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, 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, 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     // TODO: repaint flags set only if the keystroke warrants it
 695     alignPanel.paintAlignment(true, true);
 696   }
 697
 698   /**
 699    * called by key handler and the hide all/show all menu items
 700    *
 701    * @param toggleSeqs
 702    * @param toggleCols
 703    */
 704   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 705   {
 706     boolean hide = false;
 707     SequenceGroup sg = viewport.getSelectionGroup();
 708     if (!toggleSeqs && !toggleCols)
 709     {
 710       // Hide everything by the current selection - this is a hack - we do the
 711       // invert and then hide
 712       // first check that there will be visible columns after the invert.
 713       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 714               && sg.getStartRes() <= sg.getEndRes()))
 715       {
 716         // now invert the sequence set, if required - empty selection implies
 717         // that no hiding is required.
 718         if (sg != null)
 719         {
 720           invertSequenceMenuItem_actionPerformed();
 721           sg = viewport.getSelectionGroup();
 722           toggleSeqs = true;
 723
 724         }
 725         viewport.expandColSelection(sg, true);
 726         // finally invert the column selection and get the new sequence
 727         // selection and indicate it should be hidden.
 728         invertColSel_actionPerformed();
 729         toggleCols = true;
 730       }
 731     }
 732
 733     if (toggleSeqs)
 734     {
 735       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 736       {
 737         hide = true;
 738         viewport.hideAllSelectedSeqs();
 739       }
 740       else if (!(toggleCols && viewport.hasSelectedColumns()))
 741       {
 742         viewport.showAllHiddenSeqs();
 743       }
 744     }
 745
 746     if (toggleCols)
 747     {
 748       if (viewport.hasSelectedColumns())
 749       {
 750         viewport.hideSelectedColumns();
 751         if (!toggleSeqs)
 752         {
 753           viewport.setSelectionGroup(sg);
 754         }
 755       }
 756       else if (!hide)
 757       {
 758         viewport.showAllHiddenColumns();
 759       }
 760       viewport.sendSelection();
 761     }
 762   }
 763
 764   @Override
 765   public void keyReleased(KeyEvent evt)
 766   {
 767   }
 768
 769   @Override
 770   public void keyTyped(KeyEvent evt)
 771   {
 772   }
 773
 774   @Override
 775   public void itemStateChanged(ItemEvent evt)
 776   {
 777     final Object source = evt.getSource();
 778     if (source == displayNonconservedMenuItem)
 779     {
 780       displayNonconservedMenuItem_actionPerformed();
 781     }
 782     else if (source == colourTextMenuItem)
 783     {
 784       colourTextMenuItem_actionPerformed();
 785     }
 786     else if (source == wrapMenuItem)
 787     {
 788       wrapMenuItem_actionPerformed();
 789     }
 790     else if (source == scaleAbove)
 791     {
 792       viewport.setScaleAboveWrapped(scaleAbove.getState());
 793     }
 794     else if (source == scaleLeft)
 795     {
 796       viewport.setScaleLeftWrapped(scaleLeft.getState());
 797     }
 798     else if (source == scaleRight)
 799     {
 800       viewport.setScaleRightWrapped(scaleRight.getState());
 801     }
 802     else if (source == seqLimits)
 803     {
 804       seqLimits_itemStateChanged();
 805     }
 806     else if (source == viewBoxesMenuItem)
 807     {
 808       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 809     }
 810     else if (source == viewTextMenuItem)
 811     {
 812       viewport.setShowText(viewTextMenuItem.getState());
 813     }
 814     else if (source == renderGapsMenuItem)
 815     {
 816       viewport.setRenderGaps(renderGapsMenuItem.getState());
 817     }
 818     else if (source == annotationPanelMenuItem)
 819     {
 820       boolean showAnnotations = annotationPanelMenuItem.getState();
 821       showAlignmentAnnotations.setEnabled(showAnnotations);
 822       showSequenceAnnotations.setEnabled(showAnnotations);
 823       viewport.setShowAnnotation(showAnnotations);
 824       alignPanel.setAnnotationVisible(showAnnotations);
 825     }
 826     else if (source == sequenceFeatures)
 827     {
 828       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 829       alignPanel.seqPanel.seqCanvas.repaint();
 830     }
 831     else if (source == showAlignmentAnnotations)
 832     {
 833       setAnnotationsVisibility();
 834     }
 835     else if (source == showSequenceAnnotations)
 836     {
 837       setAnnotationsVisibility();
 838     }
 839     else if (source == sortAnnBySequence)
 840     {
 841       boolean newState = sortAnnBySequence.getState();
 842       sortAnnByLabel.setState(false);
 843       setAnnotationSortOrder(
 844               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 845                       : SequenceAnnotationOrder.NONE);
 846       setViewportAnnotationOrder();
 847     }
 848     else if (source == sortAnnByLabel)
 849     {
 850       boolean newState = sortAnnByLabel.getState();
 851       sortAnnBySequence.setState(false);
 852       setAnnotationSortOrder(
 853               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 854                       : SequenceAnnotationOrder.NONE);
 855       setViewportAnnotationOrder();
 856     }
 857     else if (source == showAutoFirst)
 858     {
 859       showAutoLast.setState(!showAutoFirst.getState());
 860       setShowAutoCalculatedAbove(showAutoFirst.getState());
 861       setViewportAnnotationOrder();
 862     }
 863     else if (source == showAutoLast)
 864     {
 865       showAutoFirst.setState(!showAutoLast.getState());
 866       setShowAutoCalculatedAbove(showAutoFirst.getState());
 867       setViewportAnnotationOrder();
 868     }
 869     else if (source == conservationMenuItem)
 870     {
 871       conservationMenuItem_actionPerformed();
 872     }
 873     else if (source == abovePIDThreshold)
 874     {
 875       abovePIDThreshold_actionPerformed();
 876     }
 877     else if (source == applyToAllGroups)
 878     {
 879       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 880     }
 881     else if (source == autoCalculate)
 882     {
 883       viewport.autoCalculateConsensus = autoCalculate.getState();
 884     }
 885     else if (source == sortByTree)
 886     {
 887       viewport.sortByTree = sortByTree.getState();
 888     }
 889     else if (source == this.centreColumnLabelFlag)
 890     {
 891       centreColumnLabelFlag_stateChanged();
 892     }
 893     else if (source == this.followMouseOverFlag)
 894     {
 895       mouseOverFlag_stateChanged();
 896     }
 897     else if (source == showGroupConsensus)
 898     {
 899       showGroupConsensus_actionPerformed();
 900     }
 901     else if (source == showGroupConservation)
 902     {
 903       showGroupConservation_actionPerformed();
 904     }
 905     else if (source == showSequenceLogo)
 906     {
 907       showSequenceLogo_actionPerformed();
 908     }
 909     else if (source == normSequenceLogo)
 910     {
 911       normSequenceLogo_actionPerformed();
 912     }
 913     else if (source == showConsensusHistogram)
 914     {
 915       showConsensusHistogram_actionPerformed();
 916     }
 917     else if (source == applyAutoAnnotationSettings)
 918     {
 919       applyAutoAnnotationSettings_actionPerformed();
 920     }
 921     // TODO: repaint flags set only if warranted
 922     alignPanel.paintAlignment(true, true);
 923   }
 924
 925   /**
 926    * Set the visibility state of sequence-related and/or alignment-related
 927    * annotations depending on checkbox selections, and repaint.
 928    *
 929    * @param visible
 930    */
 931   private void setAnnotationsVisibility()
 932   {
 933     boolean showForAlignment = showAlignmentAnnotations.getState();
 934     boolean showForSequences = showSequenceAnnotations.getState();
 935     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 936     {
 937       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 938               .getAlignmentAnnotation())
 939       {
 940         boolean visible = (aa.sequenceRef == null ? showForAlignment
 941                 : showForSequences);
 942         aa.visible = visible;
 943       }
 944     }
 945     alignPanel.validateAnnotationDimensions(true);
 946     validate();
 947     repaint();
 948   }
 949
 950   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 951   {
 952     this.annotationSortOrder = order;
 953   }
 954
 955   /**
 956    * Set flags on the viewport that control annotation ordering
 957    */
 958   private void setViewportAnnotationOrder()
 959   {
 960     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 961     this.alignPanel.av
 962             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 963   }
 964
 965   private void setShowAutoCalculatedAbove(boolean showAbove)
 966   {
 967     this.showAutoCalculatedAbove = showAbove;
 968   }
 969
 970   private void mouseOverFlag_stateChanged()
 971   {
 972     viewport.setFollowHighlight(followMouseOverFlag.getState());
 973     // TODO: could kick the scrollTo mechanism to reset view for current
 974     // searchresults.
 975   }
 976
 977   private void centreColumnLabelFlag_stateChanged()
 978   {
 979     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 980     this.alignPanel.annotationPanel.repaint();
 981   }
 982
 983   @Override
 984   public void actionPerformed(ActionEvent evt)
 985   {
 986     viewport.applet.currentAlignFrame = this;
 987
 988     Object source = evt.getSource();
 989
 990     if (source == inputText)
 991     {
 992       inputText_actionPerformed();
 993     }
 994     else if (source == loadTree)
 995     {
 996       loadTree_actionPerformed();
 997     }
 998     else if (source == loadApplication)
 999     {
1000       launchFullApplication();
1001     }
1002     else if (source == loadAnnotations)
1003     {
1004       loadAnnotations();
1005     }
1006     else if (source == outputAnnotations)
1007     {
1008       outputAnnotations(true);
1009     }
1010     else if (source == outputFeatures)
1011     {
1012       outputFeatures(true, "Jalview");
1013     }
1014     else if (source == closeMenuItem)
1015     {
1016       closeMenuItem_actionPerformed();
1017     }
1018     else if (source == copy)
1019     {
1020       copy_actionPerformed();
1021     }
1022     else if (source == undoMenuItem)
1023     {
1024       undoMenuItem_actionPerformed();
1025     }
1026     else if (source == redoMenuItem)
1027     {
1028       redoMenuItem_actionPerformed();
1029     }
1030     else if (source == inputText)
1031     {
1032       inputText_actionPerformed();
1033     }
1034     else if (source == closeMenuItem)
1035     {
1036       closeMenuItem_actionPerformed();
1037     }
1038     else if (source == undoMenuItem)
1039     {
1040       undoMenuItem_actionPerformed();
1041     }
1042     else if (source == redoMenuItem)
1043     {
1044       redoMenuItem_actionPerformed();
1045     }
1046     else if (source == copy)
1047     {
1048       copy_actionPerformed();
1049     }
1050     else if (source == pasteNew)
1051     {
1052       pasteNew_actionPerformed();
1053     }
1054     else if (source == pasteThis)
1055     {
1056       pasteThis_actionPerformed();
1057     }
1058     else if (source == cut)
1059     {
1060       cut_actionPerformed();
1061     }
1062     else if (source == delete)
1063     {
1064       delete_actionPerformed();
1065     }
1066     else if (source == createGroup)
1067     {
1068       createGroup_actionPerformed();
1069     }
1070     else if (source == unGroup)
1071     {
1072       unGroup_actionPerformed();
1073     }
1074     else if (source == grpsFromSelection)
1075     {
1076       makeGrpsFromSelection_actionPerformed();
1077     }
1078     else if (source == deleteGroups)
1079     {
1080       deleteGroups_actionPerformed();
1081     }
1082     else if (source == selectAllSequenceMenuItem)
1083     {
1084       selectAllSequenceMenuItem_actionPerformed();
1085     }
1086     else if (source == deselectAllSequenceMenuItem)
1087     {
1088       deselectAllSequenceMenuItem_actionPerformed();
1089     }
1090     else if (source == invertSequenceMenuItem)
1091     {
1092       invertSequenceMenuItem_actionPerformed();
1093       // uncomment to slave sequence selections in split frame
1094       // viewport.sendSelection();
1095     }
1096     else if (source == invertColSel)
1097     {
1098       viewport.invertColumnSelection();
1099       alignPanel.paintAlignment(false, false);
1100       viewport.sendSelection();
1101     }
1102     else if (source == remove2LeftMenuItem)
1103     {
1104       trimAlignment(true);
1105     }
1106     else if (source == remove2RightMenuItem)
1107     {
1108       trimAlignment(false);
1109     }
1110     else if (source == removeGappedColumnMenuItem)
1111     {
1112       removeGappedColumnMenuItem_actionPerformed();
1113     }
1114     else if (source == removeAllGapsMenuItem)
1115     {
1116       removeAllGapsMenuItem_actionPerformed();
1117     }
1118     else if (source == findMenuItem)
1119     {
1120       findMenuItem_actionPerformed();
1121     }
1122     else if (source == font)
1123     {
1124       new FontChooser(alignPanel);
1125     }
1126     else if (source == newView)
1127     {
1128       newView(null);
1129     }
1130     else if (source == showColumns)
1131     {
1132       viewport.showAllHiddenColumns();
1133       alignPanel.paintAlignment(true, true);
1134       viewport.sendSelection();
1135     }
1136     else if (source == showSeqs)
1137     {
1138       viewport.showAllHiddenSeqs();
1139       alignPanel.paintAlignment(true, true);
1140       // uncomment if we want to slave sequence selections in split frame
1141       // viewport.sendSelection();
1142     }
1143     else if (source == hideColumns)
1144     {
1145       viewport.hideSelectedColumns();
1146       alignPanel.paintAlignment(true, true);
1147       viewport.sendSelection();
1148     }
1149     else if (source == hideSequences
1150             && viewport.getSelectionGroup() != null)
1151     {
1152       viewport.hideAllSelectedSeqs();
1153       alignPanel.paintAlignment(true, true);
1154       // uncomment if we want to slave sequence selections in split frame
1155       // viewport.sendSelection();
1156     }
1157     else if (source == hideAllButSelection)
1158     {
1159       toggleHiddenRegions(false, false);
1160       alignPanel.paintAlignment(true, true);
1161       viewport.sendSelection();
1162     }
1163     else if (source == hideAllSelection)
1164     {
1165       SequenceGroup sg = viewport.getSelectionGroup();
1166       viewport.expandColSelection(sg, false);
1167       viewport.hideAllSelectedSeqs();
1168       viewport.hideSelectedColumns();
1169       alignPanel.paintAlignment(true, true);
1170       viewport.sendSelection();
1171     }
1172     else if (source == showAllHidden)
1173     {
1174       viewport.showAllHiddenColumns();
1175       viewport.showAllHiddenSeqs();
1176       alignPanel.paintAlignment(true, true);
1177       viewport.sendSelection();
1178     }
1179     else if (source == showGroupConsensus)
1180     {
1181       showGroupConsensus_actionPerformed();
1182     }
1183     else if (source == showGroupConservation)
1184     {
1185       showGroupConservation_actionPerformed();
1186     }
1187     else if (source == showSequenceLogo)
1188     {
1189       showSequenceLogo_actionPerformed();
1190     }
1191     else if (source == normSequenceLogo)
1192     {
1193       normSequenceLogo_actionPerformed();
1194     }
1195     else if (source == showConsensusHistogram)
1196     {
1197       showConsensusHistogram_actionPerformed();
1198     }
1199     else if (source == applyAutoAnnotationSettings)
1200     {
1201       applyAutoAnnotationSettings_actionPerformed();
1202     }
1203     else if (source == featureSettings)
1204     {
1205       new FeatureSettings(alignPanel);
1206     }
1207     else if (source == alProperties)
1208     {
1209       StringBuffer contents = new jalview.io.AlignmentProperties(
1210               viewport.getAlignment()).formatAsString();
1211       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212       cap.setText(contents.toString());
1213       Frame frame = new Frame();
1214       frame.add(cap);
1215       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1216               .formatMessage("label.alignment_properties", new String[]
1217               { getTitle() }), 400, 250);
1218     }
1219     else if (source == overviewMenuItem)
1220     {
1221       overviewMenuItem_actionPerformed();
1222     }
1223     else if (source == noColourmenuItem)
1224     {
1225       changeColour(null);
1226     }
1227     else if (source == clustalColour)
1228     {
1229       abovePIDThreshold.setState(false);
1230       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1231     }
1232     else if (source == zappoColour)
1233     {
1234       changeColour(new ZappoColourScheme());
1235     }
1236     else if (source == taylorColour)
1237     {
1238       changeColour(new TaylorColourScheme());
1239     }
1240     else if (source == hydrophobicityColour)
1241     {
1242       changeColour(new HydrophobicColourScheme());
1243     }
1244     else if (source == helixColour)
1245     {
1246       changeColour(new HelixColourScheme());
1247     }
1248     else if (source == strandColour)
1249     {
1250       changeColour(new StrandColourScheme());
1251     }
1252     else if (source == turnColour)
1253     {
1254       changeColour(new TurnColourScheme());
1255     }
1256     else if (source == buriedColour)
1257     {
1258       changeColour(new BuriedColourScheme());
1259     }
1260     else if (source == nucleotideColour)
1261     {
1262       changeColour(new NucleotideColourScheme());
1263     }
1264     else if (source == purinePyrimidineColour)
1265     {
1266       changeColour(new PurinePyrimidineColourScheme());
1267     }
1268     // else if (source == RNAInteractionColour)
1269     // {
1270     // changeColour(new RNAInteractionColourScheme());
1271     // }
1272     else if (source == RNAHelixColour)
1273     {
1274       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1275       // new RNAHelicesColourChooser(viewport, alignPanel);
1276     }
1277     else if (source == modifyPID)
1278     {
1279       modifyPID_actionPerformed();
1280     }
1281     else if (source == modifyConservation)
1282     {
1283       modifyConservation_actionPerformed();
1284     }
1285     else if (source == userDefinedColour)
1286     {
1287       new UserDefinedColours(alignPanel, null);
1288     }
1289     else if (source == PIDColour)
1290     {
1291       changeColour(new PIDColourScheme());
1292     }
1293     else if (source == BLOSUM62Colour)
1294     {
1295       changeColour(new Blosum62ColourScheme());
1296     }
1297     else if (source == tcoffeeColour)
1298     {
1299       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1300     }
1301     else if (source == annotationColour)
1302     {
1303       new AnnotationColourChooser(viewport, alignPanel);
1304     }
1305     else if (source == annotationColumnSelection)
1306     {
1307       new AnnotationColumnChooser(viewport, alignPanel);
1308     }
1309     else if (source == sortPairwiseMenuItem)
1310     {
1311       sortPairwiseMenuItem_actionPerformed();
1312     }
1313     else if (source == sortIDMenuItem)
1314     {
1315       sortIDMenuItem_actionPerformed();
1316     }
1317     else if (source == sortLengthMenuItem)
1318     {
1319       sortLengthMenuItem_actionPerformed();
1320     }
1321     else if (source == sortGroupMenuItem)
1322     {
1323       sortGroupMenuItem_actionPerformed();
1324     }
1325     else if (source == removeRedundancyMenuItem)
1326     {
1327       removeRedundancyMenuItem_actionPerformed();
1328     }
1329     else if (source == pairwiseAlignmentMenuItem)
1330     {
1331       pairwiseAlignmentMenuItem_actionPerformed();
1332     }
1333     else if (source == PCAMenuItem)
1334     {
1335       PCAMenuItem_actionPerformed();
1336     }
1337     else if (source == averageDistanceTreeMenuItem)
1338     {
1339       averageDistanceTreeMenuItem_actionPerformed();
1340     }
1341     else if (source == neighbourTreeMenuItem)
1342     {
1343       neighbourTreeMenuItem_actionPerformed();
1344     }
1345     else if (source == njTreeBlosumMenuItem)
1346     {
1347       njTreeBlosumMenuItem_actionPerformed();
1348     }
1349     else if (source == avDistanceTreeBlosumMenuItem)
1350     {
1351       avTreeBlosumMenuItem_actionPerformed();
1352     }
1353     else if (source == documentation)
1354     {
1355       documentation_actionPerformed();
1356     }
1357     else if (source == about)
1358     {
1359       about_actionPerformed();
1360     }
1361
1362   }
1363
1364   public void inputText_actionPerformed()
1365   {
1366     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1367     Frame frame = new Frame();
1368     frame.add(cap);
1369     jalview.bin.JalviewLite.addFrame(frame,
1370             MessageManager.getString("label.input_cut_paste"), 500, 500);
1371   }
1372
1373   protected void outputText_actionPerformed(ActionEvent e)
1374   {
1375     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376     Frame frame = new Frame();
1377     frame.add(cap);
1378     JalviewLite.addFrame(frame, MessageManager
1379             .formatMessage("label.alignment_output_command", new Object[]
1380             { e.getActionCommand() }), 600, 500);
1381
1382     FileFormatI fileFormat = FileFormats.getInstance()
1383             .forName(e.getActionCommand());
1384     cap.setText(
1385             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1386                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1387   }
1388
1389   public void loadAnnotations()
1390   {
1391     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1392     cap.setText(MessageManager
1393             .getString("label.paste_features_annotations_Tcoffee_here"));
1394     cap.setAnnotationImport();
1395     Frame frame = new Frame();
1396     frame.add(cap);
1397     jalview.bin.JalviewLite.addFrame(frame,
1398             MessageManager.getString("action.paste_annotations"), 400, 300);
1399
1400   }
1401
1402   public String outputAnnotations(boolean displayTextbox)
1403   {
1404     String annotation = new AnnotationFile()
1405             .printAnnotationsForView(viewport);
1406
1407     if (displayTextbox)
1408     {
1409       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1410       Frame frame = new Frame();
1411       frame.add(cap);
1412       jalview.bin.JalviewLite.addFrame(frame,
1413               MessageManager.getString("label.annotations"), 600, 500);
1414       cap.setText(annotation);
1415     }
1416
1417     return annotation;
1418   }
1419
1420   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1421   {
1422     if (alignPanel.getFeatureRenderer() != null
1423             && viewport.getFeaturesDisplayed() != null)
1424     {
1425       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1426
1427     }
1428     return null;
1429   }
1430
1431   private List<String> getDisplayedFeatureGroups()
1432   {
1433     if (alignPanel.getFeatureRenderer() != null
1434             && viewport.getFeaturesDisplayed() != null)
1435     {
1436       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1437
1438     }
1439     return null;
1440   }
1441
1442   public String outputFeatures(boolean displayTextbox, String format)
1443   {
1444     String features;
1445     FeaturesFile formatter = new FeaturesFile();
1446     if (format.equalsIgnoreCase("Jalview"))
1447     {
1448       features = formatter.printJalviewFormat(viewport.getAlignment()
1449               .getSequencesArray(), getDisplayedFeatureCols(),
1450               getDisplayedFeatureGroups(), true);
1451     }
1452     else
1453     {
1454       features = formatter.printGffFormat(viewport.getAlignment()
1455               .getSequencesArray(), getDisplayedFeatureCols(),
1456               getDisplayedFeatureGroups(), true);
1457     }
1458
1459     if (displayTextbox)
1460     {
1461       boolean frimport = false;
1462       if (features == null || features.equals("No Features Visible"))
1463       {
1464         features = "# No features visible - paste some and import them here.";
1465         frimport = true;
1466       }
1467
1468       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1469       if (frimport)
1470       {
1471         cap.setAnnotationImport();
1472       }
1473       Frame frame = new Frame();
1474       frame.add(cap);
1475       jalview.bin.JalviewLite.addFrame(frame,
1476               MessageManager.getString("label.features"), 600, 500);
1477       cap.setText(features);
1478     }
1479     else
1480     {
1481       if (features == null)
1482       {
1483         features = "";
1484       }
1485     }
1486
1487     return features;
1488   }
1489
1490   void launchFullApplication()
1491   {
1492     StringBuffer url = new StringBuffer(jalviewServletURL);
1493
1494     // allow servlet parameters to be passed in applet parameter
1495     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1496             : "?";
1497     url.append(firstSep);
1498
1499     url.append(
1500             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1501
1502     if (viewport.applet.getParameter("features") != null)
1503     {
1504       url.append("&features=");
1505       url.append(appendProtocol(viewport.applet.getParameter("features")));
1506     }
1507
1508     if (viewport.applet.getParameter("annotations") != null)
1509     {
1510       url.append("&annotations=");
1511       url.append(
1512               appendProtocol(viewport.applet.getParameter("annotations")));
1513     }
1514
1515     if (viewport.applet.getParameter("jnetfile") != null
1516             || viewport.applet.getParameter("jpredfile") != null)
1517     {
1518       url.append("&annotations=");
1519       url.append(appendProtocol(
1520               viewport.applet.getParameter("jnetfile") != null
1521                       ? viewport.applet.getParameter("jnetfile")
1522                       : viewport.applet.getParameter("jpredfile")));
1523     }
1524
1525     if (viewport.applet.getParameter("defaultColour") != null)
1526     {
1527       url.append("&colour=" + removeWhiteSpace(
1528               viewport.applet.getParameter("defaultColour")));
1529     }
1530
1531     if (viewport.applet.getParameter("userDefinedColour") != null)
1532     {
1533       url.append("&colour=" + removeWhiteSpace(
1534               viewport.applet.getParameter("userDefinedColour")));
1535     }
1536     if (viewport.applet.getParameter("tree") != null)
1537     {
1538       url.append("&tree="
1539               + appendProtocol(viewport.applet.getParameter("tree")));
1540     }
1541     if (viewport.applet.getParameter("treeFile") != null)
1542     {
1543       url.append("&tree="
1544               + appendProtocol(viewport.applet.getParameter("treeFile")));
1545     }
1546
1547     showURL(url.toString(), "FULL_APP");
1548   }
1549
1550   String removeWhiteSpace(String colour)
1551   {
1552     StringBuffer sb = new StringBuffer();
1553     for (int i = 0; i < colour.length(); i++)
1554     {
1555       if (Character.isWhitespace(colour.charAt(i)))
1556       {
1557         sb.append("%20");
1558       }
1559       else
1560       {
1561         sb.append(colour.charAt(i));
1562       }
1563     }
1564
1565     return sb.toString();
1566   }
1567
1568   String appendProtocol(String url)
1569   {
1570     try
1571     {
1572       new URL(url);
1573       url = URLEncoder.encode(url);
1574     }
1575     /*
1576      * When we finally deprecate 1.1 compatibility, we can start to use
1577      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1578      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1579      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1580      * ex.printStackTrace(); }
1581      */
1582     catch (java.net.MalformedURLException ex)
1583     {
1584       url = viewport.applet.getCodeBase() + url;
1585     }
1586     return url;
1587   }
1588
1589   public void closeMenuItem_actionPerformed()
1590   {
1591     PaintRefresher.RemoveComponent(alignPanel);
1592     if (alignPanel.seqPanel != null
1593             && alignPanel.seqPanel.seqCanvas != null)
1594     {
1595       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1596     }
1597     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1598     {
1599       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1600     }
1601
1602     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1603     {
1604       System.exit(0);
1605     }
1606     else
1607     {
1608     }
1609     viewport = null;
1610     alignPanel = null;
1611     this.dispose();
1612   }
1613
1614   /**
1615    * TODO: JAL-1104
1616    */
1617   void updateEditMenuBar()
1618   {
1619
1620     if (viewport.getHistoryList().size() > 0)
1621     {
1622       undoMenuItem.setEnabled(true);
1623       CommandI command = viewport.getHistoryList().peek();
1624       undoMenuItem.setLabel(MessageManager
1625               .formatMessage("label.undo_command", new Object[]
1626               { command.getDescription() }));
1627     }
1628     else
1629     {
1630       undoMenuItem.setEnabled(false);
1631       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1632     }
1633
1634     if (viewport.getRedoList().size() > 0)
1635     {
1636       redoMenuItem.setEnabled(true);
1637
1638       CommandI command = viewport.getRedoList().peek();
1639       redoMenuItem.setLabel(MessageManager
1640               .formatMessage("label.redo_command", new Object[]
1641               { command.getDescription() }));
1642     }
1643     else
1644     {
1645       redoMenuItem.setEnabled(false);
1646       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1647     }
1648   }
1649
1650   /**
1651    * TODO: JAL-1104
1652    */
1653   @Override
1654   public void addHistoryItem(CommandI command)
1655   {
1656     if (command.getSize() > 0)
1657     {
1658       viewport.addToHistoryList(command);
1659       viewport.clearRedoList();
1660       updateEditMenuBar();
1661       viewport.updateHiddenColumns();
1662     }
1663   }
1664
1665   /**
1666    * TODO: JAL-1104 DOCUMENT ME!
1667    *
1668    * @param e
1669    *          DOCUMENT ME!
1670    */
1671   protected void undoMenuItem_actionPerformed()
1672   {
1673     if (viewport.getHistoryList().isEmpty())
1674     {
1675       return;
1676     }
1677
1678     CommandI command = viewport.getHistoryList().pop();
1679     viewport.addToRedoList(command);
1680     command.undoCommand(null);
1681
1682     AlignmentViewport originalSource = getOriginatingSource(command);
1683     // JBPNote Test
1684     if (originalSource != viewport)
1685     {
1686       System.err
1687               .println("Warning: Viewport object mismatch whilst undoing");
1688     }
1689     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1690                                           // viewport.getColumnSelection().getHiddenColumns()
1691                                           // != null;
1692     updateEditMenuBar();
1693     originalSource.firePropertyChange("alignment", null,
1694             originalSource.getAlignment().getSequences());
1695   }
1696
1697   /**
1698    * TODO: JAL-1104 DOCUMENT ME!
1699    *
1700    * @param e
1701    *          DOCUMENT ME!
1702    */
1703   protected void redoMenuItem_actionPerformed()
1704   {
1705     if (viewport.getRedoList().isEmpty())
1706     {
1707       return;
1708     }
1709
1710     CommandI command = viewport.getRedoList().pop();
1711     viewport.addToHistoryList(command);
1712     command.doCommand(null);
1713
1714     AlignmentViewport originalSource = getOriginatingSource(command);
1715     // JBPNote Test
1716     if (originalSource != viewport)
1717     {
1718       System.err
1719               .println("Warning: Viewport object mismatch whilst re-doing");
1720     }
1721     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1722                                           // viewport.getColumnSelection().getHiddenColumns()
1723                                           // != null;
1724
1725     updateEditMenuBar();
1726     originalSource.firePropertyChange("alignment", null,
1727             originalSource.getAlignment().getSequences());
1728   }
1729
1730   AlignmentViewport getOriginatingSource(CommandI command)
1731   {
1732     AlignmentViewport originalSource = null;
1733     // For sequence removal and addition, we need to fire
1734     // the property change event FROM the viewport where the
1735     // original alignment was altered
1736     AlignmentI al = null;
1737     if (command instanceof EditCommand)
1738     {
1739       EditCommand editCommand = (EditCommand) command;
1740       al = editCommand.getAlignment();
1741       Vector comps = PaintRefresher.components
1742               .get(viewport.getSequenceSetId());
1743       for (int i = 0; i < comps.size(); i++)
1744       {
1745         if (comps.elementAt(i) instanceof AlignmentPanel)
1746         {
1747           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1748           {
1749             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1750             break;
1751           }
1752         }
1753       }
1754     }
1755
1756     if (originalSource == null)
1757     {
1758       // The original view is closed, we must validate
1759       // the current view against the closed view first
1760       if (al != null)
1761       {
1762         PaintRefresher.validateSequences(al, viewport.getAlignment());
1763       }
1764
1765       originalSource = viewport;
1766     }
1767
1768     return originalSource;
1769   }
1770
1771   /**
1772    * Move the currently selected sequences up or down one position in the
1773    * alignment
1774    *
1775    * @param up
1776    */
1777   public void moveSelectedSequences(boolean up)
1778   {
1779     SequenceGroup sg = viewport.getSelectionGroup();
1780     if (sg == null)
1781     {
1782       return;
1783     }
1784     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1785             up ? null : viewport.getHiddenRepSequences(), up);
1786     alignPanel.paintAlignment(true, false);
1787
1788     /*
1789      * Also move cDNA/protein complement sequences
1790      */
1791     AlignViewportI complement = viewport.getCodingComplement();
1792     if (complement != null)
1793     {
1794       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1795               viewport, complement);
1796       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1797               up ? null : complement.getHiddenRepSequences(), up);
1798       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1799               false);
1800     }
1801   }
1802
1803   synchronized void slideSequences(boolean right, int size)
1804   {
1805     List<SequenceI> sg = new Vector<>();
1806     if (viewport.cursorMode)
1807     {
1808       sg.add(viewport.getAlignment()
1809               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1810     }
1811     else if (viewport.getSelectionGroup() != null
1812             && viewport.getSelectionGroup().getSize() != viewport
1813                     .getAlignment().getHeight())
1814     {
1815       sg = viewport.getSelectionGroup()
1816               .getSequences(viewport.getHiddenRepSequences());
1817     }
1818
1819     if (sg.size() < 1)
1820     {
1821       return;
1822     }
1823
1824     Vector<SequenceI> invertGroup = new Vector();
1825
1826     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1827     {
1828       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1829       {
1830         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1831       }
1832     }
1833
1834     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1835
1836     SequenceI[] seqs2 = invertGroup
1837             .toArray(new SequenceI[invertGroup.size()]);
1838     for (int i = 0; i < invertGroup.size(); i++)
1839     {
1840       seqs2[i] = invertGroup.elementAt(i);
1841     }
1842
1843     SlideSequencesCommand ssc;
1844     if (right)
1845     {
1846       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1847               viewport.getGapCharacter());
1848     }
1849     else
1850     {
1851       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1852               viewport.getGapCharacter());
1853     }
1854
1855     int groupAdjustment = 0;
1856     if (ssc.getGapsInsertedBegin() && right)
1857     {
1858       if (viewport.cursorMode)
1859       {
1860         alignPanel.seqPanel.moveCursor(size, 0);
1861       }
1862       else
1863       {
1864         groupAdjustment = size;
1865       }
1866     }
1867     else if (!ssc.getGapsInsertedBegin() && !right)
1868     {
1869       if (viewport.cursorMode)
1870       {
1871         alignPanel.seqPanel.moveCursor(-size, 0);
1872       }
1873       else
1874       {
1875         groupAdjustment = -size;
1876       }
1877     }
1878
1879     if (groupAdjustment != 0)
1880     {
1881       viewport.getSelectionGroup().setStartRes(
1882               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1883       viewport.getSelectionGroup().setEndRes(
1884               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1885     }
1886
1887     boolean appendHistoryItem = false;
1888     Deque<CommandI> historyList = viewport.getHistoryList();
1889     if (historyList != null && historyList.size() > 0
1890             && historyList.peek() instanceof SlideSequencesCommand)
1891     {
1892       appendHistoryItem = ssc.appendSlideCommand(
1893               (SlideSequencesCommand) historyList.peek());
1894     }
1895
1896     if (!appendHistoryItem)
1897     {
1898       addHistoryItem(ssc);
1899     }
1900
1901     repaint();
1902   }
1903
1904   static StringBuffer copiedSequences;
1905
1906   static Vector<int[]> copiedHiddenColumns;
1907
1908   protected void copy_actionPerformed()
1909   {
1910     if (viewport.getSelectionGroup() == null)
1911     {
1912       return;
1913     }
1914
1915     SequenceGroup sg = viewport.getSelectionGroup();
1916     copiedSequences = new StringBuffer();
1917     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1918     for (int i = 0; i < sg.getSize(); i++)
1919     {
1920       SequenceI seq = sg.getSequenceAt(i);
1921       int index = viewport.getAlignment().findIndex(seq);
1922       orderedSeqs.put(index, seq);
1923     }
1924
1925     int index = 0, startRes, endRes;
1926     char ch;
1927
1928     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1929     {
1930       copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1931               .getHiddenColumns().getHiddenColumnsCopy());
1932       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1933       for (int[] region : copiedHiddenColumns)
1934       {
1935         region[0] = region[0] - hiddenOffset;
1936         region[1] = region[1] - hiddenOffset;
1937       }
1938     }
1939     else
1940     {
1941       copiedHiddenColumns = null;
1942     }
1943
1944     for (int i = 0; i < sg.getSize(); i++)
1945     {
1946       SequenceI seq = null;
1947
1948       while (seq == null)
1949       {
1950         if (orderedSeqs.containsKey(index))
1951         {
1952           seq = orderedSeqs.get(index);
1953           index++;
1954           break;
1955         }
1956         else
1957         {
1958           index++;
1959         }
1960       }
1961
1962       // FIND START RES
1963       // Returns residue following index if gap
1964       startRes = seq.findPosition(sg.getStartRes());
1965
1966       // FIND END RES
1967       // Need to find the residue preceeding index if gap
1968       endRes = 0;
1969
1970       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1971       {
1972         ch = seq.getCharAt(j);
1973         if (!jalview.util.Comparison.isGap((ch)))
1974         {
1975           endRes++;
1976         }
1977       }
1978
1979       if (endRes > 0)
1980       {
1981         endRes += seq.getStart() - 1;
1982       }
1983
1984       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1985               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1986                       sg.getEndRes() + 1)
1987               + "\n");
1988     }
1989
1990   }
1991
1992   protected void pasteNew_actionPerformed()
1993   {
1994     paste(true);
1995   }
1996
1997   protected void pasteThis_actionPerformed()
1998   {
1999     paste(false);
2000   }
2001
2002   void paste(boolean newAlignment)
2003   {
2004     try
2005     {
2006
2007       if (copiedSequences == null)
2008       {
2009         return;
2010       }
2011
2012       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2013       Vector seqs = new Vector();
2014       while (st.hasMoreElements())
2015       {
2016         String name = st.nextToken();
2017         int start = Integer.parseInt(st.nextToken());
2018         int end = Integer.parseInt(st.nextToken());
2019         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2020       }
2021       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2022       for (int i = 0; i < seqs.size(); i++)
2023       {
2024         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2025       }
2026
2027       if (newAlignment)
2028       {
2029         String newtitle = MessageManager
2030                 .getString("label.copied_sequences");
2031         if (getTitle().startsWith(
2032                 MessageManager.getString("label.copied_sequences")))
2033         {
2034           newtitle = getTitle();
2035         }
2036         else
2037         {
2038           newtitle = newtitle.concat(MessageManager
2039                   .formatMessage("label.from_msname", new String[]
2040                   { getTitle() }));
2041         }
2042         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2043                 viewport.applet, newtitle, false);
2044         if (copiedHiddenColumns != null)
2045         {
2046           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2047           {
2048             int[] region = copiedHiddenColumns.elementAt(i);
2049             af.viewport.hideColumns(region[0], region[1]);
2050           }
2051         }
2052
2053         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2054                 frameHeight);
2055       }
2056       else
2057       {
2058         addSequences(newSeqs);
2059       }
2060
2061     } catch (Exception ex)
2062     {
2063     } // could be anything being pasted in here
2064
2065   }
2066
2067   void addSequences(SequenceI[] seqs)
2068   {
2069     for (int i = 0; i < seqs.length; i++)
2070     {
2071       viewport.getAlignment().addSequence(seqs[i]);
2072     }
2073
2074     // !newAlignment
2075     addHistoryItem(new EditCommand(
2076             MessageManager.getString("label.add_sequences"), Action.PASTE,
2077             seqs, 0, viewport.getAlignment().getWidth(),
2078             viewport.getAlignment()));
2079
2080     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2081     viewport.getAlignment().getWidth();
2082     viewport.firePropertyChange("alignment", null,
2083             viewport.getAlignment().getSequences());
2084
2085   }
2086
2087   protected void cut_actionPerformed()
2088   {
2089     copy_actionPerformed();
2090     delete_actionPerformed();
2091   }
2092
2093   protected void delete_actionPerformed()
2094   {
2095
2096     SequenceGroup sg = viewport.getSelectionGroup();
2097     if (sg == null)
2098     {
2099       return;
2100     }
2101
2102     Vector seqs = new Vector();
2103     SequenceI seq;
2104     for (int i = 0; i < sg.getSize(); i++)
2105     {
2106       seq = sg.getSequenceAt(i);
2107       seqs.addElement(seq);
2108     }
2109
2110     /*
2111      * If the cut affects all sequences, warn, remove highlighted columns
2112      */
2113     if (sg.getSize() == viewport.getAlignment().getHeight())
2114     {
2115       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2116               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2117       if (isEntireAlignWidth)
2118       {
2119         String title = MessageManager.getString("label.delete_all");
2120         Panel infoPanel = new Panel();
2121         infoPanel.setLayout(new FlowLayout());
2122         infoPanel.add(
2123                 new Label(MessageManager.getString("warn.delete_all")));
2124
2125         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2126         dialog.setMainPanel(infoPanel);
2127         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2128         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2129         dialog.setVisible(true);
2130
2131         if (!dialog.accept)
2132         {
2133           return;
2134         }
2135       }
2136       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2137               sg.getEndRes() + 1);
2138     }
2139
2140     SequenceI[] cut = new SequenceI[seqs.size()];
2141     for (int i = 0; i < seqs.size(); i++)
2142     {
2143       cut[i] = (SequenceI) seqs.elementAt(i);
2144     }
2145
2146     /*
2147      * //ADD HISTORY ITEM
2148      */
2149     addHistoryItem(new EditCommand(
2150             MessageManager.getString("label.cut_sequences"), Action.CUT,
2151             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2152             viewport.getAlignment()));
2153
2154     viewport.setSelectionGroup(null);
2155     viewport.getAlignment().deleteGroup(sg);
2156
2157     viewport.firePropertyChange("alignment", null,
2158             viewport.getAlignment().getSequences());
2159
2160     if (viewport.getAlignment().getHeight() < 1)
2161     {
2162       this.setVisible(false);
2163     }
2164     viewport.sendSelection();
2165   }
2166
2167   /**
2168    * group consensus toggled
2169    *
2170    */
2171   protected void showGroupConsensus_actionPerformed()
2172   {
2173     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2174     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2175
2176   }
2177
2178   /**
2179    * group conservation toggled.
2180    */
2181   protected void showGroupConservation_actionPerformed()
2182   {
2183     viewport.setShowGroupConservation(showGroupConservation.getState());
2184     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2185   }
2186
2187   /*
2188    * (non-Javadoc)
2189    *
2190    * @see
2191    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2192    * .event.ActionEvent)
2193    */
2194   protected void showConsensusHistogram_actionPerformed()
2195   {
2196     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2197     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2198   }
2199
2200   /*
2201    * (non-Javadoc)
2202    *
2203    * @see
2204    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2205    * .event.ActionEvent)
2206    */
2207   protected void showSequenceLogo_actionPerformed()
2208   {
2209     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2210     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2211   }
2212
2213   protected void normSequenceLogo_actionPerformed()
2214   {
2215     showSequenceLogo.setState(true);
2216     viewport.setShowSequenceLogo(true);
2217     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2218     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2219   }
2220
2221   protected void applyAutoAnnotationSettings_actionPerformed()
2222   {
2223     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2224   }
2225
2226   protected void makeGrpsFromSelection_actionPerformed()
2227   {
2228     if (avc.makeGroupsFromSelection())
2229     {
2230       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2231       alignPanel.updateAnnotation();
2232       alignPanel.paintAlignment(true, true);
2233     }
2234   }
2235
2236   protected void createGroup_actionPerformed()
2237   {
2238     avc.createGroup();
2239   }
2240
2241   protected void unGroup_actionPerformed()
2242   {
2243     if (avc.unGroup())
2244     {
2245       alignPanel.alignmentChanged();
2246     }
2247   }
2248
2249   protected void deleteGroups_actionPerformed()
2250   {
2251     if (avc.deleteGroups())
2252     {
2253       alignPanel.alignmentChanged();
2254     }
2255   }
2256
2257   public void selectAllSequenceMenuItem_actionPerformed()
2258   {
2259     SequenceGroup sg = new SequenceGroup();
2260     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2261     {
2262       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2263     }
2264     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2265     viewport.setSelectionGroup(sg);
2266     // JAL-2034 - should delegate to
2267     // alignPanel to decide if overview needs
2268     // updating.
2269     alignPanel.paintAlignment(false, false);
2270     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2271     viewport.sendSelection();
2272   }
2273
2274   public void deselectAllSequenceMenuItem_actionPerformed()
2275   {
2276     if (viewport.cursorMode)
2277     {
2278       alignPanel.seqPanel.keyboardNo1 = null;
2279       alignPanel.seqPanel.keyboardNo2 = null;
2280     }
2281     viewport.setSelectionGroup(null);
2282     viewport.getColumnSelection().clear();
2283     viewport.setSelectionGroup(null);
2284     alignPanel.idPanel.idCanvas.searchResults = null;
2285     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2286     // JAL-2034 - should delegate to
2287     // alignPanel to decide if overview needs
2288     // updating.
2289     alignPanel.paintAlignment(false, false);
2290     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2291     viewport.sendSelection();
2292   }
2293
2294   public void invertSequenceMenuItem_actionPerformed()
2295   {
2296     SequenceGroup sg = viewport.getSelectionGroup();
2297     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2298     {
2299       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2300     }
2301
2302     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2303     viewport.sendSelection();
2304   }
2305
2306   public void invertColSel_actionPerformed()
2307   {
2308     viewport.invertColumnSelection();
2309     alignPanel.paintAlignment(true, false);
2310     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2311     viewport.sendSelection();
2312   }
2313
2314   void trimAlignment(boolean trimLeft)
2315   {
2316     AlignmentI al = viewport.getAlignment();
2317     ViewportRanges ranges = viewport.getRanges();
2318     ColumnSelection colSel = viewport.getColumnSelection();
2319     int column;
2320
2321     if (!colSel.isEmpty())
2322     {
2323       if (trimLeft)
2324       {
2325         column = colSel.getMin();
2326       }
2327       else
2328       {
2329         column = colSel.getMax();
2330       }
2331
2332       SequenceI[] seqs;
2333       if (viewport.getSelectionGroup() != null)
2334       {
2335         seqs = viewport.getSelectionGroup()
2336                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2337       }
2338       else
2339       {
2340         seqs = al.getSequencesArray();
2341       }
2342
2343       TrimRegionCommand trimRegion;
2344       if (trimLeft)
2345       {
2346         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2347                 column, al);
2348         ranges.setStartRes(0);
2349       }
2350       else
2351       {
2352         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2353                 column, al);
2354       }
2355
2356       statusBar.setText(MessageManager
2357               .formatMessage("label.removed_columns", new String[]
2358               { Integer.valueOf(trimRegion.getSize()).toString() }));
2359       addHistoryItem(trimRegion);
2360
2361       for (SequenceGroup sg : al.getGroups())
2362       {
2363         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2364                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2365         {
2366           al.deleteGroup(sg);
2367         }
2368       }
2369
2370       viewport.firePropertyChange("alignment", null, al.getSequences());
2371     }
2372   }
2373
2374   public void removeGappedColumnMenuItem_actionPerformed()
2375   {
2376     AlignmentI al = viewport.getAlignment();
2377     ViewportRanges ranges = viewport.getRanges();
2378     int start = 0;
2379     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2380
2381     SequenceI[] seqs;
2382     if (viewport.getSelectionGroup() != null)
2383     {
2384       seqs = viewport.getSelectionGroup()
2385               .getSequencesAsArray(viewport.getHiddenRepSequences());
2386       start = viewport.getSelectionGroup().getStartRes();
2387       end = viewport.getSelectionGroup().getEndRes();
2388     }
2389     else
2390     {
2391       seqs = viewport.getAlignment().getSequencesArray();
2392     }
2393
2394     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2395             "Remove Gapped Columns", seqs, start, end,
2396             viewport.getAlignment());
2397
2398     addHistoryItem(removeGapCols);
2399
2400     statusBar.setText(MessageManager
2401             .formatMessage("label.removed_empty_columns", new String[]
2402             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2403
2404     // This is to maintain viewport position on first residue
2405     // of first sequence
2406     SequenceI seq = al.getSequenceAt(0);
2407     int startRes = seq.findPosition(ranges.getStartRes());
2408     // ShiftList shifts;
2409     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2410     // edit.alColumnChanges=shifts.getInverse();
2411     // if (viewport.hasHiddenColumns)
2412     // viewport.getColumnSelection().compensateForEdits(shifts);
2413     ranges.setStartRes(seq.findIndex(startRes) - 1);
2414     viewport.firePropertyChange("alignment", null, al.getSequences());
2415
2416   }
2417
2418   public void removeAllGapsMenuItem_actionPerformed()
2419   {
2420     AlignmentI al = viewport.getAlignment();
2421     ViewportRanges ranges = viewport.getRanges();
2422     int start = 0;
2423     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2424
2425     SequenceI[] seqs;
2426     if (viewport.getSelectionGroup() != null)
2427     {
2428       seqs = viewport.getSelectionGroup()
2429               .getSequencesAsArray(viewport.getHiddenRepSequences());
2430       start = viewport.getSelectionGroup().getStartRes();
2431       end = viewport.getSelectionGroup().getEndRes();
2432     }
2433     else
2434     {
2435       seqs = viewport.getAlignment().getSequencesArray();
2436     }
2437
2438     // This is to maintain viewport position on first residue
2439     // of first sequence
2440     SequenceI seq = al.getSequenceAt(0);
2441     int startRes = seq.findPosition(ranges.getStartRes());
2442
2443     addHistoryItem(
2444             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2445
2446     ranges.setStartRes(seq.findIndex(startRes) - 1);
2447
2448     viewport.firePropertyChange("alignment", null, al.getSequences());
2449
2450   }
2451
2452   public void findMenuItem_actionPerformed()
2453   {
2454     new Finder(alignPanel);
2455   }
2456
2457   /**
2458    * create a new view derived from the current view
2459    *
2460    * @param viewtitle
2461    * @return frame for the new view
2462    */
2463   public AlignFrame newView(String viewtitle)
2464   {
2465     AlignmentI newal;
2466     if (viewport.hasHiddenRows())
2467     {
2468       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2469               .getFullAlignment().getSequencesArray());
2470     }
2471     else
2472     {
2473       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2474     }
2475
2476     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2477     {
2478       for (int i = 0; i < viewport.getAlignment()
2479               .getAlignmentAnnotation().length; i++)
2480       {
2481         if (!viewport.getAlignment()
2482                 .getAlignmentAnnotation()[i].autoCalculated)
2483         {
2484           newal.addAnnotation(
2485                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2486         }
2487       }
2488     }
2489
2490     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2491
2492     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2493     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2494     PaintRefresher.Register(newaf.alignPanel,
2495             newaf.alignPanel.av.getSequenceSetId());
2496
2497     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2498             newaf.alignPanel.av.getSequenceSetId());
2499     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2500             newaf.alignPanel.av.getSequenceSetId());
2501
2502     Vector comps = PaintRefresher.components
2503             .get(viewport.getSequenceSetId());
2504     int viewSize = -1;
2505     for (int i = 0; i < comps.size(); i++)
2506     {
2507       if (comps.elementAt(i) instanceof AlignmentPanel)
2508       {
2509         viewSize++;
2510       }
2511     }
2512
2513     String title = new String(this.getTitle());
2514     if (viewtitle != null)
2515     {
2516       title = viewtitle + " ( " + title + ")";
2517     }
2518     else
2519     {
2520       if (title.indexOf("(View") > -1)
2521       {
2522         title = title.substring(0, title.indexOf("(View"));
2523       }
2524       title += "(View " + viewSize + ")";
2525     }
2526
2527     newaf.setTitle(title.toString());
2528
2529     newaf.viewport.setHistoryList(viewport.getHistoryList());
2530     newaf.viewport.setRedoList(viewport.getRedoList());
2531     return newaf;
2532   }
2533
2534   /**
2535    *
2536    * @return list of feature groups on the view
2537    */
2538   public String[] getFeatureGroups()
2539   {
2540     FeatureRenderer fr = null;
2541     if (alignPanel != null
2542             && (fr = alignPanel.getFeatureRenderer()) != null)
2543     {
2544       List<String> gps = fr.getFeatureGroups();
2545       String[] _gps = gps.toArray(new String[gps.size()]);
2546       return _gps;
2547     }
2548     return null;
2549   }
2550
2551   /**
2552    * get sequence feature groups that are hidden or shown
2553    *
2554    * @param visible
2555    *          true is visible
2556    * @return list
2557    */
2558   public String[] getFeatureGroupsOfState(boolean visible)
2559   {
2560     FeatureRenderer fr = null;
2561     if (alignPanel != null
2562             && (fr = alignPanel.getFeatureRenderer()) != null)
2563     {
2564       List<String> gps = fr.getGroups(visible);
2565       String[] _gps = gps.toArray(new String[gps.size()]);
2566       return _gps;
2567     }
2568     return null;
2569   }
2570
2571   /**
2572    * Change the display state for the given feature groups
2573    *
2574    * @param groups
2575    *          list of group strings
2576    * @param state
2577    *          visible or invisible
2578    */
2579   public void setFeatureGroupState(String[] groups, boolean state)
2580   {
2581     FeatureRenderer fr = null;
2582     this.sequenceFeatures.setState(true);
2583     viewport.setShowSequenceFeatures(true);
2584     if (alignPanel != null
2585             && (fr = alignPanel.getFeatureRenderer()) != null)
2586     {
2587
2588       fr.setGroupVisibility(Arrays.asList(groups), state);
2589       alignPanel.seqPanel.seqCanvas.repaint();
2590       if (alignPanel.overviewPanel != null)
2591       {
2592         alignPanel.overviewPanel.updateOverviewImage();
2593       }
2594     }
2595   }
2596
2597   public void seqLimits_itemStateChanged()
2598   {
2599     viewport.setShowJVSuffix(seqLimits.getState());
2600     alignPanel.fontChanged();
2601     alignPanel.paintAlignment(true, false);
2602   }
2603
2604   protected void colourTextMenuItem_actionPerformed()
2605   {
2606     viewport.setColourText(colourTextMenuItem.getState());
2607     alignPanel.paintAlignment(false, false);
2608   }
2609
2610   protected void displayNonconservedMenuItem_actionPerformed()
2611   {
2612     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2613     alignPanel.paintAlignment(false, false);
2614   }
2615
2616   protected void wrapMenuItem_actionPerformed()
2617   {
2618     viewport.setWrapAlignment(wrapMenuItem.getState());
2619     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2620     scaleAbove.setEnabled(wrapMenuItem.getState());
2621     scaleLeft.setEnabled(wrapMenuItem.getState());
2622     scaleRight.setEnabled(wrapMenuItem.getState());
2623     alignPanel.paintAlignment(true, false);
2624   }
2625
2626   public void overviewMenuItem_actionPerformed()
2627   {
2628     if (alignPanel.overviewPanel != null)
2629     {
2630       return;
2631     }
2632
2633     Frame frame = new Frame();
2634     final OverviewPanel overview = new OverviewPanel(alignPanel);
2635     frame.add(overview);
2636     // +50 must allow for applet frame window
2637     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2638             .formatMessage("label.overview_params", new String[]
2639             { this.getTitle() }), overview.getPreferredSize().width,
2640             overview.getPreferredSize().height + 50);
2641
2642     frame.pack();
2643     final AlignmentPanel ap = alignPanel;
2644     frame.addWindowListener(new WindowAdapter()
2645     {
2646       @Override
2647       public void windowClosing(WindowEvent e)
2648       {
2649         overview.dispose();
2650         if (ap != null)
2651         {
2652           ap.setOverviewPanel(null);
2653         }
2654       };
2655     });
2656
2657     alignPanel.setOverviewPanel(overview);
2658
2659   }
2660
2661   @Override
2662   public void changeColour(ColourSchemeI cs)
2663   {
2664     viewport.setGlobalColourScheme(cs);
2665
2666     alignPanel.paintAlignment(true, true);
2667   }
2668
2669   protected void modifyPID_actionPerformed()
2670   {
2671     if (viewport.getAbovePIDThreshold()
2672             && viewport.getGlobalColourScheme() != null)
2673     {
2674       SliderPanel.setPIDSliderSource(alignPanel,
2675               viewport.getResidueShading(), alignPanel.getViewName());
2676       SliderPanel.showPIDSlider();
2677     }
2678   }
2679
2680   protected void modifyConservation_actionPerformed()
2681   {
2682     if (viewport.getConservationSelected()
2683             && viewport.getGlobalColourScheme() != null)
2684     {
2685       SliderPanel.setConservationSlider(alignPanel,
2686               viewport.getResidueShading(), alignPanel.getViewName());
2687       SliderPanel.showConservationSlider();
2688     }
2689   }
2690
2691   protected void conservationMenuItem_actionPerformed()
2692   {
2693     boolean selected = conservationMenuItem.getState();
2694     modifyConservation.setEnabled(selected);
2695     viewport.setConservationSelected(selected);
2696     viewport.getResidueShading().setConservationApplied(selected);
2697
2698     changeColour(viewport.getGlobalColourScheme());
2699
2700     if (selected)
2701     {
2702       modifyConservation_actionPerformed();
2703     }
2704     else
2705     {
2706       SliderPanel.hideConservationSlider();
2707     }
2708   }
2709
2710   public void abovePIDThreshold_actionPerformed()
2711   {
2712     boolean selected = abovePIDThreshold.getState();
2713     modifyPID.setEnabled(selected);
2714     viewport.setAbovePIDThreshold(selected);
2715     if (!selected)
2716     {
2717       viewport.getResidueShading().setThreshold(0,
2718               viewport.isIgnoreGapsConsensus());
2719     }
2720
2721     changeColour(viewport.getGlobalColourScheme());
2722
2723     if (selected)
2724     {
2725       modifyPID_actionPerformed();
2726     }
2727     else
2728     {
2729       SliderPanel.hidePIDSlider();
2730     }
2731   }
2732
2733   public void sortPairwiseMenuItem_actionPerformed()
2734   {
2735     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2736     AlignmentSorter.sortByPID(viewport.getAlignment(),
2737             viewport.getAlignment().getSequenceAt(0));
2738
2739     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2740             viewport.getAlignment()));
2741     alignPanel.paintAlignment(true, false);
2742   }
2743
2744   public void sortIDMenuItem_actionPerformed()
2745   {
2746     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2747     AlignmentSorter.sortByID(viewport.getAlignment());
2748     addHistoryItem(
2749             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2750     alignPanel.paintAlignment(true, false);
2751   }
2752
2753   public void sortLengthMenuItem_actionPerformed()
2754   {
2755     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2756     AlignmentSorter.sortByLength(viewport.getAlignment());
2757     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2758             viewport.getAlignment()));
2759     alignPanel.paintAlignment(true, false);
2760   }
2761
2762   public void sortGroupMenuItem_actionPerformed()
2763   {
2764     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2765     AlignmentSorter.sortByGroup(viewport.getAlignment());
2766     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2767             viewport.getAlignment()));
2768     alignPanel.paintAlignment(true, false);
2769
2770   }
2771
2772   public void removeRedundancyMenuItem_actionPerformed()
2773   {
2774     new RedundancyPanel(alignPanel);
2775   }
2776
2777   public void pairwiseAlignmentMenuItem_actionPerformed()
2778   {
2779     if (viewport.getSelectionGroup() != null
2780             && viewport.getSelectionGroup().getSize() > 1)
2781     {
2782       Frame frame = new Frame();
2783       frame.add(new PairwiseAlignPanel(alignPanel));
2784       jalview.bin.JalviewLite.addFrame(frame,
2785               MessageManager.getString("action.pairwise_alignment"), 600,
2786               500);
2787     }
2788   }
2789
2790   public void PCAMenuItem_actionPerformed()
2791   {
2792     // are the sequences aligned?
2793     if (!viewport.getAlignment().isAligned(false))
2794     {
2795       SequenceI current;
2796       int Width = viewport.getAlignment().getWidth();
2797
2798       for (int i = 0; i < viewport.getAlignment().getSequences()
2799               .size(); i++)
2800       {
2801         current = viewport.getAlignment().getSequenceAt(i);
2802
2803         if (current.getLength() < Width)
2804         {
2805           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2806         }
2807       }
2808       alignPanel.paintAlignment(false, false);
2809     }
2810
2811     if ((viewport.getSelectionGroup() != null
2812             && viewport.getSelectionGroup().getSize() < 4
2813             && viewport.getSelectionGroup().getSize() > 0)
2814             || viewport.getAlignment().getHeight() < 4)
2815     {
2816       return;
2817     }
2818
2819     try
2820     {
2821       new PCAPanel(viewport);
2822     } catch (java.lang.OutOfMemoryError ex)
2823     {
2824     }
2825
2826   }
2827
2828   public void averageDistanceTreeMenuItem_actionPerformed()
2829   {
2830     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2831             "Average distance tree using PID");
2832   }
2833
2834   public void neighbourTreeMenuItem_actionPerformed()
2835   {
2836     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2837             "Neighbour joining tree using PID");
2838   }
2839
2840   protected void njTreeBlosumMenuItem_actionPerformed()
2841   {
2842     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2843             ScoreModels.getInstance().getBlosum62().getName(),
2844             "Neighbour joining tree using BLOSUM62");
2845   }
2846
2847   protected void avTreeBlosumMenuItem_actionPerformed()
2848   {
2849     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2850             ScoreModels.getInstance().getBlosum62().getName(),
2851             "Average distance tree using BLOSUM62");
2852   }
2853
2854   void newTreePanel(String type, String pwType, String title)
2855   {
2856     // are the sequences aligned?
2857     if (!viewport.getAlignment().isAligned(false))
2858     {
2859       SequenceI current;
2860       int Width = viewport.getAlignment().getWidth();
2861
2862       for (int i = 0; i < viewport.getAlignment().getSequences()
2863               .size(); i++)
2864       {
2865         current = viewport.getAlignment().getSequenceAt(i);
2866
2867         if (current.getLength() < Width)
2868         {
2869           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2870         }
2871       }
2872       alignPanel.paintAlignment(false, false);
2873
2874     }
2875
2876     if ((viewport.getSelectionGroup() != null
2877             && viewport.getSelectionGroup().getSize() > 1)
2878             || (viewport.getAlignment().getHeight() > 1))
2879     {
2880       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2881
2882       addTreeMenuItem(tp, title);
2883
2884       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2885     }
2886   }
2887
2888   void loadTree_actionPerformed()
2889   {
2890     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2891     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2892     cap.setTreeImport();
2893     Frame frame = new Frame();
2894     frame.add(cap);
2895     jalview.bin.JalviewLite.addFrame(frame,
2896             MessageManager.getString("label.paste_newick_file"), 400, 300);
2897   }
2898
2899   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2900   {
2901     TreePanel tp = new TreePanel(alignPanel, treeFile,
2902             MessageManager.getString("label.load_tree_from_file"), tree);
2903     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2904     addTreeMenuItem(tp, treeFile);
2905   }
2906
2907   /**
2908    * sort the alignment using the given treePanel
2909    *
2910    * @param treePanel
2911    *          tree used to sort view
2912    * @param title
2913    *          string used for undo event name
2914    */
2915   public void sortByTree(TreePanel treePanel, String title)
2916   {
2917     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2918     AlignmentSorter.sortByTree(viewport.getAlignment(),
2919             treePanel.getTree());
2920     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2921     // HistoryItem.SORT));
2922     addHistoryItem(new OrderCommand(MessageManager
2923             .formatMessage("label.order_by_params", new String[]
2924             { title }), oldOrder, viewport.getAlignment()));
2925     alignPanel.paintAlignment(true, false);
2926   }
2927
2928   /**
2929    * Do any automatic reordering of the alignment and add the necessary bits to
2930    * the menu structure for the new tree
2931    *
2932    * @param treePanel
2933    * @param title
2934    */
2935   protected void addTreeMenuItem(final TreePanel treePanel,
2936           final String title)
2937   {
2938     final MenuItem item = new MenuItem(title);
2939     sortByTreeMenu.add(item);
2940     item.addActionListener(new java.awt.event.ActionListener()
2941     {
2942       @Override
2943       public void actionPerformed(ActionEvent evt)
2944       {
2945         sortByTree(treePanel, title); // treePanel.getTitle());
2946       }
2947     });
2948
2949     treePanel.addWindowListener(new WindowAdapter()
2950     {
2951       @Override
2952       public void windowOpened(WindowEvent e)
2953       {
2954         if (viewport.sortByTree)
2955         {
2956           sortByTree(treePanel, title);
2957         }
2958         super.windowOpened(e);
2959       }
2960
2961       @Override
2962       public void windowClosing(WindowEvent e)
2963       {
2964         sortByTreeMenu.remove(item);
2965       };
2966     });
2967   }
2968
2969   public boolean sortBy(AlignmentOrder alorder, String undoname)
2970   {
2971     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2972     if (viewport.applet.debug)
2973     {
2974       System.err.println("Sorting " + alorder.getOrder().size()
2975               + " in alignment '" + getTitle() + "'");
2976     }
2977     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2978     if (undoname != null)
2979     {
2980       addHistoryItem(new OrderCommand(undoname, oldOrder,
2981               viewport.getAlignment()));
2982     }
2983     alignPanel.paintAlignment(true, false);
2984     return true;
2985   }
2986
2987   protected void documentation_actionPerformed()
2988   {
2989     alignPanel.av.applet.openJalviewHelpUrl();
2990   }
2991
2992   protected void about_actionPerformed()
2993   {
2994
2995     class AboutPanel extends Canvas
2996     {
2997       String version;
2998
2999       String builddate;
3000
3001       public AboutPanel(String version, String builddate)
3002       {
3003         this.version = version;
3004         this.builddate = builddate;
3005       }
3006
3007       @Override
3008       public void paint(Graphics g)
3009       {
3010         g.setColor(Color.white);
3011         g.fillRect(0, 0, getSize().width, getSize().height);
3012         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3013         FontMetrics fm = g.getFontMetrics();
3014         int fh = fm.getHeight();
3015         int y = 5, x = 7;
3016         g.setColor(Color.black);
3017         // TODO: update this text for each release or centrally store it for
3018         // lite and application
3019         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3020         g.drawString(MessageManager
3021                 .formatMessage("label.jalviewLite_release", new String[]
3022                 { version }), x, y += fh);
3023         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3024         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3025                 new String[]
3026                 { builddate }), x, y += fh);
3027         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3028         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3029                 y += fh * 1.5);
3030         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3031                 x + 50, y += fh + 8);
3032         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3033                 x, y += fh);
3034         g.drawString(MessageManager
3035                 .getString("label.jalview_distribution_lists"), x, y += fh);
3036         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3037                 x, y += fh + 8);
3038         g.drawString(
3039                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3040                 y += fh);
3041         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3042                 x, y += fh);
3043         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3044                 x, y += fh);
3045       }
3046     }
3047
3048     Frame frame = new Frame();
3049     frame.add(new AboutPanel(JalviewLite.getVersion(),
3050             JalviewLite.getBuildDate()));
3051     jalview.bin.JalviewLite.addFrame(frame,
3052             MessageManager.getString("label.jalview"), 580, 220);
3053
3054   }
3055
3056   public void showURL(String url, String target)
3057   {
3058     if (viewport.applet == null)
3059     {
3060       System.out.println("Not running as applet - no browser available.");
3061     }
3062     else
3063     {
3064       viewport.applet.showURL(url, target);
3065     }
3066   }
3067
3068   // ////////////////////////////////////////////////////////////////////////////////
3069   // JBuilder Graphics here
3070
3071   MenuBar alignFrameMenuBar = new MenuBar();
3072
3073   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3074
3075   MenuItem loadApplication = new MenuItem(
3076           MessageManager.getString("label.view_full_application"));
3077
3078   MenuItem loadTree = new MenuItem(
3079           MessageManager.getString("label.load_associated_tree"));
3080
3081   MenuItem loadAnnotations = new MenuItem(
3082           MessageManager.getString("label.load_features_annotations"));
3083
3084   MenuItem outputFeatures = new MenuItem(
3085           MessageManager.getString("label.export_features"));
3086
3087   MenuItem outputAnnotations = new MenuItem(
3088           MessageManager.getString("label.export_annotations"));
3089
3090   MenuItem closeMenuItem = new MenuItem(
3091           MessageManager.getString("action.close"));
3092
3093   MenuItem selectAllSequenceMenuItem = new MenuItem(
3094           MessageManager.getString("action.select_all"));
3095
3096   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3097           MessageManager.getString("action.deselect_all"));
3098
3099   MenuItem invertSequenceMenuItem = new MenuItem(
3100           MessageManager.getString("action.invert_selection"));
3101
3102   MenuItem remove2LeftMenuItem = new MenuItem();
3103
3104   MenuItem remove2RightMenuItem = new MenuItem();
3105
3106   MenuItem removeGappedColumnMenuItem = new MenuItem();
3107
3108   MenuItem removeAllGapsMenuItem = new MenuItem();
3109
3110   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3111
3112   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3113
3114   MenuItem sortPairwiseMenuItem = new MenuItem();
3115
3116   MenuItem sortIDMenuItem = new MenuItem();
3117
3118   MenuItem sortLengthMenuItem = new MenuItem();
3119
3120   MenuItem sortGroupMenuItem = new MenuItem();
3121
3122   MenuItem removeRedundancyMenuItem = new MenuItem();
3123
3124   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3125
3126   MenuItem PCAMenuItem = new MenuItem();
3127
3128   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3129
3130   MenuItem neighbourTreeMenuItem = new MenuItem();
3131
3132   BorderLayout borderLayout1 = new BorderLayout();
3133
3134   public Label statusBar = new Label();
3135
3136   MenuItem clustalColour = new MenuItem();
3137
3138   MenuItem zappoColour = new MenuItem();
3139
3140   MenuItem taylorColour = new MenuItem();
3141
3142   MenuItem hydrophobicityColour = new MenuItem();
3143
3144   MenuItem helixColour = new MenuItem();
3145
3146   MenuItem strandColour = new MenuItem();
3147
3148   MenuItem turnColour = new MenuItem();
3149
3150   MenuItem buriedColour = new MenuItem();
3151
3152   MenuItem purinePyrimidineColour = new MenuItem();
3153
3154   // MenuItem RNAInteractionColour = new MenuItem();
3155
3156   MenuItem RNAHelixColour = new MenuItem();
3157
3158   MenuItem userDefinedColour = new MenuItem();
3159
3160   MenuItem PIDColour = new MenuItem();
3161
3162   MenuItem BLOSUM62Colour = new MenuItem();
3163
3164   MenuItem tcoffeeColour = new MenuItem();
3165
3166   MenuItem njTreeBlosumMenuItem = new MenuItem();
3167
3168   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3169
3170   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3171
3172   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3173
3174   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3175
3176   MenuItem alProperties = new MenuItem(
3177           MessageManager.getString("label.alignment_props"));
3178
3179   MenuItem overviewMenuItem = new MenuItem();
3180
3181   MenuItem undoMenuItem = new MenuItem();
3182
3183   MenuItem redoMenuItem = new MenuItem();
3184
3185   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3186
3187   MenuItem noColourmenuItem = new MenuItem();
3188
3189   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3190
3191   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3192
3193   MenuItem findMenuItem = new MenuItem();
3194
3195   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3196
3197   MenuItem nucleotideColour = new MenuItem();
3198
3199   MenuItem deleteGroups = new MenuItem();
3200
3201   MenuItem grpsFromSelection = new MenuItem();
3202
3203   MenuItem createGroup = new MenuItem();
3204
3205   MenuItem unGroup = new MenuItem();
3206
3207   MenuItem delete = new MenuItem();
3208
3209   MenuItem copy = new MenuItem();
3210
3211   MenuItem cut = new MenuItem();
3212
3213   Menu pasteMenu = new Menu();
3214
3215   MenuItem pasteNew = new MenuItem();
3216
3217   MenuItem pasteThis = new MenuItem();
3218
3219   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3220
3221   MenuItem font = new MenuItem();
3222
3223   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3224
3225   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3226
3227   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3228
3229   MenuItem modifyPID = new MenuItem();
3230
3231   MenuItem modifyConservation = new MenuItem();
3232
3233   CheckboxMenuItem autoCalculate = null;
3234
3235   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3236           "Sort Alignment With New Tree", true);
3237
3238   Menu sortByTreeMenu = new Menu();
3239
3240   MenuItem inputText = new MenuItem();
3241
3242   MenuItem documentation = new MenuItem();
3243
3244   MenuItem about = new MenuItem();
3245
3246   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3253
3254   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3255
3256   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3257
3258   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3259
3260   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3261
3262   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3263
3264   /**
3265    * Initialise menus and other items
3266    *
3267    * @throws Exception
3268    */
3269   private void jbInit() throws Exception
3270   {
3271     setMenuBar(alignFrameMenuBar);
3272
3273     /*
3274      * Configure File menu items and actions
3275      */
3276     inputText
3277             .setLabel(MessageManager.getString("label.input_from_textbox"));
3278     inputText.addActionListener(this);
3279     Menu outputTextboxMenu = new Menu(
3280             MessageManager.getString("label.out_to_textbox"));
3281     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3282     {
3283       MenuItem item = new MenuItem(ff);
3284
3285       item.addActionListener(new java.awt.event.ActionListener()
3286       {
3287         @Override
3288         public void actionPerformed(ActionEvent e)
3289         {
3290           outputText_actionPerformed(e);
3291         }
3292       });
3293
3294       outputTextboxMenu.add(item);
3295     }
3296     closeMenuItem.addActionListener(this);
3297     loadApplication.addActionListener(this);
3298     loadTree.addActionListener(this);
3299     loadAnnotations.addActionListener(this);
3300     outputFeatures.addActionListener(this);
3301     outputAnnotations.addActionListener(this);
3302
3303     /*
3304      * Configure Edit menu items and actions
3305      */
3306     undoMenuItem.setEnabled(false);
3307     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3308     undoMenuItem.addActionListener(this);
3309     redoMenuItem.setEnabled(false);
3310     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3311     redoMenuItem.addActionListener(this);
3312     copy.setLabel(MessageManager.getString("action.copy"));
3313     copy.addActionListener(this);
3314     cut.setLabel(MessageManager.getString("action.cut"));
3315     cut.addActionListener(this);
3316     delete.setLabel(MessageManager.getString("action.delete"));
3317     delete.addActionListener(this);
3318     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3319     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3320     pasteNew.addActionListener(this);
3321     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3322     pasteThis.addActionListener(this);
3323     remove2LeftMenuItem
3324             .setLabel(MessageManager.getString("action.remove_left"));
3325     remove2LeftMenuItem.addActionListener(this);
3326     remove2RightMenuItem
3327             .setLabel(MessageManager.getString("action.remove_right"));
3328     remove2RightMenuItem.addActionListener(this);
3329     removeGappedColumnMenuItem.setLabel(
3330             MessageManager.getString("action.remove_empty_columns"));
3331     removeGappedColumnMenuItem.addActionListener(this);
3332     removeAllGapsMenuItem
3333             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3334     removeAllGapsMenuItem.addActionListener(this);
3335     removeRedundancyMenuItem
3336             .setLabel(MessageManager.getString("action.remove_redundancy"));
3337     removeRedundancyMenuItem.addActionListener(this);
3338
3339     /*
3340      * Configure Select menu items and actions
3341      */
3342     findMenuItem.setLabel(MessageManager.getString("action.find"));
3343     findMenuItem.addActionListener(this);
3344     selectAllSequenceMenuItem.addActionListener(this);
3345     deselectAllSequenceMenuItem.addActionListener(this);
3346     invertSequenceMenuItem.setLabel(
3347             MessageManager.getString("action.invert_sequence_selection"));
3348     invertSequenceMenuItem.addActionListener(this);
3349     invertColSel.setLabel(
3350             MessageManager.getString("action.invert_column_selection"));
3351     invertColSel.addActionListener(this);
3352     deleteGroups
3353             .setLabel(MessageManager.getString("action.undefine_groups"));
3354     deleteGroups.addActionListener(this);
3355     grpsFromSelection.setLabel(
3356             MessageManager.getString("action.make_groups_selection"));
3357     grpsFromSelection.addActionListener(this);
3358     createGroup.setLabel(MessageManager.getString("action.create_group"));
3359     createGroup.addActionListener(this);
3360     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3361     unGroup.addActionListener(this);
3362
3363     annotationColumnSelection.setLabel(
3364             MessageManager.getString("action.select_by_annotation"));
3365     annotationColumnSelection.addActionListener(this);
3366
3367     /*
3368      * Configure View menu items and actions
3369      */
3370     newView.setLabel(MessageManager.getString("action.new_view"));
3371     newView.addActionListener(this);
3372     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3373     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3374     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3375     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3376     hideColumns
3377             .setLabel(MessageManager.getString("label.selected_columns"));
3378     hideSequences
3379             .setLabel(MessageManager.getString("label.selected_sequences"));
3380     hideAllButSelection.setLabel(
3381             MessageManager.getString("label.all_but_selected_region"));
3382     hideAllSelection
3383             .setLabel(MessageManager.getString("label.selected_region"));
3384     showAllHidden.setLabel(
3385             MessageManager.getString("label.all_sequences_columns"));
3386     showColumns.addActionListener(this);
3387     showSeqs.addActionListener(this);
3388     hideColumns.addActionListener(this);
3389     hideSequences.addActionListener(this);
3390     hideAllButSelection.addActionListener(this);
3391     hideAllSelection.addActionListener(this);
3392     showAllHidden.addActionListener(this);
3393     featureSettings
3394             .setLabel(MessageManager.getString("action.feature_settings"));
3395     featureSettings.addActionListener(this);
3396     sequenceFeatures.setLabel(
3397             MessageManager.getString("label.show_sequence_features"));
3398     sequenceFeatures.addItemListener(this);
3399     sequenceFeatures.setState(false);
3400     followMouseOverFlag.setLabel(
3401             MessageManager.getString("label.automatic_scrolling"));
3402     followMouseOverFlag.addItemListener(this);
3403     alProperties.addActionListener(this);
3404     overviewMenuItem
3405             .setLabel(MessageManager.getString("label.overview_window"));
3406     overviewMenuItem.addActionListener(this);
3407
3408     /*
3409      * Configure Annotations menu items and actions
3410      */
3411     annotationPanelMenuItem
3412             .setLabel(MessageManager.getString("label.show_annotations"));
3413     annotationPanelMenuItem.addItemListener(this);
3414     showGroupConsensus
3415             .setLabel(MessageManager.getString("label.group_consensus"));
3416     showGroupConservation
3417             .setLabel(MessageManager.getString("label.group_conservation"));
3418     showConsensusHistogram.setLabel(
3419             MessageManager.getString("label.show_consensus_histogram"));
3420     showSequenceLogo.setLabel(
3421             MessageManager.getString("label.show_consensus_logo"));
3422     normSequenceLogo.setLabel(
3423             MessageManager.getString("label.norm_consensus_logo"));
3424     applyAutoAnnotationSettings
3425             .setLabel(MessageManager.getString("label.apply_all_groups"));
3426     applyAutoAnnotationSettings.setState(true);
3427     Menu autoAnnMenu = new Menu(
3428             MessageManager.getString("label.autocalculated_annotation"));
3429     showGroupConsensus.addItemListener(this);
3430     showGroupConservation.addItemListener(this);
3431     showConsensusHistogram.addItemListener(this);
3432     showSequenceLogo.addItemListener(this);
3433     normSequenceLogo.addItemListener(this);
3434     applyAutoAnnotationSettings.addItemListener(this);
3435     showAlignmentAnnotations = new CheckboxMenuItem(
3436             MessageManager.getString("label.show_all_al_annotations"));
3437     showSequenceAnnotations = new CheckboxMenuItem(
3438             MessageManager.getString("label.show_all_seq_annotations"));
3439     sortAnnBySequence = new CheckboxMenuItem(
3440             MessageManager.getString("label.sort_annotations_by_sequence"));
3441     sortAnnByLabel = new CheckboxMenuItem(
3442             MessageManager.getString("label.sort_annotations_by_label"));
3443     showAutoFirst = new CheckboxMenuItem(
3444             MessageManager.getString("label.show_first"));
3445     showAutoFirst.setState(false); // pending applet parameter
3446     setShowAutoCalculatedAbove(showAutoFirst.getState());
3447     showAutoLast = new CheckboxMenuItem(
3448             MessageManager.getString("label.show_last"));
3449     showAutoLast.setState(!showAutoFirst.getState());
3450     showAlignmentAnnotations.addItemListener(this);
3451     showSequenceAnnotations.addItemListener(this);
3452     sortAnnBySequence.addItemListener(this);
3453     sortAnnByLabel.addItemListener(this);
3454     showAutoFirst.addItemListener(this);
3455     showAutoLast.addItemListener(this);
3456
3457     /*
3458      * Configure Format menu items and actions
3459      */
3460     font.setLabel(MessageManager.getString("action.font"));
3461     font.addActionListener(this);
3462     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3463     scaleAbove.setState(true);
3464     scaleAbove.setEnabled(false);
3465     scaleAbove.addItemListener(this);
3466     scaleLeft.setEnabled(false);
3467     scaleLeft.setState(true);
3468     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3469     scaleLeft.addItemListener(this);
3470     scaleRight.setEnabled(false);
3471     scaleRight.setState(true);
3472     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3473     scaleRight.addItemListener(this);
3474     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3475     viewBoxesMenuItem.setState(true);
3476     viewBoxesMenuItem.addItemListener(this);
3477     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3478     viewTextMenuItem.setState(true);
3479     viewTextMenuItem.addItemListener(this);
3480     colourTextMenuItem
3481             .setLabel(MessageManager.getString("label.colour_text"));
3482     colourTextMenuItem.addItemListener(this);
3483     displayNonconservedMenuItem
3484             .setLabel(MessageManager.getString("label.show_non_conserved"));
3485     displayNonconservedMenuItem.addItemListener(this);
3486     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3487     wrapMenuItem.addItemListener(this);
3488     renderGapsMenuItem
3489             .setLabel(MessageManager.getString("action.show_gaps"));
3490     renderGapsMenuItem.setState(true);
3491     renderGapsMenuItem.addItemListener(this);
3492     centreColumnLabelFlag.setLabel(
3493             MessageManager.getString("label.centre_column_labels"));
3494     centreColumnLabelFlag.addItemListener(this);
3495     seqLimits.setState(true);
3496     seqLimits.setLabel(
3497             MessageManager.getString("label.show_sequence_limits"));
3498     seqLimits.addItemListener(this);
3499
3500     /*
3501      * Configure Colour menu items and actions
3502      */
3503     applyToAllGroups.setLabel(
3504             MessageManager.getString("label.apply_colour_to_all_groups"));
3505     applyToAllGroups.setState(true);
3506     applyToAllGroups.addItemListener(this);
3507     clustalColour.setLabel(
3508             MessageManager.getString("label.colourScheme_clustal"));
3509     clustalColour.addActionListener(this);
3510     zappoColour
3511             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3512     zappoColour.addActionListener(this);
3513     taylorColour.setLabel(
3514             MessageManager.getString("label.colourScheme_taylor"));
3515     taylorColour.addActionListener(this);
3516     hydrophobicityColour.setLabel(
3517             MessageManager.getString("label.colourScheme_hydrophobic"));
3518     hydrophobicityColour.addActionListener(this);
3519     helixColour.setLabel(MessageManager
3520             .getString("label.colourScheme_helix_propensity"));
3521     helixColour.addActionListener(this);
3522     strandColour.setLabel(MessageManager
3523             .getString("label.colourScheme_strand_propensity"));
3524     strandColour.addActionListener(this);
3525     turnColour.setLabel(
3526             MessageManager.getString("label.colourScheme_turn_propensity"));
3527     turnColour.addActionListener(this);
3528     buriedColour.setLabel(
3529             MessageManager.getString("label.colourScheme_buried_index"));
3530     buriedColour.addActionListener(this);
3531     purinePyrimidineColour.setLabel(MessageManager
3532             .getString("label.colourScheme_purine/pyrimidine"));
3533     purinePyrimidineColour.addActionListener(this);
3534     // RNAInteractionColour.setLabel(MessageManager
3535     // .getString("label.rna_interaction"));
3536     // RNAInteractionColour.addActionListener(this);
3537     RNAHelixColour.setLabel(
3538             MessageManager.getString("label.colourScheme_rna_helices"));
3539     RNAHelixColour.addActionListener(this);
3540     userDefinedColour
3541             .setLabel(MessageManager.getString("action.user_defined"));
3542     userDefinedColour.addActionListener(this);
3543     PIDColour.setLabel(
3544             MessageManager.getString("label.colourScheme_%_identity"));
3545     PIDColour.addActionListener(this);
3546     BLOSUM62Colour.setLabel(
3547             MessageManager.getString("label.colourScheme_blosum62"));
3548     BLOSUM62Colour.addActionListener(this);
3549     tcoffeeColour.setLabel(
3550             MessageManager.getString("label.colourScheme_t-coffee_scores"));
3551     // it will be enabled only if a score file is provided
3552     tcoffeeColour.setEnabled(false);
3553     tcoffeeColour.addActionListener(this);
3554     conservationMenuItem
3555             .setLabel(MessageManager.getString("action.by_conservation"));
3556     conservationMenuItem.addItemListener(this);
3557     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3558     noColourmenuItem.addActionListener(this);
3559     abovePIDThreshold.setLabel(
3560             MessageManager.getString("label.above_identity_threshold"));
3561     abovePIDThreshold.addItemListener(this);
3562     nucleotideColour.setLabel(
3563             MessageManager.getString("label.colourScheme_nucleotide"));
3564     nucleotideColour.addActionListener(this);
3565     modifyPID.setLabel(
3566             MessageManager.getString("label.modify_identity_threshold"));
3567     modifyPID.setEnabled(abovePIDThreshold.getState());
3568     modifyPID.addActionListener(this);
3569     modifyConservation.setLabel(MessageManager
3570             .getString("label.modify_conservation_threshold"));
3571     modifyConservation.setEnabled(conservationMenuItem.getState());
3572     modifyConservation.addActionListener(this);
3573     annotationColour
3574             .setLabel(MessageManager.getString("action.by_annotation"));
3575     annotationColour.addActionListener(this);
3576
3577     /*
3578      * Configure Calculate menu items and actions
3579      */
3580     sortPairwiseMenuItem
3581             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3582     sortPairwiseMenuItem.addActionListener(this);
3583     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3584     sortIDMenuItem.addActionListener(this);
3585     sortLengthMenuItem
3586             .setLabel(MessageManager.getString("action.by_length"));
3587     sortLengthMenuItem.addActionListener(this);
3588     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3589     sortGroupMenuItem.addActionListener(this);
3590     pairwiseAlignmentMenuItem.setLabel(
3591             MessageManager.getString("action.pairwise_alignment"));
3592     pairwiseAlignmentMenuItem.addActionListener(this);
3593     PCAMenuItem.setLabel(
3594             MessageManager.getString("label.principal_component_analysis"));
3595     PCAMenuItem.addActionListener(this);
3596     autoCalculate = new CheckboxMenuItem(
3597             MessageManager.getString("label.autocalculate_consensus"),
3598             true);
3599     averageDistanceTreeMenuItem.setLabel(
3600             MessageManager.getString("label.average_distance_identity"));
3601     averageDistanceTreeMenuItem.addActionListener(this);
3602     neighbourTreeMenuItem.setLabel(
3603             MessageManager.getString("label.neighbour_joining_identity"));
3604     neighbourTreeMenuItem.addActionListener(this);
3605     avDistanceTreeBlosumMenuItem.setLabel(
3606             MessageManager.getString("label.average_distance_blosum62"));
3607     avDistanceTreeBlosumMenuItem.addActionListener(this);
3608     njTreeBlosumMenuItem
3609             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3610     njTreeBlosumMenuItem.addActionListener(this);
3611     sortByTreeMenu
3612             .setLabel(MessageManager.getString("action.by_tree_order"));
3613     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3614     Menu calculateTreeMenu = new Menu(
3615             MessageManager.getString("action.calculate_tree"));
3616     autoCalculate.addItemListener(this);
3617     sortByTree.addItemListener(this);
3618
3619     /*
3620      * Configure Help menu items and actions
3621      */
3622     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3623     documentation.setLabel(MessageManager.getString("label.documentation"));
3624     documentation.addActionListener(this);
3625     about.setLabel(MessageManager.getString("label.about"));
3626     about.addActionListener(this);
3627
3628     /*
3629      * Add top level menus to frame
3630      */
3631     alignFrameMenuBar.add(fileMenu);
3632     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3633     alignFrameMenuBar.add(editMenu);
3634     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3635     alignFrameMenuBar.add(selectMenu);
3636     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3637     alignFrameMenuBar.add(viewMenu);
3638     Menu annotationsMenu = new Menu(
3639             MessageManager.getString("action.annotations"));
3640     alignFrameMenuBar.add(annotationsMenu);
3641     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3642     alignFrameMenuBar.add(formatMenu);
3643     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3644     alignFrameMenuBar.add(colourMenu);
3645     Menu calculateMenu = new Menu(
3646             MessageManager.getString("action.calculate"));
3647     alignFrameMenuBar.add(calculateMenu);
3648     alignFrameMenuBar.add(helpMenu);
3649
3650     /*
3651      * File menu
3652      */
3653     fileMenu.add(inputText);
3654     fileMenu.add(loadTree);
3655     fileMenu.add(loadAnnotations);
3656     fileMenu.addSeparator();
3657     fileMenu.add(outputTextboxMenu);
3658     fileMenu.add(outputFeatures);
3659     fileMenu.add(outputAnnotations);
3660     if (jalviewServletURL != null)
3661     {
3662       fileMenu.add(loadApplication);
3663     }
3664     fileMenu.addSeparator();
3665     fileMenu.add(closeMenuItem);
3666
3667     /*
3668      * Edit menu
3669      */
3670     editMenu.add(undoMenuItem);
3671     editMenu.add(redoMenuItem);
3672     editMenu.add(cut);
3673     editMenu.add(copy);
3674     pasteMenu.add(pasteNew);
3675     pasteMenu.add(pasteThis);
3676     editMenu.add(pasteMenu);
3677     editMenu.add(delete);
3678     editMenu.addSeparator();
3679     editMenu.add(remove2LeftMenuItem);
3680     editMenu.add(remove2RightMenuItem);
3681     editMenu.add(removeGappedColumnMenuItem);
3682     editMenu.add(removeAllGapsMenuItem);
3683     editMenu.add(removeRedundancyMenuItem);
3684
3685     /*
3686      * Select menu
3687      */
3688     selectMenu.add(findMenuItem);
3689     selectMenu.addSeparator();
3690     selectMenu.add(selectAllSequenceMenuItem);
3691     selectMenu.add(deselectAllSequenceMenuItem);
3692     selectMenu.add(invertSequenceMenuItem);
3693     selectMenu.add(invertColSel);
3694     selectMenu.add(createGroup);
3695     selectMenu.add(unGroup);
3696     selectMenu.add(grpsFromSelection);
3697     selectMenu.add(deleteGroups);
3698     selectMenu.add(annotationColumnSelection);
3699
3700     /*
3701      * View menu
3702      */
3703     viewMenu.add(newView);
3704     viewMenu.addSeparator();
3705     showMenu.add(showColumns);
3706     showMenu.add(showSeqs);
3707     showMenu.add(showAllHidden);
3708     viewMenu.add(showMenu);
3709     hideMenu.add(hideColumns);
3710     hideMenu.add(hideSequences);
3711     hideMenu.add(hideAllSelection);
3712     hideMenu.add(hideAllButSelection);
3713     viewMenu.add(hideMenu);
3714     viewMenu.addSeparator();
3715     viewMenu.add(followMouseOverFlag);
3716     viewMenu.addSeparator();
3717     viewMenu.add(sequenceFeatures);
3718     viewMenu.add(featureSettings);
3719     viewMenu.addSeparator();
3720     viewMenu.add(alProperties);
3721     viewMenu.addSeparator();
3722     viewMenu.add(overviewMenuItem);
3723
3724     /*
3725      * Annotations menu
3726      */
3727     annotationsMenu.add(annotationPanelMenuItem);
3728     annotationsMenu.addSeparator();
3729     annotationsMenu.add(showAlignmentAnnotations);
3730     annotationsMenu.add(showSequenceAnnotations);
3731     annotationsMenu.add(sortAnnBySequence);
3732     annotationsMenu.add(sortAnnByLabel);
3733     annotationsMenu.addSeparator();
3734     autoAnnMenu.add(showAutoFirst);
3735     autoAnnMenu.add(showAutoLast);
3736     autoAnnMenu.addSeparator();
3737     autoAnnMenu.add(applyAutoAnnotationSettings);
3738     autoAnnMenu.add(showConsensusHistogram);
3739     autoAnnMenu.add(showSequenceLogo);
3740     autoAnnMenu.add(normSequenceLogo);
3741     autoAnnMenu.addSeparator();
3742     autoAnnMenu.add(showGroupConservation);
3743     autoAnnMenu.add(showGroupConsensus);
3744     annotationsMenu.add(autoAnnMenu);
3745
3746     /*
3747      * Format menu
3748      */
3749     formatMenu.add(font);
3750     formatMenu.add(seqLimits);
3751     formatMenu.add(wrapMenuItem);
3752     formatMenu.add(scaleAbove);
3753     formatMenu.add(scaleLeft);
3754     formatMenu.add(scaleRight);
3755     formatMenu.add(viewBoxesMenuItem);
3756     formatMenu.add(viewTextMenuItem);
3757     formatMenu.add(colourTextMenuItem);
3758     formatMenu.add(displayNonconservedMenuItem);
3759     formatMenu.add(renderGapsMenuItem);
3760     formatMenu.add(centreColumnLabelFlag);
3761
3762     /*
3763      * Colour menu
3764      */
3765     colourMenu.add(applyToAllGroups);
3766     colourMenu.addSeparator();
3767     colourMenu.add(noColourmenuItem);
3768     colourMenu.add(clustalColour);
3769     colourMenu.add(BLOSUM62Colour);
3770     colourMenu.add(PIDColour);
3771     colourMenu.add(zappoColour);
3772     colourMenu.add(taylorColour);
3773     colourMenu.add(hydrophobicityColour);
3774     colourMenu.add(helixColour);
3775     colourMenu.add(strandColour);
3776     colourMenu.add(turnColour);
3777     colourMenu.add(buriedColour);
3778     colourMenu.add(nucleotideColour);
3779     colourMenu.add(purinePyrimidineColour);
3780     // colourMenu.add(RNAInteractionColour);
3781     colourMenu.add(tcoffeeColour);
3782     colourMenu.add(userDefinedColour);
3783     colourMenu.addSeparator();
3784     colourMenu.add(conservationMenuItem);
3785     colourMenu.add(modifyConservation);
3786     colourMenu.add(abovePIDThreshold);
3787     colourMenu.add(modifyPID);
3788     colourMenu.add(annotationColour);
3789     colourMenu.add(RNAHelixColour);
3790
3791     /*
3792      * Calculate menu
3793      */
3794     sortMenu.add(sortIDMenuItem);
3795     sortMenu.add(sortLengthMenuItem);
3796     sortMenu.add(sortByTreeMenu);
3797     sortMenu.add(sortGroupMenuItem);
3798     sortMenu.add(sortPairwiseMenuItem);
3799     calculateMenu.add(sortMenu);
3800     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3801     calculateTreeMenu.add(neighbourTreeMenuItem);
3802     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3803     calculateTreeMenu.add(njTreeBlosumMenuItem);
3804     calculateMenu.add(calculateTreeMenu);
3805     calculateMenu.addSeparator();
3806     calculateMenu.add(pairwiseAlignmentMenuItem);
3807     calculateMenu.add(PCAMenuItem);
3808     calculateMenu.add(autoCalculate);
3809     calculateMenu.add(sortByTree);
3810
3811     /*
3812      * Help menu
3813      */
3814     helpMenu.add(documentation);
3815     helpMenu.add(about);
3816
3817     /*
3818      * Status bar
3819      */
3820     statusBar.setBackground(Color.white);
3821     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3822     statusBar.setText(MessageManager.getString("label.status_bar"));
3823     this.add(statusBar, BorderLayout.SOUTH);
3824   }
3825
3826   @Override
3827   public void setStatus(String string)
3828   {
3829     statusBar.setText(string);
3830   };
3831
3832   MenuItem featureSettings = new MenuItem();
3833
3834   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3835
3836   MenuItem annotationColour = new MenuItem();
3837
3838   MenuItem annotationColumnSelection = new MenuItem();
3839
3840   MenuItem invertColSel = new MenuItem();
3841
3842   MenuItem showColumns = new MenuItem();
3843
3844   MenuItem showSeqs = new MenuItem();
3845
3846   MenuItem hideColumns = new MenuItem();
3847
3848   MenuItem hideSequences = new MenuItem();
3849
3850   MenuItem hideAllButSelection = new MenuItem();
3851
3852   MenuItem hideAllSelection = new MenuItem();
3853
3854   MenuItem showAllHidden = new MenuItem();
3855
3856   MenuItem newView = new MenuItem();
3857
3858   private CheckboxMenuItem showAlignmentAnnotations;
3859
3860   private CheckboxMenuItem showSequenceAnnotations;
3861
3862   private CheckboxMenuItem sortAnnBySequence;
3863
3864   private CheckboxMenuItem sortAnnByLabel;
3865
3866   private CheckboxMenuItem showAutoFirst;
3867
3868   private CheckboxMenuItem showAutoLast;
3869
3870   private SplitFrame splitFrame;
3871
3872   /**
3873    * Attach the alignFrame panels after embedding menus, if necessary. This used
3874    * to be called setEmbedded, but is now creates the dropdown menus in a
3875    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3876    *
3877    * @param reallyEmbedded
3878    *          true to attach the view to the applet area on the page rather than
3879    *          in a new window
3880    */
3881   public void createAlignFrameWindow(boolean reallyEmbedded)
3882   {
3883     if (reallyEmbedded)
3884     {
3885       embedAlignFrameInApplet(viewport.applet);
3886     }
3887     else
3888     {
3889       // //////
3890       // test and embed menu bar if necessary.
3891       //
3892       if (embedMenuIfNeeded(alignPanel))
3893       {
3894         /*
3895          * adjust for status bar height too. ? pointless as overridden by layout
3896          * manager
3897          */
3898         alignPanel.setSize(getSize().width,
3899                 getSize().height - statusBar.getHeight());
3900       }
3901       add(statusBar, BorderLayout.SOUTH);
3902       add(alignPanel, BorderLayout.CENTER);
3903       // and register with the applet so it can pass external API calls to us
3904       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3905               frameHeight);
3906     }
3907   }
3908
3909   /**
3910    * Add the components of this AlignFrame to the applet container.
3911    *
3912    * @param theApplet
3913    */
3914   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3915   {
3916     // ////
3917     // Explicitly build the embedded menu panel for the on-page applet
3918     //
3919     // view cannot be closed if its actually on the page
3920     fileMenu.remove(closeMenuItem);
3921     fileMenu.remove(3); // Remove Separator
3922     // construct embedded menu, using default font
3923     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3924     // and actually add the components to the applet area
3925     theApplet.setLayout(new BorderLayout());
3926     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3927     theApplet.add(statusBar, BorderLayout.SOUTH);
3928     // TODO should size be left to the layout manager?
3929     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3930             - embeddedMenu.getHeight() - statusBar.getHeight());
3931     theApplet.add(alignPanel, BorderLayout.CENTER);
3932     final AlignFrame me = this;
3933     theApplet.addFocusListener(new FocusListener()
3934     {
3935
3936       @Override
3937       public void focusLost(FocusEvent e)
3938       {
3939         if (theApplet.currentAlignFrame == me)
3940         {
3941           theApplet.currentAlignFrame = null;
3942         }
3943       }
3944
3945       @Override
3946       public void focusGained(FocusEvent e)
3947       {
3948         theApplet.currentAlignFrame = me;
3949       }
3950     });
3951     theApplet.validate();
3952   }
3953
3954   /**
3955    * create a new binding between structures in an existing jmol viewer instance
3956    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3957    * this does not open a new Jmol window, or modify the display of the
3958    * structures in the original jmol window. Note This method doesn't work
3959    * without an additional javascript library to exchange messages between the
3960    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3961    *
3962    * @param viewer
3963    *          JmolViewer instance
3964    * @param sequenceIds
3965    *          - sequence Ids to search for associations
3966    */
3967   public SequenceStructureBinding addStructureViewInstance(
3968           Object jmolviewer, String[] sequenceIds)
3969   {
3970     Viewer viewer = null;
3971     try
3972     {
3973       viewer = (Viewer) jmolviewer;
3974     } catch (ClassCastException ex)
3975     {
3976       System.err.println(
3977               "Unsupported viewer object :" + jmolviewer.getClass());
3978     }
3979     if (viewer == null)
3980     {
3981       System.err.println("Can't use this object as a structure viewer:"
3982               + jmolviewer.getClass());
3983       return null;
3984     }
3985     SequenceI[] seqs = null;
3986     if (sequenceIds == null || sequenceIds.length == 0)
3987     {
3988       seqs = viewport.getAlignment().getSequencesArray();
3989     }
3990     else
3991     {
3992       Vector sqi = new Vector();
3993       AlignmentI al = viewport.getAlignment();
3994       for (int sid = 0; sid < sequenceIds.length; sid++)
3995       {
3996         SequenceI sq = al.findName(sequenceIds[sid]);
3997         if (sq != null)
3998         {
3999           sqi.addElement(sq);
4000         }
4001       }
4002       if (sqi.size() > 0)
4003       {
4004         seqs = new SequenceI[sqi.size()];
4005         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4006         {
4007           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4008         }
4009       }
4010       else
4011       {
4012         return null;
4013       }
4014     }
4015     AAStructureBindingModel jmv = null;
4016     // TODO: search for a jmv that involves viewer
4017     if (jmv == null)
4018     { // create a new viewer/jalview binding.
4019       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4020     }
4021     return jmv;
4022
4023   }
4024
4025   /**
4026    * bind a pdb file to a sequence in the current view
4027    *
4028    * @param sequenceId
4029    *          - sequenceId within the dataset.
4030    * @param pdbEntryString
4031    *          - the short name for the PDB file
4032    * @param pdbFile
4033    *          - pdb file - either a URL or a valid PDB file.
4034    * @return true if binding was as success TODO: consider making an exception
4035    *         structure for indicating when PDB parsing or sequenceId location
4036    *         fails.
4037    */
4038   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4039           String pdbFile)
4040   {
4041     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4042     boolean needtoadd = false;
4043     if (toaddpdb != null)
4044     {
4045       Vector pdbe = toaddpdb.getAllPDBEntries();
4046       PDBEntry pdbentry = null;
4047       if (pdbe != null && pdbe.size() > 0)
4048       {
4049         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4050         {
4051           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4052           if (!pdbentry.getId().equals(pdbEntryString)
4053                   && !pdbentry.getFile().equals(pdbFile))
4054           {
4055             pdbentry = null;
4056           }
4057           else
4058           {
4059             continue;
4060           }
4061         }
4062       }
4063       if (pdbentry == null)
4064       {
4065         pdbentry = new PDBEntry();
4066         pdbentry.setId(pdbEntryString);
4067         pdbentry.setFile(pdbFile);
4068         needtoadd = true; // add this new entry to sequence.
4069       }
4070       // resolve data source
4071       // TODO: this code should be a refactored to an io package
4072       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4073               FileFormat.PDB);
4074       if (protocol == null)
4075       {
4076         return false;
4077       }
4078       if (needtoadd)
4079       {
4080         pdbentry.setProperty("protocol", protocol);
4081         toaddpdb.addPDBId(pdbentry);
4082         alignPanel.getStructureSelectionManager()
4083                 .registerPDBEntry(pdbentry);
4084       }
4085     }
4086     return true;
4087   }
4088
4089   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4090   {
4091     if (seqs != null)
4092     {
4093       Vector sequences = new Vector();
4094       for (int i = 0; i < seqs.length; i++)
4095       {
4096         if (seqs[i] != null)
4097         {
4098           sequences
4099                   .addElement(new Object[]
4100                   { seqs[i], (chains != null) ? chains[i] : null });
4101         }
4102       }
4103       seqs = new SequenceI[sequences.size()];
4104       chains = new String[sequences.size()];
4105       for (int i = 0, isize = sequences.size(); i < isize; i++)
4106       {
4107         Object[] oj = (Object[]) sequences.elementAt(i);
4108
4109         seqs[i] = (SequenceI) oj[0];
4110         chains[i] = (String) oj[1];
4111       }
4112     }
4113     return new Object[] { seqs, chains };
4114
4115   }
4116
4117   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4118           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4119   {
4120     // Scrub any null sequences from the array
4121     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4122     seqs = (SequenceI[]) sqch[0];
4123     chains = (String[]) sqch[1];
4124     if (seqs == null || seqs.length == 0)
4125     {
4126       System.err.println(
4127               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4128     }
4129     if (protocol == null)
4130     {
4131       String sourceType = (String) pdb.getProperty("protocol");
4132       try
4133       {
4134         protocol = DataSourceType.valueOf(sourceType);
4135       } catch (IllegalArgumentException e)
4136       {
4137         // ignore
4138       }
4139       if (protocol == null)
4140       {
4141         System.err.println("Couldn't work out protocol to open structure: "
4142                 + pdb.getId());
4143         return;
4144       }
4145     }
4146     if (applet.useXtrnalSviewer)
4147     {
4148       // register the association(s) and quit, don't create any windows.
4149       if (StructureSelectionManager.getStructureSelectionManager(applet)
4150               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4151       {
4152         System.err.println("Failed to map " + pdb.getFile() + " ("
4153                 + protocol + ") to any sequences");
4154       }
4155       return;
4156     }
4157     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4158     {
4159       // can only do alignments with Jmol
4160       // find the last jmol window assigned to this alignment
4161       AppletJmol ajm = null, tajm;
4162       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4163       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4164       {
4165         tajm = (AppletJmol) jmols.elementAt(i);
4166         if (tajm.ap.alignFrame == this)
4167         {
4168           ajm = tajm;
4169           break;
4170         }
4171       }
4172       if (ajm != null)
4173       {
4174         System.err.println(
4175                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4176         // try and add the pdb structure
4177         // ajm.addS
4178         ajm = null;
4179       }
4180     }
4181     // otherwise, create a new window
4182     if (applet.jmolAvailable)
4183     {
4184       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4185       applet.lastFrameX += 40;
4186       applet.lastFrameY += 40;
4187     }
4188     else
4189     {
4190       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4191     }
4192
4193   }
4194
4195   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4196           SequenceI[][] seqs, String[][] chains, String[] protocols)
4197   {
4198     // TODO Auto-generated method stub
4199     System.err.println("Aligned Structure View: Not yet implemented.");
4200   }
4201
4202   /**
4203    * modify the current selection, providing the user has not made a selection
4204    * already.
4205    *
4206    * @param sel
4207    *          - sequences from this alignment
4208    * @param csel
4209    *          - columns to be selected on the alignment
4210    */
4211   public void select(SequenceGroup sel, ColumnSelection csel,
4212           HiddenColumns hidden)
4213   {
4214     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4215   }
4216
4217   public void scrollTo(int row, int column)
4218   {
4219     alignPanel.seqPanel.scrollTo(row, column);
4220   }
4221
4222   public void scrollToRow(int row)
4223   {
4224     alignPanel.seqPanel.scrollToRow(row);
4225   }
4226
4227   public void scrollToColumn(int column)
4228   {
4229     alignPanel.seqPanel.scrollToColumn(column);
4230   }
4231
4232   /**
4233    * @return the alignments unique ID.
4234    */
4235   public String getSequenceSetId()
4236   {
4237     return viewport.getSequenceSetId();
4238   }
4239
4240   /**
4241    * Load the (T-Coffee) score file from the specified url
4242    *
4243    * @param source
4244    *          File/URL/T-COFFEE score file contents
4245    * @throws IOException
4246    * @return true if alignment was annotated with data from source
4247    */
4248   public boolean loadScoreFile(String source) throws IOException
4249   {
4250
4251     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4252             AppletFormatAdapter.checkProtocol(source));
4253     if (!file.isValid())
4254     {
4255       // TODO: raise dialog for gui
4256       System.err.println("Problems parsing T-Coffee scores: "
4257               + file.getWarningMessage());
4258       System.err.println("Origin was:\n" + source);
4259       return false;
4260     }
4261
4262     /*
4263      * check that the score matrix matches the alignment dimensions
4264      */
4265     AlignmentI aln;
4266     if ((aln = viewport.getAlignment()) != null
4267             && (aln.getHeight() != file.getHeight()
4268                     || aln.getWidth() != file.getWidth()))
4269     {
4270       // TODO: raise a dialog box here rather than bomb out.
4271       System.err.println(
4272               "The scores matrix does not match the alignment dimensions");
4273
4274     }
4275
4276     // TODO add parameter to indicate if matching should be done
4277     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4278     {
4279       alignPanel.fontChanged();
4280       tcoffeeColour.setEnabled(true);
4281       // switch to this color
4282       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4283       return true;
4284     }
4285     else
4286     {
4287       System.err.println("Problems resolving T-Coffee scores:");
4288       if (file.getWarningMessage() != null)
4289       {
4290         System.err.println(file.getWarningMessage());
4291       }
4292     }
4293     return false;
4294   }
4295
4296   public SplitFrame getSplitFrame()
4297   {
4298     return this.splitFrame;
4299   }
4300
4301   public void setSplitFrame(SplitFrame sf)
4302   {
4303     this.splitFrame = sf;
4304   }
4305
4306   // may not need this
4307   @Override
4308   public void setShowSeqFeatures(boolean b)
4309   {
4310     // showSeqFeatures.setSelected(b);
4311     viewport.setShowSequenceFeatures(b);
4312
4313   }
4314
4315   @Override
4316   public void setMenusForViewport()
4317   {
4318     // setMenusFromViewport(viewport);
4319
4320   }
4321
4322   @Override
4323   public void refreshFeatureUI(boolean enableIfNecessary)
4324   {
4325     if (enableIfNecessary)
4326     {
4327       sequenceFeatures.setState(true);
4328       alignPanel.av.setShowSequenceFeatures(true);
4329     }
4330   }
4331
4332   @Override
4333   public FeatureSettingsControllerI getFeatureSettingsUI()
4334   {
4335     return alignPanel.av.featureSettings;
4336   }
4337
4338 }