconservedMenuItem_actionPerformed()
2601   {
2602     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2603     alignPanel.paintAlignment(true);
2604   }
2605
2606   protected void wrapMenuItem_actionPerformed()
2607   {
2608     viewport.setWrapAlignment(wrapMenuItem.getState());
2609     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2610     scaleAbove.setEnabled(wrapMenuItem.getState());
2611     scaleLeft.setEnabled(wrapMenuItem.getState());
2612     scaleRight.setEnabled(wrapMenuItem.getState());
2613     alignPanel.paintAlignment(true);
2614   }
2615
2616   public void overviewMenuItem_actionPerformed()
2617   {
2618     if (alignPanel.overviewPanel != null)
2619     {
2620       return;
2621     }
2622
2623     Frame frame = new Frame();
2624     final OverviewPanel overview = new OverviewPanel(alignPanel);
2625     frame.add(overview);
2626     // +50 must allow for applet frame window
2627     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2628             .formatMessage("label.overview_params", new String[]
2629             { this.getTitle() }), overview.getPreferredSize().width,
2630             overview.getPreferredSize().height + 50);
2631
2632     frame.pack();
2633     final AlignmentPanel ap = alignPanel;
2634     frame.addWindowListener(new WindowAdapter()
2635     {
2636       @Override
2637       public void windowClosing(WindowEvent e)
2638       {
2639         overview.dispose();
2640         if (ap != null)
2641         {
2642           ap.setOverviewPanel(null);
2643         }
2644       };
2645     });
2646
2647     alignPanel.setOverviewPanel(overview);
2648
2649   }
2650
2651   @Override
2652   public void changeColour(ColourSchemeI cs)
2653   {
2654     viewport.setGlobalColourScheme(cs);
2655
2656     alignPanel.paintAlignment(true);
2657   }
2658
2659   protected void modifyPID_actionPerformed()
2660   {
2661     if (viewport.getAbovePIDThreshold()
2662             && viewport.getGlobalColourScheme() != null)
2663     {
2664       SliderPanel.setPIDSliderSource(alignPanel,
2665               viewport.getResidueShading(), alignPanel.getViewName());
2666       SliderPanel.showPIDSlider();
2667     }
2668   }
2669
2670   protected void modifyConservation_actionPerformed()
2671   {
2672     if (viewport.getConservationSelected()
2673             && viewport.getGlobalColourScheme() != null)
2674     {
2675       SliderPanel.setConservationSlider(alignPanel,
2676               viewport.getResidueShading(), alignPanel.getViewName());
2677       SliderPanel.showConservationSlider();
2678     }
2679   }
2680
2681   protected void conservationMenuItem_actionPerformed()
2682   {
2683     boolean selected = conservationMenuItem.getState();
2684     modifyConservation.setEnabled(selected);
2685     viewport.setConservationSelected(selected);
2686     viewport.getResidueShading().setConservationApplied(selected);
2687
2688     changeColour(viewport.getGlobalColourScheme());
2689
2690     if (selected)
2691     {
2692       modifyConservation_actionPerformed();
2693     }
2694     else
2695     {
2696       SliderPanel.hideConservationSlider();
2697     }
2698   }
2699
2700   public void abovePIDThreshold_actionPerformed()
2701   {
2702     boolean selected = abovePIDThreshold.getState();
2703     modifyPID.setEnabled(selected);
2704     viewport.setAbovePIDThreshold(selected);
2705     if (!selected)
2706     {
2707       viewport.getResidueShading().setThreshold(0,
2708               viewport.isIgnoreGapsConsensus());
2709     }
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(),
2727             viewport.getAlignment().getSequenceAt(0));
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(
2739             new OrderCommand("ID Sort", oldOrder, 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()
2789               .size(); i++)
2790       {
2791         current = viewport.getAlignment().getSequenceAt(i);
2792
2793         if (current.getLength() < Width)
2794         {
2795           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2796         }
2797       }
2798       alignPanel.paintAlignment(true);
2799     }
2800
2801     if ((viewport.getSelectionGroup() != null
2802             && viewport.getSelectionGroup().getSize() < 4
2803             && viewport.getSelectionGroup().getSize() > 0)
2804             || viewport.getAlignment().getHeight() < 4)
2805     {
2806       return;
2807     }
2808
2809     try
2810     {
2811       new PCAPanel(viewport);
2812     } catch (java.lang.OutOfMemoryError ex)
2813     {
2814     }
2815
2816   }
2817
2818   public void averageDistanceTreeMenuItem_actionPerformed()
2819   {
2820     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2821             "Average distance tree using PID");
2822   }
2823
2824   public void neighbourTreeMenuItem_actionPerformed()
2825   {
2826     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2827             "Neighbour joining tree using PID");
2828   }
2829
2830   protected void njTreeBlosumMenuItem_actionPerformed()
2831   {
2832     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2833             ScoreModels.getInstance().getBlosum62().getName(),
2834             "Neighbour joining tree using BLOSUM62");
2835   }
2836
2837   protected void avTreeBlosumMenuItem_actionPerformed()
2838   {
2839     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2840             ScoreModels.getInstance().getBlosum62().getName(),
2841             "Average distance tree using BLOSUM62");
2842   }
2843
2844   void newTreePanel(String type, String pwType, String title)
2845   {
2846     // are the sequences aligned?
2847     if (!viewport.getAlignment().isAligned(false))
2848     {
2849       SequenceI current;
2850       int Width = viewport.getAlignment().getWidth();
2851
2852       for (int i = 0; i < viewport.getAlignment().getSequences()
2853               .size(); i++)
2854       {
2855         current = viewport.getAlignment().getSequenceAt(i);
2856
2857         if (current.getLength() < Width)
2858         {
2859           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2860         }
2861       }
2862       alignPanel.paintAlignment(true);
2863
2864     }
2865
2866     if ((viewport.getSelectionGroup() != null
2867             && viewport.getSelectionGroup().getSize() > 1)
2868             || (viewport.getAlignment().getHeight() > 1))
2869     {
2870       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2871
2872       addTreeMenuItem(tp, title);
2873
2874       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2875     }
2876   }
2877
2878   void loadTree_actionPerformed()
2879   {
2880     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2881     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2882     cap.setTreeImport();
2883     Frame frame = new Frame();
2884     frame.add(cap);
2885     jalview.bin.JalviewLite.addFrame(frame,
2886             MessageManager.getString("label.paste_newick_file"), 400, 300);
2887   }
2888
2889   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2890   {
2891     TreePanel tp = new TreePanel(alignPanel, treeFile,
2892             MessageManager.getString("label.load_tree_from_file"), tree);
2893     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2894     addTreeMenuItem(tp, treeFile);
2895   }
2896
2897   /**
2898    * sort the alignment using the given treePanel
2899    *
2900    * @param treePanel
2901    *          tree used to sort view
2902    * @param title
2903    *          string used for undo event name
2904    */
2905   public void sortByTree(TreePanel treePanel, String title)
2906   {
2907     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2908     AlignmentSorter.sortByTree(viewport.getAlignment(),
2909             treePanel.getTree());
2910     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2911     // HistoryItem.SORT));
2912     addHistoryItem(new OrderCommand(MessageManager
2913             .formatMessage("label.order_by_params", new String[]
2914             { title }), oldOrder, viewport.getAlignment()));
2915     alignPanel.paintAlignment(true);
2916   }
2917
2918   /**
2919    * Do any automatic reordering of the alignment and add the necessary bits to
2920    * the menu structure for the new tree
2921    *
2922    * @param treePanel
2923    * @param title
2924    */
2925   protected void addTreeMenuItem(final TreePanel treePanel,
2926           final String title)
2927   {
2928     final MenuItem item = new MenuItem(title);
2929     sortByTreeMenu.add(item);
2930     item.addActionListener(new java.awt.event.ActionListener()
2931     {
2932       @Override
2933       public void actionPerformed(ActionEvent evt)
2934       {
2935         sortByTree(treePanel, title); // treePanel.getTitle());
2936       }
2937     });
2938
2939     treePanel.addWindowListener(new WindowAdapter()
2940     {
2941       @Override
2942       public void windowOpened(WindowEvent e)
2943       {
2944         if (viewport.sortByTree)
2945         {
2946           sortByTree(treePanel, title);
2947         }
2948         super.windowOpened(e);
2949       }
2950
2951       @Override
2952       public void windowClosing(WindowEvent e)
2953       {
2954         sortByTreeMenu.remove(item);
2955       };
2956     });
2957   }
2958
2959   public boolean sortBy(AlignmentOrder alorder, String undoname)
2960   {
2961     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2962     if (viewport.applet.debug)
2963     {
2964       System.err.println("Sorting " + alorder.getOrder().size()
2965               + " in alignment '" + getTitle() + "'");
2966     }
2967     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2968     if (undoname != null)
2969     {
2970       addHistoryItem(new OrderCommand(undoname, oldOrder,
2971               viewport.getAlignment()));
2972     }
2973     alignPanel.paintAlignment(true);
2974     return true;
2975   }
2976
2977   protected void documentation_actionPerformed()
2978   {
2979     alignPanel.av.applet.openJalviewHelpUrl();
2980   }
2981
2982   protected void about_actionPerformed()
2983   {
2984
2985     class AboutPanel extends Canvas
2986     {
2987       String version;
2988
2989       String builddate;
2990
2991       public AboutPanel(String version, String builddate)
2992       {
2993         this.version = version;
2994         this.builddate = builddate;
2995       }
2996
2997       @Override
2998       public void paint(Graphics g)
2999       {
3000         g.setColor(Color.white);
3001         g.fillRect(0, 0, getSize().width, getSize().height);
3002         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3003         FontMetrics fm = g.getFontMetrics();
3004         int fh = fm.getHeight();
3005         int y = 5, x = 7;
3006         g.setColor(Color.black);
3007         // TODO: update this text for each release or centrally store it for
3008         // lite and application
3009         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3010         g.drawString(MessageManager
3011                 .formatMessage("label.jalviewLite_release", new String[]
3012                 { version }), x, y += fh);
3013         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3014         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3015                 new String[]
3016                 { builddate }), x, y += fh);
3017         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3018         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3019                 y += fh * 1.5);
3020         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3021                 x + 50, y += fh + 8);
3022         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3023                 x, y += fh);
3024         g.drawString(MessageManager
3025                 .getString("label.jalview_distribution_lists"), x, y += fh);
3026         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3027                 x, y += fh + 8);
3028         g.drawString(
3029                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3030                 y += fh);
3031         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3032                 x, y += fh);
3033         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3034                 x, y += fh);
3035       }
3036     }
3037
3038     Frame frame = new Frame();
3039     frame.add(new AboutPanel(JalviewLite.getVersion(),
3040             JalviewLite.getBuildDate()));
3041     jalview.bin.JalviewLite.addFrame(frame,
3042             MessageManager.getString("label.jalview"), 580, 220);
3043
3044   }
3045
3046   public void showURL(String url, String target)
3047   {
3048     if (viewport.applet == null)
3049     {
3050       System.out.println("Not running as applet - no browser available.");
3051     }
3052     else
3053     {
3054       viewport.applet.showURL(url, target);
3055     }
3056   }
3057
3058   // ////////////////////////////////////////////////////////////////////////////////
3059   // JBuilder Graphics here
3060
3061   MenuBar alignFrameMenuBar = new MenuBar();
3062
3063   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3064
3065   MenuItem loadApplication = new MenuItem(
3066           MessageManager.getString("label.view_full_application"));
3067
3068   MenuItem loadTree = new MenuItem(
3069           MessageManager.getString("label.load_associated_tree"));
3070
3071   MenuItem loadAnnotations = new MenuItem(
3072           MessageManager.getString("label.load_features_annotations"));
3073
3074   MenuItem outputFeatures = new MenuItem(
3075           MessageManager.getString("label.export_features"));
3076
3077   MenuItem outputAnnotations = new MenuItem(
3078           MessageManager.getString("label.export_annotations"));
3079
3080   MenuItem closeMenuItem = new MenuItem(
3081           MessageManager.getString("action.close"));
3082
3083   MenuItem selectAllSequenceMenuItem = new MenuItem(
3084           MessageManager.getString("action.select_all"));
3085
3086   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3087           MessageManager.getString("action.deselect_all"));
3088
3089   MenuItem invertSequenceMenuItem = new MenuItem(
3090           MessageManager.getString("action.invert_selection"));
3091
3092   MenuItem remove2LeftMenuItem = new MenuItem();
3093
3094   MenuItem remove2RightMenuItem = new MenuItem();
3095
3096   MenuItem removeGappedColumnMenuItem = new MenuItem();
3097
3098   MenuItem removeAllGapsMenuItem = new MenuItem();
3099
3100   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3101
3102   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3103
3104   MenuItem sortPairwiseMenuItem = new MenuItem();
3105
3106   MenuItem sortIDMenuItem = new MenuItem();
3107
3108   MenuItem sortLengthMenuItem = new MenuItem();
3109
3110   MenuItem sortGroupMenuItem = new MenuItem();
3111
3112   MenuItem removeRedundancyMenuItem = new MenuItem();
3113
3114   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3115
3116   MenuItem PCAMenuItem = new MenuItem();
3117
3118   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3119
3120   MenuItem neighbourTreeMenuItem = new MenuItem();
3121
3122   BorderLayout borderLayout1 = new BorderLayout();
3123
3124   public Label statusBar = new Label();
3125
3126   MenuItem clustalColour = new MenuItem();
3127
3128   MenuItem zappoColour = new MenuItem();
3129
3130   MenuItem taylorColour = new MenuItem();
3131
3132   MenuItem hydrophobicityColour = new MenuItem();
3133
3134   MenuItem helixColour = new MenuItem();
3135
3136   MenuItem strandColour = new MenuItem();
3137
3138   MenuItem turnColour = new MenuItem();
3139
3140   MenuItem buriedColour = new MenuItem();
3141
3142   MenuItem purinePyrimidineColour = new MenuItem();
3143
3144   // MenuItem RNAInteractionColour = new MenuItem();
3145
3146   MenuItem RNAHelixColour = new MenuItem();
3147
3148   MenuItem userDefinedColour = new MenuItem();
3149
3150   MenuItem PIDColour = new MenuItem();
3151
3152   MenuItem BLOSUM62Colour = new MenuItem();
3153
3154   MenuItem tcoffeeColour = new MenuItem();
3155
3156   MenuItem njTreeBlosumMenuItem = new MenuItem();
3157
3158   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3159
3160   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3161
3162   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3163
3164   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3165
3166   MenuItem alProperties = new MenuItem(
3167           MessageManager.getString("label.alignment_props"));
3168
3169   MenuItem overviewMenuItem = new MenuItem();
3170
3171   MenuItem undoMenuItem = new MenuItem();
3172
3173   MenuItem redoMenuItem = new MenuItem();
3174
3175   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3176
3177   MenuItem noColourmenuItem = new MenuItem();
3178
3179   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3180
3181   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3182
3183   MenuItem findMenuItem = new MenuItem();
3184
3185   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3186
3187   MenuItem nucleotideColour = new MenuItem();
3188
3189   MenuItem deleteGroups = new MenuItem();
3190
3191   MenuItem grpsFromSelection = new MenuItem();
3192
3193   MenuItem createGroup = new MenuItem();
3194
3195   MenuItem unGroup = new MenuItem();
3196
3197   MenuItem delete = new MenuItem();
3198
3199   MenuItem copy = new MenuItem();
3200
3201   MenuItem cut = new MenuItem();
3202
3203   Menu pasteMenu = new Menu();
3204
3205   MenuItem pasteNew = new MenuItem();
3206
3207   MenuItem pasteThis = new MenuItem();
3208
3209   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3210
3211   MenuItem font = new MenuItem();
3212
3213   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3218
3219   MenuItem modifyPID = new MenuItem();
3220
3221   MenuItem modifyConservation = new MenuItem();
3222
3223   CheckboxMenuItem autoCalculate = null;
3224
3225   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3226           "Sort Alignment With New Tree", true);
3227
3228   Menu sortByTreeMenu = new Menu();
3229
3230   MenuItem inputText = new MenuItem();
3231
3232   MenuItem documentation = new MenuItem();
3233
3234   MenuItem about = new MenuItem();
3235
3236   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3237
3238   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3253
3254   /**
3255    * Initialise menus and other items
3256    *
3257    * @throws Exception
3258    */
3259   private void jbInit() throws Exception
3260   {
3261     setMenuBar(alignFrameMenuBar);
3262
3263     /*
3264      * Configure File menu items and actions
3265      */
3266     inputText
3267             .setLabel(MessageManager.getString("label.input_from_textbox"));
3268     inputText.addActionListener(this);
3269     Menu outputTextboxMenu = new Menu(
3270             MessageManager.getString("label.out_to_textbox"));
3271     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3272     {
3273       MenuItem item = new MenuItem(ff);
3274
3275       item.addActionListener(new java.awt.event.ActionListener()
3276       {
3277         @Override
3278         public void actionPerformed(ActionEvent e)
3279         {
3280           outputText_actionPerformed(e);
3281         }
3282       });
3283
3284       outputTextboxMenu.add(item);
3285     }
3286     closeMenuItem.addActionListener(this);
3287     loadApplication.addActionListener(this);
3288     loadTree.addActionListener(this);
3289     loadAnnotations.addActionListener(this);
3290     outputFeatures.addActionListener(this);
3291     outputAnnotations.addActionListener(this);
3292
3293     /*
3294      * Configure Edit menu items and actions
3295      */
3296     undoMenuItem.setEnabled(false);
3297     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3298     undoMenuItem.addActionListener(this);
3299     redoMenuItem.setEnabled(false);
3300     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3301     redoMenuItem.addActionListener(this);
3302     copy.setLabel(MessageManager.getString("action.copy"));
3303     copy.addActionListener(this);
3304     cut.setLabel(MessageManager.getString("action.cut"));
3305     cut.addActionListener(this);
3306     delete.setLabel(MessageManager.getString("action.delete"));
3307     delete.addActionListener(this);
3308     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3309     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3310     pasteNew.addActionListener(this);
3311     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3312     pasteThis.addActionListener(this);
3313     remove2LeftMenuItem
3314             .setLabel(MessageManager.getString("action.remove_left"));
3315     remove2LeftMenuItem.addActionListener(this);
3316     remove2RightMenuItem
3317             .setLabel(MessageManager.getString("action.remove_right"));
3318     remove2RightMenuItem.addActionListener(this);
3319     removeGappedColumnMenuItem.setLabel(
3320             MessageManager.getString("action.remove_empty_columns"));
3321     removeGappedColumnMenuItem.addActionListener(this);
3322     removeAllGapsMenuItem
3323             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3324     removeAllGapsMenuItem.addActionListener(this);
3325     removeRedundancyMenuItem
3326             .setLabel(MessageManager.getString("action.remove_redundancy"));
3327     removeRedundancyMenuItem.addActionListener(this);
3328
3329     /*
3330      * Configure Select menu items and actions
3331      */
3332     findMenuItem.setLabel(MessageManager.getString("action.find"));
3333     findMenuItem.addActionListener(this);
3334     selectAllSequenceMenuItem.addActionListener(this);
3335     deselectAllSequenceMenuItem.addActionListener(this);
3336     invertSequenceMenuItem.setLabel(
3337             MessageManager.getString("action.invert_sequence_selection"));
3338     invertSequenceMenuItem.addActionListener(this);
3339     invertColSel.setLabel(
3340             MessageManager.getString("action.invert_column_selection"));
3341     invertColSel.addActionListener(this);
3342     deleteGroups
3343             .setLabel(MessageManager.getString("action.undefine_groups"));
3344     deleteGroups.addActionListener(this);
3345     grpsFromSelection.setLabel(
3346             MessageManager.getString("action.make_groups_selection"));
3347     grpsFromSelection.addActionListener(this);
3348     createGroup.setLabel(MessageManager.getString("action.create_group"));
3349     createGroup.addActionListener(this);
3350     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3351     unGroup.addActionListener(this);
3352
3353     annotationColumnSelection.setLabel(
3354             MessageManager.getString("action.select_by_annotation"));
3355     annotationColumnSelection.addActionListener(this);
3356
3357     /*
3358      * Configure View menu items and actions
3359      */
3360     newView.setLabel(MessageManager.getString("action.new_view"));
3361     newView.addActionListener(this);
3362     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3363     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3364     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3365     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3366     hideColumns
3367             .setLabel(MessageManager.getString("label.selected_columns"));
3368     hideSequences
3369             .setLabel(MessageManager.getString("label.selected_sequences"));
3370     hideAllButSelection.setLabel(
3371             MessageManager.getString("label.all_but_selected_region"));
3372     hideAllSelection
3373             .setLabel(MessageManager.getString("label.selected_region"));
3374     showAllHidden.setLabel(
3375             MessageManager.getString("label.all_sequences_columns"));
3376     showColumns.addActionListener(this);
3377     showSeqs.addActionListener(this);
3378     hideColumns.addActionListener(this);
3379     hideSequences.addActionListener(this);
3380     hideAllButSelection.addActionListener(this);
3381     hideAllSelection.addActionListener(this);
3382     showAllHidden.addActionListener(this);
3383     featureSettings
3384             .setLabel(MessageManager.getString("action.feature_settings"));
3385     featureSettings.addActionListener(this);
3386     sequenceFeatures.setLabel(
3387             MessageManager.getString("label.show_sequence_features"));
3388     sequenceFeatures.addItemListener(this);
3389     sequenceFeatures.setState(false);
3390     followMouseOverFlag.setLabel(
3391             MessageManager.getString("label.automatic_scrolling"));
3392     followMouseOverFlag.addItemListener(this);
3393     alProperties.addActionListener(this);
3394     overviewMenuItem
3395             .setLabel(MessageManager.getString("label.overview_window"));
3396     overviewMenuItem.addActionListener(this);
3397
3398     /*
3399      * Configure Annotations menu items and actions
3400      */
3401     annotationPanelMenuItem
3402             .setLabel(MessageManager.getString("label.show_annotations"));
3403     annotationPanelMenuItem.addItemListener(this);
3404     showGroupConsensus
3405             .setLabel(MessageManager.getString("label.group_consensus"));
3406     showGroupConservation
3407             .setLabel(MessageManager.getString("label.group_conservation"));
3408     showConsensusHistogram.setLabel(
3409             MessageManager.getString("label.show_consensus_histogram"));
3410     showSequenceLogo.setLabel(
3411             MessageManager.getString("label.show_consensus_logo"));
3412     normSequenceLogo.setLabel(
3413             MessageManager.getString("label.norm_consensus_logo"));
3414     applyAutoAnnotationSettings
3415             .setLabel(MessageManager.getString("label.apply_all_groups"));
3416     applyAutoAnnotationSettings.setState(true);
3417     Menu autoAnnMenu = new Menu(
3418             MessageManager.getString("label.autocalculated_annotation"));
3419     showGroupConsensus.addItemListener(this);
3420     showGroupConservation.addItemListener(this);
3421     showConsensusHistogram.addItemListener(this);
3422     showSequenceLogo.addItemListener(this);
3423     normSequenceLogo.addItemListener(this);
3424     applyAutoAnnotationSettings.addItemListener(this);
3425     showAlignmentAnnotations = new CheckboxMenuItem(
3426             MessageManager.getString("label.show_all_al_annotations"));
3427     showSequenceAnnotations = new CheckboxMenuItem(
3428             MessageManager.getString("label.show_all_seq_annotations"));
3429     sortAnnBySequence = new CheckboxMenuItem(
3430             MessageManager.getString("label.sort_annotations_by_sequence"));
3431     sortAnnByLabel = new CheckboxMenuItem(
3432             MessageManager.getString("label.sort_annotations_by_label"));
3433     showAutoFirst = new CheckboxMenuItem(
3434             MessageManager.getString("label.show_first"));
3435     showAutoFirst.setState(false); // pending applet parameter
3436     setShowAutoCalculatedAbove(showAutoFirst.getState());
3437     showAutoLast = new CheckboxMenuItem(
3438             MessageManager.getString("label.show_last"));
3439     showAutoLast.setState(!showAutoFirst.getState());
3440     showAlignmentAnnotations.addItemListener(this);
3441     showSequenceAnnotations.addItemListener(this);
3442     sortAnnBySequence.addItemListener(this);
3443     sortAnnByLabel.addItemListener(this);
3444     showAutoFirst.addItemListener(this);
3445     showAutoLast.addItemListener(this);
3446
3447     /*
3448      * Configure Format menu items and actions
3449      */
3450     font.setLabel(MessageManager.getString("action.font"));
3451     font.addActionListener(this);
3452     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3453     scaleAbove.setState(true);
3454     scaleAbove.setEnabled(false);
3455     scaleAbove.addItemListener(this);
3456     scaleLeft.setEnabled(false);
3457     scaleLeft.setState(true);
3458     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3459     scaleLeft.addItemListener(this);
3460     scaleRight.setEnabled(false);
3461     scaleRight.setState(true);
3462     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3463     scaleRight.addItemListener(this);
3464     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3465     viewBoxesMenuItem.setState(true);
3466     viewBoxesMenuItem.addItemListener(this);
3467     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3468     viewTextMenuItem.setState(true);
3469     viewTextMenuItem.addItemListener(this);
3470     colourTextMenuItem
3471             .setLabel(MessageManager.getString("label.colour_text"));
3472     colourTextMenuItem.addItemListener(this);
3473     displayNonconservedMenuItem
3474             .setLabel(MessageManager.getString("label.show_non_conserved"));
3475     displayNonconservedMenuItem.addItemListener(this);
3476     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3477     wrapMenuItem.addItemListener(this);
3478     renderGapsMenuItem
3479             .setLabel(MessageManager.getString("action.show_gaps"));
3480     renderGapsMenuItem.setState(true);
3481     renderGapsMenuItem.addItemListener(this);
3482     centreColumnLabelFlag.setLabel(
3483             MessageManager.getString("label.centre_column_labels"));
3484     centreColumnLabelFlag.addItemListener(this);
3485     seqLimits.setState(true);
3486     seqLimits.setLabel(
3487             MessageManager.getString("label.show_sequence_limits"));
3488     seqLimits.addItemListener(this);
3489
3490     /*
3491      * Configure Colour menu items and actions
3492      */
3493     applyToAllGroups.setLabel(
3494             MessageManager.getString("label.apply_colour_to_all_groups"));
3495     applyToAllGroups.setState(true);
3496     applyToAllGroups.addItemListener(this);
3497     clustalColour.setLabel(
3498             MessageManager.getString("label.colourScheme_clustal"));
3499     clustalColour.addActionListener(this);
3500     zappoColour
3501             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3502     zappoColour.addActionListener(this);
3503     taylorColour.setLabel(
3504             MessageManager.getString("label.colourScheme_taylor"));
3505     taylorColour.addActionListener(this);
3506     hydrophobicityColour.setLabel(
3507             MessageManager.getString("label.colourScheme_hydrophobic"));
3508     hydrophobicityColour.addActionListener(this);
3509     helixColour.setLabel(MessageManager
3510             .getString("label.colourScheme_helix_propensity"));
3511     helixColour.addActionListener(this);
3512     strandColour.setLabel(MessageManager
3513             .getString("label.colourScheme_strand_propensity"));
3514     strandColour.addActionListener(this);
3515     turnColour.setLabel(
3516             MessageManager.getString("label.colourScheme_turn_propensity"));
3517     turnColour.addActionListener(this);
3518     buriedColour.setLabel(
3519             MessageManager.getString("label.colourScheme_buried_index"));
3520     buriedColour.addActionListener(this);
3521     purinePyrimidineColour.setLabel(MessageManager
3522             .getString("label.colourScheme_purine/pyrimidine"));
3523     purinePyrimidineColour.addActionListener(this);
3524     // RNAInteractionColour.setLabel(MessageManager
3525     // .getString("label.rna_interaction"));
3526     // RNAInteractionColour.addActionListener(this);
3527     RNAHelixColour.setLabel(
3528             MessageManager.getString("label.colourScheme_rna_helices"));
3529     RNAHelixColour.addActionListener(this);
3530     userDefinedColour
3531             .setLabel(MessageManager.getString("action.user_defined"));
3532     userDefinedColour.addActionListener(this);
3533     PIDColour.setLabel(
3534             MessageManager.getString("label.colourScheme_%_identity"));
3535     PIDColour.addActionListener(this);
3536     BLOSUM62Colour.setLabel(
3537             MessageManager.getString("label.colourScheme_blosum62"));
3538     BLOSUM62Colour.addActionListener(this);
3539     tcoffeeColour.setLabel(
3540             MessageManager.getString("label.colourScheme_t-coffee_scores"));
3541     // it will be enabled only if a score file is provided
3542     tcoffeeColour.setEnabled(false);
3543     tcoffeeColour.addActionListener(this);
3544     conservationMenuItem
3545             .setLabel(MessageManager.getString("action.by_conservation"));
3546     conservationMenuItem.addItemListener(this);
3547     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3548     noColourmenuItem.addActionListener(this);
3549     abovePIDThreshold.setLabel(
3550             MessageManager.getString("label.above_identity_threshold"));
3551     abovePIDThreshold.addItemListener(this);
3552     nucleotideColour.setLabel(
3553             MessageManager.getString("label.colourScheme_nucleotide"));
3554     nucleotideColour.addActionListener(this);
3555     modifyPID.setLabel(
3556             MessageManager.getString("label.modify_identity_threshold"));
3557     modifyPID.setEnabled(abovePIDThreshold.getState());
3558     modifyPID.addActionListener(this);
3559     modifyConservation.setLabel(MessageManager
3560             .getString("label.modify_conservation_threshold"));
3561     modifyConservation.setEnabled(conservationMenuItem.getState());
3562     modifyConservation.addActionListener(this);
3563     annotationColour
3564             .setLabel(MessageManager.getString("action.by_annotation"));
3565     annotationColour.addActionListener(this);
3566
3567     /*
3568      * Configure Calculate menu items and actions
3569      */
3570     sortPairwiseMenuItem
3571             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3572     sortPairwiseMenuItem.addActionListener(this);
3573     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3574     sortIDMenuItem.addActionListener(this);
3575     sortLengthMenuItem
3576             .setLabel(MessageManager.getString("action.by_length"));
3577     sortLengthMenuItem.addActionListener(this);
3578     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3579     sortGroupMenuItem.addActionListener(this);
3580     pairwiseAlignmentMenuItem.setLabel(
3581             MessageManager.getString("action.pairwise_alignment"));
3582     pairwiseAlignmentMenuItem.addActionListener(this);
3583     PCAMenuItem.setLabel(
3584             MessageManager.getString("label.principal_component_analysis"));
3585     PCAMenuItem.addActionListener(this);
3586     autoCalculate = new CheckboxMenuItem(
3587             MessageManager.getString("label.autocalculate_consensus"),
3588             true);
3589     averageDistanceTreeMenuItem.setLabel(
3590             MessageManager.getString("label.average_distance_identity"));
3591     averageDistanceTreeMenuItem.addActionListener(this);
3592     neighbourTreeMenuItem.setLabel(
3593             MessageManager.getString("label.neighbour_joining_identity"));
3594     neighbourTreeMenuItem.addActionListener(this);
3595     avDistanceTreeBlosumMenuItem.setLabel(
3596             MessageManager.getString("label.average_distance_blosum62"));
3597     avDistanceTreeBlosumMenuItem.addActionListener(this);
3598     njTreeBlosumMenuItem
3599             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3600     njTreeBlosumMenuItem.addActionListener(this);
3601     sortByTreeMenu
3602             .setLabel(MessageManager.getString("action.by_tree_order"));
3603     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3604     Menu calculateTreeMenu = new Menu(
3605             MessageManager.getString("action.calculate_tree"));
3606     autoCalculate.addItemListener(this);
3607     sortByTree.addItemListener(this);
3608
3609     /*
3610      * Configure Help menu items and actions
3611      */
3612     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3613     documentation.setLabel(MessageManager.getString("label.documentation"));
3614     documentation.addActionListener(this);
3615     about.setLabel(MessageManager.getString("label.about"));
3616     about.addActionListener(this);
3617
3618     /*
3619      * Add top level menus to frame
3620      */
3621     alignFrameMenuBar.add(fileMenu);
3622     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3623     alignFrameMenuBar.add(editMenu);
3624     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3625     alignFrameMenuBar.add(selectMenu);
3626     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3627     alignFrameMenuBar.add(viewMenu);
3628     Menu annotationsMenu = new Menu(
3629             MessageManager.getString("action.annotations"));
3630     alignFrameMenuBar.add(annotationsMenu);
3631     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3632     alignFrameMenuBar.add(formatMenu);
3633     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3634     alignFrameMenuBar.add(colourMenu);
3635     Menu calculateMenu = new Menu(
3636             MessageManager.getString("action.calculate"));
3637     alignFrameMenuBar.add(calculateMenu);
3638     alignFrameMenuBar.add(helpMenu);
3639
3640     /*
3641      * File menu
3642      */
3643     fileMenu.add(inputText);
3644     fileMenu.add(loadTree);
3645     fileMenu.add(loadAnnotations);
3646     fileMenu.addSeparator();
3647     fileMenu.add(outputTextboxMenu);
3648     fileMenu.add(outputFeatures);
3649     fileMenu.add(outputAnnotations);
3650     if (jalviewServletURL != null)
3651     {
3652       fileMenu.add(loadApplication);
3653     }
3654     fileMenu.addSeparator();
3655     fileMenu.add(closeMenuItem);
3656
3657     /*
3658      * Edit menu
3659      */
3660     editMenu.add(undoMenuItem);
3661     editMenu.add(redoMenuItem);
3662     editMenu.add(cut);
3663     editMenu.add(copy);
3664     pasteMenu.add(pasteNew);
3665     pasteMenu.add(pasteThis);
3666     editMenu.add(pasteMenu);
3667     editMenu.add(delete);
3668     editMenu.addSeparator();
3669     editMenu.add(remove2LeftMenuItem);
3670     editMenu.add(remove2RightMenuItem);
3671     editMenu.add(removeGappedColumnMenuItem);
3672     editMenu.add(removeAllGapsMenuItem);
3673     editMenu.add(removeRedundancyMenuItem);
3674
3675     /*
3676      * Select menu
3677      */
3678     selectMenu.add(findMenuItem);
3679     selectMenu.addSeparator();
3680     selectMenu.add(selectAllSequenceMenuItem);
3681     selectMenu.add(deselectAllSequenceMenuItem);
3682     selectMenu.add(invertSequenceMenuItem);
3683     selectMenu.add(invertColSel);
3684     selectMenu.add(createGroup);
3685     selectMenu.add(unGroup);
3686     selectMenu.add(grpsFromSelection);
3687     selectMenu.add(deleteGroups);
3688     selectMenu.add(annotationColumnSelection);
3689
3690     /*
3691      * View menu
3692      */
3693     viewMenu.add(newView);
3694     viewMenu.addSeparator();
3695     showMenu.add(showColumns);
3696     showMenu.add(showSeqs);
3697     showMenu.add(showAllHidden);
3698     viewMenu.add(showMenu);
3699     hideMenu.add(hideColumns);
3700     hideMenu.add(hideSequences);
3701     hideMenu.add(hideAllSelection);
3702     hideMenu.add(hideAllButSelection);
3703     viewMenu.add(hideMenu);
3704     viewMenu.addSeparator();
3705     viewMenu.add(followMouseOverFlag);
3706     viewMenu.addSeparator();
3707     viewMenu.add(sequenceFeatures);
3708     viewMenu.add(featureSettings);
3709     viewMenu.addSeparator();
3710     viewMenu.add(alProperties);
3711     viewMenu.addSeparator();
3712     viewMenu.add(overviewMenuItem);
3713
3714     /*
3715      * Annotations menu
3716      */
3717     annotationsMenu.add(annotationPanelMenuItem);
3718     annotationsMenu.addSeparator();
3719     annotationsMenu.add(showAlignmentAnnotations);
3720     annotationsMenu.add(showSequenceAnnotations);
3721     annotationsMenu.add(sortAnnBySequence);
3722     annotationsMenu.add(sortAnnByLabel);
3723     annotationsMenu.addSeparator();
3724     autoAnnMenu.add(showAutoFirst);
3725     autoAnnMenu.add(showAutoLast);
3726     autoAnnMenu.addSeparator();
3727     autoAnnMenu.add(applyAutoAnnotationSettings);
3728     autoAnnMenu.add(showConsensusHistogram);
3729     autoAnnMenu.add(showSequenceLogo);
3730     autoAnnMenu.add(normSequenceLogo);
3731     autoAnnMenu.addSeparator();
3732     autoAnnMenu.add(showGroupConservation);
3733     autoAnnMenu.add(showGroupConsensus);
3734     annotationsMenu.add(autoAnnMenu);
3735
3736     /*
3737      * Format menu
3738      */
3739     formatMenu.add(font);
3740     formatMenu.add(seqLimits);
3741     formatMenu.add(wrapMenuItem);
3742     formatMenu.add(scaleAbove);
3743     formatMenu.add(scaleLeft);
3744     formatMenu.add(scaleRight);
3745     formatMenu.add(viewBoxesMenuItem);
3746     formatMenu.add(viewTextMenuItem);
3747     formatMenu.add(colourTextMenuItem);
3748     formatMenu.add(displayNonconservedMenuItem);
3749     formatMenu.add(renderGapsMenuItem);
3750     formatMenu.add(centreColumnLabelFlag);
3751
3752     /*
3753      * Colour menu
3754      */
3755     colourMenu.add(applyToAllGroups);
3756     colourMenu.addSeparator();
3757     colourMenu.add(noColourmenuItem);
3758     colourMenu.add(clustalColour);
3759     colourMenu.add(BLOSUM62Colour);
3760     colourMenu.add(PIDColour);
3761     colourMenu.add(zappoColour);
3762     colourMenu.add(taylorColour);
3763     colourMenu.add(hydrophobicityColour);
3764     colourMenu.add(helixColour);
3765     colourMenu.add(strandColour);
3766     colourMenu.add(turnColour);
3767     colourMenu.add(buriedColour);
3768     colourMenu.add(nucleotideColour);
3769     colourMenu.add(purinePyrimidineColour);
3770     // colourMenu.add(RNAInteractionColour);
3771     colourMenu.add(tcoffeeColour);
3772     colourMenu.add(userDefinedColour);
3773     colourMenu.addSeparator();
3774     colourMenu.add(conservationMenuItem);
3775     colourMenu.add(modifyConservation);
3776     colourMenu.add(abovePIDThreshold);
3777     colourMenu.add(modifyPID);
3778     colourMenu.add(annotationColour);
3779     colourMenu.add(RNAHelixColour);
3780
3781     /*
3782      * Calculate menu
3783      */
3784     sortMenu.add(sortIDMenuItem);
3785     sortMenu.add(sortLengthMenuItem);
3786     sortMenu.add(sortByTreeMenu);
3787     sortMenu.add(sortGroupMenuItem);
3788     sortMenu.add(sortPairwiseMenuItem);
3789     calculateMenu.add(sortMenu);
3790     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3791     calculateTreeMenu.add(neighbourTreeMenuItem);
3792     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3793     calculateTreeMenu.add(njTreeBlosumMenuItem);
3794     calculateMenu.add(calculateTreeMenu);
3795     calculateMenu.addSeparator();
3796     calculateMenu.add(pairwiseAlignmentMenuItem);
3797     calculateMenu.add(PCAMenuItem);
3798     calculateMenu.add(autoCalculate);
3799     calculateMenu.add(sortByTree);
3800
3801     /*
3802      * Help menu
3803      */
3804     helpMenu.add(documentation);
3805     helpMenu.add(about);
3806
3807     /*
3808      * Status bar
3809      */
3810     statusBar.setBackground(Color.white);
3811     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3812     statusBar.setText(MessageManager.getString("label.status_bar"));
3813     this.add(statusBar, BorderLayout.SOUTH);
3814   }
3815
3816   @Override
3817   public void setStatus(String string)
3818   {
3819     statusBar.setText(string);
3820   };
3821
3822   MenuItem featureSettings = new MenuItem();
3823
3824   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3825
3826   MenuItem annotationColour = new MenuItem();
3827
3828   MenuItem annotationColumnSelection = new MenuItem();
3829
3830   MenuItem invertColSel = new MenuItem();
3831
3832   MenuItem showColumns = new MenuItem();
3833
3834   MenuItem showSeqs = new MenuItem();
3835
3836   MenuItem hideColumns = new MenuItem();
3837
3838   MenuItem hideSequences = new MenuItem();
3839
3840   MenuItem hideAllButSelection = new MenuItem();
3841
3842   MenuItem hideAllSelection = new MenuItem();
3843
3844   MenuItem showAllHidden = new MenuItem();
3845
3846   MenuItem newView = new MenuItem();
3847
3848   private CheckboxMenuItem showAlignmentAnnotations;
3849
3850   private CheckboxMenuItem showSequenceAnnotations;
3851
3852   private CheckboxMenuItem sortAnnBySequence;
3853
3854   private CheckboxMenuItem sortAnnByLabel;
3855
3856   private CheckboxMenuItem showAutoFirst;
3857
3858   private CheckboxMenuItem showAutoLast;
3859
3860   private SplitFrame splitFrame;
3861
3862   /**
3863    * Attach the alignFrame panels after embedding menus, if necessary. This used
3864    * to be called setEmbedded, but is now creates the dropdown menus in a
3865    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3866    *
3867    * @param reallyEmbedded
3868    *          true to attach the view to the applet area on the page rather than
3869    *          in a new window
3870    */
3871   public void createAlignFrameWindow(boolean reallyEmbedded)
3872   {
3873     if (reallyEmbedded)
3874     {
3875       embedAlignFrameInApplet(viewport.applet);
3876     }
3877     else
3878     {
3879       // //////
3880       // test and embed menu bar if necessary.
3881       //
3882       if (embedMenuIfNeeded(alignPanel))
3883       {
3884         /*
3885          * adjust for status bar height too. ? pointless as overridden by layout
3886          * manager
3887          */
3888         alignPanel.setSize(getSize().width,
3889                 getSize().height - statusBar.getHeight());
3890       }
3891       add(statusBar, BorderLayout.SOUTH);
3892       add(alignPanel, BorderLayout.CENTER);
3893       // and register with the applet so it can pass external API calls to us
3894       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3895               frameHeight);
3896     }
3897   }
3898
3899   /**
3900    * Add the components of this AlignFrame to the applet container.
3901    *
3902    * @param theApplet
3903    */
3904   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3905   {
3906     // ////
3907     // Explicitly build the embedded menu panel for the on-page applet
3908     //
3909     // view cannot be closed if its actually on the page
3910     fileMenu.remove(closeMenuItem);
3911     fileMenu.remove(3); // Remove Separator
3912     // construct embedded menu, using default font
3913     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3914     // and actually add the components to the applet area
3915     theApplet.setLayout(new BorderLayout());
3916     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3917     theApplet.add(statusBar, BorderLayout.SOUTH);
3918     // TODO should size be left to the layout manager?
3919     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3920             - embeddedMenu.getHeight() - statusBar.getHeight());
3921     theApplet.add(alignPanel, BorderLayout.CENTER);
3922     final AlignFrame me = this;
3923     theApplet.addFocusListener(new FocusListener()
3924     {
3925
3926       @Override
3927       public void focusLost(FocusEvent e)
3928       {
3929         if (theApplet.currentAlignFrame == me)
3930         {
3931           theApplet.currentAlignFrame = null;
3932         }
3933       }
3934
3935       @Override
3936       public void focusGained(FocusEvent e)
3937       {
3938         theApplet.currentAlignFrame = me;
3939       }
3940     });
3941     theApplet.validate();
3942   }
3943
3944   /**
3945    * create a new binding between structures in an existing jmol viewer instance
3946    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3947    * this does not open a new Jmol window, or modify the display of the
3948    * structures in the original jmol window. Note This method doesn't work
3949    * without an additional javascript library to exchange messages between the
3950    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3951    *
3952    * @param viewer
3953    *          JmolViewer instance
3954    * @param sequenceIds
3955    *          - sequence Ids to search for associations
3956    */
3957   public SequenceStructureBinding addStructureViewInstance(
3958           Object jmolviewer, String[] sequenceIds)
3959   {
3960     Viewer viewer = null;
3961     try
3962     {
3963       viewer = (Viewer) jmolviewer;
3964     } catch (ClassCastException ex)
3965     {
3966       System.err.println(
3967               "Unsupported viewer object :" + jmolviewer.getClass());
3968     }
3969     if (viewer == null)
3970     {
3971       System.err.println("Can't use this object as a structure viewer:"
3972               + jmolviewer.getClass());
3973       return null;
3974     }
3975     SequenceI[] seqs = null;
3976     if (sequenceIds == null || sequenceIds.length == 0)
3977     {
3978       seqs = viewport.getAlignment().getSequencesArray();
3979     }
3980     else
3981     {
3982       Vector sqi = new Vector();
3983       AlignmentI al = viewport.getAlignment();
3984       for (int sid = 0; sid < sequenceIds.length; sid++)
3985       {
3986         SequenceI sq = al.findName(sequenceIds[sid]);
3987         if (sq != null)
3988         {
3989           sqi.addElement(sq);
3990         }
3991       }
3992       if (sqi.size() > 0)
3993       {
3994         seqs = new SequenceI[sqi.size()];
3995         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3996         {
3997           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3998         }
3999       }
4000       else
4001       {
4002         return null;
4003       }
4004     }
4005     AAStructureBindingModel jmv = null;
4006     // TODO: search for a jmv that involves viewer
4007     if (jmv == null)
4008     { // create a new viewer/jalview binding.
4009       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4010     }
4011     return jmv;
4012
4013   }
4014
4015   /**
4016    * bind a pdb file to a sequence in the current view
4017    *
4018    * @param sequenceId
4019    *          - sequenceId within the dataset.
4020    * @param pdbEntryString
4021    *          - the short name for the PDB file
4022    * @param pdbFile
4023    *          - pdb file - either a URL or a valid PDB file.
4024    * @return true if binding was as success TODO: consider making an exception
4025    *         structure for indicating when PDB parsing or sequenceId location
4026    *         fails.
4027    */
4028   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4029           String pdbFile)
4030   {
4031     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4032     boolean needtoadd = false;
4033     if (toaddpdb != null)
4034     {
4035       Vector pdbe = toaddpdb.getAllPDBEntries();
4036       PDBEntry pdbentry = null;
4037       if (pdbe != null && pdbe.size() > 0)
4038       {
4039         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4040         {
4041           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4042           if (!pdbentry.getId().equals(pdbEntryString)
4043                   && !pdbentry.getFile().equals(pdbFile))
4044           {
4045             pdbentry = null;
4046           }
4047           else
4048           {
4049             continue;
4050           }
4051         }
4052       }
4053       if (pdbentry == null)
4054       {
4055         pdbentry = new PDBEntry();
4056         pdbentry.setId(pdbEntryString);
4057         pdbentry.setFile(pdbFile);
4058         needtoadd = true; // add this new entry to sequence.
4059       }
4060       // resolve data source
4061       // TODO: this code should be a refactored to an io package
4062       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4063               FileFormat.PDB);
4064       if (protocol == null)
4065       {
4066         return false;
4067       }
4068       if (needtoadd)
4069       {
4070         pdbentry.setProperty("protocol", protocol);
4071         toaddpdb.addPDBId(pdbentry);
4072         alignPanel.getStructureSelectionManager()
4073                 .registerPDBEntry(pdbentry);
4074       }
4075     }
4076     return true;
4077   }
4078
4079   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4080   {
4081     if (seqs != null)
4082     {
4083       Vector sequences = new Vector();
4084       for (int i = 0; i < seqs.length; i++)
4085       {
4086         if (seqs[i] != null)
4087         {
4088           sequences
4089                   .addElement(new Object[]
4090                   { seqs[i], (chains != null) ? chains[i] : null });
4091         }
4092       }
4093       seqs = new SequenceI[sequences.size()];
4094       chains = new String[sequences.size()];
4095       for (int i = 0, isize = sequences.size(); i < isize; i++)
4096       {
4097         Object[] oj = (Object[]) sequences.elementAt(i);
4098
4099         seqs[i] = (SequenceI) oj[0];
4100         chains[i] = (String) oj[1];
4101       }
4102     }
4103     return new Object[] { seqs, chains };
4104
4105   }
4106
4107   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4108           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4109   {
4110     // Scrub any null sequences from the array
4111     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4112     seqs = (SequenceI[]) sqch[0];
4113     chains = (String[]) sqch[1];
4114     if (seqs == null || seqs.length == 0)
4115     {
4116       System.err.println(
4117               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4118     }
4119     if (protocol == null)
4120     {
4121       String sourceType = (String) pdb.getProperty("protocol");
4122       try
4123       {
4124         protocol = DataSourceType.valueOf(sourceType);
4125       } catch (IllegalArgumentException e)
4126       {
4127         // ignore
4128       }
4129       if (protocol == null)
4130       {
4131         System.err.println("Couldn't work out protocol to open structure: "
4132                 + pdb.getId());
4133         return;
4134       }
4135     }
4136     if (applet.useXtrnalSviewer)
4137     {
4138       // register the association(s) and quit, don't create any windows.
4139       if (StructureSelectionManager.getStructureSelectionManager(applet)
4140               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4141       {
4142         System.err.println("Failed to map " + pdb.getFile() + " ("
4143                 + protocol + ") to any sequences");
4144       }
4145       return;
4146     }
4147     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4148     {
4149       // can only do alignments with Jmol
4150       // find the last jmol window assigned to this alignment
4151       AppletJmol ajm = null, tajm;
4152       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4153       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4154       {
4155         tajm = (AppletJmol) jmols.elementAt(i);
4156         if (tajm.ap.alignFrame == this)
4157         {
4158           ajm = tajm;
4159           break;
4160         }
4161       }
4162       if (ajm != null)
4163       {
4164         System.err.println(
4165                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4166         // try and add the pdb structure
4167         // ajm.addS
4168         ajm = null;
4169       }
4170     }
4171     // otherwise, create a new window
4172     if (applet.jmolAvailable)
4173     {
4174       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4175       applet.lastFrameX += 40;
4176       applet.lastFrameY += 40;
4177     }
4178     else
4179     {
4180       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4181     }
4182
4183   }
4184
4185   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4186           SequenceI[][] seqs, String[][] chains, String[] protocols)
4187   {
4188     // TODO Auto-generated method stub
4189     System.err.println("Aligned Structure View: Not yet implemented.");
4190   }
4191
4192   /**
4193    * modify the current selection, providing the user has not made a selection
4194    * already.
4195    *
4196    * @param sel
4197    *          - sequences from this alignment
4198    * @param csel
4199    *          - columns to be selected on the alignment
4200    */
4201   public void select(SequenceGroup sel, ColumnSelection csel,
4202           HiddenColumns hidden)
4203   {
4204     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4205   }
4206
4207   public void scrollTo(int row, int column)
4208   {
4209     alignPanel.seqPanel.scrollTo(row, column);
4210   }
4211
4212   public void scrollToRow(int row)
4213   {
4214     alignPanel.seqPanel.scrollToRow(row);
4215   }
4216
4217   public void scrollToColumn(int column)
4218   {
4219     alignPanel.seqPanel.scrollToColumn(column);
4220   }
4221
4222   /**
4223    * @return the alignments unique ID.
4224    */
4225   public String getSequenceSetId()
4226   {
4227     return viewport.getSequenceSetId();
4228   }
4229
4230   /**
4231    * Load the (T-Coffee) score file from the specified url
4232    *
4233    * @param source
4234    *          File/URL/T-COFFEE score file contents
4235    * @throws IOException
4236    * @return true if alignment was annotated with data from source
4237    */
4238   public boolean loadScoreFile(String source) throws IOException
4239   {
4240
4241     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4242             AppletFormatAdapter.checkProtocol(source));
4243     if (!file.isValid())
4244     {
4245       // TODO: raise dialog for gui
4246       System.err.println("Problems parsing T-Coffee scores: "
4247               + file.getWarningMessage());
4248       System.err.println("Origin was:\n" + source);
4249       return false;
4250     }
4251
4252     /*
4253      * check that the score matrix matches the alignment dimensions
4254      */
4255     AlignmentI aln;
4256     if ((aln = viewport.getAlignment()) != null
4257             && (aln.getHeight() != file.getHeight()
4258                     || aln.getWidth() != file.getWidth()))
4259     {
4260       // TODO: raise a dialog box here rather than bomb out.
4261       System.err.println(
4262               "The scores matrix does not match the alignment dimensions");
4263
4264     }
4265
4266     // TODO add parameter to indicate if matching should be done
4267     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4268     {
4269       alignPanel.fontChanged();
4270       tcoffeeColour.setEnabled(true);
4271       // switch to this color
4272       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4273       return true;
4274     }
4275     else
4276     {
4277       System.err.println("Problems resolving T-Coffee scores:");
4278       if (file.getWarningMessage() != null)
4279       {
4280         System.err.println(file.getWarningMessage());
4281       }
4282     }
4283     return false;
4284   }
4285
4286   public SplitFrame getSplitFrame()
4287   {
4288     return this.splitFrame;
4289   }
4290
4291   public void setSplitFrame(SplitFrame sf)
4292   {
4293     this.splitFrame = sf;
4294   }
4295
4296   // may not need this
4297   @Override
4298   public void setShowSeqFeatures(boolean b)
4299   {
4300     // showSeqFeatures.setSelected(b);
4301     viewport.setShowSequenceFeatures(b);
4302
4303   }
4304
4305   @Override
4306   public void setMenusForViewport()
4307   {
4308     // setMenusFromViewport(viewport);
4309
4310   }
4311
4312   @Override
4313   public void refreshFeatureUI(boolean enableIfNecessary)
4314   {
4315     if (enableIfNecessary)
4316     {
4317       sequenceFeatures.setState(true);
4318       alignPanel.av.setShowSequenceFeatures(true);
4319     }
4320   }
4321
4322   @Override
4323   public FeatureSettingsControllerI getFeatureSettingsUI()
4324   {
4325     return alignPanel.av.featureSettings;
4326   }
4327
4328 }