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,
 177           String title, 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,
 184           String title, boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237
 238     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 239     followMouseOverFlag.setState(viewport.isFollowHighlight());
 240     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 241     showGroupConservation.setState(viewport.isShowGroupConservation());
 242     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 243     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 244     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 245     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 246     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 247     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 248     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showAlignmentAnnotations.setState(true);
 250     showSequenceAnnotations.setState(false);
 251
 252     seqLimits.setState(viewport.getShowJVSuffix());
 253
 254     if (applet != null)
 255     {
 256       String param = applet.getParameter("sortBy");
 257       if (param != null)
 258       {
 259         if (param.equalsIgnoreCase("Id"))
 260         {
 261           sortIDMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Pairwise Identity"))
 264         {
 265           sortPairwiseMenuItem_actionPerformed();
 266         }
 267         else if (param.equalsIgnoreCase("Length"))
 268         {
 269           sortLengthMenuItem_actionPerformed();
 270         }
 271       }
 272
 273       param = applet.getParameter("wrap");
 274       if (param != null)
 275       {
 276         if (param.equalsIgnoreCase("true"))
 277         {
 278           wrapMenuItem.setState(true);
 279           wrapMenuItem_actionPerformed();
 280         }
 281       }
 282       param = applet.getParameter("centrecolumnlabels");
 283       if (param != null)
 284       {
 285         centreColumnLabelFlag.setState(true);
 286         centreColumnLabelFlag_stateChanged();
 287       }
 288
 289     }
 290     if (viewport.getAlignment().isNucleotide())
 291     {
 292       conservationMenuItem.setEnabled(false);
 293       clustalColour.setEnabled(false);
 294       BLOSUM62Colour.setEnabled(false);
 295       zappoColour.setEnabled(false);
 296       taylorColour.setEnabled(false);
 297       hydrophobicityColour.setEnabled(false);
 298       helixColour.setEnabled(false);
 299       strandColour.setEnabled(false);
 300       turnColour.setEnabled(false);
 301       buriedColour.setEnabled(false);
 302       viewport.updateStrucConsensus(alignPanel);
 303       if (viewport.getAlignment().hasRNAStructure())
 304       {
 305         RNAHelixColour.setEnabled(true);
 306       }
 307       else
 308       {
 309         RNAHelixColour.setEnabled(false);
 310       }
 311     }
 312     else
 313     {
 314       RNAHelixColour.setEnabled(false);
 315       purinePyrimidineColour.setEnabled(false);
 316       nucleotideColour.setEnabled(false);
 317     }
 318     // Some JVMS send keyevents to Top frame or lowest panel,
 319     // Havent worked out why yet. So add to both this frame and seqCanvas for
 320     // now
 321     this.addKeyListener(this);
 322     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 323     alignPanel.idPanel.idCanvas.addKeyListener(this);
 324     alignPanel.scalePanel.addKeyListener(this);
 325     alignPanel.annotationPanel.addKeyListener(this);
 326     alignPanel.annotationPanelHolder.addKeyListener(this);
 327     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 328     alignPanel.alabels.addKeyListener(this);
 329
 330     setAnnotationsVisibility();
 331
 332     if (addToDisplay)
 333     {
 334       addToDisplay(embedded);
 335     }
 336   }
 337
 338   /**
 339    * @param embedded
 340    */
 341   public void addToDisplay(boolean embedded)
 342   {
 343     createAlignFrameWindow(embedded);
 344     validate();
 345     alignPanel.adjustAnnotationHeight();
 346     alignPanel.paintAlignment(true);
 347   }
 348
 349   public AlignViewport getAlignViewport()
 350   {
 351     return viewport;
 352   }
 353
 354   public SeqCanvas getSeqcanvas()
 355   {
 356     return alignPanel.seqPanel.seqCanvas;
 357   }
 358
 359   /**
 360    * Load a features file onto the alignment
 361    *
 362    * @param file
 363    *          file URL, content, or other resolvable path
 364    * @param type
 365    *          is protocol for accessing data referred to by file
 366    */
 367
 368   public boolean parseFeaturesFile(String file, DataSourceType type)
 369   {
 370     return parseFeaturesFile(file, type, true);
 371   }
 372
 373   /**
 374    * Load a features file onto the alignment
 375    *
 376    * @param file
 377    *          file URL, content, or other resolvable path
 378    * @param sourceType
 379    *          is protocol for accessing data referred to by file
 380    * @param autoenabledisplay
 381    *          when true, display features flag will be automatically enabled if
 382    *          features are loaded
 383    * @return true if data parsed as a features file
 384    */
 385   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 386           boolean autoenabledisplay)
 387   {
 388     boolean featuresFile = false;
 389     try
 390     {
 391       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 392               .getFeatureRenderer().getFeatureColours();
 393       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 394               "relaxedidmatch", false);
 395       featuresFile = new FeaturesFile(file, sourceType).parse(
 396               viewport.getAlignment(), colours, true, relaxedIdMatching);
 397     } catch (Exception ex)
 398     {
 399       ex.printStackTrace();
 400     }
 401
 402     if (featuresFile)
 403     {
 404       if (autoenabledisplay)
 405       {
 406         viewport.setShowSequenceFeatures(true);
 407         sequenceFeatures.setState(true);
 408       }
 409       if (alignPanel.seqPanel.seqCanvas.fr != null)
 410       {
 411         // update the min/max ranges where necessary
 412         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 413       }
 414       if (viewport.featureSettings != null)
 415       {
 416         viewport.featureSettings.refreshTable();
 417       }
 418       alignPanel.paintAlignment(true);
 419       statusBar.setText(MessageManager
 420               .getString("label.successfully_added_features_alignment"));
 421     }
 422     return featuresFile;
 423   }
 424
 425   @Override
 426   public void keyPressed(KeyEvent evt)
 427   {
 428     ViewportRanges ranges = viewport.getRanges();
 429
 430     if (viewport.cursorMode
 431             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 432                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 433                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 434             && Character.isDigit(evt.getKeyChar()))
 435     {
 436       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 437     }
 438
 439     switch (evt.getKeyCode())
 440     {
 441     case 27: // escape key
 442       deselectAllSequenceMenuItem_actionPerformed();
 443
 444       alignPanel.alabels.cancelDrag();
 445       break;
 446     case KeyEvent.VK_X:
 447       if (evt.isControlDown() || evt.isMetaDown())
 448       {
 449         cut_actionPerformed();
 450       }
 451       break;
 452     case KeyEvent.VK_C:
 453       if (viewport.cursorMode && !evt.isControlDown())
 454       {
 455         alignPanel.seqPanel.setCursorColumn();
 456       }
 457       if (evt.isControlDown() || evt.isMetaDown())
 458       {
 459         copy_actionPerformed();
 460       }
 461       break;
 462     case KeyEvent.VK_V:
 463       if (evt.isControlDown())
 464       {
 465         paste(evt.isShiftDown());
 466       }
 467       break;
 468     case KeyEvent.VK_A:
 469       if (evt.isControlDown() || evt.isMetaDown())
 470       {
 471         selectAllSequenceMenuItem_actionPerformed();
 472       }
 473       break;
 474     case KeyEvent.VK_DOWN:
 475       if (viewport.cursorMode)
 476       {
 477         alignPanel.seqPanel.moveCursor(0, 1);
 478       }
 479       else
 480       {
 481         moveSelectedSequences(false);
 482       }
 483       break;
 484
 485     case KeyEvent.VK_UP:
 486       if (viewport.cursorMode)
 487       {
 488         alignPanel.seqPanel.moveCursor(0, -1);
 489       }
 490       else
 491       {
 492         moveSelectedSequences(true);
 493       }
 494       break;
 495
 496     case KeyEvent.VK_LEFT:
 497       if (evt.isAltDown() || !viewport.cursorMode)
 498       {
 499         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 500       }
 501       else
 502       {
 503         alignPanel.seqPanel.moveCursor(-1, 0);
 504       }
 505       break;
 506
 507     case KeyEvent.VK_RIGHT:
 508       if (evt.isAltDown() || !viewport.cursorMode)
 509       {
 510         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 511       }
 512       else
 513       {
 514         alignPanel.seqPanel.moveCursor(1, 0);
 515       }
 516       break;
 517
 518     case KeyEvent.VK_SPACE:
 519       if (viewport.cursorMode)
 520       {
 521         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 522                 || evt.isShiftDown() || evt.isAltDown());
 523       }
 524       break;
 525
 526     case KeyEvent.VK_DELETE:
 527     case KeyEvent.VK_BACK_SPACE:
 528       if (viewport.cursorMode)
 529       {
 530         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 531                 || evt.isShiftDown() || evt.isAltDown());
 532       }
 533       else
 534       {
 535         cut_actionPerformed();
 536         alignPanel.seqPanel.seqCanvas.repaint();
 537       }
 538       break;
 539
 540     case KeyEvent.VK_S:
 541       if (viewport.cursorMode)
 542       {
 543         alignPanel.seqPanel.setCursorRow();
 544       }
 545       break;
 546     case KeyEvent.VK_P:
 547       if (viewport.cursorMode)
 548       {
 549         alignPanel.seqPanel.setCursorPosition();
 550       }
 551       break;
 552
 553     case KeyEvent.VK_ENTER:
 554     case KeyEvent.VK_COMMA:
 555       if (viewport.cursorMode)
 556       {
 557         alignPanel.seqPanel.setCursorRowAndColumn();
 558       }
 559       break;
 560
 561     case KeyEvent.VK_Q:
 562       if (viewport.cursorMode)
 563       {
 564         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 565       }
 566       break;
 567     case KeyEvent.VK_M:
 568       if (viewport.cursorMode)
 569       {
 570         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 571       }
 572       break;
 573
 574     case KeyEvent.VK_F2:
 575       viewport.cursorMode = !viewport.cursorMode;
 576       statusBar.setText(MessageManager.formatMessage(
 577               "label.keyboard_editing_mode",
 578               new String[] { (viewport.cursorMode ? "on" : "off") }));
 579       if (viewport.cursorMode)
 580       {
 581         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 582         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 583       }
 584       break;
 585
 586     case KeyEvent.VK_F:
 587       if (evt.isControlDown())
 588       {
 589         findMenuItem_actionPerformed();
 590       }
 591       break;
 592
 593     case KeyEvent.VK_H:
 594     {
 595       boolean toggleSeqs = !evt.isControlDown();
 596       boolean toggleCols = !evt.isShiftDown();
 597       toggleHiddenRegions(toggleSeqs, toggleCols);
 598       break;
 599     }
 600
 601     case KeyEvent.VK_PAGE_UP:
 602       ranges.pageUp();
 603       break;
 604
 605     case KeyEvent.VK_PAGE_DOWN:
 606       ranges.pageDown();
 607       break;
 608
 609     case KeyEvent.VK_Z:
 610       if (evt.isControlDown())
 611       {
 612         undoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_Y:
 617       if (evt.isControlDown())
 618       {
 619         redoMenuItem_actionPerformed();
 620       }
 621       break;
 622
 623     case KeyEvent.VK_L:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(true);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_R:
 631       if (evt.isControlDown())
 632       {
 633         trimAlignment(false);
 634       }
 635       break;
 636
 637     case KeyEvent.VK_E:
 638       if (evt.isControlDown())
 639       {
 640         if (evt.isShiftDown())
 641         {
 642           this.removeAllGapsMenuItem_actionPerformed();
 643         }
 644         else
 645         {
 646           removeGappedColumnMenuItem_actionPerformed();
 647         }
 648       }
 649       break;
 650     case KeyEvent.VK_I:
 651       if (evt.isControlDown())
 652       {
 653         if (evt.isAltDown())
 654         {
 655           invertColSel_actionPerformed();
 656         }
 657         else
 658         {
 659           invertSequenceMenuItem_actionPerformed();
 660         }
 661       }
 662       break;
 663
 664     case KeyEvent.VK_G:
 665       if (evt.isControlDown())
 666       {
 667         if (evt.isShiftDown())
 668         {
 669           this.unGroup_actionPerformed();
 670         }
 671         else
 672         {
 673           this.createGroup_actionPerformed();
 674         }
 675       }
 676       break;
 677
 678     case KeyEvent.VK_U:
 679       if (evt.isControlDown())
 680       {
 681         this.deleteGroups_actionPerformed();
 682       }
 683       break;
 684
 685     case KeyEvent.VK_T:
 686       if (evt.isControlDown())
 687       {
 688         newView(null);
 689       }
 690       break;
 691
 692     }
 693     alignPanel.paintAlignment(true);
 694   }
 695
 696   /**
 697    * called by key handler and the hide all/show all menu items
 698    *
 699    * @param toggleSeqs
 700    * @param toggleCols
 701    */
 702   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 703   {
 704     boolean hide = false;
 705     SequenceGroup sg = viewport.getSelectionGroup();
 706     if (!toggleSeqs && !toggleCols)
 707     {
 708       // Hide everything by the current selection - this is a hack - we do the
 709       // invert and then hide
 710       // first check that there will be visible columns after the invert.
 711       if (viewport.hasSelectedColumns()
 712               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 713                       .getEndRes()))
 714       {
 715         // now invert the sequence set, if required - empty selection implies
 716         // that no hiding is required.
 717         if (sg != null)
 718         {
 719           invertSequenceMenuItem_actionPerformed();
 720           sg = viewport.getSelectionGroup();
 721           toggleSeqs = true;
 722
 723         }
 724         viewport.expandColSelection(sg, true);
 725         // finally invert the column selection and get the new sequence
 726         // selection and indicate it should be hidden.
 727         invertColSel_actionPerformed();
 728         toggleCols = true;
 729       }
 730     }
 731
 732     if (toggleSeqs)
 733     {
 734       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 735       {
 736         hide = true;
 737         viewport.hideAllSelectedSeqs();
 738       }
 739       else if (!(toggleCols && viewport.hasSelectedColumns()))
 740       {
 741         viewport.showAllHiddenSeqs();
 742       }
 743     }
 744
 745     if (toggleCols)
 746     {
 747       if (viewport.hasSelectedColumns())
 748       {
 749         viewport.hideSelectedColumns();
 750         if (!toggleSeqs)
 751         {
 752           viewport.setSelectionGroup(sg);
 753         }
 754       }
 755       else if (!hide)
 756       {
 757         viewport.showAllHiddenColumns();
 758       }
 759       viewport.sendSelection();
 760     }
 761   }
 762
 763   @Override
 764   public void keyReleased(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void keyTyped(KeyEvent evt)
 770   {
 771   }
 772
 773   @Override
 774   public void itemStateChanged(ItemEvent evt)
 775   {
 776     final Object source = evt.getSource();
 777     if (source == displayNonconservedMenuItem)
 778     {
 779       displayNonconservedMenuItem_actionPerformed();
 780     }
 781     else if (source == colourTextMenuItem)
 782     {
 783       colourTextMenuItem_actionPerformed();
 784     }
 785     else if (source == wrapMenuItem)
 786     {
 787       wrapMenuItem_actionPerformed();
 788     }
 789     else if (source == scaleAbove)
 790     {
 791       viewport.setScaleAboveWrapped(scaleAbove.getState());
 792     }
 793     else if (source == scaleLeft)
 794     {
 795       viewport.setScaleLeftWrapped(scaleLeft.getState());
 796     }
 797     else if (source == scaleRight)
 798     {
 799       viewport.setScaleRightWrapped(scaleRight.getState());
 800     }
 801     else if (source == seqLimits)
 802     {
 803       seqLimits_itemStateChanged();
 804     }
 805     else if (source == viewBoxesMenuItem)
 806     {
 807       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 808     }
 809     else if (source == viewTextMenuItem)
 810     {
 811       viewport.setShowText(viewTextMenuItem.getState());
 812     }
 813     else if (source == renderGapsMenuItem)
 814     {
 815       viewport.setRenderGaps(renderGapsMenuItem.getState());
 816     }
 817     else if (source == annotationPanelMenuItem)
 818     {
 819       boolean showAnnotations = annotationPanelMenuItem.getState();
 820       showAlignmentAnnotations.setEnabled(showAnnotations);
 821       showSequenceAnnotations.setEnabled(showAnnotations);
 822       viewport.setShowAnnotation(showAnnotations);
 823       alignPanel.setAnnotationVisible(showAnnotations);
 824     }
 825     else if (source == sequenceFeatures)
 826     {
 827       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 828       alignPanel.seqPanel.seqCanvas.repaint();
 829     }
 830     else if (source == showAlignmentAnnotations)
 831     {
 832       setAnnotationsVisibility();
 833     }
 834     else if (source == showSequenceAnnotations)
 835     {
 836       setAnnotationsVisibility();
 837     }
 838     else if (source == sortAnnBySequence)
 839     {
 840       boolean newState = sortAnnBySequence.getState();
 841       sortAnnByLabel.setState(false);
 842       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 843               : SequenceAnnotationOrder.NONE);
 844       setViewportAnnotationOrder();
 845     }
 846     else if (source == sortAnnByLabel)
 847     {
 848       boolean newState = sortAnnByLabel.getState();
 849       sortAnnBySequence.setState(false);
 850       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 851               : SequenceAnnotationOrder.NONE);
 852       setViewportAnnotationOrder();
 853     }
 854     else if (source == showAutoFirst)
 855     {
 856       showAutoLast.setState(!showAutoFirst.getState());
 857       setShowAutoCalculatedAbove(showAutoFirst.getState());
 858       setViewportAnnotationOrder();
 859     }
 860     else if (source == showAutoLast)
 861     {
 862       showAutoFirst.setState(!showAutoLast.getState());
 863       setShowAutoCalculatedAbove(showAutoFirst.getState());
 864       setViewportAnnotationOrder();
 865     }
 866     else if (source == conservationMenuItem)
 867     {
 868       conservationMenuItem_actionPerformed();
 869     }
 870     else if (source == abovePIDThreshold)
 871     {
 872       abovePIDThreshold_actionPerformed();
 873     }
 874     else if (source == applyToAllGroups)
 875     {
 876       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 877     }
 878     else if (source == autoCalculate)
 879     {
 880       viewport.autoCalculateConsensus = autoCalculate.getState();
 881     }
 882     else if (source == sortByTree)
 883     {
 884       viewport.sortByTree = sortByTree.getState();
 885     }
 886     else if (source == this.centreColumnLabelFlag)
 887     {
 888       centreColumnLabelFlag_stateChanged();
 889     }
 890     else if (source == this.followMouseOverFlag)
 891     {
 892       mouseOverFlag_stateChanged();
 893     }
 894     else if (source == showGroupConsensus)
 895     {
 896       showGroupConsensus_actionPerformed();
 897     }
 898     else if (source == showGroupConservation)
 899     {
 900       showGroupConservation_actionPerformed();
 901     }
 902     else if (source == showSequenceLogo)
 903     {
 904       showSequenceLogo_actionPerformed();
 905     }
 906     else if (source == normSequenceLogo)
 907     {
 908       normSequenceLogo_actionPerformed();
 909     }
 910     else if (source == showConsensusHistogram)
 911     {
 912       showConsensusHistogram_actionPerformed();
 913     }
 914     else if (source == applyAutoAnnotationSettings)
 915     {
 916       applyAutoAnnotationSettings_actionPerformed();
 917     }
 918     alignPanel.paintAlignment(true);
 919   }
 920
 921   /**
 922    * Set the visibility state of sequence-related and/or alignment-related
 923    * annotations depending on checkbox selections, and repaint.
 924    *
 925    * @param visible
 926    */
 927   private void setAnnotationsVisibility()
 928   {
 929     boolean showForAlignment = showAlignmentAnnotations.getState();
 930     boolean showForSequences = showSequenceAnnotations.getState();
 931     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 932     {
 933       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 934               .getAlignmentAnnotation())
 935       {
 936         boolean visible = (aa.sequenceRef == null ? showForAlignment
 937                 : showForSequences);
 938         aa.visible = visible;
 939       }
 940     }
 941     alignPanel.validateAnnotationDimensions(true);
 942     validate();
 943     repaint();
 944   }
 945
 946   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 947   {
 948     this.annotationSortOrder = order;
 949   }
 950
 951   /**
 952    * Set flags on the viewport that control annotation ordering
 953    */
 954   private void setViewportAnnotationOrder()
 955   {
 956     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 957     this.alignPanel.av
 958             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 959   }
 960
 961   private void setShowAutoCalculatedAbove(boolean showAbove)
 962   {
 963     this.showAutoCalculatedAbove = showAbove;
 964   }
 965
 966   private void mouseOverFlag_stateChanged()
 967   {
 968     viewport.setFollowHighlight(followMouseOverFlag.getState());
 969     // TODO: could kick the scrollTo mechanism to reset view for current
 970     // searchresults.
 971   }
 972
 973   private void centreColumnLabelFlag_stateChanged()
 974   {
 975     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 976     this.alignPanel.annotationPanel.repaint();
 977   }
 978
 979   @Override
 980   public void actionPerformed(ActionEvent evt)
 981   {
 982     viewport.applet.currentAlignFrame = this;
 983
 984     Object source = evt.getSource();
 985
 986     if (source == inputText)
 987     {
 988       inputText_actionPerformed();
 989     }
 990     else if (source == loadTree)
 991     {
 992       loadTree_actionPerformed();
 993     }
 994     else if (source == loadApplication)
 995     {
 996       launchFullApplication();
 997     }
 998     else if (source == loadAnnotations)
 999     {
1000       loadAnnotations();
1001     }
1002     else if (source == outputAnnotations)
1003     {
1004       outputAnnotations(true);
1005     }
1006     else if (source == outputFeatures)
1007     {
1008       outputFeatures(true, "Jalview");
1009     }
1010     else if (source == closeMenuItem)
1011     {
1012       closeMenuItem_actionPerformed();
1013     }
1014     else if (source == copy)
1015     {
1016       copy_actionPerformed();
1017     }
1018     else if (source == undoMenuItem)
1019     {
1020       undoMenuItem_actionPerformed();
1021     }
1022     else if (source == redoMenuItem)
1023     {
1024       redoMenuItem_actionPerformed();
1025     }
1026     else if (source == inputText)
1027     {
1028       inputText_actionPerformed();
1029     }
1030     else if (source == closeMenuItem)
1031     {
1032       closeMenuItem_actionPerformed();
1033     }
1034     else if (source == undoMenuItem)
1035     {
1036       undoMenuItem_actionPerformed();
1037     }
1038     else if (source == redoMenuItem)
1039     {
1040       redoMenuItem_actionPerformed();
1041     }
1042     else if (source == copy)
1043     {
1044       copy_actionPerformed();
1045     }
1046     else if (source == pasteNew)
1047     {
1048       pasteNew_actionPerformed();
1049     }
1050     else if (source == pasteThis)
1051     {
1052       pasteThis_actionPerformed();
1053     }
1054     else if (source == cut)
1055     {
1056       cut_actionPerformed();
1057     }
1058     else if (source == delete)
1059     {
1060       delete_actionPerformed();
1061     }
1062     else if (source == createGroup)
1063     {
1064       createGroup_actionPerformed();
1065     }
1066     else if (source == unGroup)
1067     {
1068       unGroup_actionPerformed();
1069     }
1070     else if (source == grpsFromSelection)
1071     {
1072       makeGrpsFromSelection_actionPerformed();
1073     }
1074     else if (source == deleteGroups)
1075     {
1076       deleteGroups_actionPerformed();
1077     }
1078     else if (source == selectAllSequenceMenuItem)
1079     {
1080       selectAllSequenceMenuItem_actionPerformed();
1081     }
1082     else if (source == deselectAllSequenceMenuItem)
1083     {
1084       deselectAllSequenceMenuItem_actionPerformed();
1085     }
1086     else if (source == invertSequenceMenuItem)
1087     {
1088       invertSequenceMenuItem_actionPerformed();
1089       // uncomment to slave sequence selections in split frame
1090       // viewport.sendSelection();
1091     }
1092     else if (source == invertColSel)
1093     {
1094       viewport.invertColumnSelection();
1095       alignPanel.paintAlignment(true);
1096       viewport.sendSelection();
1097     }
1098     else if (source == remove2LeftMenuItem)
1099     {
1100       trimAlignment(true);
1101     }
1102     else if (source == remove2RightMenuItem)
1103     {
1104       trimAlignment(false);
1105     }
1106     else if (source == removeGappedColumnMenuItem)
1107     {
1108       removeGappedColumnMenuItem_actionPerformed();
1109     }
1110     else if (source == removeAllGapsMenuItem)
1111     {
1112       removeAllGapsMenuItem_actionPerformed();
1113     }
1114     else if (source == findMenuItem)
1115     {
1116       findMenuItem_actionPerformed();
1117     }
1118     else if (source == font)
1119     {
1120       new FontChooser(alignPanel);
1121     }
1122     else if (source == newView)
1123     {
1124       newView(null);
1125     }
1126     else if (source == showColumns)
1127     {
1128       viewport.showAllHiddenColumns();
1129       alignPanel.paintAlignment(true);
1130       viewport.sendSelection();
1131     }
1132     else if (source == showSeqs)
1133     {
1134       viewport.showAllHiddenSeqs();
1135       alignPanel.paintAlignment(true);
1136       // uncomment if we want to slave sequence selections in split frame
1137       // viewport.sendSelection();
1138     }
1139     else if (source == hideColumns)
1140     {
1141       viewport.hideSelectedColumns();
1142       alignPanel.paintAlignment(true);
1143       viewport.sendSelection();
1144     }
1145     else if (source == hideSequences
1146             && viewport.getSelectionGroup() != null)
1147     {
1148       viewport.hideAllSelectedSeqs();
1149       alignPanel.paintAlignment(true);
1150       // uncomment if we want to slave sequence selections in split frame
1151       // viewport.sendSelection();
1152     }
1153     else if (source == hideAllButSelection)
1154     {
1155       toggleHiddenRegions(false, false);
1156       alignPanel.paintAlignment(true);
1157       viewport.sendSelection();
1158     }
1159     else if (source == hideAllSelection)
1160     {
1161       SequenceGroup sg = viewport.getSelectionGroup();
1162       viewport.expandColSelection(sg, false);
1163       viewport.hideAllSelectedSeqs();
1164       viewport.hideSelectedColumns();
1165       alignPanel.paintAlignment(true);
1166       viewport.sendSelection();
1167     }
1168     else if (source == showAllHidden)
1169     {
1170       viewport.showAllHiddenColumns();
1171       viewport.showAllHiddenSeqs();
1172       alignPanel.paintAlignment(true);
1173       viewport.sendSelection();
1174     }
1175     else if (source == showGroupConsensus)
1176     {
1177       showGroupConsensus_actionPerformed();
1178     }
1179     else if (source == showGroupConservation)
1180     {
1181       showGroupConservation_actionPerformed();
1182     }
1183     else if (source == showSequenceLogo)
1184     {
1185       showSequenceLogo_actionPerformed();
1186     }
1187     else if (source == normSequenceLogo)
1188     {
1189       normSequenceLogo_actionPerformed();
1190     }
1191     else if (source == showConsensusHistogram)
1192     {
1193       showConsensusHistogram_actionPerformed();
1194     }
1195     else if (source == applyAutoAnnotationSettings)
1196     {
1197       applyAutoAnnotationSettings_actionPerformed();
1198     }
1199     else if (source == featureSettings)
1200     {
1201       new FeatureSettings(alignPanel);
1202     }
1203     else if (source == alProperties)
1204     {
1205       StringBuffer contents = new jalview.io.AlignmentProperties(
1206               viewport.getAlignment()).formatAsString();
1207       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1208       cap.setText(contents.toString());
1209       Frame frame = new Frame();
1210       frame.add(cap);
1211       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1212               "label.alignment_properties", new String[] { getTitle() }),
1213               400, 250);
1214     }
1215     else if (source == overviewMenuItem)
1216     {
1217       overviewMenuItem_actionPerformed();
1218     }
1219     else if (source == noColourmenuItem)
1220     {
1221       changeColour(null);
1222     }
1223     else if (source == clustalColour)
1224     {
1225       abovePIDThreshold.setState(false);
1226       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1227     }
1228     else if (source == zappoColour)
1229     {
1230       changeColour(new ZappoColourScheme());
1231     }
1232     else if (source == taylorColour)
1233     {
1234       changeColour(new TaylorColourScheme());
1235     }
1236     else if (source == hydrophobicityColour)
1237     {
1238       changeColour(new HydrophobicColourScheme());
1239     }
1240     else if (source == helixColour)
1241     {
1242       changeColour(new HelixColourScheme());
1243     }
1244     else if (source == strandColour)
1245     {
1246       changeColour(new StrandColourScheme());
1247     }
1248     else if (source == turnColour)
1249     {
1250       changeColour(new TurnColourScheme());
1251     }
1252     else if (source == buriedColour)
1253     {
1254       changeColour(new BuriedColourScheme());
1255     }
1256     else if (source == nucleotideColour)
1257     {
1258       changeColour(new NucleotideColourScheme());
1259     }
1260     else if (source == purinePyrimidineColour)
1261     {
1262       changeColour(new PurinePyrimidineColourScheme());
1263     }
1264     // else if (source == RNAInteractionColour)
1265     // {
1266     // changeColour(new RNAInteractionColourScheme());
1267     // }
1268     else if (source == RNAHelixColour)
1269     {
1270       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1271       // new RNAHelicesColourChooser(viewport, alignPanel);
1272     }
1273     else if (source == modifyPID)
1274     {
1275       modifyPID_actionPerformed();
1276     }
1277     else if (source == modifyConservation)
1278     {
1279       modifyConservation_actionPerformed();
1280     }
1281     else if (source == userDefinedColour)
1282     {
1283       new UserDefinedColours(alignPanel, null);
1284     }
1285     else if (source == PIDColour)
1286     {
1287       changeColour(new PIDColourScheme());
1288     }
1289     else if (source == BLOSUM62Colour)
1290     {
1291       changeColour(new Blosum62ColourScheme());
1292     }
1293     else if (source == tcoffeeColour)
1294     {
1295       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1296     }
1297     else if (source == annotationColour)
1298     {
1299       new AnnotationColourChooser(viewport, alignPanel);
1300     }
1301     else if (source == annotationColumnSelection)
1302     {
1303       new AnnotationColumnChooser(viewport, alignPanel);
1304     }
1305     else if (source == sortPairwiseMenuItem)
1306     {
1307       sortPairwiseMenuItem_actionPerformed();
1308     }
1309     else if (source == sortIDMenuItem)
1310     {
1311       sortIDMenuItem_actionPerformed();
1312     }
1313     else if (source == sortLengthMenuItem)
1314     {
1315       sortLengthMenuItem_actionPerformed();
1316     }
1317     else if (source == sortGroupMenuItem)
1318     {
1319       sortGroupMenuItem_actionPerformed();
1320     }
1321     else if (source == removeRedundancyMenuItem)
1322     {
1323       removeRedundancyMenuItem_actionPerformed();
1324     }
1325     else if (source == pairwiseAlignmentMenuItem)
1326     {
1327       pairwiseAlignmentMenuItem_actionPerformed();
1328     }
1329     else if (source == PCAMenuItem)
1330     {
1331       PCAMenuItem_actionPerformed();
1332     }
1333     else if (source == averageDistanceTreeMenuItem)
1334     {
1335       averageDistanceTreeMenuItem_actionPerformed();
1336     }
1337     else if (source == neighbourTreeMenuItem)
1338     {
1339       neighbourTreeMenuItem_actionPerformed();
1340     }
1341     else if (source == njTreeBlosumMenuItem)
1342     {
1343       njTreeBlosumMenuItem_actionPerformed();
1344     }
1345     else if (source == avDistanceTreeBlosumMenuItem)
1346     {
1347       avTreeBlosumMenuItem_actionPerformed();
1348     }
1349     else if (source == documentation)
1350     {
1351       documentation_actionPerformed();
1352     }
1353     else if (source == about)
1354     {
1355       about_actionPerformed();
1356     }
1357
1358   }
1359
1360   public void inputText_actionPerformed()
1361   {
1362     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1363     Frame frame = new Frame();
1364     frame.add(cap);
1365     jalview.bin.JalviewLite.addFrame(frame,
1366             MessageManager.getString("label.input_cut_paste"), 500, 500);
1367   }
1368
1369   protected void outputText_actionPerformed(ActionEvent e)
1370   {
1371     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1372     Frame frame = new Frame();
1373     frame.add(cap);
1374     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1375             "label.alignment_output_command",
1376             new Object[] { e.getActionCommand() }), 600, 500);
1377
1378     FileFormatI fileFormat = FileFormats.getInstance().forName(
1379             e.getActionCommand());
1380     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1381             fileFormat, viewport.getAlignment(),
1382             viewport.getShowJVSuffix()));
1383   }
1384
1385   public void loadAnnotations()
1386   {
1387     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1388     cap.setText(MessageManager
1389             .getString("label.paste_features_annotations_Tcoffee_here"));
1390     cap.setAnnotationImport();
1391     Frame frame = new Frame();
1392     frame.add(cap);
1393     jalview.bin.JalviewLite.addFrame(frame,
1394             MessageManager.getString("action.paste_annotations"), 400, 300);
1395
1396   }
1397
1398   public String outputAnnotations(boolean displayTextbox)
1399   {
1400     String annotation = new AnnotationFile()
1401             .printAnnotationsForView(viewport);
1402
1403     if (displayTextbox)
1404     {
1405       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1406       Frame frame = new Frame();
1407       frame.add(cap);
1408       jalview.bin.JalviewLite.addFrame(frame,
1409               MessageManager.getString("label.annotations"), 600, 500);
1410       cap.setText(annotation);
1411     }
1412
1413     return annotation;
1414   }
1415
1416   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1417   {
1418     if (alignPanel.getFeatureRenderer() != null
1419             && viewport.getFeaturesDisplayed() != null)
1420     {
1421       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1422
1423     }
1424     return null;
1425   }
1426
1427   private List<String> getDisplayedFeatureGroups()
1428   {
1429     if (alignPanel.getFeatureRenderer() != null
1430             && viewport.getFeaturesDisplayed() != null)
1431     {
1432       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1433
1434     }
1435     return null;
1436   }
1437
1438   public String outputFeatures(boolean displayTextbox, String format)
1439   {
1440     String features;
1441     FeaturesFile formatter = new FeaturesFile();
1442     if (format.equalsIgnoreCase("Jalview"))
1443     {
1444       features = formatter.printJalviewFormat(viewport.getAlignment()
1445               .getSequencesArray(), getDisplayedFeatureCols(),
1446               getDisplayedFeatureGroups(), true);
1447     }
1448     else
1449     {
1450       features = formatter.printGffFormat(viewport.getAlignment()
1451               .getSequencesArray(), getDisplayedFeatureCols(),
1452               getDisplayedFeatureGroups(), true);
1453     }
1454
1455     if (displayTextbox)
1456     {
1457       boolean frimport = false;
1458       if (features == null || features.equals("No Features Visible"))
1459       {
1460         features = "# No features visible - paste some and import them here.";
1461         frimport = true;
1462       }
1463
1464       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1465       if (frimport)
1466       {
1467         cap.setAnnotationImport();
1468       }
1469       Frame frame = new Frame();
1470       frame.add(cap);
1471       jalview.bin.JalviewLite.addFrame(frame,
1472               MessageManager.getString("label.features"), 600, 500);
1473       cap.setText(features);
1474     }
1475     else
1476     {
1477       if (features == null)
1478       {
1479         features = "";
1480       }
1481     }
1482
1483     return features;
1484   }
1485
1486   void launchFullApplication()
1487   {
1488     StringBuffer url = new StringBuffer(jalviewServletURL);
1489
1490     // allow servlet parameters to be passed in applet parameter
1491     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1492             : "?";
1493     url.append(firstSep);
1494
1495     url.append("open="
1496             + appendProtocol(viewport.applet.getParameter("file")));
1497
1498     if (viewport.applet.getParameter("features") != null)
1499     {
1500       url.append("&features=");
1501       url.append(appendProtocol(viewport.applet.getParameter("features")));
1502     }
1503
1504     if (viewport.applet.getParameter("annotations") != null)
1505     {
1506       url.append("&annotations=");
1507       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1508     }
1509
1510     if (viewport.applet.getParameter("jnetfile") != null
1511             || viewport.applet.getParameter("jpredfile") != null)
1512     {
1513       url.append("&annotations=");
1514       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1515               .getParameter("jnetfile") : viewport.applet
1516               .getParameter("jpredfile")));
1517     }
1518
1519     if (viewport.applet.getParameter("defaultColour") != null)
1520     {
1521       url.append("&colour="
1522               + removeWhiteSpace(viewport.applet
1523                       .getParameter("defaultColour")));
1524     }
1525
1526     if (viewport.applet.getParameter("userDefinedColour") != null)
1527     {
1528       url.append("&colour="
1529               + removeWhiteSpace(viewport.applet
1530                       .getParameter("userDefinedColour")));
1531     }
1532     if (viewport.applet.getParameter("tree") != null)
1533     {
1534       url.append("&tree="
1535               + appendProtocol(viewport.applet.getParameter("tree")));
1536     }
1537     if (viewport.applet.getParameter("treeFile") != null)
1538     {
1539       url.append("&tree="
1540               + appendProtocol(viewport.applet.getParameter("treeFile")));
1541     }
1542
1543     showURL(url.toString(), "FULL_APP");
1544   }
1545
1546   String removeWhiteSpace(String colour)
1547   {
1548     StringBuffer sb = new StringBuffer();
1549     for (int i = 0; i < colour.length(); i++)
1550     {
1551       if (Character.isWhitespace(colour.charAt(i)))
1552       {
1553         sb.append("%20");
1554       }
1555       else
1556       {
1557         sb.append(colour.charAt(i));
1558       }
1559     }
1560
1561     return sb.toString();
1562   }
1563
1564   String appendProtocol(String url)
1565   {
1566     try
1567     {
1568       new URL(url);
1569       url = URLEncoder.encode(url);
1570     }
1571     /*
1572      * When we finally deprecate 1.1 compatibility, we can start to use
1573      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1574      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1575      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1576      * ex.printStackTrace(); }
1577      */
1578     catch (java.net.MalformedURLException ex)
1579     {
1580       url = viewport.applet.getCodeBase() + url;
1581     }
1582     return url;
1583   }
1584
1585   public void closeMenuItem_actionPerformed()
1586   {
1587     PaintRefresher.RemoveComponent(alignPanel);
1588     if (alignPanel.seqPanel != null
1589             && alignPanel.seqPanel.seqCanvas != null)
1590     {
1591       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1592     }
1593     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1594     {
1595       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1596     }
1597
1598     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1599     {
1600       System.exit(0);
1601     }
1602     else
1603     {
1604     }
1605     viewport = null;
1606     alignPanel = null;
1607     this.dispose();
1608   }
1609
1610   /**
1611    * TODO: JAL-1104
1612    */
1613   void updateEditMenuBar()
1614   {
1615
1616     if (viewport.getHistoryList().size() > 0)
1617     {
1618       undoMenuItem.setEnabled(true);
1619       CommandI command = viewport.getHistoryList().peek();
1620       undoMenuItem.setLabel(MessageManager.formatMessage(
1621               "label.undo_command",
1622               new Object[] { command.getDescription() }));
1623     }
1624     else
1625     {
1626       undoMenuItem.setEnabled(false);
1627       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1628     }
1629
1630     if (viewport.getRedoList().size() > 0)
1631     {
1632       redoMenuItem.setEnabled(true);
1633
1634       CommandI command = viewport.getRedoList().peek();
1635       redoMenuItem.setLabel(MessageManager.formatMessage(
1636               "label.redo_command",
1637               new Object[] { command.getDescription() }));
1638     }
1639     else
1640     {
1641       redoMenuItem.setEnabled(false);
1642       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1643     }
1644   }
1645
1646   /**
1647    * TODO: JAL-1104
1648    */
1649   @Override
1650   public void addHistoryItem(CommandI command)
1651   {
1652     if (command.getSize() > 0)
1653     {
1654       viewport.addToHistoryList(command);
1655       viewport.clearRedoList();
1656       updateEditMenuBar();
1657       viewport.updateHiddenColumns();
1658     }
1659   }
1660
1661   /**
1662    * TODO: JAL-1104 DOCUMENT ME!
1663    *
1664    * @param e
1665    *          DOCUMENT ME!
1666    */
1667   protected void undoMenuItem_actionPerformed()
1668   {
1669     if (viewport.getHistoryList().isEmpty())
1670     {
1671       return;
1672     }
1673
1674     CommandI command = viewport.getHistoryList().pop();
1675     viewport.addToRedoList(command);
1676     command.undoCommand(null);
1677
1678     AlignmentViewport originalSource = getOriginatingSource(command);
1679     // JBPNote Test
1680     if (originalSource != viewport)
1681     {
1682       System.err
1683               .println("Warning: Viewport object mismatch whilst undoing");
1684     }
1685     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1686                                           // viewport.getColumnSelection().getHiddenColumns()
1687                                           // != null;
1688     updateEditMenuBar();
1689     originalSource.firePropertyChange("alignment", null, originalSource
1690             .getAlignment().getSequences());
1691   }
1692
1693   /**
1694    * TODO: JAL-1104 DOCUMENT ME!
1695    *
1696    * @param e
1697    *          DOCUMENT ME!
1698    */
1699   protected void redoMenuItem_actionPerformed()
1700   {
1701     if (viewport.getRedoList().isEmpty())
1702     {
1703       return;
1704     }
1705
1706     CommandI command = viewport.getRedoList().pop();
1707     viewport.addToHistoryList(command);
1708     command.doCommand(null);
1709
1710     AlignmentViewport originalSource = getOriginatingSource(command);
1711     // JBPNote Test
1712     if (originalSource != viewport)
1713     {
1714       System.err
1715               .println("Warning: Viewport object mismatch whilst re-doing");
1716     }
1717     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1718                                           // viewport.getColumnSelection().getHiddenColumns()
1719                                           // != null;
1720
1721     updateEditMenuBar();
1722     originalSource.firePropertyChange("alignment", null, originalSource
1723             .getAlignment().getSequences());
1724   }
1725
1726   AlignmentViewport getOriginatingSource(CommandI command)
1727   {
1728     AlignmentViewport originalSource = null;
1729     // For sequence removal and addition, we need to fire
1730     // the property change event FROM the viewport where the
1731     // original alignment was altered
1732     AlignmentI al = null;
1733     if (command instanceof EditCommand)
1734     {
1735       EditCommand editCommand = (EditCommand) command;
1736       al = editCommand.getAlignment();
1737       Vector comps = (Vector) PaintRefresher.components.get(viewport
1738               .getSequenceSetId());
1739       for (int i = 0; i < comps.size(); i++)
1740       {
1741         if (comps.elementAt(i) instanceof AlignmentPanel)
1742         {
1743           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1744           {
1745             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1746             break;
1747           }
1748         }
1749       }
1750     }
1751
1752     if (originalSource == null)
1753     {
1754       // The original view is closed, we must validate
1755       // the current view against the closed view first
1756       if (al != null)
1757       {
1758         PaintRefresher.validateSequences(al, viewport.getAlignment());
1759       }
1760
1761       originalSource = viewport;
1762     }
1763
1764     return originalSource;
1765   }
1766
1767   /**
1768    * Move the currently selected sequences up or down one position in the
1769    * alignment
1770    *
1771    * @param up
1772    */
1773   public void moveSelectedSequences(boolean up)
1774   {
1775     SequenceGroup sg = viewport.getSelectionGroup();
1776     if (sg == null)
1777     {
1778       return;
1779     }
1780     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1781             up ? null : viewport.getHiddenRepSequences(), up);
1782     alignPanel.paintAlignment(true);
1783
1784     /*
1785      * Also move cDNA/protein complement sequences
1786      */
1787     AlignViewportI complement = viewport.getCodingComplement();
1788     if (complement != null)
1789     {
1790       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1791               viewport, complement);
1792       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1793               up ? null : complement.getHiddenRepSequences(), up);
1794       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1795     }
1796   }
1797
1798   synchronized void slideSequences(boolean right, int size)
1799   {
1800     List<SequenceI> sg = new Vector<>();
1801     if (viewport.cursorMode)
1802     {
1803       sg.add(viewport.getAlignment().getSequenceAt(
1804               alignPanel.seqPanel.seqCanvas.cursorY));
1805     }
1806     else if (viewport.getSelectionGroup() != null
1807             && viewport.getSelectionGroup().getSize() != viewport
1808                     .getAlignment().getHeight())
1809     {
1810       sg = viewport.getSelectionGroup().getSequences(
1811               viewport.getHiddenRepSequences());
1812     }
1813
1814     if (sg.size() < 1)
1815     {
1816       return;
1817     }
1818
1819     Vector<SequenceI> invertGroup = new Vector();
1820
1821     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1822     {
1823       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1824       {
1825         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1826       }
1827     }
1828
1829     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1830
1831     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1832             .size()]);
1833     for (int i = 0; i < invertGroup.size(); i++)
1834     {
1835       seqs2[i] = invertGroup.elementAt(i);
1836     }
1837
1838     SlideSequencesCommand ssc;
1839     if (right)
1840     {
1841       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1842               size, viewport.getGapCharacter());
1843     }
1844     else
1845     {
1846       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1847               size, viewport.getGapCharacter());
1848     }
1849
1850     int groupAdjustment = 0;
1851     if (ssc.getGapsInsertedBegin() && right)
1852     {
1853       if (viewport.cursorMode)
1854       {
1855         alignPanel.seqPanel.moveCursor(size, 0);
1856       }
1857       else
1858       {
1859         groupAdjustment = size;
1860       }
1861     }
1862     else if (!ssc.getGapsInsertedBegin() && !right)
1863     {
1864       if (viewport.cursorMode)
1865       {
1866         alignPanel.seqPanel.moveCursor(-size, 0);
1867       }
1868       else
1869       {
1870         groupAdjustment = -size;
1871       }
1872     }
1873
1874     if (groupAdjustment != 0)
1875     {
1876       viewport.getSelectionGroup().setStartRes(
1877               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1878       viewport.getSelectionGroup().setEndRes(
1879               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1880     }
1881
1882     boolean appendHistoryItem = false;
1883     Deque<CommandI> historyList = viewport.getHistoryList();
1884     if (historyList != null && historyList.size() > 0
1885             && historyList.peek() instanceof SlideSequencesCommand)
1886     {
1887       appendHistoryItem = ssc
1888               .appendSlideCommand((SlideSequencesCommand) historyList
1889                       .peek());
1890     }
1891
1892     if (!appendHistoryItem)
1893     {
1894       addHistoryItem(ssc);
1895     }
1896
1897     repaint();
1898   }
1899
1900   static StringBuffer copiedSequences;
1901
1902   static Vector<int[]> copiedHiddenColumns;
1903
1904   protected void copy_actionPerformed()
1905   {
1906     if (viewport.getSelectionGroup() == null)
1907     {
1908       return;
1909     }
1910
1911     SequenceGroup sg = viewport.getSelectionGroup();
1912     copiedSequences = new StringBuffer();
1913     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1914     for (int i = 0; i < sg.getSize(); i++)
1915     {
1916       SequenceI seq = sg.getSequenceAt(i);
1917       int index = viewport.getAlignment().findIndex(seq);
1918       orderedSeqs.put(index, seq);
1919     }
1920
1921     int index = 0, startRes, endRes;
1922     char ch;
1923
1924     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1925     {
1926       copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1927               .getHiddenColumns().getHiddenColumnsCopy());
1928       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1929       for (int[] region : copiedHiddenColumns)
1930       {
1931         region[0] = region[0] - hiddenOffset;
1932         region[1] = region[1] - hiddenOffset;
1933       }
1934     }
1935     else
1936     {
1937       copiedHiddenColumns = null;
1938     }
1939
1940     for (int i = 0; i < sg.getSize(); i++)
1941     {
1942       SequenceI seq = null;
1943
1944       while (seq == null)
1945       {
1946         if (orderedSeqs.containsKey(index))
1947         {
1948           seq = orderedSeqs.get(index);
1949           index++;
1950           break;
1951         }
1952         else
1953         {
1954           index++;
1955         }
1956       }
1957
1958       // FIND START RES
1959       // Returns residue following index if gap
1960       startRes = seq.findPosition(sg.getStartRes());
1961
1962       // FIND END RES
1963       // Need to find the residue preceeding index if gap
1964       endRes = 0;
1965
1966       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1967       {
1968         ch = seq.getCharAt(j);
1969         if (!jalview.util.Comparison.isGap((ch)))
1970         {
1971           endRes++;
1972         }
1973       }
1974
1975       if (endRes > 0)
1976       {
1977         endRes += seq.getStart() - 1;
1978       }
1979
1980       copiedSequences.append(seq.getName()
1981               + "\t"
1982               + startRes
1983               + "\t"
1984               + endRes
1985               + "\t"
1986               + seq.getSequenceAsString(sg.getStartRes(),
1987                       sg.getEndRes() + 1) + "\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.formatMessage(
2039                   "label.from_msname", new String[] { getTitle() }));
2040         }
2041         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2042                 viewport.applet, newtitle, false);
2043         if (copiedHiddenColumns != null)
2044         {
2045           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2046           {
2047             int[] region = copiedHiddenColumns.elementAt(i);
2048             af.viewport.hideColumns(region[0], region[1]);
2049           }
2050         }
2051
2052         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2053                 frameHeight);
2054       }
2055       else
2056       {
2057         addSequences(newSeqs);
2058       }
2059
2060     } catch (Exception ex)
2061     {
2062     } // could be anything being pasted in here
2063
2064   }
2065
2066   void addSequences(SequenceI[] seqs)
2067   {
2068     for (int i = 0; i < seqs.length; i++)
2069     {
2070       viewport.getAlignment().addSequence(seqs[i]);
2071     }
2072
2073     // !newAlignment
2074     addHistoryItem(new EditCommand(
2075             MessageManager.getString("label.add_sequences"), Action.PASTE,
2076             seqs, 0, viewport.getAlignment().getWidth(),
2077             viewport.getAlignment()));
2078
2079     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2080     viewport.getAlignment().getWidth();
2081     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2082             .getSequences());
2083
2084   }
2085
2086   protected void cut_actionPerformed()
2087   {
2088     copy_actionPerformed();
2089     delete_actionPerformed();
2090   }
2091
2092   protected void delete_actionPerformed()
2093   {
2094
2095     SequenceGroup sg = viewport.getSelectionGroup();
2096     if (sg == null)
2097     {
2098       return;
2099     }
2100
2101     Vector seqs = new Vector();
2102     SequenceI seq;
2103     for (int i = 0; i < sg.getSize(); i++)
2104     {
2105       seq = sg.getSequenceAt(i);
2106       seqs.addElement(seq);
2107     }
2108
2109     /*
2110      * If the cut affects all sequences, warn, remove highlighted columns
2111      */
2112     if (sg.getSize() == viewport.getAlignment().getHeight())
2113     {
2114       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2115               .getAlignment().getWidth()) ? true : false;
2116       if (isEntireAlignWidth)
2117       {
2118         String title = MessageManager.getString("label.delete_all");
2119         Panel infoPanel = new Panel();
2120         infoPanel.setLayout(new FlowLayout());
2121         infoPanel
2122                 .add(new Label(MessageManager.getString("warn.delete_all")));
2123
2124         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2125         dialog.setMainPanel(infoPanel);
2126         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2127         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2128         dialog.setVisible(true);
2129
2130         if (!dialog.accept)
2131         {
2132           return;
2133         }
2134       }
2135       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2136               sg.getEndRes() + 1);
2137     }
2138
2139     SequenceI[] cut = new SequenceI[seqs.size()];
2140     for (int i = 0; i < seqs.size(); i++)
2141     {
2142       cut[i] = (SequenceI) seqs.elementAt(i);
2143     }
2144
2145     /*
2146      * //ADD HISTORY ITEM
2147      */
2148     addHistoryItem(new EditCommand(
2149             MessageManager.getString("label.cut_sequences"), Action.CUT,
2150             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2151             viewport.getAlignment()));
2152
2153     viewport.setSelectionGroup(null);
2154     viewport.getAlignment().deleteGroup(sg);
2155
2156     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2157             .getSequences());
2158
2159     if (viewport.getAlignment().getHeight() < 1)
2160     {
2161       this.setVisible(false);
2162     }
2163     viewport.sendSelection();
2164   }
2165
2166   /**
2167    * group consensus toggled
2168    *
2169    */
2170   protected void showGroupConsensus_actionPerformed()
2171   {
2172     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2173     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174
2175   }
2176
2177   /**
2178    * group conservation toggled.
2179    */
2180   protected void showGroupConservation_actionPerformed()
2181   {
2182     viewport.setShowGroupConservation(showGroupConservation.getState());
2183     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184   }
2185
2186   /*
2187    * (non-Javadoc)
2188    *
2189    * @see
2190    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2191    * .event.ActionEvent)
2192    */
2193   protected void showConsensusHistogram_actionPerformed()
2194   {
2195     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197   }
2198
2199   /*
2200    * (non-Javadoc)
2201    *
2202    * @see
2203    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2204    * .event.ActionEvent)
2205    */
2206   protected void showSequenceLogo_actionPerformed()
2207   {
2208     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2209     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2210   }
2211
2212   protected void normSequenceLogo_actionPerformed()
2213   {
2214     showSequenceLogo.setState(true);
2215     viewport.setShowSequenceLogo(true);
2216     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2217     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2218   }
2219
2220   protected void applyAutoAnnotationSettings_actionPerformed()
2221   {
2222     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2223   }
2224
2225   protected void makeGrpsFromSelection_actionPerformed()
2226   {
2227     if (avc.makeGroupsFromSelection())
2228     {
2229       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2230       alignPanel.updateAnnotation();
2231       alignPanel.paintAlignment(true);
2232     }
2233   }
2234
2235   protected void createGroup_actionPerformed()
2236   {
2237     avc.createGroup();
2238   }
2239
2240   protected void unGroup_actionPerformed()
2241   {
2242     if (avc.unGroup())
2243     {
2244       alignPanel.alignmentChanged();
2245     }
2246   }
2247
2248   protected void deleteGroups_actionPerformed()
2249   {
2250     if (avc.deleteGroups())
2251     {
2252       alignPanel.alignmentChanged();
2253     }
2254   }
2255
2256   public void selectAllSequenceMenuItem_actionPerformed()
2257   {
2258     SequenceGroup sg = new SequenceGroup();
2259     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2260     {
2261       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2262     }
2263     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2264     viewport.setSelectionGroup(sg);
2265     // JAL-2034 - should delegate to
2266     // alignPanel to decide if overview needs
2267     // updating.
2268     alignPanel.paintAlignment(false);
2269     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2270     viewport.sendSelection();
2271   }
2272
2273   public void deselectAllSequenceMenuItem_actionPerformed()
2274   {
2275     if (viewport.cursorMode)
2276     {
2277       alignPanel.seqPanel.keyboardNo1 = null;
2278       alignPanel.seqPanel.keyboardNo2 = null;
2279     }
2280     viewport.setSelectionGroup(null);
2281     viewport.getColumnSelection().clear();
2282     viewport.setSelectionGroup(null);
2283     alignPanel.idPanel.idCanvas.searchResults = null;
2284     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2285     // JAL-2034 - should delegate to
2286     // alignPanel to decide if overview needs
2287     // updating.
2288     alignPanel.paintAlignment(false);
2289     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2290     viewport.sendSelection();
2291   }
2292
2293   public void invertSequenceMenuItem_actionPerformed()
2294   {
2295     SequenceGroup sg = viewport.getSelectionGroup();
2296     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2297     {
2298       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2299     }
2300
2301     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2302     viewport.sendSelection();
2303   }
2304
2305   public void invertColSel_actionPerformed()
2306   {
2307     viewport.invertColumnSelection();
2308     alignPanel.paintAlignment(true);
2309     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2310     viewport.sendSelection();
2311   }
2312
2313   void trimAlignment(boolean trimLeft)
2314   {
2315     AlignmentI al = viewport.getAlignment();
2316     ViewportRanges ranges = viewport.getRanges();
2317     ColumnSelection colSel = viewport.getColumnSelection();
2318     int column;
2319
2320     if (!colSel.isEmpty())
2321     {
2322       if (trimLeft)
2323       {
2324         column = colSel.getMin();
2325       }
2326       else
2327       {
2328         column = colSel.getMax();
2329       }
2330
2331       SequenceI[] seqs;
2332       if (viewport.getSelectionGroup() != null)
2333       {
2334         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2335                 viewport.getHiddenRepSequences());
2336       }
2337       else
2338       {
2339         seqs = al.getSequencesArray();
2340       }
2341
2342       TrimRegionCommand trimRegion;
2343       if (trimLeft)
2344       {
2345         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2346                 column, al);
2347         ranges.setStartRes(0);
2348       }
2349       else
2350       {
2351         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2352                 column, al);
2353       }
2354
2355       statusBar.setText(MessageManager.formatMessage(
2356               "label.removed_columns",
2357               new String[] { Integer.valueOf(trimRegion.getSize())
2358                       .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().getSequencesAsArray(
2385               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.formatMessage(
2401             "label.removed_empty_columns",
2402             new String[] { Integer.valueOf(removeGapCols.getSize())
2403                     .toString() }));
2404
2405     // This is to maintain viewport position on first residue
2406     // of first sequence
2407     SequenceI seq = al.getSequenceAt(0);
2408     int startRes = seq.findPosition(ranges.getStartRes());
2409     // ShiftList shifts;
2410     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2411     // edit.alColumnChanges=shifts.getInverse();
2412     // if (viewport.hasHiddenColumns)
2413     // viewport.getColumnSelection().compensateForEdits(shifts);
2414     ranges.setStartRes(seq.findIndex(startRes) - 1);
2415     viewport.firePropertyChange("alignment", null, al.getSequences());
2416
2417   }
2418
2419   public void removeAllGapsMenuItem_actionPerformed()
2420   {
2421     AlignmentI al = viewport.getAlignment();
2422     ViewportRanges ranges = viewport.getRanges();
2423     int start = 0;
2424     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2425
2426     SequenceI[] seqs;
2427     if (viewport.getSelectionGroup() != null)
2428     {
2429       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2430               viewport.getHiddenRepSequences());
2431       start = viewport.getSelectionGroup().getStartRes();
2432       end = viewport.getSelectionGroup().getEndRes();
2433     }
2434     else
2435     {
2436       seqs = viewport.getAlignment().getSequencesArray();
2437     }
2438
2439     // This is to maintain viewport position on first residue
2440     // of first sequence
2441     SequenceI seq = al.getSequenceAt(0);
2442     int startRes = seq.findPosition(ranges.getStartRes());
2443
2444     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2445             al));
2446
2447     ranges.setStartRes(seq.findIndex(startRes) - 1);
2448
2449     viewport.firePropertyChange("alignment", null, al.getSequences());
2450
2451   }
2452
2453   public void findMenuItem_actionPerformed()
2454   {
2455     new Finder(alignPanel);
2456   }
2457
2458   /**
2459    * create a new view derived from the current view
2460    *
2461    * @param viewtitle
2462    * @return frame for the new view
2463    */
2464   public AlignFrame newView(String viewtitle)
2465   {
2466     AlignmentI newal;
2467     if (viewport.hasHiddenRows())
2468     {
2469       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2470               .getFullAlignment().getSequencesArray());
2471     }
2472     else
2473     {
2474       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2475     }
2476
2477     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2478     {
2479       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2480       {
2481         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2482         {
2483           newal.addAnnotation(viewport.getAlignment()
2484                   .getAlignmentAnnotation()[i]);
2485         }
2486       }
2487     }
2488
2489     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2490
2491     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2492     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2493     PaintRefresher.Register(newaf.alignPanel,
2494             newaf.alignPanel.av.getSequenceSetId());
2495
2496     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2497             newaf.alignPanel.av.getSequenceSetId());
2498     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2499             newaf.alignPanel.av.getSequenceSetId());
2500
2501     Vector comps = (Vector) PaintRefresher.components.get(viewport
2502             .getSequenceSetId());
2503     int viewSize = -1;
2504     for (int i = 0; i < comps.size(); i++)
2505     {
2506       if (comps.elementAt(i) instanceof AlignmentPanel)
2507       {
2508         viewSize++;
2509       }
2510     }
2511
2512     String title = new String(this.getTitle());
2513     if (viewtitle != null)
2514     {
2515       title = viewtitle + " ( " + title + ")";
2516     }
2517     else
2518     {
2519       if (title.indexOf("(View") > -1)
2520       {
2521         title = title.substring(0, title.indexOf("(View"));
2522       }
2523       title += "(View " + viewSize + ")";
2524     }
2525
2526     newaf.setTitle(title.toString());
2527
2528     newaf.viewport.setHistoryList(viewport.getHistoryList());
2529     newaf.viewport.setRedoList(viewport.getRedoList());
2530     return newaf;
2531   }
2532
2533   /**
2534    *
2535    * @return list of feature groups on the view
2536    */
2537   public String[] getFeatureGroups()
2538   {
2539     FeatureRenderer fr = null;
2540     if (alignPanel != null
2541             && (fr = alignPanel.getFeatureRenderer()) != null)
2542     {
2543       List<String> gps = fr.getFeatureGroups();
2544       String[] _gps = gps.toArray(new String[gps.size()]);
2545       return _gps;
2546     }
2547     return null;
2548   }
2549
2550   /**
2551    * get sequence feature groups that are hidden or shown
2552    *
2553    * @param visible
2554    *          true is visible
2555    * @return list
2556    */
2557   public String[] getFeatureGroupsOfState(boolean visible)
2558   {
2559     FeatureRenderer fr = null;
2560     if (alignPanel != null
2561             && (fr = alignPanel.getFeatureRenderer()) != null)
2562     {
2563       List<String> gps = fr.getGroups(visible);
2564       String[] _gps = gps.toArray(new String[gps.size()]);
2565       return _gps;
2566     }
2567     return null;
2568   }
2569
2570   /**
2571    * Change the display state for the given feature groups
2572    *
2573    * @param groups
2574    *          list of group strings
2575    * @param state
2576    *          visible or invisible
2577    */
2578   public void setFeatureGroupState(String[] groups, boolean state)
2579   {
2580     FeatureRenderer fr = null;
2581     this.sequenceFeatures.setState(true);
2582     viewport.setShowSequenceFeatures(true);
2583     if (alignPanel != null
2584             && (fr = alignPanel.getFeatureRenderer()) != null)
2585     {
2586
2587       fr.setGroupVisibility(Arrays.asList(groups), state);
2588       alignPanel.seqPanel.seqCanvas.repaint();
2589       if (alignPanel.overviewPanel != null)
2590       {
2591         alignPanel.overviewPanel.updateOverviewImage();
2592       }
2593     }
2594   }
2595
2596   public void seqLimits_itemStateChanged()
2597   {
2598     viewport.setShowJVSuffix(seqLimits.getState());
2599     alignPanel.fontChanged();
2600     alignPanel.paintAlignment(true);
2601   }
2602
2603   protected void colourTextMenuItem_actionPerformed()
2604   {
2605     viewport.setColourText(colourTextMenuItem.getState());
2606     alignPanel.paintAlignment(true);
2607   }
2608
2609   protected void displayNonconservedMenuItem_actionPerformed()
2610   {
2611     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2612     alignPanel.paintAlignment(true);
2613   }
2614
2615   protected void wrapMenuItem_actionPerformed()
2616   {
2617     viewport.setWrapAlignment(wrapMenuItem.getState());
2618     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2619     scaleAbove.setEnabled(wrapMenuItem.getState());
2620     scaleLeft.setEnabled(wrapMenuItem.getState());
2621     scaleRight.setEnabled(wrapMenuItem.getState());
2622     alignPanel.paintAlignment(true);
2623   }
2624
2625   public void overviewMenuItem_actionPerformed()
2626   {
2627     if (alignPanel.overviewPanel != null)
2628     {
2629       return;
2630     }
2631
2632     Frame frame = new Frame();
2633     final OverviewPanel overview = new OverviewPanel(alignPanel);
2634     frame.add(overview);
2635     // +50 must allow for applet frame window
2636     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2637             "label.overview_params", new String[] { this.getTitle() }),
2638             overview.getPreferredSize().width,
2639             overview.getPreferredSize().height + 50);
2640
2641     frame.pack();
2642     final AlignmentPanel ap = alignPanel;
2643     frame.addWindowListener(new WindowAdapter()
2644     {
2645       @Override
2646       public void windowClosing(WindowEvent e)
2647       {
2648         overview.dispose();
2649         if (ap != null)
2650         {
2651           ap.setOverviewPanel(null);
2652         }
2653       };
2654     });
2655
2656     alignPanel.setOverviewPanel(overview);
2657
2658   }
2659
2660   @Override
2661   public void changeColour(ColourSchemeI cs)
2662   {
2663     viewport.setGlobalColourScheme(cs);
2664
2665     alignPanel.paintAlignment(true);
2666   }
2667
2668   protected void modifyPID_actionPerformed()
2669   {
2670     if (viewport.getAbovePIDThreshold()
2671             && viewport.getGlobalColourScheme() != null)
2672     {
2673       SliderPanel.setPIDSliderSource(alignPanel,
2674               viewport.getResidueShading(), alignPanel.getViewName());
2675       SliderPanel.showPIDSlider();
2676     }
2677   }
2678
2679   protected void modifyConservation_actionPerformed()
2680   {
2681     if (viewport.getConservationSelected()
2682             && viewport.getGlobalColourScheme() != null)
2683     {
2684       SliderPanel.setConservationSlider(alignPanel,
2685               viewport.getResidueShading(), alignPanel.getViewName());
2686       SliderPanel.showConservationSlider();
2687     }
2688   }
2689
2690   protected void conservationMenuItem_actionPerformed()
2691   {
2692     boolean selected = conservationMenuItem.getState();
2693     modifyConservation.setEnabled(selected);
2694     viewport.setConservationSelected(selected);
2695     viewport.getResidueShading().setConservationApplied(selected);
2696
2697     changeColour(viewport.getGlobalColourScheme());
2698
2699     if (selected)
2700     {
2701       modifyConservation_actionPerformed();
2702     }
2703     else
2704     {
2705       SliderPanel.hideConservationSlider();
2706     }
2707   }
2708
2709   public void abovePIDThreshold_actionPerformed()
2710   {
2711     boolean selected = abovePIDThreshold.getState();
2712     modifyPID.setEnabled(selected);
2713     viewport.setAbovePIDThreshold(selected);
2714     if (!selected)
2715     {
2716       viewport.getResidueShading().setThreshold(0,
2717               viewport.isIgnoreGapsConsensus());
2718     }
2719
2720     changeColour(viewport.getGlobalColourScheme());
2721
2722     if (selected)
2723     {
2724       modifyPID_actionPerformed();
2725     }
2726     else
2727     {
2728       SliderPanel.hidePIDSlider();
2729     }
2730   }
2731
2732   public void sortPairwiseMenuItem_actionPerformed()
2733   {
2734     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2735     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2736             .getAlignment().getSequenceAt(0));
2737
2738     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2739             viewport.getAlignment()));
2740     alignPanel.paintAlignment(true);
2741   }
2742
2743   public void sortIDMenuItem_actionPerformed()
2744   {
2745     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2746     AlignmentSorter.sortByID(viewport.getAlignment());
2747     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2748             viewport.getAlignment()));
2749     alignPanel.paintAlignment(true);
2750   }
2751
2752   public void sortLengthMenuItem_actionPerformed()
2753   {
2754     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2755     AlignmentSorter.sortByLength(viewport.getAlignment());
2756     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2757             viewport.getAlignment()));
2758     alignPanel.paintAlignment(true);
2759   }
2760
2761   public void sortGroupMenuItem_actionPerformed()
2762   {
2763     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2764     AlignmentSorter.sortByGroup(viewport.getAlignment());
2765     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2766             viewport.getAlignment()));
2767     alignPanel.paintAlignment(true);
2768
2769   }
2770
2771   public void removeRedundancyMenuItem_actionPerformed()
2772   {
2773     new RedundancyPanel(alignPanel);
2774   }
2775
2776   public void pairwiseAlignmentMenuItem_actionPerformed()
2777   {
2778     if (viewport.getSelectionGroup() != null
2779             && viewport.getSelectionGroup().getSize() > 1)
2780     {
2781       Frame frame = new Frame();
2782       frame.add(new PairwiseAlignPanel(alignPanel));
2783       jalview.bin.JalviewLite.addFrame(frame,
2784               MessageManager.getString("action.pairwise_alignment"), 600,
2785               500);
2786     }
2787   }
2788
2789   public void PCAMenuItem_actionPerformed()
2790   {
2791     // are the sequences aligned?
2792     if (!viewport.getAlignment().isAligned(false))
2793     {
2794       SequenceI current;
2795       int Width = viewport.getAlignment().getWidth();
2796
2797       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2798       {
2799         current = viewport.getAlignment().getSequenceAt(i);
2800
2801         if (current.getLength() < Width)
2802         {
2803           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2804         }
2805       }
2806       alignPanel.paintAlignment(true);
2807     }
2808
2809     if ((viewport.getSelectionGroup() != null
2810             && viewport.getSelectionGroup().getSize() < 4 && viewport
2811             .getSelectionGroup().getSize() > 0)
2812             || viewport.getAlignment().getHeight() < 4)
2813     {
2814       return;
2815     }
2816
2817     try
2818     {
2819       new PCAPanel(viewport);
2820     } catch (java.lang.OutOfMemoryError ex)
2821     {
2822     }
2823
2824   }
2825
2826   public void averageDistanceTreeMenuItem_actionPerformed()
2827   {
2828     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2829             "Average distance tree using PID");
2830   }
2831
2832   public void neighbourTreeMenuItem_actionPerformed()
2833   {
2834     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2835             "Neighbour joining tree using PID");
2836   }
2837
2838   protected void njTreeBlosumMenuItem_actionPerformed()
2839   {
2840     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2841             .getBlosum62().getName(),
2842             "Neighbour joining tree using BLOSUM62");
2843   }
2844
2845   protected void avTreeBlosumMenuItem_actionPerformed()
2846   {
2847     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2848             .getBlosum62().getName(),
2849             "Average distance tree using BLOSUM62");
2850   }
2851
2852   void newTreePanel(String type, String pwType, String title)
2853   {
2854     // are the sequences aligned?
2855     if (!viewport.getAlignment().isAligned(false))
2856     {
2857       SequenceI current;
2858       int Width = viewport.getAlignment().getWidth();
2859
2860       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2861       {
2862         current = viewport.getAlignment().getSequenceAt(i);
2863
2864         if (current.getLength() < Width)
2865         {
2866           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2867         }
2868       }
2869       alignPanel.paintAlignment(true);
2870
2871     }
2872
2873     if ((viewport.getSelectionGroup() != null && viewport
2874             .getSelectionGroup().getSize() > 1)
2875             || (viewport.getAlignment().getHeight() > 1))
2876     {
2877       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2878
2879       addTreeMenuItem(tp, title);
2880
2881       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2882     }
2883   }
2884
2885   void loadTree_actionPerformed()
2886   {
2887     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2888     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2889     cap.setTreeImport();
2890     Frame frame = new Frame();
2891     frame.add(cap);
2892     jalview.bin.JalviewLite.addFrame(frame,
2893             MessageManager.getString("label.paste_newick_file"), 400, 300);
2894   }
2895
2896   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2897   {
2898     TreePanel tp = new TreePanel(alignPanel, treeFile,
2899             MessageManager.getString("label.load_tree_from_file"), tree);
2900     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2901     addTreeMenuItem(tp, treeFile);
2902   }
2903
2904   /**
2905    * sort the alignment using the given treePanel
2906    *
2907    * @param treePanel
2908    *          tree used to sort view
2909    * @param title
2910    *          string used for undo event name
2911    */
2912   public void sortByTree(TreePanel treePanel, String title)
2913   {
2914     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2915     AlignmentSorter
2916             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2917     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2918     // HistoryItem.SORT));
2919     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2920             "label.order_by_params", new String[] { title }), oldOrder,
2921             viewport.getAlignment()));
2922     alignPanel.paintAlignment(true);
2923   }
2924
2925   /**
2926    * Do any automatic reordering of the alignment and add the necessary bits to
2927    * the menu structure for the new tree
2928    *
2929    * @param treePanel
2930    * @param title
2931    */
2932   protected void addTreeMenuItem(final TreePanel treePanel,
2933           final String title)
2934   {
2935     final MenuItem item = new MenuItem(title);
2936     sortByTreeMenu.add(item);
2937     item.addActionListener(new java.awt.event.ActionListener()
2938     {
2939       @Override
2940       public void actionPerformed(ActionEvent evt)
2941       {
2942         sortByTree(treePanel, title); // treePanel.getTitle());
2943       }
2944     });
2945
2946     treePanel.addWindowListener(new WindowAdapter()
2947     {
2948       @Override
2949       public void windowOpened(WindowEvent e)
2950       {
2951         if (viewport.sortByTree)
2952         {
2953           sortByTree(treePanel, title);
2954         }
2955         super.windowOpened(e);
2956       }
2957
2958       @Override
2959       public void windowClosing(WindowEvent e)
2960       {
2961         sortByTreeMenu.remove(item);
2962       };
2963     });
2964   }
2965
2966   public boolean sortBy(AlignmentOrder alorder, String undoname)
2967   {
2968     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2969     if (viewport.applet.debug)
2970     {
2971       System.err.println("Sorting " + alorder.getOrder().size()
2972               + " in alignment '" + getTitle() + "'");
2973     }
2974     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2975     if (undoname != null)
2976     {
2977       addHistoryItem(new OrderCommand(undoname, oldOrder,
2978               viewport.getAlignment()));
2979     }
2980     alignPanel.paintAlignment(true);
2981     return true;
2982   }
2983
2984   protected void documentation_actionPerformed()
2985   {
2986     alignPanel.av.applet.openJalviewHelpUrl();
2987   }
2988
2989   protected void about_actionPerformed()
2990   {
2991
2992     class AboutPanel extends Canvas
2993     {
2994       String version;
2995
2996       String builddate;
2997
2998       public AboutPanel(String version, String builddate)
2999       {
3000         this.version = version;
3001         this.builddate = builddate;
3002       }
3003
3004       @Override
3005       public void paint(Graphics g)
3006       {
3007         g.setColor(Color.white);
3008         g.fillRect(0, 0, getSize().width, getSize().height);
3009         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3010         FontMetrics fm = g.getFontMetrics();
3011         int fh = fm.getHeight();
3012         int y = 5, x = 7;
3013         g.setColor(Color.black);
3014         // TODO: update this text for each release or centrally store it for
3015         // lite and application
3016         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3017         g.drawString(MessageManager.formatMessage(
3018                 "label.jalviewLite_release", new String[] { version }), x,
3019                 y += fh);
3020         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3021         g.drawString(MessageManager.formatMessage(
3022                 "label.jaview_build_date", new String[] { builddate }), x,
3023                 y += fh);
3024         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3025         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3026                 x, y += fh * 1.5);
3027         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3028                 x + 50, y += fh + 8);
3029         g.drawString(
3030                 MessageManager.getString("label.jalview_dev_managers"), x,
3031                 y += fh);
3032         g.drawString(MessageManager
3033                 .getString("label.jalview_distribution_lists"), x, y += fh);
3034         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3035                 x, y += fh + 8);
3036         g.drawString(
3037                 MessageManager.getString("label.jalview_cite_1_authors"),
3038                 x, y += fh);
3039         g.drawString(
3040                 MessageManager.getString("label.jalview_cite_1_title"), x,
3041                 y += fh);
3042         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3043                 x, y += fh);
3044       }
3045     }
3046
3047     Frame frame = new Frame();
3048     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3049             .getBuildDate()));
3050     jalview.bin.JalviewLite.addFrame(frame,
3051             MessageManager.getString("label.jalview"), 580, 220);
3052
3053   }
3054
3055   public void showURL(String url, String target)
3056   {
3057     if (viewport.applet == null)
3058     {
3059       System.out.println("Not running as applet - no browser available.");
3060     }
3061     else
3062     {
3063       viewport.applet.showURL(url, target);
3064     }
3065   }
3066
3067   // ////////////////////////////////////////////////////////////////////////////////
3068   // JBuilder Graphics here
3069
3070   MenuBar alignFrameMenuBar = new MenuBar();
3071
3072   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3073
3074   MenuItem loadApplication = new MenuItem(
3075           MessageManager.getString("label.view_full_application"));
3076
3077   MenuItem loadTree = new MenuItem(
3078           MessageManager.getString("label.load_associated_tree"));
3079
3080   MenuItem loadAnnotations = new MenuItem(
3081           MessageManager.getString("label.load_features_annotations"));
3082
3083   MenuItem outputFeatures = new MenuItem(
3084           MessageManager.getString("label.export_features"));
3085
3086   MenuItem outputAnnotations = new MenuItem(
3087           MessageManager.getString("label.export_annotations"));
3088
3089   MenuItem closeMenuItem = new MenuItem(
3090           MessageManager.getString("action.close"));
3091
3092   MenuItem selectAllSequenceMenuItem = new MenuItem(
3093           MessageManager.getString("action.select_all"));
3094
3095   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3096           MessageManager.getString("action.deselect_all"));
3097
3098   MenuItem invertSequenceMenuItem = new MenuItem(
3099           MessageManager.getString("action.invert_selection"));
3100
3101   MenuItem remove2LeftMenuItem = new MenuItem();
3102
3103   MenuItem remove2RightMenuItem = new MenuItem();
3104
3105   MenuItem removeGappedColumnMenuItem = new MenuItem();
3106
3107   MenuItem removeAllGapsMenuItem = new MenuItem();
3108
3109   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3110
3111   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3112
3113   MenuItem sortPairwiseMenuItem = new MenuItem();
3114
3115   MenuItem sortIDMenuItem = new MenuItem();
3116
3117   MenuItem sortLengthMenuItem = new MenuItem();
3118
3119   MenuItem sortGroupMenuItem = new MenuItem();
3120
3121   MenuItem removeRedundancyMenuItem = new MenuItem();
3122
3123   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3124
3125   MenuItem PCAMenuItem = new MenuItem();
3126
3127   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3128
3129   MenuItem neighbourTreeMenuItem = new MenuItem();
3130
3131   BorderLayout borderLayout1 = new BorderLayout();
3132
3133   public Label statusBar = new Label();
3134
3135   MenuItem clustalColour = new MenuItem();
3136
3137   MenuItem zappoColour = new MenuItem();
3138
3139   MenuItem taylorColour = new MenuItem();
3140
3141   MenuItem hydrophobicityColour = new MenuItem();
3142
3143   MenuItem helixColour = new MenuItem();
3144
3145   MenuItem strandColour = new MenuItem();
3146
3147   MenuItem turnColour = new MenuItem();
3148
3149   MenuItem buriedColour = new MenuItem();
3150
3151   MenuItem purinePyrimidineColour = new MenuItem();
3152
3153   // MenuItem RNAInteractionColour = new MenuItem();
3154
3155   MenuItem RNAHelixColour = new MenuItem();
3156
3157   MenuItem userDefinedColour = new MenuItem();
3158
3159   MenuItem PIDColour = new MenuItem();
3160
3161   MenuItem BLOSUM62Colour = new MenuItem();
3162
3163   MenuItem tcoffeeColour = new MenuItem();
3164
3165   MenuItem njTreeBlosumMenuItem = new MenuItem();
3166
3167   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3168
3169   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3170
3171   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3174
3175   MenuItem alProperties = new MenuItem(
3176           MessageManager.getString("label.alignment_props"));
3177
3178   MenuItem overviewMenuItem = new MenuItem();
3179
3180   MenuItem undoMenuItem = new MenuItem();
3181
3182   MenuItem redoMenuItem = new MenuItem();
3183
3184   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3185
3186   MenuItem noColourmenuItem = new MenuItem();
3187
3188   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3189
3190   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3191
3192   MenuItem findMenuItem = new MenuItem();
3193
3194   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3195
3196   MenuItem nucleotideColour = new MenuItem();
3197
3198   MenuItem deleteGroups = new MenuItem();
3199
3200   MenuItem grpsFromSelection = new MenuItem();
3201
3202   MenuItem createGroup = new MenuItem();
3203
3204   MenuItem unGroup = new MenuItem();
3205
3206   MenuItem delete = new MenuItem();
3207
3208   MenuItem copy = new MenuItem();
3209
3210   MenuItem cut = new MenuItem();
3211
3212   Menu pasteMenu = new Menu();
3213
3214   MenuItem pasteNew = new MenuItem();
3215
3216   MenuItem pasteThis = new MenuItem();
3217
3218   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3219
3220   MenuItem font = new MenuItem();
3221
3222   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3223
3224   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3225
3226   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3227
3228   MenuItem modifyPID = new MenuItem();
3229
3230   MenuItem modifyConservation = new MenuItem();
3231
3232   CheckboxMenuItem autoCalculate = null;
3233
3234   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3235           "Sort Alignment With New Tree", true);
3236
3237   Menu sortByTreeMenu = new Menu();
3238
3239   MenuItem inputText = new MenuItem();
3240
3241   MenuItem documentation = new MenuItem();
3242
3243   MenuItem about = new MenuItem();
3244
3245   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3246
3247   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3248
3249   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3250
3251   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3252
3253   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3254
3255   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3256
3257   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3258
3259   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3260
3261   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3262
3263   /**
3264    * Initialise menus and other items
3265    *
3266    * @throws Exception
3267    */
3268   private void jbInit() throws Exception
3269   {
3270     setMenuBar(alignFrameMenuBar);
3271
3272     /*
3273      * Configure File menu items and actions
3274      */
3275     inputText
3276             .setLabel(MessageManager.getString("label.input_from_textbox"));
3277     inputText.addActionListener(this);
3278     Menu outputTextboxMenu = new Menu(
3279             MessageManager.getString("label.out_to_textbox"));
3280     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3281     {
3282       MenuItem item = new MenuItem(ff);
3283
3284       item.addActionListener(new java.awt.event.ActionListener()
3285       {
3286         @Override
3287         public void actionPerformed(ActionEvent e)
3288         {
3289           outputText_actionPerformed(e);
3290         }
3291       });
3292
3293       outputTextboxMenu.add(item);
3294     }
3295     closeMenuItem.addActionListener(this);
3296     loadApplication.addActionListener(this);
3297     loadTree.addActionListener(this);
3298     loadAnnotations.addActionListener(this);
3299     outputFeatures.addActionListener(this);
3300     outputAnnotations.addActionListener(this);
3301
3302     /*
3303      * Configure Edit menu items and actions
3304      */
3305     undoMenuItem.setEnabled(false);
3306     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3307     undoMenuItem.addActionListener(this);
3308     redoMenuItem.setEnabled(false);
3309     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3310     redoMenuItem.addActionListener(this);
3311     copy.setLabel(MessageManager.getString("action.copy"));
3312     copy.addActionListener(this);
3313     cut.setLabel(MessageManager.getString("action.cut"));
3314     cut.addActionListener(this);
3315     delete.setLabel(MessageManager.getString("action.delete"));
3316     delete.addActionListener(this);
3317     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3318     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3319     pasteNew.addActionListener(this);
3320     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3321     pasteThis.addActionListener(this);
3322     remove2LeftMenuItem.setLabel(MessageManager
3323             .getString("action.remove_left"));
3324     remove2LeftMenuItem.addActionListener(this);
3325     remove2RightMenuItem.setLabel(MessageManager
3326             .getString("action.remove_right"));
3327     remove2RightMenuItem.addActionListener(this);
3328     removeGappedColumnMenuItem.setLabel(MessageManager
3329             .getString("action.remove_empty_columns"));
3330     removeGappedColumnMenuItem.addActionListener(this);
3331     removeAllGapsMenuItem.setLabel(MessageManager
3332             .getString("action.remove_all_gaps"));
3333     removeAllGapsMenuItem.addActionListener(this);
3334     removeRedundancyMenuItem.setLabel(MessageManager
3335             .getString("action.remove_redundancy"));
3336     removeRedundancyMenuItem.addActionListener(this);
3337
3338     /*
3339      * Configure Select menu items and actions
3340      */
3341     findMenuItem.setLabel(MessageManager.getString("action.find"));
3342     findMenuItem.addActionListener(this);
3343     selectAllSequenceMenuItem.addActionListener(this);
3344     deselectAllSequenceMenuItem.addActionListener(this);
3345     invertSequenceMenuItem.setLabel(MessageManager
3346             .getString("action.invert_sequence_selection"));
3347     invertSequenceMenuItem.addActionListener(this);
3348     invertColSel.setLabel(MessageManager
3349             .getString("action.invert_column_selection"));
3350     invertColSel.addActionListener(this);
3351     deleteGroups.setLabel(MessageManager
3352             .getString("action.undefine_groups"));
3353     deleteGroups.addActionListener(this);
3354     grpsFromSelection.setLabel(MessageManager
3355             .getString("action.make_groups_selection"));
3356     grpsFromSelection.addActionListener(this);
3357     createGroup.setLabel(MessageManager.getString("action.create_group"));
3358     createGroup.addActionListener(this);
3359     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3360     unGroup.addActionListener(this);
3361
3362     annotationColumnSelection.setLabel(MessageManager
3363             .getString("action.select_by_annotation"));
3364     annotationColumnSelection.addActionListener(this);
3365
3366     /*
3367      * Configure View menu items and actions
3368      */
3369     newView.setLabel(MessageManager.getString("action.new_view"));
3370     newView.addActionListener(this);
3371     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3372     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3373     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3374     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3375     hideColumns
3376             .setLabel(MessageManager.getString("label.selected_columns"));
3377     hideSequences.setLabel(MessageManager
3378             .getString("label.selected_sequences"));
3379     hideAllButSelection.setLabel(MessageManager
3380             .getString("label.all_but_selected_region"));
3381     hideAllSelection.setLabel(MessageManager
3382             .getString("label.selected_region"));
3383     showAllHidden.setLabel(MessageManager
3384             .getString("label.all_sequences_columns"));
3385     showColumns.addActionListener(this);
3386     showSeqs.addActionListener(this);
3387     hideColumns.addActionListener(this);
3388     hideSequences.addActionListener(this);
3389     hideAllButSelection.addActionListener(this);
3390     hideAllSelection.addActionListener(this);
3391     showAllHidden.addActionListener(this);
3392     featureSettings.setLabel(MessageManager
3393             .getString("action.feature_settings"));
3394     featureSettings.addActionListener(this);
3395     sequenceFeatures.setLabel(MessageManager
3396             .getString("label.show_sequence_features"));
3397     sequenceFeatures.addItemListener(this);
3398     sequenceFeatures.setState(false);
3399     followMouseOverFlag.setLabel(MessageManager
3400             .getString("label.automatic_scrolling"));
3401     followMouseOverFlag.addItemListener(this);
3402     alProperties.addActionListener(this);
3403     overviewMenuItem.setLabel(MessageManager
3404             .getString("label.overview_window"));
3405     overviewMenuItem.addActionListener(this);
3406
3407     /*
3408      * Configure Annotations menu items and actions
3409      */
3410     annotationPanelMenuItem.setLabel(MessageManager
3411             .getString("label.show_annotations"));
3412     annotationPanelMenuItem.addItemListener(this);
3413     showGroupConsensus.setLabel(MessageManager
3414             .getString("label.group_consensus"));
3415     showGroupConservation.setLabel(MessageManager
3416             .getString("label.group_conservation"));
3417     showConsensusHistogram.setLabel(MessageManager
3418             .getString("label.show_consensus_histogram"));
3419     showSequenceLogo.setLabel(MessageManager
3420             .getString("label.show_consensus_logo"));
3421     normSequenceLogo.setLabel(MessageManager
3422             .getString("label.norm_consensus_logo"));
3423     applyAutoAnnotationSettings.setLabel(MessageManager
3424             .getString("label.apply_all_groups"));
3425     applyAutoAnnotationSettings.setState(true);
3426     Menu autoAnnMenu = new Menu(
3427             MessageManager.getString("label.autocalculated_annotation"));
3428     showGroupConsensus.addItemListener(this);
3429     showGroupConservation.addItemListener(this);
3430     showConsensusHistogram.addItemListener(this);
3431     showSequenceLogo.addItemListener(this);
3432     normSequenceLogo.addItemListener(this);
3433     applyAutoAnnotationSettings.addItemListener(this);
3434     showAlignmentAnnotations = new CheckboxMenuItem(
3435             MessageManager.getString("label.show_all_al_annotations"));
3436     showSequenceAnnotations = new CheckboxMenuItem(
3437             MessageManager.getString("label.show_all_seq_annotations"));
3438     sortAnnBySequence = new CheckboxMenuItem(
3439             MessageManager.getString("label.sort_annotations_by_sequence"));
3440     sortAnnByLabel = new CheckboxMenuItem(
3441             MessageManager.getString("label.sort_annotations_by_label"));
3442     showAutoFirst = new CheckboxMenuItem(
3443             MessageManager.getString("label.show_first"));
3444     showAutoFirst.setState(false); // pending applet parameter
3445     setShowAutoCalculatedAbove(showAutoFirst.getState());
3446     showAutoLast = new CheckboxMenuItem(
3447             MessageManager.getString("label.show_last"));
3448     showAutoLast.setState(!showAutoFirst.getState());
3449     showAlignmentAnnotations.addItemListener(this);
3450     showSequenceAnnotations.addItemListener(this);
3451     sortAnnBySequence.addItemListener(this);
3452     sortAnnByLabel.addItemListener(this);
3453     showAutoFirst.addItemListener(this);
3454     showAutoLast.addItemListener(this);
3455
3456     /*
3457      * Configure Format menu items and actions
3458      */
3459     font.setLabel(MessageManager.getString("action.font"));
3460     font.addActionListener(this);
3461     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3462     scaleAbove.setState(true);
3463     scaleAbove.setEnabled(false);
3464     scaleAbove.addItemListener(this);
3465     scaleLeft.setEnabled(false);
3466     scaleLeft.setState(true);
3467     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3468     scaleLeft.addItemListener(this);
3469     scaleRight.setEnabled(false);
3470     scaleRight.setState(true);
3471     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3472     scaleRight.addItemListener(this);
3473     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3474     viewBoxesMenuItem.setState(true);
3475     viewBoxesMenuItem.addItemListener(this);
3476     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3477     viewTextMenuItem.setState(true);
3478     viewTextMenuItem.addItemListener(this);
3479     colourTextMenuItem.setLabel(MessageManager
3480             .getString("label.colour_text"));
3481     colourTextMenuItem.addItemListener(this);
3482     displayNonconservedMenuItem.setLabel(MessageManager
3483             .getString("label.show_non_conserved"));
3484     displayNonconservedMenuItem.addItemListener(this);
3485     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3486     wrapMenuItem.addItemListener(this);
3487     renderGapsMenuItem.setLabel(MessageManager
3488             .getString("action.show_gaps"));
3489     renderGapsMenuItem.setState(true);
3490     renderGapsMenuItem.addItemListener(this);
3491     centreColumnLabelFlag.setLabel(MessageManager
3492             .getString("label.centre_column_labels"));
3493     centreColumnLabelFlag.addItemListener(this);
3494     seqLimits.setState(true);
3495     seqLimits.setLabel(MessageManager
3496             .getString("label.show_sequence_limits"));
3497     seqLimits.addItemListener(this);
3498
3499     /*
3500      * Configure Colour menu items and actions
3501      */
3502     applyToAllGroups.setLabel(MessageManager
3503             .getString("label.apply_colour_to_all_groups"));
3504     applyToAllGroups.setState(true);
3505     applyToAllGroups.addItemListener(this);
3506     clustalColour.setLabel(MessageManager
3507             .getString("label.colourScheme_clustal"));
3508     clustalColour.addActionListener(this);
3509     zappoColour.setLabel(MessageManager
3510             .getString("label.colourScheme_zappo"));
3511     zappoColour.addActionListener(this);
3512     taylorColour.setLabel(MessageManager
3513             .getString("label.colourScheme_taylor"));
3514     taylorColour.addActionListener(this);
3515     hydrophobicityColour.setLabel(MessageManager
3516             .getString("label.colourScheme_hydrophobic"));
3517     hydrophobicityColour.addActionListener(this);
3518     helixColour.setLabel(MessageManager
3519             .getString("label.colourScheme_helix_propensity"));
3520     helixColour.addActionListener(this);
3521     strandColour.setLabel(MessageManager
3522             .getString("label.colourScheme_strand_propensity"));
3523     strandColour.addActionListener(this);
3524     turnColour.setLabel(MessageManager
3525             .getString("label.colourScheme_turn_propensity"));
3526     turnColour.addActionListener(this);
3527     buriedColour.setLabel(MessageManager
3528             .getString("label.colourScheme_buried_index"));
3529     buriedColour.addActionListener(this);
3530     purinePyrimidineColour.setLabel(MessageManager
3531             .getString("label.colourScheme_purine/pyrimidine"));
3532     purinePyrimidineColour.addActionListener(this);
3533     // RNAInteractionColour.setLabel(MessageManager
3534     // .getString("label.rna_interaction"));
3535     // RNAInteractionColour.addActionListener(this);
3536     RNAHelixColour.setLabel(MessageManager
3537             .getString("label.colourScheme_rna_helices"));
3538     RNAHelixColour.addActionListener(this);
3539     userDefinedColour.setLabel(MessageManager
3540             .getString("action.user_defined"));
3541     userDefinedColour.addActionListener(this);
3542     PIDColour.setLabel(MessageManager
3543             .getString("label.colourScheme_%_identity"));
3544     PIDColour.addActionListener(this);
3545     BLOSUM62Colour.setLabel(MessageManager
3546             .getString("label.colourScheme_blosum62"));
3547     BLOSUM62Colour.addActionListener(this);
3548     tcoffeeColour.setLabel(MessageManager
3549             .getString("label.colourScheme_t-coffee_scores"));
3550     // it will be enabled only if a score file is provided
3551     tcoffeeColour.setEnabled(false);
3552     tcoffeeColour.addActionListener(this);
3553     conservationMenuItem.setLabel(MessageManager
3554             .getString("action.by_conservation"));
3555     conservationMenuItem.addItemListener(this);
3556     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3557     noColourmenuItem.addActionListener(this);
3558     abovePIDThreshold.setLabel(MessageManager
3559             .getString("label.above_identity_threshold"));
3560     abovePIDThreshold.addItemListener(this);
3561     nucleotideColour.setLabel(MessageManager
3562             .getString("label.colourScheme_nucleotide"));
3563     nucleotideColour.addActionListener(this);
3564     modifyPID.setLabel(MessageManager
3565             .getString("label.modify_identity_threshold"));
3566     modifyPID.setEnabled(abovePIDThreshold.getState());
3567     modifyPID.addActionListener(this);
3568     modifyConservation.setLabel(MessageManager
3569             .getString("label.modify_conservation_threshold"));
3570     modifyConservation.setEnabled(conservationMenuItem.getState());
3571     modifyConservation.addActionListener(this);
3572     annotationColour.setLabel(MessageManager
3573             .getString("action.by_annotation"));
3574     annotationColour.addActionListener(this);
3575
3576     /*
3577      * Configure Calculate menu items and actions
3578      */
3579     sortPairwiseMenuItem.setLabel(MessageManager
3580             .getString("action.by_pairwise_id"));
3581     sortPairwiseMenuItem.addActionListener(this);
3582     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3583     sortIDMenuItem.addActionListener(this);
3584     sortLengthMenuItem.setLabel(MessageManager
3585             .getString("action.by_length"));
3586     sortLengthMenuItem.addActionListener(this);
3587     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3588     sortGroupMenuItem.addActionListener(this);
3589     pairwiseAlignmentMenuItem.setLabel(MessageManager
3590             .getString("action.pairwise_alignment"));
3591     pairwiseAlignmentMenuItem.addActionListener(this);
3592     PCAMenuItem.setLabel(MessageManager
3593             .getString("label.principal_component_analysis"));
3594     PCAMenuItem.addActionListener(this);
3595     autoCalculate = new CheckboxMenuItem(
3596             MessageManager.getString("label.autocalculate_consensus"), true);
3597     averageDistanceTreeMenuItem.setLabel(MessageManager
3598             .getString("label.average_distance_identity"));
3599     averageDistanceTreeMenuItem.addActionListener(this);
3600     neighbourTreeMenuItem.setLabel(MessageManager
3601             .getString("label.neighbour_joining_identity"));
3602     neighbourTreeMenuItem.addActionListener(this);
3603     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3604             .getString("label.average_distance_blosum62"));
3605     avDistanceTreeBlosumMenuItem.addActionListener(this);
3606     njTreeBlosumMenuItem.setLabel(MessageManager
3607             .getString("label.neighbour_blosum62"));
3608     njTreeBlosumMenuItem.addActionListener(this);
3609     sortByTreeMenu.setLabel(MessageManager
3610             .getString("action.by_tree_order"));
3611     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3612     Menu calculateTreeMenu = new Menu(
3613             MessageManager.getString("action.calculate_tree"));
3614     autoCalculate.addItemListener(this);
3615     sortByTree.addItemListener(this);
3616
3617     /*
3618      * Configure Help menu items and actions
3619      */
3620     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3621     documentation.setLabel(MessageManager.getString("label.documentation"));
3622     documentation.addActionListener(this);
3623     about.setLabel(MessageManager.getString("label.about"));
3624     about.addActionListener(this);
3625
3626     /*
3627      * Add top level menus to frame
3628      */
3629     alignFrameMenuBar.add(fileMenu);
3630     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3631     alignFrameMenuBar.add(editMenu);
3632     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3633     alignFrameMenuBar.add(selectMenu);
3634     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3635     alignFrameMenuBar.add(viewMenu);
3636     Menu annotationsMenu = new Menu(
3637             MessageManager.getString("action.annotations"));
3638     alignFrameMenuBar.add(annotationsMenu);
3639     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3640     alignFrameMenuBar.add(formatMenu);
3641     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3642     alignFrameMenuBar.add(colourMenu);
3643     Menu calculateMenu = new Menu(
3644             MessageManager.getString("action.calculate"));
3645     alignFrameMenuBar.add(calculateMenu);
3646     alignFrameMenuBar.add(helpMenu);
3647
3648     /*
3649      * File menu
3650      */
3651     fileMenu.add(inputText);
3652     fileMenu.add(loadTree);
3653     fileMenu.add(loadAnnotations);
3654     fileMenu.addSeparator();
3655     fileMenu.add(outputTextboxMenu);
3656     fileMenu.add(outputFeatures);
3657     fileMenu.add(outputAnnotations);
3658     if (jalviewServletURL != null)
3659     {
3660       fileMenu.add(loadApplication);
3661     }
3662     fileMenu.addSeparator();
3663     fileMenu.add(closeMenuItem);
3664
3665     /*
3666      * Edit menu
3667      */
3668     editMenu.add(undoMenuItem);
3669     editMenu.add(redoMenuItem);
3670     editMenu.add(cut);
3671     editMenu.add(copy);
3672     pasteMenu.add(pasteNew);
3673     pasteMenu.add(pasteThis);
3674     editMenu.add(pasteMenu);
3675     editMenu.add(delete);
3676     editMenu.addSeparator();
3677     editMenu.add(remove2LeftMenuItem);
3678     editMenu.add(remove2RightMenuItem);
3679     editMenu.add(removeGappedColumnMenuItem);
3680     editMenu.add(removeAllGapsMenuItem);
3681     editMenu.add(removeRedundancyMenuItem);
3682
3683     /*
3684      * Select menu
3685      */
3686     selectMenu.add(findMenuItem);
3687     selectMenu.addSeparator();
3688     selectMenu.add(selectAllSequenceMenuItem);
3689     selectMenu.add(deselectAllSequenceMenuItem);
3690     selectMenu.add(invertSequenceMenuItem);
3691     selectMenu.add(invertColSel);
3692     selectMenu.add(createGroup);
3693     selectMenu.add(unGroup);
3694     selectMenu.add(grpsFromSelection);
3695     selectMenu.add(deleteGroups);
3696     selectMenu.add(annotationColumnSelection);
3697
3698     /*
3699      * View menu
3700      */
3701     viewMenu.add(newView);
3702     viewMenu.addSeparator();
3703     showMenu.add(showColumns);
3704     showMenu.add(showSeqs);
3705     showMenu.add(showAllHidden);
3706     viewMenu.add(showMenu);
3707     hideMenu.add(hideColumns);
3708     hideMenu.add(hideSequences);
3709     hideMenu.add(hideAllSelection);
3710     hideMenu.add(hideAllButSelection);
3711     viewMenu.add(hideMenu);
3712     viewMenu.addSeparator();
3713     viewMenu.add(followMouseOverFlag);
3714     viewMenu.addSeparator();
3715     viewMenu.add(sequenceFeatures);
3716     viewMenu.add(featureSettings);
3717     viewMenu.addSeparator();
3718     viewMenu.add(alProperties);
3719     viewMenu.addSeparator();
3720     viewMenu.add(overviewMenuItem);
3721
3722     /*
3723      * Annotations menu
3724      */
3725     annotationsMenu.add(annotationPanelMenuItem);
3726     annotationsMenu.addSeparator();
3727     annotationsMenu.add(showAlignmentAnnotations);
3728     annotationsMenu.add(showSequenceAnnotations);
3729     annotationsMenu.add(sortAnnBySequence);
3730     annotationsMenu.add(sortAnnByLabel);
3731     annotationsMenu.addSeparator();
3732     autoAnnMenu.add(showAutoFirst);
3733     autoAnnMenu.add(showAutoLast);
3734     autoAnnMenu.addSeparator();
3735     autoAnnMenu.add(applyAutoAnnotationSettings);
3736     autoAnnMenu.add(showConsensusHistogram);
3737     autoAnnMenu.add(showSequenceLogo);
3738     autoAnnMenu.add(normSequenceLogo);
3739     autoAnnMenu.addSeparator();
3740     autoAnnMenu.add(showGroupConservation);
3741     autoAnnMenu.add(showGroupConsensus);
3742     annotationsMenu.add(autoAnnMenu);
3743
3744     /*
3745      * Format menu
3746      */
3747     formatMenu.add(font);
3748     formatMenu.add(seqLimits);
3749     formatMenu.add(wrapMenuItem);
3750     formatMenu.add(scaleAbove);
3751     formatMenu.add(scaleLeft);
3752     formatMenu.add(scaleRight);
3753     formatMenu.add(viewBoxesMenuItem);
3754     formatMenu.add(viewTextMenuItem);
3755     formatMenu.add(colourTextMenuItem);
3756     formatMenu.add(displayNonconservedMenuItem);
3757     formatMenu.add(renderGapsMenuItem);
3758     formatMenu.add(centreColumnLabelFlag);
3759
3760     /*
3761      * Colour menu
3762      */
3763     colourMenu.add(applyToAllGroups);
3764     colourMenu.addSeparator();
3765     colourMenu.add(noColourmenuItem);
3766     colourMenu.add(clustalColour);
3767     colourMenu.add(BLOSUM62Colour);
3768     colourMenu.add(PIDColour);
3769     colourMenu.add(zappoColour);
3770     colourMenu.add(taylorColour);
3771     colourMenu.add(hydrophobicityColour);
3772     colourMenu.add(helixColour);
3773     colourMenu.add(strandColour);
3774     colourMenu.add(turnColour);
3775     colourMenu.add(buriedColour);
3776     colourMenu.add(nucleotideColour);
3777     colourMenu.add(purinePyrimidineColour);
3778     // colourMenu.add(RNAInteractionColour);
3779     colourMenu.add(tcoffeeColour);
3780     colourMenu.add(userDefinedColour);
3781     colourMenu.addSeparator();
3782     colourMenu.add(conservationMenuItem);
3783     colourMenu.add(modifyConservation);
3784     colourMenu.add(abovePIDThreshold);
3785     colourMenu.add(modifyPID);
3786     colourMenu.add(annotationColour);
3787     colourMenu.add(RNAHelixColour);
3788
3789     /*
3790      * Calculate menu
3791      */
3792     sortMenu.add(sortIDMenuItem);
3793     sortMenu.add(sortLengthMenuItem);
3794     sortMenu.add(sortByTreeMenu);
3795     sortMenu.add(sortGroupMenuItem);
3796     sortMenu.add(sortPairwiseMenuItem);
3797     calculateMenu.add(sortMenu);
3798     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3799     calculateTreeMenu.add(neighbourTreeMenuItem);
3800     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3801     calculateTreeMenu.add(njTreeBlosumMenuItem);
3802     calculateMenu.add(calculateTreeMenu);
3803     calculateMenu.addSeparator();
3804     calculateMenu.add(pairwiseAlignmentMenuItem);
3805     calculateMenu.add(PCAMenuItem);
3806     calculateMenu.add(autoCalculate);
3807     calculateMenu.add(sortByTree);
3808
3809     /*
3810      * Help menu
3811      */
3812     helpMenu.add(documentation);
3813     helpMenu.add(about);
3814
3815     /*
3816      * Status bar
3817      */
3818     statusBar.setBackground(Color.white);
3819     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3820     statusBar.setText(MessageManager.getString("label.status_bar"));
3821     this.add(statusBar, BorderLayout.SOUTH);
3822   }
3823
3824   @Override
3825   public void setStatus(String string)
3826   {
3827     statusBar.setText(string);
3828   };
3829
3830   MenuItem featureSettings = new MenuItem();
3831
3832   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3833
3834   MenuItem annotationColour = new MenuItem();
3835
3836   MenuItem annotationColumnSelection = new MenuItem();
3837
3838   MenuItem invertColSel = new MenuItem();
3839
3840   MenuItem showColumns = new MenuItem();
3841
3842   MenuItem showSeqs = new MenuItem();
3843
3844   MenuItem hideColumns = new MenuItem();
3845
3846   MenuItem hideSequences = new MenuItem();
3847
3848   MenuItem hideAllButSelection = new MenuItem();
3849
3850   MenuItem hideAllSelection = new MenuItem();
3851
3852   MenuItem showAllHidden = new MenuItem();
3853
3854   MenuItem newView = new MenuItem();
3855
3856   private CheckboxMenuItem showAlignmentAnnotations;
3857
3858   private CheckboxMenuItem showSequenceAnnotations;
3859
3860   private CheckboxMenuItem sortAnnBySequence;
3861
3862   private CheckboxMenuItem sortAnnByLabel;
3863
3864   private CheckboxMenuItem showAutoFirst;
3865
3866   private CheckboxMenuItem showAutoLast;
3867
3868   private SplitFrame splitFrame;
3869
3870   /**
3871    * Attach the alignFrame panels after embedding menus, if necessary. This used
3872    * to be called setEmbedded, but is now creates the dropdown menus in a
3873    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3874    *
3875    * @param reallyEmbedded
3876    *          true to attach the view to the applet area on the page rather than
3877    *          in a new window
3878    */
3879   public void createAlignFrameWindow(boolean reallyEmbedded)
3880   {
3881     if (reallyEmbedded)
3882     {
3883       embedAlignFrameInApplet(viewport.applet);
3884     }
3885     else
3886     {
3887       // //////
3888       // test and embed menu bar if necessary.
3889       //
3890       if (embedMenuIfNeeded(alignPanel))
3891       {
3892         /*
3893          * adjust for status bar height too. ? pointless as overridden by layout
3894          * manager
3895          */
3896         alignPanel.setSize(getSize().width,
3897                 getSize().height - statusBar.getHeight());
3898       }
3899       add(statusBar, BorderLayout.SOUTH);
3900       add(alignPanel, BorderLayout.CENTER);
3901       // and register with the applet so it can pass external API calls to us
3902       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3903               frameHeight);
3904     }
3905   }
3906
3907   /**
3908    * Add the components of this AlignFrame to the applet container.
3909    *
3910    * @param theApplet
3911    */
3912   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3913   {
3914     // ////
3915     // Explicitly build the embedded menu panel for the on-page applet
3916     //
3917     // view cannot be closed if its actually on the page
3918     fileMenu.remove(closeMenuItem);
3919     fileMenu.remove(3); // Remove Separator
3920     // construct embedded menu, using default font
3921     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3922     // and actually add the components to the applet area
3923     theApplet.setLayout(new BorderLayout());
3924     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3925     theApplet.add(statusBar, BorderLayout.SOUTH);
3926     // TODO should size be left to the layout manager?
3927     alignPanel.setSize(theApplet.getSize().width,
3928             theApplet.getSize().height - embeddedMenu.getHeight()
3929                     - statusBar.getHeight());
3930     theApplet.add(alignPanel, BorderLayout.CENTER);
3931     final AlignFrame me = this;
3932     theApplet.addFocusListener(new FocusListener()
3933     {
3934
3935       @Override
3936       public void focusLost(FocusEvent e)
3937       {
3938         if (theApplet.currentAlignFrame == me)
3939         {
3940           theApplet.currentAlignFrame = null;
3941         }
3942       }
3943
3944       @Override
3945       public void focusGained(FocusEvent e)
3946       {
3947         theApplet.currentAlignFrame = me;
3948       }
3949     });
3950     theApplet.validate();
3951   }
3952
3953   /**
3954    * create a new binding between structures in an existing jmol viewer instance
3955    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3956    * this does not open a new Jmol window, or modify the display of the
3957    * structures in the original jmol window. Note This method doesn't work
3958    * without an additional javascript library to exchange messages between the
3959    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3960    *
3961    * @param viewer
3962    *          JmolViewer instance
3963    * @param sequenceIds
3964    *          - sequence Ids to search for associations
3965    */
3966   public SequenceStructureBinding addStructureViewInstance(
3967           Object jmolviewer, String[] sequenceIds)
3968   {
3969     Viewer viewer = null;
3970     try
3971     {
3972       viewer = (Viewer) jmolviewer;
3973     } catch (ClassCastException ex)
3974     {
3975       System.err.println("Unsupported viewer object :"
3976               + jmolviewer.getClass());
3977     }
3978     if (viewer == null)
3979     {
3980       System.err.println("Can't use this object as a structure viewer:"
3981               + jmolviewer.getClass());
3982       return null;
3983     }
3984     SequenceI[] seqs = null;
3985     if (sequenceIds == null || sequenceIds.length == 0)
3986     {
3987       seqs = viewport.getAlignment().getSequencesArray();
3988     }
3989     else
3990     {
3991       Vector sqi = new Vector();
3992       AlignmentI al = viewport.getAlignment();
3993       for (int sid = 0; sid < sequenceIds.length; sid++)
3994       {
3995         SequenceI sq = al.findName(sequenceIds[sid]);
3996         if (sq != null)
3997         {
3998           sqi.addElement(sq);
3999         }
4000       }
4001       if (sqi.size() > 0)
4002       {
4003         seqs = new SequenceI[sqi.size()];
4004         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4005         {
4006           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4007         }
4008       }
4009       else
4010       {
4011         return null;
4012       }
4013     }
4014     AAStructureBindingModel jmv = null;
4015     // TODO: search for a jmv that involves viewer
4016     if (jmv == null)
4017     { // create a new viewer/jalview binding.
4018       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4019     }
4020     return jmv;
4021
4022   }
4023
4024   /**
4025    * bind a pdb file to a sequence in the current view
4026    *
4027    * @param sequenceId
4028    *          - sequenceId within the dataset.
4029    * @param pdbEntryString
4030    *          - the short name for the PDB file
4031    * @param pdbFile
4032    *          - pdb file - either a URL or a valid PDB file.
4033    * @return true if binding was as success TODO: consider making an exception
4034    *         structure for indicating when PDB parsing or sequenceId location
4035    *         fails.
4036    */
4037   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4038           String pdbFile)
4039   {
4040     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4041     boolean needtoadd = false;
4042     if (toaddpdb != null)
4043     {
4044       Vector pdbe = toaddpdb.getAllPDBEntries();
4045       PDBEntry pdbentry = null;
4046       if (pdbe != null && pdbe.size() > 0)
4047       {
4048         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4049         {
4050           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4051           if (!pdbentry.getId().equals(pdbEntryString)
4052                   && !pdbentry.getFile().equals(pdbFile))
4053           {
4054             pdbentry = null;
4055           }
4056           else
4057           {
4058             continue;
4059           }
4060         }
4061       }
4062       if (pdbentry == null)
4063       {
4064         pdbentry = new PDBEntry();
4065         pdbentry.setId(pdbEntryString);
4066         pdbentry.setFile(pdbFile);
4067         needtoadd = true; // add this new entry to sequence.
4068       }
4069       // resolve data source
4070       // TODO: this code should be a refactored to an io package
4071       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4072               pdbFile, FileFormat.PDB);
4073       if (protocol == null)
4074       {
4075         return false;
4076       }
4077       if (needtoadd)
4078       {
4079         pdbentry.setProperty("protocol", protocol);
4080         toaddpdb.addPDBId(pdbentry);
4081         alignPanel.getStructureSelectionManager()
4082                 .registerPDBEntry(pdbentry);
4083       }
4084     }
4085     return true;
4086   }
4087
4088   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4089   {
4090     if (seqs != null)
4091     {
4092       Vector sequences = new Vector();
4093       for (int i = 0; i < seqs.length; i++)
4094       {
4095         if (seqs[i] != null)
4096         {
4097           sequences.addElement(new Object[] { seqs[i],
4098               (chains != null) ? chains[i] : null });
4099         }
4100       }
4101       seqs = new SequenceI[sequences.size()];
4102       chains = new String[sequences.size()];
4103       for (int i = 0, isize = sequences.size(); i < isize; i++)
4104       {
4105         Object[] oj = (Object[]) sequences.elementAt(i);
4106
4107         seqs[i] = (SequenceI) oj[0];
4108         chains[i] = (String) oj[1];
4109       }
4110     }
4111     return new Object[] { seqs, chains };
4112
4113   }
4114
4115   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4116           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4117   {
4118     // Scrub any null sequences from the array
4119     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4120     seqs = (SequenceI[]) sqch[0];
4121     chains = (String[]) sqch[1];
4122     if (seqs == null || seqs.length == 0)
4123     {
4124       System.err
4125               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4126     }
4127     if (protocol == null)
4128     {
4129       String sourceType = (String) pdb.getProperty("protocol");
4130       try
4131       {
4132         protocol = DataSourceType.valueOf(sourceType);
4133       } catch (IllegalArgumentException e)
4134       {
4135         // ignore
4136       }
4137       if (protocol == null)
4138       {
4139         System.err.println("Couldn't work out protocol to open structure: "
4140                 + pdb.getId());
4141         return;
4142       }
4143     }
4144     if (applet.useXtrnalSviewer)
4145     {
4146       // register the association(s) and quit, don't create any windows.
4147       if (StructureSelectionManager.getStructureSelectionManager(applet)
4148               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4149       {
4150         System.err.println("Failed to map " + pdb.getFile() + " ("
4151                 + protocol + ") to any sequences");
4152       }
4153       return;
4154     }
4155     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4156     {
4157       // can only do alignments with Jmol
4158       // find the last jmol window assigned to this alignment
4159       AppletJmol ajm = null, tajm;
4160       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4161       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4162       {
4163         tajm = (AppletJmol) jmols.elementAt(i);
4164         if (tajm.ap.alignFrame == this)
4165         {
4166           ajm = tajm;
4167           break;
4168         }
4169       }
4170       if (ajm != null)
4171       {
4172         System.err
4173                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4174         // try and add the pdb structure
4175         // ajm.addS
4176         ajm = null;
4177       }
4178     }
4179     // otherwise, create a new window
4180     if (applet.jmolAvailable)
4181     {
4182       new AppletJmol(pdb, seqs, chains, alignPanel,
4183               protocol);
4184       applet.lastFrameX += 40;
4185       applet.lastFrameY += 40;
4186     }
4187     else
4188     {
4189       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4190     }
4191
4192   }
4193
4194   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4195           SequenceI[][] seqs, String[][] chains, String[] protocols)
4196   {
4197     // TODO Auto-generated method stub
4198     System.err.println("Aligned Structure View: Not yet implemented.");
4199   }
4200
4201   /**
4202    * modify the current selection, providing the user has not made a selection
4203    * already.
4204    *
4205    * @param sel
4206    *          - sequences from this alignment
4207    * @param csel
4208    *          - columns to be selected on the alignment
4209    */
4210   public void select(SequenceGroup sel, ColumnSelection csel,
4211           HiddenColumns hidden)
4212   {
4213     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4214   }
4215
4216   public void scrollTo(int row, int column)
4217   {
4218     alignPanel.seqPanel.scrollTo(row, column);
4219   }
4220
4221   public void scrollToRow(int row)
4222   {
4223     alignPanel.seqPanel.scrollToRow(row);
4224   }
4225
4226   public void scrollToColumn(int column)
4227   {
4228     alignPanel.seqPanel.scrollToColumn(column);
4229   }
4230
4231   /**
4232    * @return the alignments unique ID.
4233    */
4234   public String getSequenceSetId()
4235   {
4236     return viewport.getSequenceSetId();
4237   }
4238
4239   /**
4240    * Load the (T-Coffee) score file from the specified url
4241    *
4242    * @param source
4243    *          File/URL/T-COFFEE score file contents
4244    * @throws IOException
4245    * @return true if alignment was annotated with data from source
4246    */
4247   public boolean loadScoreFile(String source) throws IOException
4248   {
4249
4250     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4251             AppletFormatAdapter.checkProtocol(source));
4252     if (!file.isValid())
4253     {
4254       // TODO: raise dialog for gui
4255       System.err.println("Problems parsing T-Coffee scores: "
4256               + file.getWarningMessage());
4257       System.err.println("Origin was:\n" + source);
4258       return false;
4259     }
4260
4261     /*
4262      * check that the score matrix matches the alignment dimensions
4263      */
4264     AlignmentI aln;
4265     if ((aln = viewport.getAlignment()) != null
4266             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4267                     .getWidth()))
4268     {
4269       // TODO: raise a dialog box here rather than bomb out.
4270       System.err
4271               .println("The scores matrix does not match the alignment dimensions");
4272
4273     }
4274
4275     // TODO add parameter to indicate if matching should be done
4276     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4277     {
4278       alignPanel.fontChanged();
4279       tcoffeeColour.setEnabled(true);
4280       // switch to this color
4281       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4282       return true;
4283     }
4284     else
4285     {
4286       System.err.println("Problems resolving T-Coffee scores:");
4287       if (file.getWarningMessage() != null)
4288       {
4289         System.err.println(file.getWarningMessage());
4290       }
4291     }
4292     return false;
4293   }
4294
4295   public SplitFrame getSplitFrame()
4296   {
4297     return this.splitFrame;
4298   }
4299
4300   public void setSplitFrame(SplitFrame sf)
4301   {
4302     this.splitFrame = sf;
4303   }
4304
4305   // may not need this
4306   @Override
4307   public void setShowSeqFeatures(boolean b)
4308   {
4309     // showSeqFeatures.setSelected(b);
4310     viewport.setShowSequenceFeatures(b);
4311
4312   }
4313
4314   @Override
4315   public void setMenusForViewport()
4316   {
4317     // setMenusFromViewport(viewport);
4318
4319   }
4320
4321   @Override
4322   public void refreshFeatureUI(boolean enableIfNecessary)
4323   {
4324     if (enableIfNecessary)
4325     {
4326       sequenceFeatures.setState(true);
4327       alignPanel.av.setShowSequenceFeatures(true);
4328     }
4329   }
4330
4331   @Override
4332   public FeatureSettingsControllerI getFeatureSettingsUI()
4333   {
4334     return alignPanel.av.featureSettings;
4335   }
4336
4337 }