src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.analysis.TreeBuilder;
  26 import jalview.analysis.scoremodels.PIDModel;
  27 import jalview.analysis.scoremodels.ScoreModels;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.FeatureColourI;
  32 import jalview.api.FeatureRenderer;
  33 import jalview.api.FeatureSettingsControllerI;
  34 import jalview.api.SequenceStructureBinding;
  35 import jalview.bin.JalviewLite;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentAnnotation;
  46 import jalview.datamodel.AlignmentI;
  47 import jalview.datamodel.AlignmentOrder;
  48 import jalview.datamodel.ColumnSelection;
  49 import jalview.datamodel.HiddenColumns;
  50 import jalview.datamodel.PDBEntry;
  51 import jalview.datamodel.Sequence;
  52 import jalview.datamodel.SequenceGroup;
  53 import jalview.datamodel.SequenceI;
  54 import jalview.io.AnnotationFile;
  55 import jalview.io.AppletFormatAdapter;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FeaturesFile;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileFormatI;
  60 import jalview.io.FileFormats;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColour;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.ZappoColourScheme;
  77 import jalview.structure.StructureSelectionManager;
  78 import jalview.structures.models.AAStructureBindingModel;
  79 import jalview.util.MappingUtils;
  80 import jalview.util.MessageManager;
  81 import jalview.viewmodel.AlignmentViewport;
  82 import jalview.viewmodel.ViewportRanges;
  83
  84 import java.awt.BorderLayout;
  85 import java.awt.Canvas;
  86 import java.awt.CheckboxMenuItem;
  87 import java.awt.Color;
  88 import java.awt.FlowLayout;
  89 import java.awt.Font;
  90 import java.awt.FontMetrics;
  91 import java.awt.Frame;
  92 import java.awt.Graphics;
  93 import java.awt.Label;
  94 import java.awt.Menu;
  95 import java.awt.MenuBar;
  96 import java.awt.MenuItem;
  97 import java.awt.Panel;
  98 import java.awt.event.ActionEvent;
  99 import java.awt.event.ActionListener;
 100 import java.awt.event.FocusEvent;
 101 import java.awt.event.FocusListener;
 102 import java.awt.event.ItemEvent;
 103 import java.awt.event.ItemListener;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.KeyListener;
 106 import java.awt.event.WindowAdapter;
 107 import java.awt.event.WindowEvent;
 108 import java.io.IOException;
 109 import java.net.URL;
 110 import java.net.URLEncoder;
 111 import java.util.Arrays;
 112 import java.util.Deque;
 113 import java.util.HashMap;
 114 import java.util.List;
 115 import java.util.Map;
 116 import java.util.StringTokenizer;
 117 import java.util.Vector;
 118
 119 import org.jmol.viewer.Viewer;
 120
 121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 122         ItemListener, KeyListener, AlignViewControllerGuiI
 123 {
 124   public AlignViewControllerI avc;
 125
 126   public AlignmentPanel alignPanel;
 127
 128   public AlignViewport viewport;
 129
 130   // width and height may be overridden by applet parameters
 131   int frameWidth = 700;
 132
 133   int frameHeight = 500;
 134
 135   String jalviewServletURL;
 136
 137   /*
 138    * Flag for showing autocalculated consensus above or below other consensus
 139    * rows
 140    */
 141   private boolean showAutoCalculatedAbove;
 142
 143   private SequenceAnnotationOrder annotationSortOrder;
 144
 145   /**
 146    * Constructor that creates the frame and adds it to the display.
 147    *
 148    * @param al
 149    * @param applet
 150    * @param title
 151    * @param embedded
 152    */
 153   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 154           boolean embedded)
 155   {
 156     this(al, applet, title, embedded, true);
 157   }
 158
 159   /**
 160    * Constructor that optionally allows the frame to be displayed or only
 161    * created.
 162    *
 163    * @param al
 164    * @param applet
 165    * @param title
 166    * @param embedded
 167    * @param addToDisplay
 168    */
 169   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 170           boolean embedded, boolean addToDisplay)
 171   {
 172     this(al, null, null, applet, title, embedded, addToDisplay);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           HiddenColumns hidden, JalviewLite applet, String title,
 177           boolean embedded)
 178   {
 179     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 180   }
 181
 182   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 183           HiddenColumns hidden, JalviewLite applet, String title,
 184           boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237
 238     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 239     followMouseOverFlag.setState(viewport.isFollowHighlight());
 240     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 241     showGroupConservation.setState(viewport.isShowGroupConservation());
 242     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 243     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 244     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 245     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 246     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 247     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 248     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showAlignmentAnnotations.setState(true);
 250     showSequenceAnnotations.setState(false);
 251
 252     seqLimits.setState(viewport.getShowJVSuffix());
 253
 254     if (applet != null)
 255     {
 256       String param = applet.getParameter("sortBy");
 257       if (param != null)
 258       {
 259         if (param.equalsIgnoreCase("Id"))
 260         {
 261           sortIDMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Pairwise Identity"))
 264         {
 265           sortPairwiseMenuItem_actionPerformed();
 266         }
 267         else if (param.equalsIgnoreCase("Length"))
 268         {
 269           sortLengthMenuItem_actionPerformed();
 270         }
 271       }
 272
 273       param = applet.getParameter("wrap");
 274       if (param != null)
 275       {
 276         if (param.equalsIgnoreCase("true"))
 277         {
 278           wrapMenuItem.setState(true);
 279           wrapMenuItem_actionPerformed();
 280         }
 281       }
 282       param = applet.getParameter("centrecolumnlabels");
 283       if (param != null)
 284       {
 285         centreColumnLabelFlag.setState(true);
 286         centreColumnLabelFlag_stateChanged();
 287       }
 288
 289     }
 290     if (viewport.getAlignment().isNucleotide())
 291     {
 292       conservationMenuItem.setEnabled(false);
 293       clustalColour.setEnabled(false);
 294       BLOSUM62Colour.setEnabled(false);
 295       zappoColour.setEnabled(false);
 296       taylorColour.setEnabled(false);
 297       hydrophobicityColour.setEnabled(false);
 298       helixColour.setEnabled(false);
 299       strandColour.setEnabled(false);
 300       turnColour.setEnabled(false);
 301       buriedColour.setEnabled(false);
 302       viewport.updateStrucConsensus(alignPanel);
 303       if (viewport.getAlignment().hasRNAStructure())
 304       {
 305         RNAHelixColour.setEnabled(true);
 306       }
 307       else
 308       {
 309         RNAHelixColour.setEnabled(false);
 310       }
 311     }
 312     else
 313     {
 314       RNAHelixColour.setEnabled(false);
 315       purinePyrimidineColour.setEnabled(false);
 316       nucleotideColour.setEnabled(false);
 317     }
 318     // Some JVMS send keyevents to Top frame or lowest panel,
 319     // Havent worked out why yet. So add to both this frame and seqCanvas for
 320     // now
 321     this.addKeyListener(this);
 322     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 323     alignPanel.idPanel.idCanvas.addKeyListener(this);
 324     alignPanel.scalePanel.addKeyListener(this);
 325     alignPanel.annotationPanel.addKeyListener(this);
 326     alignPanel.annotationPanelHolder.addKeyListener(this);
 327     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 328     alignPanel.alabels.addKeyListener(this);
 329
 330     setAnnotationsVisibility();
 331
 332     if (addToDisplay)
 333     {
 334       addToDisplay(embedded);
 335     }
 336   }
 337
 338   /**
 339    * @param embedded
 340    */
 341   public void addToDisplay(boolean embedded)
 342   {
 343     createAlignFrameWindow(embedded);
 344     validate();
 345     alignPanel.adjustAnnotationHeight();
 346     alignPanel.paintAlignment(true);
 347   }
 348
 349   public AlignViewport getAlignViewport()
 350   {
 351     return viewport;
 352   }
 353
 354   public SeqCanvas getSeqcanvas()
 355   {
 356     return alignPanel.seqPanel.seqCanvas;
 357   }
 358
 359   /**
 360    * Load a features file onto the alignment
 361    *
 362    * @param file
 363    *          file URL, content, or other resolvable path
 364    * @param type
 365    *          is protocol for accessing data referred to by file
 366    */
 367
 368   public boolean parseFeaturesFile(String file, DataSourceType type)
 369   {
 370     return parseFeaturesFile(file, type, true);
 371   }
 372
 373   /**
 374    * Load a features file onto the alignment
 375    *
 376    * @param file
 377    *          file URL, content, or other resolvable path
 378    * @param sourceType
 379    *          is protocol for accessing data referred to by file
 380    * @param autoenabledisplay
 381    *          when true, display features flag will be automatically enabled if
 382    *          features are loaded
 383    * @return true if data parsed as a features file
 384    */
 385   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 386           boolean autoenabledisplay)
 387   {
 388     boolean featuresFile = false;
 389     try
 390     {
 391       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 392               .getFeatureRenderer().getFeatureColours();
 393       boolean relaxedIdMatching = viewport.applet
 394               .getDefaultParameter("relaxedidmatch", false);
 395       featuresFile = new FeaturesFile(file, sourceType).parse(
 396               viewport.getAlignment(), colours, true, relaxedIdMatching);
 397     } catch (Exception ex)
 398     {
 399       ex.printStackTrace();
 400     }
 401
 402     if (featuresFile)
 403     {
 404       if (autoenabledisplay)
 405       {
 406         viewport.setShowSequenceFeatures(true);
 407         sequenceFeatures.setState(true);
 408       }
 409       if (alignPanel.seqPanel.seqCanvas.fr != null)
 410       {
 411         // update the min/max ranges where necessary
 412         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 413       }
 414       if (viewport.featureSettings != null)
 415       {
 416         viewport.featureSettings.refreshTable();
 417       }
 418       alignPanel.paintAlignment(true);
 419       statusBar.setText(MessageManager
 420               .getString("label.successfully_added_features_alignment"));
 421     }
 422     return featuresFile;
 423   }
 424
 425   @Override
 426   public void keyPressed(KeyEvent evt)
 427   {
 428     ViewportRanges ranges = viewport.getRanges();
 429
 430     if (viewport.cursorMode
 431             && ((evt.getKeyCode() >= KeyEvent.VK_0
 432                     && evt.getKeyCode() <= KeyEvent.VK_9)
 433                     || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 434                             && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 435             && Character.isDigit(evt.getKeyChar()))
 436     {
 437       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 438     }
 439
 440     switch (evt.getKeyCode())
 441     {
 442     case 27: // escape key
 443       deselectAllSequenceMenuItem_actionPerformed();
 444
 445       alignPanel.alabels.cancelDrag();
 446       break;
 447     case KeyEvent.VK_X:
 448       if (evt.isControlDown() || evt.isMetaDown())
 449       {
 450         cut_actionPerformed();
 451       }
 452       break;
 453     case KeyEvent.VK_C:
 454       if (viewport.cursorMode && !evt.isControlDown())
 455       {
 456         alignPanel.seqPanel.setCursorColumn();
 457       }
 458       if (evt.isControlDown() || evt.isMetaDown())
 459       {
 460         copy_actionPerformed();
 461       }
 462       break;
 463     case KeyEvent.VK_V:
 464       if (evt.isControlDown())
 465       {
 466         paste(evt.isShiftDown());
 467       }
 468       break;
 469     case KeyEvent.VK_A:
 470       if (evt.isControlDown() || evt.isMetaDown())
 471       {
 472         selectAllSequenceMenuItem_actionPerformed();
 473       }
 474       break;
 475     case KeyEvent.VK_DOWN:
 476       if (viewport.cursorMode)
 477       {
 478         alignPanel.seqPanel.moveCursor(0, 1);
 479       }
 480       else
 481       {
 482         moveSelectedSequences(false);
 483       }
 484       break;
 485
 486     case KeyEvent.VK_UP:
 487       if (viewport.cursorMode)
 488       {
 489         alignPanel.seqPanel.moveCursor(0, -1);
 490       }
 491       else
 492       {
 493         moveSelectedSequences(true);
 494       }
 495       break;
 496
 497     case KeyEvent.VK_LEFT:
 498       if (evt.isAltDown() || !viewport.cursorMode)
 499       {
 500         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 501       }
 502       else
 503       {
 504         alignPanel.seqPanel.moveCursor(-1, 0);
 505       }
 506       break;
 507
 508     case KeyEvent.VK_RIGHT:
 509       if (evt.isAltDown() || !viewport.cursorMode)
 510       {
 511         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 512       }
 513       else
 514       {
 515         alignPanel.seqPanel.moveCursor(1, 0);
 516       }
 517       break;
 518
 519     case KeyEvent.VK_SPACE:
 520       if (viewport.cursorMode)
 521       {
 522         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 523                 || evt.isShiftDown() || evt.isAltDown());
 524       }
 525       break;
 526
 527     case KeyEvent.VK_DELETE:
 528     case KeyEvent.VK_BACK_SPACE:
 529       if (viewport.cursorMode)
 530       {
 531         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 532                 || evt.isShiftDown() || evt.isAltDown());
 533       }
 534       else
 535       {
 536         cut_actionPerformed();
 537         alignPanel.seqPanel.seqCanvas.repaint();
 538       }
 539       break;
 540
 541     case KeyEvent.VK_S:
 542       if (viewport.cursorMode)
 543       {
 544         alignPanel.seqPanel.setCursorRow();
 545       }
 546       break;
 547     case KeyEvent.VK_P:
 548       if (viewport.cursorMode)
 549       {
 550         alignPanel.seqPanel.setCursorPosition();
 551       }
 552       break;
 553
 554     case KeyEvent.VK_ENTER:
 555     case KeyEvent.VK_COMMA:
 556       if (viewport.cursorMode)
 557       {
 558         alignPanel.seqPanel.setCursorRowAndColumn();
 559       }
 560       break;
 561
 562     case KeyEvent.VK_Q:
 563       if (viewport.cursorMode)
 564       {
 565         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 566       }
 567       break;
 568     case KeyEvent.VK_M:
 569       if (viewport.cursorMode)
 570       {
 571         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 572       }
 573       break;
 574
 575     case KeyEvent.VK_F2:
 576       viewport.cursorMode = !viewport.cursorMode;
 577       statusBar.setText(MessageManager
 578               .formatMessage("label.keyboard_editing_mode", new String[]
 579               { (viewport.cursorMode ? "on" : "off") }));
 580       if (viewport.cursorMode)
 581       {
 582         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 583         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 584       }
 585       break;
 586
 587     case KeyEvent.VK_F:
 588       if (evt.isControlDown())
 589       {
 590         findMenuItem_actionPerformed();
 591       }
 592       break;
 593
 594     case KeyEvent.VK_H:
 595     {
 596       boolean toggleSeqs = !evt.isControlDown();
 597       boolean toggleCols = !evt.isShiftDown();
 598       toggleHiddenRegions(toggleSeqs, toggleCols);
 599       break;
 600     }
 601
 602     case KeyEvent.VK_PAGE_UP:
 603       ranges.pageUp();
 604       break;
 605
 606     case KeyEvent.VK_PAGE_DOWN:
 607       ranges.pageDown();
 608       break;
 609
 610     case KeyEvent.VK_Z:
 611       if (evt.isControlDown())
 612       {
 613         undoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_Y:
 618       if (evt.isControlDown())
 619       {
 620         redoMenuItem_actionPerformed();
 621       }
 622       break;
 623
 624     case KeyEvent.VK_L:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(true);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_R:
 632       if (evt.isControlDown())
 633       {
 634         trimAlignment(false);
 635       }
 636       break;
 637
 638     case KeyEvent.VK_E:
 639       if (evt.isControlDown())
 640       {
 641         if (evt.isShiftDown())
 642         {
 643           this.removeAllGapsMenuItem_actionPerformed();
 644         }
 645         else
 646         {
 647           removeGappedColumnMenuItem_actionPerformed();
 648         }
 649       }
 650       break;
 651     case KeyEvent.VK_I:
 652       if (evt.isControlDown())
 653       {
 654         if (evt.isAltDown())
 655         {
 656           invertColSel_actionPerformed();
 657         }
 658         else
 659         {
 660           invertSequenceMenuItem_actionPerformed();
 661         }
 662       }
 663       break;
 664
 665     case KeyEvent.VK_G:
 666       if (evt.isControlDown())
 667       {
 668         if (evt.isShiftDown())
 669         {
 670           this.unGroup_actionPerformed();
 671         }
 672         else
 673         {
 674           this.createGroup_actionPerformed();
 675         }
 676       }
 677       break;
 678
 679     case KeyEvent.VK_U:
 680       if (evt.isControlDown())
 681       {
 682         this.deleteGroups_actionPerformed();
 683       }
 684       break;
 685
 686     case KeyEvent.VK_T:
 687       if (evt.isControlDown())
 688       {
 689         newView(null);
 690       }
 691       break;
 692
 693     }
 694     alignPanel.paintAlignment(true);
 695   }
 696
 697   /**
 698    * called by key handler and the hide all/show all menu items
 699    *
 700    * @param toggleSeqs
 701    * @param toggleCols
 702    */
 703   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 704   {
 705     boolean hide = false;
 706     SequenceGroup sg = viewport.getSelectionGroup();
 707     if (!toggleSeqs && !toggleCols)
 708     {
 709       // Hide everything by the current selection - this is a hack - we do the
 710       // invert and then hide
 711       // first check that there will be visible columns after the invert.
 712       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 713               && sg.getStartRes() <= sg.getEndRes()))
 714       {
 715         // now invert the sequence set, if required - empty selection implies
 716         // that no hiding is required.
 717         if (sg != null)
 718         {
 719           invertSequenceMenuItem_actionPerformed();
 720           sg = viewport.getSelectionGroup();
 721           toggleSeqs = true;
 722
 723         }
 724         viewport.expandColSelection(sg, true);
 725         // finally invert the column selection and get the new sequence
 726         // selection and indicate it should be hidden.
 727         invertColSel_actionPerformed();
 728         toggleCols = true;
 729       }
 730     }
 731
 732     if (toggleSeqs)
 733     {
 734       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 735       {
 736         hide = true;
 737         viewport.hideAllSelectedSeqs();
 738       }
 739       else if (!(toggleCols && viewport.hasSelectedColumns()))
 740       {
 741         viewport.showAllHiddenSeqs();
 742       }
 743     }
 744
 745     if (toggleCols)
 746     {
 747       if (viewport.hasSelectedColumns())
 748       {
 749         viewport.hideSelectedColumns();
 750         if (!toggleSeqs)
 751         {
 752           viewport.setSelectionGroup(sg);
 753         }
 754       }
 755       else if (!hide)
 756       {
 757         viewport.showAllHiddenColumns();
 758       }
 759       viewport.sendSelection();
 760     }
 761   }
 762
 763   @Override
 764   public void keyReleased(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void keyTyped(KeyEvent evt)
 770   {
 771   }
 772
 773   @Override
 774   public void itemStateChanged(ItemEvent evt)
 775   {
 776     final Object source = evt.getSource();
 777     if (source == displayNonconservedMenuItem)
 778     {
 779       displayNonconservedMenuItem_actionPerformed();
 780     }
 781     else if (source == colourTextMenuItem)
 782     {
 783       colourTextMenuItem_actionPerformed();
 784     }
 785     else if (source == wrapMenuItem)
 786     {
 787       wrapMenuItem_actionPerformed();
 788     }
 789     else if (source == scaleAbove)
 790     {
 791       viewport.setScaleAboveWrapped(scaleAbove.getState());
 792     }
 793     else if (source == scaleLeft)
 794     {
 795       viewport.setScaleLeftWrapped(scaleLeft.getState());
 796     }
 797     else if (source == scaleRight)
 798     {
 799       viewport.setScaleRightWrapped(scaleRight.getState());
 800     }
 801     else if (source == seqLimits)
 802     {
 803       seqLimits_itemStateChanged();
 804     }
 805     else if (source == viewBoxesMenuItem)
 806     {
 807       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 808     }
 809     else if (source == viewTextMenuItem)
 810     {
 811       viewport.setShowText(viewTextMenuItem.getState());
 812     }
 813     else if (source == renderGapsMenuItem)
 814     {
 815       viewport.setRenderGaps(renderGapsMenuItem.getState());
 816     }
 817     else if (source == annotationPanelMenuItem)
 818     {
 819       boolean showAnnotations = annotationPanelMenuItem.getState();
 820       showAlignmentAnnotations.setEnabled(showAnnotations);
 821       showSequenceAnnotations.setEnabled(showAnnotations);
 822       viewport.setShowAnnotation(showAnnotations);
 823       alignPanel.setAnnotationVisible(showAnnotations);
 824     }
 825     else if (source == sequenceFeatures)
 826     {
 827       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 828       alignPanel.seqPanel.seqCanvas.repaint();
 829     }
 830     else if (source == showAlignmentAnnotations)
 831     {
 832       setAnnotationsVisibility();
 833     }
 834     else if (source == showSequenceAnnotations)
 835     {
 836       setAnnotationsVisibility();
 837     }
 838     else if (source == sortAnnBySequence)
 839     {
 840       boolean newState = sortAnnBySequence.getState();
 841       sortAnnByLabel.setState(false);
 842       setAnnotationSortOrder(
 843               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 844                       : SequenceAnnotationOrder.NONE);
 845       setViewportAnnotationOrder();
 846     }
 847     else if (source == sortAnnByLabel)
 848     {
 849       boolean newState = sortAnnByLabel.getState();
 850       sortAnnBySequence.setState(false);
 851       setAnnotationSortOrder(
 852               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 853                       : SequenceAnnotationOrder.NONE);
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == showAutoFirst)
 857     {
 858       showAutoLast.setState(!showAutoFirst.getState());
 859       setShowAutoCalculatedAbove(showAutoFirst.getState());
 860       setViewportAnnotationOrder();
 861     }
 862     else if (source == showAutoLast)
 863     {
 864       showAutoFirst.setState(!showAutoLast.getState());
 865       setShowAutoCalculatedAbove(showAutoFirst.getState());
 866       setViewportAnnotationOrder();
 867     }
 868     else if (source == conservationMenuItem)
 869     {
 870       conservationMenuItem_actionPerformed();
 871     }
 872     else if (source == abovePIDThreshold)
 873     {
 874       abovePIDThreshold_actionPerformed();
 875     }
 876     else if (source == applyToAllGroups)
 877     {
 878       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 879     }
 880     else if (source == autoCalculate)
 881     {
 882       viewport.autoCalculateConsensus = autoCalculate.getState();
 883     }
 884     else if (source == sortByTree)
 885     {
 886       viewport.sortByTree = sortByTree.getState();
 887     }
 888     else if (source == this.centreColumnLabelFlag)
 889     {
 890       centreColumnLabelFlag_stateChanged();
 891     }
 892     else if (source == this.followMouseOverFlag)
 893     {
 894       mouseOverFlag_stateChanged();
 895     }
 896     else if (source == showGroupConsensus)
 897     {
 898       showGroupConsensus_actionPerformed();
 899     }
 900     else if (source == showGroupConservation)
 901     {
 902       showGroupConservation_actionPerformed();
 903     }
 904     else if (source == showSequenceLogo)
 905     {
 906       showSequenceLogo_actionPerformed();
 907     }
 908     else if (source == normSequenceLogo)
 909     {
 910       normSequenceLogo_actionPerformed();
 911     }
 912     else if (source == showConsensusHistogram)
 913     {
 914       showConsensusHistogram_actionPerformed();
 915     }
 916     else if (source == applyAutoAnnotationSettings)
 917     {
 918       applyAutoAnnotationSettings_actionPerformed();
 919     }
 920     alignPanel.paintAlignment(true);
 921   }
 922
 923   /**
 924    * Set the visibility state of sequence-related and/or alignment-related
 925    * annotations depending on checkbox selections, and repaint.
 926    *
 927    * @param visible
 928    */
 929   private void setAnnotationsVisibility()
 930   {
 931     boolean showForAlignment = showAlignmentAnnotations.getState();
 932     boolean showForSequences = showSequenceAnnotations.getState();
 933     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 934     {
 935       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 936               .getAlignmentAnnotation())
 937       {
 938         boolean visible = (aa.sequenceRef == null ? showForAlignment
 939                 : showForSequences);
 940         aa.visible = visible;
 941       }
 942     }
 943     alignPanel.validateAnnotationDimensions(true);
 944     validate();
 945     repaint();
 946   }
 947
 948   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 949   {
 950     this.annotationSortOrder = order;
 951   }
 952
 953   /**
 954    * Set flags on the viewport that control annotation ordering
 955    */
 956   private void setViewportAnnotationOrder()
 957   {
 958     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 959     this.alignPanel.av
 960             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 961   }
 962
 963   private void setShowAutoCalculatedAbove(boolean showAbove)
 964   {
 965     this.showAutoCalculatedAbove = showAbove;
 966   }
 967
 968   private void mouseOverFlag_stateChanged()
 969   {
 970     viewport.setFollowHighlight(followMouseOverFlag.getState());
 971     // TODO: could kick the scrollTo mechanism to reset view for current
 972     // searchresults.
 973   }
 974
 975   private void centreColumnLabelFlag_stateChanged()
 976   {
 977     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 978     this.alignPanel.annotationPanel.repaint();
 979   }
 980
 981   @Override
 982   public void actionPerformed(ActionEvent evt)
 983   {
 984     viewport.applet.currentAlignFrame = this;
 985
 986     Object source = evt.getSource();
 987
 988     if (source == inputText)
 989     {
 990       inputText_actionPerformed();
 991     }
 992     else if (source == loadTree)
 993     {
 994       loadTree_actionPerformed();
 995     }
 996     else if (source == loadApplication)
 997     {
 998       launchFullApplication();
 999     }
1000     else if (source == loadAnnotations)
1001     {
1002       loadAnnotations();
1003     }
1004     else if (source == outputAnnotations)
1005     {
1006       outputAnnotations(true);
1007     }
1008     else if (source == outputFeatures)
1009     {
1010       outputFeatures(true, "Jalview");
1011     }
1012     else if (source == closeMenuItem)
1013     {
1014       closeMenuItem_actionPerformed();
1015     }
1016     else if (source == copy)
1017     {
1018       copy_actionPerformed();
1019     }
1020     else if (source == undoMenuItem)
1021     {
1022       undoMenuItem_actionPerformed();
1023     }
1024     else if (source == redoMenuItem)
1025     {
1026       redoMenuItem_actionPerformed();
1027     }
1028     else if (source == inputText)
1029     {
1030       inputText_actionPerformed();
1031     }
1032     else if (source == closeMenuItem)
1033     {
1034       closeMenuItem_actionPerformed();
1035     }
1036     else if (source == undoMenuItem)
1037     {
1038       undoMenuItem_actionPerformed();
1039     }
1040     else if (source == redoMenuItem)
1041     {
1042       redoMenuItem_actionPerformed();
1043     }
1044     else if (source == copy)
1045     {
1046       copy_actionPerformed();
1047     }
1048     else if (source == pasteNew)
1049     {
1050       pasteNew_actionPerformed();
1051     }
1052     else if (source == pasteThis)
1053     {
1054       pasteThis_actionPerformed();
1055     }
1056     else if (source == cut)
1057     {
1058       cut_actionPerformed();
1059     }
1060     else if (source == delete)
1061     {
1062       delete_actionPerformed();
1063     }
1064     else if (source == createGroup)
1065     {
1066       createGroup_actionPerformed();
1067     }
1068     else if (source == unGroup)
1069     {
1070       unGroup_actionPerformed();
1071     }
1072     else if (source == grpsFromSelection)
1073     {
1074       makeGrpsFromSelection_actionPerformed();
1075     }
1076     else if (source == deleteGroups)
1077     {
1078       deleteGroups_actionPerformed();
1079     }
1080     else if (source == selectAllSequenceMenuItem)
1081     {
1082       selectAllSequenceMenuItem_actionPerformed();
1083     }
1084     else if (source == deselectAllSequenceMenuItem)
1085     {
1086       deselectAllSequenceMenuItem_actionPerformed();
1087     }
1088     else if (source == invertSequenceMenuItem)
1089     {
1090       invertSequenceMenuItem_actionPerformed();
1091       // uncomment to slave sequence selections in split frame
1092       // viewport.sendSelection();
1093     }
1094     else if (source == invertColSel)
1095     {
1096       viewport.invertColumnSelection();
1097       alignPanel.paintAlignment(true);
1098       viewport.sendSelection();
1099     }
1100     else if (source == remove2LeftMenuItem)
1101     {
1102       trimAlignment(true);
1103     }
1104     else if (source == remove2RightMenuItem)
1105     {
1106       trimAlignment(false);
1107     }
1108     else if (source == removeGappedColumnMenuItem)
1109     {
1110       removeGappedColumnMenuItem_actionPerformed();
1111     }
1112     else if (source == removeAllGapsMenuItem)
1113     {
1114       removeAllGapsMenuItem_actionPerformed();
1115     }
1116     else if (source == findMenuItem)
1117     {
1118       findMenuItem_actionPerformed();
1119     }
1120     else if (source == font)
1121     {
1122       new FontChooser(alignPanel);
1123     }
1124     else if (source == newView)
1125     {
1126       newView(null);
1127     }
1128     else if (source == showColumns)
1129     {
1130       viewport.showAllHiddenColumns();
1131       alignPanel.paintAlignment(true);
1132       viewport.sendSelection();
1133     }
1134     else if (source == showSeqs)
1135     {
1136       viewport.showAllHiddenSeqs();
1137       alignPanel.paintAlignment(true);
1138       // uncomment if we want to slave sequence selections in split frame
1139       // viewport.sendSelection();
1140     }
1141     else if (source == hideColumns)
1142     {
1143       viewport.hideSelectedColumns();
1144       alignPanel.paintAlignment(true);
1145       viewport.sendSelection();
1146     }
1147     else if (source == hideSequences
1148             && viewport.getSelectionGroup() != null)
1149     {
1150       viewport.hideAllSelectedSeqs();
1151       alignPanel.paintAlignment(true);
1152       // uncomment if we want to slave sequence selections in split frame
1153       // viewport.sendSelection();
1154     }
1155     else if (source == hideAllButSelection)
1156     {
1157       toggleHiddenRegions(false, false);
1158       alignPanel.paintAlignment(true);
1159       viewport.sendSelection();
1160     }
1161     else if (source == hideAllSelection)
1162     {
1163       SequenceGroup sg = viewport.getSelectionGroup();
1164       viewport.expandColSelection(sg, false);
1165       viewport.hideAllSelectedSeqs();
1166       viewport.hideSelectedColumns();
1167       alignPanel.paintAlignment(true);
1168       viewport.sendSelection();
1169     }
1170     else if (source == showAllHidden)
1171     {
1172       viewport.showAllHiddenColumns();
1173       viewport.showAllHiddenSeqs();
1174       alignPanel.paintAlignment(true);
1175       viewport.sendSelection();
1176     }
1177     else if (source == showGroupConsensus)
1178     {
1179       showGroupConsensus_actionPerformed();
1180     }
1181     else if (source == showGroupConservation)
1182     {
1183       showGroupConservation_actionPerformed();
1184     }
1185     else if (source == showSequenceLogo)
1186     {
1187       showSequenceLogo_actionPerformed();
1188     }
1189     else if (source == normSequenceLogo)
1190     {
1191       normSequenceLogo_actionPerformed();
1192     }
1193     else if (source == showConsensusHistogram)
1194     {
1195       showConsensusHistogram_actionPerformed();
1196     }
1197     else if (source == applyAutoAnnotationSettings)
1198     {
1199       applyAutoAnnotationSettings_actionPerformed();
1200     }
1201     else if (source == featureSettings)
1202     {
1203       new FeatureSettings(alignPanel);
1204     }
1205     else if (source == alProperties)
1206     {
1207       StringBuffer contents = new jalview.io.AlignmentProperties(
1208               viewport.getAlignment()).formatAsString();
1209       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1210       cap.setText(contents.toString());
1211       Frame frame = new Frame();
1212       frame.add(cap);
1213       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1214               .formatMessage("label.alignment_properties", new String[]
1215               { getTitle() }), 400, 250);
1216     }
1217     else if (source == overviewMenuItem)
1218     {
1219       overviewMenuItem_actionPerformed();
1220     }
1221     else if (source == noColourmenuItem)
1222     {
1223       changeColour(null);
1224     }
1225     else if (source == clustalColour)
1226     {
1227       abovePIDThreshold.setState(false);
1228       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1229     }
1230     else if (source == zappoColour)
1231     {
1232       changeColour(new ZappoColourScheme());
1233     }
1234     else if (source == taylorColour)
1235     {
1236       changeColour(new TaylorColourScheme());
1237     }
1238     else if (source == hydrophobicityColour)
1239     {
1240       changeColour(new HydrophobicColourScheme());
1241     }
1242     else if (source == helixColour)
1243     {
1244       changeColour(new HelixColourScheme());
1245     }
1246     else if (source == strandColour)
1247     {
1248       changeColour(new StrandColourScheme());
1249     }
1250     else if (source == turnColour)
1251     {
1252       changeColour(new TurnColourScheme());
1253     }
1254     else if (source == buriedColour)
1255     {
1256       changeColour(new BuriedColourScheme());
1257     }
1258     else if (source == nucleotideColour)
1259     {
1260       changeColour(new NucleotideColourScheme());
1261     }
1262     else if (source == purinePyrimidineColour)
1263     {
1264       changeColour(new PurinePyrimidineColourScheme());
1265     }
1266     // else if (source == RNAInteractionColour)
1267     // {
1268     // changeColour(new RNAInteractionColourScheme());
1269     // }
1270     else if (source == RNAHelixColour)
1271     {
1272       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1273       // new RNAHelicesColourChooser(viewport, alignPanel);
1274     }
1275     else if (source == modifyPID)
1276     {
1277       modifyPID_actionPerformed();
1278     }
1279     else if (source == modifyConservation)
1280     {
1281       modifyConservation_actionPerformed();
1282     }
1283     else if (source == userDefinedColour)
1284     {
1285       new UserDefinedColours(alignPanel, null);
1286     }
1287     else if (source == PIDColour)
1288     {
1289       changeColour(new PIDColourScheme());
1290     }
1291     else if (source == BLOSUM62Colour)
1292     {
1293       changeColour(new Blosum62ColourScheme());
1294     }
1295     else if (source == tcoffeeColour)
1296     {
1297       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1298     }
1299     else if (source == annotationColour)
1300     {
1301       new AnnotationColourChooser(viewport, alignPanel);
1302     }
1303     else if (source == annotationColumnSelection)
1304     {
1305       new AnnotationColumnChooser(viewport, alignPanel);
1306     }
1307     else if (source == sortPairwiseMenuItem)
1308     {
1309       sortPairwiseMenuItem_actionPerformed();
1310     }
1311     else if (source == sortIDMenuItem)
1312     {
1313       sortIDMenuItem_actionPerformed();
1314     }
1315     else if (source == sortLengthMenuItem)
1316     {
1317       sortLengthMenuItem_actionPerformed();
1318     }
1319     else if (source == sortGroupMenuItem)
1320     {
1321       sortGroupMenuItem_actionPerformed();
1322     }
1323     else if (source == removeRedundancyMenuItem)
1324     {
1325       removeRedundancyMenuItem_actionPerformed();
1326     }
1327     else if (source == pairwiseAlignmentMenuItem)
1328     {
1329       pairwiseAlignmentMenuItem_actionPerformed();
1330     }
1331     else if (source == PCAMenuItem)
1332     {
1333       PCAMenuItem_actionPerformed();
1334     }
1335     else if (source == averageDistanceTreeMenuItem)
1336     {
1337       averageDistanceTreeMenuItem_actionPerformed();
1338     }
1339     else if (source == neighbourTreeMenuItem)
1340     {
1341       neighbourTreeMenuItem_actionPerformed();
1342     }
1343     else if (source == njTreeBlosumMenuItem)
1344     {
1345       njTreeBlosumMenuItem_actionPerformed();
1346     }
1347     else if (source == avDistanceTreeBlosumMenuItem)
1348     {
1349       avTreeBlosumMenuItem_actionPerformed();
1350     }
1351     else if (source == documentation)
1352     {
1353       documentation_actionPerformed();
1354     }
1355     else if (source == about)
1356     {
1357       about_actionPerformed();
1358     }
1359
1360   }
1361
1362   public void inputText_actionPerformed()
1363   {
1364     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1365     Frame frame = new Frame();
1366     frame.add(cap);
1367     jalview.bin.JalviewLite.addFrame(frame,
1368             MessageManager.getString("label.input_cut_paste"), 500, 500);
1369   }
1370
1371   protected void outputText_actionPerformed(ActionEvent e)
1372   {
1373     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1374     Frame frame = new Frame();
1375     frame.add(cap);
1376     JalviewLite.addFrame(frame, MessageManager
1377             .formatMessage("label.alignment_output_command", new Object[]
1378             { e.getActionCommand() }), 600, 500);
1379
1380     FileFormatI fileFormat = FileFormats.getInstance()
1381             .forName(e.getActionCommand());
1382     cap.setText(
1383             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1384                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1385   }
1386
1387   public void loadAnnotations()
1388   {
1389     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1390     cap.setText(MessageManager
1391             .getString("label.paste_features_annotations_Tcoffee_here"));
1392     cap.setAnnotationImport();
1393     Frame frame = new Frame();
1394     frame.add(cap);
1395     jalview.bin.JalviewLite.addFrame(frame,
1396             MessageManager.getString("action.paste_annotations"), 400, 300);
1397
1398   }
1399
1400   public String outputAnnotations(boolean displayTextbox)
1401   {
1402     String annotation = new AnnotationFile()
1403             .printAnnotationsForView(viewport);
1404
1405     if (displayTextbox)
1406     {
1407       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1408       Frame frame = new Frame();
1409       frame.add(cap);
1410       jalview.bin.JalviewLite.addFrame(frame,
1411               MessageManager.getString("label.annotations"), 600, 500);
1412       cap.setText(annotation);
1413     }
1414
1415     return annotation;
1416   }
1417
1418   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1419   {
1420     if (alignPanel.getFeatureRenderer() != null
1421             && viewport.getFeaturesDisplayed() != null)
1422     {
1423       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1424
1425     }
1426     return null;
1427   }
1428
1429   public String outputFeatures(boolean displayTextbox, String format)
1430   {
1431     String features;
1432     FeaturesFile formatter = new FeaturesFile();
1433     if (format.equalsIgnoreCase("Jalview"))
1434     {
1435       features = formatter.printJalviewFormat(
1436               viewport.getAlignment().getSequencesArray(),
1437               getDisplayedFeatureCols());
1438     }
1439     else
1440     {
1441       features = formatter.printGffFormat(
1442               viewport.getAlignment().getSequencesArray(),
1443               getDisplayedFeatureCols());
1444     }
1445
1446     if (displayTextbox)
1447     {
1448       boolean frimport = false;
1449       if (features == null || features.equals("No Features Visible"))
1450       {
1451         features = "# No features visible - paste some and import them here.";
1452         frimport = true;
1453       }
1454
1455       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1456       if (frimport)
1457       {
1458         cap.setAnnotationImport();
1459       }
1460       Frame frame = new Frame();
1461       frame.add(cap);
1462       jalview.bin.JalviewLite.addFrame(frame,
1463               MessageManager.getString("label.features"), 600, 500);
1464       cap.setText(features);
1465     }
1466     else
1467     {
1468       if (features == null)
1469       {
1470         features = "";
1471       }
1472     }
1473
1474     return features;
1475   }
1476
1477   void launchFullApplication()
1478   {
1479     StringBuffer url = new StringBuffer(jalviewServletURL);
1480
1481     // allow servlet parameters to be passed in applet parameter
1482     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1483             : "?";
1484     url.append(firstSep);
1485
1486     url.append(
1487             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1488
1489     if (viewport.applet.getParameter("features") != null)
1490     {
1491       url.append("&features=");
1492       url.append(appendProtocol(viewport.applet.getParameter("features")));
1493     }
1494
1495     if (viewport.applet.getParameter("annotations") != null)
1496     {
1497       url.append("&annotations=");
1498       url.append(
1499               appendProtocol(viewport.applet.getParameter("annotations")));
1500     }
1501
1502     if (viewport.applet.getParameter("jnetfile") != null
1503             || viewport.applet.getParameter("jpredfile") != null)
1504     {
1505       url.append("&annotations=");
1506       url.append(appendProtocol(
1507               viewport.applet.getParameter("jnetfile") != null
1508                       ? viewport.applet.getParameter("jnetfile")
1509                       : viewport.applet.getParameter("jpredfile")));
1510     }
1511
1512     if (viewport.applet.getParameter("defaultColour") != null)
1513     {
1514       url.append("&colour=" + removeWhiteSpace(
1515               viewport.applet.getParameter("defaultColour")));
1516     }
1517
1518     if (viewport.applet.getParameter("userDefinedColour") != null)
1519     {
1520       url.append("&colour=" + removeWhiteSpace(
1521               viewport.applet.getParameter("userDefinedColour")));
1522     }
1523     if (viewport.applet.getParameter("tree") != null)
1524     {
1525       url.append("&tree="
1526               + appendProtocol(viewport.applet.getParameter("tree")));
1527     }
1528     if (viewport.applet.getParameter("treeFile") != null)
1529     {
1530       url.append("&tree="
1531               + appendProtocol(viewport.applet.getParameter("treeFile")));
1532     }
1533
1534     showURL(url.toString(), "FULL_APP");
1535   }
1536
1537   String removeWhiteSpace(String colour)
1538   {
1539     StringBuffer sb = new StringBuffer();
1540     for (int i = 0; i < colour.length(); i++)
1541     {
1542       if (Character.isWhitespace(colour.charAt(i)))
1543       {
1544         sb.append("%20");
1545       }
1546       else
1547       {
1548         sb.append(colour.charAt(i));
1549       }
1550     }
1551
1552     return sb.toString();
1553   }
1554
1555   String appendProtocol(String url)
1556   {
1557     try
1558     {
1559       new URL(url);
1560       url = URLEncoder.encode(url);
1561     }
1562     /*
1563      * When we finally deprecate 1.1 compatibility, we can start to use
1564      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1565      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1566      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1567      * ex.printStackTrace(); }
1568      */
1569     catch (java.net.MalformedURLException ex)
1570     {
1571       url = viewport.applet.getCodeBase() + url;
1572     }
1573     return url;
1574   }
1575
1576   public void closeMenuItem_actionPerformed()
1577   {
1578     PaintRefresher.RemoveComponent(alignPanel);
1579     if (alignPanel.seqPanel != null
1580             && alignPanel.seqPanel.seqCanvas != null)
1581     {
1582       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1583     }
1584     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1585     {
1586       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1587     }
1588
1589     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1590     {
1591       System.exit(0);
1592     }
1593     else
1594     {
1595     }
1596     viewport = null;
1597     alignPanel = null;
1598     this.dispose();
1599   }
1600
1601   /**
1602    * TODO: JAL-1104
1603    */
1604   void updateEditMenuBar()
1605   {
1606
1607     if (viewport.getHistoryList().size() > 0)
1608     {
1609       undoMenuItem.setEnabled(true);
1610       CommandI command = viewport.getHistoryList().peek();
1611       undoMenuItem.setLabel(MessageManager
1612               .formatMessage("label.undo_command", new Object[]
1613               { command.getDescription() }));
1614     }
1615     else
1616     {
1617       undoMenuItem.setEnabled(false);
1618       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1619     }
1620
1621     if (viewport.getRedoList().size() > 0)
1622     {
1623       redoMenuItem.setEnabled(true);
1624
1625       CommandI command = viewport.getRedoList().peek();
1626       redoMenuItem.setLabel(MessageManager
1627               .formatMessage("label.redo_command", new Object[]
1628               { command.getDescription() }));
1629     }
1630     else
1631     {
1632       redoMenuItem.setEnabled(false);
1633       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1634     }
1635   }
1636
1637   /**
1638    * TODO: JAL-1104
1639    */
1640   @Override
1641   public void addHistoryItem(CommandI command)
1642   {
1643     if (command.getSize() > 0)
1644     {
1645       viewport.addToHistoryList(command);
1646       viewport.clearRedoList();
1647       updateEditMenuBar();
1648       viewport.updateHiddenColumns();
1649     }
1650   }
1651
1652   /**
1653    * TODO: JAL-1104 DOCUMENT ME!
1654    *
1655    * @param e
1656    *          DOCUMENT ME!
1657    */
1658   protected void undoMenuItem_actionPerformed()
1659   {
1660     if (viewport.getHistoryList().isEmpty())
1661     {
1662       return;
1663     }
1664
1665     CommandI command = viewport.getHistoryList().pop();
1666     viewport.addToRedoList(command);
1667     command.undoCommand(null);
1668
1669     AlignmentViewport originalSource = getOriginatingSource(command);
1670     // JBPNote Test
1671     if (originalSource != viewport)
1672     {
1673       System.err
1674               .println("Warning: Viewport object mismatch whilst undoing");
1675     }
1676     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1677                                           // viewport.getColumnSelection().getHiddenColumns()
1678                                           // != null;
1679     updateEditMenuBar();
1680     originalSource.firePropertyChange("alignment", null,
1681             originalSource.getAlignment().getSequences());
1682   }
1683
1684   /**
1685    * TODO: JAL-1104 DOCUMENT ME!
1686    *
1687    * @param e
1688    *          DOCUMENT ME!
1689    */
1690   protected void redoMenuItem_actionPerformed()
1691   {
1692     if (viewport.getRedoList().isEmpty())
1693     {
1694       return;
1695     }
1696
1697     CommandI command = viewport.getRedoList().pop();
1698     viewport.addToHistoryList(command);
1699     command.doCommand(null);
1700
1701     AlignmentViewport originalSource = getOriginatingSource(command);
1702     // JBPNote Test
1703     if (originalSource != viewport)
1704     {
1705       System.err
1706               .println("Warning: Viewport object mismatch whilst re-doing");
1707     }
1708     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1709                                           // viewport.getColumnSelection().getHiddenColumns()
1710                                           // != null;
1711
1712     updateEditMenuBar();
1713     originalSource.firePropertyChange("alignment", null,
1714             originalSource.getAlignment().getSequences());
1715   }
1716
1717   AlignmentViewport getOriginatingSource(CommandI command)
1718   {
1719     AlignmentViewport originalSource = null;
1720     // For sequence removal and addition, we need to fire
1721     // the property change event FROM the viewport where the
1722     // original alignment was altered
1723     AlignmentI al = null;
1724     if (command instanceof EditCommand)
1725     {
1726       EditCommand editCommand = (EditCommand) command;
1727       al = editCommand.getAlignment();
1728       Vector comps = (Vector) PaintRefresher.components
1729               .get(viewport.getSequenceSetId());
1730       for (int i = 0; i < comps.size(); i++)
1731       {
1732         if (comps.elementAt(i) instanceof AlignmentPanel)
1733         {
1734           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1735           {
1736             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1737             break;
1738           }
1739         }
1740       }
1741     }
1742
1743     if (originalSource == null)
1744     {
1745       // The original view is closed, we must validate
1746       // the current view against the closed view first
1747       if (al != null)
1748       {
1749         PaintRefresher.validateSequences(al, viewport.getAlignment());
1750       }
1751
1752       originalSource = viewport;
1753     }
1754
1755     return originalSource;
1756   }
1757
1758   /**
1759    * Move the currently selected sequences up or down one position in the
1760    * alignment
1761    *
1762    * @param up
1763    */
1764   public void moveSelectedSequences(boolean up)
1765   {
1766     SequenceGroup sg = viewport.getSelectionGroup();
1767     if (sg == null)
1768     {
1769       return;
1770     }
1771     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1772             up ? null : viewport.getHiddenRepSequences(), up);
1773     alignPanel.paintAlignment(true);
1774
1775     /*
1776      * Also move cDNA/protein complement sequences
1777      */
1778     AlignViewportI complement = viewport.getCodingComplement();
1779     if (complement != null)
1780     {
1781       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1782               viewport, complement);
1783       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1784               up ? null : complement.getHiddenRepSequences(), up);
1785       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1786     }
1787   }
1788
1789   synchronized void slideSequences(boolean right, int size)
1790   {
1791     List<SequenceI> sg = new Vector<>();
1792     if (viewport.cursorMode)
1793     {
1794       sg.add(viewport.getAlignment()
1795               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1796     }
1797     else if (viewport.getSelectionGroup() != null
1798             && viewport.getSelectionGroup().getSize() != viewport
1799                     .getAlignment().getHeight())
1800     {
1801       sg = viewport.getSelectionGroup()
1802               .getSequences(viewport.getHiddenRepSequences());
1803     }
1804
1805     if (sg.size() < 1)
1806     {
1807       return;
1808     }
1809
1810     Vector<SequenceI> invertGroup = new Vector();
1811
1812     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1813     {
1814       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1815       {
1816         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1817       }
1818     }
1819
1820     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1821
1822     SequenceI[] seqs2 = invertGroup
1823             .toArray(new SequenceI[invertGroup.size()]);
1824     for (int i = 0; i < invertGroup.size(); i++)
1825     {
1826       seqs2[i] = invertGroup.elementAt(i);
1827     }
1828
1829     SlideSequencesCommand ssc;
1830     if (right)
1831     {
1832       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1833               viewport.getGapCharacter());
1834     }
1835     else
1836     {
1837       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1838               viewport.getGapCharacter());
1839     }
1840
1841     int groupAdjustment = 0;
1842     if (ssc.getGapsInsertedBegin() && right)
1843     {
1844       if (viewport.cursorMode)
1845       {
1846         alignPanel.seqPanel.moveCursor(size, 0);
1847       }
1848       else
1849       {
1850         groupAdjustment = size;
1851       }
1852     }
1853     else if (!ssc.getGapsInsertedBegin() && !right)
1854     {
1855       if (viewport.cursorMode)
1856       {
1857         alignPanel.seqPanel.moveCursor(-size, 0);
1858       }
1859       else
1860       {
1861         groupAdjustment = -size;
1862       }
1863     }
1864
1865     if (groupAdjustment != 0)
1866     {
1867       viewport.getSelectionGroup().setStartRes(
1868               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1869       viewport.getSelectionGroup().setEndRes(
1870               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1871     }
1872
1873     boolean appendHistoryItem = false;
1874     Deque<CommandI> historyList = viewport.getHistoryList();
1875     if (historyList != null && historyList.size() > 0
1876             && historyList.peek() instanceof SlideSequencesCommand)
1877     {
1878       appendHistoryItem = ssc.appendSlideCommand(
1879               (SlideSequencesCommand) historyList.peek());
1880     }
1881
1882     if (!appendHistoryItem)
1883     {
1884       addHistoryItem(ssc);
1885     }
1886
1887     repaint();
1888   }
1889
1890   static StringBuffer copiedSequences;
1891
1892   static Vector<int[]> copiedHiddenColumns;
1893
1894   protected void copy_actionPerformed()
1895   {
1896     if (viewport.getSelectionGroup() == null)
1897     {
1898       return;
1899     }
1900
1901     SequenceGroup sg = viewport.getSelectionGroup();
1902     copiedSequences = new StringBuffer();
1903     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1904     for (int i = 0; i < sg.getSize(); i++)
1905     {
1906       SequenceI seq = sg.getSequenceAt(i);
1907       int index = viewport.getAlignment().findIndex(seq);
1908       orderedSeqs.put(index, seq);
1909     }
1910
1911     int index = 0, startRes, endRes;
1912     char ch;
1913
1914     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1915     {
1916       copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1917               .getHiddenColumns().getHiddenColumnsCopy());
1918       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1919       for (int[] region : copiedHiddenColumns)
1920       {
1921         region[0] = region[0] - hiddenOffset;
1922         region[1] = region[1] - hiddenOffset;
1923       }
1924     }
1925     else
1926     {
1927       copiedHiddenColumns = null;
1928     }
1929
1930     for (int i = 0; i < sg.getSize(); i++)
1931     {
1932       SequenceI seq = null;
1933
1934       while (seq == null)
1935       {
1936         if (orderedSeqs.containsKey(index))
1937         {
1938           seq = orderedSeqs.get(index);
1939           index++;
1940           break;
1941         }
1942         else
1943         {
1944           index++;
1945         }
1946       }
1947
1948       // FIND START RES
1949       // Returns residue following index if gap
1950       startRes = seq.findPosition(sg.getStartRes());
1951
1952       // FIND END RES
1953       // Need to find the residue preceeding index if gap
1954       endRes = 0;
1955
1956       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1957       {
1958         ch = seq.getCharAt(j);
1959         if (!jalview.util.Comparison.isGap((ch)))
1960         {
1961           endRes++;
1962         }
1963       }
1964
1965       if (endRes > 0)
1966       {
1967         endRes += seq.getStart() - 1;
1968       }
1969
1970       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1971               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1972                       sg.getEndRes() + 1)
1973               + "\n");
1974     }
1975
1976   }
1977
1978   protected void pasteNew_actionPerformed()
1979   {
1980     paste(true);
1981   }
1982
1983   protected void pasteThis_actionPerformed()
1984   {
1985     paste(false);
1986   }
1987
1988   void paste(boolean newAlignment)
1989   {
1990     try
1991     {
1992
1993       if (copiedSequences == null)
1994       {
1995         return;
1996       }
1997
1998       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1999       Vector seqs = new Vector();
2000       while (st.hasMoreElements())
2001       {
2002         String name = st.nextToken();
2003         int start = Integer.parseInt(st.nextToken());
2004         int end = Integer.parseInt(st.nextToken());
2005         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2006       }
2007       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2008       for (int i = 0; i < seqs.size(); i++)
2009       {
2010         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2011       }
2012
2013       if (newAlignment)
2014       {
2015         String newtitle = MessageManager
2016                 .getString("label.copied_sequences");
2017         if (getTitle().startsWith(
2018                 MessageManager.getString("label.copied_sequences")))
2019         {
2020           newtitle = getTitle();
2021         }
2022         else
2023         {
2024           newtitle = newtitle.concat(MessageManager
2025                   .formatMessage("label.from_msname", new String[]
2026                   { getTitle() }));
2027         }
2028         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2029                 viewport.applet, newtitle, false);
2030         if (copiedHiddenColumns != null)
2031         {
2032           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2033           {
2034             int[] region = copiedHiddenColumns.elementAt(i);
2035             af.viewport.hideColumns(region[0], region[1]);
2036           }
2037         }
2038
2039         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2040                 frameHeight);
2041       }
2042       else
2043       {
2044         addSequences(newSeqs);
2045       }
2046
2047     } catch (Exception ex)
2048     {
2049     } // could be anything being pasted in here
2050
2051   }
2052
2053   void addSequences(SequenceI[] seqs)
2054   {
2055     for (int i = 0; i < seqs.length; i++)
2056     {
2057       viewport.getAlignment().addSequence(seqs[i]);
2058     }
2059
2060     // !newAlignment
2061     addHistoryItem(new EditCommand(
2062             MessageManager.getString("label.add_sequences"), Action.PASTE,
2063             seqs, 0, viewport.getAlignment().getWidth(),
2064             viewport.getAlignment()));
2065
2066     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2067     viewport.getAlignment().getWidth();
2068     viewport.firePropertyChange("alignment", null,
2069             viewport.getAlignment().getSequences());
2070
2071   }
2072
2073   protected void cut_actionPerformed()
2074   {
2075     copy_actionPerformed();
2076     delete_actionPerformed();
2077   }
2078
2079   protected void delete_actionPerformed()
2080   {
2081
2082     SequenceGroup sg = viewport.getSelectionGroup();
2083     if (sg == null)
2084     {
2085       return;
2086     }
2087
2088     Vector seqs = new Vector();
2089     SequenceI seq;
2090     for (int i = 0; i < sg.getSize(); i++)
2091     {
2092       seq = sg.getSequenceAt(i);
2093       seqs.addElement(seq);
2094     }
2095
2096     /*
2097      * If the cut affects all sequences, warn, remove highlighted columns
2098      */
2099     if (sg.getSize() == viewport.getAlignment().getHeight())
2100     {
2101       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2102               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2103       if (isEntireAlignWidth)
2104       {
2105         String title = MessageManager.getString("label.delete_all");
2106         Panel infoPanel = new Panel();
2107         infoPanel.setLayout(new FlowLayout());
2108         infoPanel.add(
2109                 new Label(MessageManager.getString("warn.delete_all")));
2110
2111         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2112         dialog.setMainPanel(infoPanel);
2113         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2114         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2115         dialog.setVisible(true);
2116
2117         if (!dialog.accept)
2118         {
2119           return;
2120         }
2121       }
2122       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2123               sg.getEndRes() + 1);
2124     }
2125
2126     SequenceI[] cut = new SequenceI[seqs.size()];
2127     for (int i = 0; i < seqs.size(); i++)
2128     {
2129       cut[i] = (SequenceI) seqs.elementAt(i);
2130     }
2131
2132     /*
2133      * //ADD HISTORY ITEM
2134      */
2135     addHistoryItem(new EditCommand(
2136             MessageManager.getString("label.cut_sequences"), Action.CUT,
2137             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2138             viewport.getAlignment()));
2139
2140     viewport.setSelectionGroup(null);
2141     viewport.getAlignment().deleteGroup(sg);
2142
2143     viewport.firePropertyChange("alignment", null,
2144             viewport.getAlignment().getSequences());
2145
2146     if (viewport.getAlignment().getHeight() < 1)
2147     {
2148       this.setVisible(false);
2149     }
2150     viewport.sendSelection();
2151   }
2152
2153   /**
2154    * group consensus toggled
2155    *
2156    */
2157   protected void showGroupConsensus_actionPerformed()
2158   {
2159     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2160     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2161
2162   }
2163
2164   /**
2165    * group conservation toggled.
2166    */
2167   protected void showGroupConservation_actionPerformed()
2168   {
2169     viewport.setShowGroupConservation(showGroupConservation.getState());
2170     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2171   }
2172
2173   /*
2174    * (non-Javadoc)
2175    *
2176    * @see
2177    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2178    * .event.ActionEvent)
2179    */
2180   protected void showConsensusHistogram_actionPerformed()
2181   {
2182     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2183     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184   }
2185
2186   /*
2187    * (non-Javadoc)
2188    *
2189    * @see
2190    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2191    * .event.ActionEvent)
2192    */
2193   protected void showSequenceLogo_actionPerformed()
2194   {
2195     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197   }
2198
2199   protected void normSequenceLogo_actionPerformed()
2200   {
2201     showSequenceLogo.setState(true);
2202     viewport.setShowSequenceLogo(true);
2203     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2204     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2205   }
2206
2207   protected void applyAutoAnnotationSettings_actionPerformed()
2208   {
2209     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2210   }
2211
2212   protected void makeGrpsFromSelection_actionPerformed()
2213   {
2214     if (avc.makeGroupsFromSelection())
2215     {
2216       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2217       alignPanel.updateAnnotation();
2218       alignPanel.paintAlignment(true);
2219     }
2220   }
2221
2222   protected void createGroup_actionPerformed()
2223   {
2224     avc.createGroup();
2225   }
2226
2227   protected void unGroup_actionPerformed()
2228   {
2229     if (avc.unGroup())
2230     {
2231       alignPanel.alignmentChanged();
2232     }
2233   }
2234
2235   protected void deleteGroups_actionPerformed()
2236   {
2237     if (avc.deleteGroups())
2238     {
2239       alignPanel.alignmentChanged();
2240     }
2241   }
2242
2243   public void selectAllSequenceMenuItem_actionPerformed()
2244   {
2245     SequenceGroup sg = new SequenceGroup();
2246     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2247     {
2248       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2249     }
2250     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2251     viewport.setSelectionGroup(sg);
2252     // JAL-2034 - should delegate to
2253     // alignPanel to decide if overview needs
2254     // updating.
2255     alignPanel.paintAlignment(false);
2256     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257     viewport.sendSelection();
2258   }
2259
2260   public void deselectAllSequenceMenuItem_actionPerformed()
2261   {
2262     if (viewport.cursorMode)
2263     {
2264       alignPanel.seqPanel.keyboardNo1 = null;
2265       alignPanel.seqPanel.keyboardNo2 = null;
2266     }
2267     viewport.setSelectionGroup(null);
2268     viewport.getColumnSelection().clear();
2269     viewport.setSelectionGroup(null);
2270     alignPanel.idPanel.idCanvas.searchResults = null;
2271     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2272     // JAL-2034 - should delegate to
2273     // alignPanel to decide if overview needs
2274     // updating.
2275     alignPanel.paintAlignment(false);
2276     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277     viewport.sendSelection();
2278   }
2279
2280   public void invertSequenceMenuItem_actionPerformed()
2281   {
2282     SequenceGroup sg = viewport.getSelectionGroup();
2283     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2284     {
2285       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2286     }
2287
2288     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289     viewport.sendSelection();
2290   }
2291
2292   public void invertColSel_actionPerformed()
2293   {
2294     viewport.invertColumnSelection();
2295     alignPanel.paintAlignment(true);
2296     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2297     viewport.sendSelection();
2298   }
2299
2300   void trimAlignment(boolean trimLeft)
2301   {
2302     AlignmentI al = viewport.getAlignment();
2303     ViewportRanges ranges = viewport.getRanges();
2304     ColumnSelection colSel = viewport.getColumnSelection();
2305     int column;
2306
2307     if (!colSel.isEmpty())
2308     {
2309       if (trimLeft)
2310       {
2311         column = colSel.getMin();
2312       }
2313       else
2314       {
2315         column = colSel.getMax();
2316       }
2317
2318       SequenceI[] seqs;
2319       if (viewport.getSelectionGroup() != null)
2320       {
2321         seqs = viewport.getSelectionGroup()
2322                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2323       }
2324       else
2325       {
2326         seqs = al.getSequencesArray();
2327       }
2328
2329       TrimRegionCommand trimRegion;
2330       if (trimLeft)
2331       {
2332         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2333                 column, al);
2334         ranges.setStartRes(0);
2335       }
2336       else
2337       {
2338         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2339                 column, al);
2340       }
2341
2342       statusBar.setText(MessageManager
2343               .formatMessage("label.removed_columns", new String[]
2344               { Integer.valueOf(trimRegion.getSize()).toString() }));
2345       addHistoryItem(trimRegion);
2346
2347       for (SequenceGroup sg : al.getGroups())
2348       {
2349         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2350                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2351         {
2352           al.deleteGroup(sg);
2353         }
2354       }
2355
2356       viewport.firePropertyChange("alignment", null, al.getSequences());
2357     }
2358   }
2359
2360   public void removeGappedColumnMenuItem_actionPerformed()
2361   {
2362     AlignmentI al = viewport.getAlignment();
2363     ViewportRanges ranges = viewport.getRanges();
2364     int start = 0;
2365     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2366
2367     SequenceI[] seqs;
2368     if (viewport.getSelectionGroup() != null)
2369     {
2370       seqs = viewport.getSelectionGroup()
2371               .getSequencesAsArray(viewport.getHiddenRepSequences());
2372       start = viewport.getSelectionGroup().getStartRes();
2373       end = viewport.getSelectionGroup().getEndRes();
2374     }
2375     else
2376     {
2377       seqs = viewport.getAlignment().getSequencesArray();
2378     }
2379
2380     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2381             "Remove Gapped Columns", seqs, start, end,
2382             viewport.getAlignment());
2383
2384     addHistoryItem(removeGapCols);
2385
2386     statusBar.setText(MessageManager
2387             .formatMessage("label.removed_empty_columns", new String[]
2388             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2389
2390     // This is to maintain viewport position on first residue
2391     // of first sequence
2392     SequenceI seq = al.getSequenceAt(0);
2393     int startRes = seq.findPosition(ranges.getStartRes());
2394     // ShiftList shifts;
2395     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2396     // edit.alColumnChanges=shifts.getInverse();
2397     // if (viewport.hasHiddenColumns)
2398     // viewport.getColumnSelection().compensateForEdits(shifts);
2399     ranges.setStartRes(seq.findIndex(startRes) - 1);
2400     viewport.firePropertyChange("alignment", null, al.getSequences());
2401
2402   }
2403
2404   public void removeAllGapsMenuItem_actionPerformed()
2405   {
2406     AlignmentI al = viewport.getAlignment();
2407     ViewportRanges ranges = viewport.getRanges();
2408     int start = 0;
2409     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2410
2411     SequenceI[] seqs;
2412     if (viewport.getSelectionGroup() != null)
2413     {
2414       seqs = viewport.getSelectionGroup()
2415               .getSequencesAsArray(viewport.getHiddenRepSequences());
2416       start = viewport.getSelectionGroup().getStartRes();
2417       end = viewport.getSelectionGroup().getEndRes();
2418     }
2419     else
2420     {
2421       seqs = viewport.getAlignment().getSequencesArray();
2422     }
2423
2424     // This is to maintain viewport position on first residue
2425     // of first sequence
2426     SequenceI seq = al.getSequenceAt(0);
2427     int startRes = seq.findPosition(ranges.getStartRes());
2428
2429     addHistoryItem(
2430             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2431
2432     ranges.setStartRes(seq.findIndex(startRes) - 1);
2433
2434     viewport.firePropertyChange("alignment", null, al.getSequences());
2435
2436   }
2437
2438   public void findMenuItem_actionPerformed()
2439   {
2440     new Finder(alignPanel);
2441   }
2442
2443   /**
2444    * create a new view derived from the current view
2445    *
2446    * @param viewtitle
2447    * @return frame for the new view
2448    */
2449   public AlignFrame newView(String viewtitle)
2450   {
2451     AlignmentI newal;
2452     if (viewport.hasHiddenRows())
2453     {
2454       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2455               .getFullAlignment().getSequencesArray());
2456     }
2457     else
2458     {
2459       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2460     }
2461
2462     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2463     {
2464       for (int i = 0; i < viewport.getAlignment()
2465               .getAlignmentAnnotation().length; i++)
2466       {
2467         if (!viewport.getAlignment()
2468                 .getAlignmentAnnotation()[i].autoCalculated)
2469         {
2470           newal.addAnnotation(
2471                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2472         }
2473       }
2474     }
2475
2476     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2477
2478     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2479     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2480     PaintRefresher.Register(newaf.alignPanel,
2481             newaf.alignPanel.av.getSequenceSetId());
2482
2483     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2484             newaf.alignPanel.av.getSequenceSetId());
2485     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2486             newaf.alignPanel.av.getSequenceSetId());
2487
2488     Vector comps = (Vector) PaintRefresher.components
2489             .get(viewport.getSequenceSetId());
2490     int viewSize = -1;
2491     for (int i = 0; i < comps.size(); i++)
2492     {
2493       if (comps.elementAt(i) instanceof AlignmentPanel)
2494       {
2495         viewSize++;
2496       }
2497     }
2498
2499     String title = new String(this.getTitle());
2500     if (viewtitle != null)
2501     {
2502       title = viewtitle + " ( " + title + ")";
2503     }
2504     else
2505     {
2506       if (title.indexOf("(View") > -1)
2507       {
2508         title = title.substring(0, title.indexOf("(View"));
2509       }
2510       title += "(View " + viewSize + ")";
2511     }
2512
2513     newaf.setTitle(title.toString());
2514
2515     newaf.viewport.setHistoryList(viewport.getHistoryList());
2516     newaf.viewport.setRedoList(viewport.getRedoList());
2517     return newaf;
2518   }
2519
2520   /**
2521    *
2522    * @return list of feature groups on the view
2523    */
2524   public String[] getFeatureGroups()
2525   {
2526     FeatureRenderer fr = null;
2527     if (alignPanel != null
2528             && (fr = alignPanel.getFeatureRenderer()) != null)
2529     {
2530       List<String> gps = fr.getFeatureGroups();
2531       String[] _gps = gps.toArray(new String[gps.size()]);
2532       return _gps;
2533     }
2534     return null;
2535   }
2536
2537   /**
2538    * get sequence feature groups that are hidden or shown
2539    *
2540    * @param visible
2541    *          true is visible
2542    * @return list
2543    */
2544   public String[] getFeatureGroupsOfState(boolean visible)
2545   {
2546     FeatureRenderer fr = null;
2547     if (alignPanel != null
2548             && (fr = alignPanel.getFeatureRenderer()) != null)
2549     {
2550       List<String> gps = fr.getGroups(visible);
2551       String[] _gps = gps.toArray(new String[gps.size()]);
2552       return _gps;
2553     }
2554     return null;
2555   }
2556
2557   /**
2558    * Change the display state for the given feature groups
2559    *
2560    * @param groups
2561    *          list of group strings
2562    * @param state
2563    *          visible or invisible
2564    */
2565   public void setFeatureGroupState(String[] groups, boolean state)
2566   {
2567     FeatureRenderer fr = null;
2568     this.sequenceFeatures.setState(true);
2569     viewport.setShowSequenceFeatures(true);
2570     if (alignPanel != null
2571             && (fr = alignPanel.getFeatureRenderer()) != null)
2572     {
2573
2574       fr.setGroupVisibility(Arrays.asList(groups), state);
2575       alignPanel.seqPanel.seqCanvas.repaint();
2576       if (alignPanel.overviewPanel != null)
2577       {
2578         alignPanel.overviewPanel.updateOverviewImage();
2579       }
2580     }
2581   }
2582
2583   public void seqLimits_itemStateChanged()
2584   {
2585     viewport.setShowJVSuffix(seqLimits.getState());
2586     alignPanel.fontChanged();
2587     alignPanel.paintAlignment(true);
2588   }
2589
2590   protected void colourTextMenuItem_actionPerformed()
2591   {
2592     viewport.setColourText(colourTextMenuItem.getState());
2593     alignPanel.paintAlignment(true);
2594   }
2595
2596   protected void displayNonconservedMenuItem_actionPerformed()
2597   {
2598     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2599     alignPanel.paintAlignment(true);
2600   }
2601
2602   protected void wrapMenuItem_actionPerformed()
2603   {
2604     viewport.setWrapAlignment(wrapMenuItem.getState());
2605     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2606     scaleAbove.setEnabled(wrapMenuItem.getState());
2607     scaleLeft.setEnabled(wrapMenuItem.getState());
2608     scaleRight.setEnabled(wrapMenuItem.getState());
2609     alignPanel.paintAlignment(true);
2610   }
2611
2612   public void overviewMenuItem_actionPerformed()
2613   {
2614     if (alignPanel.overviewPanel != null)
2615     {
2616       return;
2617     }
2618
2619     Frame frame = new Frame();
2620     final OverviewPanel overview = new OverviewPanel(alignPanel);
2621     frame.add(overview);
2622     // +50 must allow for applet frame window
2623     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2624             .formatMessage("label.overview_params", new String[]
2625             { this.getTitle() }), overview.getPreferredSize().width,
2626             overview.getPreferredSize().height + 50);
2627
2628     frame.pack();
2629     final AlignmentPanel ap = alignPanel;
2630     frame.addWindowListener(new WindowAdapter()
2631     {
2632       @Override
2633       public void windowClosing(WindowEvent e)
2634       {
2635         overview.dispose();
2636         if (ap != null)
2637         {
2638           ap.setOverviewPanel(null);
2639         }
2640       };
2641     });
2642
2643     alignPanel.setOverviewPanel(overview);
2644
2645   }
2646
2647   @Override
2648   public void changeColour(ColourSchemeI cs)
2649   {
2650     viewport.setGlobalColourScheme(cs);
2651
2652     alignPanel.paintAlignment(true);
2653   }
2654
2655   protected void modifyPID_actionPerformed()
2656   {
2657     if (viewport.getAbovePIDThreshold()
2658             && viewport.getGlobalColourScheme() != null)
2659     {
2660       SliderPanel.setPIDSliderSource(alignPanel,
2661               viewport.getResidueShading(), alignPanel.getViewName());
2662       SliderPanel.showPIDSlider();
2663     }
2664   }
2665
2666   protected void modifyConservation_actionPerformed()
2667   {
2668     if (viewport.getConservationSelected()
2669             && viewport.getGlobalColourScheme() != null)
2670     {
2671       SliderPanel.setConservationSlider(alignPanel,
2672               viewport.getResidueShading(), alignPanel.getViewName());
2673       SliderPanel.showConservationSlider();
2674     }
2675   }
2676
2677   protected void conservationMenuItem_actionPerformed()
2678   {
2679     boolean selected = conservationMenuItem.getState();
2680     modifyConservation.setEnabled(selected);
2681     viewport.setConservationSelected(selected);
2682     viewport.getResidueShading().setConservationApplied(selected);
2683
2684     changeColour(viewport.getGlobalColourScheme());
2685
2686     if (selected)
2687     {
2688       modifyConservation_actionPerformed();
2689     }
2690     else
2691     {
2692       SliderPanel.hideConservationSlider();
2693     }
2694   }
2695
2696   public void abovePIDThreshold_actionPerformed()
2697   {
2698     boolean selected = abovePIDThreshold.getState();
2699     modifyPID.setEnabled(selected);
2700     viewport.setAbovePIDThreshold(selected);
2701     if (!selected)
2702     {
2703       viewport.getResidueShading().setThreshold(0,
2704               viewport.isIgnoreGapsConsensus());
2705     }
2706
2707     changeColour(viewport.getGlobalColourScheme());
2708
2709     if (selected)
2710     {
2711       modifyPID_actionPerformed();
2712     }
2713     else
2714     {
2715       SliderPanel.hidePIDSlider();
2716     }
2717   }
2718
2719   public void sortPairwiseMenuItem_actionPerformed()
2720   {
2721     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2722     AlignmentSorter.sortByPID(viewport.getAlignment(),
2723             viewport.getAlignment().getSequenceAt(0));
2724
2725     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2726             viewport.getAlignment()));
2727     alignPanel.paintAlignment(true);
2728   }
2729
2730   public void sortIDMenuItem_actionPerformed()
2731   {
2732     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2733     AlignmentSorter.sortByID(viewport.getAlignment());
2734     addHistoryItem(
2735             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2736     alignPanel.paintAlignment(true);
2737   }
2738
2739   public void sortLengthMenuItem_actionPerformed()
2740   {
2741     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2742     AlignmentSorter.sortByLength(viewport.getAlignment());
2743     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2744             viewport.getAlignment()));
2745     alignPanel.paintAlignment(true);
2746   }
2747
2748   public void sortGroupMenuItem_actionPerformed()
2749   {
2750     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2751     AlignmentSorter.sortByGroup(viewport.getAlignment());
2752     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2753             viewport.getAlignment()));
2754     alignPanel.paintAlignment(true);
2755
2756   }
2757
2758   public void removeRedundancyMenuItem_actionPerformed()
2759   {
2760     new RedundancyPanel(alignPanel);
2761   }
2762
2763   public void pairwiseAlignmentMenuItem_actionPerformed()
2764   {
2765     if (viewport.getSelectionGroup() != null
2766             && viewport.getSelectionGroup().getSize() > 1)
2767     {
2768       Frame frame = new Frame();
2769       frame.add(new PairwiseAlignPanel(alignPanel));
2770       jalview.bin.JalviewLite.addFrame(frame,
2771               MessageManager.getString("action.pairwise_alignment"), 600,
2772               500);
2773     }
2774   }
2775
2776   public void PCAMenuItem_actionPerformed()
2777   {
2778     // are the sequences aligned?
2779     if (!viewport.getAlignment().isAligned(false))
2780     {
2781       SequenceI current;
2782       int Width = viewport.getAlignment().getWidth();
2783
2784       for (int i = 0; i < viewport.getAlignment().getSequences()
2785               .size(); i++)
2786       {
2787         current = viewport.getAlignment().getSequenceAt(i);
2788
2789         if (current.getLength() < Width)
2790         {
2791           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2792         }
2793       }
2794       alignPanel.paintAlignment(true);
2795     }
2796
2797     if ((viewport.getSelectionGroup() != null
2798             && viewport.getSelectionGroup().getSize() < 4
2799             && viewport.getSelectionGroup().getSize() > 0)
2800             || viewport.getAlignment().getHeight() < 4)
2801     {
2802       return;
2803     }
2804
2805     try
2806     {
2807       new PCAPanel(viewport);
2808     } catch (java.lang.OutOfMemoryError ex)
2809     {
2810     }
2811
2812   }
2813
2814   public void averageDistanceTreeMenuItem_actionPerformed()
2815   {
2816     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2817             "Average distance tree using PID");
2818   }
2819
2820   public void neighbourTreeMenuItem_actionPerformed()
2821   {
2822     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2823             "Neighbour joining tree using PID");
2824   }
2825
2826   protected void njTreeBlosumMenuItem_actionPerformed()
2827   {
2828     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2829             ScoreModels.getInstance().getBlosum62().getName(),
2830             "Neighbour joining tree using BLOSUM62");
2831   }
2832
2833   protected void avTreeBlosumMenuItem_actionPerformed()
2834   {
2835     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2836             ScoreModels.getInstance().getBlosum62().getName(),
2837             "Average distance tree using BLOSUM62");
2838   }
2839
2840   void newTreePanel(String type, String pwType, String title)
2841   {
2842     // are the sequences aligned?
2843     if (!viewport.getAlignment().isAligned(false))
2844     {
2845       SequenceI current;
2846       int Width = viewport.getAlignment().getWidth();
2847
2848       for (int i = 0; i < viewport.getAlignment().getSequences()
2849               .size(); i++)
2850       {
2851         current = viewport.getAlignment().getSequenceAt(i);
2852
2853         if (current.getLength() < Width)
2854         {
2855           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2856         }
2857       }
2858       alignPanel.paintAlignment(true);
2859
2860     }
2861
2862     if ((viewport.getSelectionGroup() != null
2863             && viewport.getSelectionGroup().getSize() > 1)
2864             || (viewport.getAlignment().getHeight() > 1))
2865     {
2866       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2867
2868       addTreeMenuItem(tp, title);
2869
2870       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2871     }
2872   }
2873
2874   void loadTree_actionPerformed()
2875   {
2876     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2877     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2878     cap.setTreeImport();
2879     Frame frame = new Frame();
2880     frame.add(cap);
2881     jalview.bin.JalviewLite.addFrame(frame,
2882             MessageManager.getString("label.paste_newick_file"), 400, 300);
2883   }
2884
2885   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2886   {
2887     TreePanel tp = new TreePanel(alignPanel, treeFile,
2888             MessageManager.getString("label.load_tree_from_file"), tree);
2889     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2890     addTreeMenuItem(tp, treeFile);
2891   }
2892
2893   /**
2894    * sort the alignment using the given treePanel
2895    *
2896    * @param treePanel
2897    *          tree used to sort view
2898    * @param title
2899    *          string used for undo event name
2900    */
2901   public void sortByTree(TreePanel treePanel, String title)
2902   {
2903     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2904     AlignmentSorter.sortByTree(viewport.getAlignment(),
2905             treePanel.getTree());
2906     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2907     // HistoryItem.SORT));
2908     addHistoryItem(new OrderCommand(MessageManager
2909             .formatMessage("label.order_by_params", new String[]
2910             { title }), oldOrder, viewport.getAlignment()));
2911     alignPanel.paintAlignment(true);
2912   }
2913
2914   /**
2915    * Do any automatic reordering of the alignment and add the necessary bits to
2916    * the menu structure for the new tree
2917    *
2918    * @param treePanel
2919    * @param title
2920    */
2921   protected void addTreeMenuItem(final TreePanel treePanel,
2922           final String title)
2923   {
2924     final MenuItem item = new MenuItem(title);
2925     sortByTreeMenu.add(item);
2926     item.addActionListener(new java.awt.event.ActionListener()
2927     {
2928       @Override
2929       public void actionPerformed(ActionEvent evt)
2930       {
2931         sortByTree(treePanel, title); // treePanel.getTitle());
2932       }
2933     });
2934
2935     treePanel.addWindowListener(new WindowAdapter()
2936     {
2937       @Override
2938       public void windowOpened(WindowEvent e)
2939       {
2940         if (viewport.sortByTree)
2941         {
2942           sortByTree(treePanel, title);
2943         }
2944         super.windowOpened(e);
2945       }
2946
2947       @Override
2948       public void windowClosing(WindowEvent e)
2949       {
2950         sortByTreeMenu.remove(item);
2951       };
2952     });
2953   }
2954
2955   public boolean sortBy(AlignmentOrder alorder, String undoname)
2956   {
2957     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2958     if (viewport.applet.debug)
2959     {
2960       System.err.println("Sorting " + alorder.getOrder().size()
2961               + " in alignment '" + getTitle() + "'");
2962     }
2963     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2964     if (undoname != null)
2965     {
2966       addHistoryItem(new OrderCommand(undoname, oldOrder,
2967               viewport.getAlignment()));
2968     }
2969     alignPanel.paintAlignment(true);
2970     return true;
2971   }
2972
2973   protected void documentation_actionPerformed()
2974   {
2975     alignPanel.av.applet.openJalviewHelpUrl();
2976   }
2977
2978   protected void about_actionPerformed()
2979   {
2980
2981     class AboutPanel extends Canvas
2982     {
2983       String version;
2984
2985       String builddate;
2986
2987       public AboutPanel(String version, String builddate)
2988       {
2989         this.version = version;
2990         this.builddate = builddate;
2991       }
2992
2993       @Override
2994       public void paint(Graphics g)
2995       {
2996         g.setColor(Color.white);
2997         g.fillRect(0, 0, getSize().width, getSize().height);
2998         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2999         FontMetrics fm = g.getFontMetrics();
3000         int fh = fm.getHeight();
3001         int y = 5, x = 7;
3002         g.setColor(Color.black);
3003         // TODO: update this text for each release or centrally store it for
3004         // lite and application
3005         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3006         g.drawString(MessageManager
3007                 .formatMessage("label.jalviewLite_release", new String[]
3008                 { version }), x, y += fh);
3009         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3010         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3011                 new String[]
3012                 { builddate }), x, y += fh);
3013         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3014         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3015                 y += fh * 1.5);
3016         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3017                 x + 50, y += fh + 8);
3018         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3019                 x, y += fh);
3020         g.drawString(MessageManager
3021                 .getString("label.jalview_distribution_lists"), x, y += fh);
3022         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3023                 x, y += fh + 8);
3024         g.drawString(
3025                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3026                 y += fh);
3027         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3028                 x, y += fh);
3029         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3030                 x, y += fh);
3031       }
3032     }
3033
3034     Frame frame = new Frame();
3035     frame.add(new AboutPanel(JalviewLite.getVersion(),
3036             JalviewLite.getBuildDate()));
3037     jalview.bin.JalviewLite.addFrame(frame,
3038             MessageManager.getString("label.jalview"), 580, 220);
3039
3040   }
3041
3042   public void showURL(String url, String target)
3043   {
3044     if (viewport.applet == null)
3045     {
3046       System.out.println("Not running as applet - no browser available.");
3047     }
3048     else
3049     {
3050       viewport.applet.showURL(url, target);
3051     }
3052   }
3053
3054   // ////////////////////////////////////////////////////////////////////////////////
3055   // JBuilder Graphics here
3056
3057   MenuBar alignFrameMenuBar = new MenuBar();
3058
3059   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3060
3061   MenuItem loadApplication = new MenuItem(
3062           MessageManager.getString("label.view_full_application"));
3063
3064   MenuItem loadTree = new MenuItem(
3065           MessageManager.getString("label.load_associated_tree"));
3066
3067   MenuItem loadAnnotations = new MenuItem(
3068           MessageManager.getString("label.load_features_annotations"));
3069
3070   MenuItem outputFeatures = new MenuItem(
3071           MessageManager.getString("label.export_features"));
3072
3073   MenuItem outputAnnotations = new MenuItem(
3074           MessageManager.getString("label.export_annotations"));
3075
3076   MenuItem closeMenuItem = new MenuItem(
3077           MessageManager.getString("action.close"));
3078
3079   MenuItem selectAllSequenceMenuItem = new MenuItem(
3080           MessageManager.getString("action.select_all"));
3081
3082   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3083           MessageManager.getString("action.deselect_all"));
3084
3085   MenuItem invertSequenceMenuItem = new MenuItem(
3086           MessageManager.getString("action.invert_selection"));
3087
3088   MenuItem remove2LeftMenuItem = new MenuItem();
3089
3090   MenuItem remove2RightMenuItem = new MenuItem();
3091
3092   MenuItem removeGappedColumnMenuItem = new MenuItem();
3093
3094   MenuItem removeAllGapsMenuItem = new MenuItem();
3095
3096   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3097
3098   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3099
3100   MenuItem sortPairwiseMenuItem = new MenuItem();
3101
3102   MenuItem sortIDMenuItem = new MenuItem();
3103
3104   MenuItem sortLengthMenuItem = new MenuItem();
3105
3106   MenuItem sortGroupMenuItem = new MenuItem();
3107
3108   MenuItem removeRedundancyMenuItem = new MenuItem();
3109
3110   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3111
3112   MenuItem PCAMenuItem = new MenuItem();
3113
3114   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3115
3116   MenuItem neighbourTreeMenuItem = new MenuItem();
3117
3118   BorderLayout borderLayout1 = new BorderLayout();
3119
3120   public Label statusBar = new Label();
3121
3122   MenuItem clustalColour = new MenuItem();
3123
3124   MenuItem zappoColour = new MenuItem();
3125
3126   MenuItem taylorColour = new MenuItem();
3127
3128   MenuItem hydrophobicityColour = new MenuItem();
3129
3130   MenuItem helixColour = new MenuItem();
3131
3132   MenuItem strandColour = new MenuItem();
3133
3134   MenuItem turnColour = new MenuItem();
3135
3136   MenuItem buriedColour = new MenuItem();
3137
3138   MenuItem purinePyrimidineColour = new MenuItem();
3139
3140   // MenuItem RNAInteractionColour = new MenuItem();
3141
3142   MenuItem RNAHelixColour = new MenuItem();
3143
3144   MenuItem userDefinedColour = new MenuItem();
3145
3146   MenuItem PIDColour = new MenuItem();
3147
3148   MenuItem BLOSUM62Colour = new MenuItem();
3149
3150   MenuItem tcoffeeColour = new MenuItem();
3151
3152   MenuItem njTreeBlosumMenuItem = new MenuItem();
3153
3154   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3155
3156   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3157
3158   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3159
3160   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3161
3162   MenuItem alProperties = new MenuItem(
3163           MessageManager.getString("label.alignment_props"));
3164
3165   MenuItem overviewMenuItem = new MenuItem();
3166
3167   MenuItem undoMenuItem = new MenuItem();
3168
3169   MenuItem redoMenuItem = new MenuItem();
3170
3171   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3172
3173   MenuItem noColourmenuItem = new MenuItem();
3174
3175   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3176
3177   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3178
3179   MenuItem findMenuItem = new MenuItem();
3180
3181   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3182
3183   MenuItem nucleotideColour = new MenuItem();
3184
3185   MenuItem deleteGroups = new MenuItem();
3186
3187   MenuItem grpsFromSelection = new MenuItem();
3188
3189   MenuItem createGroup = new MenuItem();
3190
3191   MenuItem unGroup = new MenuItem();
3192
3193   MenuItem delete = new MenuItem();
3194
3195   MenuItem copy = new MenuItem();
3196
3197   MenuItem cut = new MenuItem();
3198
3199   Menu pasteMenu = new Menu();
3200
3201   MenuItem pasteNew = new MenuItem();
3202
3203   MenuItem pasteThis = new MenuItem();
3204
3205   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3206
3207   MenuItem font = new MenuItem();
3208
3209   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3214
3215   MenuItem modifyPID = new MenuItem();
3216
3217   MenuItem modifyConservation = new MenuItem();
3218
3219   CheckboxMenuItem autoCalculate = null;
3220
3221   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3222           "Sort Alignment With New Tree", true);
3223
3224   Menu sortByTreeMenu = new Menu();
3225
3226   MenuItem inputText = new MenuItem();
3227
3228   MenuItem documentation = new MenuItem();
3229
3230   MenuItem about = new MenuItem();
3231
3232   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3233
3234   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3235
3236   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3237
3238   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3249
3250   /**
3251    * Initialise menus and other items
3252    *
3253    * @throws Exception
3254    */
3255   private void jbInit() throws Exception
3256   {
3257     setMenuBar(alignFrameMenuBar);
3258
3259     /*
3260      * Configure File menu items and actions
3261      */
3262     inputText
3263             .setLabel(MessageManager.getString("label.input_from_textbox"));
3264     inputText.addActionListener(this);
3265     Menu outputTextboxMenu = new Menu(
3266             MessageManager.getString("label.out_to_textbox"));
3267     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3268     {
3269       MenuItem item = new MenuItem(ff);
3270
3271       item.addActionListener(new java.awt.event.ActionListener()
3272       {
3273         @Override
3274         public void actionPerformed(ActionEvent e)
3275         {
3276           outputText_actionPerformed(e);
3277         }
3278       });
3279
3280       outputTextboxMenu.add(item);
3281     }
3282     closeMenuItem.addActionListener(this);
3283     loadApplication.addActionListener(this);
3284     loadTree.addActionListener(this);
3285     loadAnnotations.addActionListener(this);
3286     outputFeatures.addActionListener(this);
3287     outputAnnotations.addActionListener(this);
3288
3289     /*
3290      * Configure Edit menu items and actions
3291      */
3292     undoMenuItem.setEnabled(false);
3293     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3294     undoMenuItem.addActionListener(this);
3295     redoMenuItem.setEnabled(false);
3296     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3297     redoMenuItem.addActionListener(this);
3298     copy.setLabel(MessageManager.getString("action.copy"));
3299     copy.addActionListener(this);
3300     cut.setLabel(MessageManager.getString("action.cut"));
3301     cut.addActionListener(this);
3302     delete.setLabel(MessageManager.getString("action.delete"));
3303     delete.addActionListener(this);
3304     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3305     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3306     pasteNew.addActionListener(this);
3307     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3308     pasteThis.addActionListener(this);
3309     remove2LeftMenuItem
3310             .setLabel(MessageManager.getString("action.remove_left"));
3311     remove2LeftMenuItem.addActionListener(this);
3312     remove2RightMenuItem
3313             .setLabel(MessageManager.getString("action.remove_right"));
3314     remove2RightMenuItem.addActionListener(this);
3315     removeGappedColumnMenuItem.setLabel(
3316             MessageManager.getString("action.remove_empty_columns"));
3317     removeGappedColumnMenuItem.addActionListener(this);
3318     removeAllGapsMenuItem
3319             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3320     removeAllGapsMenuItem.addActionListener(this);
3321     removeRedundancyMenuItem
3322             .setLabel(MessageManager.getString("action.remove_redundancy"));
3323     removeRedundancyMenuItem.addActionListener(this);
3324
3325     /*
3326      * Configure Select menu items and actions
3327      */
3328     findMenuItem.setLabel(MessageManager.getString("action.find"));
3329     findMenuItem.addActionListener(this);
3330     selectAllSequenceMenuItem.addActionListener(this);
3331     deselectAllSequenceMenuItem.addActionListener(this);
3332     invertSequenceMenuItem.setLabel(
3333             MessageManager.getString("action.invert_sequence_selection"));
3334     invertSequenceMenuItem.addActionListener(this);
3335     invertColSel.setLabel(
3336             MessageManager.getString("action.invert_column_selection"));
3337     invertColSel.addActionListener(this);
3338     deleteGroups
3339             .setLabel(MessageManager.getString("action.undefine_groups"));
3340     deleteGroups.addActionListener(this);
3341     grpsFromSelection.setLabel(
3342             MessageManager.getString("action.make_groups_selection"));
3343     grpsFromSelection.addActionListener(this);
3344     createGroup.setLabel(MessageManager.getString("action.create_group"));
3345     createGroup.addActionListener(this);
3346     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3347     unGroup.addActionListener(this);
3348
3349     annotationColumnSelection.setLabel(
3350             MessageManager.getString("action.select_by_annotation"));
3351     annotationColumnSelection.addActionListener(this);
3352
3353     /*
3354      * Configure View menu items and actions
3355      */
3356     newView.setLabel(MessageManager.getString("action.new_view"));
3357     newView.addActionListener(this);
3358     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3359     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3360     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3361     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3362     hideColumns
3363             .setLabel(MessageManager.getString("label.selected_columns"));
3364     hideSequences
3365             .setLabel(MessageManager.getString("label.selected_sequences"));
3366     hideAllButSelection.setLabel(
3367             MessageManager.getString("label.all_but_selected_region"));
3368     hideAllSelection
3369             .setLabel(MessageManager.getString("label.selected_region"));
3370     showAllHidden.setLabel(
3371             MessageManager.getString("label.all_sequences_columns"));
3372     showColumns.addActionListener(this);
3373     showSeqs.addActionListener(this);
3374     hideColumns.addActionListener(this);
3375     hideSequences.addActionListener(this);
3376     hideAllButSelection.addActionListener(this);
3377     hideAllSelection.addActionListener(this);
3378     showAllHidden.addActionListener(this);
3379     featureSettings
3380             .setLabel(MessageManager.getString("action.feature_settings"));
3381     featureSettings.addActionListener(this);
3382     sequenceFeatures.setLabel(
3383             MessageManager.getString("label.show_sequence_features"));
3384     sequenceFeatures.addItemListener(this);
3385     sequenceFeatures.setState(false);
3386     followMouseOverFlag.setLabel(
3387             MessageManager.getString("label.automatic_scrolling"));
3388     followMouseOverFlag.addItemListener(this);
3389     alProperties.addActionListener(this);
3390     overviewMenuItem
3391             .setLabel(MessageManager.getString("label.overview_window"));
3392     overviewMenuItem.addActionListener(this);
3393
3394     /*
3395      * Configure Annotations menu items and actions
3396      */
3397     annotationPanelMenuItem
3398             .setLabel(MessageManager.getString("label.show_annotations"));
3399     annotationPanelMenuItem.addItemListener(this);
3400     showGroupConsensus
3401             .setLabel(MessageManager.getString("label.group_consensus"));
3402     showGroupConservation
3403             .setLabel(MessageManager.getString("label.group_conservation"));
3404     showConsensusHistogram.setLabel(
3405             MessageManager.getString("label.show_consensus_histogram"));
3406     showSequenceLogo.setLabel(
3407             MessageManager.getString("label.show_consensus_logo"));
3408     normSequenceLogo.setLabel(
3409             MessageManager.getString("label.norm_consensus_logo"));
3410     applyAutoAnnotationSettings
3411             .setLabel(MessageManager.getString("label.apply_all_groups"));
3412     applyAutoAnnotationSettings.setState(true);
3413     Menu autoAnnMenu = new Menu(
3414             MessageManager.getString("label.autocalculated_annotation"));
3415     showGroupConsensus.addItemListener(this);
3416     showGroupConservation.addItemListener(this);
3417     showConsensusHistogram.addItemListener(this);
3418     showSequenceLogo.addItemListener(this);
3419     normSequenceLogo.addItemListener(this);
3420     applyAutoAnnotationSettings.addItemListener(this);
3421     showAlignmentAnnotations = new CheckboxMenuItem(
3422             MessageManager.getString("label.show_all_al_annotations"));
3423     showSequenceAnnotations = new CheckboxMenuItem(
3424             MessageManager.getString("label.show_all_seq_annotations"));
3425     sortAnnBySequence = new CheckboxMenuItem(
3426             MessageManager.getString("label.sort_annotations_by_sequence"));
3427     sortAnnByLabel = new CheckboxMenuItem(
3428             MessageManager.getString("label.sort_annotations_by_label"));
3429     showAutoFirst = new CheckboxMenuItem(
3430             MessageManager.getString("label.show_first"));
3431     showAutoFirst.setState(false); // pending applet parameter
3432     setShowAutoCalculatedAbove(showAutoFirst.getState());
3433     showAutoLast = new CheckboxMenuItem(
3434             MessageManager.getString("label.show_last"));
3435     showAutoLast.setState(!showAutoFirst.getState());
3436     showAlignmentAnnotations.addItemListener(this);
3437     showSequenceAnnotations.addItemListener(this);
3438     sortAnnBySequence.addItemListener(this);
3439     sortAnnByLabel.addItemListener(this);
3440     showAutoFirst.addItemListener(this);
3441     showAutoLast.addItemListener(this);
3442
3443     /*
3444      * Configure Format menu items and actions
3445      */
3446     font.setLabel(MessageManager.getString("action.font"));
3447     font.addActionListener(this);
3448     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3449     scaleAbove.setState(true);
3450     scaleAbove.setEnabled(false);
3451     scaleAbove.addItemListener(this);
3452     scaleLeft.setEnabled(false);
3453     scaleLeft.setState(true);
3454     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3455     scaleLeft.addItemListener(this);
3456     scaleRight.setEnabled(false);
3457     scaleRight.setState(true);
3458     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3459     scaleRight.addItemListener(this);
3460     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3461     viewBoxesMenuItem.setState(true);
3462     viewBoxesMenuItem.addItemListener(this);
3463     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3464     viewTextMenuItem.setState(true);
3465     viewTextMenuItem.addItemListener(this);
3466     colourTextMenuItem
3467             .setLabel(MessageManager.getString("label.colour_text"));
3468     colourTextMenuItem.addItemListener(this);
3469     displayNonconservedMenuItem
3470             .setLabel(MessageManager.getString("label.show_non_conserved"));
3471     displayNonconservedMenuItem.addItemListener(this);
3472     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3473     wrapMenuItem.addItemListener(this);
3474     renderGapsMenuItem
3475             .setLabel(MessageManager.getString("action.show_gaps"));
3476     renderGapsMenuItem.setState(true);
3477     renderGapsMenuItem.addItemListener(this);
3478     centreColumnLabelFlag.setLabel(
3479             MessageManager.getString("label.centre_column_labels"));
3480     centreColumnLabelFlag.addItemListener(this);
3481     seqLimits.setState(true);
3482     seqLimits.setLabel(
3483             MessageManager.getString("label.show_sequence_limits"));
3484     seqLimits.addItemListener(this);
3485
3486     /*
3487      * Configure Colour menu items and actions
3488      */
3489     applyToAllGroups.setLabel(
3490             MessageManager.getString("label.apply_colour_to_all_groups"));
3491     applyToAllGroups.setState(true);
3492     applyToAllGroups.addItemListener(this);
3493     clustalColour.setLabel(
3494             MessageManager.getString("label.colourScheme_clustal"));
3495     clustalColour.addActionListener(this);
3496     zappoColour
3497             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3498     zappoColour.addActionListener(this);
3499     taylorColour.setLabel(
3500             MessageManager.getString("label.colourScheme_taylor"));
3501     taylorColour.addActionListener(this);
3502     hydrophobicityColour.setLabel(
3503             MessageManager.getString("label.colourScheme_hydrophobic"));
3504     hydrophobicityColour.addActionListener(this);
3505     helixColour.setLabel(MessageManager
3506             .getString("label.colourScheme_helix_propensity"));
3507     helixColour.addActionListener(this);
3508     strandColour.setLabel(MessageManager
3509             .getString("label.colourScheme_strand_propensity"));
3510     strandColour.addActionListener(this);
3511     turnColour.setLabel(
3512             MessageManager.getString("label.colourScheme_turn_propensity"));
3513     turnColour.addActionListener(this);
3514     buriedColour.setLabel(
3515             MessageManager.getString("label.colourScheme_buried_index"));
3516     buriedColour.addActionListener(this);
3517     purinePyrimidineColour.setLabel(MessageManager
3518             .getString("label.colourScheme_purine/pyrimidine"));
3519     purinePyrimidineColour.addActionListener(this);
3520     // RNAInteractionColour.setLabel(MessageManager
3521     // .getString("label.rna_interaction"));
3522     // RNAInteractionColour.addActionListener(this);
3523     RNAHelixColour.setLabel(
3524             MessageManager.getString("label.colourScheme_rna_helices"));
3525     RNAHelixColour.addActionListener(this);
3526     userDefinedColour
3527             .setLabel(MessageManager.getString("action.user_defined"));
3528     userDefinedColour.addActionListener(this);
3529     PIDColour.setLabel(
3530             MessageManager.getString("label.colourScheme_%_identity"));
3531     PIDColour.addActionListener(this);
3532     BLOSUM62Colour.setLabel(
3533             MessageManager.getString("label.colourScheme_blosum62"));
3534     BLOSUM62Colour.addActionListener(this);
3535     tcoffeeColour.setLabel(
3536             MessageManager.getString("label.colourScheme_t-coffee_scores"));
3537     // it will be enabled only if a score file is provided
3538     tcoffeeColour.setEnabled(false);
3539     tcoffeeColour.addActionListener(this);
3540     conservationMenuItem
3541             .setLabel(MessageManager.getString("action.by_conservation"));
3542     conservationMenuItem.addItemListener(this);
3543     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3544     noColourmenuItem.addActionListener(this);
3545     abovePIDThreshold.setLabel(
3546             MessageManager.getString("label.above_identity_threshold"));
3547     abovePIDThreshold.addItemListener(this);
3548     nucleotideColour.setLabel(
3549             MessageManager.getString("label.colourScheme_nucleotide"));
3550     nucleotideColour.addActionListener(this);
3551     modifyPID.setLabel(
3552             MessageManager.getString("label.modify_identity_threshold"));
3553     modifyPID.setEnabled(abovePIDThreshold.getState());
3554     modifyPID.addActionListener(this);
3555     modifyConservation.setLabel(MessageManager
3556             .getString("label.modify_conservation_threshold"));
3557     modifyConservation.setEnabled(conservationMenuItem.getState());
3558     modifyConservation.addActionListener(this);
3559     annotationColour
3560             .setLabel(MessageManager.getString("action.by_annotation"));
3561     annotationColour.addActionListener(this);
3562
3563     /*
3564      * Configure Calculate menu items and actions
3565      */
3566     sortPairwiseMenuItem
3567             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3568     sortPairwiseMenuItem.addActionListener(this);
3569     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3570     sortIDMenuItem.addActionListener(this);
3571     sortLengthMenuItem
3572             .setLabel(MessageManager.getString("action.by_length"));
3573     sortLengthMenuItem.addActionListener(this);
3574     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3575     sortGroupMenuItem.addActionListener(this);
3576     pairwiseAlignmentMenuItem.setLabel(
3577             MessageManager.getString("action.pairwise_alignment"));
3578     pairwiseAlignmentMenuItem.addActionListener(this);
3579     PCAMenuItem.setLabel(
3580             MessageManager.getString("label.principal_component_analysis"));
3581     PCAMenuItem.addActionListener(this);
3582     autoCalculate = new CheckboxMenuItem(
3583             MessageManager.getString("label.autocalculate_consensus"),
3584             true);
3585     averageDistanceTreeMenuItem.setLabel(
3586             MessageManager.getString("label.average_distance_identity"));
3587     averageDistanceTreeMenuItem.addActionListener(this);
3588     neighbourTreeMenuItem.setLabel(
3589             MessageManager.getString("label.neighbour_joining_identity"));
3590     neighbourTreeMenuItem.addActionListener(this);
3591     avDistanceTreeBlosumMenuItem.setLabel(
3592             MessageManager.getString("label.average_distance_blosum62"));
3593     avDistanceTreeBlosumMenuItem.addActionListener(this);
3594     njTreeBlosumMenuItem
3595             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3596     njTreeBlosumMenuItem.addActionListener(this);
3597     sortByTreeMenu
3598             .setLabel(MessageManager.getString("action.by_tree_order"));
3599     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3600     Menu calculateTreeMenu = new Menu(
3601             MessageManager.getString("action.calculate_tree"));
3602     autoCalculate.addItemListener(this);
3603     sortByTree.addItemListener(this);
3604
3605     /*
3606      * Configure Help menu items and actions
3607      */
3608     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3609     documentation.setLabel(MessageManager.getString("label.documentation"));
3610     documentation.addActionListener(this);
3611     about.setLabel(MessageManager.getString("label.about"));
3612     about.addActionListener(this);
3613
3614     /*
3615      * Add top level menus to frame
3616      */
3617     alignFrameMenuBar.add(fileMenu);
3618     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3619     alignFrameMenuBar.add(editMenu);
3620     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3621     alignFrameMenuBar.add(selectMenu);
3622     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3623     alignFrameMenuBar.add(viewMenu);
3624     Menu annotationsMenu = new Menu(
3625             MessageManager.getString("action.annotations"));
3626     alignFrameMenuBar.add(annotationsMenu);
3627     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3628     alignFrameMenuBar.add(formatMenu);
3629     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3630     alignFrameMenuBar.add(colourMenu);
3631     Menu calculateMenu = new Menu(
3632             MessageManager.getString("action.calculate"));
3633     alignFrameMenuBar.add(calculateMenu);
3634     alignFrameMenuBar.add(helpMenu);
3635
3636     /*
3637      * File menu
3638      */
3639     fileMenu.add(inputText);
3640     fileMenu.add(loadTree);
3641     fileMenu.add(loadAnnotations);
3642     fileMenu.addSeparator();
3643     fileMenu.add(outputTextboxMenu);
3644     fileMenu.add(outputFeatures);
3645     fileMenu.add(outputAnnotations);
3646     if (jalviewServletURL != null)
3647     {
3648       fileMenu.add(loadApplication);
3649     }
3650     fileMenu.addSeparator();
3651     fileMenu.add(closeMenuItem);
3652
3653     /*
3654      * Edit menu
3655      */
3656     editMenu.add(undoMenuItem);
3657     editMenu.add(redoMenuItem);
3658     editMenu.add(cut);
3659     editMenu.add(copy);
3660     pasteMenu.add(pasteNew);
3661     pasteMenu.add(pasteThis);
3662     editMenu.add(pasteMenu);
3663     editMenu.add(delete);
3664     editMenu.addSeparator();
3665     editMenu.add(remove2LeftMenuItem);
3666     editMenu.add(remove2RightMenuItem);
3667     editMenu.add(removeGappedColumnMenuItem);
3668     editMenu.add(removeAllGapsMenuItem);
3669     editMenu.add(removeRedundancyMenuItem);
3670
3671     /*
3672      * Select menu
3673      */
3674     selectMenu.add(findMenuItem);
3675     selectMenu.addSeparator();
3676     selectMenu.add(selectAllSequenceMenuItem);
3677     selectMenu.add(deselectAllSequenceMenuItem);
3678     selectMenu.add(invertSequenceMenuItem);
3679     selectMenu.add(invertColSel);
3680     selectMenu.add(createGroup);
3681     selectMenu.add(unGroup);
3682     selectMenu.add(grpsFromSelection);
3683     selectMenu.add(deleteGroups);
3684     selectMenu.add(annotationColumnSelection);
3685
3686     /*
3687      * View menu
3688      */
3689     viewMenu.add(newView);
3690     viewMenu.addSeparator();
3691     showMenu.add(showColumns);
3692     showMenu.add(showSeqs);
3693     showMenu.add(showAllHidden);
3694     viewMenu.add(showMenu);
3695     hideMenu.add(hideColumns);
3696     hideMenu.add(hideSequences);
3697     hideMenu.add(hideAllSelection);
3698     hideMenu.add(hideAllButSelection);
3699     viewMenu.add(hideMenu);
3700     viewMenu.addSeparator();
3701     viewMenu.add(followMouseOverFlag);
3702     viewMenu.addSeparator();
3703     viewMenu.add(sequenceFeatures);
3704     viewMenu.add(featureSettings);
3705     viewMenu.addSeparator();
3706     viewMenu.add(alProperties);
3707     viewMenu.addSeparator();
3708     viewMenu.add(overviewMenuItem);
3709
3710     /*
3711      * Annotations menu
3712      */
3713     annotationsMenu.add(annotationPanelMenuItem);
3714     annotationsMenu.addSeparator();
3715     annotationsMenu.add(showAlignmentAnnotations);
3716     annotationsMenu.add(showSequenceAnnotations);
3717     annotationsMenu.add(sortAnnBySequence);
3718     annotationsMenu.add(sortAnnByLabel);
3719     annotationsMenu.addSeparator();
3720     autoAnnMenu.add(showAutoFirst);
3721     autoAnnMenu.add(showAutoLast);
3722     autoAnnMenu.addSeparator();
3723     autoAnnMenu.add(applyAutoAnnotationSettings);
3724     autoAnnMenu.add(showConsensusHistogram);
3725     autoAnnMenu.add(showSequenceLogo);
3726     autoAnnMenu.add(normSequenceLogo);
3727     autoAnnMenu.addSeparator();
3728     autoAnnMenu.add(showGroupConservation);
3729     autoAnnMenu.add(showGroupConsensus);
3730     annotationsMenu.add(autoAnnMenu);
3731
3732     /*
3733      * Format menu
3734      */
3735     formatMenu.add(font);
3736     formatMenu.add(seqLimits);
3737     formatMenu.add(wrapMenuItem);
3738     formatMenu.add(scaleAbove);
3739     formatMenu.add(scaleLeft);
3740     formatMenu.add(scaleRight);
3741     formatMenu.add(viewBoxesMenuItem);
3742     formatMenu.add(viewTextMenuItem);
3743     formatMenu.add(colourTextMenuItem);
3744     formatMenu.add(displayNonconservedMenuItem);
3745     formatMenu.add(renderGapsMenuItem);
3746     formatMenu.add(centreColumnLabelFlag);
3747
3748     /*
3749      * Colour menu
3750      */
3751     colourMenu.add(applyToAllGroups);
3752     colourMenu.addSeparator();
3753     colourMenu.add(noColourmenuItem);
3754     colourMenu.add(clustalColour);
3755     colourMenu.add(BLOSUM62Colour);
3756     colourMenu.add(PIDColour);
3757     colourMenu.add(zappoColour);
3758     colourMenu.add(taylorColour);
3759     colourMenu.add(hydrophobicityColour);
3760     colourMenu.add(helixColour);
3761     colourMenu.add(strandColour);
3762     colourMenu.add(turnColour);
3763     colourMenu.add(buriedColour);
3764     colourMenu.add(nucleotideColour);
3765     colourMenu.add(purinePyrimidineColour);
3766     // colourMenu.add(RNAInteractionColour);
3767     colourMenu.add(tcoffeeColour);
3768     colourMenu.add(userDefinedColour);
3769     colourMenu.addSeparator();
3770     colourMenu.add(conservationMenuItem);
3771     colourMenu.add(modifyConservation);
3772     colourMenu.add(abovePIDThreshold);
3773     colourMenu.add(modifyPID);
3774     colourMenu.add(annotationColour);
3775     colourMenu.add(RNAHelixColour);
3776
3777     /*
3778      * Calculate menu
3779      */
3780     sortMenu.add(sortIDMenuItem);
3781     sortMenu.add(sortLengthMenuItem);
3782     sortMenu.add(sortByTreeMenu);
3783     sortMenu.add(sortGroupMenuItem);
3784     sortMenu.add(sortPairwiseMenuItem);
3785     calculateMenu.add(sortMenu);
3786     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3787     calculateTreeMenu.add(neighbourTreeMenuItem);
3788     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3789     calculateTreeMenu.add(njTreeBlosumMenuItem);
3790     calculateMenu.add(calculateTreeMenu);
3791     calculateMenu.addSeparator();
3792     calculateMenu.add(pairwiseAlignmentMenuItem);
3793     calculateMenu.add(PCAMenuItem);
3794     calculateMenu.add(autoCalculate);
3795     calculateMenu.add(sortByTree);
3796
3797     /*
3798      * Help menu
3799      */
3800     helpMenu.add(documentation);
3801     helpMenu.add(about);
3802
3803     /*
3804      * Status bar
3805      */
3806     statusBar.setBackground(Color.white);
3807     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3808     statusBar.setText(MessageManager.getString("label.status_bar"));
3809     this.add(statusBar, BorderLayout.SOUTH);
3810   }
3811
3812   @Override
3813   public void setStatus(String string)
3814   {
3815     statusBar.setText(string);
3816   };
3817
3818   MenuItem featureSettings = new MenuItem();
3819
3820   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3821
3822   MenuItem annotationColour = new MenuItem();
3823
3824   MenuItem annotationColumnSelection = new MenuItem();
3825
3826   MenuItem invertColSel = new MenuItem();
3827
3828   MenuItem showColumns = new MenuItem();
3829
3830   MenuItem showSeqs = new MenuItem();
3831
3832   MenuItem hideColumns = new MenuItem();
3833
3834   MenuItem hideSequences = new MenuItem();
3835
3836   MenuItem hideAllButSelection = new MenuItem();
3837
3838   MenuItem hideAllSelection = new MenuItem();
3839
3840   MenuItem showAllHidden = new MenuItem();
3841
3842   MenuItem newView = new MenuItem();
3843
3844   private CheckboxMenuItem showAlignmentAnnotations;
3845
3846   private CheckboxMenuItem showSequenceAnnotations;
3847
3848   private CheckboxMenuItem sortAnnBySequence;
3849
3850   private CheckboxMenuItem sortAnnByLabel;
3851
3852   private CheckboxMenuItem showAutoFirst;
3853
3854   private CheckboxMenuItem showAutoLast;
3855
3856   private SplitFrame splitFrame;
3857
3858   /**
3859    * Attach the alignFrame panels after embedding menus, if necessary. This used
3860    * to be called setEmbedded, but is now creates the dropdown menus in a
3861    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3862    *
3863    * @param reallyEmbedded
3864    *          true to attach the view to the applet area on the page rather than
3865    *          in a new window
3866    */
3867   public void createAlignFrameWindow(boolean reallyEmbedded)
3868   {
3869     if (reallyEmbedded)
3870     {
3871       embedAlignFrameInApplet(viewport.applet);
3872     }
3873     else
3874     {
3875       // //////
3876       // test and embed menu bar if necessary.
3877       //
3878       if (embedMenuIfNeeded(alignPanel))
3879       {
3880         /*
3881          * adjust for status bar height too. ? pointless as overridden by layout
3882          * manager
3883          */
3884         alignPanel.setSize(getSize().width,
3885                 getSize().height - statusBar.getHeight());
3886       }
3887       add(statusBar, BorderLayout.SOUTH);
3888       add(alignPanel, BorderLayout.CENTER);
3889       // and register with the applet so it can pass external API calls to us
3890       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3891               frameHeight);
3892     }
3893   }
3894
3895   /**
3896    * Add the components of this AlignFrame to the applet container.
3897    *
3898    * @param theApplet
3899    */
3900   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3901   {
3902     // ////
3903     // Explicitly build the embedded menu panel for the on-page applet
3904     //
3905     // view cannot be closed if its actually on the page
3906     fileMenu.remove(closeMenuItem);
3907     fileMenu.remove(3); // Remove Separator
3908     // construct embedded menu, using default font
3909     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3910     // and actually add the components to the applet area
3911     theApplet.setLayout(new BorderLayout());
3912     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3913     theApplet.add(statusBar, BorderLayout.SOUTH);
3914     // TODO should size be left to the layout manager?
3915     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3916             - embeddedMenu.getHeight() - statusBar.getHeight());
3917     theApplet.add(alignPanel, BorderLayout.CENTER);
3918     final AlignFrame me = this;
3919     theApplet.addFocusListener(new FocusListener()
3920     {
3921
3922       @Override
3923       public void focusLost(FocusEvent e)
3924       {
3925         if (theApplet.currentAlignFrame == me)
3926         {
3927           theApplet.currentAlignFrame = null;
3928         }
3929       }
3930
3931       @Override
3932       public void focusGained(FocusEvent e)
3933       {
3934         theApplet.currentAlignFrame = me;
3935       }
3936     });
3937     theApplet.validate();
3938   }
3939
3940   /**
3941    * create a new binding between structures in an existing jmol viewer instance
3942    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3943    * this does not open a new Jmol window, or modify the display of the
3944    * structures in the original jmol window. Note This method doesn't work
3945    * without an additional javascript library to exchange messages between the
3946    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3947    *
3948    * @param viewer
3949    *          JmolViewer instance
3950    * @param sequenceIds
3951    *          - sequence Ids to search for associations
3952    */
3953   public SequenceStructureBinding addStructureViewInstance(
3954           Object jmolviewer, String[] sequenceIds)
3955   {
3956     Viewer viewer = null;
3957     try
3958     {
3959       viewer = (Viewer) jmolviewer;
3960     } catch (ClassCastException ex)
3961     {
3962       System.err.println(
3963               "Unsupported viewer object :" + jmolviewer.getClass());
3964     }
3965     if (viewer == null)
3966     {
3967       System.err.println("Can't use this object as a structure viewer:"
3968               + jmolviewer.getClass());
3969       return null;
3970     }
3971     SequenceI[] seqs = null;
3972     if (sequenceIds == null || sequenceIds.length == 0)
3973     {
3974       seqs = viewport.getAlignment().getSequencesArray();
3975     }
3976     else
3977     {
3978       Vector sqi = new Vector();
3979       AlignmentI al = viewport.getAlignment();
3980       for (int sid = 0; sid < sequenceIds.length; sid++)
3981       {
3982         SequenceI sq = al.findName(sequenceIds[sid]);
3983         if (sq != null)
3984         {
3985           sqi.addElement(sq);
3986         }
3987       }
3988       if (sqi.size() > 0)
3989       {
3990         seqs = new SequenceI[sqi.size()];
3991         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3992         {
3993           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3994         }
3995       }
3996       else
3997       {
3998         return null;
3999       }
4000     }
4001     AAStructureBindingModel jmv = null;
4002     // TODO: search for a jmv that involves viewer
4003     if (jmv == null)
4004     { // create a new viewer/jalview binding.
4005       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4006     }
4007     return jmv;
4008
4009   }
4010
4011   /**
4012    * bind a pdb file to a sequence in the current view
4013    *
4014    * @param sequenceId
4015    *          - sequenceId within the dataset.
4016    * @param pdbEntryString
4017    *          - the short name for the PDB file
4018    * @param pdbFile
4019    *          - pdb file - either a URL or a valid PDB file.
4020    * @return true if binding was as success TODO: consider making an exception
4021    *         structure for indicating when PDB parsing or sequenceId location
4022    *         fails.
4023    */
4024   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4025           String pdbFile)
4026   {
4027     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4028     boolean needtoadd = false;
4029     if (toaddpdb != null)
4030     {
4031       Vector pdbe = toaddpdb.getAllPDBEntries();
4032       PDBEntry pdbentry = null;
4033       if (pdbe != null && pdbe.size() > 0)
4034       {
4035         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4036         {
4037           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4038           if (!pdbentry.getId().equals(pdbEntryString)
4039                   && !pdbentry.getFile().equals(pdbFile))
4040           {
4041             pdbentry = null;
4042           }
4043           else
4044           {
4045             continue;
4046           }
4047         }
4048       }
4049       if (pdbentry == null)
4050       {
4051         pdbentry = new PDBEntry();
4052         pdbentry.setId(pdbEntryString);
4053         pdbentry.setFile(pdbFile);
4054         needtoadd = true; // add this new entry to sequence.
4055       }
4056       // resolve data source
4057       // TODO: this code should be a refactored to an io package
4058       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4059               FileFormat.PDB);
4060       if (protocol == null)
4061       {
4062         return false;
4063       }
4064       if (needtoadd)
4065       {
4066         pdbentry.setProperty("protocol", protocol);
4067         toaddpdb.addPDBId(pdbentry);
4068         alignPanel.getStructureSelectionManager()
4069                 .registerPDBEntry(pdbentry);
4070       }
4071     }
4072     return true;
4073   }
4074
4075   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4076   {
4077     if (seqs != null)
4078     {
4079       Vector sequences = new Vector();
4080       for (int i = 0; i < seqs.length; i++)
4081       {
4082         if (seqs[i] != null)
4083         {
4084           sequences
4085                   .addElement(new Object[]
4086                   { seqs[i], (chains != null) ? chains[i] : null });
4087         }
4088       }
4089       seqs = new SequenceI[sequences.size()];
4090       chains = new String[sequences.size()];
4091       for (int i = 0, isize = sequences.size(); i < isize; i++)
4092       {
4093         Object[] oj = (Object[]) sequences.elementAt(i);
4094
4095         seqs[i] = (SequenceI) oj[0];
4096         chains[i] = (String) oj[1];
4097       }
4098     }
4099     return new Object[] { seqs, chains };
4100
4101   }
4102
4103   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4104           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4105   {
4106     // Scrub any null sequences from the array
4107     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4108     seqs = (SequenceI[]) sqch[0];
4109     chains = (String[]) sqch[1];
4110     if (seqs == null || seqs.length == 0)
4111     {
4112       System.err.println(
4113               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4114     }
4115     if (protocol == null)
4116     {
4117       String sourceType = (String) pdb.getProperty("protocol");
4118       try
4119       {
4120         protocol = DataSourceType.valueOf(sourceType);
4121       } catch (IllegalArgumentException e)
4122       {
4123         // ignore
4124       }
4125       if (protocol == null)
4126       {
4127         System.err.println("Couldn't work out protocol to open structure: "
4128                 + pdb.getId());
4129         return;
4130       }
4131     }
4132     if (applet.useXtrnalSviewer)
4133     {
4134       // register the association(s) and quit, don't create any windows.
4135       if (StructureSelectionManager.getStructureSelectionManager(applet)
4136               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4137       {
4138         System.err.println("Failed to map " + pdb.getFile() + " ("
4139                 + protocol + ") to any sequences");
4140       }
4141       return;
4142     }
4143     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4144     {
4145       // can only do alignments with Jmol
4146       // find the last jmol window assigned to this alignment
4147       AppletJmol ajm = null, tajm;
4148       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4149       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4150       {
4151         tajm = (AppletJmol) jmols.elementAt(i);
4152         if (tajm.ap.alignFrame == this)
4153         {
4154           ajm = tajm;
4155           break;
4156         }
4157       }
4158       if (ajm != null)
4159       {
4160         System.err.println(
4161                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4162         // try and add the pdb structure
4163         // ajm.addS
4164         ajm = null;
4165       }
4166     }
4167     // otherwise, create a new window
4168     if (applet.jmolAvailable)
4169     {
4170       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4171       applet.lastFrameX += 40;
4172       applet.lastFrameY += 40;
4173     }
4174     else
4175     {
4176       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4177     }
4178
4179   }
4180
4181   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4182           SequenceI[][] seqs, String[][] chains, String[] protocols)
4183   {
4184     // TODO Auto-generated method stub
4185     System.err.println("Aligned Structure View: Not yet implemented.");
4186   }
4187
4188   /**
4189    * modify the current selection, providing the user has not made a selection
4190    * already.
4191    *
4192    * @param sel
4193    *          - sequences from this alignment
4194    * @param csel
4195    *          - columns to be selected on the alignment
4196    */
4197   public void select(SequenceGroup sel, ColumnSelection csel,
4198           HiddenColumns hidden)
4199   {
4200     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4201   }
4202
4203   public void scrollTo(int row, int column)
4204   {
4205     alignPanel.seqPanel.scrollTo(row, column);
4206   }
4207
4208   public void scrollToRow(int row)
4209   {
4210     alignPanel.seqPanel.scrollToRow(row);
4211   }
4212
4213   public void scrollToColumn(int column)
4214   {
4215     alignPanel.seqPanel.scrollToColumn(column);
4216   }
4217
4218   /**
4219    * @return the alignments unique ID.
4220    */
4221   public String getSequenceSetId()
4222   {
4223     return viewport.getSequenceSetId();
4224   }
4225
4226   /**
4227    * Load the (T-Coffee) score file from the specified url
4228    *
4229    * @param source
4230    *          File/URL/T-COFFEE score file contents
4231    * @throws IOException
4232    * @return true if alignment was annotated with data from source
4233    */
4234   public boolean loadScoreFile(String source) throws IOException
4235   {
4236
4237     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4238             AppletFormatAdapter.checkProtocol(source));
4239     if (!file.isValid())
4240     {
4241       // TODO: raise dialog for gui
4242       System.err.println("Problems parsing T-Coffee scores: "
4243               + file.getWarningMessage());
4244       System.err.println("Origin was:\n" + source);
4245       return false;
4246     }
4247
4248     /*
4249      * check that the score matrix matches the alignment dimensions
4250      */
4251     AlignmentI aln;
4252     if ((aln = viewport.getAlignment()) != null
4253             && (aln.getHeight() != file.getHeight()
4254                     || aln.getWidth() != file.getWidth()))
4255     {
4256       // TODO: raise a dialog box here rather than bomb out.
4257       System.err.println(
4258               "The scores matrix does not match the alignment dimensions");
4259
4260     }
4261
4262     // TODO add parameter to indicate if matching should be done
4263     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4264     {
4265       alignPanel.fontChanged();
4266       tcoffeeColour.setEnabled(true);
4267       // switch to this color
4268       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4269       return true;
4270     }
4271     else
4272     {
4273       System.err.println("Problems resolving T-Coffee scores:");
4274       if (file.getWarningMessage() != null)
4275       {
4276         System.err.println(file.getWarningMessage());
4277       }
4278     }
4279     return false;
4280   }
4281
4282   public SplitFrame getSplitFrame()
4283   {
4284     return this.splitFrame;
4285   }
4286
4287   public void setSplitFrame(SplitFrame sf)
4288   {
4289     this.splitFrame = sf;
4290   }
4291
4292   // may not need this
4293   @Override
4294   public void setShowSeqFeatures(boolean b)
4295   {
4296     // showSeqFeatures.setSelected(b);
4297     viewport.setShowSequenceFeatures(b);
4298
4299   }
4300
4301   @Override
4302   public void setMenusForViewport()
4303   {
4304     // setMenusFromViewport(viewport);
4305
4306   }
4307
4308   @Override
4309   public void refreshFeatureUI(boolean enableIfNecessary)
4310   {
4311     if (enableIfNecessary)
4312     {
4313       sequenceFeatures.setState(true);
4314       alignPanel.av.setShowSequenceFeatures(true);
4315     }
4316   }
4317
4318   @Override
4319   public FeatureSettingsControllerI getFeatureSettingsUI()
4320   {
4321     return alignPanel.av.featureSettings;
4322   }
4323
4324 }