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     boolean featuresFile = false;
 368     try
 369     {
 370       Map<String, Object> colours = alignPanel.seqPanel.seqCanvas
 371               .getFeatureRenderer().getFeatureColours();
 372       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 373               "relaxedidmatch", false);
 374       featuresFile = new FeaturesFile(file, type).parse(
 375               viewport.getAlignment(), colours, true, relaxedIdMatching);
 376     } catch (Exception ex)
 377     {
 378       ex.printStackTrace();
 379     }
 380
 381     if (featuresFile)
 382     {
 383       if (autoenabledisplay)
 384       {
 385         viewport.setShowSequenceFeatures(true);
 386         sequenceFeatures.setState(true);
 387       }
 388       if (alignPanel.seqPanel.seqCanvas.fr != null)
 389       {
 390         // update the min/max ranges where necessary
 391         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 392       }
 393       if (viewport.featureSettings != null)
 394       {
 395         viewport.featureSettings.refreshTable();
 396       }
 397       alignPanel.paintAlignment(true);
 398       statusBar.setText(MessageManager
 399               .getString("label.successfully_added_features_alignment"));
 400     }
 401     return featuresFile;
 402   }
 403
 404   @Override
 405   public void keyPressed(KeyEvent evt)
 406   {
 407     if (viewport.cursorMode
 408             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 409                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 410                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 411             && Character.isDigit(evt.getKeyChar()))
 412     {
 413       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 414     }
 415
 416     switch (evt.getKeyCode())
 417     {
 418     case 27: // escape key
 419       deselectAllSequenceMenuItem_actionPerformed();
 420
 421       alignPanel.alabels.cancelDrag();
 422       break;
 423     case KeyEvent.VK_X:
 424       if (evt.isControlDown() || evt.isMetaDown())
 425       {
 426         cut_actionPerformed();
 427       }
 428       break;
 429     case KeyEvent.VK_C:
 430       if (viewport.cursorMode && !evt.isControlDown())
 431       {
 432         alignPanel.seqPanel.setCursorColumn();
 433       }
 434       if (evt.isControlDown() || evt.isMetaDown())
 435       {
 436         copy_actionPerformed();
 437       }
 438       break;
 439     case KeyEvent.VK_V:
 440       if (evt.isControlDown())
 441       {
 442         paste(evt.isShiftDown());
 443       }
 444       break;
 445     case KeyEvent.VK_A:
 446       if (evt.isControlDown() || evt.isMetaDown())
 447       {
 448         selectAllSequenceMenuItem_actionPerformed();
 449       }
 450       break;
 451     case KeyEvent.VK_DOWN:
 452       if (viewport.cursorMode)
 453       {
 454         alignPanel.seqPanel.moveCursor(0, 1);
 455       }
 456       else
 457       {
 458         moveSelectedSequences(false);
 459       }
 460       break;
 461
 462     case KeyEvent.VK_UP:
 463       if (viewport.cursorMode)
 464       {
 465         alignPanel.seqPanel.moveCursor(0, -1);
 466       }
 467       else
 468       {
 469         moveSelectedSequences(true);
 470       }
 471       break;
 472
 473     case KeyEvent.VK_LEFT:
 474       if (evt.isAltDown() || !viewport.cursorMode)
 475       {
 476         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 477       }
 478       else
 479       {
 480         alignPanel.seqPanel.moveCursor(-1, 0);
 481       }
 482       break;
 483
 484     case KeyEvent.VK_RIGHT:
 485       if (evt.isAltDown() || !viewport.cursorMode)
 486       {
 487         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 488       }
 489       else
 490       {
 491         alignPanel.seqPanel.moveCursor(1, 0);
 492       }
 493       break;
 494
 495     case KeyEvent.VK_SPACE:
 496       if (viewport.cursorMode)
 497       {
 498         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 499                 || evt.isShiftDown() || evt.isAltDown());
 500       }
 501       break;
 502
 503     case KeyEvent.VK_DELETE:
 504     case KeyEvent.VK_BACK_SPACE:
 505       if (viewport.cursorMode)
 506       {
 507         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 508                 || evt.isShiftDown() || evt.isAltDown());
 509       }
 510       else
 511       {
 512         cut_actionPerformed();
 513         alignPanel.seqPanel.seqCanvas.repaint();
 514       }
 515       break;
 516
 517     case KeyEvent.VK_S:
 518       if (viewport.cursorMode)
 519       {
 520         alignPanel.seqPanel.setCursorRow();
 521       }
 522       break;
 523     case KeyEvent.VK_P:
 524       if (viewport.cursorMode)
 525       {
 526         alignPanel.seqPanel.setCursorPosition();
 527       }
 528       break;
 529
 530     case KeyEvent.VK_ENTER:
 531     case KeyEvent.VK_COMMA:
 532       if (viewport.cursorMode)
 533       {
 534         alignPanel.seqPanel.setCursorRowAndColumn();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_Q:
 539       if (viewport.cursorMode)
 540       {
 541         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 542       }
 543       break;
 544     case KeyEvent.VK_M:
 545       if (viewport.cursorMode)
 546       {
 547         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 548       }
 549       break;
 550
 551     case KeyEvent.VK_F2:
 552       viewport.cursorMode = !viewport.cursorMode;
 553       statusBar.setText(MessageManager.formatMessage(
 554               "label.keyboard_editing_mode",
 555               new String[] { (viewport.cursorMode ? "on" : "off") }));
 556       if (viewport.cursorMode)
 557       {
 558         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 559         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 560       }
 561       break;
 562
 563     case KeyEvent.VK_F:
 564       if (evt.isControlDown())
 565       {
 566         findMenuItem_actionPerformed();
 567       }
 568       break;
 569
 570     case KeyEvent.VK_H:
 571     {
 572       boolean toggleSeqs = !evt.isControlDown();
 573       boolean toggleCols = !evt.isShiftDown();
 574       toggleHiddenRegions(toggleSeqs, toggleCols);
 575       break;
 576     }
 577
 578     case KeyEvent.VK_PAGE_UP:
 579       if (viewport.getWrapAlignment())
 580       {
 581         alignPanel.scrollUp(true);
 582       }
 583       else
 584       {
 585         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 586                 - viewport.endSeq + viewport.startSeq);
 587       }
 588       break;
 589
 590     case KeyEvent.VK_PAGE_DOWN:
 591       if (viewport.getWrapAlignment())
 592       {
 593         alignPanel.scrollUp(false);
 594       }
 595       else
 596       {
 597         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 598                 + viewport.endSeq - viewport.startSeq);
 599       }
 600       break;
 601
 602     case KeyEvent.VK_Z:
 603       if (evt.isControlDown())
 604       {
 605         undoMenuItem_actionPerformed();
 606       }
 607       break;
 608
 609     case KeyEvent.VK_Y:
 610       if (evt.isControlDown())
 611       {
 612         redoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_L:
 617       if (evt.isControlDown())
 618       {
 619         trimAlignment(true);
 620       }
 621       break;
 622
 623     case KeyEvent.VK_R:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(false);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_E:
 631       if (evt.isControlDown())
 632       {
 633         if (evt.isShiftDown())
 634         {
 635           this.removeAllGapsMenuItem_actionPerformed();
 636         }
 637         else
 638         {
 639           removeGappedColumnMenuItem_actionPerformed();
 640         }
 641       }
 642       break;
 643     case KeyEvent.VK_I:
 644       if (evt.isControlDown())
 645       {
 646         if (evt.isAltDown())
 647         {
 648           invertColSel_actionPerformed();
 649         }
 650         else
 651         {
 652           invertSequenceMenuItem_actionPerformed();
 653         }
 654       }
 655       break;
 656
 657     case KeyEvent.VK_G:
 658       if (evt.isControlDown())
 659       {
 660         if (evt.isShiftDown())
 661         {
 662           this.unGroup_actionPerformed();
 663         }
 664         else
 665         {
 666           this.createGroup_actionPerformed();
 667         }
 668       }
 669       break;
 670
 671     case KeyEvent.VK_U:
 672       if (evt.isControlDown())
 673       {
 674         this.deleteGroups_actionPerformed();
 675       }
 676       break;
 677
 678     case KeyEvent.VK_T:
 679       if (evt.isControlDown())
 680       {
 681         newView(null);
 682       }
 683       break;
 684
 685     }
 686     alignPanel.paintAlignment(true);
 687   }
 688
 689   /**
 690    * called by key handler and the hide all/show all menu items
 691    *
 692    * @param toggleSeqs
 693    * @param toggleCols
 694    */
 695   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 696   {
 697     boolean hide = false;
 698     SequenceGroup sg = viewport.getSelectionGroup();
 699     if (!toggleSeqs && !toggleCols)
 700     {
 701       // Hide everything by the current selection - this is a hack - we do the
 702       // invert and then hide
 703       // first check that there will be visible columns after the invert.
 704       if ((viewport.getColumnSelection() != null
 705               && viewport.getColumnSelection().getSelected() != null && viewport
 706               .getColumnSelection().getSelected().size() > 0)
 707               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 708                       .getEndRes()))
 709       {
 710         // now invert the sequence set, if required - empty selection implies
 711         // that no hiding is required.
 712         if (sg != null)
 713         {
 714           invertSequenceMenuItem_actionPerformed();
 715           sg = viewport.getSelectionGroup();
 716           toggleSeqs = true;
 717
 718         }
 719         viewport.expandColSelection(sg, true);
 720         // finally invert the column selection and get the new sequence
 721         // selection and indicate it should be hidden.
 722         invertColSel_actionPerformed();
 723         toggleCols = true;
 724       }
 725     }
 726
 727     if (toggleSeqs)
 728     {
 729       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 730       {
 731         hide = true;
 732         viewport.hideAllSelectedSeqs();
 733       }
 734       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 735               .size() > 0))
 736       {
 737         viewport.showAllHiddenSeqs();
 738       }
 739     }
 740
 741     if (toggleCols)
 742     {
 743       if (viewport.getColumnSelection().getSelected().size() > 0)
 744       {
 745         viewport.hideSelectedColumns();
 746         if (!toggleSeqs)
 747         {
 748           viewport.setSelectionGroup(sg);
 749         }
 750       }
 751       else if (!hide)
 752       {
 753         viewport.showAllHiddenColumns();
 754       }
 755     }
 756   }
 757
 758   @Override
 759   public void keyReleased(KeyEvent evt)
 760   {
 761   }
 762
 763   @Override
 764   public void keyTyped(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void itemStateChanged(ItemEvent evt)
 770   {
 771     final Object source = evt.getSource();
 772     if (source == displayNonconservedMenuItem)
 773     {
 774       displayNonconservedMenuItem_actionPerformed();
 775     }
 776     else if (source == colourTextMenuItem)
 777     {
 778       colourTextMenuItem_actionPerformed();
 779     }
 780     else if (source == wrapMenuItem)
 781     {
 782       wrapMenuItem_actionPerformed();
 783     }
 784     else if (source == scaleAbove)
 785     {
 786       viewport.setScaleAboveWrapped(scaleAbove.getState());
 787     }
 788     else if (source == scaleLeft)
 789     {
 790       viewport.setScaleLeftWrapped(scaleLeft.getState());
 791     }
 792     else if (source == scaleRight)
 793     {
 794       viewport.setScaleRightWrapped(scaleRight.getState());
 795     }
 796     else if (source == seqLimits)
 797     {
 798       seqLimits_itemStateChanged();
 799     }
 800     else if (source == viewBoxesMenuItem)
 801     {
 802       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 803     }
 804     else if (source == viewTextMenuItem)
 805     {
 806       viewport.setShowText(viewTextMenuItem.getState());
 807     }
 808     else if (source == renderGapsMenuItem)
 809     {
 810       viewport.setRenderGaps(renderGapsMenuItem.getState());
 811     }
 812     else if (source == annotationPanelMenuItem)
 813     {
 814       boolean showAnnotations = annotationPanelMenuItem.getState();
 815       showAlignmentAnnotations.setEnabled(showAnnotations);
 816       showSequenceAnnotations.setEnabled(showAnnotations);
 817       viewport.setShowAnnotation(showAnnotations);
 818       alignPanel.setAnnotationVisible(showAnnotations);
 819     }
 820     else if (source == sequenceFeatures)
 821     {
 822       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 823       alignPanel.seqPanel.seqCanvas.repaint();
 824     }
 825     else if (source == showAlignmentAnnotations)
 826     {
 827       setAnnotationsVisibility();
 828     }
 829     else if (source == showSequenceAnnotations)
 830     {
 831       setAnnotationsVisibility();
 832     }
 833     else if (source == sortAnnBySequence)
 834     {
 835       boolean newState = sortAnnBySequence.getState();
 836       sortAnnByLabel.setState(false);
 837       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 838               : SequenceAnnotationOrder.NONE);
 839       setViewportAnnotationOrder();
 840     }
 841     else if (source == sortAnnByLabel)
 842     {
 843       boolean newState = sortAnnByLabel.getState();
 844       sortAnnBySequence.setState(false);
 845       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 846               : SequenceAnnotationOrder.NONE);
 847       setViewportAnnotationOrder();
 848     }
 849     else if (source == showAutoFirst)
 850     {
 851       showAutoLast.setState(!showAutoFirst.getState());
 852       setShowAutoCalculatedAbove(showAutoFirst.getState());
 853       setViewportAnnotationOrder();
 854     }
 855     else if (source == showAutoLast)
 856     {
 857       showAutoFirst.setState(!showAutoLast.getState());
 858       setShowAutoCalculatedAbove(showAutoFirst.getState());
 859       setViewportAnnotationOrder();
 860     }
 861     else if (source == conservationMenuItem)
 862     {
 863       conservationMenuItem_actionPerformed();
 864     }
 865     else if (source == abovePIDThreshold)
 866     {
 867       abovePIDThreshold_actionPerformed();
 868     }
 869     else if (source == applyToAllGroups)
 870     {
 871       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 872     }
 873     else if (source == autoCalculate)
 874     {
 875       viewport.autoCalculateConsensus = autoCalculate.getState();
 876     }
 877     else if (source == sortByTree)
 878     {
 879       viewport.sortByTree = sortByTree.getState();
 880     }
 881     else if (source == this.centreColumnLabelFlag)
 882     {
 883       centreColumnLabelFlag_stateChanged();
 884     }
 885     else if (source == this.followMouseOverFlag)
 886     {
 887       mouseOverFlag_stateChanged();
 888     }
 889     else if (source == showGroupConsensus)
 890     {
 891       showGroupConsensus_actionPerformed();
 892     }
 893     else if (source == showGroupConservation)
 894     {
 895       showGroupConservation_actionPerformed();
 896     }
 897     else if (source == showSequenceLogo)
 898     {
 899       showSequenceLogo_actionPerformed();
 900     }
 901     else if (source == normSequenceLogo)
 902     {
 903       normSequenceLogo_actionPerformed();
 904     }
 905     else if (source == showConsensusHistogram)
 906     {
 907       showConsensusHistogram_actionPerformed();
 908     }
 909     else if (source == applyAutoAnnotationSettings)
 910     {
 911       applyAutoAnnotationSettings_actionPerformed();
 912     }
 913     alignPanel.paintAlignment(true);
 914   }
 915
 916   /**
 917    * Set the visibility state of sequence-related and/or alignment-related
 918    * annotations depending on checkbox selections, and repaint.
 919    *
 920    * @param visible
 921    */
 922   private void setAnnotationsVisibility()
 923   {
 924     boolean showForAlignment = showAlignmentAnnotations.getState();
 925     boolean showForSequences = showSequenceAnnotations.getState();
 926     for (AlignmentAnnotation aa : alignPanel.getAlignment()
 927             .getAlignmentAnnotation())
 928     {
 929       boolean visible = (aa.sequenceRef == null ? showForAlignment
 930               : showForSequences);
 931       aa.visible = visible;
 932     }
 933     alignPanel.validateAnnotationDimensions(true);
 934     validate();
 935     repaint();
 936   }
 937
 938   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 939   {
 940     this.annotationSortOrder = order;
 941   }
 942
 943   /**
 944    * Set flags on the viewport that control annotation ordering
 945    */
 946   private void setViewportAnnotationOrder()
 947   {
 948     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 949     this.alignPanel.av
 950             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 951   }
 952
 953   private void setShowAutoCalculatedAbove(boolean showAbove)
 954   {
 955     this.showAutoCalculatedAbove = showAbove;
 956   }
 957
 958   private void mouseOverFlag_stateChanged()
 959   {
 960     viewport.setFollowHighlight(followMouseOverFlag.getState());
 961     // TODO: could kick the scrollTo mechanism to reset view for current
 962     // searchresults.
 963   }
 964
 965   private void centreColumnLabelFlag_stateChanged()
 966   {
 967     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 968     this.alignPanel.annotationPanel.repaint();
 969   }
 970
 971   @Override
 972   public void actionPerformed(ActionEvent evt)
 973   {
 974     viewport.applet.currentAlignFrame = this;
 975
 976     Object source = evt.getSource();
 977
 978     if (source == inputText)
 979     {
 980       inputText_actionPerformed();
 981     }
 982     else if (source == loadTree)
 983     {
 984       loadTree_actionPerformed();
 985     }
 986     else if (source == loadApplication)
 987     {
 988       launchFullApplication();
 989     }
 990     else if (source == loadAnnotations)
 991     {
 992       loadAnnotations();
 993     }
 994     else if (source == outputAnnotations)
 995     {
 996       outputAnnotations(true);
 997     }
 998     else if (source == outputFeatures)
 999     {
1000       outputFeatures(true, "Jalview");
1001     }
1002     else if (source == closeMenuItem)
1003     {
1004       closeMenuItem_actionPerformed();
1005     }
1006     else if (source == copy)
1007     {
1008       copy_actionPerformed();
1009     }
1010     else if (source == undoMenuItem)
1011     {
1012       undoMenuItem_actionPerformed();
1013     }
1014     else if (source == redoMenuItem)
1015     {
1016       redoMenuItem_actionPerformed();
1017     }
1018     else if (source == inputText)
1019     {
1020       inputText_actionPerformed();
1021     }
1022     else if (source == closeMenuItem)
1023     {
1024       closeMenuItem_actionPerformed();
1025     }
1026     else if (source == undoMenuItem)
1027     {
1028       undoMenuItem_actionPerformed();
1029     }
1030     else if (source == redoMenuItem)
1031     {
1032       redoMenuItem_actionPerformed();
1033     }
1034     else if (source == copy)
1035     {
1036       copy_actionPerformed();
1037     }
1038     else if (source == pasteNew)
1039     {
1040       pasteNew_actionPerformed();
1041     }
1042     else if (source == pasteThis)
1043     {
1044       pasteThis_actionPerformed();
1045     }
1046     else if (source == cut)
1047     {
1048       cut_actionPerformed();
1049     }
1050     else if (source == delete)
1051     {
1052       delete_actionPerformed();
1053     }
1054     else if (source == grpsFromSelection)
1055     {
1056       makeGrpsFromSelection_actionPerformed();
1057     }
1058     else if (source == deleteGroups)
1059     {
1060       deleteGroups_actionPerformed();
1061     }
1062     else if (source == selectAllSequenceMenuItem)
1063     {
1064       selectAllSequenceMenuItem_actionPerformed();
1065     }
1066     else if (source == deselectAllSequenceMenuItem)
1067     {
1068       deselectAllSequenceMenuItem_actionPerformed();
1069     }
1070     else if (source == invertSequenceMenuItem)
1071     {
1072       invertSequenceMenuItem_actionPerformed();
1073     }
1074     else if (source == invertColSel)
1075     {
1076       viewport.invertColumnSelection();
1077       alignPanel.paintAlignment(true);
1078     }
1079     else if (source == remove2LeftMenuItem)
1080     {
1081       trimAlignment(true);
1082     }
1083     else if (source == remove2RightMenuItem)
1084     {
1085       trimAlignment(false);
1086     }
1087     else if (source == removeGappedColumnMenuItem)
1088     {
1089       removeGappedColumnMenuItem_actionPerformed();
1090     }
1091     else if (source == removeAllGapsMenuItem)
1092     {
1093       removeAllGapsMenuItem_actionPerformed();
1094     }
1095     else if (source == findMenuItem)
1096     {
1097       findMenuItem_actionPerformed();
1098     }
1099     else if (source == font)
1100     {
1101       new FontChooser(alignPanel);
1102     }
1103     else if (source == newView)
1104     {
1105       newView(null);
1106     }
1107     else if (source == showColumns)
1108     {
1109       viewport.showAllHiddenColumns();
1110       alignPanel.paintAlignment(true);
1111     }
1112     else if (source == showSeqs)
1113     {
1114       viewport.showAllHiddenSeqs();
1115       alignPanel.paintAlignment(true);
1116     }
1117     else if (source == hideColumns)
1118     {
1119       viewport.hideSelectedColumns();
1120       alignPanel.paintAlignment(true);
1121     }
1122     else if (source == hideSequences
1123             && viewport.getSelectionGroup() != null)
1124     {
1125       viewport.hideAllSelectedSeqs();
1126       alignPanel.paintAlignment(true);
1127     }
1128     else if (source == hideAllButSelection)
1129     {
1130       toggleHiddenRegions(false, false);
1131       alignPanel.paintAlignment(true);
1132     }
1133     else if (source == hideAllSelection)
1134     {
1135       SequenceGroup sg = viewport.getSelectionGroup();
1136       viewport.expandColSelection(sg, false);
1137       viewport.hideAllSelectedSeqs();
1138       viewport.hideSelectedColumns();
1139       alignPanel.paintAlignment(true);
1140     }
1141     else if (source == showAllHidden)
1142     {
1143       viewport.showAllHiddenColumns();
1144       viewport.showAllHiddenSeqs();
1145       alignPanel.paintAlignment(true);
1146     }
1147     else if (source == showGroupConsensus)
1148     {
1149       showGroupConsensus_actionPerformed();
1150     }
1151     else if (source == showGroupConservation)
1152     {
1153       showGroupConservation_actionPerformed();
1154     }
1155     else if (source == showSequenceLogo)
1156     {
1157       showSequenceLogo_actionPerformed();
1158     }
1159     else if (source == normSequenceLogo)
1160     {
1161       normSequenceLogo_actionPerformed();
1162     }
1163     else if (source == showConsensusHistogram)
1164     {
1165       showConsensusHistogram_actionPerformed();
1166     }
1167     else if (source == applyAutoAnnotationSettings)
1168     {
1169       applyAutoAnnotationSettings_actionPerformed();
1170     }
1171     else if (source == featureSettings)
1172     {
1173       new FeatureSettings(alignPanel);
1174     }
1175     else if (source == alProperties)
1176     {
1177       StringBuffer contents = new jalview.io.AlignmentProperties(
1178               viewport.getAlignment()).formatAsString();
1179       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1180       cap.setText(contents.toString());
1181       Frame frame = new Frame();
1182       frame.add(cap);
1183       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1184               "label.alignment_properties", new String[] { getTitle() }),
1185               400, 250);
1186     }
1187     else if (source == overviewMenuItem)
1188     {
1189       overviewMenuItem_actionPerformed();
1190     }
1191     else if (source == noColourmenuItem)
1192     {
1193       changeColour(null);
1194     }
1195     else if (source == clustalColour)
1196     {
1197       abovePIDThreshold.setState(false);
1198       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1199     }
1200     else if (source == zappoColour)
1201     {
1202       changeColour(new ZappoColourScheme());
1203     }
1204     else if (source == taylorColour)
1205     {
1206       changeColour(new TaylorColourScheme());
1207     }
1208     else if (source == hydrophobicityColour)
1209     {
1210       changeColour(new HydrophobicColourScheme());
1211     }
1212     else if (source == helixColour)
1213     {
1214       changeColour(new HelixColourScheme());
1215     }
1216     else if (source == strandColour)
1217     {
1218       changeColour(new StrandColourScheme());
1219     }
1220     else if (source == turnColour)
1221     {
1222       changeColour(new TurnColourScheme());
1223     }
1224     else if (source == buriedColour)
1225     {
1226       changeColour(new BuriedColourScheme());
1227     }
1228     else if (source == nucleotideColour)
1229     {
1230       changeColour(new NucleotideColourScheme());
1231     }
1232     else if (source == purinePyrimidineColour)
1233     {
1234       changeColour(new PurinePyrimidineColourScheme());
1235     }
1236     // else if (source == RNAInteractionColour)
1237     // {
1238     // changeColour(new RNAInteractionColourScheme());
1239     // }
1240     else if (source == RNAHelixColour)
1241     {
1242       new RNAHelicesColourChooser(viewport, alignPanel);
1243     }
1244     else if (source == modifyPID)
1245     {
1246       modifyPID_actionPerformed();
1247     }
1248     else if (source == modifyConservation)
1249     {
1250       modifyConservation_actionPerformed();
1251     }
1252     else if (source == userDefinedColour)
1253     {
1254       new UserDefinedColours(alignPanel, null);
1255     }
1256     else if (source == PIDColour)
1257     {
1258       changeColour(new PIDColourScheme());
1259     }
1260     else if (source == BLOSUM62Colour)
1261     {
1262       changeColour(new Blosum62ColourScheme());
1263     }
1264     else if (source == tcoffeeColour)
1265     {
1266       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1267     }
1268     else if (source == annotationColour)
1269     {
1270       new AnnotationColourChooser(viewport, alignPanel);
1271     }
1272     else if (source == annotationColumnSelection)
1273     {
1274       new AnnotationColumnChooser(viewport, alignPanel);
1275     }
1276     else if (source == sortPairwiseMenuItem)
1277     {
1278       sortPairwiseMenuItem_actionPerformed();
1279     }
1280     else if (source == sortIDMenuItem)
1281     {
1282       sortIDMenuItem_actionPerformed();
1283     }
1284     else if (source == sortLengthMenuItem)
1285     {
1286       sortLengthMenuItem_actionPerformed();
1287     }
1288     else if (source == sortGroupMenuItem)
1289     {
1290       sortGroupMenuItem_actionPerformed();
1291     }
1292     else if (source == removeRedundancyMenuItem)
1293     {
1294       removeRedundancyMenuItem_actionPerformed();
1295     }
1296     else if (source == pairwiseAlignmentMenuItem)
1297     {
1298       pairwiseAlignmentMenuItem_actionPerformed();
1299     }
1300     else if (source == PCAMenuItem)
1301     {
1302       PCAMenuItem_actionPerformed();
1303     }
1304     else if (source == averageDistanceTreeMenuItem)
1305     {
1306       averageDistanceTreeMenuItem_actionPerformed();
1307     }
1308     else if (source == neighbourTreeMenuItem)
1309     {
1310       neighbourTreeMenuItem_actionPerformed();
1311     }
1312     else if (source == njTreeBlosumMenuItem)
1313     {
1314       njTreeBlosumMenuItem_actionPerformed();
1315     }
1316     else if (source == avDistanceTreeBlosumMenuItem)
1317     {
1318       avTreeBlosumMenuItem_actionPerformed();
1319     }
1320     else if (source == documentation)
1321     {
1322       documentation_actionPerformed();
1323     }
1324     else if (source == about)
1325     {
1326       about_actionPerformed();
1327     }
1328
1329   }
1330
1331   public void inputText_actionPerformed()
1332   {
1333     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1334     Frame frame = new Frame();
1335     frame.add(cap);
1336     jalview.bin.JalviewLite.addFrame(frame,
1337             MessageManager.getString("label.input_cut_paste"), 500, 500);
1338   }
1339
1340   protected void outputText_actionPerformed(ActionEvent e)
1341   {
1342     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1343     Frame frame = new Frame();
1344     frame.add(cap);
1345     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1346             "label.alignment_output_command",
1347             new Object[] { e.getActionCommand() }), 600, 500);
1348
1349     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1350     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1351             e.getActionCommand(), viewport.getAlignment(),
1352             viewport.getShowJVSuffix()));
1353   }
1354
1355   public void loadAnnotations()
1356   {
1357     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1358     cap.setText(MessageManager
1359             .getString("label.paste_features_annotations_Tcoffee_here"));
1360     cap.setAnnotationImport();
1361     Frame frame = new Frame();
1362     frame.add(cap);
1363     jalview.bin.JalviewLite.addFrame(frame,
1364             MessageManager.getString("action.paste_annotations"), 400, 300);
1365
1366   }
1367
1368   public String outputAnnotations(boolean displayTextbox)
1369   {
1370     String annotation = new AnnotationFile()
1371             .printAnnotationsForView(viewport);
1372
1373     if (displayTextbox)
1374     {
1375       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1376       Frame frame = new Frame();
1377       frame.add(cap);
1378       jalview.bin.JalviewLite.addFrame(frame,
1379               MessageManager.getString("label.annotations"), 600, 500);
1380       cap.setText(annotation);
1381     }
1382
1383     return annotation;
1384   }
1385
1386   private Map<String, Object> getDisplayedFeatureCols()
1387   {
1388     if (alignPanel.getFeatureRenderer() != null
1389             && viewport.getFeaturesDisplayed() != null)
1390     {
1391       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1392
1393     }
1394     return null;
1395   }
1396
1397   public String outputFeatures(boolean displayTextbox, String format)
1398   {
1399     String features;
1400     FeaturesFile formatter = new FeaturesFile();
1401     if (format.equalsIgnoreCase("Jalview"))
1402     {
1403       features = formatter.printJalviewFormat(viewport
1404               .getAlignment().getSequencesArray(),
1405               getDisplayedFeatureCols());
1406     }
1407     else
1408     {
1409       features = formatter.printGffFormat(viewport.getAlignment()
1410               .getSequencesArray(), getDisplayedFeatureCols());
1411     }
1412
1413     if (displayTextbox)
1414     {
1415       boolean frimport = false;
1416       if (features == null || features.equals("No Features Visible"))
1417       {
1418         features = "# No features visible - paste some and import them here.";
1419         frimport = true;
1420       }
1421
1422       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1423       if (frimport)
1424       {
1425         cap.setAnnotationImport();
1426       }
1427       Frame frame = new Frame();
1428       frame.add(cap);
1429       jalview.bin.JalviewLite.addFrame(frame,
1430               MessageManager.getString("label.features"), 600, 500);
1431       cap.setText(features);
1432     }
1433     else
1434     {
1435       if (features == null)
1436       {
1437         features = "";
1438       }
1439     }
1440
1441     return features;
1442   }
1443
1444   void launchFullApplication()
1445   {
1446     StringBuffer url = new StringBuffer(jalviewServletURL);
1447
1448     // allow servlet parameters to be passed in applet parameter
1449     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1450             : "?";
1451     url.append(firstSep);
1452
1453     url.append("open="
1454             + appendProtocol(viewport.applet.getParameter("file")));
1455
1456     if (viewport.applet.getParameter("features") != null)
1457     {
1458       url.append("&features=");
1459       url.append(appendProtocol(viewport.applet.getParameter("features")));
1460     }
1461
1462     if (viewport.applet.getParameter("annotations") != null)
1463     {
1464       url.append("&annotations=");
1465       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1466     }
1467
1468     if (viewport.applet.getParameter("jnetfile") != null)
1469     {
1470       url.append("&annotations=");
1471       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1472     }
1473
1474     if (viewport.applet.getParameter("defaultColour") != null)
1475     {
1476       url.append("&colour="
1477               + removeWhiteSpace(viewport.applet
1478                       .getParameter("defaultColour")));
1479     }
1480
1481     if (viewport.applet.getParameter("userDefinedColour") != null)
1482     {
1483       url.append("&colour="
1484               + removeWhiteSpace(viewport.applet
1485                       .getParameter("userDefinedColour")));
1486     }
1487     if (viewport.applet.getParameter("tree") != null)
1488     {
1489       url.append("&tree="
1490               + appendProtocol(viewport.applet.getParameter("tree")));
1491     }
1492     if (viewport.applet.getParameter("treeFile") != null)
1493     {
1494       url.append("&tree="
1495               + appendProtocol(viewport.applet.getParameter("treeFile")));
1496     }
1497
1498     showURL(url.toString(), "FULL_APP");
1499   }
1500
1501   String removeWhiteSpace(String colour)
1502   {
1503     StringBuffer sb = new StringBuffer();
1504     for (int i = 0; i < colour.length(); i++)
1505     {
1506       if (Character.isWhitespace(colour.charAt(i)))
1507       {
1508         sb.append("%20");
1509       }
1510       else
1511       {
1512         sb.append(colour.charAt(i));
1513       }
1514     }
1515
1516     return sb.toString();
1517   }
1518
1519   String appendProtocol(String url)
1520   {
1521     try
1522     {
1523       new URL(url);
1524       url = URLEncoder.encode(url);
1525     }
1526     /*
1527      * When we finally deprecate 1.1 compatibility, we can start to use
1528      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1529      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1530      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1531      * ex.printStackTrace(); }
1532      */
1533     catch (java.net.MalformedURLException ex)
1534     {
1535       url = viewport.applet.getCodeBase() + url;
1536     }
1537     return url;
1538   }
1539
1540   public void closeMenuItem_actionPerformed()
1541   {
1542     PaintRefresher.RemoveComponent(alignPanel);
1543     if (alignPanel.seqPanel != null
1544             && alignPanel.seqPanel.seqCanvas != null)
1545     {
1546       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1547     }
1548     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1549     {
1550       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1551     }
1552
1553     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1554     {
1555       System.exit(0);
1556     }
1557     else
1558     {
1559     }
1560     viewport = null;
1561     alignPanel = null;
1562     this.dispose();
1563   }
1564
1565   /**
1566    * TODO: JAL-1104
1567    */
1568   void updateEditMenuBar()
1569   {
1570
1571     if (viewport.getHistoryList().size() > 0)
1572     {
1573       undoMenuItem.setEnabled(true);
1574       CommandI command = viewport.getHistoryList().peek();
1575       undoMenuItem.setLabel(MessageManager.formatMessage(
1576               "label.undo_command",
1577               new Object[] { command.getDescription() }));
1578     }
1579     else
1580     {
1581       undoMenuItem.setEnabled(false);
1582       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1583     }
1584
1585     if (viewport.getRedoList().size() > 0)
1586     {
1587       redoMenuItem.setEnabled(true);
1588
1589       CommandI command = viewport.getRedoList().peek();
1590       redoMenuItem.setLabel(MessageManager.formatMessage(
1591               "label.redo_command",
1592               new Object[] { command.getDescription() }));
1593     }
1594     else
1595     {
1596       redoMenuItem.setEnabled(false);
1597       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1598     }
1599   }
1600
1601   /**
1602    * TODO: JAL-1104
1603    */
1604   @Override
1605   public void addHistoryItem(CommandI command)
1606   {
1607     if (command.getSize() > 0)
1608     {
1609       viewport.addToHistoryList(command);
1610       viewport.clearRedoList();
1611       updateEditMenuBar();
1612       viewport.updateHiddenColumns();
1613     }
1614   }
1615
1616   /**
1617    * TODO: JAL-1104 DOCUMENT ME!
1618    *
1619    * @param e
1620    *          DOCUMENT ME!
1621    */
1622   protected void undoMenuItem_actionPerformed()
1623   {
1624     if (viewport.getHistoryList().isEmpty())
1625     {
1626       return;
1627     }
1628
1629     CommandI command = viewport.getHistoryList().pop();
1630     viewport.addToRedoList(command);
1631     command.undoCommand(null);
1632
1633     AlignmentViewport originalSource = getOriginatingSource(command);
1634     // JBPNote Test
1635     if (originalSource != viewport)
1636     {
1637       System.err
1638               .println("Warning: Viewport object mismatch whilst undoing");
1639     }
1640     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1641                                           // viewport.getColumnSelection().getHiddenColumns()
1642                                           // != null;
1643     updateEditMenuBar();
1644     originalSource.firePropertyChange("alignment", null, originalSource
1645             .getAlignment().getSequences());
1646   }
1647
1648   /**
1649    * TODO: JAL-1104 DOCUMENT ME!
1650    *
1651    * @param e
1652    *          DOCUMENT ME!
1653    */
1654   protected void redoMenuItem_actionPerformed()
1655   {
1656     if (viewport.getRedoList().isEmpty())
1657     {
1658       return;
1659     }
1660
1661     CommandI command = viewport.getRedoList().pop();
1662     viewport.addToHistoryList(command);
1663     command.doCommand(null);
1664
1665     AlignmentViewport originalSource = getOriginatingSource(command);
1666     // JBPNote Test
1667     if (originalSource != viewport)
1668     {
1669       System.err
1670               .println("Warning: Viewport object mismatch whilst re-doing");
1671     }
1672     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1673                                           // viewport.getColumnSelection().getHiddenColumns()
1674                                           // != null;
1675
1676     updateEditMenuBar();
1677     originalSource.firePropertyChange("alignment", null, originalSource
1678             .getAlignment().getSequences());
1679   }
1680
1681   AlignmentViewport getOriginatingSource(CommandI command)
1682   {
1683     AlignmentViewport originalSource = null;
1684     // For sequence removal and addition, we need to fire
1685     // the property change event FROM the viewport where the
1686     // original alignment was altered
1687     AlignmentI al = null;
1688     if (command instanceof EditCommand)
1689     {
1690       EditCommand editCommand = (EditCommand) command;
1691       al = editCommand.getAlignment();
1692       Vector comps = (Vector) PaintRefresher.components.get(viewport
1693               .getSequenceSetId());
1694       for (int i = 0; i < comps.size(); i++)
1695       {
1696         if (comps.elementAt(i) instanceof AlignmentPanel)
1697         {
1698           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1699           {
1700             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1701             break;
1702           }
1703         }
1704       }
1705     }
1706
1707     if (originalSource == null)
1708     {
1709       // The original view is closed, we must validate
1710       // the current view against the closed view first
1711       if (al != null)
1712       {
1713         PaintRefresher.validateSequences(al, viewport.getAlignment());
1714       }
1715
1716       originalSource = viewport;
1717     }
1718
1719     return originalSource;
1720   }
1721
1722   /**
1723    * Move the currently selected sequences up or down one position in the
1724    * alignment
1725    *
1726    * @param up
1727    */
1728   public void moveSelectedSequences(boolean up)
1729   {
1730     SequenceGroup sg = viewport.getSelectionGroup();
1731     if (sg == null)
1732     {
1733       return;
1734     }
1735     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1736             up ? null : viewport.getHiddenRepSequences(), up);
1737     alignPanel.paintAlignment(true);
1738
1739     /*
1740      * Also move cDNA/protein complement sequences
1741      */
1742     AlignViewportI complement = viewport.getCodingComplement();
1743     if (complement != null)
1744     {
1745       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1746               viewport, complement);
1747       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1748               up ? null : complement.getHiddenRepSequences(), up);
1749       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1750     }
1751   }
1752
1753   synchronized void slideSequences(boolean right, int size)
1754   {
1755     List<SequenceI> sg = new Vector<SequenceI>();
1756     if (viewport.cursorMode)
1757     {
1758       sg.add(viewport.getAlignment().getSequenceAt(
1759               alignPanel.seqPanel.seqCanvas.cursorY));
1760     }
1761     else if (viewport.getSelectionGroup() != null
1762             && viewport.getSelectionGroup().getSize() != viewport
1763                     .getAlignment().getHeight())
1764     {
1765       sg = viewport.getSelectionGroup().getSequences(
1766               viewport.getHiddenRepSequences());
1767     }
1768
1769     if (sg.size() < 1)
1770     {
1771       return;
1772     }
1773
1774     Vector<SequenceI> invertGroup = new Vector();
1775
1776     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1777     {
1778       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1779       {
1780         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1781       }
1782     }
1783
1784     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1785
1786     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1787             .size()]);
1788     for (int i = 0; i < invertGroup.size(); i++)
1789     {
1790       seqs2[i] = invertGroup.elementAt(i);
1791     }
1792
1793     SlideSequencesCommand ssc;
1794     if (right)
1795     {
1796       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1797               size, viewport.getGapCharacter());
1798     }
1799     else
1800     {
1801       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1802               size, viewport.getGapCharacter());
1803     }
1804
1805     int groupAdjustment = 0;
1806     if (ssc.getGapsInsertedBegin() && right)
1807     {
1808       if (viewport.cursorMode)
1809       {
1810         alignPanel.seqPanel.moveCursor(size, 0);
1811       }
1812       else
1813       {
1814         groupAdjustment = size;
1815       }
1816     }
1817     else if (!ssc.getGapsInsertedBegin() && !right)
1818     {
1819       if (viewport.cursorMode)
1820       {
1821         alignPanel.seqPanel.moveCursor(-size, 0);
1822       }
1823       else
1824       {
1825         groupAdjustment = -size;
1826       }
1827     }
1828
1829     if (groupAdjustment != 0)
1830     {
1831       viewport.getSelectionGroup().setStartRes(
1832               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1833       viewport.getSelectionGroup().setEndRes(
1834               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1835     }
1836
1837     boolean appendHistoryItem = false;
1838     Deque<CommandI> historyList = viewport.getHistoryList();
1839     if (historyList != null && historyList.size() > 0
1840             && historyList.peek() instanceof SlideSequencesCommand)
1841     {
1842       appendHistoryItem = ssc
1843               .appendSlideCommand((SlideSequencesCommand) historyList
1844                       .peek());
1845     }
1846
1847     if (!appendHistoryItem)
1848     {
1849       addHistoryItem(ssc);
1850     }
1851
1852     repaint();
1853   }
1854
1855   static StringBuffer copiedSequences;
1856
1857   static Vector copiedHiddenColumns;
1858
1859   protected void copy_actionPerformed()
1860   {
1861     if (viewport.getSelectionGroup() == null)
1862     {
1863       return;
1864     }
1865
1866     SequenceGroup sg = viewport.getSelectionGroup();
1867     copiedSequences = new StringBuffer();
1868     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1869     for (int i = 0; i < sg.getSize(); i++)
1870     {
1871       SequenceI seq = sg.getSequenceAt(i);
1872       int index = viewport.getAlignment().findIndex(seq);
1873       orderedSeqs.put(index, seq);
1874     }
1875
1876     int index = 0, startRes, endRes;
1877     char ch;
1878
1879     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1880     {
1881       copiedHiddenColumns = new Vector();
1882       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1883       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1884       {
1885         copiedHiddenColumns.addElement(new int[] {
1886             region[0] - hiddenOffset, region[1] - hiddenOffset });
1887       }
1888     }
1889     else
1890     {
1891       copiedHiddenColumns = null;
1892     }
1893
1894     for (int i = 0; i < sg.getSize(); i++)
1895     {
1896       SequenceI seq = null;
1897
1898       while (seq == null)
1899       {
1900         if (orderedSeqs.containsKey(index))
1901         {
1902           seq = orderedSeqs.get(index);
1903           index++;
1904           break;
1905         }
1906         else
1907         {
1908           index++;
1909         }
1910       }
1911
1912       // FIND START RES
1913       // Returns residue following index if gap
1914       startRes = seq.findPosition(sg.getStartRes());
1915
1916       // FIND END RES
1917       // Need to find the residue preceeding index if gap
1918       endRes = 0;
1919
1920       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1921       {
1922         ch = seq.getCharAt(j);
1923         if (!jalview.util.Comparison.isGap((ch)))
1924         {
1925           endRes++;
1926         }
1927       }
1928
1929       if (endRes > 0)
1930       {
1931         endRes += seq.getStart() - 1;
1932       }
1933
1934       copiedSequences.append(seq.getName()
1935               + "\t"
1936               + startRes
1937               + "\t"
1938               + endRes
1939               + "\t"
1940               + seq.getSequenceAsString(sg.getStartRes(),
1941                       sg.getEndRes() + 1) + "\n");
1942     }
1943
1944   }
1945
1946   protected void pasteNew_actionPerformed()
1947   {
1948     paste(true);
1949   }
1950
1951   protected void pasteThis_actionPerformed()
1952   {
1953     paste(false);
1954   }
1955
1956   void paste(boolean newAlignment)
1957   {
1958     try
1959     {
1960
1961       if (copiedSequences == null)
1962       {
1963         return;
1964       }
1965
1966       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1967       Vector seqs = new Vector();
1968       while (st.hasMoreElements())
1969       {
1970         String name = st.nextToken();
1971         int start = Integer.parseInt(st.nextToken());
1972         int end = Integer.parseInt(st.nextToken());
1973         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1974       }
1975       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1976       for (int i = 0; i < seqs.size(); i++)
1977       {
1978         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1979       }
1980
1981       if (newAlignment)
1982       {
1983         String newtitle = MessageManager
1984                 .getString("label.copied_sequences");
1985         if (getTitle().startsWith(
1986                 MessageManager.getString("label.copied_sequences")))
1987         {
1988           newtitle = getTitle();
1989         }
1990         else
1991         {
1992           newtitle = newtitle.concat(MessageManager.formatMessage(
1993                   "label.from_msname", new String[] { getTitle() }));
1994         }
1995         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1996                 viewport.applet, newtitle, false);
1997         if (copiedHiddenColumns != null)
1998         {
1999           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2000           {
2001             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2002             af.viewport.hideColumns(region[0], region[1]);
2003           }
2004         }
2005
2006         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2007                 frameHeight);
2008       }
2009       else
2010       {
2011         addSequences(newSeqs);
2012       }
2013
2014     } catch (Exception ex)
2015     {
2016     } // could be anything being pasted in here
2017
2018   }
2019
2020   void addSequences(SequenceI[] seqs)
2021   {
2022     for (int i = 0; i < seqs.length; i++)
2023     {
2024       viewport.getAlignment().addSequence(seqs[i]);
2025     }
2026
2027     // !newAlignment
2028     addHistoryItem(new EditCommand(
2029             MessageManager.getString("label.add_sequences"), Action.PASTE,
2030             seqs, 0, viewport.getAlignment().getWidth(),
2031             viewport.getAlignment()));
2032
2033     viewport.setEndSeq(viewport.getAlignment().getHeight());
2034     viewport.getAlignment().getWidth();
2035     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2036             .getSequences());
2037
2038   }
2039
2040   protected void cut_actionPerformed()
2041   {
2042     copy_actionPerformed();
2043     delete_actionPerformed();
2044   }
2045
2046   protected void delete_actionPerformed()
2047   {
2048
2049     SequenceGroup sg = viewport.getSelectionGroup();
2050     if (sg == null)
2051     {
2052       return;
2053     }
2054
2055     Vector seqs = new Vector();
2056     SequenceI seq;
2057     for (int i = 0; i < sg.getSize(); i++)
2058     {
2059       seq = sg.getSequenceAt(i);
2060       seqs.addElement(seq);
2061     }
2062
2063     /*
2064      * If the cut affects all sequences, warn, remove highlighted columns
2065      */
2066     if (sg.getSize() == viewport.getAlignment().getHeight())
2067     {
2068       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2069               .getAlignment().getWidth()) ? true : false;
2070       if (isEntireAlignWidth)
2071       {
2072         String title = MessageManager.getString("label.delete_all");
2073         Panel infoPanel = new Panel();
2074         infoPanel.setLayout(new FlowLayout());
2075         infoPanel
2076                 .add(new Label(MessageManager.getString("warn.delete_all")));
2077
2078         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2079         dialog.setMainPanel(infoPanel);
2080         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2081         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2082         dialog.setVisible(true);
2083
2084         if (!dialog.accept)
2085         {
2086           return;
2087         }
2088       }
2089       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2090               sg.getEndRes() + 1);
2091     }
2092
2093     SequenceI[] cut = new SequenceI[seqs.size()];
2094     for (int i = 0; i < seqs.size(); i++)
2095     {
2096       cut[i] = (SequenceI) seqs.elementAt(i);
2097     }
2098
2099     /*
2100      * //ADD HISTORY ITEM
2101      */
2102     addHistoryItem(new EditCommand(
2103             MessageManager.getString("label.cut_sequences"), Action.CUT,
2104             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2105             viewport.getAlignment()));
2106
2107     viewport.setSelectionGroup(null);
2108     viewport.getAlignment().deleteGroup(sg);
2109
2110     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2111             .getSequences());
2112
2113     if (viewport.getAlignment().getHeight() < 1)
2114     {
2115       this.setVisible(false);
2116     }
2117     viewport.sendSelection();
2118   }
2119
2120   /**
2121    * group consensus toggled
2122    *
2123    */
2124   protected void showGroupConsensus_actionPerformed()
2125   {
2126     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2127     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2128
2129   }
2130
2131   /**
2132    * group conservation toggled.
2133    */
2134   protected void showGroupConservation_actionPerformed()
2135   {
2136     viewport.setShowGroupConservation(showGroupConservation.getState());
2137     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2138   }
2139
2140   /*
2141    * (non-Javadoc)
2142    *
2143    * @see
2144    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2145    * .event.ActionEvent)
2146    */
2147   protected void showConsensusHistogram_actionPerformed()
2148   {
2149     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2150     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2151   }
2152
2153   /*
2154    * (non-Javadoc)
2155    *
2156    * @see
2157    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2158    * .event.ActionEvent)
2159    */
2160   protected void showSequenceLogo_actionPerformed()
2161   {
2162     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2163     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2164   }
2165
2166   protected void normSequenceLogo_actionPerformed()
2167   {
2168     showSequenceLogo.setState(true);
2169     viewport.setShowSequenceLogo(true);
2170     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2171     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2172   }
2173
2174   protected void applyAutoAnnotationSettings_actionPerformed()
2175   {
2176     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2177   }
2178
2179   protected void makeGrpsFromSelection_actionPerformed()
2180   {
2181     if (avc.makeGroupsFromSelection())
2182     {
2183       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2184       alignPanel.updateAnnotation();
2185       alignPanel.paintAlignment(true);
2186     }
2187   }
2188
2189   protected void createGroup_actionPerformed()
2190   {
2191     avc.createGroup();
2192   }
2193
2194   protected void unGroup_actionPerformed()
2195   {
2196     if (avc.unGroup())
2197     {
2198       alignPanel.alignmentChanged();
2199     }
2200   }
2201
2202   protected void deleteGroups_actionPerformed()
2203   {
2204     if (avc.deleteGroups())
2205     {
2206       alignPanel.alignmentChanged();
2207     }
2208   }
2209
2210   public void selectAllSequenceMenuItem_actionPerformed()
2211   {
2212     SequenceGroup sg = new SequenceGroup();
2213     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2214     {
2215       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2216     }
2217     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2218     viewport.setSelectionGroup(sg);
2219     alignPanel.paintAlignment(true);
2220     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2221     viewport.sendSelection();
2222   }
2223
2224   public void deselectAllSequenceMenuItem_actionPerformed()
2225   {
2226     if (viewport.cursorMode)
2227     {
2228       alignPanel.seqPanel.keyboardNo1 = null;
2229       alignPanel.seqPanel.keyboardNo2 = null;
2230     }
2231     viewport.setSelectionGroup(null);
2232     viewport.getColumnSelection().clear();
2233     viewport.setSelectionGroup(null);
2234     alignPanel.idPanel.idCanvas.searchResults = null;
2235     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2236     alignPanel.paintAlignment(true);
2237     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2238     viewport.sendSelection();
2239   }
2240
2241   public void invertSequenceMenuItem_actionPerformed()
2242   {
2243     SequenceGroup sg = viewport.getSelectionGroup();
2244     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2245     {
2246       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2247     }
2248
2249     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2250     viewport.sendSelection();
2251   }
2252
2253   public void invertColSel_actionPerformed()
2254   {
2255     viewport.invertColumnSelection();
2256     alignPanel.paintAlignment(true);
2257     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2258     viewport.sendSelection();
2259   }
2260
2261   void trimAlignment(boolean trimLeft)
2262   {
2263     ColumnSelection colSel = viewport.getColumnSelection();
2264     int column;
2265
2266     if (colSel.size() > 0)
2267     {
2268       if (trimLeft)
2269       {
2270         column = colSel.getMin();
2271       }
2272       else
2273       {
2274         column = colSel.getMax();
2275       }
2276
2277       SequenceI[] seqs;
2278       if (viewport.getSelectionGroup() != null)
2279       {
2280         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2281                 viewport.getHiddenRepSequences());
2282       }
2283       else
2284       {
2285         seqs = viewport.getAlignment().getSequencesArray();
2286       }
2287
2288       TrimRegionCommand trimRegion;
2289       if (trimLeft)
2290       {
2291         trimRegion = new TrimRegionCommand("Remove Left",
2292                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2293                 viewport.getAlignment(), viewport.getColumnSelection(),
2294                 viewport.getSelectionGroup());
2295         viewport.setStartRes(0);
2296       }
2297       else
2298       {
2299         trimRegion = new TrimRegionCommand("Remove Right",
2300                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2301                 viewport.getAlignment(), viewport.getColumnSelection(),
2302                 viewport.getSelectionGroup());
2303       }
2304
2305       statusBar.setText(MessageManager.formatMessage(
2306               "label.removed_columns",
2307               new String[] { Integer.valueOf(trimRegion.getSize())
2308                       .toString() }));
2309       addHistoryItem(trimRegion);
2310
2311       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2312       {
2313         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2314                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2315         {
2316           viewport.getAlignment().deleteGroup(sg);
2317         }
2318       }
2319
2320       viewport.firePropertyChange("alignment", null, viewport
2321               .getAlignment().getSequences());
2322     }
2323   }
2324
2325   public void removeGappedColumnMenuItem_actionPerformed()
2326   {
2327     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2328
2329     SequenceI[] seqs;
2330     if (viewport.getSelectionGroup() != null)
2331     {
2332       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2333               viewport.getHiddenRepSequences());
2334       start = viewport.getSelectionGroup().getStartRes();
2335       end = viewport.getSelectionGroup().getEndRes();
2336     }
2337     else
2338     {
2339       seqs = viewport.getAlignment().getSequencesArray();
2340     }
2341
2342     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2343             "Remove Gapped Columns", seqs, start, end,
2344             viewport.getAlignment());
2345
2346     addHistoryItem(removeGapCols);
2347
2348     statusBar.setText(MessageManager.formatMessage(
2349             "label.removed_empty_columns",
2350             new String[] { Integer.valueOf(removeGapCols.getSize())
2351                     .toString() }));
2352
2353     // This is to maintain viewport position on first residue
2354     // of first sequence
2355     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2356     int startRes = seq.findPosition(viewport.startRes);
2357     // ShiftList shifts;
2358     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2359     // edit.alColumnChanges=shifts.getInverse();
2360     // if (viewport.hasHiddenColumns)
2361     // viewport.getColumnSelection().compensateForEdits(shifts);
2362     viewport.setStartRes(seq.findIndex(startRes) - 1);
2363     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2364             .getSequences());
2365
2366   }
2367
2368   public void removeAllGapsMenuItem_actionPerformed()
2369   {
2370     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2371
2372     SequenceI[] seqs;
2373     if (viewport.getSelectionGroup() != null)
2374     {
2375       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2376               viewport.getHiddenRepSequences());
2377       start = viewport.getSelectionGroup().getStartRes();
2378       end = viewport.getSelectionGroup().getEndRes();
2379     }
2380     else
2381     {
2382       seqs = viewport.getAlignment().getSequencesArray();
2383     }
2384
2385     // This is to maintain viewport position on first residue
2386     // of first sequence
2387     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2388     int startRes = seq.findPosition(viewport.startRes);
2389
2390     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2391             viewport.getAlignment()));
2392
2393     viewport.setStartRes(seq.findIndex(startRes) - 1);
2394
2395     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2396             .getSequences());
2397
2398   }
2399
2400   public void findMenuItem_actionPerformed()
2401   {
2402     new Finder(alignPanel);
2403   }
2404
2405   /**
2406    * create a new view derived from the current view
2407    *
2408    * @param viewtitle
2409    * @return frame for the new view
2410    */
2411   public AlignFrame newView(String viewtitle)
2412   {
2413     AlignmentI newal;
2414     if (viewport.hasHiddenRows())
2415     {
2416       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2417               .getFullAlignment().getSequencesArray());
2418     }
2419     else
2420     {
2421       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2422     }
2423
2424     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2425     {
2426       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2427       {
2428         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2429         {
2430           newal.addAnnotation(viewport.getAlignment()
2431                   .getAlignmentAnnotation()[i]);
2432         }
2433       }
2434     }
2435
2436     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2437
2438     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2439     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2440     PaintRefresher.Register(newaf.alignPanel,
2441             newaf.alignPanel.av.getSequenceSetId());
2442
2443     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2444             newaf.alignPanel.av.getSequenceSetId());
2445     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2446             newaf.alignPanel.av.getSequenceSetId());
2447
2448     Vector comps = (Vector) PaintRefresher.components.get(viewport
2449             .getSequenceSetId());
2450     int viewSize = -1;
2451     for (int i = 0; i < comps.size(); i++)
2452     {
2453       if (comps.elementAt(i) instanceof AlignmentPanel)
2454       {
2455         viewSize++;
2456       }
2457     }
2458
2459     String title = new String(this.getTitle());
2460     if (viewtitle != null)
2461     {
2462       title = viewtitle + " ( " + title + ")";
2463     }
2464     else
2465     {
2466       if (title.indexOf("(View") > -1)
2467       {
2468         title = title.substring(0, title.indexOf("(View"));
2469       }
2470       title += "(View " + viewSize + ")";
2471     }
2472
2473     newaf.setTitle(title.toString());
2474
2475     newaf.viewport.setHistoryList(viewport.getHistoryList());
2476     newaf.viewport.setRedoList(viewport.getRedoList());
2477     return newaf;
2478   }
2479
2480   /**
2481    *
2482    * @return list of feature groups on the view
2483    */
2484   public String[] getFeatureGroups()
2485   {
2486     FeatureRenderer fr = null;
2487     if (alignPanel != null
2488             && (fr = alignPanel.getFeatureRenderer()) != null)
2489     {
2490       List<String> gps = fr.getFeatureGroups();
2491       String[] _gps = gps.toArray(new String[gps.size()]);
2492       return _gps;
2493     }
2494     return null;
2495   }
2496
2497   /**
2498    * get sequence feature groups that are hidden or shown
2499    *
2500    * @param visible
2501    *          true is visible
2502    * @return list
2503    */
2504   public String[] getFeatureGroupsOfState(boolean visible)
2505   {
2506     FeatureRenderer fr = null;
2507     if (alignPanel != null
2508             && (fr = alignPanel.getFeatureRenderer()) != null)
2509     {
2510       List<String> gps = fr.getGroups(visible);
2511       String[] _gps = gps.toArray(new String[gps.size()]);
2512       return _gps;
2513     }
2514     return null;
2515   }
2516
2517   /**
2518    * Change the display state for the given feature groups
2519    *
2520    * @param groups
2521    *          list of group strings
2522    * @param state
2523    *          visible or invisible
2524    */
2525   public void setFeatureGroupState(String[] groups, boolean state)
2526   {
2527     FeatureRenderer fr = null;
2528     this.sequenceFeatures.setState(true);
2529     viewport.setShowSequenceFeatures(true);
2530     if (alignPanel != null
2531             && (fr = alignPanel.getFeatureRenderer()) != null)
2532     {
2533
2534       fr.setGroupVisibility(Arrays.asList(groups), state);
2535       alignPanel.seqPanel.seqCanvas.repaint();
2536       if (alignPanel.overviewPanel != null)
2537       {
2538         alignPanel.overviewPanel.updateOverviewImage();
2539       }
2540     }
2541   }
2542
2543   public void seqLimits_itemStateChanged()
2544   {
2545     viewport.setShowJVSuffix(seqLimits.getState());
2546     alignPanel.fontChanged();
2547     alignPanel.paintAlignment(true);
2548   }
2549
2550   protected void colourTextMenuItem_actionPerformed()
2551   {
2552     viewport.setColourText(colourTextMenuItem.getState());
2553     alignPanel.paintAlignment(true);
2554   }
2555
2556   protected void displayNonconservedMenuItem_actionPerformed()
2557   {
2558     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2559     alignPanel.paintAlignment(true);
2560   }
2561
2562   protected void wrapMenuItem_actionPerformed()
2563   {
2564     viewport.setWrapAlignment(wrapMenuItem.getState());
2565     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2566     scaleAbove.setEnabled(wrapMenuItem.getState());
2567     scaleLeft.setEnabled(wrapMenuItem.getState());
2568     scaleRight.setEnabled(wrapMenuItem.getState());
2569     alignPanel.paintAlignment(true);
2570   }
2571
2572   public void overviewMenuItem_actionPerformed()
2573   {
2574     if (alignPanel.overviewPanel != null)
2575     {
2576       return;
2577     }
2578
2579     Frame frame = new Frame();
2580     OverviewPanel overview = new OverviewPanel(alignPanel);
2581     frame.add(overview);
2582     // +50 must allow for applet frame window
2583     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2584             "label.overview_params", new String[] { this.getTitle() }),
2585             overview.getPreferredSize().width,
2586             overview.getPreferredSize().height + 50);
2587
2588     frame.pack();
2589     final AlignmentPanel ap = alignPanel;
2590     frame.addWindowListener(new WindowAdapter()
2591     {
2592       @Override
2593       public void windowClosing(WindowEvent e)
2594       {
2595         if (ap != null)
2596         {
2597           ap.setOverviewPanel(null);
2598         }
2599       };
2600     });
2601
2602     alignPanel.setOverviewPanel(overview);
2603
2604   }
2605
2606   @Override
2607   public void changeColour(ColourSchemeI cs)
2608   {
2609
2610     if (cs != null)
2611     {
2612       if (viewport.getAbovePIDThreshold())
2613       {
2614         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2615                 cs, "Background"));
2616       }
2617
2618       if (viewport.getConservationSelected())
2619       {
2620         cs.setConservationApplied(true);
2621         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2622                 cs, "Background"));
2623       }
2624       else
2625       {
2626         cs.setConservationApplied(false);
2627       }
2628     }
2629     viewport.setGlobalColourScheme(cs);
2630
2631     alignPanel.paintAlignment(true);
2632   }
2633
2634   protected void modifyPID_actionPerformed()
2635   {
2636     if (viewport.getAbovePIDThreshold()
2637             && viewport.getGlobalColourScheme() != null)
2638     {
2639       SliderPanel.setPIDSliderSource(alignPanel,
2640               viewport.getGlobalColourScheme(), "Background");
2641       SliderPanel.showPIDSlider();
2642     }
2643   }
2644
2645   protected void modifyConservation_actionPerformed()
2646   {
2647     if (viewport.getConservationSelected()
2648             && viewport.getGlobalColourScheme() != null)
2649     {
2650       SliderPanel.setConservationSlider(alignPanel,
2651               viewport.getGlobalColourScheme(), "Background");
2652       SliderPanel.showConservationSlider();
2653     }
2654   }
2655
2656   protected void conservationMenuItem_actionPerformed()
2657   {
2658     viewport.setConservationSelected(conservationMenuItem.getState());
2659
2660     viewport.setAbovePIDThreshold(false);
2661     abovePIDThreshold.setState(false);
2662
2663     changeColour(viewport.getGlobalColourScheme());
2664
2665     modifyConservation_actionPerformed();
2666   }
2667
2668   public void abovePIDThreshold_actionPerformed()
2669   {
2670     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2671
2672     conservationMenuItem.setState(false);
2673     viewport.setConservationSelected(false);
2674
2675     changeColour(viewport.getGlobalColourScheme());
2676
2677     modifyPID_actionPerformed();
2678   }
2679
2680   public void sortPairwiseMenuItem_actionPerformed()
2681   {
2682     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2683     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2684             .getAlignment().getSequenceAt(0), null);
2685
2686     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2687             viewport.getAlignment()));
2688     alignPanel.paintAlignment(true);
2689   }
2690
2691   public void sortIDMenuItem_actionPerformed()
2692   {
2693     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2694     AlignmentSorter.sortByID(viewport.getAlignment());
2695     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2696             viewport.getAlignment()));
2697     alignPanel.paintAlignment(true);
2698   }
2699
2700   public void sortLengthMenuItem_actionPerformed()
2701   {
2702     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2703     AlignmentSorter.sortByLength(viewport.getAlignment());
2704     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2705             viewport.getAlignment()));
2706     alignPanel.paintAlignment(true);
2707   }
2708
2709   public void sortGroupMenuItem_actionPerformed()
2710   {
2711     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2712     AlignmentSorter.sortByGroup(viewport.getAlignment());
2713     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2714             viewport.getAlignment()));
2715     alignPanel.paintAlignment(true);
2716
2717   }
2718
2719   public void removeRedundancyMenuItem_actionPerformed()
2720   {
2721     new RedundancyPanel(alignPanel);
2722   }
2723
2724   public void pairwiseAlignmentMenuItem_actionPerformed()
2725   {
2726     if (viewport.getSelectionGroup() != null
2727             && viewport.getSelectionGroup().getSize() > 1)
2728     {
2729       Frame frame = new Frame();
2730       frame.add(new PairwiseAlignPanel(alignPanel));
2731       jalview.bin.JalviewLite.addFrame(frame,
2732               MessageManager.getString("action.pairwise_alignment"), 600,
2733               500);
2734     }
2735   }
2736
2737   public void PCAMenuItem_actionPerformed()
2738   {
2739     // are the sequences aligned?
2740     if (!viewport.getAlignment().isAligned(false))
2741     {
2742       SequenceI current;
2743       int Width = viewport.getAlignment().getWidth();
2744
2745       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2746       {
2747         current = viewport.getAlignment().getSequenceAt(i);
2748
2749         if (current.getLength() < Width)
2750         {
2751           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2752         }
2753       }
2754       alignPanel.paintAlignment(true);
2755     }
2756
2757     if ((viewport.getSelectionGroup() != null
2758             && viewport.getSelectionGroup().getSize() < 4 && viewport
2759             .getSelectionGroup().getSize() > 0)
2760             || viewport.getAlignment().getHeight() < 4)
2761     {
2762       return;
2763     }
2764
2765     try
2766     {
2767       new PCAPanel(viewport);
2768     } catch (java.lang.OutOfMemoryError ex)
2769     {
2770     }
2771
2772   }
2773
2774   public void averageDistanceTreeMenuItem_actionPerformed()
2775   {
2776     NewTreePanel("AV", "PID", "Average distance tree using PID");
2777   }
2778
2779   public void neighbourTreeMenuItem_actionPerformed()
2780   {
2781     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2782   }
2783
2784   protected void njTreeBlosumMenuItem_actionPerformed()
2785   {
2786     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2787   }
2788
2789   protected void avTreeBlosumMenuItem_actionPerformed()
2790   {
2791     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2792   }
2793
2794   void NewTreePanel(String type, String pwType, String title)
2795   {
2796     // are the sequences aligned?
2797     if (!viewport.getAlignment().isAligned(false))
2798     {
2799       SequenceI current;
2800       int Width = viewport.getAlignment().getWidth();
2801
2802       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2803       {
2804         current = viewport.getAlignment().getSequenceAt(i);
2805
2806         if (current.getLength() < Width)
2807         {
2808           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2809         }
2810       }
2811       alignPanel.paintAlignment(true);
2812
2813     }
2814
2815     if ((viewport.getSelectionGroup() != null && viewport
2816             .getSelectionGroup().getSize() > 1)
2817             || (viewport.getAlignment().getHeight() > 1))
2818     {
2819       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2820
2821       addTreeMenuItem(tp, title);
2822
2823       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2824     }
2825   }
2826
2827   void loadTree_actionPerformed()
2828   {
2829     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2830     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2831     cap.setTreeImport();
2832     Frame frame = new Frame();
2833     frame.add(cap);
2834     jalview.bin.JalviewLite.addFrame(frame,
2835             MessageManager.getString("label.paste_newick_file"), 400, 300);
2836   }
2837
2838   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2839   {
2840     TreePanel tp = new TreePanel(alignPanel, treeFile,
2841             MessageManager.getString("label.load_tree_from_file"), tree);
2842     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2843     addTreeMenuItem(tp, treeFile);
2844   }
2845
2846   /**
2847    * sort the alignment using the given treePanel
2848    *
2849    * @param treePanel
2850    *          tree used to sort view
2851    * @param title
2852    *          string used for undo event name
2853    */
2854   public void sortByTree(TreePanel treePanel, String title)
2855   {
2856     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2857     AlignmentSorter
2858             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2859     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2860     // HistoryItem.SORT));
2861     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2862             "label.order_by_params", new String[] { title }), oldOrder,
2863             viewport.getAlignment()));
2864     alignPanel.paintAlignment(true);
2865   }
2866
2867   /**
2868    * Do any automatic reordering of the alignment and add the necessary bits to
2869    * the menu structure for the new tree
2870    *
2871    * @param treePanel
2872    * @param title
2873    */
2874   protected void addTreeMenuItem(final TreePanel treePanel,
2875           final String title)
2876   {
2877     final MenuItem item = new MenuItem(title);
2878     sortByTreeMenu.add(item);
2879     item.addActionListener(new java.awt.event.ActionListener()
2880     {
2881       @Override
2882       public void actionPerformed(ActionEvent evt)
2883       {
2884         sortByTree(treePanel, title); // treePanel.getTitle());
2885       }
2886     });
2887
2888     treePanel.addWindowListener(new WindowAdapter()
2889     {
2890       @Override
2891       public void windowOpened(WindowEvent e)
2892       {
2893         if (viewport.sortByTree)
2894         {
2895           sortByTree(treePanel, title);
2896         }
2897         super.windowOpened(e);
2898       }
2899
2900       @Override
2901       public void windowClosing(WindowEvent e)
2902       {
2903         sortByTreeMenu.remove(item);
2904       };
2905     });
2906   }
2907
2908   public boolean sortBy(AlignmentOrder alorder, String undoname)
2909   {
2910     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2911     if (viewport.applet.debug)
2912     {
2913       System.err.println("Sorting " + alorder.getOrder().size()
2914               + " in alignment '" + getTitle() + "'");
2915     }
2916     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2917     if (undoname != null)
2918     {
2919       addHistoryItem(new OrderCommand(undoname, oldOrder,
2920               viewport.getAlignment()));
2921     }
2922     alignPanel.paintAlignment(true);
2923     return true;
2924   }
2925
2926   protected void documentation_actionPerformed()
2927   {
2928     alignPanel.av.applet.openJalviewHelpUrl();
2929   }
2930
2931   protected void about_actionPerformed()
2932   {
2933
2934     class AboutPanel extends Canvas
2935     {
2936       String version;
2937
2938       String builddate;
2939
2940       public AboutPanel(String version, String builddate)
2941       {
2942         this.version = version;
2943         this.builddate = builddate;
2944       }
2945
2946       @Override
2947       public void paint(Graphics g)
2948       {
2949         g.setColor(Color.white);
2950         g.fillRect(0, 0, getSize().width, getSize().height);
2951         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2952         FontMetrics fm = g.getFontMetrics();
2953         int fh = fm.getHeight();
2954         int y = 5, x = 7;
2955         g.setColor(Color.black);
2956         // TODO: update this text for each release or centrally store it for
2957         // lite and application
2958         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2959         g.drawString(MessageManager.formatMessage(
2960                 "label.jalviewLite_release", new String[] { version }), x,
2961                 y += fh);
2962         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2963         g.drawString(MessageManager.formatMessage(
2964                 "label.jaview_build_date", new String[] { builddate }), x,
2965                 y += fh);
2966         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2967         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2968                 x, y += fh * 1.5);
2969         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2970                 x + 50, y += fh + 8);
2971         g.drawString(
2972                 MessageManager.getString("label.jalview_dev_managers"), x,
2973                 y += fh);
2974         g.drawString(MessageManager
2975                 .getString("label.jalview_distribution_lists"), x, y += fh);
2976         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2977                 x, y += fh + 8);
2978         g.drawString(
2979                 MessageManager.getString("label.jalview_cite_1_authors"),
2980                 x, y += fh);
2981         g.drawString(
2982                 MessageManager.getString("label.jalview_cite_1_title"), x,
2983                 y += fh);
2984         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2985                 x, y += fh);
2986       }
2987     }
2988
2989     Frame frame = new Frame();
2990     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2991             .getBuildDate()));
2992     jalview.bin.JalviewLite.addFrame(frame,
2993             MessageManager.getString("label.jalview"), 580, 220);
2994
2995   }
2996
2997   public void showURL(String url, String target)
2998   {
2999     if (viewport.applet == null)
3000     {
3001       System.out.println("Not running as applet - no browser available.");
3002     }
3003     else
3004     {
3005       viewport.applet.showURL(url, target);
3006     }
3007   }
3008
3009   // ////////////////////////////////////////////////////////////////////////////////
3010   // JBuilder Graphics here
3011
3012   MenuBar alignFrameMenuBar = new MenuBar();
3013
3014   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3015
3016   MenuItem loadApplication = new MenuItem(
3017           MessageManager.getString("label.view_full_application"));
3018
3019   MenuItem loadTree = new MenuItem(
3020           MessageManager.getString("label.load_associated_tree"));
3021
3022   MenuItem loadAnnotations = new MenuItem(
3023           MessageManager.getString("label.load_features_annotations"));
3024
3025   MenuItem outputFeatures = new MenuItem(
3026           MessageManager.getString("label.export_features"));
3027
3028   MenuItem outputAnnotations = new MenuItem(
3029           MessageManager.getString("label.export_annotations"));
3030
3031   MenuItem closeMenuItem = new MenuItem(
3032           MessageManager.getString("action.close"));
3033
3034   MenuItem selectAllSequenceMenuItem = new MenuItem(
3035           MessageManager.getString("action.select_all"));
3036
3037   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3038           MessageManager.getString("action.deselect_all"));
3039
3040   MenuItem invertSequenceMenuItem = new MenuItem(
3041           MessageManager.getString("action.invert_selection"));
3042
3043   MenuItem remove2LeftMenuItem = new MenuItem();
3044
3045   MenuItem remove2RightMenuItem = new MenuItem();
3046
3047   MenuItem removeGappedColumnMenuItem = new MenuItem();
3048
3049   MenuItem removeAllGapsMenuItem = new MenuItem();
3050
3051   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3052
3053   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3054
3055   MenuItem sortPairwiseMenuItem = new MenuItem();
3056
3057   MenuItem sortIDMenuItem = new MenuItem();
3058
3059   MenuItem sortLengthMenuItem = new MenuItem();
3060
3061   MenuItem sortGroupMenuItem = new MenuItem();
3062
3063   MenuItem removeRedundancyMenuItem = new MenuItem();
3064
3065   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3066
3067   MenuItem PCAMenuItem = new MenuItem();
3068
3069   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3070
3071   MenuItem neighbourTreeMenuItem = new MenuItem();
3072
3073   BorderLayout borderLayout1 = new BorderLayout();
3074
3075   public Label statusBar = new Label();
3076
3077   MenuItem clustalColour = new MenuItem();
3078
3079   MenuItem zappoColour = new MenuItem();
3080
3081   MenuItem taylorColour = new MenuItem();
3082
3083   MenuItem hydrophobicityColour = new MenuItem();
3084
3085   MenuItem helixColour = new MenuItem();
3086
3087   MenuItem strandColour = new MenuItem();
3088
3089   MenuItem turnColour = new MenuItem();
3090
3091   MenuItem buriedColour = new MenuItem();
3092
3093   MenuItem purinePyrimidineColour = new MenuItem();
3094
3095   // MenuItem RNAInteractionColour = new MenuItem();
3096
3097   MenuItem RNAHelixColour = new MenuItem();
3098
3099   MenuItem userDefinedColour = new MenuItem();
3100
3101   MenuItem PIDColour = new MenuItem();
3102
3103   MenuItem BLOSUM62Colour = new MenuItem();
3104
3105   MenuItem tcoffeeColour = new MenuItem();
3106
3107   MenuItem njTreeBlosumMenuItem = new MenuItem();
3108
3109   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3110
3111   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3112
3113   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3114
3115   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3116
3117   MenuItem alProperties = new MenuItem(
3118           MessageManager.getString("label.alignment_props"));
3119
3120   MenuItem overviewMenuItem = new MenuItem();
3121
3122   MenuItem undoMenuItem = new MenuItem();
3123
3124   MenuItem redoMenuItem = new MenuItem();
3125
3126   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3127
3128   MenuItem noColourmenuItem = new MenuItem();
3129
3130   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3131
3132   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3133
3134   MenuItem findMenuItem = new MenuItem();
3135
3136   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3137
3138   MenuItem nucleotideColour = new MenuItem();
3139
3140   MenuItem deleteGroups = new MenuItem();
3141
3142   MenuItem grpsFromSelection = new MenuItem();
3143
3144   MenuItem createGroup = new MenuItem();
3145
3146   MenuItem unGroup = new MenuItem();
3147
3148   MenuItem delete = new MenuItem();
3149
3150   MenuItem copy = new MenuItem();
3151
3152   MenuItem cut = new MenuItem();
3153
3154   Menu pasteMenu = new Menu();
3155
3156   MenuItem pasteNew = new MenuItem();
3157
3158   MenuItem pasteThis = new MenuItem();
3159
3160   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3161
3162   MenuItem font = new MenuItem();
3163
3164   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3165
3166   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3167
3168   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3169
3170   MenuItem modifyPID = new MenuItem();
3171
3172   MenuItem modifyConservation = new MenuItem();
3173
3174   CheckboxMenuItem autoCalculate = null;
3175
3176   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3177           "Sort Alignment With New Tree", true);
3178
3179   Menu sortByTreeMenu = new Menu();
3180
3181   MenuItem inputText = new MenuItem();
3182
3183   MenuItem documentation = new MenuItem();
3184
3185   MenuItem about = new MenuItem();
3186
3187   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3188
3189   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3190
3191   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3192
3193   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3194
3195   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3196
3197   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3198
3199   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3200
3201   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3202
3203   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3204
3205   /**
3206    * Initialise menus and other items
3207    *
3208    * @throws Exception
3209    */
3210   private void jbInit() throws Exception
3211   {
3212     setMenuBar(alignFrameMenuBar);
3213
3214     /*
3215      * Configure File menu items and actions
3216      */
3217     inputText
3218             .setLabel(MessageManager.getString("label.input_from_textbox"));
3219     inputText.addActionListener(this);
3220     Menu outputTextboxMenu = new Menu(
3221             MessageManager.getString("label.out_to_textbox"));
3222     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3223     {
3224
3225       MenuItem item = new MenuItem(
3226               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3227
3228       item.addActionListener(new java.awt.event.ActionListener()
3229       {
3230         @Override
3231         public void actionPerformed(ActionEvent e)
3232         {
3233           outputText_actionPerformed(e);
3234         }
3235       });
3236
3237       outputTextboxMenu.add(item);
3238     }
3239     closeMenuItem.addActionListener(this);
3240     loadApplication.addActionListener(this);
3241     loadTree.addActionListener(this);
3242     loadAnnotations.addActionListener(this);
3243     outputFeatures.addActionListener(this);
3244     outputAnnotations.addActionListener(this);
3245
3246     /*
3247      * Configure Edit menu items and actions
3248      */
3249     undoMenuItem.setEnabled(false);
3250     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3251     undoMenuItem.addActionListener(this);
3252     redoMenuItem.setEnabled(false);
3253     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3254     redoMenuItem.addActionListener(this);
3255     copy.setLabel(MessageManager.getString("action.copy"));
3256     copy.addActionListener(this);
3257     cut.setLabel(MessageManager.getString("action.cut"));
3258     cut.addActionListener(this);
3259     delete.setLabel(MessageManager.getString("action.delete"));
3260     delete.addActionListener(this);
3261     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3262     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3263     pasteNew.addActionListener(this);
3264     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3265     pasteThis.addActionListener(this);
3266     remove2LeftMenuItem.setLabel(MessageManager
3267             .getString("action.remove_left"));
3268     remove2LeftMenuItem.addActionListener(this);
3269     remove2RightMenuItem.setLabel(MessageManager
3270             .getString("action.remove_right"));
3271     remove2RightMenuItem.addActionListener(this);
3272     removeGappedColumnMenuItem.setLabel(MessageManager
3273             .getString("action.remove_empty_columns"));
3274     removeGappedColumnMenuItem.addActionListener(this);
3275     removeAllGapsMenuItem.setLabel(MessageManager
3276             .getString("action.remove_all_gaps"));
3277     removeAllGapsMenuItem.addActionListener(this);
3278     removeRedundancyMenuItem.setLabel(MessageManager
3279             .getString("action.remove_redundancy"));
3280     removeRedundancyMenuItem.addActionListener(this);
3281
3282     /*
3283      * Configure Select menu items and actions
3284      */
3285     findMenuItem.setLabel(MessageManager.getString("action.find"));
3286     findMenuItem.addActionListener(this);
3287     selectAllSequenceMenuItem.addActionListener(this);
3288     deselectAllSequenceMenuItem.addActionListener(this);
3289     invertSequenceMenuItem.setLabel(MessageManager
3290             .getString("action.invert_sequence_selection"));
3291     invertSequenceMenuItem.addActionListener(this);
3292     invertColSel.setLabel(MessageManager
3293             .getString("action.invert_column_selection"));
3294     invertColSel.addActionListener(this);
3295     deleteGroups.setLabel(MessageManager
3296             .getString("action.undefine_groups"));
3297     deleteGroups.addActionListener(this);
3298     grpsFromSelection.setLabel(MessageManager
3299             .getString("action.make_groups_selection"));
3300     grpsFromSelection.addActionListener(this);
3301     createGroup.setLabel(MessageManager.getString("action.create_group"));
3302     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3303     annotationColumnSelection.setLabel(MessageManager
3304             .getString("action.select_by_annotation"));
3305     annotationColumnSelection.addActionListener(this);
3306
3307     /*
3308      * Configure View menu items and actions
3309      */
3310     newView.setLabel(MessageManager.getString("action.new_view"));
3311     newView.addActionListener(this);
3312     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3313     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3314     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3315     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3316     hideColumns
3317             .setLabel(MessageManager.getString("label.selected_columns"));
3318     hideSequences.setLabel(MessageManager
3319             .getString("label.selected_sequences"));
3320     hideAllButSelection.setLabel(MessageManager
3321             .getString("label.all_but_selected_region"));
3322     hideAllSelection.setLabel(MessageManager
3323             .getString("label.selected_region"));
3324     showAllHidden.setLabel(MessageManager
3325             .getString("label.all_sequences_columns"));
3326     showColumns.addActionListener(this);
3327     showSeqs.addActionListener(this);
3328     hideColumns.addActionListener(this);
3329     hideSequences.addActionListener(this);
3330     hideAllButSelection.addActionListener(this);
3331     hideAllSelection.addActionListener(this);
3332     showAllHidden.addActionListener(this);
3333     featureSettings.setLabel(MessageManager
3334             .getString("action.feature_settings"));
3335     featureSettings.addActionListener(this);
3336     sequenceFeatures.setLabel(MessageManager
3337             .getString("label.show_sequence_features"));
3338     sequenceFeatures.addItemListener(this);
3339     sequenceFeatures.setState(false);
3340     followMouseOverFlag.setLabel(MessageManager
3341             .getString("label.automatic_scrolling"));
3342     followMouseOverFlag.addItemListener(this);
3343     alProperties.addActionListener(this);
3344     overviewMenuItem.setLabel(MessageManager
3345             .getString("label.overview_window"));
3346     overviewMenuItem.addActionListener(this);
3347
3348     /*
3349      * Configure Annotations menu items and actions
3350      */
3351     annotationPanelMenuItem.setLabel(MessageManager
3352             .getString("label.show_annotations"));
3353     annotationPanelMenuItem.addItemListener(this);
3354     showGroupConsensus.setLabel(MessageManager
3355             .getString("label.group_consensus"));
3356     showGroupConservation.setLabel(MessageManager
3357             .getString("label.group_conservation"));
3358     showConsensusHistogram.setLabel(MessageManager
3359             .getString("label.show_consensus_histogram"));
3360     showSequenceLogo.setLabel(MessageManager
3361             .getString("label.show_consensus_logo"));
3362     normSequenceLogo.setLabel(MessageManager
3363             .getString("label.norm_consensus_logo"));
3364     applyAutoAnnotationSettings.setLabel(MessageManager
3365             .getString("label.apply_all_groups"));
3366     applyAutoAnnotationSettings.setState(true);
3367     Menu autoAnnMenu = new Menu(
3368             MessageManager.getString("label.autocalculated_annotation"));
3369     showGroupConsensus.addItemListener(this);
3370     showGroupConservation.addItemListener(this);
3371     showConsensusHistogram.addItemListener(this);
3372     showSequenceLogo.addItemListener(this);
3373     normSequenceLogo.addItemListener(this);
3374     applyAutoAnnotationSettings.addItemListener(this);
3375     showAlignmentAnnotations = new CheckboxMenuItem(
3376             MessageManager.getString("label.show_all_al_annotations"));
3377     showSequenceAnnotations = new CheckboxMenuItem(
3378             MessageManager.getString("label.show_all_seq_annotations"));
3379     sortAnnBySequence = new CheckboxMenuItem(
3380             MessageManager.getString("label.sort_annotations_by_sequence"));
3381     sortAnnByLabel = new CheckboxMenuItem(
3382             MessageManager.getString("label.sort_annotations_by_label"));
3383     showAutoFirst = new CheckboxMenuItem(
3384             MessageManager.getString("label.show_first"));
3385     showAutoFirst.setState(false); // pending applet parameter
3386     setShowAutoCalculatedAbove(showAutoFirst.getState());
3387     showAutoLast = new CheckboxMenuItem(
3388             MessageManager.getString("label.show_last"));
3389     showAutoLast.setState(!showAutoFirst.getState());
3390     showAlignmentAnnotations.addItemListener(this);
3391     showSequenceAnnotations.addItemListener(this);
3392     sortAnnBySequence.addItemListener(this);
3393     sortAnnByLabel.addItemListener(this);
3394     showAutoFirst.addItemListener(this);
3395     showAutoLast.addItemListener(this);
3396
3397     /*
3398      * Configure Format menu items and actions
3399      */
3400     font.setLabel(MessageManager.getString("action.font"));
3401     font.addActionListener(this);
3402     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3403     scaleAbove.setState(true);
3404     scaleAbove.setEnabled(false);
3405     scaleAbove.addItemListener(this);
3406     scaleLeft.setEnabled(false);
3407     scaleLeft.setState(true);
3408     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3409     scaleLeft.addItemListener(this);
3410     scaleRight.setEnabled(false);
3411     scaleRight.setState(true);
3412     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3413     scaleRight.addItemListener(this);
3414     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3415     viewBoxesMenuItem.setState(true);
3416     viewBoxesMenuItem.addItemListener(this);
3417     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3418     viewTextMenuItem.setState(true);
3419     viewTextMenuItem.addItemListener(this);
3420     colourTextMenuItem.setLabel(MessageManager
3421             .getString("label.colour_text"));
3422     colourTextMenuItem.addItemListener(this);
3423     displayNonconservedMenuItem.setLabel(MessageManager
3424             .getString("label.show_non_conversed"));
3425     displayNonconservedMenuItem.addItemListener(this);
3426     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3427     wrapMenuItem.addItemListener(this);
3428     renderGapsMenuItem.setLabel(MessageManager
3429             .getString("action.show_gaps"));
3430     renderGapsMenuItem.setState(true);
3431     renderGapsMenuItem.addItemListener(this);
3432     centreColumnLabelFlag.setLabel(MessageManager
3433             .getString("label.centre_column_labels"));
3434     centreColumnLabelFlag.addItemListener(this);
3435     seqLimits.setState(true);
3436     seqLimits.setLabel(MessageManager
3437             .getString("label.show_sequence_limits"));
3438     seqLimits.addItemListener(this);
3439
3440     /*
3441      * Configure Colour menu items and actions
3442      */
3443     applyToAllGroups.setLabel(MessageManager
3444             .getString("label.apply_colour_to_all_groups"));
3445     applyToAllGroups.setState(true);
3446     applyToAllGroups.addItemListener(this);
3447     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3448     clustalColour.addActionListener(this);
3449     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3450     zappoColour.addActionListener(this);
3451     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3452     taylorColour.addActionListener(this);
3453     hydrophobicityColour.setLabel(MessageManager
3454             .getString("label.hydrophobicity"));
3455     hydrophobicityColour.addActionListener(this);
3456     helixColour
3457             .setLabel(MessageManager.getString("label.helix_propensity"));
3458     helixColour.addActionListener(this);
3459     strandColour.setLabel(MessageManager
3460             .getString("label.strand_propensity"));
3461     strandColour.addActionListener(this);
3462     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3463     turnColour.addActionListener(this);
3464     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3465     buriedColour.addActionListener(this);
3466     purinePyrimidineColour.setLabel(MessageManager
3467             .getString("label.purine_pyrimidine"));
3468     purinePyrimidineColour.addActionListener(this);
3469     // RNAInteractionColour.setLabel(MessageManager
3470     // .getString("label.rna_interaction"));
3471     // RNAInteractionColour.addActionListener(this);
3472     RNAHelixColour.setLabel(MessageManager
3473             .getString("action.by_rna_helixes"));
3474     RNAHelixColour.addActionListener(this);
3475     userDefinedColour.setLabel(MessageManager
3476             .getString("action.user_defined"));
3477     userDefinedColour.addActionListener(this);
3478     PIDColour.setLabel(MessageManager
3479             .getString("label.percentage_identity"));
3480     PIDColour.addActionListener(this);
3481     BLOSUM62Colour.setLabel(MessageManager
3482             .getString("label.blosum62_score"));
3483     BLOSUM62Colour.addActionListener(this);
3484     tcoffeeColour
3485             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3486     // it will be enabled only if a score file is provided
3487     tcoffeeColour.setEnabled(false);
3488     tcoffeeColour.addActionListener(this);
3489     conservationMenuItem.setLabel(MessageManager
3490             .getString("action.by_conservation"));
3491     conservationMenuItem.addItemListener(this);
3492     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3493     noColourmenuItem.addActionListener(this);
3494     abovePIDThreshold.setLabel(MessageManager
3495             .getString("label.above_identity_threshold"));
3496     abovePIDThreshold.addItemListener(this);
3497     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3498     nucleotideColour.addActionListener(this);
3499     modifyPID.setLabel(MessageManager
3500             .getString("label.modify_identity_thereshold"));
3501     modifyPID.addActionListener(this);
3502     modifyConservation.setLabel(MessageManager
3503             .getString("label.modify_conservation_thereshold"));
3504     modifyConservation.addActionListener(this);
3505     annotationColour.setLabel(MessageManager
3506             .getString("action.by_annotation"));
3507     annotationColour.addActionListener(this);
3508
3509     /*
3510      * Configure Calculate menu items and actions
3511      */
3512     sortPairwiseMenuItem.setLabel(MessageManager
3513             .getString("action.by_pairwise_id"));
3514     sortPairwiseMenuItem.addActionListener(this);
3515     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3516     sortIDMenuItem.addActionListener(this);
3517     sortLengthMenuItem.setLabel(MessageManager
3518             .getString("action.by_length"));
3519     sortLengthMenuItem.addActionListener(this);
3520     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3521     sortGroupMenuItem.addActionListener(this);
3522     pairwiseAlignmentMenuItem.setLabel(MessageManager
3523             .getString("action.pairwise_alignment"));
3524     pairwiseAlignmentMenuItem.addActionListener(this);
3525     PCAMenuItem.setLabel(MessageManager
3526             .getString("label.principal_component_analysis"));
3527     PCAMenuItem.addActionListener(this);
3528     autoCalculate = new CheckboxMenuItem(
3529             MessageManager.getString("label.autocalculate_consensus"), true);
3530     averageDistanceTreeMenuItem.setLabel(MessageManager
3531             .getString("label.average_distance_identity"));
3532     averageDistanceTreeMenuItem.addActionListener(this);
3533     neighbourTreeMenuItem.setLabel(MessageManager
3534             .getString("label.neighbour_joining_identity"));
3535     neighbourTreeMenuItem.addActionListener(this);
3536     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3537             .getString("label.average_distance_bloslum62"));
3538     avDistanceTreeBlosumMenuItem.addActionListener(this);
3539     njTreeBlosumMenuItem.setLabel(MessageManager
3540             .getString("label.neighbour_blosum62"));
3541     njTreeBlosumMenuItem.addActionListener(this);
3542     sortByTreeMenu.setLabel(MessageManager
3543             .getString("action.by_tree_order"));
3544     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3545     Menu calculateTreeMenu = new Menu(
3546             MessageManager.getString("action.calculate_tree"));
3547     autoCalculate.addItemListener(this);
3548     sortByTree.addItemListener(this);
3549
3550     /*
3551      * Configure Help menu items and actions
3552      */
3553     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3554     documentation.setLabel(MessageManager.getString("label.documentation"));
3555     documentation.addActionListener(this);
3556     about.setLabel(MessageManager.getString("label.about"));
3557     about.addActionListener(this);
3558
3559     /*
3560      * Add top level menus to frame
3561      */
3562     alignFrameMenuBar.add(fileMenu);
3563     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3564     alignFrameMenuBar.add(editMenu);
3565     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3566     alignFrameMenuBar.add(selectMenu);
3567     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3568     alignFrameMenuBar.add(viewMenu);
3569     Menu annotationsMenu = new Menu(
3570             MessageManager.getString("action.annotations"));
3571     alignFrameMenuBar.add(annotationsMenu);
3572     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3573     alignFrameMenuBar.add(formatMenu);
3574     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3575     alignFrameMenuBar.add(colourMenu);
3576     Menu calculateMenu = new Menu(
3577             MessageManager.getString("action.calculate"));
3578     alignFrameMenuBar.add(calculateMenu);
3579     alignFrameMenuBar.add(helpMenu);
3580
3581     /*
3582      * File menu
3583      */
3584     fileMenu.add(inputText);
3585     fileMenu.add(loadTree);
3586     fileMenu.add(loadAnnotations);
3587     fileMenu.addSeparator();
3588     fileMenu.add(outputTextboxMenu);
3589     fileMenu.add(outputFeatures);
3590     fileMenu.add(outputAnnotations);
3591     if (jalviewServletURL != null)
3592     {
3593       fileMenu.add(loadApplication);
3594     }
3595     fileMenu.addSeparator();
3596     fileMenu.add(closeMenuItem);
3597
3598     /*
3599      * Edit menu
3600      */
3601     editMenu.add(undoMenuItem);
3602     editMenu.add(redoMenuItem);
3603     editMenu.add(cut);
3604     editMenu.add(copy);
3605     pasteMenu.add(pasteNew);
3606     pasteMenu.add(pasteThis);
3607     editMenu.add(pasteMenu);
3608     editMenu.add(delete);
3609     editMenu.addSeparator();
3610     editMenu.add(remove2LeftMenuItem);
3611     editMenu.add(remove2RightMenuItem);
3612     editMenu.add(removeGappedColumnMenuItem);
3613     editMenu.add(removeAllGapsMenuItem);
3614     editMenu.add(removeRedundancyMenuItem);
3615
3616     /*
3617      * Select menu
3618      */
3619     selectMenu.add(findMenuItem);
3620     selectMenu.addSeparator();
3621     selectMenu.add(selectAllSequenceMenuItem);
3622     selectMenu.add(deselectAllSequenceMenuItem);
3623     selectMenu.add(invertSequenceMenuItem);
3624     selectMenu.add(invertColSel);
3625     selectMenu.add(createGroup);
3626     selectMenu.add(unGroup);
3627     selectMenu.add(grpsFromSelection);
3628     selectMenu.add(deleteGroups);
3629     selectMenu.add(annotationColumnSelection);
3630
3631     /*
3632      * View menu
3633      */
3634     viewMenu.add(newView);
3635     viewMenu.addSeparator();
3636     showMenu.add(showColumns);
3637     showMenu.add(showSeqs);
3638     showMenu.add(showAllHidden);
3639     viewMenu.add(showMenu);
3640     hideMenu.add(hideColumns);
3641     hideMenu.add(hideSequences);
3642     hideMenu.add(hideAllSelection);
3643     hideMenu.add(hideAllButSelection);
3644     viewMenu.add(hideMenu);
3645     viewMenu.addSeparator();
3646     viewMenu.add(followMouseOverFlag);
3647     viewMenu.addSeparator();
3648     viewMenu.add(sequenceFeatures);
3649     viewMenu.add(featureSettings);
3650     viewMenu.addSeparator();
3651     viewMenu.add(alProperties);
3652     viewMenu.addSeparator();
3653     viewMenu.add(overviewMenuItem);
3654
3655     /*
3656      * Annotations menu
3657      */
3658     annotationsMenu.add(annotationPanelMenuItem);
3659     annotationsMenu.addSeparator();
3660     annotationsMenu.add(showAlignmentAnnotations);
3661     annotationsMenu.add(showSequenceAnnotations);
3662     annotationsMenu.add(sortAnnBySequence);
3663     annotationsMenu.add(sortAnnByLabel);
3664     annotationsMenu.addSeparator();
3665     autoAnnMenu.add(showAutoFirst);
3666     autoAnnMenu.add(showAutoLast);
3667     autoAnnMenu.addSeparator();
3668     autoAnnMenu.add(applyAutoAnnotationSettings);
3669     autoAnnMenu.add(showConsensusHistogram);
3670     autoAnnMenu.add(showSequenceLogo);
3671     autoAnnMenu.add(normSequenceLogo);
3672     autoAnnMenu.addSeparator();
3673     autoAnnMenu.add(showGroupConservation);
3674     autoAnnMenu.add(showGroupConsensus);
3675     annotationsMenu.add(autoAnnMenu);
3676
3677     /*
3678      * Format menu
3679      */
3680     formatMenu.add(font);
3681     formatMenu.add(seqLimits);
3682     formatMenu.add(wrapMenuItem);
3683     formatMenu.add(scaleAbove);
3684     formatMenu.add(scaleLeft);
3685     formatMenu.add(scaleRight);
3686     formatMenu.add(viewBoxesMenuItem);
3687     formatMenu.add(viewTextMenuItem);
3688     formatMenu.add(colourTextMenuItem);
3689     formatMenu.add(displayNonconservedMenuItem);
3690     formatMenu.add(renderGapsMenuItem);
3691     formatMenu.add(centreColumnLabelFlag);
3692
3693     /*
3694      * Colour menu
3695      */
3696     colourMenu.add(applyToAllGroups);
3697     colourMenu.addSeparator();
3698     colourMenu.add(noColourmenuItem);
3699     colourMenu.add(clustalColour);
3700     colourMenu.add(BLOSUM62Colour);
3701     colourMenu.add(PIDColour);
3702     colourMenu.add(zappoColour);
3703     colourMenu.add(taylorColour);
3704     colourMenu.add(hydrophobicityColour);
3705     colourMenu.add(helixColour);
3706     colourMenu.add(strandColour);
3707     colourMenu.add(turnColour);
3708     colourMenu.add(buriedColour);
3709     colourMenu.add(nucleotideColour);
3710     colourMenu.add(purinePyrimidineColour);
3711     // colourMenu.add(RNAInteractionColour);
3712     colourMenu.add(tcoffeeColour);
3713     colourMenu.add(userDefinedColour);
3714     colourMenu.addSeparator();
3715     colourMenu.add(conservationMenuItem);
3716     colourMenu.add(modifyConservation);
3717     colourMenu.add(abovePIDThreshold);
3718     colourMenu.add(modifyPID);
3719     colourMenu.add(annotationColour);
3720     colourMenu.add(RNAHelixColour);
3721
3722     /*
3723      * Calculate menu
3724      */
3725     sortMenu.add(sortIDMenuItem);
3726     sortMenu.add(sortLengthMenuItem);
3727     sortMenu.add(sortByTreeMenu);
3728     sortMenu.add(sortGroupMenuItem);
3729     sortMenu.add(sortPairwiseMenuItem);
3730     calculateMenu.add(sortMenu);
3731     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3732     calculateTreeMenu.add(neighbourTreeMenuItem);
3733     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3734     calculateTreeMenu.add(njTreeBlosumMenuItem);
3735     calculateMenu.add(calculateTreeMenu);
3736     calculateMenu.addSeparator();
3737     calculateMenu.add(pairwiseAlignmentMenuItem);
3738     calculateMenu.add(PCAMenuItem);
3739     calculateMenu.add(autoCalculate);
3740     calculateMenu.add(sortByTree);
3741
3742     /*
3743      * Help menu
3744      */
3745     helpMenu.add(documentation);
3746     helpMenu.add(about);
3747
3748     /*
3749      * Status bar
3750      */
3751     statusBar.setBackground(Color.white);
3752     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3753     statusBar.setText(MessageManager.getString("label.status_bar"));
3754     this.add(statusBar, BorderLayout.SOUTH);
3755   }
3756
3757   @Override
3758   public void setStatus(String string)
3759   {
3760     statusBar.setText(string);
3761   };
3762
3763   MenuItem featureSettings = new MenuItem();
3764
3765   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3766
3767   MenuItem annotationColour = new MenuItem();
3768
3769   MenuItem annotationColumnSelection = new MenuItem();
3770
3771   MenuItem invertColSel = new MenuItem();
3772
3773   MenuItem showColumns = new MenuItem();
3774
3775   MenuItem showSeqs = new MenuItem();
3776
3777   MenuItem hideColumns = new MenuItem();
3778
3779   MenuItem hideSequences = new MenuItem();
3780
3781   MenuItem hideAllButSelection = new MenuItem();
3782
3783   MenuItem hideAllSelection = new MenuItem();
3784
3785   MenuItem showAllHidden = new MenuItem();
3786
3787   MenuItem newView = new MenuItem();
3788
3789   private CheckboxMenuItem showAlignmentAnnotations;
3790
3791   private CheckboxMenuItem showSequenceAnnotations;
3792
3793   private CheckboxMenuItem sortAnnBySequence;
3794
3795   private CheckboxMenuItem sortAnnByLabel;
3796
3797   private CheckboxMenuItem showAutoFirst;
3798
3799   private CheckboxMenuItem showAutoLast;
3800
3801   private SplitFrame splitFrame;
3802
3803   /**
3804    * Attach the alignFrame panels after embedding menus, if necessary. This used
3805    * to be called setEmbedded, but is now creates the dropdown menus in a
3806    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3807    *
3808    * @param reallyEmbedded
3809    *          true to attach the view to the applet area on the page rather than
3810    *          in a new window
3811    */
3812   public void createAlignFrameWindow(boolean reallyEmbedded)
3813   {
3814     if (reallyEmbedded)
3815     {
3816       embedAlignFrameInApplet(viewport.applet);
3817     }
3818     else
3819     {
3820       // //////
3821       // test and embed menu bar if necessary.
3822       //
3823       if (embedMenuIfNeeded(alignPanel))
3824       {
3825         /*
3826          * adjust for status bar height too. ? pointless as overridden by layout
3827          * manager
3828          */
3829         alignPanel.setSize(getSize().width,
3830                 getSize().height - statusBar.getHeight());
3831       }
3832       add(statusBar, BorderLayout.SOUTH);
3833       add(alignPanel, BorderLayout.CENTER);
3834       // and register with the applet so it can pass external API calls to us
3835       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3836               frameHeight);
3837     }
3838   }
3839
3840   /**
3841    * Add the components of this AlignFrame to the applet container.
3842    *
3843    * @param theApplet
3844    */
3845   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3846   {
3847     // ////
3848     // Explicitly build the embedded menu panel for the on-page applet
3849     //
3850     // view cannot be closed if its actually on the page
3851     fileMenu.remove(closeMenuItem);
3852     fileMenu.remove(3); // Remove Separator
3853     // construct embedded menu, using default font
3854     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3855     // and actually add the components to the applet area
3856     theApplet.setLayout(new BorderLayout());
3857     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3858     theApplet.add(statusBar, BorderLayout.SOUTH);
3859     // TODO should size be left to the layout manager?
3860     alignPanel.setSize(theApplet.getSize().width,
3861             theApplet.getSize().height - embeddedMenu.getHeight()
3862                     - statusBar.getHeight());
3863     theApplet.add(alignPanel, BorderLayout.CENTER);
3864     final AlignFrame me = this;
3865     theApplet.addFocusListener(new FocusListener()
3866     {
3867
3868       @Override
3869       public void focusLost(FocusEvent e)
3870       {
3871         if (theApplet.currentAlignFrame == me)
3872         {
3873           theApplet.currentAlignFrame = null;
3874         }
3875       }
3876
3877       @Override
3878       public void focusGained(FocusEvent e)
3879       {
3880         theApplet.currentAlignFrame = me;
3881       }
3882     });
3883     theApplet.validate();
3884   }
3885
3886   /**
3887    * create a new binding between structures in an existing jmol viewer instance
3888    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3889    * this does not open a new Jmol window, or modify the display of the
3890    * structures in the original jmol window. Note This method doesn't work
3891    * without an additional javascript library to exchange messages between the
3892    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3893    *
3894    * @param viewer
3895    *          JmolViewer instance
3896    * @param sequenceIds
3897    *          - sequence Ids to search for associations
3898    */
3899   public SequenceStructureBinding addStructureViewInstance(
3900           Object jmolviewer, String[] sequenceIds)
3901   {
3902     Viewer viewer = null;
3903     try
3904     {
3905       viewer = (Viewer) jmolviewer;
3906     } catch (ClassCastException ex)
3907     {
3908       System.err.println("Unsupported viewer object :"
3909               + jmolviewer.getClass());
3910     }
3911     if (viewer == null)
3912     {
3913       System.err.println("Can't use this object as a structure viewer:"
3914               + jmolviewer.getClass());
3915       return null;
3916     }
3917     SequenceI[] seqs = null;
3918     if (sequenceIds == null || sequenceIds.length == 0)
3919     {
3920       seqs = viewport.getAlignment().getSequencesArray();
3921     }
3922     else
3923     {
3924       Vector sqi = new Vector();
3925       AlignmentI al = viewport.getAlignment();
3926       for (int sid = 0; sid < sequenceIds.length; sid++)
3927       {
3928         SequenceI sq = al.findName(sequenceIds[sid]);
3929         if (sq != null)
3930         {
3931           sqi.addElement(sq);
3932         }
3933       }
3934       if (sqi.size() > 0)
3935       {
3936         seqs = new SequenceI[sqi.size()];
3937         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3938         {
3939           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3940         }
3941       }
3942       else
3943       {
3944         return null;
3945       }
3946     }
3947     AAStructureBindingModel jmv = null;
3948     // TODO: search for a jmv that involves viewer
3949     if (jmv == null)
3950     { // create a new viewer/jalview binding.
3951       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3952     }
3953     return jmv;
3954
3955   }
3956
3957   /**
3958    * bind a pdb file to a sequence in the current view
3959    *
3960    * @param sequenceId
3961    *          - sequenceId within the dataset.
3962    * @param pdbEntryString
3963    *          - the short name for the PDB file
3964    * @param pdbFile
3965    *          - pdb file - either a URL or a valid PDB file.
3966    * @return true if binding was as success TODO: consider making an exception
3967    *         structure for indicating when PDB parsing or sequenceId location
3968    *         fails.
3969    */
3970   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3971           String pdbFile)
3972   {
3973     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3974     boolean needtoadd = false;
3975     if (toaddpdb != null)
3976     {
3977       Vector pdbe = toaddpdb.getAllPDBEntries();
3978       PDBEntry pdbentry = null;
3979       if (pdbe != null && pdbe.size() > 0)
3980       {
3981         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3982         {
3983           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3984           if (!pdbentry.getId().equals(pdbEntryString)
3985                   && !pdbentry.getFile().equals(pdbFile))
3986           {
3987             pdbentry = null;
3988           }
3989           else
3990           {
3991             continue;
3992           }
3993         }
3994       }
3995       if (pdbentry == null)
3996       {
3997         pdbentry = new PDBEntry();
3998         pdbentry.setId(pdbEntryString);
3999         pdbentry.setFile(pdbFile);
4000         needtoadd = true; // add this new entry to sequence.
4001       }
4002       // resolve data source
4003       // TODO: this code should be a refactored to an io package
4004       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4005       if (protocol == null)
4006       {
4007         return false;
4008       }
4009       if (needtoadd)
4010       {
4011         // make a note of the access mode and add
4012         if (pdbentry.getProperty() == null)
4013         {
4014           pdbentry.setProperty(new Hashtable());
4015         }
4016         pdbentry.getProperty().put("protocol", protocol);
4017         toaddpdb.addPDBId(pdbentry);
4018         alignPanel.getStructureSelectionManager()
4019                 .registerPDBEntry(pdbentry);
4020       }
4021     }
4022     return true;
4023   }
4024
4025   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4026   {
4027     if (seqs != null)
4028     {
4029       Vector sequences = new Vector();
4030       for (int i = 0; i < seqs.length; i++)
4031       {
4032         if (seqs[i] != null)
4033         {
4034           sequences.addElement(new Object[] { seqs[i],
4035               (chains != null) ? chains[i] : null });
4036         }
4037       }
4038       seqs = new SequenceI[sequences.size()];
4039       chains = new String[sequences.size()];
4040       for (int i = 0, isize = sequences.size(); i < isize; i++)
4041       {
4042         Object[] oj = (Object[]) sequences.elementAt(i);
4043
4044         seqs[i] = (SequenceI) oj[0];
4045         chains[i] = (String) oj[1];
4046       }
4047     }
4048     return new Object[] { seqs, chains };
4049
4050   }
4051
4052   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4053           SequenceI[] seqs, String[] chains, String protocol)
4054   {
4055     // Scrub any null sequences from the array
4056     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4057     seqs = (SequenceI[]) sqch[0];
4058     chains = (String[]) sqch[1];
4059     if (seqs == null || seqs.length == 0)
4060     {
4061       System.err
4062               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4063     }
4064     if (protocol == null || protocol.trim().length() == 0
4065             || protocol.equals("null"))
4066     {
4067       protocol = (String) pdb.getProperty().get("protocol");
4068       if (protocol == null)
4069       {
4070         System.err.println("Couldn't work out protocol to open structure: "
4071                 + pdb.getId());
4072         return;
4073       }
4074     }
4075     if (applet.useXtrnalSviewer)
4076     {
4077       // register the association(s) and quit, don't create any windows.
4078       if (StructureSelectionManager.getStructureSelectionManager(applet)
4079               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4080       {
4081         System.err.println("Failed to map " + pdb.getFile() + " ("
4082                 + protocol + ") to any sequences");
4083       }
4084       return;
4085     }
4086     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4087     {
4088       // can only do alignments with Jmol
4089       // find the last jmol window assigned to this alignment
4090       jalview.appletgui.AppletJmol ajm = null, tajm;
4091       Vector jmols = applet
4092               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4093       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4094       {
4095         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4096         if (tajm.ap.alignFrame == this)
4097         {
4098           ajm = tajm;
4099           break;
4100         }
4101       }
4102       if (ajm != null)
4103       {
4104         System.err
4105                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4106         // try and add the pdb structure
4107         // ajm.addS
4108         ajm = null;
4109       }
4110     }
4111     // otherwise, create a new window
4112     if (applet.jmolAvailable)
4113     {
4114       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4115               protocol);
4116       applet.lastFrameX += 40;
4117       applet.lastFrameY += 40;
4118     }
4119     else
4120     {
4121       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4122     }
4123
4124   }
4125
4126   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4127           SequenceI[][] seqs, String[][] chains, String[] protocols)
4128   {
4129     // TODO Auto-generated method stub
4130     System.err.println("Aligned Structure View: Not yet implemented.");
4131   }
4132
4133   /**
4134    * modify the current selection, providing the user has not made a selection
4135    * already.
4136    *
4137    * @param sel
4138    *          - sequences from this alignment
4139    * @param csel
4140    *          - columns to be selected on the alignment
4141    */
4142   public void select(SequenceGroup sel, ColumnSelection csel)
4143   {
4144     alignPanel.seqPanel.selection(sel, csel, null);
4145   }
4146
4147   public void scrollTo(int row, int column)
4148   {
4149     alignPanel.seqPanel.scrollTo(row, column);
4150   }
4151
4152   public void scrollToRow(int row)
4153   {
4154     alignPanel.seqPanel.scrollToRow(row);
4155   }
4156
4157   public void scrollToColumn(int column)
4158   {
4159     alignPanel.seqPanel.scrollToColumn(column);
4160   }
4161
4162   /**
4163    * @return the alignments unique ID.
4164    */
4165   public String getSequenceSetId()
4166   {
4167     return viewport.getSequenceSetId();
4168   }
4169
4170   /**
4171    * Load the (T-Coffee) score file from the specified url
4172    *
4173    * @param source
4174    *          File/URL/T-COFFEE score file contents
4175    * @throws IOException
4176    * @return true if alignment was annotated with data from source
4177    */
4178   public boolean loadScoreFile(String source) throws IOException
4179   {
4180
4181     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4182             AppletFormatAdapter.checkProtocol(source));
4183     if (!file.isValid())
4184     {
4185       // TODO: raise dialog for gui
4186       System.err.println("Problems parsing T-Coffee scores: "
4187               + file.getWarningMessage());
4188       System.err.println("Origin was:\n" + source);
4189       return false;
4190     }
4191
4192     /*
4193      * check that the score matrix matches the alignment dimensions
4194      */
4195     AlignmentI aln;
4196     if ((aln = viewport.getAlignment()) != null
4197             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4198                     .getWidth()))
4199     {
4200       // TODO: raise a dialog box here rather than bomb out.
4201       System.err
4202               .println("The scores matrix does not match the alignment dimensions");
4203
4204     }
4205
4206     // TODO add parameter to indicate if matching should be done
4207     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4208     {
4209       alignPanel.fontChanged();
4210       tcoffeeColour.setEnabled(true);
4211       // switch to this color
4212       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4213       return true;
4214     }
4215     else
4216     {
4217       System.err.println("Problems resolving T-Coffee scores:");
4218       if (file.getWarningMessage() != null)
4219       {
4220         System.err.println(file.getWarningMessage());
4221       }
4222     }
4223     return false;
4224   }
4225
4226   public SplitFrame getSplitFrame()
4227   {
4228     return this.splitFrame;
4229   }
4230
4231   public void setSplitFrame(SplitFrame sf)
4232   {
4233     this.splitFrame = sf;
4234   }
4235
4236   // may not need this
4237   @Override
4238   public void setShowSeqFeatures(boolean b)
4239   {
4240     // showSeqFeatures.setSelected(b);
4241     viewport.setShowSequenceFeatures(b);
4242
4243   }
4244
4245   @Override
4246   public void setMenusForViewport()
4247   {
4248     // setMenusFromViewport(viewport);
4249
4250   }
4251
4252   @Override
4253   public void refreshFeatureUI(boolean enableIfNecessary)
4254   {
4255     if (enableIfNecessary)
4256     {
4257       sequenceFeatures.setState(true);
4258       alignPanel.av.setShowSequenceFeatures(true);
4259     }
4260   }
4261
4262   @Override
4263   public FeatureSettingsControllerI getFeatureSettingsUI()
4264   {
4265     return alignPanel.av.featureSettings;
4266   }
4267
4268 }