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.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.TCoffeeScoreFile;
  56 import jalview.schemes.Blosum62ColourScheme;
  57 import jalview.schemes.BuriedColourScheme;
  58 import jalview.schemes.ClustalxColourScheme;
  59 import jalview.schemes.ColourSchemeI;
  60 import jalview.schemes.HelixColourScheme;
  61 import jalview.schemes.HydrophobicColourScheme;
  62 import jalview.schemes.NucleotideColourScheme;
  63 import jalview.schemes.PIDColourScheme;
  64 import jalview.schemes.PurinePyrimidineColourScheme;
  65 import jalview.schemes.RNAHelicesColourChooser;
  66 import jalview.schemes.StrandColourScheme;
  67 import jalview.schemes.TCoffeeColourScheme;
  68 import jalview.schemes.TaylorColourScheme;
  69 import jalview.schemes.TurnColourScheme;
  70 import jalview.schemes.ZappoColourScheme;
  71 import jalview.structure.StructureSelectionManager;
  72 import jalview.structures.models.AAStructureBindingModel;
  73 import jalview.util.MappingUtils;
  74 import jalview.util.MessageManager;
  75 import jalview.viewmodel.AlignmentViewport;
  76
  77 import java.awt.BorderLayout;
  78 import java.awt.Canvas;
  79 import java.awt.CheckboxMenuItem;
  80 import java.awt.Color;
  81 import java.awt.FlowLayout;
  82 import java.awt.Font;
  83 import java.awt.FontMetrics;
  84 import java.awt.Frame;
  85 import java.awt.Graphics;
  86 import java.awt.Label;
  87 import java.awt.Menu;
  88 import java.awt.MenuBar;
  89 import java.awt.MenuItem;
  90 import java.awt.Panel;
  91 import java.awt.event.ActionEvent;
  92 import java.awt.event.ActionListener;
  93 import java.awt.event.FocusEvent;
  94 import java.awt.event.FocusListener;
  95 import java.awt.event.ItemEvent;
  96 import java.awt.event.ItemListener;
  97 import java.awt.event.KeyEvent;
  98 import java.awt.event.KeyListener;
  99 import java.awt.event.WindowAdapter;
 100 import java.awt.event.WindowEvent;
 101 import java.io.IOException;
 102 import java.net.URL;
 103 import java.net.URLEncoder;
 104 import java.util.Arrays;
 105 import java.util.Deque;
 106 import java.util.HashMap;
 107 import java.util.List;
 108 import java.util.Map;
 109 import java.util.StringTokenizer;
 110 import java.util.Vector;
 111
 112 import org.jmol.viewer.Viewer;
 113
 114 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 115         ItemListener, KeyListener, AlignViewControllerGuiI
 116 {
 117   public AlignViewControllerI avc;
 118
 119   public AlignmentPanel alignPanel;
 120
 121   public AlignViewport viewport;
 122
 123   // width and height may be overridden by applet parameters
 124   int frameWidth = 700;
 125
 126   int frameHeight = 500;
 127
 128   String jalviewServletURL;
 129
 130   /*
 131    * Flag for showing autocalculated consensus above or below other consensus
 132    * rows
 133    */
 134   private boolean showAutoCalculatedAbove;
 135
 136   private SequenceAnnotationOrder annotationSortOrder;
 137
 138   /**
 139    * Constructor that creates the frame and adds it to the display.
 140    *
 141    * @param al
 142    * @param applet
 143    * @param title
 144    * @param embedded
 145    */
 146   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 147           boolean embedded)
 148   {
 149     this(al, applet, title, embedded, true);
 150   }
 151
 152   /**
 153    * Constructor that optionally allows the frame to be displayed or only
 154    * created.
 155    *
 156    * @param al
 157    * @param applet
 158    * @param title
 159    * @param embedded
 160    * @param addToDisplay
 161    */
 162   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 163           boolean embedded, boolean addToDisplay)
 164   {
 165     this(al, null, null, applet, title, embedded, addToDisplay);
 166   }
 167
 168   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 169           ColumnSelection columnSelection, JalviewLite applet,
 170           String title, boolean embedded)
 171   {
 172     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           ColumnSelection columnSelection, JalviewLite applet,
 177           String title, boolean embedded, boolean addToDisplay)
 178   {
 179     if (applet != null)
 180     {
 181       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception ex)
 188     {
 189       ex.printStackTrace();
 190     }
 191     // need to get window geometry before we calculate alignment layout
 192     if (applet != null)
 193     {
 194       String param;
 195       try
 196       {
 197         param = applet.getParameter("windowWidth");
 198         if (param != null)
 199         {
 200           int width = Integer.parseInt(param);
 201           frameWidth = width;
 202         }
 203         param = applet.getParameter("windowHeight");
 204         if (param != null)
 205         {
 206           int height = Integer.parseInt(param);
 207           frameHeight = height;
 208         }
 209       } catch (Exception ex)
 210       {
 211       }
 212     }
 213     viewport = new AlignViewport(al, applet);
 214
 215     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 216     {
 217       viewport.hideSequence(hiddenSeqs);
 218     }
 219     if (columnSelection != null)
 220     {
 221       viewport.setColumnSelection(columnSelection);
 222     }
 223     viewport.setScaleAboveWrapped(scaleAbove.getState());
 224
 225     alignPanel = new AlignmentPanel(this, viewport);
 226     avc = new jalview.controller.AlignViewController(this, viewport,
 227             alignPanel);
 228     viewport.updateConservation(alignPanel);
 229     viewport.updateConsensus(alignPanel);
 230
 231     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 232     followMouseOverFlag.setState(viewport.isFollowHighlight());
 233     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 234     showGroupConservation.setState(viewport.isShowGroupConservation());
 235     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 236     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 237     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 238     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 239     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 240     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 242     showAlignmentAnnotations.setState(true);
 243     showSequenceAnnotations.setState(false);
 244
 245     seqLimits.setState(viewport.getShowJVSuffix());
 246
 247     if (applet != null)
 248     {
 249       String param = applet.getParameter("sortBy");
 250       if (param != null)
 251       {
 252         if (param.equalsIgnoreCase("Id"))
 253         {
 254           sortIDMenuItem_actionPerformed();
 255         }
 256         else if (param.equalsIgnoreCase("Pairwise Identity"))
 257         {
 258           sortPairwiseMenuItem_actionPerformed();
 259         }
 260         else if (param.equalsIgnoreCase("Length"))
 261         {
 262           sortLengthMenuItem_actionPerformed();
 263         }
 264       }
 265
 266       param = applet.getParameter("wrap");
 267       if (param != null)
 268       {
 269         if (param.equalsIgnoreCase("true"))
 270         {
 271           wrapMenuItem.setState(true);
 272           wrapMenuItem_actionPerformed();
 273         }
 274       }
 275       param = applet.getParameter("centrecolumnlabels");
 276       if (param != null)
 277       {
 278         centreColumnLabelFlag.setState(true);
 279         centreColumnLabelFlag_stateChanged();
 280       }
 281
 282     }
 283     if (viewport.getAlignment().isNucleotide())
 284     {
 285       viewport.updateStrucConsensus(alignPanel);
 286       if (viewport.getAlignment().hasRNAStructure())
 287       {
 288         RNAHelixColour.setEnabled(true);
 289       }
 290       else
 291       {
 292         RNAHelixColour.setEnabled(false);
 293       }
 294     }
 295     else
 296     {
 297       RNAHelixColour.setEnabled(false);
 298       purinePyrimidineColour.setEnabled(false);
 299     }
 300     // Some JVMS send keyevents to Top frame or lowest panel,
 301     // Havent worked out why yet. So add to both this frame and seqCanvas for
 302     // now
 303     this.addKeyListener(this);
 304     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 305     alignPanel.idPanel.idCanvas.addKeyListener(this);
 306     alignPanel.scalePanel.addKeyListener(this);
 307     alignPanel.annotationPanel.addKeyListener(this);
 308     alignPanel.annotationPanelHolder.addKeyListener(this);
 309     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 310     alignPanel.alabels.addKeyListener(this);
 311
 312     setAnnotationsVisibility();
 313
 314     if (addToDisplay)
 315     {
 316       addToDisplay(embedded);
 317     }
 318   }
 319
 320   /**
 321    * @param embedded
 322    */
 323   public void addToDisplay(boolean embedded)
 324   {
 325     createAlignFrameWindow(embedded);
 326     validate();
 327     alignPanel.adjustAnnotationHeight();
 328     alignPanel.paintAlignment(true);
 329   }
 330
 331   public AlignViewport getAlignViewport()
 332   {
 333     return viewport;
 334   }
 335
 336   public SeqCanvas getSeqcanvas()
 337   {
 338     return alignPanel.seqPanel.seqCanvas;
 339   }
 340
 341   /**
 342    * Load a features file onto the alignment
 343    *
 344    * @param file
 345    *          file URL, content, or other resolvable path
 346    * @param type
 347    *          is protocol for accessing data referred to by file
 348    */
 349
 350   public boolean parseFeaturesFile(String file, DataSourceType type)
 351   {
 352     return parseFeaturesFile(file, type, true);
 353   }
 354
 355   /**
 356    * Load a features file onto the alignment
 357    *
 358    * @param file
 359    *          file URL, content, or other resolvable path
 360    * @param sourceType
 361    *          is protocol for accessing data referred to by file
 362    * @param autoenabledisplay
 363    *          when true, display features flag will be automatically enabled if
 364    *          features are loaded
 365    * @return true if data parsed as a features file
 366    */
 367   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 368           boolean autoenabledisplay)
 369   {
 370     boolean featuresFile = false;
 371     try
 372     {
 373       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 374               .getFeatureRenderer().getFeatureColours();
 375       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 376               "relaxedidmatch", false);
 377       featuresFile = new FeaturesFile(file, sourceType).parse(
 378               viewport.getAlignment(), colours, true, relaxedIdMatching);
 379     } catch (Exception ex)
 380     {
 381       ex.printStackTrace();
 382     }
 383
 384     if (featuresFile)
 385     {
 386       if (autoenabledisplay)
 387       {
 388         viewport.setShowSequenceFeatures(true);
 389         sequenceFeatures.setState(true);
 390       }
 391       if (alignPanel.seqPanel.seqCanvas.fr != null)
 392       {
 393         // update the min/max ranges where necessary
 394         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 395       }
 396       if (viewport.featureSettings != null)
 397       {
 398         viewport.featureSettings.refreshTable();
 399       }
 400       alignPanel.paintAlignment(true);
 401       statusBar.setText(MessageManager
 402               .getString("label.successfully_added_features_alignment"));
 403     }
 404     return featuresFile;
 405   }
 406
 407   @Override
 408   public void keyPressed(KeyEvent evt)
 409   {
 410     if (viewport.cursorMode
 411             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 412                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 413                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 414             && Character.isDigit(evt.getKeyChar()))
 415     {
 416       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 417     }
 418
 419     switch (evt.getKeyCode())
 420     {
 421     case 27: // escape key
 422       deselectAllSequenceMenuItem_actionPerformed();
 423
 424       alignPanel.alabels.cancelDrag();
 425       break;
 426     case KeyEvent.VK_X:
 427       if (evt.isControlDown() || evt.isMetaDown())
 428       {
 429         cut_actionPerformed();
 430       }
 431       break;
 432     case KeyEvent.VK_C:
 433       if (viewport.cursorMode && !evt.isControlDown())
 434       {
 435         alignPanel.seqPanel.setCursorColumn();
 436       }
 437       if (evt.isControlDown() || evt.isMetaDown())
 438       {
 439         copy_actionPerformed();
 440       }
 441       break;
 442     case KeyEvent.VK_V:
 443       if (evt.isControlDown())
 444       {
 445         paste(evt.isShiftDown());
 446       }
 447       break;
 448     case KeyEvent.VK_A:
 449       if (evt.isControlDown() || evt.isMetaDown())
 450       {
 451         selectAllSequenceMenuItem_actionPerformed();
 452       }
 453       break;
 454     case KeyEvent.VK_DOWN:
 455       if (viewport.cursorMode)
 456       {
 457         alignPanel.seqPanel.moveCursor(0, 1);
 458       }
 459       else
 460       {
 461         moveSelectedSequences(false);
 462       }
 463       break;
 464
 465     case KeyEvent.VK_UP:
 466       if (viewport.cursorMode)
 467       {
 468         alignPanel.seqPanel.moveCursor(0, -1);
 469       }
 470       else
 471       {
 472         moveSelectedSequences(true);
 473       }
 474       break;
 475
 476     case KeyEvent.VK_LEFT:
 477       if (evt.isAltDown() || !viewport.cursorMode)
 478       {
 479         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 480       }
 481       else
 482       {
 483         alignPanel.seqPanel.moveCursor(-1, 0);
 484       }
 485       break;
 486
 487     case KeyEvent.VK_RIGHT:
 488       if (evt.isAltDown() || !viewport.cursorMode)
 489       {
 490         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 491       }
 492       else
 493       {
 494         alignPanel.seqPanel.moveCursor(1, 0);
 495       }
 496       break;
 497
 498     case KeyEvent.VK_SPACE:
 499       if (viewport.cursorMode)
 500       {
 501         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 502                 || evt.isShiftDown() || evt.isAltDown());
 503       }
 504       break;
 505
 506     case KeyEvent.VK_DELETE:
 507     case KeyEvent.VK_BACK_SPACE:
 508       if (viewport.cursorMode)
 509       {
 510         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 511                 || evt.isShiftDown() || evt.isAltDown());
 512       }
 513       else
 514       {
 515         cut_actionPerformed();
 516         alignPanel.seqPanel.seqCanvas.repaint();
 517       }
 518       break;
 519
 520     case KeyEvent.VK_S:
 521       if (viewport.cursorMode)
 522       {
 523         alignPanel.seqPanel.setCursorRow();
 524       }
 525       break;
 526     case KeyEvent.VK_P:
 527       if (viewport.cursorMode)
 528       {
 529         alignPanel.seqPanel.setCursorPosition();
 530       }
 531       break;
 532
 533     case KeyEvent.VK_ENTER:
 534     case KeyEvent.VK_COMMA:
 535       if (viewport.cursorMode)
 536       {
 537         alignPanel.seqPanel.setCursorRowAndColumn();
 538       }
 539       break;
 540
 541     case KeyEvent.VK_Q:
 542       if (viewport.cursorMode)
 543       {
 544         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 545       }
 546       break;
 547     case KeyEvent.VK_M:
 548       if (viewport.cursorMode)
 549       {
 550         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 551       }
 552       break;
 553
 554     case KeyEvent.VK_F2:
 555       viewport.cursorMode = !viewport.cursorMode;
 556       statusBar.setText(MessageManager.formatMessage(
 557               "label.keyboard_editing_mode",
 558               new String[] { (viewport.cursorMode ? "on" : "off") }));
 559       if (viewport.cursorMode)
 560       {
 561         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 562         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 563       }
 564       break;
 565
 566     case KeyEvent.VK_F:
 567       if (evt.isControlDown())
 568       {
 569         findMenuItem_actionPerformed();
 570       }
 571       break;
 572
 573     case KeyEvent.VK_H:
 574     {
 575       boolean toggleSeqs = !evt.isControlDown();
 576       boolean toggleCols = !evt.isShiftDown();
 577       toggleHiddenRegions(toggleSeqs, toggleCols);
 578       break;
 579     }
 580
 581     case KeyEvent.VK_PAGE_UP:
 582       if (viewport.getWrapAlignment())
 583       {
 584         alignPanel.scrollUp(true);
 585       }
 586       else
 587       {
 588         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 589                 - viewport.endSeq + viewport.startSeq);
 590       }
 591       break;
 592
 593     case KeyEvent.VK_PAGE_DOWN:
 594       if (viewport.getWrapAlignment())
 595       {
 596         alignPanel.scrollUp(false);
 597       }
 598       else
 599       {
 600         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 601                 + viewport.endSeq - viewport.startSeq);
 602       }
 603       break;
 604
 605     case KeyEvent.VK_Z:
 606       if (evt.isControlDown())
 607       {
 608         undoMenuItem_actionPerformed();
 609       }
 610       break;
 611
 612     case KeyEvent.VK_Y:
 613       if (evt.isControlDown())
 614       {
 615         redoMenuItem_actionPerformed();
 616       }
 617       break;
 618
 619     case KeyEvent.VK_L:
 620       if (evt.isControlDown())
 621       {
 622         trimAlignment(true);
 623       }
 624       break;
 625
 626     case KeyEvent.VK_R:
 627       if (evt.isControlDown())
 628       {
 629         trimAlignment(false);
 630       }
 631       break;
 632
 633     case KeyEvent.VK_E:
 634       if (evt.isControlDown())
 635       {
 636         if (evt.isShiftDown())
 637         {
 638           this.removeAllGapsMenuItem_actionPerformed();
 639         }
 640         else
 641         {
 642           removeGappedColumnMenuItem_actionPerformed();
 643         }
 644       }
 645       break;
 646     case KeyEvent.VK_I:
 647       if (evt.isControlDown())
 648       {
 649         if (evt.isAltDown())
 650         {
 651           invertColSel_actionPerformed();
 652         }
 653         else
 654         {
 655           invertSequenceMenuItem_actionPerformed();
 656         }
 657       }
 658       break;
 659
 660     case KeyEvent.VK_G:
 661       if (evt.isControlDown())
 662       {
 663         if (evt.isShiftDown())
 664         {
 665           this.unGroup_actionPerformed();
 666         }
 667         else
 668         {
 669           this.createGroup_actionPerformed();
 670         }
 671       }
 672       break;
 673
 674     case KeyEvent.VK_U:
 675       if (evt.isControlDown())
 676       {
 677         this.deleteGroups_actionPerformed();
 678       }
 679       break;
 680
 681     case KeyEvent.VK_T:
 682       if (evt.isControlDown())
 683       {
 684         newView(null);
 685       }
 686       break;
 687
 688     }
 689     alignPanel.paintAlignment(true);
 690   }
 691
 692   /**
 693    * called by key handler and the hide all/show all menu items
 694    *
 695    * @param toggleSeqs
 696    * @param toggleCols
 697    */
 698   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 699   {
 700     boolean hide = false;
 701     SequenceGroup sg = viewport.getSelectionGroup();
 702     if (!toggleSeqs && !toggleCols)
 703     {
 704       // Hide everything by the current selection - this is a hack - we do the
 705       // invert and then hide
 706       // first check that there will be visible columns after the invert.
 707       if (viewport.hasSelectedColumns()
 708               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 709                       .getEndRes()))
 710       {
 711         // now invert the sequence set, if required - empty selection implies
 712         // that no hiding is required.
 713         if (sg != null)
 714         {
 715           invertSequenceMenuItem_actionPerformed();
 716           sg = viewport.getSelectionGroup();
 717           toggleSeqs = true;
 718
 719         }
 720         viewport.expandColSelection(sg, true);
 721         // finally invert the column selection and get the new sequence
 722         // selection and indicate it should be hidden.
 723         invertColSel_actionPerformed();
 724         toggleCols = true;
 725       }
 726     }
 727
 728     if (toggleSeqs)
 729     {
 730       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 731       {
 732         hide = true;
 733         viewport.hideAllSelectedSeqs();
 734       }
 735       else if (!(toggleCols && viewport.hasSelectedColumns()))
 736       {
 737         viewport.showAllHiddenSeqs();
 738       }
 739     }
 740
 741     if (toggleCols)
 742     {
 743       if (viewport.hasSelectedColumns())
 744       {
 745         viewport.hideSelectedColumns();
 746         if (!toggleSeqs)
 747         {
 748           viewport.setSelectionGroup(sg);
 749         }
 750       }
 751       else if (!hide)
 752       {
 753         viewport.showAllHiddenColumns();
 754       }
 755       viewport.sendSelection();
 756     }
 757   }
 758
 759   @Override
 760   public void keyReleased(KeyEvent evt)
 761   {
 762   }
 763
 764   @Override
 765   public void keyTyped(KeyEvent evt)
 766   {
 767   }
 768
 769   @Override
 770   public void itemStateChanged(ItemEvent evt)
 771   {
 772     final Object source = evt.getSource();
 773     if (source == displayNonconservedMenuItem)
 774     {
 775       displayNonconservedMenuItem_actionPerformed();
 776     }
 777     else if (source == colourTextMenuItem)
 778     {
 779       colourTextMenuItem_actionPerformed();
 780     }
 781     else if (source == wrapMenuItem)
 782     {
 783       wrapMenuItem_actionPerformed();
 784     }
 785     else if (source == scaleAbove)
 786     {
 787       viewport.setScaleAboveWrapped(scaleAbove.getState());
 788     }
 789     else if (source == scaleLeft)
 790     {
 791       viewport.setScaleLeftWrapped(scaleLeft.getState());
 792     }
 793     else if (source == scaleRight)
 794     {
 795       viewport.setScaleRightWrapped(scaleRight.getState());
 796     }
 797     else if (source == seqLimits)
 798     {
 799       seqLimits_itemStateChanged();
 800     }
 801     else if (source == viewBoxesMenuItem)
 802     {
 803       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 804     }
 805     else if (source == viewTextMenuItem)
 806     {
 807       viewport.setShowText(viewTextMenuItem.getState());
 808     }
 809     else if (source == renderGapsMenuItem)
 810     {
 811       viewport.setRenderGaps(renderGapsMenuItem.getState());
 812     }
 813     else if (source == annotationPanelMenuItem)
 814     {
 815       boolean showAnnotations = annotationPanelMenuItem.getState();
 816       showAlignmentAnnotations.setEnabled(showAnnotations);
 817       showSequenceAnnotations.setEnabled(showAnnotations);
 818       viewport.setShowAnnotation(showAnnotations);
 819       alignPanel.setAnnotationVisible(showAnnotations);
 820     }
 821     else if (source == sequenceFeatures)
 822     {
 823       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 824       alignPanel.seqPanel.seqCanvas.repaint();
 825     }
 826     else if (source == showAlignmentAnnotations)
 827     {
 828       setAnnotationsVisibility();
 829     }
 830     else if (source == showSequenceAnnotations)
 831     {
 832       setAnnotationsVisibility();
 833     }
 834     else if (source == sortAnnBySequence)
 835     {
 836       boolean newState = sortAnnBySequence.getState();
 837       sortAnnByLabel.setState(false);
 838       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 839               : SequenceAnnotationOrder.NONE);
 840       setViewportAnnotationOrder();
 841     }
 842     else if (source == sortAnnByLabel)
 843     {
 844       boolean newState = sortAnnByLabel.getState();
 845       sortAnnBySequence.setState(false);
 846       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 847               : SequenceAnnotationOrder.NONE);
 848       setViewportAnnotationOrder();
 849     }
 850     else if (source == showAutoFirst)
 851     {
 852       showAutoLast.setState(!showAutoFirst.getState());
 853       setShowAutoCalculatedAbove(showAutoFirst.getState());
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == showAutoLast)
 857     {
 858       showAutoFirst.setState(!showAutoLast.getState());
 859       setShowAutoCalculatedAbove(showAutoFirst.getState());
 860       setViewportAnnotationOrder();
 861     }
 862     else if (source == conservationMenuItem)
 863     {
 864       conservationMenuItem_actionPerformed();
 865     }
 866     else if (source == abovePIDThreshold)
 867     {
 868       abovePIDThreshold_actionPerformed();
 869     }
 870     else if (source == applyToAllGroups)
 871     {
 872       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 873     }
 874     else if (source == autoCalculate)
 875     {
 876       viewport.autoCalculateConsensus = autoCalculate.getState();
 877     }
 878     else if (source == sortByTree)
 879     {
 880       viewport.sortByTree = sortByTree.getState();
 881     }
 882     else if (source == this.centreColumnLabelFlag)
 883     {
 884       centreColumnLabelFlag_stateChanged();
 885     }
 886     else if (source == this.followMouseOverFlag)
 887     {
 888       mouseOverFlag_stateChanged();
 889     }
 890     else if (source == showGroupConsensus)
 891     {
 892       showGroupConsensus_actionPerformed();
 893     }
 894     else if (source == showGroupConservation)
 895     {
 896       showGroupConservation_actionPerformed();
 897     }
 898     else if (source == showSequenceLogo)
 899     {
 900       showSequenceLogo_actionPerformed();
 901     }
 902     else if (source == normSequenceLogo)
 903     {
 904       normSequenceLogo_actionPerformed();
 905     }
 906     else if (source == showConsensusHistogram)
 907     {
 908       showConsensusHistogram_actionPerformed();
 909     }
 910     else if (source == applyAutoAnnotationSettings)
 911     {
 912       applyAutoAnnotationSettings_actionPerformed();
 913     }
 914     alignPanel.paintAlignment(true);
 915   }
 916
 917   /**
 918    * Set the visibility state of sequence-related and/or alignment-related
 919    * annotations depending on checkbox selections, and repaint.
 920    *
 921    * @param visible
 922    */
 923   private void setAnnotationsVisibility()
 924   {
 925     boolean showForAlignment = showAlignmentAnnotations.getState();
 926     boolean showForSequences = showSequenceAnnotations.getState();
 927     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 928     {
 929       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 930               .getAlignmentAnnotation())
 931       {
 932         boolean visible = (aa.sequenceRef == null ? showForAlignment
 933                 : showForSequences);
 934         aa.visible = visible;
 935       }
 936     }
 937     alignPanel.validateAnnotationDimensions(true);
 938     validate();
 939     repaint();
 940   }
 941
 942   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 943   {
 944     this.annotationSortOrder = order;
 945   }
 946
 947   /**
 948    * Set flags on the viewport that control annotation ordering
 949    */
 950   private void setViewportAnnotationOrder()
 951   {
 952     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 953     this.alignPanel.av
 954             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 955   }
 956
 957   private void setShowAutoCalculatedAbove(boolean showAbove)
 958   {
 959     this.showAutoCalculatedAbove = showAbove;
 960   }
 961
 962   private void mouseOverFlag_stateChanged()
 963   {
 964     viewport.setFollowHighlight(followMouseOverFlag.getState());
 965     // TODO: could kick the scrollTo mechanism to reset view for current
 966     // searchresults.
 967   }
 968
 969   private void centreColumnLabelFlag_stateChanged()
 970   {
 971     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 972     this.alignPanel.annotationPanel.repaint();
 973   }
 974
 975   @Override
 976   public void actionPerformed(ActionEvent evt)
 977   {
 978     viewport.applet.currentAlignFrame = this;
 979
 980     Object source = evt.getSource();
 981
 982     if (source == inputText)
 983     {
 984       inputText_actionPerformed();
 985     }
 986     else if (source == loadTree)
 987     {
 988       loadTree_actionPerformed();
 989     }
 990     else if (source == loadApplication)
 991     {
 992       launchFullApplication();
 993     }
 994     else if (source == loadAnnotations)
 995     {
 996       loadAnnotations();
 997     }
 998     else if (source == outputAnnotations)
 999     {
1000       outputAnnotations(true);
1001     }
1002     else if (source == outputFeatures)
1003     {
1004       outputFeatures(true, "Jalview");
1005     }
1006     else if (source == closeMenuItem)
1007     {
1008       closeMenuItem_actionPerformed();
1009     }
1010     else if (source == copy)
1011     {
1012       copy_actionPerformed();
1013     }
1014     else if (source == undoMenuItem)
1015     {
1016       undoMenuItem_actionPerformed();
1017     }
1018     else if (source == redoMenuItem)
1019     {
1020       redoMenuItem_actionPerformed();
1021     }
1022     else if (source == inputText)
1023     {
1024       inputText_actionPerformed();
1025     }
1026     else if (source == closeMenuItem)
1027     {
1028       closeMenuItem_actionPerformed();
1029     }
1030     else if (source == undoMenuItem)
1031     {
1032       undoMenuItem_actionPerformed();
1033     }
1034     else if (source == redoMenuItem)
1035     {
1036       redoMenuItem_actionPerformed();
1037     }
1038     else if (source == copy)
1039     {
1040       copy_actionPerformed();
1041     }
1042     else if (source == pasteNew)
1043     {
1044       pasteNew_actionPerformed();
1045     }
1046     else if (source == pasteThis)
1047     {
1048       pasteThis_actionPerformed();
1049     }
1050     else if (source == cut)
1051     {
1052       cut_actionPerformed();
1053     }
1054     else if (source == delete)
1055     {
1056       delete_actionPerformed();
1057     }
1058     else if (source == grpsFromSelection)
1059     {
1060       makeGrpsFromSelection_actionPerformed();
1061     }
1062     else if (source == deleteGroups)
1063     {
1064       deleteGroups_actionPerformed();
1065     }
1066     else if (source == selectAllSequenceMenuItem)
1067     {
1068       selectAllSequenceMenuItem_actionPerformed();
1069     }
1070     else if (source == deselectAllSequenceMenuItem)
1071     {
1072       deselectAllSequenceMenuItem_actionPerformed();
1073     }
1074     else if (source == invertSequenceMenuItem)
1075     {
1076       invertSequenceMenuItem_actionPerformed();
1077       // uncomment to slave sequence selections in split frame
1078       // viewport.sendSelection();
1079     }
1080     else if (source == invertColSel)
1081     {
1082       viewport.invertColumnSelection();
1083       alignPanel.paintAlignment(true);
1084       viewport.sendSelection();
1085     }
1086     else if (source == remove2LeftMenuItem)
1087     {
1088       trimAlignment(true);
1089     }
1090     else if (source == remove2RightMenuItem)
1091     {
1092       trimAlignment(false);
1093     }
1094     else if (source == removeGappedColumnMenuItem)
1095     {
1096       removeGappedColumnMenuItem_actionPerformed();
1097     }
1098     else if (source == removeAllGapsMenuItem)
1099     {
1100       removeAllGapsMenuItem_actionPerformed();
1101     }
1102     else if (source == findMenuItem)
1103     {
1104       findMenuItem_actionPerformed();
1105     }
1106     else if (source == font)
1107     {
1108       new FontChooser(alignPanel);
1109     }
1110     else if (source == newView)
1111     {
1112       newView(null);
1113     }
1114     else if (source == showColumns)
1115     {
1116       viewport.showAllHiddenColumns();
1117       alignPanel.paintAlignment(true);
1118       viewport.sendSelection();
1119     }
1120     else if (source == showSeqs)
1121     {
1122       viewport.showAllHiddenSeqs();
1123       alignPanel.paintAlignment(true);
1124       // uncomment if we want to slave sequence selections in split frame
1125       // viewport.sendSelection();
1126     }
1127     else if (source == hideColumns)
1128     {
1129       viewport.hideSelectedColumns();
1130       alignPanel.paintAlignment(true);
1131       viewport.sendSelection();
1132     }
1133     else if (source == hideSequences
1134             && viewport.getSelectionGroup() != null)
1135     {
1136       viewport.hideAllSelectedSeqs();
1137       alignPanel.paintAlignment(true);
1138       // uncomment if we want to slave sequence selections in split frame
1139       // viewport.sendSelection();
1140     }
1141     else if (source == hideAllButSelection)
1142     {
1143       toggleHiddenRegions(false, false);
1144       alignPanel.paintAlignment(true);
1145       viewport.sendSelection();
1146     }
1147     else if (source == hideAllSelection)
1148     {
1149       SequenceGroup sg = viewport.getSelectionGroup();
1150       viewport.expandColSelection(sg, false);
1151       viewport.hideAllSelectedSeqs();
1152       viewport.hideSelectedColumns();
1153       alignPanel.paintAlignment(true);
1154       viewport.sendSelection();
1155     }
1156     else if (source == showAllHidden)
1157     {
1158       viewport.showAllHiddenColumns();
1159       viewport.showAllHiddenSeqs();
1160       alignPanel.paintAlignment(true);
1161       viewport.sendSelection();
1162     }
1163     else if (source == showGroupConsensus)
1164     {
1165       showGroupConsensus_actionPerformed();
1166     }
1167     else if (source == showGroupConservation)
1168     {
1169       showGroupConservation_actionPerformed();
1170     }
1171     else if (source == showSequenceLogo)
1172     {
1173       showSequenceLogo_actionPerformed();
1174     }
1175     else if (source == normSequenceLogo)
1176     {
1177       normSequenceLogo_actionPerformed();
1178     }
1179     else if (source == showConsensusHistogram)
1180     {
1181       showConsensusHistogram_actionPerformed();
1182     }
1183     else if (source == applyAutoAnnotationSettings)
1184     {
1185       applyAutoAnnotationSettings_actionPerformed();
1186     }
1187     else if (source == featureSettings)
1188     {
1189       new FeatureSettings(alignPanel);
1190     }
1191     else if (source == alProperties)
1192     {
1193       StringBuffer contents = new jalview.io.AlignmentProperties(
1194               viewport.getAlignment()).formatAsString();
1195       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1196       cap.setText(contents.toString());
1197       Frame frame = new Frame();
1198       frame.add(cap);
1199       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1200               "label.alignment_properties", new String[] { getTitle() }),
1201               400, 250);
1202     }
1203     else if (source == overviewMenuItem)
1204     {
1205       overviewMenuItem_actionPerformed();
1206     }
1207     else if (source == noColourmenuItem)
1208     {
1209       changeColour(null);
1210     }
1211     else if (source == clustalColour)
1212     {
1213       abovePIDThreshold.setState(false);
1214       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1215     }
1216     else if (source == zappoColour)
1217     {
1218       changeColour(new ZappoColourScheme());
1219     }
1220     else if (source == taylorColour)
1221     {
1222       changeColour(new TaylorColourScheme());
1223     }
1224     else if (source == hydrophobicityColour)
1225     {
1226       changeColour(new HydrophobicColourScheme());
1227     }
1228     else if (source == helixColour)
1229     {
1230       changeColour(new HelixColourScheme());
1231     }
1232     else if (source == strandColour)
1233     {
1234       changeColour(new StrandColourScheme());
1235     }
1236     else if (source == turnColour)
1237     {
1238       changeColour(new TurnColourScheme());
1239     }
1240     else if (source == buriedColour)
1241     {
1242       changeColour(new BuriedColourScheme());
1243     }
1244     else if (source == nucleotideColour)
1245     {
1246       changeColour(new NucleotideColourScheme());
1247     }
1248     else if (source == purinePyrimidineColour)
1249     {
1250       changeColour(new PurinePyrimidineColourScheme());
1251     }
1252     // else if (source == RNAInteractionColour)
1253     // {
1254     // changeColour(new RNAInteractionColourScheme());
1255     // }
1256     else if (source == RNAHelixColour)
1257     {
1258       new RNAHelicesColourChooser(viewport, alignPanel);
1259     }
1260     else if (source == modifyPID)
1261     {
1262       modifyPID_actionPerformed();
1263     }
1264     else if (source == modifyConservation)
1265     {
1266       modifyConservation_actionPerformed();
1267     }
1268     else if (source == userDefinedColour)
1269     {
1270       new UserDefinedColours(alignPanel, null);
1271     }
1272     else if (source == PIDColour)
1273     {
1274       changeColour(new PIDColourScheme());
1275     }
1276     else if (source == BLOSUM62Colour)
1277     {
1278       changeColour(new Blosum62ColourScheme());
1279     }
1280     else if (source == tcoffeeColour)
1281     {
1282       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1283     }
1284     else if (source == annotationColour)
1285     {
1286       new AnnotationColourChooser(viewport, alignPanel);
1287     }
1288     else if (source == annotationColumnSelection)
1289     {
1290       new AnnotationColumnChooser(viewport, alignPanel);
1291     }
1292     else if (source == sortPairwiseMenuItem)
1293     {
1294       sortPairwiseMenuItem_actionPerformed();
1295     }
1296     else if (source == sortIDMenuItem)
1297     {
1298       sortIDMenuItem_actionPerformed();
1299     }
1300     else if (source == sortLengthMenuItem)
1301     {
1302       sortLengthMenuItem_actionPerformed();
1303     }
1304     else if (source == sortGroupMenuItem)
1305     {
1306       sortGroupMenuItem_actionPerformed();
1307     }
1308     else if (source == removeRedundancyMenuItem)
1309     {
1310       removeRedundancyMenuItem_actionPerformed();
1311     }
1312     else if (source == pairwiseAlignmentMenuItem)
1313     {
1314       pairwiseAlignmentMenuItem_actionPerformed();
1315     }
1316     else if (source == PCAMenuItem)
1317     {
1318       PCAMenuItem_actionPerformed();
1319     }
1320     else if (source == averageDistanceTreeMenuItem)
1321     {
1322       averageDistanceTreeMenuItem_actionPerformed();
1323     }
1324     else if (source == neighbourTreeMenuItem)
1325     {
1326       neighbourTreeMenuItem_actionPerformed();
1327     }
1328     else if (source == njTreeBlosumMenuItem)
1329     {
1330       njTreeBlosumMenuItem_actionPerformed();
1331     }
1332     else if (source == avDistanceTreeBlosumMenuItem)
1333     {
1334       avTreeBlosumMenuItem_actionPerformed();
1335     }
1336     else if (source == documentation)
1337     {
1338       documentation_actionPerformed();
1339     }
1340     else if (source == about)
1341     {
1342       about_actionPerformed();
1343     }
1344
1345   }
1346
1347   public void inputText_actionPerformed()
1348   {
1349     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1350     Frame frame = new Frame();
1351     frame.add(cap);
1352     jalview.bin.JalviewLite.addFrame(frame,
1353             MessageManager.getString("label.input_cut_paste"), 500, 500);
1354   }
1355
1356   protected void outputText_actionPerformed(ActionEvent e)
1357   {
1358     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1359     Frame frame = new Frame();
1360     frame.add(cap);
1361     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1362             "label.alignment_output_command",
1363             new Object[] { e.getActionCommand() }), 600, 500);
1364
1365     FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1366     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1367             fileFormat, viewport.getAlignment(),
1368             viewport.getShowJVSuffix()));
1369   }
1370
1371   public void loadAnnotations()
1372   {
1373     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1374     cap.setText(MessageManager
1375             .getString("label.paste_features_annotations_Tcoffee_here"));
1376     cap.setAnnotationImport();
1377     Frame frame = new Frame();
1378     frame.add(cap);
1379     jalview.bin.JalviewLite.addFrame(frame,
1380             MessageManager.getString("action.paste_annotations"), 400, 300);
1381
1382   }
1383
1384   public String outputAnnotations(boolean displayTextbox)
1385   {
1386     String annotation = new AnnotationFile()
1387             .printAnnotationsForView(viewport);
1388
1389     if (displayTextbox)
1390     {
1391       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1392       Frame frame = new Frame();
1393       frame.add(cap);
1394       jalview.bin.JalviewLite.addFrame(frame,
1395               MessageManager.getString("label.annotations"), 600, 500);
1396       cap.setText(annotation);
1397     }
1398
1399     return annotation;
1400   }
1401
1402   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1403   {
1404     if (alignPanel.getFeatureRenderer() != null
1405             && viewport.getFeaturesDisplayed() != null)
1406     {
1407       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1408
1409     }
1410     return null;
1411   }
1412
1413   public String outputFeatures(boolean displayTextbox, String format)
1414   {
1415     String features;
1416     FeaturesFile formatter = new FeaturesFile();
1417     if (format.equalsIgnoreCase("Jalview"))
1418     {
1419       features = formatter.printJalviewFormat(viewport.getAlignment()
1420               .getSequencesArray(), getDisplayedFeatureCols());
1421     }
1422     else
1423     {
1424       features = formatter.printGffFormat(viewport.getAlignment()
1425               .getSequencesArray(), getDisplayedFeatureCols());
1426     }
1427
1428     if (displayTextbox)
1429     {
1430       boolean frimport = false;
1431       if (features == null || features.equals("No Features Visible"))
1432       {
1433         features = "# No features visible - paste some and import them here.";
1434         frimport = true;
1435       }
1436
1437       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1438       if (frimport)
1439       {
1440         cap.setAnnotationImport();
1441       }
1442       Frame frame = new Frame();
1443       frame.add(cap);
1444       jalview.bin.JalviewLite.addFrame(frame,
1445               MessageManager.getString("label.features"), 600, 500);
1446       cap.setText(features);
1447     }
1448     else
1449     {
1450       if (features == null)
1451       {
1452         features = "";
1453       }
1454     }
1455
1456     return features;
1457   }
1458
1459   void launchFullApplication()
1460   {
1461     StringBuffer url = new StringBuffer(jalviewServletURL);
1462
1463     // allow servlet parameters to be passed in applet parameter
1464     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1465             : "?";
1466     url.append(firstSep);
1467
1468     url.append("open="
1469             + appendProtocol(viewport.applet.getParameter("file")));
1470
1471     if (viewport.applet.getParameter("features") != null)
1472     {
1473       url.append("&features=");
1474       url.append(appendProtocol(viewport.applet.getParameter("features")));
1475     }
1476
1477     if (viewport.applet.getParameter("annotations") != null)
1478     {
1479       url.append("&annotations=");
1480       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1481     }
1482
1483     if (viewport.applet.getParameter("jnetfile") != null
1484             || viewport.applet.getParameter("jpredfile") != null)
1485     {
1486       url.append("&annotations=");
1487       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1488               .getParameter("jnetfile") : viewport.applet
1489               .getParameter("jpredfile")));
1490     }
1491
1492     if (viewport.applet.getParameter("defaultColour") != null)
1493     {
1494       url.append("&colour="
1495               + removeWhiteSpace(viewport.applet
1496                       .getParameter("defaultColour")));
1497     }
1498
1499     if (viewport.applet.getParameter("userDefinedColour") != null)
1500     {
1501       url.append("&colour="
1502               + removeWhiteSpace(viewport.applet
1503                       .getParameter("userDefinedColour")));
1504     }
1505     if (viewport.applet.getParameter("tree") != null)
1506     {
1507       url.append("&tree="
1508               + appendProtocol(viewport.applet.getParameter("tree")));
1509     }
1510     if (viewport.applet.getParameter("treeFile") != null)
1511     {
1512       url.append("&tree="
1513               + appendProtocol(viewport.applet.getParameter("treeFile")));
1514     }
1515
1516     showURL(url.toString(), "FULL_APP");
1517   }
1518
1519   String removeWhiteSpace(String colour)
1520   {
1521     StringBuffer sb = new StringBuffer();
1522     for (int i = 0; i < colour.length(); i++)
1523     {
1524       if (Character.isWhitespace(colour.charAt(i)))
1525       {
1526         sb.append("%20");
1527       }
1528       else
1529       {
1530         sb.append(colour.charAt(i));
1531       }
1532     }
1533
1534     return sb.toString();
1535   }
1536
1537   String appendProtocol(String url)
1538   {
1539     try
1540     {
1541       new URL(url);
1542       url = URLEncoder.encode(url);
1543     }
1544     /*
1545      * When we finally deprecate 1.1 compatibility, we can start to use
1546      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1547      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1548      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1549      * ex.printStackTrace(); }
1550      */
1551     catch (java.net.MalformedURLException ex)
1552     {
1553       url = viewport.applet.getCodeBase() + url;
1554     }
1555     return url;
1556   }
1557
1558   public void closeMenuItem_actionPerformed()
1559   {
1560     PaintRefresher.RemoveComponent(alignPanel);
1561     if (alignPanel.seqPanel != null
1562             && alignPanel.seqPanel.seqCanvas != null)
1563     {
1564       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1565     }
1566     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1567     {
1568       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1569     }
1570
1571     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1572     {
1573       System.exit(0);
1574     }
1575     else
1576     {
1577     }
1578     viewport = null;
1579     alignPanel = null;
1580     this.dispose();
1581   }
1582
1583   /**
1584    * TODO: JAL-1104
1585    */
1586   void updateEditMenuBar()
1587   {
1588
1589     if (viewport.getHistoryList().size() > 0)
1590     {
1591       undoMenuItem.setEnabled(true);
1592       CommandI command = viewport.getHistoryList().peek();
1593       undoMenuItem.setLabel(MessageManager.formatMessage(
1594               "label.undo_command",
1595               new Object[] { command.getDescription() }));
1596     }
1597     else
1598     {
1599       undoMenuItem.setEnabled(false);
1600       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1601     }
1602
1603     if (viewport.getRedoList().size() > 0)
1604     {
1605       redoMenuItem.setEnabled(true);
1606
1607       CommandI command = viewport.getRedoList().peek();
1608       redoMenuItem.setLabel(MessageManager.formatMessage(
1609               "label.redo_command",
1610               new Object[] { command.getDescription() }));
1611     }
1612     else
1613     {
1614       redoMenuItem.setEnabled(false);
1615       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1616     }
1617   }
1618
1619   /**
1620    * TODO: JAL-1104
1621    */
1622   @Override
1623   public void addHistoryItem(CommandI command)
1624   {
1625     if (command.getSize() > 0)
1626     {
1627       viewport.addToHistoryList(command);
1628       viewport.clearRedoList();
1629       updateEditMenuBar();
1630       viewport.updateHiddenColumns();
1631     }
1632   }
1633
1634   /**
1635    * TODO: JAL-1104 DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   protected void undoMenuItem_actionPerformed()
1641   {
1642     if (viewport.getHistoryList().isEmpty())
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getHistoryList().pop();
1648     viewport.addToRedoList(command);
1649     command.undoCommand(null);
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     // JBPNote Test
1653     if (originalSource != viewport)
1654     {
1655       System.err
1656               .println("Warning: Viewport object mismatch whilst undoing");
1657     }
1658     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1659                                           // viewport.getColumnSelection().getHiddenColumns()
1660                                           // != null;
1661     updateEditMenuBar();
1662     originalSource.firePropertyChange("alignment", null, originalSource
1663             .getAlignment().getSequences());
1664   }
1665
1666   /**
1667    * TODO: JAL-1104 DOCUMENT ME!
1668    *
1669    * @param e
1670    *          DOCUMENT ME!
1671    */
1672   protected void redoMenuItem_actionPerformed()
1673   {
1674     if (viewport.getRedoList().isEmpty())
1675     {
1676       return;
1677     }
1678
1679     CommandI command = viewport.getRedoList().pop();
1680     viewport.addToHistoryList(command);
1681     command.doCommand(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 re-doing");
1689     }
1690     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1691                                           // viewport.getColumnSelection().getHiddenColumns()
1692                                           // != null;
1693
1694     updateEditMenuBar();
1695     originalSource.firePropertyChange("alignment", null, originalSource
1696             .getAlignment().getSequences());
1697   }
1698
1699   AlignmentViewport getOriginatingSource(CommandI command)
1700   {
1701     AlignmentViewport originalSource = null;
1702     // For sequence removal and addition, we need to fire
1703     // the property change event FROM the viewport where the
1704     // original alignment was altered
1705     AlignmentI al = null;
1706     if (command instanceof EditCommand)
1707     {
1708       EditCommand editCommand = (EditCommand) command;
1709       al = editCommand.getAlignment();
1710       Vector comps = (Vector) PaintRefresher.components.get(viewport
1711               .getSequenceSetId());
1712       for (int i = 0; i < comps.size(); i++)
1713       {
1714         if (comps.elementAt(i) instanceof AlignmentPanel)
1715         {
1716           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1717           {
1718             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1719             break;
1720           }
1721         }
1722       }
1723     }
1724
1725     if (originalSource == null)
1726     {
1727       // The original view is closed, we must validate
1728       // the current view against the closed view first
1729       if (al != null)
1730       {
1731         PaintRefresher.validateSequences(al, viewport.getAlignment());
1732       }
1733
1734       originalSource = viewport;
1735     }
1736
1737     return originalSource;
1738   }
1739
1740   /**
1741    * Move the currently selected sequences up or down one position in the
1742    * alignment
1743    *
1744    * @param up
1745    */
1746   public void moveSelectedSequences(boolean up)
1747   {
1748     SequenceGroup sg = viewport.getSelectionGroup();
1749     if (sg == null)
1750     {
1751       return;
1752     }
1753     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1754             up ? null : viewport.getHiddenRepSequences(), up);
1755     alignPanel.paintAlignment(true);
1756
1757     /*
1758      * Also move cDNA/protein complement sequences
1759      */
1760     AlignViewportI complement = viewport.getCodingComplement();
1761     if (complement != null)
1762     {
1763       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1764               viewport, complement);
1765       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1766               up ? null : complement.getHiddenRepSequences(), up);
1767       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1768     }
1769   }
1770
1771   synchronized void slideSequences(boolean right, int size)
1772   {
1773     List<SequenceI> sg = new Vector<SequenceI>();
1774     if (viewport.cursorMode)
1775     {
1776       sg.add(viewport.getAlignment().getSequenceAt(
1777               alignPanel.seqPanel.seqCanvas.cursorY));
1778     }
1779     else if (viewport.getSelectionGroup() != null
1780             && viewport.getSelectionGroup().getSize() != viewport
1781                     .getAlignment().getHeight())
1782     {
1783       sg = viewport.getSelectionGroup().getSequences(
1784               viewport.getHiddenRepSequences());
1785     }
1786
1787     if (sg.size() < 1)
1788     {
1789       return;
1790     }
1791
1792     Vector<SequenceI> invertGroup = new Vector();
1793
1794     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1795     {
1796       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1797       {
1798         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1799       }
1800     }
1801
1802     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1803
1804     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1805             .size()]);
1806     for (int i = 0; i < invertGroup.size(); i++)
1807     {
1808       seqs2[i] = invertGroup.elementAt(i);
1809     }
1810
1811     SlideSequencesCommand ssc;
1812     if (right)
1813     {
1814       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1815               size, viewport.getGapCharacter());
1816     }
1817     else
1818     {
1819       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1820               size, viewport.getGapCharacter());
1821     }
1822
1823     int groupAdjustment = 0;
1824     if (ssc.getGapsInsertedBegin() && right)
1825     {
1826       if (viewport.cursorMode)
1827       {
1828         alignPanel.seqPanel.moveCursor(size, 0);
1829       }
1830       else
1831       {
1832         groupAdjustment = size;
1833       }
1834     }
1835     else if (!ssc.getGapsInsertedBegin() && !right)
1836     {
1837       if (viewport.cursorMode)
1838       {
1839         alignPanel.seqPanel.moveCursor(-size, 0);
1840       }
1841       else
1842       {
1843         groupAdjustment = -size;
1844       }
1845     }
1846
1847     if (groupAdjustment != 0)
1848     {
1849       viewport.getSelectionGroup().setStartRes(
1850               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1851       viewport.getSelectionGroup().setEndRes(
1852               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1853     }
1854
1855     boolean appendHistoryItem = false;
1856     Deque<CommandI> historyList = viewport.getHistoryList();
1857     if (historyList != null && historyList.size() > 0
1858             && historyList.peek() instanceof SlideSequencesCommand)
1859     {
1860       appendHistoryItem = ssc
1861               .appendSlideCommand((SlideSequencesCommand) historyList
1862                       .peek());
1863     }
1864
1865     if (!appendHistoryItem)
1866     {
1867       addHistoryItem(ssc);
1868     }
1869
1870     repaint();
1871   }
1872
1873   static StringBuffer copiedSequences;
1874
1875   static Vector copiedHiddenColumns;
1876
1877   protected void copy_actionPerformed()
1878   {
1879     if (viewport.getSelectionGroup() == null)
1880     {
1881       return;
1882     }
1883
1884     SequenceGroup sg = viewport.getSelectionGroup();
1885     copiedSequences = new StringBuffer();
1886     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1887     for (int i = 0; i < sg.getSize(); i++)
1888     {
1889       SequenceI seq = sg.getSequenceAt(i);
1890       int index = viewport.getAlignment().findIndex(seq);
1891       orderedSeqs.put(index, seq);
1892     }
1893
1894     int index = 0, startRes, endRes;
1895     char ch;
1896
1897     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1898     {
1899       copiedHiddenColumns = new Vector();
1900       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1901       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1902       {
1903         copiedHiddenColumns.addElement(new int[] {
1904             region[0] - hiddenOffset, region[1] - hiddenOffset });
1905       }
1906     }
1907     else
1908     {
1909       copiedHiddenColumns = null;
1910     }
1911
1912     for (int i = 0; i < sg.getSize(); i++)
1913     {
1914       SequenceI seq = null;
1915
1916       while (seq == null)
1917       {
1918         if (orderedSeqs.containsKey(index))
1919         {
1920           seq = orderedSeqs.get(index);
1921           index++;
1922           break;
1923         }
1924         else
1925         {
1926           index++;
1927         }
1928       }
1929
1930       // FIND START RES
1931       // Returns residue following index if gap
1932       startRes = seq.findPosition(sg.getStartRes());
1933
1934       // FIND END RES
1935       // Need to find the residue preceeding index if gap
1936       endRes = 0;
1937
1938       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1939       {
1940         ch = seq.getCharAt(j);
1941         if (!jalview.util.Comparison.isGap((ch)))
1942         {
1943           endRes++;
1944         }
1945       }
1946
1947       if (endRes > 0)
1948       {
1949         endRes += seq.getStart() - 1;
1950       }
1951
1952       copiedSequences.append(seq.getName()
1953               + "\t"
1954               + startRes
1955               + "\t"
1956               + endRes
1957               + "\t"
1958               + seq.getSequenceAsString(sg.getStartRes(),
1959                       sg.getEndRes() + 1) + "\n");
1960     }
1961
1962   }
1963
1964   protected void pasteNew_actionPerformed()
1965   {
1966     paste(true);
1967   }
1968
1969   protected void pasteThis_actionPerformed()
1970   {
1971     paste(false);
1972   }
1973
1974   void paste(boolean newAlignment)
1975   {
1976     try
1977     {
1978
1979       if (copiedSequences == null)
1980       {
1981         return;
1982       }
1983
1984       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1985       Vector seqs = new Vector();
1986       while (st.hasMoreElements())
1987       {
1988         String name = st.nextToken();
1989         int start = Integer.parseInt(st.nextToken());
1990         int end = Integer.parseInt(st.nextToken());
1991         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1992       }
1993       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1994       for (int i = 0; i < seqs.size(); i++)
1995       {
1996         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1997       }
1998
1999       if (newAlignment)
2000       {
2001         String newtitle = MessageManager
2002                 .getString("label.copied_sequences");
2003         if (getTitle().startsWith(
2004                 MessageManager.getString("label.copied_sequences")))
2005         {
2006           newtitle = getTitle();
2007         }
2008         else
2009         {
2010           newtitle = newtitle.concat(MessageManager.formatMessage(
2011                   "label.from_msname", new String[] { getTitle() }));
2012         }
2013         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2014                 viewport.applet, newtitle, false);
2015         if (copiedHiddenColumns != null)
2016         {
2017           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2018           {
2019             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2020             af.viewport.hideColumns(region[0], region[1]);
2021           }
2022         }
2023
2024         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2025                 frameHeight);
2026       }
2027       else
2028       {
2029         addSequences(newSeqs);
2030       }
2031
2032     } catch (Exception ex)
2033     {
2034     } // could be anything being pasted in here
2035
2036   }
2037
2038   void addSequences(SequenceI[] seqs)
2039   {
2040     for (int i = 0; i < seqs.length; i++)
2041     {
2042       viewport.getAlignment().addSequence(seqs[i]);
2043     }
2044
2045     // !newAlignment
2046     addHistoryItem(new EditCommand(
2047             MessageManager.getString("label.add_sequences"), Action.PASTE,
2048             seqs, 0, viewport.getAlignment().getWidth(),
2049             viewport.getAlignment()));
2050
2051     viewport.setEndSeq(viewport.getAlignment().getHeight());
2052     viewport.getAlignment().getWidth();
2053     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2054             .getSequences());
2055
2056   }
2057
2058   protected void cut_actionPerformed()
2059   {
2060     copy_actionPerformed();
2061     delete_actionPerformed();
2062   }
2063
2064   protected void delete_actionPerformed()
2065   {
2066
2067     SequenceGroup sg = viewport.getSelectionGroup();
2068     if (sg == null)
2069     {
2070       return;
2071     }
2072
2073     Vector seqs = new Vector();
2074     SequenceI seq;
2075     for (int i = 0; i < sg.getSize(); i++)
2076     {
2077       seq = sg.getSequenceAt(i);
2078       seqs.addElement(seq);
2079     }
2080
2081     /*
2082      * If the cut affects all sequences, warn, remove highlighted columns
2083      */
2084     if (sg.getSize() == viewport.getAlignment().getHeight())
2085     {
2086       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2087               .getAlignment().getWidth()) ? true : false;
2088       if (isEntireAlignWidth)
2089       {
2090         String title = MessageManager.getString("label.delete_all");
2091         Panel infoPanel = new Panel();
2092         infoPanel.setLayout(new FlowLayout());
2093         infoPanel
2094                 .add(new Label(MessageManager.getString("warn.delete_all")));
2095
2096         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2097         dialog.setMainPanel(infoPanel);
2098         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2099         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2100         dialog.setVisible(true);
2101
2102         if (!dialog.accept)
2103         {
2104           return;
2105         }
2106       }
2107       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2108               sg.getEndRes() + 1);
2109     }
2110
2111     SequenceI[] cut = new SequenceI[seqs.size()];
2112     for (int i = 0; i < seqs.size(); i++)
2113     {
2114       cut[i] = (SequenceI) seqs.elementAt(i);
2115     }
2116
2117     /*
2118      * //ADD HISTORY ITEM
2119      */
2120     addHistoryItem(new EditCommand(
2121             MessageManager.getString("label.cut_sequences"), Action.CUT,
2122             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2123             viewport.getAlignment()));
2124
2125     viewport.setSelectionGroup(null);
2126     viewport.getAlignment().deleteGroup(sg);
2127
2128     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2129             .getSequences());
2130
2131     if (viewport.getAlignment().getHeight() < 1)
2132     {
2133       this.setVisible(false);
2134     }
2135     viewport.sendSelection();
2136   }
2137
2138   /**
2139    * group consensus toggled
2140    *
2141    */
2142   protected void showGroupConsensus_actionPerformed()
2143   {
2144     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2145     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2146
2147   }
2148
2149   /**
2150    * group conservation toggled.
2151    */
2152   protected void showGroupConservation_actionPerformed()
2153   {
2154     viewport.setShowGroupConservation(showGroupConservation.getState());
2155     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2156   }
2157
2158   /*
2159    * (non-Javadoc)
2160    *
2161    * @see
2162    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2163    * .event.ActionEvent)
2164    */
2165   protected void showConsensusHistogram_actionPerformed()
2166   {
2167     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2168     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2169   }
2170
2171   /*
2172    * (non-Javadoc)
2173    *
2174    * @see
2175    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2176    * .event.ActionEvent)
2177    */
2178   protected void showSequenceLogo_actionPerformed()
2179   {
2180     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2181     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2182   }
2183
2184   protected void normSequenceLogo_actionPerformed()
2185   {
2186     showSequenceLogo.setState(true);
2187     viewport.setShowSequenceLogo(true);
2188     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2189     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190   }
2191
2192   protected void applyAutoAnnotationSettings_actionPerformed()
2193   {
2194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195   }
2196
2197   protected void makeGrpsFromSelection_actionPerformed()
2198   {
2199     if (avc.makeGroupsFromSelection())
2200     {
2201       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2202       alignPanel.updateAnnotation();
2203       alignPanel.paintAlignment(true);
2204     }
2205   }
2206
2207   protected void createGroup_actionPerformed()
2208   {
2209     avc.createGroup();
2210   }
2211
2212   protected void unGroup_actionPerformed()
2213   {
2214     if (avc.unGroup())
2215     {
2216       alignPanel.alignmentChanged();
2217     }
2218   }
2219
2220   protected void deleteGroups_actionPerformed()
2221   {
2222     if (avc.deleteGroups())
2223     {
2224       alignPanel.alignmentChanged();
2225     }
2226   }
2227
2228   public void selectAllSequenceMenuItem_actionPerformed()
2229   {
2230     SequenceGroup sg = new SequenceGroup();
2231     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2232     {
2233       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2234     }
2235     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2236     viewport.setSelectionGroup(sg);
2237     // JAL-2034 - should delegate to
2238     // alignPanel to decide if overview needs
2239     // updating.
2240     alignPanel.paintAlignment(false);
2241     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2242     viewport.sendSelection();
2243   }
2244
2245   public void deselectAllSequenceMenuItem_actionPerformed()
2246   {
2247     if (viewport.cursorMode)
2248     {
2249       alignPanel.seqPanel.keyboardNo1 = null;
2250       alignPanel.seqPanel.keyboardNo2 = null;
2251     }
2252     viewport.setSelectionGroup(null);
2253     viewport.getColumnSelection().clear();
2254     viewport.setSelectionGroup(null);
2255     alignPanel.idPanel.idCanvas.searchResults = null;
2256     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2257     // JAL-2034 - should delegate to
2258     // alignPanel to decide if overview needs
2259     // updating.
2260     alignPanel.paintAlignment(false);
2261     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2262     viewport.sendSelection();
2263   }
2264
2265   public void invertSequenceMenuItem_actionPerformed()
2266   {
2267     SequenceGroup sg = viewport.getSelectionGroup();
2268     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2269     {
2270       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2271     }
2272
2273     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2274     viewport.sendSelection();
2275   }
2276
2277   public void invertColSel_actionPerformed()
2278   {
2279     viewport.invertColumnSelection();
2280     alignPanel.paintAlignment(true);
2281     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2282     viewport.sendSelection();
2283   }
2284
2285   void trimAlignment(boolean trimLeft)
2286   {
2287     ColumnSelection colSel = viewport.getColumnSelection();
2288     int column;
2289
2290     if (!colSel.isEmpty())
2291     {
2292       if (trimLeft)
2293       {
2294         column = colSel.getMin();
2295       }
2296       else
2297       {
2298         column = colSel.getMax();
2299       }
2300
2301       SequenceI[] seqs;
2302       if (viewport.getSelectionGroup() != null)
2303       {
2304         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2305                 viewport.getHiddenRepSequences());
2306       }
2307       else
2308       {
2309         seqs = viewport.getAlignment().getSequencesArray();
2310       }
2311
2312       TrimRegionCommand trimRegion;
2313       if (trimLeft)
2314       {
2315         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2316                 column, viewport.getAlignment());
2317         viewport.setStartRes(0);
2318       }
2319       else
2320       {
2321         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2322                 column, viewport.getAlignment());
2323       }
2324
2325       statusBar.setText(MessageManager.formatMessage(
2326               "label.removed_columns",
2327               new String[] { Integer.valueOf(trimRegion.getSize())
2328                       .toString() }));
2329       addHistoryItem(trimRegion);
2330
2331       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2332       {
2333         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2334                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2335         {
2336           viewport.getAlignment().deleteGroup(sg);
2337         }
2338       }
2339
2340       viewport.firePropertyChange("alignment", null, viewport
2341               .getAlignment().getSequences());
2342     }
2343   }
2344
2345   public void removeGappedColumnMenuItem_actionPerformed()
2346   {
2347     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2348
2349     SequenceI[] seqs;
2350     if (viewport.getSelectionGroup() != null)
2351     {
2352       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2353               viewport.getHiddenRepSequences());
2354       start = viewport.getSelectionGroup().getStartRes();
2355       end = viewport.getSelectionGroup().getEndRes();
2356     }
2357     else
2358     {
2359       seqs = viewport.getAlignment().getSequencesArray();
2360     }
2361
2362     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2363             "Remove Gapped Columns", seqs, start, end,
2364             viewport.getAlignment());
2365
2366     addHistoryItem(removeGapCols);
2367
2368     statusBar.setText(MessageManager.formatMessage(
2369             "label.removed_empty_columns",
2370             new String[] { Integer.valueOf(removeGapCols.getSize())
2371                     .toString() }));
2372
2373     // This is to maintain viewport position on first residue
2374     // of first sequence
2375     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2376     int startRes = seq.findPosition(viewport.startRes);
2377     // ShiftList shifts;
2378     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2379     // edit.alColumnChanges=shifts.getInverse();
2380     // if (viewport.hasHiddenColumns)
2381     // viewport.getColumnSelection().compensateForEdits(shifts);
2382     viewport.setStartRes(seq.findIndex(startRes) - 1);
2383     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2384             .getSequences());
2385
2386   }
2387
2388   public void removeAllGapsMenuItem_actionPerformed()
2389   {
2390     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2391
2392     SequenceI[] seqs;
2393     if (viewport.getSelectionGroup() != null)
2394     {
2395       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2396               viewport.getHiddenRepSequences());
2397       start = viewport.getSelectionGroup().getStartRes();
2398       end = viewport.getSelectionGroup().getEndRes();
2399     }
2400     else
2401     {
2402       seqs = viewport.getAlignment().getSequencesArray();
2403     }
2404
2405     // This is to maintain viewport position on first residue
2406     // of first sequence
2407     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2408     int startRes = seq.findPosition(viewport.startRes);
2409
2410     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2411             viewport.getAlignment()));
2412
2413     viewport.setStartRes(seq.findIndex(startRes) - 1);
2414
2415     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2416             .getSequences());
2417
2418   }
2419
2420   public void findMenuItem_actionPerformed()
2421   {
2422     new Finder(alignPanel);
2423   }
2424
2425   /**
2426    * create a new view derived from the current view
2427    *
2428    * @param viewtitle
2429    * @return frame for the new view
2430    */
2431   public AlignFrame newView(String viewtitle)
2432   {
2433     AlignmentI newal;
2434     if (viewport.hasHiddenRows())
2435     {
2436       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2437               .getFullAlignment().getSequencesArray());
2438     }
2439     else
2440     {
2441       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2442     }
2443
2444     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2445     {
2446       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2447       {
2448         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2449         {
2450           newal.addAnnotation(viewport.getAlignment()
2451                   .getAlignmentAnnotation()[i]);
2452         }
2453       }
2454     }
2455
2456     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2457
2458     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2459     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2460     PaintRefresher.Register(newaf.alignPanel,
2461             newaf.alignPanel.av.getSequenceSetId());
2462
2463     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2464             newaf.alignPanel.av.getSequenceSetId());
2465     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2466             newaf.alignPanel.av.getSequenceSetId());
2467
2468     Vector comps = (Vector) PaintRefresher.components.get(viewport
2469             .getSequenceSetId());
2470     int viewSize = -1;
2471     for (int i = 0; i < comps.size(); i++)
2472     {
2473       if (comps.elementAt(i) instanceof AlignmentPanel)
2474       {
2475         viewSize++;
2476       }
2477     }
2478
2479     String title = new String(this.getTitle());
2480     if (viewtitle != null)
2481     {
2482       title = viewtitle + " ( " + title + ")";
2483     }
2484     else
2485     {
2486       if (title.indexOf("(View") > -1)
2487       {
2488         title = title.substring(0, title.indexOf("(View"));
2489       }
2490       title += "(View " + viewSize + ")";
2491     }
2492
2493     newaf.setTitle(title.toString());
2494
2495     newaf.viewport.setHistoryList(viewport.getHistoryList());
2496     newaf.viewport.setRedoList(viewport.getRedoList());
2497     return newaf;
2498   }
2499
2500   /**
2501    *
2502    * @return list of feature groups on the view
2503    */
2504   public String[] getFeatureGroups()
2505   {
2506     FeatureRenderer fr = null;
2507     if (alignPanel != null
2508             && (fr = alignPanel.getFeatureRenderer()) != null)
2509     {
2510       List<String> gps = fr.getFeatureGroups();
2511       String[] _gps = gps.toArray(new String[gps.size()]);
2512       return _gps;
2513     }
2514     return null;
2515   }
2516
2517   /**
2518    * get sequence feature groups that are hidden or shown
2519    *
2520    * @param visible
2521    *          true is visible
2522    * @return list
2523    */
2524   public String[] getFeatureGroupsOfState(boolean visible)
2525   {
2526     FeatureRenderer fr = null;
2527     if (alignPanel != null
2528             && (fr = alignPanel.getFeatureRenderer()) != null)
2529     {
2530       List<String> gps = fr.getGroups(visible);
2531       String[] _gps = gps.toArray(new String[gps.size()]);
2532       return _gps;
2533     }
2534     return null;
2535   }
2536
2537   /**
2538    * Change the display state for the given feature groups
2539    *
2540    * @param groups
2541    *          list of group strings
2542    * @param state
2543    *          visible or invisible
2544    */
2545   public void setFeatureGroupState(String[] groups, boolean state)
2546   {
2547     FeatureRenderer fr = null;
2548     this.sequenceFeatures.setState(true);
2549     viewport.setShowSequenceFeatures(true);
2550     if (alignPanel != null
2551             && (fr = alignPanel.getFeatureRenderer()) != null)
2552     {
2553
2554       fr.setGroupVisibility(Arrays.asList(groups), state);
2555       alignPanel.seqPanel.seqCanvas.repaint();
2556       if (alignPanel.overviewPanel != null)
2557       {
2558         alignPanel.overviewPanel.updateOverviewImage();
2559       }
2560     }
2561   }
2562
2563   public void seqLimits_itemStateChanged()
2564   {
2565     viewport.setShowJVSuffix(seqLimits.getState());
2566     alignPanel.fontChanged();
2567     alignPanel.paintAlignment(true);
2568   }
2569
2570   protected void colourTextMenuItem_actionPerformed()
2571   {
2572     viewport.setColourText(colourTextMenuItem.getState());
2573     alignPanel.paintAlignment(true);
2574   }
2575
2576   protected void displayNonconservedMenuItem_actionPerformed()
2577   {
2578     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2579     alignPanel.paintAlignment(true);
2580   }
2581
2582   protected void wrapMenuItem_actionPerformed()
2583   {
2584     viewport.setWrapAlignment(wrapMenuItem.getState());
2585     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2586     scaleAbove.setEnabled(wrapMenuItem.getState());
2587     scaleLeft.setEnabled(wrapMenuItem.getState());
2588     scaleRight.setEnabled(wrapMenuItem.getState());
2589     alignPanel.paintAlignment(true);
2590   }
2591
2592   public void overviewMenuItem_actionPerformed()
2593   {
2594     if (alignPanel.overviewPanel != null)
2595     {
2596       return;
2597     }
2598
2599     Frame frame = new Frame();
2600     OverviewPanel overview = new OverviewPanel(alignPanel);
2601     frame.add(overview);
2602     // +50 must allow for applet frame window
2603     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2604             "label.overview_params", new String[] { this.getTitle() }),
2605             overview.getPreferredSize().width,
2606             overview.getPreferredSize().height + 50);
2607
2608     frame.pack();
2609     final AlignmentPanel ap = alignPanel;
2610     frame.addWindowListener(new WindowAdapter()
2611     {
2612       @Override
2613       public void windowClosing(WindowEvent e)
2614       {
2615         if (ap != null)
2616         {
2617           ap.setOverviewPanel(null);
2618         }
2619       };
2620     });
2621
2622     alignPanel.setOverviewPanel(overview);
2623
2624   }
2625
2626   @Override
2627   public void changeColour(ColourSchemeI cs)
2628   {
2629
2630     if (cs != null)
2631     {
2632       if (viewport.getAbovePIDThreshold())
2633       {
2634         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2635                 cs, "Background"));
2636       }
2637
2638       if (viewport.getConservationSelected())
2639       {
2640         cs.setConservationApplied(true);
2641         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2642                 cs, "Background"));
2643       }
2644       else
2645       {
2646         cs.setConservationApplied(false);
2647       }
2648     }
2649     viewport.setGlobalColourScheme(cs);
2650
2651     alignPanel.paintAlignment(true);
2652   }
2653
2654   protected void modifyPID_actionPerformed()
2655   {
2656     if (viewport.getAbovePIDThreshold()
2657             && viewport.getGlobalColourScheme() != null)
2658     {
2659       SliderPanel.setPIDSliderSource(alignPanel,
2660               viewport.getGlobalColourScheme(), "Background");
2661       SliderPanel.showPIDSlider();
2662     }
2663   }
2664
2665   protected void modifyConservation_actionPerformed()
2666   {
2667     if (viewport.getConservationSelected()
2668             && viewport.getGlobalColourScheme() != null)
2669     {
2670       SliderPanel.setConservationSlider(alignPanel,
2671               viewport.getGlobalColourScheme(), "Background");
2672       SliderPanel.showConservationSlider();
2673     }
2674   }
2675
2676   protected void conservationMenuItem_actionPerformed()
2677   {
2678     viewport.setConservationSelected(conservationMenuItem.getState());
2679
2680     viewport.setAbovePIDThreshold(false);
2681     abovePIDThreshold.setState(false);
2682
2683     changeColour(viewport.getGlobalColourScheme());
2684
2685     modifyConservation_actionPerformed();
2686   }
2687
2688   public void abovePIDThreshold_actionPerformed()
2689   {
2690     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2691
2692     conservationMenuItem.setState(false);
2693     viewport.setConservationSelected(false);
2694
2695     changeColour(viewport.getGlobalColourScheme());
2696
2697     modifyPID_actionPerformed();
2698   }
2699
2700   public void sortPairwiseMenuItem_actionPerformed()
2701   {
2702     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2703     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2704             .getAlignment().getSequenceAt(0), null);
2705
2706     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2707             viewport.getAlignment()));
2708     alignPanel.paintAlignment(true);
2709   }
2710
2711   public void sortIDMenuItem_actionPerformed()
2712   {
2713     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2714     AlignmentSorter.sortByID(viewport.getAlignment());
2715     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2716             viewport.getAlignment()));
2717     alignPanel.paintAlignment(true);
2718   }
2719
2720   public void sortLengthMenuItem_actionPerformed()
2721   {
2722     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723     AlignmentSorter.sortByLength(viewport.getAlignment());
2724     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2725             viewport.getAlignment()));
2726     alignPanel.paintAlignment(true);
2727   }
2728
2729   public void sortGroupMenuItem_actionPerformed()
2730   {
2731     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2732     AlignmentSorter.sortByGroup(viewport.getAlignment());
2733     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2734             viewport.getAlignment()));
2735     alignPanel.paintAlignment(true);
2736
2737   }
2738
2739   public void removeRedundancyMenuItem_actionPerformed()
2740   {
2741     new RedundancyPanel(alignPanel);
2742   }
2743
2744   public void pairwiseAlignmentMenuItem_actionPerformed()
2745   {
2746     if (viewport.getSelectionGroup() != null
2747             && viewport.getSelectionGroup().getSize() > 1)
2748     {
2749       Frame frame = new Frame();
2750       frame.add(new PairwiseAlignPanel(alignPanel));
2751       jalview.bin.JalviewLite.addFrame(frame,
2752               MessageManager.getString("action.pairwise_alignment"), 600,
2753               500);
2754     }
2755   }
2756
2757   public void PCAMenuItem_actionPerformed()
2758   {
2759     // are the sequences aligned?
2760     if (!viewport.getAlignment().isAligned(false))
2761     {
2762       SequenceI current;
2763       int Width = viewport.getAlignment().getWidth();
2764
2765       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2766       {
2767         current = viewport.getAlignment().getSequenceAt(i);
2768
2769         if (current.getLength() < Width)
2770         {
2771           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2772         }
2773       }
2774       alignPanel.paintAlignment(true);
2775     }
2776
2777     if ((viewport.getSelectionGroup() != null
2778             && viewport.getSelectionGroup().getSize() < 4 && viewport
2779             .getSelectionGroup().getSize() > 0)
2780             || viewport.getAlignment().getHeight() < 4)
2781     {
2782       return;
2783     }
2784
2785     try
2786     {
2787       new PCAPanel(viewport);
2788     } catch (java.lang.OutOfMemoryError ex)
2789     {
2790     }
2791
2792   }
2793
2794   public void averageDistanceTreeMenuItem_actionPerformed()
2795   {
2796     NewTreePanel("AV", "PID", "Average distance tree using PID");
2797   }
2798
2799   public void neighbourTreeMenuItem_actionPerformed()
2800   {
2801     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2802   }
2803
2804   protected void njTreeBlosumMenuItem_actionPerformed()
2805   {
2806     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2807   }
2808
2809   protected void avTreeBlosumMenuItem_actionPerformed()
2810   {
2811     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2812   }
2813
2814   void NewTreePanel(String type, String pwType, String title)
2815   {
2816     // are the sequences aligned?
2817     if (!viewport.getAlignment().isAligned(false))
2818     {
2819       SequenceI current;
2820       int Width = viewport.getAlignment().getWidth();
2821
2822       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2823       {
2824         current = viewport.getAlignment().getSequenceAt(i);
2825
2826         if (current.getLength() < Width)
2827         {
2828           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2829         }
2830       }
2831       alignPanel.paintAlignment(true);
2832
2833     }
2834
2835     if ((viewport.getSelectionGroup() != null && viewport
2836             .getSelectionGroup().getSize() > 1)
2837             || (viewport.getAlignment().getHeight() > 1))
2838     {
2839       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2840
2841       addTreeMenuItem(tp, title);
2842
2843       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2844     }
2845   }
2846
2847   void loadTree_actionPerformed()
2848   {
2849     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2850     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2851     cap.setTreeImport();
2852     Frame frame = new Frame();
2853     frame.add(cap);
2854     jalview.bin.JalviewLite.addFrame(frame,
2855             MessageManager.getString("label.paste_newick_file"), 400, 300);
2856   }
2857
2858   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2859   {
2860     TreePanel tp = new TreePanel(alignPanel, treeFile,
2861             MessageManager.getString("label.load_tree_from_file"), tree);
2862     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2863     addTreeMenuItem(tp, treeFile);
2864   }
2865
2866   /**
2867    * sort the alignment using the given treePanel
2868    *
2869    * @param treePanel
2870    *          tree used to sort view
2871    * @param title
2872    *          string used for undo event name
2873    */
2874   public void sortByTree(TreePanel treePanel, String title)
2875   {
2876     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2877     AlignmentSorter
2878             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2879     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2880     // HistoryItem.SORT));
2881     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2882             "label.order_by_params", new String[] { title }), oldOrder,
2883             viewport.getAlignment()));
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   /**
2888    * Do any automatic reordering of the alignment and add the necessary bits to
2889    * the menu structure for the new tree
2890    *
2891    * @param treePanel
2892    * @param title
2893    */
2894   protected void addTreeMenuItem(final TreePanel treePanel,
2895           final String title)
2896   {
2897     final MenuItem item = new MenuItem(title);
2898     sortByTreeMenu.add(item);
2899     item.addActionListener(new java.awt.event.ActionListener()
2900     {
2901       @Override
2902       public void actionPerformed(ActionEvent evt)
2903       {
2904         sortByTree(treePanel, title); // treePanel.getTitle());
2905       }
2906     });
2907
2908     treePanel.addWindowListener(new WindowAdapter()
2909     {
2910       @Override
2911       public void windowOpened(WindowEvent e)
2912       {
2913         if (viewport.sortByTree)
2914         {
2915           sortByTree(treePanel, title);
2916         }
2917         super.windowOpened(e);
2918       }
2919
2920       @Override
2921       public void windowClosing(WindowEvent e)
2922       {
2923         sortByTreeMenu.remove(item);
2924       };
2925     });
2926   }
2927
2928   public boolean sortBy(AlignmentOrder alorder, String undoname)
2929   {
2930     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2931     if (viewport.applet.debug)
2932     {
2933       System.err.println("Sorting " + alorder.getOrder().size()
2934               + " in alignment '" + getTitle() + "'");
2935     }
2936     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2937     if (undoname != null)
2938     {
2939       addHistoryItem(new OrderCommand(undoname, oldOrder,
2940               viewport.getAlignment()));
2941     }
2942     alignPanel.paintAlignment(true);
2943     return true;
2944   }
2945
2946   protected void documentation_actionPerformed()
2947   {
2948     alignPanel.av.applet.openJalviewHelpUrl();
2949   }
2950
2951   protected void about_actionPerformed()
2952   {
2953
2954     class AboutPanel extends Canvas
2955     {
2956       String version;
2957
2958       String builddate;
2959
2960       public AboutPanel(String version, String builddate)
2961       {
2962         this.version = version;
2963         this.builddate = builddate;
2964       }
2965
2966       @Override
2967       public void paint(Graphics g)
2968       {
2969         g.setColor(Color.white);
2970         g.fillRect(0, 0, getSize().width, getSize().height);
2971         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2972         FontMetrics fm = g.getFontMetrics();
2973         int fh = fm.getHeight();
2974         int y = 5, x = 7;
2975         g.setColor(Color.black);
2976         // TODO: update this text for each release or centrally store it for
2977         // lite and application
2978         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2979         g.drawString(MessageManager.formatMessage(
2980                 "label.jalviewLite_release", new String[] { version }), x,
2981                 y += fh);
2982         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2983         g.drawString(MessageManager.formatMessage(
2984                 "label.jaview_build_date", new String[] { builddate }), x,
2985                 y += fh);
2986         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2987         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2988                 x, y += fh * 1.5);
2989         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2990                 x + 50, y += fh + 8);
2991         g.drawString(
2992                 MessageManager.getString("label.jalview_dev_managers"), x,
2993                 y += fh);
2994         g.drawString(MessageManager
2995                 .getString("label.jalview_distribution_lists"), x, y += fh);
2996         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2997                 x, y += fh + 8);
2998         g.drawString(
2999                 MessageManager.getString("label.jalview_cite_1_authors"),
3000                 x, y += fh);
3001         g.drawString(
3002                 MessageManager.getString("label.jalview_cite_1_title"), x,
3003                 y += fh);
3004         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3005                 x, y += fh);
3006       }
3007     }
3008
3009     Frame frame = new Frame();
3010     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3011             .getBuildDate()));
3012     jalview.bin.JalviewLite.addFrame(frame,
3013             MessageManager.getString("label.jalview"), 580, 220);
3014
3015   }
3016
3017   public void showURL(String url, String target)
3018   {
3019     if (viewport.applet == null)
3020     {
3021       System.out.println("Not running as applet - no browser available.");
3022     }
3023     else
3024     {
3025       viewport.applet.showURL(url, target);
3026     }
3027   }
3028
3029   // ////////////////////////////////////////////////////////////////////////////////
3030   // JBuilder Graphics here
3031
3032   MenuBar alignFrameMenuBar = new MenuBar();
3033
3034   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3035
3036   MenuItem loadApplication = new MenuItem(
3037           MessageManager.getString("label.view_full_application"));
3038
3039   MenuItem loadTree = new MenuItem(
3040           MessageManager.getString("label.load_associated_tree"));
3041
3042   MenuItem loadAnnotations = new MenuItem(
3043           MessageManager.getString("label.load_features_annotations"));
3044
3045   MenuItem outputFeatures = new MenuItem(
3046           MessageManager.getString("label.export_features"));
3047
3048   MenuItem outputAnnotations = new MenuItem(
3049           MessageManager.getString("label.export_annotations"));
3050
3051   MenuItem closeMenuItem = new MenuItem(
3052           MessageManager.getString("action.close"));
3053
3054   MenuItem selectAllSequenceMenuItem = new MenuItem(
3055           MessageManager.getString("action.select_all"));
3056
3057   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3058           MessageManager.getString("action.deselect_all"));
3059
3060   MenuItem invertSequenceMenuItem = new MenuItem(
3061           MessageManager.getString("action.invert_selection"));
3062
3063   MenuItem remove2LeftMenuItem = new MenuItem();
3064
3065   MenuItem remove2RightMenuItem = new MenuItem();
3066
3067   MenuItem removeGappedColumnMenuItem = new MenuItem();
3068
3069   MenuItem removeAllGapsMenuItem = new MenuItem();
3070
3071   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3072
3073   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3074
3075   MenuItem sortPairwiseMenuItem = new MenuItem();
3076
3077   MenuItem sortIDMenuItem = new MenuItem();
3078
3079   MenuItem sortLengthMenuItem = new MenuItem();
3080
3081   MenuItem sortGroupMenuItem = new MenuItem();
3082
3083   MenuItem removeRedundancyMenuItem = new MenuItem();
3084
3085   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3086
3087   MenuItem PCAMenuItem = new MenuItem();
3088
3089   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3090
3091   MenuItem neighbourTreeMenuItem = new MenuItem();
3092
3093   BorderLayout borderLayout1 = new BorderLayout();
3094
3095   public Label statusBar = new Label();
3096
3097   MenuItem clustalColour = new MenuItem();
3098
3099   MenuItem zappoColour = new MenuItem();
3100
3101   MenuItem taylorColour = new MenuItem();
3102
3103   MenuItem hydrophobicityColour = new MenuItem();
3104
3105   MenuItem helixColour = new MenuItem();
3106
3107   MenuItem strandColour = new MenuItem();
3108
3109   MenuItem turnColour = new MenuItem();
3110
3111   MenuItem buriedColour = new MenuItem();
3112
3113   MenuItem purinePyrimidineColour = new MenuItem();
3114
3115   // MenuItem RNAInteractionColour = new MenuItem();
3116
3117   MenuItem RNAHelixColour = new MenuItem();
3118
3119   MenuItem userDefinedColour = new MenuItem();
3120
3121   MenuItem PIDColour = new MenuItem();
3122
3123   MenuItem BLOSUM62Colour = new MenuItem();
3124
3125   MenuItem tcoffeeColour = new MenuItem();
3126
3127   MenuItem njTreeBlosumMenuItem = new MenuItem();
3128
3129   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3130
3131   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3132
3133   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3134
3135   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3136
3137   MenuItem alProperties = new MenuItem(
3138           MessageManager.getString("label.alignment_props"));
3139
3140   MenuItem overviewMenuItem = new MenuItem();
3141
3142   MenuItem undoMenuItem = new MenuItem();
3143
3144   MenuItem redoMenuItem = new MenuItem();
3145
3146   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3147
3148   MenuItem noColourmenuItem = new MenuItem();
3149
3150   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3151
3152   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3153
3154   MenuItem findMenuItem = new MenuItem();
3155
3156   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3157
3158   MenuItem nucleotideColour = new MenuItem();
3159
3160   MenuItem deleteGroups = new MenuItem();
3161
3162   MenuItem grpsFromSelection = new MenuItem();
3163
3164   MenuItem createGroup = new MenuItem();
3165
3166   MenuItem unGroup = new MenuItem();
3167
3168   MenuItem delete = new MenuItem();
3169
3170   MenuItem copy = new MenuItem();
3171
3172   MenuItem cut = new MenuItem();
3173
3174   Menu pasteMenu = new Menu();
3175
3176   MenuItem pasteNew = new MenuItem();
3177
3178   MenuItem pasteThis = new MenuItem();
3179
3180   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3181
3182   MenuItem font = new MenuItem();
3183
3184   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3185
3186   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3187
3188   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3189
3190   MenuItem modifyPID = new MenuItem();
3191
3192   MenuItem modifyConservation = new MenuItem();
3193
3194   CheckboxMenuItem autoCalculate = null;
3195
3196   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3197           "Sort Alignment With New Tree", true);
3198
3199   Menu sortByTreeMenu = new Menu();
3200
3201   MenuItem inputText = new MenuItem();
3202
3203   MenuItem documentation = new MenuItem();
3204
3205   MenuItem about = new MenuItem();
3206
3207   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3208
3209   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3222
3223   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3224
3225   /**
3226    * Initialise menus and other items
3227    *
3228    * @throws Exception
3229    */
3230   private void jbInit() throws Exception
3231   {
3232     setMenuBar(alignFrameMenuBar);
3233
3234     /*
3235      * Configure File menu items and actions
3236      */
3237     inputText
3238             .setLabel(MessageManager.getString("label.input_from_textbox"));
3239     inputText.addActionListener(this);
3240     Menu outputTextboxMenu = new Menu(
3241             MessageManager.getString("label.out_to_textbox"));
3242     for (String ff : FileFormat.getWritableFormats(true))
3243     {
3244       MenuItem item = new MenuItem(ff);
3245
3246       item.addActionListener(new java.awt.event.ActionListener()
3247       {
3248         @Override
3249         public void actionPerformed(ActionEvent e)
3250         {
3251           outputText_actionPerformed(e);
3252         }
3253       });
3254
3255       outputTextboxMenu.add(item);
3256     }
3257     closeMenuItem.addActionListener(this);
3258     loadApplication.addActionListener(this);
3259     loadTree.addActionListener(this);
3260     loadAnnotations.addActionListener(this);
3261     outputFeatures.addActionListener(this);
3262     outputAnnotations.addActionListener(this);
3263
3264     /*
3265      * Configure Edit menu items and actions
3266      */
3267     undoMenuItem.setEnabled(false);
3268     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3269     undoMenuItem.addActionListener(this);
3270     redoMenuItem.setEnabled(false);
3271     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3272     redoMenuItem.addActionListener(this);
3273     copy.setLabel(MessageManager.getString("action.copy"));
3274     copy.addActionListener(this);
3275     cut.setLabel(MessageManager.getString("action.cut"));
3276     cut.addActionListener(this);
3277     delete.setLabel(MessageManager.getString("action.delete"));
3278     delete.addActionListener(this);
3279     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3280     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3281     pasteNew.addActionListener(this);
3282     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3283     pasteThis.addActionListener(this);
3284     remove2LeftMenuItem.setLabel(MessageManager
3285             .getString("action.remove_left"));
3286     remove2LeftMenuItem.addActionListener(this);
3287     remove2RightMenuItem.setLabel(MessageManager
3288             .getString("action.remove_right"));
3289     remove2RightMenuItem.addActionListener(this);
3290     removeGappedColumnMenuItem.setLabel(MessageManager
3291             .getString("action.remove_empty_columns"));
3292     removeGappedColumnMenuItem.addActionListener(this);
3293     removeAllGapsMenuItem.setLabel(MessageManager
3294             .getString("action.remove_all_gaps"));
3295     removeAllGapsMenuItem.addActionListener(this);
3296     removeRedundancyMenuItem.setLabel(MessageManager
3297             .getString("action.remove_redundancy"));
3298     removeRedundancyMenuItem.addActionListener(this);
3299
3300     /*
3301      * Configure Select menu items and actions
3302      */
3303     findMenuItem.setLabel(MessageManager.getString("action.find"));
3304     findMenuItem.addActionListener(this);
3305     selectAllSequenceMenuItem.addActionListener(this);
3306     deselectAllSequenceMenuItem.addActionListener(this);
3307     invertSequenceMenuItem.setLabel(MessageManager
3308             .getString("action.invert_sequence_selection"));
3309     invertSequenceMenuItem.addActionListener(this);
3310     invertColSel.setLabel(MessageManager
3311             .getString("action.invert_column_selection"));
3312     invertColSel.addActionListener(this);
3313     deleteGroups.setLabel(MessageManager
3314             .getString("action.undefine_groups"));
3315     deleteGroups.addActionListener(this);
3316     grpsFromSelection.setLabel(MessageManager
3317             .getString("action.make_groups_selection"));
3318     grpsFromSelection.addActionListener(this);
3319     createGroup.setLabel(MessageManager.getString("action.create_group"));
3320     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3321     annotationColumnSelection.setLabel(MessageManager
3322             .getString("action.select_by_annotation"));
3323     annotationColumnSelection.addActionListener(this);
3324
3325     /*
3326      * Configure View menu items and actions
3327      */
3328     newView.setLabel(MessageManager.getString("action.new_view"));
3329     newView.addActionListener(this);
3330     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3331     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3332     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3333     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3334     hideColumns
3335             .setLabel(MessageManager.getString("label.selected_columns"));
3336     hideSequences.setLabel(MessageManager
3337             .getString("label.selected_sequences"));
3338     hideAllButSelection.setLabel(MessageManager
3339             .getString("label.all_but_selected_region"));
3340     hideAllSelection.setLabel(MessageManager
3341             .getString("label.selected_region"));
3342     showAllHidden.setLabel(MessageManager
3343             .getString("label.all_sequences_columns"));
3344     showColumns.addActionListener(this);
3345     showSeqs.addActionListener(this);
3346     hideColumns.addActionListener(this);
3347     hideSequences.addActionListener(this);
3348     hideAllButSelection.addActionListener(this);
3349     hideAllSelection.addActionListener(this);
3350     showAllHidden.addActionListener(this);
3351     featureSettings.setLabel(MessageManager
3352             .getString("action.feature_settings"));
3353     featureSettings.addActionListener(this);
3354     sequenceFeatures.setLabel(MessageManager
3355             .getString("label.show_sequence_features"));
3356     sequenceFeatures.addItemListener(this);
3357     sequenceFeatures.setState(false);
3358     followMouseOverFlag.setLabel(MessageManager
3359             .getString("label.automatic_scrolling"));
3360     followMouseOverFlag.addItemListener(this);
3361     alProperties.addActionListener(this);
3362     overviewMenuItem.setLabel(MessageManager
3363             .getString("label.overview_window"));
3364     overviewMenuItem.addActionListener(this);
3365
3366     /*
3367      * Configure Annotations menu items and actions
3368      */
3369     annotationPanelMenuItem.setLabel(MessageManager
3370             .getString("label.show_annotations"));
3371     annotationPanelMenuItem.addItemListener(this);
3372     showGroupConsensus.setLabel(MessageManager
3373             .getString("label.group_consensus"));
3374     showGroupConservation.setLabel(MessageManager
3375             .getString("label.group_conservation"));
3376     showConsensusHistogram.setLabel(MessageManager
3377             .getString("label.show_consensus_histogram"));
3378     showSequenceLogo.setLabel(MessageManager
3379             .getString("label.show_consensus_logo"));
3380     normSequenceLogo.setLabel(MessageManager
3381             .getString("label.norm_consensus_logo"));
3382     applyAutoAnnotationSettings.setLabel(MessageManager
3383             .getString("label.apply_all_groups"));
3384     applyAutoAnnotationSettings.setState(true);
3385     Menu autoAnnMenu = new Menu(
3386             MessageManager.getString("label.autocalculated_annotation"));
3387     showGroupConsensus.addItemListener(this);
3388     showGroupConservation.addItemListener(this);
3389     showConsensusHistogram.addItemListener(this);
3390     showSequenceLogo.addItemListener(this);
3391     normSequenceLogo.addItemListener(this);
3392     applyAutoAnnotationSettings.addItemListener(this);
3393     showAlignmentAnnotations = new CheckboxMenuItem(
3394             MessageManager.getString("label.show_all_al_annotations"));
3395     showSequenceAnnotations = new CheckboxMenuItem(
3396             MessageManager.getString("label.show_all_seq_annotations"));
3397     sortAnnBySequence = new CheckboxMenuItem(
3398             MessageManager.getString("label.sort_annotations_by_sequence"));
3399     sortAnnByLabel = new CheckboxMenuItem(
3400             MessageManager.getString("label.sort_annotations_by_label"));
3401     showAutoFirst = new CheckboxMenuItem(
3402             MessageManager.getString("label.show_first"));
3403     showAutoFirst.setState(false); // pending applet parameter
3404     setShowAutoCalculatedAbove(showAutoFirst.getState());
3405     showAutoLast = new CheckboxMenuItem(
3406             MessageManager.getString("label.show_last"));
3407     showAutoLast.setState(!showAutoFirst.getState());
3408     showAlignmentAnnotations.addItemListener(this);
3409     showSequenceAnnotations.addItemListener(this);
3410     sortAnnBySequence.addItemListener(this);
3411     sortAnnByLabel.addItemListener(this);
3412     showAutoFirst.addItemListener(this);
3413     showAutoLast.addItemListener(this);
3414
3415     /*
3416      * Configure Format menu items and actions
3417      */
3418     font.setLabel(MessageManager.getString("action.font"));
3419     font.addActionListener(this);
3420     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3421     scaleAbove.setState(true);
3422     scaleAbove.setEnabled(false);
3423     scaleAbove.addItemListener(this);
3424     scaleLeft.setEnabled(false);
3425     scaleLeft.setState(true);
3426     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3427     scaleLeft.addItemListener(this);
3428     scaleRight.setEnabled(false);
3429     scaleRight.setState(true);
3430     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3431     scaleRight.addItemListener(this);
3432     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3433     viewBoxesMenuItem.setState(true);
3434     viewBoxesMenuItem.addItemListener(this);
3435     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3436     viewTextMenuItem.setState(true);
3437     viewTextMenuItem.addItemListener(this);
3438     colourTextMenuItem.setLabel(MessageManager
3439             .getString("label.colour_text"));
3440     colourTextMenuItem.addItemListener(this);
3441     displayNonconservedMenuItem.setLabel(MessageManager
3442             .getString("label.show_non_conversed"));
3443     displayNonconservedMenuItem.addItemListener(this);
3444     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3445     wrapMenuItem.addItemListener(this);
3446     renderGapsMenuItem.setLabel(MessageManager
3447             .getString("action.show_gaps"));
3448     renderGapsMenuItem.setState(true);
3449     renderGapsMenuItem.addItemListener(this);
3450     centreColumnLabelFlag.setLabel(MessageManager
3451             .getString("label.centre_column_labels"));
3452     centreColumnLabelFlag.addItemListener(this);
3453     seqLimits.setState(true);
3454     seqLimits.setLabel(MessageManager
3455             .getString("label.show_sequence_limits"));
3456     seqLimits.addItemListener(this);
3457
3458     /*
3459      * Configure Colour menu items and actions
3460      */
3461     applyToAllGroups.setLabel(MessageManager
3462             .getString("label.apply_colour_to_all_groups"));
3463     applyToAllGroups.setState(true);
3464     applyToAllGroups.addItemListener(this);
3465     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3466     clustalColour.addActionListener(this);
3467     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3468     zappoColour.addActionListener(this);
3469     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3470     taylorColour.addActionListener(this);
3471     hydrophobicityColour.setLabel(MessageManager
3472             .getString("label.hydrophobicity"));
3473     hydrophobicityColour.addActionListener(this);
3474     helixColour
3475             .setLabel(MessageManager.getString("label.helix_propensity"));
3476     helixColour.addActionListener(this);
3477     strandColour.setLabel(MessageManager
3478             .getString("label.strand_propensity"));
3479     strandColour.addActionListener(this);
3480     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3481     turnColour.addActionListener(this);
3482     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3483     buriedColour.addActionListener(this);
3484     purinePyrimidineColour.setLabel(MessageManager
3485             .getString("label.purine_pyrimidine"));
3486     purinePyrimidineColour.addActionListener(this);
3487     // RNAInteractionColour.setLabel(MessageManager
3488     // .getString("label.rna_interaction"));
3489     // RNAInteractionColour.addActionListener(this);
3490     RNAHelixColour.setLabel(MessageManager
3491             .getString("action.by_rna_helixes"));
3492     RNAHelixColour.addActionListener(this);
3493     userDefinedColour.setLabel(MessageManager
3494             .getString("action.user_defined"));
3495     userDefinedColour.addActionListener(this);
3496     PIDColour.setLabel(MessageManager
3497             .getString("label.percentage_identity"));
3498     PIDColour.addActionListener(this);
3499     BLOSUM62Colour.setLabel(MessageManager
3500             .getString("label.blosum62_score"));
3501     BLOSUM62Colour.addActionListener(this);
3502     tcoffeeColour
3503             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3504     // it will be enabled only if a score file is provided
3505     tcoffeeColour.setEnabled(false);
3506     tcoffeeColour.addActionListener(this);
3507     conservationMenuItem.setLabel(MessageManager
3508             .getString("action.by_conservation"));
3509     conservationMenuItem.addItemListener(this);
3510     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3511     noColourmenuItem.addActionListener(this);
3512     abovePIDThreshold.setLabel(MessageManager
3513             .getString("label.above_identity_threshold"));
3514     abovePIDThreshold.addItemListener(this);
3515     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3516     nucleotideColour.addActionListener(this);
3517     modifyPID.setLabel(MessageManager
3518             .getString("label.modify_identity_threshold"));
3519     modifyPID.addActionListener(this);
3520     modifyConservation.setLabel(MessageManager
3521             .getString("label.modify_conservation_threshold"));
3522     modifyConservation.addActionListener(this);
3523     annotationColour.setLabel(MessageManager
3524             .getString("action.by_annotation"));
3525     annotationColour.addActionListener(this);
3526
3527     /*
3528      * Configure Calculate menu items and actions
3529      */
3530     sortPairwiseMenuItem.setLabel(MessageManager
3531             .getString("action.by_pairwise_id"));
3532     sortPairwiseMenuItem.addActionListener(this);
3533     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3534     sortIDMenuItem.addActionListener(this);
3535     sortLengthMenuItem.setLabel(MessageManager
3536             .getString("action.by_length"));
3537     sortLengthMenuItem.addActionListener(this);
3538     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3539     sortGroupMenuItem.addActionListener(this);
3540     pairwiseAlignmentMenuItem.setLabel(MessageManager
3541             .getString("action.pairwise_alignment"));
3542     pairwiseAlignmentMenuItem.addActionListener(this);
3543     PCAMenuItem.setLabel(MessageManager
3544             .getString("label.principal_component_analysis"));
3545     PCAMenuItem.addActionListener(this);
3546     autoCalculate = new CheckboxMenuItem(
3547             MessageManager.getString("label.autocalculate_consensus"), true);
3548     averageDistanceTreeMenuItem.setLabel(MessageManager
3549             .getString("label.average_distance_identity"));
3550     averageDistanceTreeMenuItem.addActionListener(this);
3551     neighbourTreeMenuItem.setLabel(MessageManager
3552             .getString("label.neighbour_joining_identity"));
3553     neighbourTreeMenuItem.addActionListener(this);
3554     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3555             .getString("label.average_distance_bloslum62"));
3556     avDistanceTreeBlosumMenuItem.addActionListener(this);
3557     njTreeBlosumMenuItem.setLabel(MessageManager
3558             .getString("label.neighbour_blosum62"));
3559     njTreeBlosumMenuItem.addActionListener(this);
3560     sortByTreeMenu.setLabel(MessageManager
3561             .getString("action.by_tree_order"));
3562     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3563     Menu calculateTreeMenu = new Menu(
3564             MessageManager.getString("action.calculate_tree"));
3565     autoCalculate.addItemListener(this);
3566     sortByTree.addItemListener(this);
3567
3568     /*
3569      * Configure Help menu items and actions
3570      */
3571     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3572     documentation.setLabel(MessageManager.getString("label.documentation"));
3573     documentation.addActionListener(this);
3574     about.setLabel(MessageManager.getString("label.about"));
3575     about.addActionListener(this);
3576
3577     /*
3578      * Add top level menus to frame
3579      */
3580     alignFrameMenuBar.add(fileMenu);
3581     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3582     alignFrameMenuBar.add(editMenu);
3583     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3584     alignFrameMenuBar.add(selectMenu);
3585     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3586     alignFrameMenuBar.add(viewMenu);
3587     Menu annotationsMenu = new Menu(
3588             MessageManager.getString("action.annotations"));
3589     alignFrameMenuBar.add(annotationsMenu);
3590     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3591     alignFrameMenuBar.add(formatMenu);
3592     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3593     alignFrameMenuBar.add(colourMenu);
3594     Menu calculateMenu = new Menu(
3595             MessageManager.getString("action.calculate"));
3596     alignFrameMenuBar.add(calculateMenu);
3597     alignFrameMenuBar.add(helpMenu);
3598
3599     /*
3600      * File menu
3601      */
3602     fileMenu.add(inputText);
3603     fileMenu.add(loadTree);
3604     fileMenu.add(loadAnnotations);
3605     fileMenu.addSeparator();
3606     fileMenu.add(outputTextboxMenu);
3607     fileMenu.add(outputFeatures);
3608     fileMenu.add(outputAnnotations);
3609     if (jalviewServletURL != null)
3610     {
3611       fileMenu.add(loadApplication);
3612     }
3613     fileMenu.addSeparator();
3614     fileMenu.add(closeMenuItem);
3615
3616     /*
3617      * Edit menu
3618      */
3619     editMenu.add(undoMenuItem);
3620     editMenu.add(redoMenuItem);
3621     editMenu.add(cut);
3622     editMenu.add(copy);
3623     pasteMenu.add(pasteNew);
3624     pasteMenu.add(pasteThis);
3625     editMenu.add(pasteMenu);
3626     editMenu.add(delete);
3627     editMenu.addSeparator();
3628     editMenu.add(remove2LeftMenuItem);
3629     editMenu.add(remove2RightMenuItem);
3630     editMenu.add(removeGappedColumnMenuItem);
3631     editMenu.add(removeAllGapsMenuItem);
3632     editMenu.add(removeRedundancyMenuItem);
3633
3634     /*
3635      * Select menu
3636      */
3637     selectMenu.add(findMenuItem);
3638     selectMenu.addSeparator();
3639     selectMenu.add(selectAllSequenceMenuItem);
3640     selectMenu.add(deselectAllSequenceMenuItem);
3641     selectMenu.add(invertSequenceMenuItem);
3642     selectMenu.add(invertColSel);
3643     selectMenu.add(createGroup);
3644     selectMenu.add(unGroup);
3645     selectMenu.add(grpsFromSelection);
3646     selectMenu.add(deleteGroups);
3647     selectMenu.add(annotationColumnSelection);
3648
3649     /*
3650      * View menu
3651      */
3652     viewMenu.add(newView);
3653     viewMenu.addSeparator();
3654     showMenu.add(showColumns);
3655     showMenu.add(showSeqs);
3656     showMenu.add(showAllHidden);
3657     viewMenu.add(showMenu);
3658     hideMenu.add(hideColumns);
3659     hideMenu.add(hideSequences);
3660     hideMenu.add(hideAllSelection);
3661     hideMenu.add(hideAllButSelection);
3662     viewMenu.add(hideMenu);
3663     viewMenu.addSeparator();
3664     viewMenu.add(followMouseOverFlag);
3665     viewMenu.addSeparator();
3666     viewMenu.add(sequenceFeatures);
3667     viewMenu.add(featureSettings);
3668     viewMenu.addSeparator();
3669     viewMenu.add(alProperties);
3670     viewMenu.addSeparator();
3671     viewMenu.add(overviewMenuItem);
3672
3673     /*
3674      * Annotations menu
3675      */
3676     annotationsMenu.add(annotationPanelMenuItem);
3677     annotationsMenu.addSeparator();
3678     annotationsMenu.add(showAlignmentAnnotations);
3679     annotationsMenu.add(showSequenceAnnotations);
3680     annotationsMenu.add(sortAnnBySequence);
3681     annotationsMenu.add(sortAnnByLabel);
3682     annotationsMenu.addSeparator();
3683     autoAnnMenu.add(showAutoFirst);
3684     autoAnnMenu.add(showAutoLast);
3685     autoAnnMenu.addSeparator();
3686     autoAnnMenu.add(applyAutoAnnotationSettings);
3687     autoAnnMenu.add(showConsensusHistogram);
3688     autoAnnMenu.add(showSequenceLogo);
3689     autoAnnMenu.add(normSequenceLogo);
3690     autoAnnMenu.addSeparator();
3691     autoAnnMenu.add(showGroupConservation);
3692     autoAnnMenu.add(showGroupConsensus);
3693     annotationsMenu.add(autoAnnMenu);
3694
3695     /*
3696      * Format menu
3697      */
3698     formatMenu.add(font);
3699     formatMenu.add(seqLimits);
3700     formatMenu.add(wrapMenuItem);
3701     formatMenu.add(scaleAbove);
3702     formatMenu.add(scaleLeft);
3703     formatMenu.add(scaleRight);
3704     formatMenu.add(viewBoxesMenuItem);
3705     formatMenu.add(viewTextMenuItem);
3706     formatMenu.add(colourTextMenuItem);
3707     formatMenu.add(displayNonconservedMenuItem);
3708     formatMenu.add(renderGapsMenuItem);
3709     formatMenu.add(centreColumnLabelFlag);
3710
3711     /*
3712      * Colour menu
3713      */
3714     colourMenu.add(applyToAllGroups);
3715     colourMenu.addSeparator();
3716     colourMenu.add(noColourmenuItem);
3717     colourMenu.add(clustalColour);
3718     colourMenu.add(BLOSUM62Colour);
3719     colourMenu.add(PIDColour);
3720     colourMenu.add(zappoColour);
3721     colourMenu.add(taylorColour);
3722     colourMenu.add(hydrophobicityColour);
3723     colourMenu.add(helixColour);
3724     colourMenu.add(strandColour);
3725     colourMenu.add(turnColour);
3726     colourMenu.add(buriedColour);
3727     colourMenu.add(nucleotideColour);
3728     colourMenu.add(purinePyrimidineColour);
3729     // colourMenu.add(RNAInteractionColour);
3730     colourMenu.add(tcoffeeColour);
3731     colourMenu.add(userDefinedColour);
3732     colourMenu.addSeparator();
3733     colourMenu.add(conservationMenuItem);
3734     colourMenu.add(modifyConservation);
3735     colourMenu.add(abovePIDThreshold);
3736     colourMenu.add(modifyPID);
3737     colourMenu.add(annotationColour);
3738     colourMenu.add(RNAHelixColour);
3739
3740     /*
3741      * Calculate menu
3742      */
3743     sortMenu.add(sortIDMenuItem);
3744     sortMenu.add(sortLengthMenuItem);
3745     sortMenu.add(sortByTreeMenu);
3746     sortMenu.add(sortGroupMenuItem);
3747     sortMenu.add(sortPairwiseMenuItem);
3748     calculateMenu.add(sortMenu);
3749     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3750     calculateTreeMenu.add(neighbourTreeMenuItem);
3751     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3752     calculateTreeMenu.add(njTreeBlosumMenuItem);
3753     calculateMenu.add(calculateTreeMenu);
3754     calculateMenu.addSeparator();
3755     calculateMenu.add(pairwiseAlignmentMenuItem);
3756     calculateMenu.add(PCAMenuItem);
3757     calculateMenu.add(autoCalculate);
3758     calculateMenu.add(sortByTree);
3759
3760     /*
3761      * Help menu
3762      */
3763     helpMenu.add(documentation);
3764     helpMenu.add(about);
3765
3766     /*
3767      * Status bar
3768      */
3769     statusBar.setBackground(Color.white);
3770     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3771     statusBar.setText(MessageManager.getString("label.status_bar"));
3772     this.add(statusBar, BorderLayout.SOUTH);
3773   }
3774
3775   @Override
3776   public void setStatus(String string)
3777   {
3778     statusBar.setText(string);
3779   };
3780
3781   MenuItem featureSettings = new MenuItem();
3782
3783   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3784
3785   MenuItem annotationColour = new MenuItem();
3786
3787   MenuItem annotationColumnSelection = new MenuItem();
3788
3789   MenuItem invertColSel = new MenuItem();
3790
3791   MenuItem showColumns = new MenuItem();
3792
3793   MenuItem showSeqs = new MenuItem();
3794
3795   MenuItem hideColumns = new MenuItem();
3796
3797   MenuItem hideSequences = new MenuItem();
3798
3799   MenuItem hideAllButSelection = new MenuItem();
3800
3801   MenuItem hideAllSelection = new MenuItem();
3802
3803   MenuItem showAllHidden = new MenuItem();
3804
3805   MenuItem newView = new MenuItem();
3806
3807   private CheckboxMenuItem showAlignmentAnnotations;
3808
3809   private CheckboxMenuItem showSequenceAnnotations;
3810
3811   private CheckboxMenuItem sortAnnBySequence;
3812
3813   private CheckboxMenuItem sortAnnByLabel;
3814
3815   private CheckboxMenuItem showAutoFirst;
3816
3817   private CheckboxMenuItem showAutoLast;
3818
3819   private SplitFrame splitFrame;
3820
3821   /**
3822    * Attach the alignFrame panels after embedding menus, if necessary. This used
3823    * to be called setEmbedded, but is now creates the dropdown menus in a
3824    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3825    *
3826    * @param reallyEmbedded
3827    *          true to attach the view to the applet area on the page rather than
3828    *          in a new window
3829    */
3830   public void createAlignFrameWindow(boolean reallyEmbedded)
3831   {
3832     if (reallyEmbedded)
3833     {
3834       embedAlignFrameInApplet(viewport.applet);
3835     }
3836     else
3837     {
3838       // //////
3839       // test and embed menu bar if necessary.
3840       //
3841       if (embedMenuIfNeeded(alignPanel))
3842       {
3843         /*
3844          * adjust for status bar height too. ? pointless as overridden by layout
3845          * manager
3846          */
3847         alignPanel.setSize(getSize().width,
3848                 getSize().height - statusBar.getHeight());
3849       }
3850       add(statusBar, BorderLayout.SOUTH);
3851       add(alignPanel, BorderLayout.CENTER);
3852       // and register with the applet so it can pass external API calls to us
3853       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3854               frameHeight);
3855     }
3856   }
3857
3858   /**
3859    * Add the components of this AlignFrame to the applet container.
3860    *
3861    * @param theApplet
3862    */
3863   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3864   {
3865     // ////
3866     // Explicitly build the embedded menu panel for the on-page applet
3867     //
3868     // view cannot be closed if its actually on the page
3869     fileMenu.remove(closeMenuItem);
3870     fileMenu.remove(3); // Remove Separator
3871     // construct embedded menu, using default font
3872     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3873     // and actually add the components to the applet area
3874     theApplet.setLayout(new BorderLayout());
3875     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3876     theApplet.add(statusBar, BorderLayout.SOUTH);
3877     // TODO should size be left to the layout manager?
3878     alignPanel.setSize(theApplet.getSize().width,
3879             theApplet.getSize().height - embeddedMenu.getHeight()
3880                     - statusBar.getHeight());
3881     theApplet.add(alignPanel, BorderLayout.CENTER);
3882     final AlignFrame me = this;
3883     theApplet.addFocusListener(new FocusListener()
3884     {
3885
3886       @Override
3887       public void focusLost(FocusEvent e)
3888       {
3889         if (theApplet.currentAlignFrame == me)
3890         {
3891           theApplet.currentAlignFrame = null;
3892         }
3893       }
3894
3895       @Override
3896       public void focusGained(FocusEvent e)
3897       {
3898         theApplet.currentAlignFrame = me;
3899       }
3900     });
3901     theApplet.validate();
3902   }
3903
3904   /**
3905    * create a new binding between structures in an existing jmol viewer instance
3906    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3907    * this does not open a new Jmol window, or modify the display of the
3908    * structures in the original jmol window. Note This method doesn't work
3909    * without an additional javascript library to exchange messages between the
3910    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3911    *
3912    * @param viewer
3913    *          JmolViewer instance
3914    * @param sequenceIds
3915    *          - sequence Ids to search for associations
3916    */
3917   public SequenceStructureBinding addStructureViewInstance(
3918           Object jmolviewer, String[] sequenceIds)
3919   {
3920     Viewer viewer = null;
3921     try
3922     {
3923       viewer = (Viewer) jmolviewer;
3924     } catch (ClassCastException ex)
3925     {
3926       System.err.println("Unsupported viewer object :"
3927               + jmolviewer.getClass());
3928     }
3929     if (viewer == null)
3930     {
3931       System.err.println("Can't use this object as a structure viewer:"
3932               + jmolviewer.getClass());
3933       return null;
3934     }
3935     SequenceI[] seqs = null;
3936     if (sequenceIds == null || sequenceIds.length == 0)
3937     {
3938       seqs = viewport.getAlignment().getSequencesArray();
3939     }
3940     else
3941     {
3942       Vector sqi = new Vector();
3943       AlignmentI al = viewport.getAlignment();
3944       for (int sid = 0; sid < sequenceIds.length; sid++)
3945       {
3946         SequenceI sq = al.findName(sequenceIds[sid]);
3947         if (sq != null)
3948         {
3949           sqi.addElement(sq);
3950         }
3951       }
3952       if (sqi.size() > 0)
3953       {
3954         seqs = new SequenceI[sqi.size()];
3955         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3956         {
3957           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3958         }
3959       }
3960       else
3961       {
3962         return null;
3963       }
3964     }
3965     AAStructureBindingModel jmv = null;
3966     // TODO: search for a jmv that involves viewer
3967     if (jmv == null)
3968     { // create a new viewer/jalview binding.
3969       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3970     }
3971     return jmv;
3972
3973   }
3974
3975   /**
3976    * bind a pdb file to a sequence in the current view
3977    *
3978    * @param sequenceId
3979    *          - sequenceId within the dataset.
3980    * @param pdbEntryString
3981    *          - the short name for the PDB file
3982    * @param pdbFile
3983    *          - pdb file - either a URL or a valid PDB file.
3984    * @return true if binding was as success TODO: consider making an exception
3985    *         structure for indicating when PDB parsing or sequenceId location
3986    *         fails.
3987    */
3988   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3989           String pdbFile)
3990   {
3991     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3992     boolean needtoadd = false;
3993     if (toaddpdb != null)
3994     {
3995       Vector pdbe = toaddpdb.getAllPDBEntries();
3996       PDBEntry pdbentry = null;
3997       if (pdbe != null && pdbe.size() > 0)
3998       {
3999         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4000         {
4001           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4002           if (!pdbentry.getId().equals(pdbEntryString)
4003                   && !pdbentry.getFile().equals(pdbFile))
4004           {
4005             pdbentry = null;
4006           }
4007           else
4008           {
4009             continue;
4010           }
4011         }
4012       }
4013       if (pdbentry == null)
4014       {
4015         pdbentry = new PDBEntry();
4016         pdbentry.setId(pdbEntryString);
4017         pdbentry.setFile(pdbFile);
4018         needtoadd = true; // add this new entry to sequence.
4019       }
4020       // resolve data source
4021       // TODO: this code should be a refactored to an io package
4022       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4023               pdbFile, FileFormat.PDB);
4024       if (protocol == null)
4025       {
4026         return false;
4027       }
4028       if (needtoadd)
4029       {
4030         pdbentry.setProperty("protocol", protocol);
4031         toaddpdb.addPDBId(pdbentry);
4032         alignPanel.getStructureSelectionManager()
4033                 .registerPDBEntry(pdbentry);
4034       }
4035     }
4036     return true;
4037   }
4038
4039   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4040   {
4041     if (seqs != null)
4042     {
4043       Vector sequences = new Vector();
4044       for (int i = 0; i < seqs.length; i++)
4045       {
4046         if (seqs[i] != null)
4047         {
4048           sequences.addElement(new Object[] { seqs[i],
4049               (chains != null) ? chains[i] : null });
4050         }
4051       }
4052       seqs = new SequenceI[sequences.size()];
4053       chains = new String[sequences.size()];
4054       for (int i = 0, isize = sequences.size(); i < isize; i++)
4055       {
4056         Object[] oj = (Object[]) sequences.elementAt(i);
4057
4058         seqs[i] = (SequenceI) oj[0];
4059         chains[i] = (String) oj[1];
4060       }
4061     }
4062     return new Object[] { seqs, chains };
4063
4064   }
4065
4066   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4067           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4068   {
4069     // Scrub any null sequences from the array
4070     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4071     seqs = (SequenceI[]) sqch[0];
4072     chains = (String[]) sqch[1];
4073     if (seqs == null || seqs.length == 0)
4074     {
4075       System.err
4076               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4077     }
4078     if (protocol == null)
4079     {
4080       String sourceType = (String) pdb.getProperty("protocol");
4081       try
4082       {
4083         protocol = DataSourceType.valueOf(sourceType);
4084       } catch (IllegalArgumentException e)
4085       {
4086         // ignore
4087       }
4088       if (protocol == null)
4089       {
4090         System.err.println("Couldn't work out protocol to open structure: "
4091                 + pdb.getId());
4092         return;
4093       }
4094     }
4095     if (applet.useXtrnalSviewer)
4096     {
4097       // register the association(s) and quit, don't create any windows.
4098       if (StructureSelectionManager.getStructureSelectionManager(applet)
4099               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4100       {
4101         System.err.println("Failed to map " + pdb.getFile() + " ("
4102                 + protocol + ") to any sequences");
4103       }
4104       return;
4105     }
4106     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4107     {
4108       // can only do alignments with Jmol
4109       // find the last jmol window assigned to this alignment
4110       AppletJmol ajm = null, tajm;
4111       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4112       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4113       {
4114         tajm = (AppletJmol) jmols.elementAt(i);
4115         if (tajm.ap.alignFrame == this)
4116         {
4117           ajm = tajm;
4118           break;
4119         }
4120       }
4121       if (ajm != null)
4122       {
4123         System.err
4124                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4125         // try and add the pdb structure
4126         // ajm.addS
4127         ajm = null;
4128       }
4129     }
4130     // otherwise, create a new window
4131     if (applet.jmolAvailable)
4132     {
4133       new AppletJmol(pdb, seqs, chains, alignPanel,
4134               protocol);
4135       applet.lastFrameX += 40;
4136       applet.lastFrameY += 40;
4137     }
4138     else
4139     {
4140       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4141     }
4142
4143   }
4144
4145   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4146           SequenceI[][] seqs, String[][] chains, String[] protocols)
4147   {
4148     // TODO Auto-generated method stub
4149     System.err.println("Aligned Structure View: Not yet implemented.");
4150   }
4151
4152   /**
4153    * modify the current selection, providing the user has not made a selection
4154    * already.
4155    *
4156    * @param sel
4157    *          - sequences from this alignment
4158    * @param csel
4159    *          - columns to be selected on the alignment
4160    */
4161   public void select(SequenceGroup sel, ColumnSelection csel)
4162   {
4163     alignPanel.seqPanel.selection(sel, csel, null);
4164   }
4165
4166   public void scrollTo(int row, int column)
4167   {
4168     alignPanel.seqPanel.scrollTo(row, column);
4169   }
4170
4171   public void scrollToRow(int row)
4172   {
4173     alignPanel.seqPanel.scrollToRow(row);
4174   }
4175
4176   public void scrollToColumn(int column)
4177   {
4178     alignPanel.seqPanel.scrollToColumn(column);
4179   }
4180
4181   /**
4182    * @return the alignments unique ID.
4183    */
4184   public String getSequenceSetId()
4185   {
4186     return viewport.getSequenceSetId();
4187   }
4188
4189   /**
4190    * Load the (T-Coffee) score file from the specified url
4191    *
4192    * @param source
4193    *          File/URL/T-COFFEE score file contents
4194    * @throws IOException
4195    * @return true if alignment was annotated with data from source
4196    */
4197   public boolean loadScoreFile(String source) throws IOException
4198   {
4199
4200     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4201             AppletFormatAdapter.checkProtocol(source));
4202     if (!file.isValid())
4203     {
4204       // TODO: raise dialog for gui
4205       System.err.println("Problems parsing T-Coffee scores: "
4206               + file.getWarningMessage());
4207       System.err.println("Origin was:\n" + source);
4208       return false;
4209     }
4210
4211     /*
4212      * check that the score matrix matches the alignment dimensions
4213      */
4214     AlignmentI aln;
4215     if ((aln = viewport.getAlignment()) != null
4216             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4217                     .getWidth()))
4218     {
4219       // TODO: raise a dialog box here rather than bomb out.
4220       System.err
4221               .println("The scores matrix does not match the alignment dimensions");
4222
4223     }
4224
4225     // TODO add parameter to indicate if matching should be done
4226     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4227     {
4228       alignPanel.fontChanged();
4229       tcoffeeColour.setEnabled(true);
4230       // switch to this color
4231       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4232       return true;
4233     }
4234     else
4235     {
4236       System.err.println("Problems resolving T-Coffee scores:");
4237       if (file.getWarningMessage() != null)
4238       {
4239         System.err.println(file.getWarningMessage());
4240       }
4241     }
4242     return false;
4243   }
4244
4245   public SplitFrame getSplitFrame()
4246   {
4247     return this.splitFrame;
4248   }
4249
4250   public void setSplitFrame(SplitFrame sf)
4251   {
4252     this.splitFrame = sf;
4253   }
4254
4255   // may not need this
4256   @Override
4257   public void setShowSeqFeatures(boolean b)
4258   {
4259     // showSeqFeatures.setSelected(b);
4260     viewport.setShowSequenceFeatures(b);
4261
4262   }
4263
4264   @Override
4265   public void setMenusForViewport()
4266   {
4267     // setMenusFromViewport(viewport);
4268
4269   }
4270
4271   @Override
4272   public void refreshFeatureUI(boolean enableIfNecessary)
4273   {
4274     if (enableIfNecessary)
4275     {
4276       sequenceFeatures.setState(true);
4277       alignPanel.av.setShowSequenceFeatures(true);
4278     }
4279   }
4280
4281   @Override
4282   public FeatureSettingsControllerI getFeatureSettingsUI()
4283   {
4284     return alignPanel.av.featureSettings;
4285   }
4286
4287 }