src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.analysis.TreeBuilder;
  26 import jalview.analysis.scoremodels.PIDModel;
  27 import jalview.analysis.scoremodels.ScoreModels;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.FeatureColourI;
  32 import jalview.api.FeatureRenderer;
  33 import jalview.api.FeatureSettingsControllerI;
  34 import jalview.api.SequenceStructureBinding;
  35 import jalview.bin.JalviewLite;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentAnnotation;
  46 import jalview.datamodel.AlignmentI;
  47 import jalview.datamodel.AlignmentOrder;
  48 import jalview.datamodel.ColumnSelection;
  49 import jalview.datamodel.HiddenColumns;
  50 import jalview.datamodel.PDBEntry;
  51 import jalview.datamodel.Sequence;
  52 import jalview.datamodel.SequenceGroup;
  53 import jalview.datamodel.SequenceI;
  54 import jalview.io.AnnotationFile;
  55 import jalview.io.AppletFormatAdapter;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FeaturesFile;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileFormatI;
  60 import jalview.io.FileFormats;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColour;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.ZappoColourScheme;
  77 import jalview.structure.StructureSelectionManager;
  78 import jalview.structures.models.AAStructureBindingModel;
  79 import jalview.util.MappingUtils;
  80 import jalview.util.MessageManager;
  81 import jalview.viewmodel.AlignmentViewport;
  82 import jalview.viewmodel.ViewportRanges;
  83
  84 import java.awt.BorderLayout;
  85 import java.awt.Canvas;
  86 import java.awt.CheckboxMenuItem;
  87 import java.awt.Color;
  88 import java.awt.FlowLayout;
  89 import java.awt.Font;
  90 import java.awt.FontMetrics;
  91 import java.awt.Frame;
  92 import java.awt.Graphics;
  93 import java.awt.Label;
  94 import java.awt.Menu;
  95 import java.awt.MenuBar;
  96 import java.awt.MenuItem;
  97 import java.awt.Panel;
  98 import java.awt.event.ActionEvent;
  99 import java.awt.event.ActionListener;
 100 import java.awt.event.FocusEvent;
 101 import java.awt.event.FocusListener;
 102 import java.awt.event.ItemEvent;
 103 import java.awt.event.ItemListener;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.KeyListener;
 106 import java.awt.event.WindowAdapter;
 107 import java.awt.event.WindowEvent;
 108 import java.io.IOException;
 109 import java.net.URL;
 110 import java.net.URLEncoder;
 111 import java.util.Arrays;
 112 import java.util.Deque;
 113 import java.util.HashMap;
 114 import java.util.List;
 115 import java.util.Map;
 116 import java.util.StringTokenizer;
 117 import java.util.Vector;
 118
 119 import org.jmol.viewer.Viewer;
 120
 121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 122         ItemListener, KeyListener, AlignViewControllerGuiI
 123 {
 124   public AlignViewControllerI avc;
 125
 126   public AlignmentPanel alignPanel;
 127
 128   public AlignViewport viewport;
 129
 130   // width and height may be overridden by applet parameters
 131   int frameWidth = 700;
 132
 133   int frameHeight = 500;
 134
 135   String jalviewServletURL;
 136
 137   /*
 138    * Flag for showing autocalculated consensus above or below other consensus
 139    * rows
 140    */
 141   private boolean showAutoCalculatedAbove;
 142
 143   private SequenceAnnotationOrder annotationSortOrder;
 144
 145   /**
 146    * Constructor that creates the frame and adds it to the display.
 147    *
 148    * @param al
 149    * @param applet
 150    * @param title
 151    * @param embedded
 152    */
 153   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 154           boolean embedded)
 155   {
 156     this(al, applet, title, embedded, true);
 157   }
 158
 159   /**
 160    * Constructor that optionally allows the frame to be displayed or only
 161    * created.
 162    *
 163    * @param al
 164    * @param applet
 165    * @param title
 166    * @param embedded
 167    * @param addToDisplay
 168    */
 169   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 170           boolean embedded, boolean addToDisplay)
 171   {
 172     this(al, null, null, applet, title, embedded, addToDisplay);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           HiddenColumns hidden, JalviewLite applet, String title,
 177           boolean embedded)
 178   {
 179     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 180   }
 181
 182   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 183           HiddenColumns hidden, JalviewLite applet, String title,
 184           boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237
 238     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 239     followMouseOverFlag.setState(viewport.isFollowHighlight());
 240     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 241     showGroupConservation.setState(viewport.isShowGroupConservation());
 242     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 243     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 244     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 245     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 246     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 247     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 248     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showAlignmentAnnotations.setState(true);
 250     showSequenceAnnotations.setState(false);
 251
 252     seqLimits.setState(viewport.getShowJVSuffix());
 253
 254     if (applet != null)
 255     {
 256       String param = applet.getParameter("sortBy");
 257       if (param != null)
 258       {
 259         if (param.equalsIgnoreCase("Id"))
 260         {
 261           sortIDMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Pairwise Identity"))
 264         {
 265           sortPairwiseMenuItem_actionPerformed();
 266         }
 267         else if (param.equalsIgnoreCase("Length"))
 268         {
 269           sortLengthMenuItem_actionPerformed();
 270         }
 271       }
 272
 273       param = applet.getParameter("wrap");
 274       if (param != null)
 275       {
 276         if (param.equalsIgnoreCase("true"))
 277         {
 278           wrapMenuItem.setState(true);
 279           wrapMenuItem_actionPerformed();
 280         }
 281       }
 282       param = applet.getParameter("centrecolumnlabels");
 283       if (param != null)
 284       {
 285         centreColumnLabelFlag.setState(true);
 286         centreColumnLabelFlag_stateChanged();
 287       }
 288
 289     }
 290     if (viewport.getAlignment().isNucleotide())
 291     {
 292       conservationMenuItem.setEnabled(false);
 293       clustalColour.setEnabled(false);
 294       BLOSUM62Colour.setEnabled(false);
 295       zappoColour.setEnabled(false);
 296       taylorColour.setEnabled(false);
 297       hydrophobicityColour.setEnabled(false);
 298       helixColour.setEnabled(false);
 299       strandColour.setEnabled(false);
 300       turnColour.setEnabled(false);
 301       buriedColour.setEnabled(false);
 302       viewport.updateStrucConsensus(alignPanel);
 303       if (viewport.getAlignment().hasRNAStructure())
 304       {
 305         RNAHelixColour.setEnabled(true);
 306       }
 307       else
 308       {
 309         RNAHelixColour.setEnabled(false);
 310       }
 311     }
 312     else
 313     {
 314       RNAHelixColour.setEnabled(false);
 315       purinePyrimidineColour.setEnabled(false);
 316       nucleotideColour.setEnabled(false);
 317     }
 318     // Some JVMS send keyevents to Top frame or lowest panel,
 319     // Havent worked out why yet. So add to both this frame and seqCanvas for
 320     // now
 321     this.addKeyListener(this);
 322     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 323     alignPanel.idPanel.idCanvas.addKeyListener(this);
 324     alignPanel.scalePanel.addKeyListener(this);
 325     alignPanel.annotationPanel.addKeyListener(this);
 326     alignPanel.annotationPanelHolder.addKeyListener(this);
 327     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 328     alignPanel.alabels.addKeyListener(this);
 329
 330     setAnnotationsVisibility();
 331
 332     if (addToDisplay)
 333     {
 334       addToDisplay(embedded);
 335     }
 336   }
 337
 338   /**
 339    * @param embedded
 340    */
 341   public void addToDisplay(boolean embedded)
 342   {
 343     createAlignFrameWindow(embedded);
 344     validate();
 345     alignPanel.adjustAnnotationHeight();
 346     alignPanel.paintAlignment(true, true);
 347   }
 348
 349   public AlignViewport getAlignViewport()
 350   {
 351     return viewport;
 352   }
 353
 354   public SeqCanvas getSeqcanvas()
 355   {
 356     return alignPanel.seqPanel.seqCanvas;
 357   }
 358
 359   /**
 360    * Load a features file onto the alignment
 361    *
 362    * @param file
 363    *          file URL, content, or other resolvable path
 364    * @param type
 365    *          is protocol for accessing data referred to by file
 366    */
 367
 368   public boolean parseFeaturesFile(String file, DataSourceType type)
 369   {
 370     return parseFeaturesFile(file, type, true);
 371   }
 372
 373   /**
 374    * Load a features file onto the alignment
 375    *
 376    * @param file
 377    *          file URL, content, or other resolvable path
 378    * @param sourceType
 379    *          is protocol for accessing data referred to by file
 380    * @param autoenabledisplay
 381    *          when true, display features flag will be automatically enabled if
 382    *          features are loaded
 383    * @return true if data parsed as a features file
 384    */
 385   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 386           boolean autoenabledisplay)
 387   {
 388     boolean featuresFile = false;
 389     try
 390     {
 391       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 392               .getFeatureRenderer().getFeatureColours();
 393       boolean relaxedIdMatching = viewport.applet
 394               .getDefaultParameter("relaxedidmatch", false);
 395       featuresFile = new FeaturesFile(file, sourceType).parse(
 396               viewport.getAlignment(), colours, true, relaxedIdMatching);
 397     } catch (Exception ex)
 398     {
 399       ex.printStackTrace();
 400     }
 401
 402     if (featuresFile)
 403     {
 404       if (autoenabledisplay)
 405       {
 406         viewport.setShowSequenceFeatures(true);
 407         sequenceFeatures.setState(true);
 408       }
 409       if (alignPanel.seqPanel.seqCanvas.fr != null)
 410       {
 411         // update the min/max ranges where necessary
 412         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 413       }
 414       if (viewport.featureSettings != null)
 415       {
 416         viewport.featureSettings.refreshTable();
 417       }
 418       alignPanel.paintAlignment(true, true);
 419       setStatus(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       setStatus(MessageManager
 578               .formatMessage("label.keyboard_editing_mode", new String[]
 579               { (viewport.cursorMode ? "on" : "off") }));
 580       if (viewport.cursorMode)
 581       {
 582         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 583         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 584       }
 585       break;
 586
 587     case KeyEvent.VK_F:
 588       if (evt.isControlDown())
 589       {
 590         findMenuItem_actionPerformed();
 591       }
 592       break;
 593
 594     case KeyEvent.VK_H:
 595     {
 596       boolean toggleSeqs = !evt.isControlDown();
 597       boolean toggleCols = !evt.isShiftDown();
 598       toggleHiddenRegions(toggleSeqs, toggleCols);
 599       break;
 600     }
 601
 602     case KeyEvent.VK_PAGE_UP:
 603       ranges.pageUp();
 604       break;
 605
 606     case KeyEvent.VK_PAGE_DOWN:
 607       ranges.pageDown();
 608       break;
 609
 610     case KeyEvent.VK_Z:
 611       if (evt.isControlDown())
 612       {
 613         undoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_Y:
 618       if (evt.isControlDown())
 619       {
 620         redoMenuItem_actionPerformed();
 621       }
 622       break;
 623
 624     case KeyEvent.VK_L:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(true);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_R:
 632       if (evt.isControlDown())
 633       {
 634         trimAlignment(false);
 635       }
 636       break;
 637
 638     case KeyEvent.VK_E:
 639       if (evt.isControlDown())
 640       {
 641         if (evt.isShiftDown())
 642         {
 643           this.removeAllGapsMenuItem_actionPerformed();
 644         }
 645         else
 646         {
 647           removeGappedColumnMenuItem_actionPerformed();
 648         }
 649       }
 650       break;
 651     case KeyEvent.VK_I:
 652       if (evt.isControlDown())
 653       {
 654         if (evt.isAltDown())
 655         {
 656           invertColSel_actionPerformed();
 657         }
 658         else
 659         {
 660           invertSequenceMenuItem_actionPerformed();
 661         }
 662       }
 663       break;
 664
 665     case KeyEvent.VK_G:
 666       if (evt.isControlDown())
 667       {
 668         if (evt.isShiftDown())
 669         {
 670           this.unGroup_actionPerformed();
 671         }
 672         else
 673         {
 674           this.createGroup_actionPerformed();
 675         }
 676       }
 677       break;
 678
 679     case KeyEvent.VK_U:
 680       if (evt.isControlDown())
 681       {
 682         this.deleteGroups_actionPerformed();
 683       }
 684       break;
 685
 686     case KeyEvent.VK_T:
 687       if (evt.isControlDown())
 688       {
 689         newView(null);
 690       }
 691       break;
 692
 693     }
 694     // TODO: repaint flags set only if the keystroke warrants it
 695     alignPanel.paintAlignment(true, true);
 696   }
 697
 698   /**
 699    * called by key handler and the hide all/show all menu items
 700    *
 701    * @param toggleSeqs
 702    * @param toggleCols
 703    */
 704   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 705   {
 706     boolean hide = false;
 707     SequenceGroup sg = viewport.getSelectionGroup();
 708     if (!toggleSeqs && !toggleCols)
 709     {
 710       // Hide everything by the current selection - this is a hack - we do the
 711       // invert and then hide
 712       // first check that there will be visible columns after the invert.
 713       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 714               && sg.getStartRes() <= sg.getEndRes()))
 715       {
 716         // now invert the sequence set, if required - empty selection implies
 717         // that no hiding is required.
 718         if (sg != null)
 719         {
 720           invertSequenceMenuItem_actionPerformed();
 721           sg = viewport.getSelectionGroup();
 722           toggleSeqs = true;
 723
 724         }
 725         viewport.expandColSelection(sg, true);
 726         // finally invert the column selection and get the new sequence
 727         // selection and indicate it should be hidden.
 728         invertColSel_actionPerformed();
 729         toggleCols = true;
 730       }
 731     }
 732
 733     if (toggleSeqs)
 734     {
 735       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 736       {
 737         hide = true;
 738         viewport.hideAllSelectedSeqs();
 739       }
 740       else if (!(toggleCols && viewport.hasSelectedColumns()))
 741       {
 742         viewport.showAllHiddenSeqs();
 743       }
 744     }
 745
 746     if (toggleCols)
 747     {
 748       if (viewport.hasSelectedColumns())
 749       {
 750         viewport.hideSelectedColumns();
 751         if (!toggleSeqs)
 752         {
 753           viewport.setSelectionGroup(sg);
 754         }
 755       }
 756       else if (!hide)
 757       {
 758         viewport.showAllHiddenColumns();
 759       }
 760       viewport.sendSelection();
 761     }
 762   }
 763
 764   @Override
 765   public void keyReleased(KeyEvent evt)
 766   {
 767   }
 768
 769   @Override
 770   public void keyTyped(KeyEvent evt)
 771   {
 772   }
 773
 774   @Override
 775   public void itemStateChanged(ItemEvent evt)
 776   {
 777     final Object source = evt.getSource();
 778     if (source == displayNonconservedMenuItem)
 779     {
 780       displayNonconservedMenuItem_actionPerformed();
 781     }
 782     else if (source == colourTextMenuItem)
 783     {
 784       colourTextMenuItem_actionPerformed();
 785     }
 786     else if (source == wrapMenuItem)
 787     {
 788       wrapMenuItem_actionPerformed();
 789     }
 790     else if (source == scaleAbove)
 791     {
 792       viewport.setScaleAboveWrapped(scaleAbove.getState());
 793     }
 794     else if (source == scaleLeft)
 795     {
 796       viewport.setScaleLeftWrapped(scaleLeft.getState());
 797     }
 798     else if (source == scaleRight)
 799     {
 800       viewport.setScaleRightWrapped(scaleRight.getState());
 801     }
 802     else if (source == seqLimits)
 803     {
 804       seqLimits_itemStateChanged();
 805     }
 806     else if (source == viewBoxesMenuItem)
 807     {
 808       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 809     }
 810     else if (source == viewTextMenuItem)
 811     {
 812       viewport.setShowText(viewTextMenuItem.getState());
 813     }
 814     else if (source == renderGapsMenuItem)
 815     {
 816       viewport.setRenderGaps(renderGapsMenuItem.getState());
 817     }
 818     else if (source == annotationPanelMenuItem)
 819     {
 820       boolean showAnnotations = annotationPanelMenuItem.getState();
 821       showAlignmentAnnotations.setEnabled(showAnnotations);
 822       showSequenceAnnotations.setEnabled(showAnnotations);
 823       viewport.setShowAnnotation(showAnnotations);
 824       alignPanel.setAnnotationVisible(showAnnotations);
 825     }
 826     else if (source == sequenceFeatures)
 827     {
 828       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 829       alignPanel.seqPanel.seqCanvas.repaint();
 830     }
 831     else if (source == showAlignmentAnnotations)
 832     {
 833       setAnnotationsVisibility();
 834     }
 835     else if (source == showSequenceAnnotations)
 836     {
 837       setAnnotationsVisibility();
 838     }
 839     else if (source == sortAnnBySequence)
 840     {
 841       boolean newState = sortAnnBySequence.getState();
 842       sortAnnByLabel.setState(false);
 843       setAnnotationSortOrder(
 844               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 845                       : SequenceAnnotationOrder.NONE);
 846       setViewportAnnotationOrder();
 847     }
 848     else if (source == sortAnnByLabel)
 849     {
 850       boolean newState = sortAnnByLabel.getState();
 851       sortAnnBySequence.setState(false);
 852       setAnnotationSortOrder(
 853               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 854                       : SequenceAnnotationOrder.NONE);
 855       setViewportAnnotationOrder();
 856     }
 857     else if (source == showAutoFirst)
 858     {
 859       showAutoLast.setState(!showAutoFirst.getState());
 860       setShowAutoCalculatedAbove(showAutoFirst.getState());
 861       setViewportAnnotationOrder();
 862     }
 863     else if (source == showAutoLast)
 864     {
 865       showAutoFirst.setState(!showAutoLast.getState());
 866       setShowAutoCalculatedAbove(showAutoFirst.getState());
 867       setViewportAnnotationOrder();
 868     }
 869     else if (source == conservationMenuItem)
 870     {
 871       conservationMenuItem_actionPerformed();
 872     }
 873     else if (source == abovePIDThreshold)
 874     {
 875       abovePIDThreshold_actionPerformed();
 876     }
 877     else if (source == applyToAllGroups)
 878     {
 879       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 880     }
 881     else if (source == autoCalculate)
 882     {
 883       viewport.autoCalculateConsensus = autoCalculate.getState();
 884     }
 885     else if (source == sortByTree)
 886     {
 887       viewport.sortByTree = sortByTree.getState();
 888     }
 889     else if (source == this.centreColumnLabelFlag)
 890     {
 891       centreColumnLabelFlag_stateChanged();
 892     }
 893     else if (source == this.followMouseOverFlag)
 894     {
 895       mouseOverFlag_stateChanged();
 896     }
 897     else if (source == showGroupConsensus)
 898     {
 899       showGroupConsensus_actionPerformed();
 900     }
 901     else if (source == showGroupConservation)
 902     {
 903       showGroupConservation_actionPerformed();
 904     }
 905     else if (source == showSequenceLogo)
 906     {
 907       showSequenceLogo_actionPerformed();
 908     }
 909     else if (source == normSequenceLogo)
 910     {
 911       normSequenceLogo_actionPerformed();
 912     }
 913     else if (source == showConsensusHistogram)
 914     {
 915       showConsensusHistogram_actionPerformed();
 916     }
 917     else if (source == applyAutoAnnotationSettings)
 918     {
 919       applyAutoAnnotationSettings_actionPerformed();
 920     }
 921     // TODO: repaint flags set only if warranted
 922     alignPanel.paintAlignment(true, true);
 923   }
 924
 925   /**
 926    * Set the visibility state of sequence-related and/or alignment-related
 927    * annotations depending on checkbox selections, and repaint.
 928    *
 929    * @param visible
 930    */
 931   private void setAnnotationsVisibility()
 932   {
 933     boolean showForAlignment = showAlignmentAnnotations.getState();
 934     boolean showForSequences = showSequenceAnnotations.getState();
 935     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 936     {
 937       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 938               .getAlignmentAnnotation())
 939       {
 940         boolean visible = (aa.sequenceRef == null ? showForAlignment
 941                 : showForSequences);
 942         aa.visible = visible;
 943       }
 944     }
 945     alignPanel.validateAnnotationDimensions(true);
 946     validate();
 947     repaint();
 948   }
 949
 950   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 951   {
 952     this.annotationSortOrder = order;
 953   }
 954
 955   /**
 956    * Set flags on the viewport that control annotation ordering
 957    */
 958   private void setViewportAnnotationOrder()
 959   {
 960     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 961     this.alignPanel.av
 962             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 963   }
 964
 965   private void setShowAutoCalculatedAbove(boolean showAbove)
 966   {
 967     this.showAutoCalculatedAbove = showAbove;
 968   }
 969
 970   private void mouseOverFlag_stateChanged()
 971   {
 972     viewport.setFollowHighlight(followMouseOverFlag.getState());
 973     // TODO: could kick the scrollTo mechanism to reset view for current
 974     // searchresults.
 975   }
 976
 977   private void centreColumnLabelFlag_stateChanged()
 978   {
 979     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 980     this.alignPanel.annotationPanel.repaint();
 981   }
 982
 983   @Override
 984   public void actionPerformed(ActionEvent evt)
 985   {
 986     viewport.applet.currentAlignFrame = this;
 987
 988     Object source = evt.getSource();
 989
 990     if (source == inputText)
 991     {
 992       inputText_actionPerformed();
 993     }
 994     else if (source == loadTree)
 995     {
 996       loadTree_actionPerformed();
 997     }
 998     else if (source == loadApplication)
 999     {
1000       launchFullApplication();
1001     }
1002     else if (source == loadAnnotations)
1003     {
1004       loadAnnotations();
1005     }
1006     else if (source == outputAnnotations)
1007     {
1008       outputAnnotations(true);
1009     }
1010     else if (source == outputFeatures)
1011     {
1012       outputFeatures(true, "Jalview");
1013     }
1014     else if (source == closeMenuItem)
1015     {
1016       closeMenuItem_actionPerformed();
1017     }
1018     else if (source == copy)
1019     {
1020       copy_actionPerformed();
1021     }
1022     else if (source == undoMenuItem)
1023     {
1024       undoMenuItem_actionPerformed();
1025     }
1026     else if (source == redoMenuItem)
1027     {
1028       redoMenuItem_actionPerformed();
1029     }
1030     else if (source == inputText)
1031     {
1032       inputText_actionPerformed();
1033     }
1034     else if (source == closeMenuItem)
1035     {
1036       closeMenuItem_actionPerformed();
1037     }
1038     else if (source == undoMenuItem)
1039     {
1040       undoMenuItem_actionPerformed();
1041     }
1042     else if (source == redoMenuItem)
1043     {
1044       redoMenuItem_actionPerformed();
1045     }
1046     else if (source == copy)
1047     {
1048       copy_actionPerformed();
1049     }
1050     else if (source == pasteNew)
1051     {
1052       pasteNew_actionPerformed();
1053     }
1054     else if (source == pasteThis)
1055     {
1056       pasteThis_actionPerformed();
1057     }
1058     else if (source == cut)
1059     {
1060       cut_actionPerformed();
1061     }
1062     else if (source == delete)
1063     {
1064       delete_actionPerformed();
1065     }
1066     else if (source == createGroup)
1067     {
1068       createGroup_actionPerformed();
1069     }
1070     else if (source == unGroup)
1071     {
1072       unGroup_actionPerformed();
1073     }
1074     else if (source == grpsFromSelection)
1075     {
1076       makeGrpsFromSelection_actionPerformed();
1077     }
1078     else if (source == deleteGroups)
1079     {
1080       deleteGroups_actionPerformed();
1081     }
1082     else if (source == selectAllSequenceMenuItem)
1083     {
1084       selectAllSequenceMenuItem_actionPerformed();
1085     }
1086     else if (source == deselectAllSequenceMenuItem)
1087     {
1088       deselectAllSequenceMenuItem_actionPerformed();
1089     }
1090     else if (source == invertSequenceMenuItem)
1091     {
1092       invertSequenceMenuItem_actionPerformed();
1093       // uncomment to slave sequence selections in split frame
1094       // viewport.sendSelection();
1095     }
1096     else if (source == invertColSel)
1097     {
1098       viewport.invertColumnSelection();
1099       alignPanel.paintAlignment(false, false);
1100       viewport.sendSelection();
1101     }
1102     else if (source == remove2LeftMenuItem)
1103     {
1104       trimAlignment(true);
1105     }
1106     else if (source == remove2RightMenuItem)
1107     {
1108       trimAlignment(false);
1109     }
1110     else if (source == removeGappedColumnMenuItem)
1111     {
1112       removeGappedColumnMenuItem_actionPerformed();
1113     }
1114     else if (source == removeAllGapsMenuItem)
1115     {
1116       removeAllGapsMenuItem_actionPerformed();
1117     }
1118     else if (source == findMenuItem)
1119     {
1120       findMenuItem_actionPerformed();
1121     }
1122     else if (source == font)
1123     {
1124       new FontChooser(alignPanel);
1125     }
1126     else if (source == newView)
1127     {
1128       newView(null);
1129     }
1130     else if (source == showColumns)
1131     {
1132       viewport.showAllHiddenColumns();
1133       alignPanel.paintAlignment(true, true);
1134       viewport.sendSelection();
1135     }
1136     else if (source == showSeqs)
1137     {
1138       viewport.showAllHiddenSeqs();
1139       alignPanel.paintAlignment(true, true);
1140       // uncomment if we want to slave sequence selections in split frame
1141       // viewport.sendSelection();
1142     }
1143     else if (source == hideColumns)
1144     {
1145       viewport.hideSelectedColumns();
1146       alignPanel.paintAlignment(true, true);
1147       viewport.sendSelection();
1148     }
1149     else if (source == hideSequences
1150             && viewport.getSelectionGroup() != null)
1151     {
1152       viewport.hideAllSelectedSeqs();
1153       alignPanel.paintAlignment(true, true);
1154       // uncomment if we want to slave sequence selections in split frame
1155       // viewport.sendSelection();
1156     }
1157     else if (source == hideAllButSelection)
1158     {
1159       toggleHiddenRegions(false, false);
1160       alignPanel.paintAlignment(true, true);
1161       viewport.sendSelection();
1162     }
1163     else if (source == hideAllSelection)
1164     {
1165       SequenceGroup sg = viewport.getSelectionGroup();
1166       viewport.expandColSelection(sg, false);
1167       viewport.hideAllSelectedSeqs();
1168       viewport.hideSelectedColumns();
1169       alignPanel.paintAlignment(true, true);
1170       viewport.sendSelection();
1171     }
1172     else if (source == showAllHidden)
1173     {
1174       viewport.showAllHiddenColumns();
1175       viewport.showAllHiddenSeqs();
1176       alignPanel.paintAlignment(true, true);
1177       viewport.sendSelection();
1178     }
1179     else if (source == showGroupConsensus)
1180     {
1181       showGroupConsensus_actionPerformed();
1182     }
1183     else if (source == showGroupConservation)
1184     {
1185       showGroupConservation_actionPerformed();
1186     }
1187     else if (source == showSequenceLogo)
1188     {
1189       showSequenceLogo_actionPerformed();
1190     }
1191     else if (source == normSequenceLogo)
1192     {
1193       normSequenceLogo_actionPerformed();
1194     }
1195     else if (source == showConsensusHistogram)
1196     {
1197       showConsensusHistogram_actionPerformed();
1198     }
1199     else if (source == applyAutoAnnotationSettings)
1200     {
1201       applyAutoAnnotationSettings_actionPerformed();
1202     }
1203     else if (source == featureSettings)
1204     {
1205       new FeatureSettings(alignPanel);
1206     }
1207     else if (source == alProperties)
1208     {
1209       StringBuffer contents = new jalview.io.AlignmentProperties(
1210               viewport.getAlignment()).formatAsString();
1211       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212       cap.setText(contents.toString());
1213       Frame frame = new Frame();
1214       frame.add(cap);
1215       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1216               .formatMessage("label.alignment_properties", new String[]
1217               { getTitle() }), 400, 250);
1218     }
1219     else if (source == overviewMenuItem)
1220     {
1221       overviewMenuItem_actionPerformed();
1222     }
1223     else if (source == noColourmenuItem)
1224     {
1225       changeColour(null);
1226     }
1227     else if (source == clustalColour)
1228     {
1229       abovePIDThreshold.setState(false);
1230       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1231     }
1232     else if (source == zappoColour)
1233     {
1234       changeColour(new ZappoColourScheme());
1235     }
1236     else if (source == taylorColour)
1237     {
1238       changeColour(new TaylorColourScheme());
1239     }
1240     else if (source == hydrophobicityColour)
1241     {
1242       changeColour(new HydrophobicColourScheme());
1243     }
1244     else if (source == helixColour)
1245     {
1246       changeColour(new HelixColourScheme());
1247     }
1248     else if (source == strandColour)
1249     {
1250       changeColour(new StrandColourScheme());
1251     }
1252     else if (source == turnColour)
1253     {
1254       changeColour(new TurnColourScheme());
1255     }
1256     else if (source == buriedColour)
1257     {
1258       changeColour(new BuriedColourScheme());
1259     }
1260     else if (source == nucleotideColour)
1261     {
1262       changeColour(new NucleotideColourScheme());
1263     }
1264     else if (source == purinePyrimidineColour)
1265     {
1266       changeColour(new PurinePyrimidineColourScheme());
1267     }
1268     // else if (source == RNAInteractionColour)
1269     // {
1270     // changeColour(new RNAInteractionColourScheme());
1271     // }
1272     else if (source == RNAHelixColour)
1273     {
1274       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1275       // new RNAHelicesColourChooser(viewport, alignPanel);
1276     }
1277     else if (source == modifyPID)
1278     {
1279       modifyPID_actionPerformed();
1280     }
1281     else if (source == modifyConservation)
1282     {
1283       modifyConservation_actionPerformed();
1284     }
1285     else if (source == userDefinedColour)
1286     {
1287       new UserDefinedColours(alignPanel, null);
1288     }
1289     else if (source == PIDColour)
1290     {
1291       changeColour(new PIDColourScheme());
1292     }
1293     else if (source == BLOSUM62Colour)
1294     {
1295       changeColour(new Blosum62ColourScheme());
1296     }
1297     else if (source == tcoffeeColour)
1298     {
1299       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1300     }
1301     else if (source == annotationColour)
1302     {
1303       new AnnotationColourChooser(viewport, alignPanel);
1304     }
1305     else if (source == annotationColumnSelection)
1306     {
1307       new AnnotationColumnChooser(viewport, alignPanel);
1308     }
1309     else if (source == sortPairwiseMenuItem)
1310     {
1311       sortPairwiseMenuItem_actionPerformed();
1312     }
1313     else if (source == sortIDMenuItem)
1314     {
1315       sortIDMenuItem_actionPerformed();
1316     }
1317     else if (source == sortLengthMenuItem)
1318     {
1319       sortLengthMenuItem_actionPerformed();
1320     }
1321     else if (source == sortGroupMenuItem)
1322     {
1323       sortGroupMenuItem_actionPerformed();
1324     }
1325     else if (source == removeRedundancyMenuItem)
1326     {
1327       removeRedundancyMenuItem_actionPerformed();
1328     }
1329     else if (source == pairwiseAlignmentMenuItem)
1330     {
1331       pairwiseAlignmentMenuItem_actionPerformed();
1332     }
1333     else if (source == PCAMenuItem)
1334     {
1335       PCAMenuItem_actionPerformed();
1336     }
1337     else if (source == averageDistanceTreeMenuItem)
1338     {
1339       averageDistanceTreeMenuItem_actionPerformed();
1340     }
1341     else if (source == neighbourTreeMenuItem)
1342     {
1343       neighbourTreeMenuItem_actionPerformed();
1344     }
1345     else if (source == njTreeBlosumMenuItem)
1346     {
1347       njTreeBlosumMenuItem_actionPerformed();
1348     }
1349     else if (source == avDistanceTreeBlosumMenuItem)
1350     {
1351       avTreeBlosumMenuItem_actionPerformed();
1352     }
1353     else if (source == documentation)
1354     {
1355       documentation_actionPerformed();
1356     }
1357     else if (source == about)
1358     {
1359       about_actionPerformed();
1360     }
1361
1362   }
1363
1364   public void inputText_actionPerformed()
1365   {
1366     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1367     Frame frame = new Frame();
1368     frame.add(cap);
1369     jalview.bin.JalviewLite.addFrame(frame,
1370             MessageManager.getString("label.input_cut_paste"), 500, 500);
1371   }
1372
1373   protected void outputText_actionPerformed(ActionEvent e)
1374   {
1375     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376     Frame frame = new Frame();
1377     frame.add(cap);
1378     JalviewLite.addFrame(frame, MessageManager
1379             .formatMessage("label.alignment_output_command", new Object[]
1380             { e.getActionCommand() }), 600, 500);
1381
1382     FileFormatI fileFormat = FileFormats.getInstance()
1383             .forName(e.getActionCommand());
1384     cap.setText(
1385             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1386                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1387   }
1388
1389   public void loadAnnotations()
1390   {
1391     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1392     cap.setText(MessageManager
1393             .getString("label.paste_features_annotations_Tcoffee_here"));
1394     cap.setAnnotationImport();
1395     Frame frame = new Frame();
1396     frame.add(cap);
1397     jalview.bin.JalviewLite.addFrame(frame,
1398             MessageManager.getString("action.paste_annotations"), 400, 300);
1399
1400   }
1401
1402   public String outputAnnotations(boolean displayTextbox)
1403   {
1404     String annotation = new AnnotationFile()
1405             .printAnnotationsForView(viewport);
1406
1407     if (displayTextbox)
1408     {
1409       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1410       Frame frame = new Frame();
1411       frame.add(cap);
1412       jalview.bin.JalviewLite.addFrame(frame,
1413               MessageManager.getString("label.annotations"), 600, 500);
1414       cap.setText(annotation);
1415     }
1416
1417     return annotation;
1418   }
1419
1420   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1421   {
1422     if (alignPanel.getFeatureRenderer() != null
1423             && viewport.getFeaturesDisplayed() != null)
1424     {
1425       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1426
1427     }
1428     return null;
1429   }
1430
1431   private List<String> getDisplayedFeatureGroups()
1432   {
1433     if (alignPanel.getFeatureRenderer() != null
1434             && viewport.getFeaturesDisplayed() != null)
1435     {
1436       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1437
1438     }
1439     return null;
1440   }
1441
1442   public String outputFeatures(boolean displayTextbox, String format)
1443   {
1444     String features;
1445     FeaturesFile formatter = new FeaturesFile();
1446     if (format.equalsIgnoreCase("Jalview"))
1447     {
1448       features = formatter.printJalviewFormat(
1449               viewport.getAlignment().getSequencesArray(),
1450               alignPanel.getFeatureRenderer(), true);
1451     }
1452     else
1453     {
1454       features = formatter.printGffFormat(viewport.getAlignment()
1455               .getSequencesArray(), alignPanel.getFeatureRenderer(), true);
1456     }
1457
1458     if (displayTextbox)
1459     {
1460       boolean frimport = false;
1461       if (features == null || features.equals("No Features Visible"))
1462       {
1463         features = "# No features visible - paste some and import them here.";
1464         frimport = true;
1465       }
1466
1467       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1468       if (frimport)
1469       {
1470         cap.setAnnotationImport();
1471       }
1472       Frame frame = new Frame();
1473       frame.add(cap);
1474       jalview.bin.JalviewLite.addFrame(frame,
1475               MessageManager.getString("label.features"), 600, 500);
1476       cap.setText(features);
1477     }
1478     else
1479     {
1480       if (features == null)
1481       {
1482         features = "";
1483       }
1484     }
1485
1486     return features;
1487   }
1488
1489   void launchFullApplication()
1490   {
1491     StringBuffer url = new StringBuffer(jalviewServletURL);
1492
1493     // allow servlet parameters to be passed in applet parameter
1494     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1495             : "?";
1496     url.append(firstSep);
1497
1498     url.append(
1499             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1500
1501     if (viewport.applet.getParameter("features") != null)
1502     {
1503       url.append("&features=");
1504       url.append(appendProtocol(viewport.applet.getParameter("features")));
1505     }
1506
1507     if (viewport.applet.getParameter("annotations") != null)
1508     {
1509       url.append("&annotations=");
1510       url.append(
1511               appendProtocol(viewport.applet.getParameter("annotations")));
1512     }
1513
1514     if (viewport.applet.getParameter("jnetfile") != null
1515             || viewport.applet.getParameter("jpredfile") != null)
1516     {
1517       url.append("&annotations=");
1518       url.append(appendProtocol(
1519               viewport.applet.getParameter("jnetfile") != null
1520                       ? viewport.applet.getParameter("jnetfile")
1521                       : viewport.applet.getParameter("jpredfile")));
1522     }
1523
1524     if (viewport.applet.getParameter("defaultColour") != null)
1525     {
1526       url.append("&colour=" + removeWhiteSpace(
1527               viewport.applet.getParameter("defaultColour")));
1528     }
1529
1530     if (viewport.applet.getParameter("userDefinedColour") != null)
1531     {
1532       url.append("&colour=" + removeWhiteSpace(
1533               viewport.applet.getParameter("userDefinedColour")));
1534     }
1535     if (viewport.applet.getParameter("tree") != null)
1536     {
1537       url.append("&tree="
1538               + appendProtocol(viewport.applet.getParameter("tree")));
1539     }
1540     if (viewport.applet.getParameter("treeFile") != null)
1541     {
1542       url.append("&tree="
1543               + appendProtocol(viewport.applet.getParameter("treeFile")));
1544     }
1545
1546     showURL(url.toString(), "FULL_APP");
1547   }
1548
1549   String removeWhiteSpace(String colour)
1550   {
1551     StringBuffer sb = new StringBuffer();
1552     for (int i = 0; i < colour.length(); i++)
1553     {
1554       if (Character.isWhitespace(colour.charAt(i)))
1555       {
1556         sb.append("%20");
1557       }
1558       else
1559       {
1560         sb.append(colour.charAt(i));
1561       }
1562     }
1563
1564     return sb.toString();
1565   }
1566
1567   String appendProtocol(String url)
1568   {
1569     try
1570     {
1571       new URL(url);
1572       url = URLEncoder.encode(url);
1573     }
1574     /*
1575      * When we finally deprecate 1.1 compatibility, we can start to use
1576      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1577      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1578      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1579      * ex.printStackTrace(); }
1580      */
1581     catch (java.net.MalformedURLException ex)
1582     {
1583       url = viewport.applet.getCodeBase() + url;
1584     }
1585     return url;
1586   }
1587
1588   public void closeMenuItem_actionPerformed()
1589   {
1590     PaintRefresher.RemoveComponent(alignPanel);
1591     if (alignPanel.seqPanel != null
1592             && alignPanel.seqPanel.seqCanvas != null)
1593     {
1594       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1595     }
1596     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1597     {
1598       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1599     }
1600
1601     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1602     {
1603       System.exit(0);
1604     }
1605
1606     viewport = null;
1607     if (alignPanel != null && alignPanel.overviewPanel != null)
1608     {
1609       alignPanel.overviewPanel.dispose();
1610     }
1611     alignPanel = null;
1612     this.dispose();
1613   }
1614
1615   /**
1616    * TODO: JAL-1104
1617    */
1618   void updateEditMenuBar()
1619   {
1620
1621     if (viewport.getHistoryList().size() > 0)
1622     {
1623       undoMenuItem.setEnabled(true);
1624       CommandI command = viewport.getHistoryList().peek();
1625       undoMenuItem.setLabel(MessageManager
1626               .formatMessage("label.undo_command", new Object[]
1627               { command.getDescription() }));
1628     }
1629     else
1630     {
1631       undoMenuItem.setEnabled(false);
1632       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1633     }
1634
1635     if (viewport.getRedoList().size() > 0)
1636     {
1637       redoMenuItem.setEnabled(true);
1638
1639       CommandI command = viewport.getRedoList().peek();
1640       redoMenuItem.setLabel(MessageManager
1641               .formatMessage("label.redo_command", new Object[]
1642               { command.getDescription() }));
1643     }
1644     else
1645     {
1646       redoMenuItem.setEnabled(false);
1647       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1648     }
1649   }
1650
1651   /**
1652    * TODO: JAL-1104
1653    */
1654   @Override
1655   public void addHistoryItem(CommandI command)
1656   {
1657     if (command.getSize() > 0)
1658     {
1659       viewport.addToHistoryList(command);
1660       viewport.clearRedoList();
1661       updateEditMenuBar();
1662       viewport.updateHiddenColumns();
1663     }
1664   }
1665
1666   /**
1667    * TODO: JAL-1104 DOCUMENT ME!
1668    *
1669    * @param e
1670    *          DOCUMENT ME!
1671    */
1672   protected void undoMenuItem_actionPerformed()
1673   {
1674     if (viewport.getHistoryList().isEmpty())
1675     {
1676       return;
1677     }
1678
1679     CommandI command = viewport.getHistoryList().pop();
1680     viewport.addToRedoList(command);
1681     command.undoCommand(null);
1682
1683     AlignmentViewport originalSource = getOriginatingSource(command);
1684     // JBPNote Test
1685     if (originalSource != viewport)
1686     {
1687       System.err
1688               .println("Warning: Viewport object mismatch whilst undoing");
1689     }
1690     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1691                                           // viewport.getColumnSelection().getHiddenColumns()
1692                                           // != null;
1693     updateEditMenuBar();
1694     originalSource.firePropertyChange("alignment", null,
1695             originalSource.getAlignment().getSequences());
1696   }
1697
1698   /**
1699    * TODO: JAL-1104 DOCUMENT ME!
1700    *
1701    * @param e
1702    *          DOCUMENT ME!
1703    */
1704   protected void redoMenuItem_actionPerformed()
1705   {
1706     if (viewport.getRedoList().isEmpty())
1707     {
1708       return;
1709     }
1710
1711     CommandI command = viewport.getRedoList().pop();
1712     viewport.addToHistoryList(command);
1713     command.doCommand(null);
1714
1715     AlignmentViewport originalSource = getOriginatingSource(command);
1716     // JBPNote Test
1717     if (originalSource != viewport)
1718     {
1719       System.err
1720               .println("Warning: Viewport object mismatch whilst re-doing");
1721     }
1722     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1723                                           // viewport.getColumnSelection().getHiddenColumns()
1724                                           // != null;
1725
1726     updateEditMenuBar();
1727     originalSource.firePropertyChange("alignment", null,
1728             originalSource.getAlignment().getSequences());
1729   }
1730
1731   AlignmentViewport getOriginatingSource(CommandI command)
1732   {
1733     AlignmentViewport originalSource = null;
1734     // For sequence removal and addition, we need to fire
1735     // the property change event FROM the viewport where the
1736     // original alignment was altered
1737     AlignmentI al = null;
1738     if (command instanceof EditCommand)
1739     {
1740       EditCommand editCommand = (EditCommand) command;
1741       al = editCommand.getAlignment();
1742       Vector comps = PaintRefresher.components
1743               .get(viewport.getSequenceSetId());
1744       for (int i = 0; i < comps.size(); i++)
1745       {
1746         if (comps.elementAt(i) instanceof AlignmentPanel)
1747         {
1748           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1749           {
1750             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1751             break;
1752           }
1753         }
1754       }
1755     }
1756
1757     if (originalSource == null)
1758     {
1759       // The original view is closed, we must validate
1760       // the current view against the closed view first
1761       if (al != null)
1762       {
1763         PaintRefresher.validateSequences(al, viewport.getAlignment());
1764       }
1765
1766       originalSource = viewport;
1767     }
1768
1769     return originalSource;
1770   }
1771
1772   /**
1773    * Move the currently selected sequences up or down one position in the
1774    * alignment
1775    *
1776    * @param up
1777    */
1778   public void moveSelectedSequences(boolean up)
1779   {
1780     SequenceGroup sg = viewport.getSelectionGroup();
1781     if (sg == null)
1782     {
1783       return;
1784     }
1785     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1786             up ? null : viewport.getHiddenRepSequences(), up);
1787     alignPanel.paintAlignment(true, false);
1788
1789     /*
1790      * Also move cDNA/protein complement sequences
1791      */
1792     AlignViewportI complement = viewport.getCodingComplement();
1793     if (complement != null)
1794     {
1795       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1796               viewport, complement);
1797       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1798               up ? null : complement.getHiddenRepSequences(), up);
1799       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1800               false);
1801     }
1802   }
1803
1804   synchronized void slideSequences(boolean right, int size)
1805   {
1806     List<SequenceI> sg = new Vector<>();
1807     if (viewport.cursorMode)
1808     {
1809       sg.add(viewport.getAlignment()
1810               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1811     }
1812     else if (viewport.getSelectionGroup() != null
1813             && viewport.getSelectionGroup().getSize() != viewport
1814                     .getAlignment().getHeight())
1815     {
1816       sg = viewport.getSelectionGroup()
1817               .getSequences(viewport.getHiddenRepSequences());
1818     }
1819
1820     if (sg.size() < 1)
1821     {
1822       return;
1823     }
1824
1825     Vector<SequenceI> invertGroup = new Vector();
1826
1827     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1828     {
1829       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1830       {
1831         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1832       }
1833     }
1834
1835     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1836
1837     SequenceI[] seqs2 = invertGroup
1838             .toArray(new SequenceI[invertGroup.size()]);
1839     for (int i = 0; i < invertGroup.size(); i++)
1840     {
1841       seqs2[i] = invertGroup.elementAt(i);
1842     }
1843
1844     SlideSequencesCommand ssc;
1845     if (right)
1846     {
1847       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1848               viewport.getGapCharacter());
1849     }
1850     else
1851     {
1852       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1853               viewport.getGapCharacter());
1854     }
1855
1856     int groupAdjustment = 0;
1857     if (ssc.getGapsInsertedBegin() && right)
1858     {
1859       if (viewport.cursorMode)
1860       {
1861         alignPanel.seqPanel.moveCursor(size, 0);
1862       }
1863       else
1864       {
1865         groupAdjustment = size;
1866       }
1867     }
1868     else if (!ssc.getGapsInsertedBegin() && !right)
1869     {
1870       if (viewport.cursorMode)
1871       {
1872         alignPanel.seqPanel.moveCursor(-size, 0);
1873       }
1874       else
1875       {
1876         groupAdjustment = -size;
1877       }
1878     }
1879
1880     if (groupAdjustment != 0)
1881     {
1882       viewport.getSelectionGroup().setStartRes(
1883               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1884       viewport.getSelectionGroup().setEndRes(
1885               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1886     }
1887
1888     boolean appendHistoryItem = false;
1889     Deque<CommandI> historyList = viewport.getHistoryList();
1890     if (historyList != null && historyList.size() > 0
1891             && historyList.peek() instanceof SlideSequencesCommand)
1892     {
1893       appendHistoryItem = ssc.appendSlideCommand(
1894               (SlideSequencesCommand) historyList.peek());
1895     }
1896
1897     if (!appendHistoryItem)
1898     {
1899       addHistoryItem(ssc);
1900     }
1901
1902     repaint();
1903   }
1904
1905   static StringBuffer copiedSequences;
1906
1907   static HiddenColumns copiedHiddenColumns;
1908
1909   protected void copy_actionPerformed()
1910   {
1911     if (viewport.getSelectionGroup() == null)
1912     {
1913       return;
1914     }
1915
1916     SequenceGroup sg = viewport.getSelectionGroup();
1917     copiedSequences = new StringBuffer();
1918     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1919     for (int i = 0; i < sg.getSize(); i++)
1920     {
1921       SequenceI seq = sg.getSequenceAt(i);
1922       int index = viewport.getAlignment().findIndex(seq);
1923       orderedSeqs.put(index, seq);
1924     }
1925
1926     int index = 0, startRes, endRes;
1927     char ch;
1928
1929     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1930     {
1931       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1932       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1933
1934       // create new HiddenColumns object with copy of hidden regions
1935       // between startRes and endRes, offset by startRes
1936       copiedHiddenColumns = new HiddenColumns(
1937               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1938               hiddenCutoff, hiddenOffset);
1939     }
1940     else
1941     {
1942       copiedHiddenColumns = null;
1943     }
1944
1945     for (int i = 0; i < sg.getSize(); i++)
1946     {
1947       SequenceI seq = null;
1948
1949       while (seq == null)
1950       {
1951         if (orderedSeqs.containsKey(index))
1952         {
1953           seq = orderedSeqs.get(index);
1954           index++;
1955           break;
1956         }
1957         else
1958         {
1959           index++;
1960         }
1961       }
1962
1963       // FIND START RES
1964       // Returns residue following index if gap
1965       startRes = seq.findPosition(sg.getStartRes());
1966
1967       // FIND END RES
1968       // Need to find the residue preceeding index if gap
1969       endRes = 0;
1970
1971       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1972       {
1973         ch = seq.getCharAt(j);
1974         if (!jalview.util.Comparison.isGap((ch)))
1975         {
1976           endRes++;
1977         }
1978       }
1979
1980       if (endRes > 0)
1981       {
1982         endRes += seq.getStart() - 1;
1983       }
1984
1985       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1986               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1987                       sg.getEndRes() + 1)
1988               + "\n");
1989     }
1990
1991   }
1992
1993   protected void pasteNew_actionPerformed()
1994   {
1995     paste(true);
1996   }
1997
1998   protected void pasteThis_actionPerformed()
1999   {
2000     paste(false);
2001   }
2002
2003   void paste(boolean newAlignment)
2004   {
2005     try
2006     {
2007       if (copiedSequences == null)
2008       {
2009         return;
2010       }
2011
2012       StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2013               "\t");
2014       Vector seqs = new Vector();
2015       while (st.hasMoreElements())
2016       {
2017         String name = st.nextToken();
2018         int start = Integer.parseInt(st.nextToken());
2019         int end = Integer.parseInt(st.nextToken());
2020         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2021       }
2022       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2023       for (int i = 0; i < seqs.size(); i++)
2024       {
2025         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2026       }
2027
2028       if (newAlignment)
2029       {
2030         String newtitle = MessageManager
2031                 .getString("label.copied_sequences");
2032         if (getTitle().startsWith(
2033                 MessageManager.getString("label.copied_sequences")))
2034         {
2035           newtitle = getTitle();
2036         }
2037         else
2038         {
2039           newtitle = newtitle.concat(MessageManager
2040                   .formatMessage("label.from_msname", new String[]
2041                   { getTitle() }));
2042         }
2043         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2044                 viewport.applet, newtitle, false);
2045         af.viewport.setHiddenColumns(copiedHiddenColumns);
2046
2047         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2048                 frameHeight);
2049       }
2050       else
2051       {
2052         addSequences(newSeqs);
2053       }
2054
2055     } catch (Exception ex)
2056     {
2057     } // could be anything being pasted in here
2058
2059   }
2060
2061   void addSequences(SequenceI[] seqs)
2062   {
2063     for (int i = 0; i < seqs.length; i++)
2064     {
2065       viewport.getAlignment().addSequence(seqs[i]);
2066     }
2067
2068     // !newAlignment
2069     addHistoryItem(new EditCommand(
2070             MessageManager.getString("label.add_sequences"), Action.PASTE,
2071             seqs, 0, viewport.getAlignment().getWidth(),
2072             viewport.getAlignment()));
2073
2074     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2075     viewport.getAlignment().getWidth();
2076     viewport.firePropertyChange("alignment", null,
2077             viewport.getAlignment().getSequences());
2078
2079   }
2080
2081   protected void cut_actionPerformed()
2082   {
2083     copy_actionPerformed();
2084     delete_actionPerformed();
2085   }
2086
2087   protected void delete_actionPerformed()
2088   {
2089
2090     SequenceGroup sg = viewport.getSelectionGroup();
2091     if (sg == null)
2092     {
2093       return;
2094     }
2095
2096     Vector seqs = new Vector();
2097     SequenceI seq;
2098     for (int i = 0; i < sg.getSize(); i++)
2099     {
2100       seq = sg.getSequenceAt(i);
2101       seqs.addElement(seq);
2102     }
2103
2104     /*
2105      * If the cut affects all sequences, warn, remove highlighted columns
2106      */
2107     if (sg.getSize() == viewport.getAlignment().getHeight())
2108     {
2109       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2110               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2111       if (isEntireAlignWidth)
2112       {
2113         String title = MessageManager.getString("label.delete_all");
2114         Panel infoPanel = new Panel();
2115         infoPanel.setLayout(new FlowLayout());
2116         infoPanel.add(
2117                 new Label(MessageManager.getString("warn.delete_all")));
2118
2119         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2120         dialog.setMainPanel(infoPanel);
2121         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2122         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2123         dialog.setVisible(true);
2124
2125         if (!dialog.accept)
2126         {
2127           return;
2128         }
2129       }
2130       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2131               sg.getEndRes() + 1);
2132     }
2133
2134     SequenceI[] cut = new SequenceI[seqs.size()];
2135     for (int i = 0; i < seqs.size(); i++)
2136     {
2137       cut[i] = (SequenceI) seqs.elementAt(i);
2138     }
2139
2140     /*
2141      * //ADD HISTORY ITEM
2142      */
2143     addHistoryItem(new EditCommand(
2144             MessageManager.getString("label.cut_sequences"), Action.CUT,
2145             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2146             viewport.getAlignment()));
2147
2148     viewport.setSelectionGroup(null);
2149     viewport.getAlignment().deleteGroup(sg);
2150
2151     viewport.firePropertyChange("alignment", null,
2152             viewport.getAlignment().getSequences());
2153
2154     if (viewport.getAlignment().getHeight() < 1)
2155     {
2156       this.setVisible(false);
2157     }
2158     viewport.sendSelection();
2159   }
2160
2161   /**
2162    * group consensus toggled
2163    *
2164    */
2165   protected void showGroupConsensus_actionPerformed()
2166   {
2167     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2168     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2169
2170   }
2171
2172   /**
2173    * group conservation toggled.
2174    */
2175   protected void showGroupConservation_actionPerformed()
2176   {
2177     viewport.setShowGroupConservation(showGroupConservation.getState());
2178     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2179   }
2180
2181   /*
2182    * (non-Javadoc)
2183    *
2184    * @see
2185    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2186    * .event.ActionEvent)
2187    */
2188   protected void showConsensusHistogram_actionPerformed()
2189   {
2190     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2191     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192   }
2193
2194   /*
2195    * (non-Javadoc)
2196    *
2197    * @see
2198    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2199    * .event.ActionEvent)
2200    */
2201   protected void showSequenceLogo_actionPerformed()
2202   {
2203     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2204     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2205   }
2206
2207   protected void normSequenceLogo_actionPerformed()
2208   {
2209     showSequenceLogo.setState(true);
2210     viewport.setShowSequenceLogo(true);
2211     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2212     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2213   }
2214
2215   protected void applyAutoAnnotationSettings_actionPerformed()
2216   {
2217     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2218   }
2219
2220   protected void makeGrpsFromSelection_actionPerformed()
2221   {
2222     if (avc.makeGroupsFromSelection())
2223     {
2224       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2225       alignPanel.updateAnnotation();
2226       alignPanel.paintAlignment(true, true);
2227     }
2228   }
2229
2230   protected void createGroup_actionPerformed()
2231   {
2232     avc.createGroup();
2233   }
2234
2235   protected void unGroup_actionPerformed()
2236   {
2237     if (avc.unGroup())
2238     {
2239       alignPanel.alignmentChanged();
2240     }
2241   }
2242
2243   protected void deleteGroups_actionPerformed()
2244   {
2245     if (avc.deleteGroups())
2246     {
2247       alignPanel.alignmentChanged();
2248     }
2249   }
2250
2251   public void selectAllSequenceMenuItem_actionPerformed()
2252   {
2253     SequenceGroup sg = new SequenceGroup();
2254     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2255     {
2256       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2257     }
2258     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2259     viewport.setSelectionGroup(sg);
2260     // JAL-2034 - should delegate to
2261     // alignPanel to decide if overview needs
2262     // updating.
2263     alignPanel.paintAlignment(false, false);
2264     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2265     viewport.sendSelection();
2266   }
2267
2268   public void deselectAllSequenceMenuItem_actionPerformed()
2269   {
2270     if (viewport.cursorMode)
2271     {
2272       alignPanel.seqPanel.keyboardNo1 = null;
2273       alignPanel.seqPanel.keyboardNo2 = null;
2274     }
2275     viewport.setSelectionGroup(null);
2276     viewport.getColumnSelection().clear();
2277     viewport.setSelectionGroup(null);
2278     alignPanel.idPanel.idCanvas.searchResults = null;
2279     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2280     // JAL-2034 - should delegate to
2281     // alignPanel to decide if overview needs
2282     // updating.
2283     alignPanel.paintAlignment(false, false);
2284     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2285     viewport.sendSelection();
2286   }
2287
2288   public void invertSequenceMenuItem_actionPerformed()
2289   {
2290     SequenceGroup sg = viewport.getSelectionGroup();
2291     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2292     {
2293       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2294     }
2295
2296     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2297     viewport.sendSelection();
2298   }
2299
2300   public void invertColSel_actionPerformed()
2301   {
2302     viewport.invertColumnSelection();
2303     alignPanel.paintAlignment(true, false);
2304     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2305     viewport.sendSelection();
2306   }
2307
2308   void trimAlignment(boolean trimLeft)
2309   {
2310     AlignmentI al = viewport.getAlignment();
2311     ViewportRanges ranges = viewport.getRanges();
2312     ColumnSelection colSel = viewport.getColumnSelection();
2313     int column;
2314
2315     if (!colSel.isEmpty())
2316     {
2317       if (trimLeft)
2318       {
2319         column = colSel.getMin();
2320       }
2321       else
2322       {
2323         column = colSel.getMax();
2324       }
2325
2326       SequenceI[] seqs;
2327       if (viewport.getSelectionGroup() != null)
2328       {
2329         seqs = viewport.getSelectionGroup()
2330                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2331       }
2332       else
2333       {
2334         seqs = al.getSequencesArray();
2335       }
2336
2337       TrimRegionCommand trimRegion;
2338       if (trimLeft)
2339       {
2340         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2341                 column, al);
2342         ranges.setStartRes(0);
2343       }
2344       else
2345       {
2346         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2347                 column, al);
2348       }
2349
2350       setStatus(MessageManager
2351               .formatMessage("label.removed_columns", new String[]
2352               { Integer.valueOf(trimRegion.getSize()).toString() }));
2353       addHistoryItem(trimRegion);
2354
2355       for (SequenceGroup sg : al.getGroups())
2356       {
2357         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2358                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2359         {
2360           al.deleteGroup(sg);
2361         }
2362       }
2363
2364       viewport.firePropertyChange("alignment", null, al.getSequences());
2365     }
2366   }
2367
2368   public void removeGappedColumnMenuItem_actionPerformed()
2369   {
2370     AlignmentI al = viewport.getAlignment();
2371     ViewportRanges ranges = viewport.getRanges();
2372     int start = 0;
2373     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2374
2375     SequenceI[] seqs;
2376     if (viewport.getSelectionGroup() != null)
2377     {
2378       seqs = viewport.getSelectionGroup()
2379               .getSequencesAsArray(viewport.getHiddenRepSequences());
2380       start = viewport.getSelectionGroup().getStartRes();
2381       end = viewport.getSelectionGroup().getEndRes();
2382     }
2383     else
2384     {
2385       seqs = viewport.getAlignment().getSequencesArray();
2386     }
2387
2388     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2389             "Remove Gapped Columns", seqs, start, end,
2390             viewport.getAlignment());
2391
2392     addHistoryItem(removeGapCols);
2393
2394     setStatus(MessageManager
2395             .formatMessage("label.removed_empty_columns", new String[]
2396             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2397
2398     // This is to maintain viewport position on first residue
2399     // of first sequence
2400     SequenceI seq = al.getSequenceAt(0);
2401     int startRes = seq.findPosition(ranges.getStartRes());
2402     // ShiftList shifts;
2403     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2404     // edit.alColumnChanges=shifts.getInverse();
2405     // if (viewport.hasHiddenColumns)
2406     // viewport.getColumnSelection().compensateForEdits(shifts);
2407     ranges.setStartRes(seq.findIndex(startRes) - 1);
2408     viewport.firePropertyChange("alignment", null, al.getSequences());
2409
2410   }
2411
2412   public void removeAllGapsMenuItem_actionPerformed()
2413   {
2414     AlignmentI al = viewport.getAlignment();
2415     ViewportRanges ranges = viewport.getRanges();
2416     int start = 0;
2417     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2418
2419     SequenceI[] seqs;
2420     if (viewport.getSelectionGroup() != null)
2421     {
2422       seqs = viewport.getSelectionGroup()
2423               .getSequencesAsArray(viewport.getHiddenRepSequences());
2424       start = viewport.getSelectionGroup().getStartRes();
2425       end = viewport.getSelectionGroup().getEndRes();
2426     }
2427     else
2428     {
2429       seqs = viewport.getAlignment().getSequencesArray();
2430     }
2431
2432     // This is to maintain viewport position on first residue
2433     // of first sequence
2434     SequenceI seq = al.getSequenceAt(0);
2435     int startRes = seq.findPosition(ranges.getStartRes());
2436
2437     addHistoryItem(
2438             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2439
2440     ranges.setStartRes(seq.findIndex(startRes) - 1);
2441
2442     viewport.firePropertyChange("alignment", null, al.getSequences());
2443
2444   }
2445
2446   public void findMenuItem_actionPerformed()
2447   {
2448     new Finder(alignPanel);
2449   }
2450
2451   /**
2452    * create a new view derived from the current view
2453    *
2454    * @param viewtitle
2455    * @return frame for the new view
2456    */
2457   public AlignFrame newView(String viewtitle)
2458   {
2459     AlignmentI newal;
2460     if (viewport.hasHiddenRows())
2461     {
2462       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2463               .getFullAlignment().getSequencesArray());
2464     }
2465     else
2466     {
2467       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2468     }
2469
2470     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2471     {
2472       for (int i = 0; i < viewport.getAlignment()
2473               .getAlignmentAnnotation().length; i++)
2474       {
2475         if (!viewport.getAlignment()
2476                 .getAlignmentAnnotation()[i].autoCalculated)
2477         {
2478           newal.addAnnotation(
2479                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2480         }
2481       }
2482     }
2483
2484     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2485
2486     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2487     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2488     PaintRefresher.Register(newaf.alignPanel,
2489             newaf.alignPanel.av.getSequenceSetId());
2490
2491     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2492             newaf.alignPanel.av.getSequenceSetId());
2493     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2494             newaf.alignPanel.av.getSequenceSetId());
2495
2496     Vector comps = PaintRefresher.components
2497             .get(viewport.getSequenceSetId());
2498     int viewSize = -1;
2499     for (int i = 0; i < comps.size(); i++)
2500     {
2501       if (comps.elementAt(i) instanceof AlignmentPanel)
2502       {
2503         viewSize++;
2504       }
2505     }
2506
2507     String title = new String(this.getTitle());
2508     if (viewtitle != null)
2509     {
2510       title = viewtitle + " ( " + title + ")";
2511     }
2512     else
2513     {
2514       if (title.indexOf("(View") > -1)
2515       {
2516         title = title.substring(0, title.indexOf("(View"));
2517       }
2518       title += "(View " + viewSize + ")";
2519     }
2520
2521     newaf.setTitle(title.toString());
2522
2523     newaf.viewport.setHistoryList(viewport.getHistoryList());
2524     newaf.viewport.setRedoList(viewport.getRedoList());
2525     return newaf;
2526   }
2527
2528   /**
2529    *
2530    * @return list of feature groups on the view
2531    */
2532   public String[] getFeatureGroups()
2533   {
2534     FeatureRenderer fr = null;
2535     if (alignPanel != null
2536             && (fr = alignPanel.getFeatureRenderer()) != null)
2537     {
2538       List<String> gps = fr.getFeatureGroups();
2539       String[] _gps = gps.toArray(new String[gps.size()]);
2540       return _gps;
2541     }
2542     return null;
2543   }
2544
2545   /**
2546    * get sequence feature groups that are hidden or shown
2547    *
2548    * @param visible
2549    *          true is visible
2550    * @return list
2551    */
2552   public String[] getFeatureGroupsOfState(boolean visible)
2553   {
2554     FeatureRenderer fr = null;
2555     if (alignPanel != null
2556             && (fr = alignPanel.getFeatureRenderer()) != null)
2557     {
2558       List<String> gps = fr.getGroups(visible);
2559       String[] _gps = gps.toArray(new String[gps.size()]);
2560       return _gps;
2561     }
2562     return null;
2563   }
2564
2565   /**
2566    * Change the display state for the given feature groups
2567    *
2568    * @param groups
2569    *          list of group strings
2570    * @param state
2571    *          visible or invisible
2572    */
2573   public void setFeatureGroupState(String[] groups, boolean state)
2574   {
2575     FeatureRenderer fr = null;
2576     this.sequenceFeatures.setState(true);
2577     viewport.setShowSequenceFeatures(true);
2578     if (alignPanel != null
2579             && (fr = alignPanel.getFeatureRenderer()) != null)
2580     {
2581
2582       fr.setGroupVisibility(Arrays.asList(groups), state);
2583       alignPanel.seqPanel.seqCanvas.repaint();
2584       if (alignPanel.overviewPanel != null)
2585       {
2586         alignPanel.overviewPanel.updateOverviewImage();
2587       }
2588     }
2589   }
2590
2591   public void seqLimits_itemStateChanged()
2592   {
2593     viewport.setShowJVSuffix(seqLimits.getState());
2594     alignPanel.fontChanged();
2595     alignPanel.paintAlignment(true, false);
2596   }
2597
2598   protected void colourTextMenuItem_actionPerformed()
2599   {
2600     viewport.setColourText(colourTextMenuItem.getState());
2601     alignPanel.paintAlignment(false, false);
2602   }
2603
2604   protected void displayNonconservedMenuItem_actionPerformed()
2605   {
2606     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2607     alignPanel.paintAlignment(false, false);
2608   }
2609
2610   protected void wrapMenuItem_actionPerformed()
2611   {
2612     viewport.setWrapAlignment(wrapMenuItem.getState());
2613     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2614     scaleAbove.setEnabled(wrapMenuItem.getState());
2615     scaleLeft.setEnabled(wrapMenuItem.getState());
2616     scaleRight.setEnabled(wrapMenuItem.getState());
2617     alignPanel.paintAlignment(true, false);
2618   }
2619
2620   public void overviewMenuItem_actionPerformed()
2621   {
2622     if (alignPanel.overviewPanel != null)
2623     {
2624       return;
2625     }
2626
2627     Frame frame = new Frame();
2628     final OverviewPanel overview = new OverviewPanel(alignPanel);
2629     frame.add(overview);
2630     // +50 must allow for applet frame window
2631     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2632             .formatMessage("label.overview_params", new String[]
2633             { this.getTitle() }), overview.getPreferredSize().width,
2634             overview.getPreferredSize().height + 50);
2635
2636     frame.pack();
2637     final AlignmentPanel ap = alignPanel;
2638     frame.addWindowListener(new WindowAdapter()
2639     {
2640       @Override
2641       public void windowClosing(WindowEvent e)
2642       {
2643         overview.dispose();
2644         if (ap != null)
2645         {
2646           ap.setOverviewPanel(null);
2647         }
2648       };
2649     });
2650
2651     alignPanel.setOverviewPanel(overview);
2652
2653   }
2654
2655   @Override
2656   public void changeColour(ColourSchemeI cs)
2657   {
2658     viewport.setGlobalColourScheme(cs);
2659
2660     alignPanel.paintAlignment(true, true);
2661   }
2662
2663   protected void modifyPID_actionPerformed()
2664   {
2665     if (viewport.getAbovePIDThreshold()
2666             && viewport.getGlobalColourScheme() != null)
2667     {
2668       SliderPanel.setPIDSliderSource(alignPanel,
2669               viewport.getResidueShading(), alignPanel.getViewName());
2670       SliderPanel.showPIDSlider();
2671     }
2672   }
2673
2674   protected void modifyConservation_actionPerformed()
2675   {
2676     if (viewport.getConservationSelected()
2677             && viewport.getGlobalColourScheme() != null)
2678     {
2679       SliderPanel.setConservationSlider(alignPanel,
2680               viewport.getResidueShading(), alignPanel.getViewName());
2681       SliderPanel.showConservationSlider();
2682     }
2683   }
2684
2685   protected void conservationMenuItem_actionPerformed()
2686   {
2687     boolean selected = conservationMenuItem.getState();
2688     modifyConservation.setEnabled(selected);
2689     viewport.setConservationSelected(selected);
2690     viewport.getResidueShading().setConservationApplied(selected);
2691
2692     changeColour(viewport.getGlobalColourScheme());
2693
2694     if (selected)
2695     {
2696       modifyConservation_actionPerformed();
2697     }
2698     else
2699     {
2700       SliderPanel.hideConservationSlider();
2701     }
2702   }
2703
2704   public void abovePIDThreshold_actionPerformed()
2705   {
2706     boolean selected = abovePIDThreshold.getState();
2707     modifyPID.setEnabled(selected);
2708     viewport.setAbovePIDThreshold(selected);
2709     if (!selected)
2710     {
2711       viewport.getResidueShading().setThreshold(0,
2712               viewport.isIgnoreGapsConsensus());
2713     }
2714
2715     changeColour(viewport.getGlobalColourScheme());
2716
2717     if (selected)
2718     {
2719       modifyPID_actionPerformed();
2720     }
2721     else
2722     {
2723       SliderPanel.hidePIDSlider();
2724     }
2725   }
2726
2727   public void sortPairwiseMenuItem_actionPerformed()
2728   {
2729     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2730     AlignmentSorter.sortByPID(viewport.getAlignment(),
2731             viewport.getAlignment().getSequenceAt(0));
2732
2733     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2734             viewport.getAlignment()));
2735     alignPanel.paintAlignment(true, false);
2736   }
2737
2738   public void sortIDMenuItem_actionPerformed()
2739   {
2740     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741     AlignmentSorter.sortByID(viewport.getAlignment());
2742     addHistoryItem(
2743             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2744     alignPanel.paintAlignment(true, false);
2745   }
2746
2747   public void sortLengthMenuItem_actionPerformed()
2748   {
2749     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2750     AlignmentSorter.sortByLength(viewport.getAlignment());
2751     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2752             viewport.getAlignment()));
2753     alignPanel.paintAlignment(true, false);
2754   }
2755
2756   public void sortGroupMenuItem_actionPerformed()
2757   {
2758     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2759     AlignmentSorter.sortByGroup(viewport.getAlignment());
2760     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2761             viewport.getAlignment()));
2762     alignPanel.paintAlignment(true, false);
2763
2764   }
2765
2766   public void removeRedundancyMenuItem_actionPerformed()
2767   {
2768     new RedundancyPanel(alignPanel);
2769   }
2770
2771   public void pairwiseAlignmentMenuItem_actionPerformed()
2772   {
2773     if (viewport.getSelectionGroup() != null
2774             && viewport.getSelectionGroup().getSize() > 1)
2775     {
2776       Frame frame = new Frame();
2777       frame.add(new PairwiseAlignPanel(alignPanel));
2778       jalview.bin.JalviewLite.addFrame(frame,
2779               MessageManager.getString("action.pairwise_alignment"), 600,
2780               500);
2781     }
2782   }
2783
2784   public void PCAMenuItem_actionPerformed()
2785   {
2786     // are the sequences aligned?
2787     if (!viewport.getAlignment().isAligned(false))
2788     {
2789       SequenceI current;
2790       int Width = viewport.getAlignment().getWidth();
2791
2792       for (int i = 0; i < viewport.getAlignment().getSequences()
2793               .size(); i++)
2794       {
2795         current = viewport.getAlignment().getSequenceAt(i);
2796
2797         if (current.getLength() < Width)
2798         {
2799           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2800         }
2801       }
2802       alignPanel.paintAlignment(false, false);
2803     }
2804
2805     if ((viewport.getSelectionGroup() != null
2806             && viewport.getSelectionGroup().getSize() < 4
2807             && viewport.getSelectionGroup().getSize() > 0)
2808             || viewport.getAlignment().getHeight() < 4)
2809     {
2810       return;
2811     }
2812
2813     try
2814     {
2815       new PCAPanel(viewport);
2816     } catch (java.lang.OutOfMemoryError ex)
2817     {
2818     }
2819
2820   }
2821
2822   public void averageDistanceTreeMenuItem_actionPerformed()
2823   {
2824     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2825             "Average distance tree using PID");
2826   }
2827
2828   public void neighbourTreeMenuItem_actionPerformed()
2829   {
2830     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2831             "Neighbour joining tree using PID");
2832   }
2833
2834   protected void njTreeBlosumMenuItem_actionPerformed()
2835   {
2836     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2837             ScoreModels.getInstance().getBlosum62().getName(),
2838             "Neighbour joining tree using BLOSUM62");
2839   }
2840
2841   protected void avTreeBlosumMenuItem_actionPerformed()
2842   {
2843     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2844             ScoreModels.getInstance().getBlosum62().getName(),
2845             "Average distance tree using BLOSUM62");
2846   }
2847
2848   void newTreePanel(String type, String pwType, String title)
2849   {
2850     // are the sequences aligned?
2851     if (!viewport.getAlignment().isAligned(false))
2852     {
2853       SequenceI current;
2854       int Width = viewport.getAlignment().getWidth();
2855
2856       for (int i = 0; i < viewport.getAlignment().getSequences()
2857               .size(); i++)
2858       {
2859         current = viewport.getAlignment().getSequenceAt(i);
2860
2861         if (current.getLength() < Width)
2862         {
2863           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2864         }
2865       }
2866       alignPanel.paintAlignment(false, false);
2867
2868     }
2869
2870     if ((viewport.getSelectionGroup() != null
2871             && viewport.getSelectionGroup().getSize() > 1)
2872             || (viewport.getAlignment().getHeight() > 1))
2873     {
2874       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2875
2876       addTreeMenuItem(tp, title);
2877
2878       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2879     }
2880   }
2881
2882   void loadTree_actionPerformed()
2883   {
2884     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2885     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2886     cap.setTreeImport();
2887     Frame frame = new Frame();
2888     frame.add(cap);
2889     jalview.bin.JalviewLite.addFrame(frame,
2890             MessageManager.getString("label.paste_newick_file"), 400, 300);
2891   }
2892
2893   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2894   {
2895     TreePanel tp = new TreePanel(alignPanel, treeFile,
2896             MessageManager.getString("label.load_tree_from_file"), tree);
2897     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2898     addTreeMenuItem(tp, treeFile);
2899   }
2900
2901   /**
2902    * sort the alignment using the given treePanel
2903    *
2904    * @param treePanel
2905    *          tree used to sort view
2906    * @param title
2907    *          string used for undo event name
2908    */
2909   public void sortByTree(TreePanel treePanel, String title)
2910   {
2911     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2912     AlignmentSorter.sortByTree(viewport.getAlignment(),
2913             treePanel.getTree());
2914     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2915     // HistoryItem.SORT));
2916     addHistoryItem(new OrderCommand(MessageManager
2917             .formatMessage("label.order_by_params", new String[]
2918             { title }), oldOrder, viewport.getAlignment()));
2919     alignPanel.paintAlignment(true, false);
2920   }
2921
2922   /**
2923    * Do any automatic reordering of the alignment and add the necessary bits to
2924    * the menu structure for the new tree
2925    *
2926    * @param treePanel
2927    * @param title
2928    */
2929   protected void addTreeMenuItem(final TreePanel treePanel,
2930           final String title)
2931   {
2932     final MenuItem item = new MenuItem(title);
2933     sortByTreeMenu.add(item);
2934     item.addActionListener(new java.awt.event.ActionListener()
2935     {
2936       @Override
2937       public void actionPerformed(ActionEvent evt)
2938       {
2939         sortByTree(treePanel, title); // treePanel.getTitle());
2940       }
2941     });
2942
2943     treePanel.addWindowListener(new WindowAdapter()
2944     {
2945       @Override
2946       public void windowOpened(WindowEvent e)
2947       {
2948         if (viewport.sortByTree)
2949         {
2950           sortByTree(treePanel, title);
2951         }
2952         super.windowOpened(e);
2953       }
2954
2955       @Override
2956       public void windowClosing(WindowEvent e)
2957       {
2958         sortByTreeMenu.remove(item);
2959       };
2960     });
2961   }
2962
2963   public boolean sortBy(AlignmentOrder alorder, String undoname)
2964   {
2965     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2966     if (viewport.applet.debug)
2967     {
2968       System.err.println("Sorting " + alorder.getOrder().size()
2969               + " in alignment '" + getTitle() + "'");
2970     }
2971     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2972     if (undoname != null)
2973     {
2974       addHistoryItem(new OrderCommand(undoname, oldOrder,
2975               viewport.getAlignment()));
2976     }
2977     alignPanel.paintAlignment(true, false);
2978     return true;
2979   }
2980
2981   protected void documentation_actionPerformed()
2982   {
2983     alignPanel.av.applet.openJalviewHelpUrl();
2984   }
2985
2986   protected void about_actionPerformed()
2987   {
2988
2989     class AboutPanel extends Canvas
2990     {
2991       String version;
2992
2993       String builddate;
2994
2995       public AboutPanel(String version, String builddate)
2996       {
2997         this.version = version;
2998         this.builddate = builddate;
2999       }
3000
3001       @Override
3002       public void paint(Graphics g)
3003       {
3004         g.setColor(Color.white);
3005         g.fillRect(0, 0, getSize().width, getSize().height);
3006         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3007         FontMetrics fm = g.getFontMetrics();
3008         int fh = fm.getHeight();
3009         int y = 5, x = 7;
3010         g.setColor(Color.black);
3011         // TODO: update this text for each release or centrally store it for
3012         // lite and application
3013         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3014         g.drawString(MessageManager
3015                 .formatMessage("label.jalviewLite_release", new String[]
3016                 { version }), x, y += fh);
3017         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3018         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3019                 new String[]
3020                 { builddate }), x, y += fh);
3021         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3022         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3023                 y += fh * 1.5);
3024         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3025                 x + 50, y += fh + 8);
3026         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3027                 x, y += fh);
3028         g.drawString(MessageManager
3029                 .getString("label.jalview_distribution_lists"), x, y += fh);
3030         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3031                 x, y += fh + 8);
3032         g.drawString(
3033                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3034                 y += fh);
3035         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3036                 x, y += fh);
3037         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3038                 x, y += fh);
3039       }
3040     }
3041
3042     Frame frame = new Frame();
3043     frame.add(new AboutPanel(JalviewLite.getVersion(),
3044             JalviewLite.getBuildDate()));
3045     jalview.bin.JalviewLite.addFrame(frame,
3046             MessageManager.getString("label.jalview"), 580, 220);
3047
3048   }
3049
3050   public void showURL(String url, String target)
3051   {
3052     if (viewport.applet == null)
3053     {
3054       System.out.println("Not running as applet - no browser available.");
3055     }
3056     else
3057     {
3058       viewport.applet.showURL(url, target);
3059     }
3060   }
3061
3062   // ////////////////////////////////////////////////////////////////////////////////
3063   // JBuilder Graphics here
3064
3065   MenuBar alignFrameMenuBar = new MenuBar();
3066
3067   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3068
3069   MenuItem loadApplication = new MenuItem(
3070           MessageManager.getString("label.view_full_application"));
3071
3072   MenuItem loadTree = new MenuItem(
3073           MessageManager.getString("label.load_associated_tree"));
3074
3075   MenuItem loadAnnotations = new MenuItem(
3076           MessageManager.getString("label.load_features_annotations"));
3077
3078   MenuItem outputFeatures = new MenuItem(
3079           MessageManager.getString("label.export_features"));
3080
3081   MenuItem outputAnnotations = new MenuItem(
3082           MessageManager.getString("label.export_annotations"));
3083
3084   MenuItem closeMenuItem = new MenuItem(
3085           MessageManager.getString("action.close"));
3086
3087   MenuItem selectAllSequenceMenuItem = new MenuItem(
3088           MessageManager.getString("action.select_all"));
3089
3090   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3091           MessageManager.getString("action.deselect_all"));
3092
3093   MenuItem invertSequenceMenuItem = new MenuItem(
3094           MessageManager.getString("action.invert_selection"));
3095
3096   MenuItem remove2LeftMenuItem = new MenuItem();
3097
3098   MenuItem remove2RightMenuItem = new MenuItem();
3099
3100   MenuItem removeGappedColumnMenuItem = new MenuItem();
3101
3102   MenuItem removeAllGapsMenuItem = new MenuItem();
3103
3104   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3105
3106   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3107
3108   MenuItem sortPairwiseMenuItem = new MenuItem();
3109
3110   MenuItem sortIDMenuItem = new MenuItem();
3111
3112   MenuItem sortLengthMenuItem = new MenuItem();
3113
3114   MenuItem sortGroupMenuItem = new MenuItem();
3115
3116   MenuItem removeRedundancyMenuItem = new MenuItem();
3117
3118   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3119
3120   MenuItem PCAMenuItem = new MenuItem();
3121
3122   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3123
3124   MenuItem neighbourTreeMenuItem = new MenuItem();
3125
3126   BorderLayout borderLayout1 = new BorderLayout();
3127
3128   public Label statusBar = new Label();
3129
3130   MenuItem clustalColour = new MenuItem();
3131
3132   MenuItem zappoColour = new MenuItem();
3133
3134   MenuItem taylorColour = new MenuItem();
3135
3136   MenuItem hydrophobicityColour = new MenuItem();
3137
3138   MenuItem helixColour = new MenuItem();
3139
3140   MenuItem strandColour = new MenuItem();
3141
3142   MenuItem turnColour = new MenuItem();
3143
3144   MenuItem buriedColour = new MenuItem();
3145
3146   MenuItem purinePyrimidineColour = new MenuItem();
3147
3148   // MenuItem RNAInteractionColour = new MenuItem();
3149
3150   MenuItem RNAHelixColour = new MenuItem();
3151
3152   MenuItem userDefinedColour = new MenuItem();
3153
3154   MenuItem PIDColour = new MenuItem();
3155
3156   MenuItem BLOSUM62Colour = new MenuItem();
3157
3158   MenuItem tcoffeeColour = new MenuItem();
3159
3160   MenuItem njTreeBlosumMenuItem = new MenuItem();
3161
3162   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3163
3164   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3165
3166   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3167
3168   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3169
3170   MenuItem alProperties = new MenuItem(
3171           MessageManager.getString("label.alignment_props"));
3172
3173   MenuItem overviewMenuItem = new MenuItem();
3174
3175   MenuItem undoMenuItem = new MenuItem();
3176
3177   MenuItem redoMenuItem = new MenuItem();
3178
3179   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3180
3181   MenuItem noColourmenuItem = new MenuItem();
3182
3183   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3184
3185   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3186
3187   MenuItem findMenuItem = new MenuItem();
3188
3189   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3190
3191   MenuItem nucleotideColour = new MenuItem();
3192
3193   MenuItem deleteGroups = new MenuItem();
3194
3195   MenuItem grpsFromSelection = new MenuItem();
3196
3197   MenuItem createGroup = new MenuItem();
3198
3199   MenuItem unGroup = new MenuItem();
3200
3201   MenuItem delete = new MenuItem();
3202
3203   MenuItem copy = new MenuItem();
3204
3205   MenuItem cut = new MenuItem();
3206
3207   Menu pasteMenu = new Menu();
3208
3209   MenuItem pasteNew = new MenuItem();
3210
3211   MenuItem pasteThis = new MenuItem();
3212
3213   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3214
3215   MenuItem font = new MenuItem();
3216
3217   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3222
3223   MenuItem modifyPID = new MenuItem();
3224
3225   MenuItem modifyConservation = new MenuItem();
3226
3227   CheckboxMenuItem autoCalculate = null;
3228
3229   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3230           "Sort Alignment With New Tree", true);
3231
3232   Menu sortByTreeMenu = new Menu();
3233
3234   MenuItem inputText = new MenuItem();
3235
3236   MenuItem documentation = new MenuItem();
3237
3238   MenuItem about = new MenuItem();
3239
3240   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3253
3254   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3255
3256   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3257
3258   /**
3259    * Initialise menus and other items
3260    *
3261    * @throws Exception
3262    */
3263   private void jbInit() throws Exception
3264   {
3265     setMenuBar(alignFrameMenuBar);
3266
3267     /*
3268      * Configure File menu items and actions
3269      */
3270     inputText
3271             .setLabel(MessageManager.getString("label.input_from_textbox"));
3272     inputText.addActionListener(this);
3273     Menu outputTextboxMenu = new Menu(
3274             MessageManager.getString("label.out_to_textbox"));
3275     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3276     {
3277       MenuItem item = new MenuItem(ff);
3278
3279       item.addActionListener(new java.awt.event.ActionListener()
3280       {
3281         @Override
3282         public void actionPerformed(ActionEvent e)
3283         {
3284           outputText_actionPerformed(e);
3285         }
3286       });
3287
3288       outputTextboxMenu.add(item);
3289     }
3290     closeMenuItem.addActionListener(this);
3291     loadApplication.addActionListener(this);
3292     loadTree.addActionListener(this);
3293     loadAnnotations.addActionListener(this);
3294     outputFeatures.addActionListener(this);
3295     outputAnnotations.addActionListener(this);
3296
3297     /*
3298      * Configure Edit menu items and actions
3299      */
3300     undoMenuItem.setEnabled(false);
3301     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3302     undoMenuItem.addActionListener(this);
3303     redoMenuItem.setEnabled(false);
3304     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3305     redoMenuItem.addActionListener(this);
3306     copy.setLabel(MessageManager.getString("action.copy"));
3307     copy.addActionListener(this);
3308     cut.setLabel(MessageManager.getString("action.cut"));
3309     cut.addActionListener(this);
3310     delete.setLabel(MessageManager.getString("action.delete"));
3311     delete.addActionListener(this);
3312     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3313     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3314     pasteNew.addActionListener(this);
3315     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3316     pasteThis.addActionListener(this);
3317     remove2LeftMenuItem
3318             .setLabel(MessageManager.getString("action.remove_left"));
3319     remove2LeftMenuItem.addActionListener(this);
3320     remove2RightMenuItem
3321             .setLabel(MessageManager.getString("action.remove_right"));
3322     remove2RightMenuItem.addActionListener(this);
3323     removeGappedColumnMenuItem.setLabel(
3324             MessageManager.getString("action.remove_empty_columns"));
3325     removeGappedColumnMenuItem.addActionListener(this);
3326     removeAllGapsMenuItem
3327             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3328     removeAllGapsMenuItem.addActionListener(this);
3329     removeRedundancyMenuItem
3330             .setLabel(MessageManager.getString("action.remove_redundancy"));
3331     removeRedundancyMenuItem.addActionListener(this);
3332
3333     /*
3334      * Configure Select menu items and actions
3335      */
3336     findMenuItem.setLabel(MessageManager.getString("action.find"));
3337     findMenuItem.addActionListener(this);
3338     selectAllSequenceMenuItem.addActionListener(this);
3339     deselectAllSequenceMenuItem.addActionListener(this);
3340     invertSequenceMenuItem.setLabel(
3341             MessageManager.getString("action.invert_sequence_selection"));
3342     invertSequenceMenuItem.addActionListener(this);
3343     invertColSel.setLabel(
3344             MessageManager.getString("action.invert_column_selection"));
3345     invertColSel.addActionListener(this);
3346     deleteGroups
3347             .setLabel(MessageManager.getString("action.undefine_groups"));
3348     deleteGroups.addActionListener(this);
3349     grpsFromSelection.setLabel(
3350             MessageManager.getString("action.make_groups_selection"));
3351     grpsFromSelection.addActionListener(this);
3352     createGroup.setLabel(MessageManager.getString("action.create_group"));
3353     createGroup.addActionListener(this);
3354     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3355     unGroup.addActionListener(this);
3356
3357     annotationColumnSelection.setLabel(
3358             MessageManager.getString("action.select_by_annotation"));
3359     annotationColumnSelection.addActionListener(this);
3360
3361     /*
3362      * Configure View menu items and actions
3363      */
3364     newView.setLabel(MessageManager.getString("action.new_view"));
3365     newView.addActionListener(this);
3366     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3367     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3368     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3369     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3370     hideColumns
3371             .setLabel(MessageManager.getString("label.selected_columns"));
3372     hideSequences
3373             .setLabel(MessageManager.getString("label.selected_sequences"));
3374     hideAllButSelection.setLabel(
3375             MessageManager.getString("label.all_but_selected_region"));
3376     hideAllSelection
3377             .setLabel(MessageManager.getString("label.selected_region"));
3378     showAllHidden.setLabel(
3379             MessageManager.getString("label.all_sequences_columns"));
3380     showColumns.addActionListener(this);
3381     showSeqs.addActionListener(this);
3382     hideColumns.addActionListener(this);
3383     hideSequences.addActionListener(this);
3384     hideAllButSelection.addActionListener(this);
3385     hideAllSelection.addActionListener(this);
3386     showAllHidden.addActionListener(this);
3387     featureSettings
3388             .setLabel(MessageManager.getString("action.feature_settings"));
3389     featureSettings.addActionListener(this);
3390     sequenceFeatures.setLabel(
3391             MessageManager.getString("label.show_sequence_features"));
3392     sequenceFeatures.addItemListener(this);
3393     sequenceFeatures.setState(false);
3394     followMouseOverFlag.setLabel(
3395             MessageManager.getString("label.automatic_scrolling"));
3396     followMouseOverFlag.addItemListener(this);
3397     alProperties.addActionListener(this);
3398     overviewMenuItem
3399             .setLabel(MessageManager.getString("label.overview_window"));
3400     overviewMenuItem.addActionListener(this);
3401
3402     /*
3403      * Configure Annotations menu items and actions
3404      */
3405     annotationPanelMenuItem
3406             .setLabel(MessageManager.getString("label.show_annotations"));
3407     annotationPanelMenuItem.addItemListener(this);
3408     showGroupConsensus
3409             .setLabel(MessageManager.getString("label.group_consensus"));
3410     showGroupConservation
3411             .setLabel(MessageManager.getString("label.group_conservation"));
3412     showConsensusHistogram.setLabel(
3413             MessageManager.getString("label.show_consensus_histogram"));
3414     showSequenceLogo.setLabel(
3415             MessageManager.getString("label.show_consensus_logo"));
3416     normSequenceLogo.setLabel(
3417             MessageManager.getString("label.norm_consensus_logo"));
3418     applyAutoAnnotationSettings
3419             .setLabel(MessageManager.getString("label.apply_all_groups"));
3420     applyAutoAnnotationSettings.setState(true);
3421     Menu autoAnnMenu = new Menu(
3422             MessageManager.getString("label.autocalculated_annotation"));
3423     showGroupConsensus.addItemListener(this);
3424     showGroupConservation.addItemListener(this);
3425     showConsensusHistogram.addItemListener(this);
3426     showSequenceLogo.addItemListener(this);
3427     normSequenceLogo.addItemListener(this);
3428     applyAutoAnnotationSettings.addItemListener(this);
3429     showAlignmentAnnotations = new CheckboxMenuItem(
3430             MessageManager.getString("label.show_all_al_annotations"));
3431     showSequenceAnnotations = new CheckboxMenuItem(
3432             MessageManager.getString("label.show_all_seq_annotations"));
3433     sortAnnBySequence = new CheckboxMenuItem(
3434             MessageManager.getString("label.sort_annotations_by_sequence"));
3435     sortAnnByLabel = new CheckboxMenuItem(
3436             MessageManager.getString("label.sort_annotations_by_label"));
3437     showAutoFirst = new CheckboxMenuItem(
3438             MessageManager.getString("label.show_first"));
3439     showAutoFirst.setState(false); // pending applet parameter
3440     setShowAutoCalculatedAbove(showAutoFirst.getState());
3441     showAutoLast = new CheckboxMenuItem(
3442             MessageManager.getString("label.show_last"));
3443     showAutoLast.setState(!showAutoFirst.getState());
3444     showAlignmentAnnotations.addItemListener(this);
3445     showSequenceAnnotations.addItemListener(this);
3446     sortAnnBySequence.addItemListener(this);
3447     sortAnnByLabel.addItemListener(this);
3448     showAutoFirst.addItemListener(this);
3449     showAutoLast.addItemListener(this);
3450
3451     /*
3452      * Configure Format menu items and actions
3453      */
3454     font.setLabel(MessageManager.getString("action.font"));
3455     font.addActionListener(this);
3456     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3457     scaleAbove.setState(true);
3458     scaleAbove.setEnabled(false);
3459     scaleAbove.addItemListener(this);
3460     scaleLeft.setEnabled(false);
3461     scaleLeft.setState(true);
3462     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3463     scaleLeft.addItemListener(this);
3464     scaleRight.setEnabled(false);
3465     scaleRight.setState(true);
3466     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3467     scaleRight.addItemListener(this);
3468     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3469     viewBoxesMenuItem.setState(true);
3470     viewBoxesMenuItem.addItemListener(this);
3471     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3472     viewTextMenuItem.setState(true);
3473     viewTextMenuItem.addItemListener(this);
3474     colourTextMenuItem
3475             .setLabel(MessageManager.getString("label.colour_text"));
3476     colourTextMenuItem.addItemListener(this);
3477     displayNonconservedMenuItem
3478             .setLabel(MessageManager.getString("label.show_non_conserved"));
3479     displayNonconservedMenuItem.addItemListener(this);
3480     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3481     wrapMenuItem.addItemListener(this);
3482     renderGapsMenuItem
3483             .setLabel(MessageManager.getString("action.show_gaps"));
3484     renderGapsMenuItem.setState(true);
3485     renderGapsMenuItem.addItemListener(this);
3486     centreColumnLabelFlag.setLabel(
3487             MessageManager.getString("label.centre_column_labels"));
3488     centreColumnLabelFlag.addItemListener(this);
3489     seqLimits.setState(true);
3490     seqLimits.setLabel(
3491             MessageManager.getString("label.show_sequence_limits"));
3492     seqLimits.addItemListener(this);
3493
3494     /*
3495      * Configure Colour menu items and actions
3496      */
3497     applyToAllGroups.setLabel(
3498             MessageManager.getString("label.apply_colour_to_all_groups"));
3499     applyToAllGroups.setState(true);
3500     applyToAllGroups.addItemListener(this);
3501     clustalColour.setLabel(
3502             MessageManager.getString("label.colourScheme_clustal"));
3503     clustalColour.addActionListener(this);
3504     zappoColour
3505             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3506     zappoColour.addActionListener(this);
3507     taylorColour.setLabel(
3508             MessageManager.getString("label.colourScheme_taylor"));
3509     taylorColour.addActionListener(this);
3510     hydrophobicityColour.setLabel(
3511             MessageManager.getString("label.colourScheme_hydrophobic"));
3512     hydrophobicityColour.addActionListener(this);
3513     helixColour.setLabel(MessageManager
3514             .getString("label.colourScheme_helix_propensity"));
3515     helixColour.addActionListener(this);
3516     strandColour.setLabel(MessageManager
3517             .getString("label.colourScheme_strand_propensity"));
3518     strandColour.addActionListener(this);
3519     turnColour.setLabel(
3520             MessageManager.getString("label.colourScheme_turn_propensity"));
3521     turnColour.addActionListener(this);
3522     buriedColour.setLabel(
3523             MessageManager.getString("label.colourScheme_buried_index"));
3524     buriedColour.addActionListener(this);
3525     purinePyrimidineColour.setLabel(MessageManager
3526             .getString("label.colourScheme_purine/pyrimidine"));
3527     purinePyrimidineColour.addActionListener(this);
3528     // RNAInteractionColour.setLabel(MessageManager
3529     // .getString("label.rna_interaction"));
3530     // RNAInteractionColour.addActionListener(this);
3531     RNAHelixColour.setLabel(
3532             MessageManager.getString("label.colourScheme_rna_helices"));
3533     RNAHelixColour.addActionListener(this);
3534     userDefinedColour
3535             .setLabel(MessageManager.getString("action.user_defined"));
3536     userDefinedColour.addActionListener(this);
3537     PIDColour.setLabel(
3538             MessageManager.getString("label.colourScheme_%_identity"));
3539     PIDColour.addActionListener(this);
3540     BLOSUM62Colour.setLabel(
3541             MessageManager.getString("label.colourScheme_blosum62"));
3542     BLOSUM62Colour.addActionListener(this);
3543     tcoffeeColour.setLabel(
3544             MessageManager.getString("label.colourScheme_t-coffee_scores"));
3545     // it will be enabled only if a score file is provided
3546     tcoffeeColour.setEnabled(false);
3547     tcoffeeColour.addActionListener(this);
3548     conservationMenuItem
3549             .setLabel(MessageManager.getString("action.by_conservation"));
3550     conservationMenuItem.addItemListener(this);
3551     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3552     noColourmenuItem.addActionListener(this);
3553     abovePIDThreshold.setLabel(
3554             MessageManager.getString("label.above_identity_threshold"));
3555     abovePIDThreshold.addItemListener(this);
3556     nucleotideColour.setLabel(
3557             MessageManager.getString("label.colourScheme_nucleotide"));
3558     nucleotideColour.addActionListener(this);
3559     modifyPID.setLabel(
3560             MessageManager.getString("label.modify_identity_threshold"));
3561     modifyPID.setEnabled(abovePIDThreshold.getState());
3562     modifyPID.addActionListener(this);
3563     modifyConservation.setLabel(MessageManager
3564             .getString("label.modify_conservation_threshold"));
3565     modifyConservation.setEnabled(conservationMenuItem.getState());
3566     modifyConservation.addActionListener(this);
3567     annotationColour
3568             .setLabel(MessageManager.getString("action.by_annotation"));
3569     annotationColour.addActionListener(this);
3570
3571     /*
3572      * Configure Calculate menu items and actions
3573      */
3574     sortPairwiseMenuItem
3575             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3576     sortPairwiseMenuItem.addActionListener(this);
3577     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3578     sortIDMenuItem.addActionListener(this);
3579     sortLengthMenuItem
3580             .setLabel(MessageManager.getString("action.by_length"));
3581     sortLengthMenuItem.addActionListener(this);
3582     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3583     sortGroupMenuItem.addActionListener(this);
3584     pairwiseAlignmentMenuItem.setLabel(
3585             MessageManager.getString("action.pairwise_alignment"));
3586     pairwiseAlignmentMenuItem.addActionListener(this);
3587     PCAMenuItem.setLabel(
3588             MessageManager.getString("label.principal_component_analysis"));
3589     PCAMenuItem.addActionListener(this);
3590     autoCalculate = new CheckboxMenuItem(
3591             MessageManager.getString("label.autocalculate_consensus"),
3592             true);
3593     averageDistanceTreeMenuItem.setLabel(
3594             MessageManager.getString("label.average_distance_identity"));
3595     averageDistanceTreeMenuItem.addActionListener(this);
3596     neighbourTreeMenuItem.setLabel(
3597             MessageManager.getString("label.neighbour_joining_identity"));
3598     neighbourTreeMenuItem.addActionListener(this);
3599     avDistanceTreeBlosumMenuItem.setLabel(
3600             MessageManager.getString("label.average_distance_blosum62"));
3601     avDistanceTreeBlosumMenuItem.addActionListener(this);
3602     njTreeBlosumMenuItem
3603             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3604     njTreeBlosumMenuItem.addActionListener(this);
3605     sortByTreeMenu
3606             .setLabel(MessageManager.getString("action.by_tree_order"));
3607     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3608     Menu calculateTreeMenu = new Menu(
3609             MessageManager.getString("action.calculate_tree"));
3610     autoCalculate.addItemListener(this);
3611     sortByTree.addItemListener(this);
3612
3613     /*
3614      * Configure Help menu items and actions
3615      */
3616     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3617     documentation.setLabel(MessageManager.getString("label.documentation"));
3618     documentation.addActionListener(this);
3619     about.setLabel(MessageManager.getString("label.about"));
3620     about.addActionListener(this);
3621
3622     /*
3623      * Add top level menus to frame
3624      */
3625     alignFrameMenuBar.add(fileMenu);
3626     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3627     alignFrameMenuBar.add(editMenu);
3628     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3629     alignFrameMenuBar.add(selectMenu);
3630     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3631     alignFrameMenuBar.add(viewMenu);
3632     Menu annotationsMenu = new Menu(
3633             MessageManager.getString("action.annotations"));
3634     alignFrameMenuBar.add(annotationsMenu);
3635     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3636     alignFrameMenuBar.add(formatMenu);
3637     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3638     alignFrameMenuBar.add(colourMenu);
3639     Menu calculateMenu = new Menu(
3640             MessageManager.getString("action.calculate"));
3641     alignFrameMenuBar.add(calculateMenu);
3642     alignFrameMenuBar.add(helpMenu);
3643
3644     /*
3645      * File menu
3646      */
3647     fileMenu.add(inputText);
3648     fileMenu.add(loadTree);
3649     fileMenu.add(loadAnnotations);
3650     fileMenu.addSeparator();
3651     fileMenu.add(outputTextboxMenu);
3652     fileMenu.add(outputFeatures);
3653     fileMenu.add(outputAnnotations);
3654     if (jalviewServletURL != null)
3655     {
3656       fileMenu.add(loadApplication);
3657     }
3658     fileMenu.addSeparator();
3659     fileMenu.add(closeMenuItem);
3660
3661     /*
3662      * Edit menu
3663      */
3664     editMenu.add(undoMenuItem);
3665     editMenu.add(redoMenuItem);
3666     editMenu.add(cut);
3667     editMenu.add(copy);
3668     pasteMenu.add(pasteNew);
3669     pasteMenu.add(pasteThis);
3670     editMenu.add(pasteMenu);
3671     editMenu.add(delete);
3672     editMenu.addSeparator();
3673     editMenu.add(remove2LeftMenuItem);
3674     editMenu.add(remove2RightMenuItem);
3675     editMenu.add(removeGappedColumnMenuItem);
3676     editMenu.add(removeAllGapsMenuItem);
3677     editMenu.add(removeRedundancyMenuItem);
3678
3679     /*
3680      * Select menu
3681      */
3682     selectMenu.add(findMenuItem);
3683     selectMenu.addSeparator();
3684     selectMenu.add(selectAllSequenceMenuItem);
3685     selectMenu.add(deselectAllSequenceMenuItem);
3686     selectMenu.add(invertSequenceMenuItem);
3687     selectMenu.add(invertColSel);
3688     selectMenu.add(createGroup);
3689     selectMenu.add(unGroup);
3690     selectMenu.add(grpsFromSelection);
3691     selectMenu.add(deleteGroups);
3692     selectMenu.add(annotationColumnSelection);
3693
3694     /*
3695      * View menu
3696      */
3697     viewMenu.add(newView);
3698     viewMenu.addSeparator();
3699     showMenu.add(showColumns);
3700     showMenu.add(showSeqs);
3701     showMenu.add(showAllHidden);
3702     viewMenu.add(showMenu);
3703     hideMenu.add(hideColumns);
3704     hideMenu.add(hideSequences);
3705     hideMenu.add(hideAllSelection);
3706     hideMenu.add(hideAllButSelection);
3707     viewMenu.add(hideMenu);
3708     viewMenu.addSeparator();
3709     viewMenu.add(followMouseOverFlag);
3710     viewMenu.addSeparator();
3711     viewMenu.add(sequenceFeatures);
3712     viewMenu.add(featureSettings);
3713     viewMenu.addSeparator();
3714     viewMenu.add(alProperties);
3715     viewMenu.addSeparator();
3716     viewMenu.add(overviewMenuItem);
3717
3718     /*
3719      * Annotations menu
3720      */
3721     annotationsMenu.add(annotationPanelMenuItem);
3722     annotationsMenu.addSeparator();
3723     annotationsMenu.add(showAlignmentAnnotations);
3724     annotationsMenu.add(showSequenceAnnotations);
3725     annotationsMenu.add(sortAnnBySequence);
3726     annotationsMenu.add(sortAnnByLabel);
3727     annotationsMenu.addSeparator();
3728     autoAnnMenu.add(showAutoFirst);
3729     autoAnnMenu.add(showAutoLast);
3730     autoAnnMenu.addSeparator();
3731     autoAnnMenu.add(applyAutoAnnotationSettings);
3732     autoAnnMenu.add(showConsensusHistogram);
3733     autoAnnMenu.add(showSequenceLogo);
3734     autoAnnMenu.add(normSequenceLogo);
3735     autoAnnMenu.addSeparator();
3736     autoAnnMenu.add(showGroupConservation);
3737     autoAnnMenu.add(showGroupConsensus);
3738     annotationsMenu.add(autoAnnMenu);
3739
3740     /*
3741      * Format menu
3742      */
3743     formatMenu.add(font);
3744     formatMenu.add(seqLimits);
3745     formatMenu.add(wrapMenuItem);
3746     formatMenu.add(scaleAbove);
3747     formatMenu.add(scaleLeft);
3748     formatMenu.add(scaleRight);
3749     formatMenu.add(viewBoxesMenuItem);
3750     formatMenu.add(viewTextMenuItem);
3751     formatMenu.add(colourTextMenuItem);
3752     formatMenu.add(displayNonconservedMenuItem);
3753     formatMenu.add(renderGapsMenuItem);
3754     formatMenu.add(centreColumnLabelFlag);
3755
3756     /*
3757      * Colour menu
3758      */
3759     colourMenu.add(applyToAllGroups);
3760     colourMenu.addSeparator();
3761     colourMenu.add(noColourmenuItem);
3762     colourMenu.add(clustalColour);
3763     colourMenu.add(BLOSUM62Colour);
3764     colourMenu.add(PIDColour);
3765     colourMenu.add(zappoColour);
3766     colourMenu.add(taylorColour);
3767     colourMenu.add(hydrophobicityColour);
3768     colourMenu.add(helixColour);
3769     colourMenu.add(strandColour);
3770     colourMenu.add(turnColour);
3771     colourMenu.add(buriedColour);
3772     colourMenu.add(nucleotideColour);
3773     colourMenu.add(purinePyrimidineColour);
3774     // colourMenu.add(RNAInteractionColour);
3775     colourMenu.add(tcoffeeColour);
3776     colourMenu.add(userDefinedColour);
3777     colourMenu.addSeparator();
3778     colourMenu.add(conservationMenuItem);
3779     colourMenu.add(modifyConservation);
3780     colourMenu.add(abovePIDThreshold);
3781     colourMenu.add(modifyPID);
3782     colourMenu.add(annotationColour);
3783     colourMenu.add(RNAHelixColour);
3784
3785     /*
3786      * Calculate menu
3787      */
3788     sortMenu.add(sortIDMenuItem);
3789     sortMenu.add(sortLengthMenuItem);
3790     sortMenu.add(sortByTreeMenu);
3791     sortMenu.add(sortGroupMenuItem);
3792     sortMenu.add(sortPairwiseMenuItem);
3793     calculateMenu.add(sortMenu);
3794     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3795     calculateTreeMenu.add(neighbourTreeMenuItem);
3796     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3797     calculateTreeMenu.add(njTreeBlosumMenuItem);
3798     calculateMenu.add(calculateTreeMenu);
3799     calculateMenu.addSeparator();
3800     calculateMenu.add(pairwiseAlignmentMenuItem);
3801     calculateMenu.add(PCAMenuItem);
3802     calculateMenu.add(autoCalculate);
3803     calculateMenu.add(sortByTree);
3804
3805     /*
3806      * Help menu
3807      */
3808     helpMenu.add(documentation);
3809     helpMenu.add(about);
3810
3811     /*
3812      * Status bar
3813      */
3814     statusBar.setBackground(Color.white);
3815     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3816     setStatus(MessageManager.getString("label.status_bar"));
3817     this.add(statusBar, BorderLayout.SOUTH);
3818   }
3819
3820   @Override
3821   public void setStatus(String string)
3822   {
3823     statusBar.setText(string);
3824   };
3825
3826   MenuItem featureSettings = new MenuItem();
3827
3828   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3829
3830   MenuItem annotationColour = new MenuItem();
3831
3832   MenuItem annotationColumnSelection = new MenuItem();
3833
3834   MenuItem invertColSel = new MenuItem();
3835
3836   MenuItem showColumns = new MenuItem();
3837
3838   MenuItem showSeqs = new MenuItem();
3839
3840   MenuItem hideColumns = new MenuItem();
3841
3842   MenuItem hideSequences = new MenuItem();
3843
3844   MenuItem hideAllButSelection = new MenuItem();
3845
3846   MenuItem hideAllSelection = new MenuItem();
3847
3848   MenuItem showAllHidden = new MenuItem();
3849
3850   MenuItem newView = new MenuItem();
3851
3852   private CheckboxMenuItem showAlignmentAnnotations;
3853
3854   private CheckboxMenuItem showSequenceAnnotations;
3855
3856   private CheckboxMenuItem sortAnnBySequence;
3857
3858   private CheckboxMenuItem sortAnnByLabel;
3859
3860   private CheckboxMenuItem showAutoFirst;
3861
3862   private CheckboxMenuItem showAutoLast;
3863
3864   private SplitFrame splitFrame;
3865
3866   /**
3867    * Attach the alignFrame panels after embedding menus, if necessary. This used
3868    * to be called setEmbedded, but is now creates the dropdown menus in a
3869    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3870    *
3871    * @param reallyEmbedded
3872    *          true to attach the view to the applet area on the page rather than
3873    *          in a new window
3874    */
3875   public void createAlignFrameWindow(boolean reallyEmbedded)
3876   {
3877     if (reallyEmbedded)
3878     {
3879       embedAlignFrameInApplet(viewport.applet);
3880     }
3881     else
3882     {
3883       // //////
3884       // test and embed menu bar if necessary.
3885       //
3886       if (embedMenuIfNeeded(alignPanel))
3887       {
3888         /*
3889          * adjust for status bar height too. ? pointless as overridden by layout
3890          * manager
3891          */
3892         alignPanel.setSize(getSize().width,
3893                 getSize().height - statusBar.getHeight());
3894       }
3895       add(statusBar, BorderLayout.SOUTH);
3896       add(alignPanel, BorderLayout.CENTER);
3897       // and register with the applet so it can pass external API calls to us
3898       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3899               frameHeight);
3900     }
3901   }
3902
3903   /**
3904    * Add the components of this AlignFrame to the applet container.
3905    *
3906    * @param theApplet
3907    */
3908   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3909   {
3910     // ////
3911     // Explicitly build the embedded menu panel for the on-page applet
3912     //
3913     // view cannot be closed if its actually on the page
3914     fileMenu.remove(closeMenuItem);
3915     fileMenu.remove(3); // Remove Separator
3916     // construct embedded menu, using default font
3917     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3918     // and actually add the components to the applet area
3919     theApplet.setLayout(new BorderLayout());
3920     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3921     theApplet.add(statusBar, BorderLayout.SOUTH);
3922     // TODO should size be left to the layout manager?
3923     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3924             - embeddedMenu.getHeight() - statusBar.getHeight());
3925     theApplet.add(alignPanel, BorderLayout.CENTER);
3926     final AlignFrame me = this;
3927     theApplet.addFocusListener(new FocusListener()
3928     {
3929
3930       @Override
3931       public void focusLost(FocusEvent e)
3932       {
3933         if (theApplet.currentAlignFrame == me)
3934         {
3935           theApplet.currentAlignFrame = null;
3936         }
3937       }
3938
3939       @Override
3940       public void focusGained(FocusEvent e)
3941       {
3942         theApplet.currentAlignFrame = me;
3943       }
3944     });
3945     theApplet.validate();
3946   }
3947
3948   /**
3949    * create a new binding between structures in an existing jmol viewer instance
3950    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3951    * this does not open a new Jmol window, or modify the display of the
3952    * structures in the original jmol window. Note This method doesn't work
3953    * without an additional javascript library to exchange messages between the
3954    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3955    *
3956    * @param viewer
3957    *          JmolViewer instance
3958    * @param sequenceIds
3959    *          - sequence Ids to search for associations
3960    */
3961   public SequenceStructureBinding addStructureViewInstance(
3962           Object jmolviewer, String[] sequenceIds)
3963   {
3964     Viewer viewer = null;
3965     try
3966     {
3967       viewer = (Viewer) jmolviewer;
3968     } catch (ClassCastException ex)
3969     {
3970       System.err.println(
3971               "Unsupported viewer object :" + jmolviewer.getClass());
3972     }
3973     if (viewer == null)
3974     {
3975       System.err.println("Can't use this object as a structure viewer:"
3976               + jmolviewer.getClass());
3977       return null;
3978     }
3979     SequenceI[] seqs = null;
3980     if (sequenceIds == null || sequenceIds.length == 0)
3981     {
3982       seqs = viewport.getAlignment().getSequencesArray();
3983     }
3984     else
3985     {
3986       Vector sqi = new Vector();
3987       AlignmentI al = viewport.getAlignment();
3988       for (int sid = 0; sid < sequenceIds.length; sid++)
3989       {
3990         SequenceI sq = al.findName(sequenceIds[sid]);
3991         if (sq != null)
3992         {
3993           sqi.addElement(sq);
3994         }
3995       }
3996       if (sqi.size() > 0)
3997       {
3998         seqs = new SequenceI[sqi.size()];
3999         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4000         {
4001           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4002         }
4003       }
4004       else
4005       {
4006         return null;
4007       }
4008     }
4009     AAStructureBindingModel jmv = null;
4010     // TODO: search for a jmv that involves viewer
4011     if (jmv == null)
4012     { // create a new viewer/jalview binding.
4013       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4014     }
4015     return jmv;
4016
4017   }
4018
4019   /**
4020    * bind a pdb file to a sequence in the current view
4021    *
4022    * @param sequenceId
4023    *          - sequenceId within the dataset.
4024    * @param pdbEntryString
4025    *          - the short name for the PDB file
4026    * @param pdbFile
4027    *          - pdb file - either a URL or a valid PDB file.
4028    * @return true if binding was as success TODO: consider making an exception
4029    *         structure for indicating when PDB parsing or sequenceId location
4030    *         fails.
4031    */
4032   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4033           String pdbFile)
4034   {
4035     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4036     boolean needtoadd = false;
4037     if (toaddpdb != null)
4038     {
4039       Vector pdbe = toaddpdb.getAllPDBEntries();
4040       PDBEntry pdbentry = null;
4041       if (pdbe != null && pdbe.size() > 0)
4042       {
4043         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4044         {
4045           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4046           if (!pdbentry.getId().equals(pdbEntryString)
4047                   && !pdbentry.getFile().equals(pdbFile))
4048           {
4049             pdbentry = null;
4050           }
4051           else
4052           {
4053             continue;
4054           }
4055         }
4056       }
4057       if (pdbentry == null)
4058       {
4059         pdbentry = new PDBEntry();
4060         pdbentry.setId(pdbEntryString);
4061         pdbentry.setFile(pdbFile);
4062         needtoadd = true; // add this new entry to sequence.
4063       }
4064       // resolve data source
4065       // TODO: this code should be a refactored to an io package
4066       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4067               FileFormat.PDB);
4068       if (protocol == null)
4069       {
4070         return false;
4071       }
4072       if (needtoadd)
4073       {
4074         pdbentry.setProperty("protocol", protocol);
4075         toaddpdb.addPDBId(pdbentry);
4076         alignPanel.getStructureSelectionManager()
4077                 .registerPDBEntry(pdbentry);
4078       }
4079     }
4080     return true;
4081   }
4082
4083   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4084   {
4085     if (seqs != null)
4086     {
4087       Vector sequences = new Vector();
4088       for (int i = 0; i < seqs.length; i++)
4089       {
4090         if (seqs[i] != null)
4091         {
4092           sequences
4093                   .addElement(new Object[]
4094                   { seqs[i], (chains != null) ? chains[i] : null });
4095         }
4096       }
4097       seqs = new SequenceI[sequences.size()];
4098       chains = new String[sequences.size()];
4099       for (int i = 0, isize = sequences.size(); i < isize; i++)
4100       {
4101         Object[] oj = (Object[]) sequences.elementAt(i);
4102
4103         seqs[i] = (SequenceI) oj[0];
4104         chains[i] = (String) oj[1];
4105       }
4106     }
4107     return new Object[] { seqs, chains };
4108
4109   }
4110
4111   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4112           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4113   {
4114     // Scrub any null sequences from the array
4115     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4116     seqs = (SequenceI[]) sqch[0];
4117     chains = (String[]) sqch[1];
4118     if (seqs == null || seqs.length == 0)
4119     {
4120       System.err.println(
4121               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4122     }
4123     if (protocol == null)
4124     {
4125       String sourceType = (String) pdb.getProperty("protocol");
4126       try
4127       {
4128         protocol = DataSourceType.valueOf(sourceType);
4129       } catch (IllegalArgumentException e)
4130       {
4131         // ignore
4132       }
4133       if (protocol == null)
4134       {
4135         System.err.println("Couldn't work out protocol to open structure: "
4136                 + pdb.getId());
4137         return;
4138       }
4139     }
4140     if (applet.useXtrnalSviewer)
4141     {
4142       // register the association(s) and quit, don't create any windows.
4143       if (StructureSelectionManager.getStructureSelectionManager(applet)
4144               .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4145       {
4146         System.err.println("Failed to map " + pdb.getFile() + " ("
4147                 + protocol + ") to any sequences");
4148       }
4149       return;
4150     }
4151     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4152     {
4153       // can only do alignments with Jmol
4154       // find the last jmol window assigned to this alignment
4155       AppletJmol ajm = null, tajm;
4156       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4157       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4158       {
4159         tajm = (AppletJmol) jmols.elementAt(i);
4160         if (tajm.ap.alignFrame == this)
4161         {
4162           ajm = tajm;
4163           break;
4164         }
4165       }
4166       if (ajm != null)
4167       {
4168         System.err.println(
4169                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4170         // try and add the pdb structure
4171         // ajm.addS
4172         ajm = null;
4173       }
4174     }
4175     // otherwise, create a new window
4176     if (applet.jmolAvailable)
4177     {
4178       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4179       applet.lastFrameX += 40;
4180       applet.lastFrameY += 40;
4181     }
4182     else
4183     {
4184       new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4185     }
4186
4187   }
4188
4189   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4190           SequenceI[][] seqs, String[][] chains, String[] protocols)
4191   {
4192     // TODO Auto-generated method stub
4193     System.err.println("Aligned Structure View: Not yet implemented.");
4194   }
4195
4196   /**
4197    * modify the current selection, providing the user has not made a selection
4198    * already.
4199    *
4200    * @param sel
4201    *          - sequences from this alignment
4202    * @param csel
4203    *          - columns to be selected on the alignment
4204    */
4205   public void select(SequenceGroup sel, ColumnSelection csel,
4206           HiddenColumns hidden)
4207   {
4208     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4209   }
4210
4211   public void scrollTo(int row, int column)
4212   {
4213     alignPanel.seqPanel.scrollTo(row, column);
4214   }
4215
4216   public void scrollToRow(int row)
4217   {
4218     alignPanel.seqPanel.scrollToRow(row);
4219   }
4220
4221   public void scrollToColumn(int column)
4222   {
4223     alignPanel.seqPanel.scrollToColumn(column);
4224   }
4225
4226   /**
4227    * @return the alignments unique ID.
4228    */
4229   public String getSequenceSetId()
4230   {
4231     return viewport.getSequenceSetId();
4232   }
4233
4234   /**
4235    * Load the (T-Coffee) score file from the specified url
4236    *
4237    * @param source
4238    *          File/URL/T-COFFEE score file contents
4239    * @throws IOException
4240    * @return true if alignment was annotated with data from source
4241    */
4242   public boolean loadScoreFile(String source) throws IOException
4243   {
4244
4245     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4246             AppletFormatAdapter.checkProtocol(source));
4247     if (!file.isValid())
4248     {
4249       // TODO: raise dialog for gui
4250       System.err.println("Problems parsing T-Coffee scores: "
4251               + file.getWarningMessage());
4252       System.err.println("Origin was:\n" + source);
4253       return false;
4254     }
4255
4256     /*
4257      * check that the score matrix matches the alignment dimensions
4258      */
4259     AlignmentI aln;
4260     if ((aln = viewport.getAlignment()) != null
4261             && (aln.getHeight() != file.getHeight()
4262                     || aln.getWidth() != file.getWidth()))
4263     {
4264       // TODO: raise a dialog box here rather than bomb out.
4265       System.err.println(
4266               "The scores matrix does not match the alignment dimensions");
4267
4268     }
4269
4270     // TODO add parameter to indicate if matching should be done
4271     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4272     {
4273       alignPanel.fontChanged();
4274       tcoffeeColour.setEnabled(true);
4275       // switch to this color
4276       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4277       return true;
4278     }
4279     else
4280     {
4281       System.err.println("Problems resolving T-Coffee scores:");
4282       if (file.getWarningMessage() != null)
4283       {
4284         System.err.println(file.getWarningMessage());
4285       }
4286     }
4287     return false;
4288   }
4289
4290   public SplitFrame getSplitFrame()
4291   {
4292     return this.splitFrame;
4293   }
4294
4295   public void setSplitFrame(SplitFrame sf)
4296   {
4297     this.splitFrame = sf;
4298   }
4299
4300   // may not need this
4301   @Override
4302   public void setShowSeqFeatures(boolean b)
4303   {
4304     // showSeqFeatures.setSelected(b);
4305     viewport.setShowSequenceFeatures(b);
4306
4307   }
4308
4309   @Override
4310   public void setMenusForViewport()
4311   {
4312     // setMenusFromViewport(viewport);
4313
4314   }
4315
4316   @Override
4317   public void refreshFeatureUI(boolean enableIfNecessary)
4318   {
4319     if (enableIfNecessary)
4320     {
4321       sequenceFeatures.setState(true);
4322       alignPanel.av.setShowSequenceFeatures(true);
4323     }
4324   }
4325
4326   @Override
4327   public FeatureSettingsControllerI getFeatureSettingsUI()
4328   {
4329     return alignPanel.av.featureSettings;
4330   }
4331
4332 }