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