src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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.Font;
  79 import java.awt.FontMetrics;
  80 import java.awt.Frame;
  81 import java.awt.Graphics;
  82 import java.awt.Label;
  83 import java.awt.Menu;
  84 import java.awt.MenuBar;
  85 import java.awt.MenuItem;
  86 import java.awt.event.ActionEvent;
  87 import java.awt.event.ActionListener;
  88 import java.awt.event.FocusEvent;
  89 import java.awt.event.FocusListener;
  90 import java.awt.event.ItemEvent;
  91 import java.awt.event.ItemListener;
  92 import java.awt.event.KeyEvent;
  93 import java.awt.event.KeyListener;
  94 import java.awt.event.WindowAdapter;
  95 import java.awt.event.WindowEvent;
  96 import java.io.IOException;
  97 import java.net.URL;
  98 import java.net.URLEncoder;
  99 import java.util.Arrays;
 100 import java.util.Deque;
 101 import java.util.HashMap;
 102 import java.util.Hashtable;
 103 import java.util.List;
 104 import java.util.Map;
 105 import java.util.StringTokenizer;
 106 import java.util.Vector;
 107
 108 import org.jmol.viewer.Viewer;
 109
 110 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 111         ItemListener, KeyListener, AlignViewControllerGuiI
 112 {
 113   public AlignViewControllerI avc;
 114
 115   public AlignmentPanel alignPanel;
 116
 117   public AlignViewport viewport;
 118
 119   // width and height may be overridden by applet parameters
 120   int frameWidth = 700;
 121
 122   int frameHeight = 500;
 123
 124   String jalviewServletURL;
 125
 126   /*
 127    * Flag for showing autocalculated consensus above or below other consensus
 128    * rows
 129    */
 130   private boolean showAutoCalculatedAbove;
 131
 132   private SequenceAnnotationOrder annotationSortOrder;
 133
 134   /**
 135    * Constructor that creates the frame and adds it to the display.
 136    *
 137    * @param al
 138    * @param applet
 139    * @param title
 140    * @param embedded
 141    */
 142   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 143           boolean embedded)
 144   {
 145     this(al, applet, title, embedded, true);
 146   }
 147
 148   /**
 149    * Constructor that optionally allows the frame to be displayed or only
 150    * created.
 151    *
 152    * @param al
 153    * @param applet
 154    * @param title
 155    * @param embedded
 156    * @param addToDisplay
 157    */
 158   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 159           boolean embedded, boolean addToDisplay)
 160   {
 161     this(al, null, null, applet, title, embedded, addToDisplay);
 162   }
 163
 164   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 165           ColumnSelection columnSelection, JalviewLite applet,
 166           String title, boolean embedded)
 167   {
 168     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 169   }
 170
 171   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 172           ColumnSelection columnSelection, JalviewLite applet,
 173           String title, boolean embedded, boolean addToDisplay)
 174   {
 175     if (applet != null)
 176     {
 177       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 178     }
 179
 180     try
 181     {
 182       jbInit();
 183     } catch (Exception ex)
 184     {
 185       ex.printStackTrace();
 186     }
 187     // need to get window geometry before we calculate alignment layout
 188     if (applet != null)
 189     {
 190       String param;
 191       try
 192       {
 193         param = applet.getParameter("windowWidth");
 194         if (param != null)
 195         {
 196           int width = Integer.parseInt(param);
 197           frameWidth = width;
 198         }
 199         param = applet.getParameter("windowHeight");
 200         if (param != null)
 201         {
 202           int height = Integer.parseInt(param);
 203           frameHeight = height;
 204         }
 205       } catch (Exception ex)
 206       {
 207       }
 208     }
 209     viewport = new AlignViewport(al, applet);
 210
 211     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 212     {
 213       viewport.hideSequence(hiddenSeqs);
 214     }
 215     if (columnSelection != null)
 216     {
 217       viewport.setColumnSelection(columnSelection);
 218     }
 219
 220     alignPanel = new AlignmentPanel(this, viewport);
 221     avc = new jalview.controller.AlignViewController(this, viewport,
 222             alignPanel);
 223     viewport.updateConservation(alignPanel);
 224     viewport.updateConsensus(alignPanel);
 225
 226     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 227     followMouseOverFlag.setState(viewport.isFollowHighlight());
 228     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 229     showGroupConservation.setState(viewport.isShowGroupConservation());
 230     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 231     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 232     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 233     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 234     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 235     showAlignmentAnnotations.setState(viewport.isShowAnnotation());
 236     showSequenceAnnotations.setState(viewport.isShowAnnotation());
 237
 238     seqLimits.setState(viewport.getShowJVSuffix());
 239
 240     if (applet != null)
 241     {
 242       String param = applet.getParameter("sortBy");
 243       if (param != null)
 244       {
 245         if (param.equalsIgnoreCase("Id"))
 246         {
 247           sortIDMenuItem_actionPerformed();
 248         }
 249         else if (param.equalsIgnoreCase("Pairwise Identity"))
 250         {
 251           sortPairwiseMenuItem_actionPerformed();
 252         }
 253         else if (param.equalsIgnoreCase("Length"))
 254         {
 255           sortLengthMenuItem_actionPerformed();
 256         }
 257       }
 258
 259       param = applet.getParameter("wrap");
 260       if (param != null)
 261       {
 262         if (param.equalsIgnoreCase("true"))
 263         {
 264           wrapMenuItem.setState(true);
 265           wrapMenuItem_actionPerformed();
 266         }
 267       }
 268       param = applet.getParameter("centrecolumnlabels");
 269       if (param != null)
 270       {
 271         centreColumnLabelFlag.setState(true);
 272         centreColumnLabelFlag_stateChanged();
 273       }
 274
 275     }
 276     if (viewport.getAlignment().isNucleotide())
 277     {
 278       viewport.updateStrucConsensus(alignPanel);
 279       if (viewport.getAlignment().hasRNAStructure())
 280       {
 281         RNAHelixColour.setEnabled(true);
 282       }
 283       else
 284       {
 285         RNAHelixColour.setEnabled(false);
 286       }
 287     }
 288     else
 289     {
 290       RNAHelixColour.setEnabled(false);
 291       purinePyrimidineColour.setEnabled(false);
 292     }
 293     // Some JVMS send keyevents to Top frame or lowest panel,
 294     // Havent worked out why yet. So add to both this frame and seqCanvas for
 295     // now
 296     this.addKeyListener(this);
 297     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 298     alignPanel.idPanel.idCanvas.addKeyListener(this);
 299     alignPanel.scalePanel.addKeyListener(this);
 300     alignPanel.annotationPanel.addKeyListener(this);
 301     alignPanel.annotationPanelHolder.addKeyListener(this);
 302     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 303     alignPanel.alabels.addKeyListener(this);
 304
 305     if (addToDisplay)
 306     {
 307       addToDisplay(embedded);
 308     }
 309   }
 310
 311   /**
 312    * @param embedded
 313    */
 314   public void addToDisplay(boolean embedded)
 315   {
 316     createAlignFrameWindow(embedded);
 317     validate();
 318     alignPanel.adjustAnnotationHeight();
 319     alignPanel.paintAlignment(true);
 320   }
 321
 322   public AlignViewport getAlignViewport()
 323   {
 324     return viewport;
 325   }
 326
 327   public SeqCanvas getSeqcanvas()
 328   {
 329     return alignPanel.seqPanel.seqCanvas;
 330   }
 331
 332   /**
 333    * Load a features file onto the alignment
 334    *
 335    * @param file
 336    *          file URL, content, or other resolvable path
 337    * @param type
 338    *          is protocol for accessing data referred to by file
 339    */
 340
 341   public boolean parseFeaturesFile(String file, String type)
 342   {
 343     return parseFeaturesFile(file, type, true);
 344   }
 345
 346   /**
 347    * Load a features file onto the alignment
 348    *
 349    * @param file
 350    *          file URL, content, or other resolvable path
 351    * @param type
 352    *          is protocol for accessing data referred to by file
 353    * @param autoenabledisplay
 354    *          when true, display features flag will be automatically enabled if
 355    *          features are loaded
 356    * @return true if data parsed as a features file
 357    */
 358   public boolean parseFeaturesFile(String file, String type,
 359           boolean autoenabledisplay)
 360   {
 361     // TODO: test if importing a features file onto an alignment which already
 362     // has features with links overwrites the original links.
 363
 364     Hashtable featureLinks = new Hashtable();
 365     boolean featuresFile = false;
 366     try
 367     {
 368       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
 369               .getAlignment(), alignPanel.seqPanel.seqCanvas
 370               .getFeatureRenderer().getFeatureColours(), featureLinks,
 371               true, viewport.applet.getDefaultParameter("relaxedidmatch",
 372                       false));
 373     } catch (Exception ex)
 374     {
 375       ex.printStackTrace();
 376     }
 377
 378     if (featuresFile)
 379     {
 380       if (featureLinks.size() > 0)
 381       {
 382         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 383       }
 384       if (autoenabledisplay)
 385       {
 386         viewport.setShowSequenceFeatures(true);
 387         sequenceFeatures.setState(true);
 388       }
 389       if (alignPanel.seqPanel.seqCanvas.fr != null)
 390       {
 391         // update the min/max ranges where necessary
 392         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 393       }
 394       if (viewport.featureSettings != null)
 395       {
 396         viewport.featureSettings.refreshTable();
 397       }
 398       alignPanel.paintAlignment(true);
 399       statusBar.setText(MessageManager
 400               .getString("label.successfully_added_features_alignment"));
 401     }
 402     return featuresFile;
 403   }
 404
 405   @Override
 406   public void keyPressed(KeyEvent evt)
 407   {
 408     if (viewport.cursorMode
 409             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 410                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 411                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 412             && Character.isDigit(evt.getKeyChar()))
 413     {
 414       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 415     }
 416
 417     switch (evt.getKeyCode())
 418     {
 419     case 27: // escape key
 420       deselectAllSequenceMenuItem_actionPerformed();
 421
 422       alignPanel.alabels.cancelDrag();
 423       break;
 424     case KeyEvent.VK_X:
 425       if (evt.isControlDown() || evt.isMetaDown())
 426       {
 427         cut_actionPerformed();
 428       }
 429       break;
 430     case KeyEvent.VK_C:
 431       if (viewport.cursorMode && !evt.isControlDown())
 432       {
 433         alignPanel.seqPanel.setCursorColumn();
 434       }
 435       if (evt.isControlDown() || evt.isMetaDown())
 436       {
 437         copy_actionPerformed();
 438       }
 439       break;
 440     case KeyEvent.VK_V:
 441       if (evt.isControlDown())
 442       {
 443         paste(evt.isShiftDown());
 444       }
 445       break;
 446     case KeyEvent.VK_A:
 447       if (evt.isControlDown() || evt.isMetaDown())
 448       {
 449         selectAllSequenceMenuItem_actionPerformed();
 450       }
 451       break;
 452     case KeyEvent.VK_DOWN:
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.moveCursor(0, 1);
 456       }
 457       else
 458       {
 459         moveSelectedSequences(false);
 460       }
 461       break;
 462
 463     case KeyEvent.VK_UP:
 464       if (viewport.cursorMode)
 465       {
 466         alignPanel.seqPanel.moveCursor(0, -1);
 467       }
 468       else
 469       {
 470         moveSelectedSequences(true);
 471       }
 472       break;
 473
 474     case KeyEvent.VK_LEFT:
 475       if (evt.isAltDown() || !viewport.cursorMode)
 476       {
 477         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 478       }
 479       else
 480       {
 481         alignPanel.seqPanel.moveCursor(-1, 0);
 482       }
 483       break;
 484
 485     case KeyEvent.VK_RIGHT:
 486       if (evt.isAltDown() || !viewport.cursorMode)
 487       {
 488         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 489       }
 490       else
 491       {
 492         alignPanel.seqPanel.moveCursor(1, 0);
 493       }
 494       break;
 495
 496     case KeyEvent.VK_SPACE:
 497       if (viewport.cursorMode)
 498       {
 499         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 500                 || evt.isShiftDown() || evt.isAltDown());
 501       }
 502       break;
 503
 504     case KeyEvent.VK_DELETE:
 505     case KeyEvent.VK_BACK_SPACE:
 506       if (viewport.cursorMode)
 507       {
 508         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 509                 || evt.isShiftDown() || evt.isAltDown());
 510       }
 511       else
 512       {
 513         cut_actionPerformed();
 514         alignPanel.seqPanel.seqCanvas.repaint();
 515       }
 516       break;
 517
 518     case KeyEvent.VK_S:
 519       if (viewport.cursorMode)
 520       {
 521         alignPanel.seqPanel.setCursorRow();
 522       }
 523       break;
 524     case KeyEvent.VK_P:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorPosition();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_ENTER:
 532     case KeyEvent.VK_COMMA:
 533       if (viewport.cursorMode)
 534       {
 535         alignPanel.seqPanel.setCursorRowAndColumn();
 536       }
 537       break;
 538
 539     case KeyEvent.VK_Q:
 540       if (viewport.cursorMode)
 541       {
 542         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 543       }
 544       break;
 545     case KeyEvent.VK_M:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_F2:
 553       viewport.cursorMode = !viewport.cursorMode;
 554       statusBar.setText(MessageManager.formatMessage(
 555               "label.keyboard_editing_mode",
 556               new String[] { (viewport.cursorMode ? "on" : "off") }));
 557       if (viewport.cursorMode)
 558       {
 559         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 560         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 561       }
 562       break;
 563
 564     case KeyEvent.VK_F:
 565       if (evt.isControlDown())
 566       {
 567         findMenuItem_actionPerformed();
 568       }
 569       break;
 570
 571     case KeyEvent.VK_H:
 572     {
 573       boolean toggleSeqs = !evt.isControlDown();
 574       boolean toggleCols = !evt.isShiftDown();
 575       toggleHiddenRegions(toggleSeqs, toggleCols);
 576       break;
 577     }
 578
 579     case KeyEvent.VK_PAGE_UP:
 580       if (viewport.getWrapAlignment())
 581       {
 582         alignPanel.scrollUp(true);
 583       }
 584       else
 585       {
 586         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 587                 - viewport.endSeq + viewport.startSeq);
 588       }
 589       break;
 590
 591     case KeyEvent.VK_PAGE_DOWN:
 592       if (viewport.getWrapAlignment())
 593       {
 594         alignPanel.scrollUp(false);
 595       }
 596       else
 597       {
 598         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 599                 + viewport.endSeq - viewport.startSeq);
 600       }
 601       break;
 602
 603     case KeyEvent.VK_Z:
 604       if (evt.isControlDown())
 605       {
 606         undoMenuItem_actionPerformed();
 607       }
 608       break;
 609
 610     case KeyEvent.VK_Y:
 611       if (evt.isControlDown())
 612       {
 613         redoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_L:
 618       if (evt.isControlDown())
 619       {
 620         trimAlignment(true);
 621       }
 622       break;
 623
 624     case KeyEvent.VK_R:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(false);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_E:
 632       if (evt.isControlDown())
 633       {
 634         if (evt.isShiftDown())
 635         {
 636           this.removeAllGapsMenuItem_actionPerformed();
 637         }
 638         else
 639         {
 640           removeGappedColumnMenuItem_actionPerformed();
 641         }
 642       }
 643       break;
 644     case KeyEvent.VK_I:
 645       if (evt.isControlDown())
 646       {
 647         if (evt.isAltDown())
 648         {
 649           invertColSel_actionPerformed();
 650         }
 651         else
 652         {
 653           invertSequenceMenuItem_actionPerformed();
 654         }
 655       }
 656       break;
 657
 658     case KeyEvent.VK_G:
 659       if (evt.isControlDown())
 660       {
 661         if (evt.isShiftDown())
 662         {
 663           this.unGroup_actionPerformed();
 664         }
 665         else
 666         {
 667           this.createGroup_actionPerformed();
 668         }
 669       }
 670       break;
 671
 672     case KeyEvent.VK_U:
 673       if (evt.isControlDown())
 674       {
 675         this.deleteGroups_actionPerformed();
 676       }
 677       break;
 678
 679     case KeyEvent.VK_T:
 680       if (evt.isControlDown())
 681       {
 682         newView(null);
 683       }
 684       break;
 685
 686     }
 687     alignPanel.paintAlignment(true);
 688   }
 689
 690   /**
 691    * called by key handler and the hide all/show all menu items
 692    *
 693    * @param toggleSeqs
 694    * @param toggleCols
 695    */
 696   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 697   {
 698     boolean hide = false;
 699     SequenceGroup sg = viewport.getSelectionGroup();
 700     if (!toggleSeqs && !toggleCols)
 701     {
 702       // Hide everything by the current selection - this is a hack - we do the
 703       // invert and then hide
 704       // first check that there will be visible columns after the invert.
 705       if ((viewport.getColumnSelection() != null
 706               && viewport.getColumnSelection().getSelected() != null && viewport
 707               .getColumnSelection().getSelected().size() > 0)
 708               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 709                       .getEndRes()))
 710       {
 711         // now invert the sequence set, if required - empty selection implies
 712         // that no hiding is required.
 713         if (sg != null)
 714         {
 715           invertSequenceMenuItem_actionPerformed();
 716           sg = viewport.getSelectionGroup();
 717           toggleSeqs = true;
 718
 719         }
 720         viewport.expandColSelection(sg, true);
 721         // finally invert the column selection and get the new sequence
 722         // selection and indicate it should be hidden.
 723         invertColSel_actionPerformed();
 724         toggleCols = true;
 725       }
 726     }
 727
 728     if (toggleSeqs)
 729     {
 730       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 731       {
 732         hide = true;
 733         viewport.hideAllSelectedSeqs();
 734       }
 735       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 736               .size() > 0))
 737       {
 738         viewport.showAllHiddenSeqs();
 739       }
 740     }
 741
 742     if (toggleCols)
 743     {
 744       if (viewport.getColumnSelection().getSelected().size() > 0)
 745       {
 746         viewport.hideSelectedColumns();
 747         if (!toggleSeqs)
 748         {
 749           viewport.setSelectionGroup(sg);
 750         }
 751       }
 752       else if (!hide)
 753       {
 754         viewport.showAllHiddenColumns();
 755       }
 756     }
 757   }
 758
 759   @Override
 760   public void keyReleased(KeyEvent evt)
 761   {
 762   }
 763
 764   @Override
 765   public void keyTyped(KeyEvent evt)
 766   {
 767   }
 768
 769   @Override
 770   public void itemStateChanged(ItemEvent evt)
 771   {
 772     final Object source = evt.getSource();
 773     if (source == displayNonconservedMenuItem)
 774     {
 775       displayNonconservedMenuItem_actionPerformed();
 776     }
 777     else if (source == colourTextMenuItem)
 778     {
 779       colourTextMenuItem_actionPerformed();
 780     }
 781     else if (source == wrapMenuItem)
 782     {
 783       wrapMenuItem_actionPerformed();
 784     }
 785     else if (source == scaleAbove)
 786     {
 787       viewport.setScaleAboveWrapped(scaleAbove.getState());
 788     }
 789     else if (source == scaleLeft)
 790     {
 791       viewport.setScaleLeftWrapped(scaleLeft.getState());
 792     }
 793     else if (source == scaleRight)
 794     {
 795       viewport.setScaleRightWrapped(scaleRight.getState());
 796     }
 797     else if (source == seqLimits)
 798     {
 799       seqLimits_itemStateChanged();
 800     }
 801     else if (source == viewBoxesMenuItem)
 802     {
 803       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 804     }
 805     else if (source == viewTextMenuItem)
 806     {
 807       viewport.setShowText(viewTextMenuItem.getState());
 808     }
 809     else if (source == renderGapsMenuItem)
 810     {
 811       viewport.setRenderGaps(renderGapsMenuItem.getState());
 812     }
 813     else if (source == annotationPanelMenuItem)
 814     {
 815       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 816       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 817     }
 818     else if (source == sequenceFeatures)
 819     {
 820       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 821       alignPanel.seqPanel.seqCanvas.repaint();
 822     }
 823     else if (source == showAlignmentAnnotations)
 824     {
 825       setAnnotationsVisibility();
 826     }
 827     else if (source == showSequenceAnnotations)
 828     {
 829       setAnnotationsVisibility();
 830     }
 831     else if (source == sortAnnBySequence)
 832     {
 833       boolean newState = sortAnnBySequence.getState();
 834       sortAnnByLabel.setState(false);
 835       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 836               : SequenceAnnotationOrder.NONE);
 837       setViewportAnnotationOrder();
 838     }
 839     else if (source == sortAnnByLabel)
 840     {
 841       boolean newState = sortAnnByLabel.getState();
 842       sortAnnBySequence.setState(false);
 843       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 844               : SequenceAnnotationOrder.NONE);
 845       setViewportAnnotationOrder();
 846     }
 847     else if (source == showAutoFirst)
 848     {
 849       showAutoLast.setState(!showAutoFirst.getState());
 850       setShowAutoCalculatedAbove(showAutoFirst.getState());
 851       setViewportAnnotationOrder();
 852     }
 853     else if (source == showAutoLast)
 854     {
 855       showAutoFirst.setState(!showAutoLast.getState());
 856       setShowAutoCalculatedAbove(showAutoFirst.getState());
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == conservationMenuItem)
 860     {
 861       conservationMenuItem_actionPerformed();
 862     }
 863     else if (source == abovePIDThreshold)
 864     {
 865       abovePIDThreshold_actionPerformed();
 866     }
 867     else if (source == applyToAllGroups)
 868     {
 869       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 870     }
 871     else if (source == autoCalculate)
 872     {
 873       viewport.autoCalculateConsensus = autoCalculate.getState();
 874     }
 875     else if (source == sortByTree)
 876     {
 877       viewport.sortByTree = sortByTree.getState();
 878     }
 879     else if (source == this.centreColumnLabelFlag)
 880     {
 881       centreColumnLabelFlag_stateChanged();
 882     }
 883     else if (source == this.followMouseOverFlag)
 884     {
 885       mouseOverFlag_stateChanged();
 886     }
 887     else if (source == showGroupConsensus)
 888     {
 889       showGroupConsensus_actionPerformed();
 890     }
 891     else if (source == showGroupConservation)
 892     {
 893       showGroupConservation_actionPerformed();
 894     }
 895     else if (source == showSequenceLogo)
 896     {
 897       showSequenceLogo_actionPerformed();
 898     }
 899     else if (source == normSequenceLogo)
 900     {
 901       normSequenceLogo_actionPerformed();
 902     }
 903     else if (source == showConsensusHistogram)
 904     {
 905       showConsensusHistogram_actionPerformed();
 906     }
 907     else if (source == applyAutoAnnotationSettings)
 908     {
 909       applyAutoAnnotationSettings_actionPerformed();
 910     }
 911     alignPanel.paintAlignment(true);
 912   }
 913
 914   /**
 915    * Set the visibility state of sequence-related and/or alignment-related
 916    * annotations depending on checkbox selections. Repaint after calling.
 917    *
 918    * @param visible
 919    */
 920   private void setAnnotationsVisibility()
 921   {
 922     boolean showForAlignment = showAlignmentAnnotations.getState();
 923     boolean showForSequences = showSequenceAnnotations.getState();
 924     for (AlignmentAnnotation aa : alignPanel.getAlignment()
 925             .getAlignmentAnnotation())
 926     {
 927       boolean visible = (aa.sequenceRef == null ? showForAlignment
 928               : showForSequences);
 929       aa.visible = visible;
 930     }
 931     alignPanel.validateAnnotationDimensions(true);
 932     validate();
 933     repaint();
 934   }
 935
 936   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 937   {
 938     this.annotationSortOrder = order;
 939   }
 940
 941   /**
 942    * Set flags on the viewport that control annotation ordering
 943    */
 944   private void setViewportAnnotationOrder()
 945   {
 946     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 947     this.alignPanel.av
 948             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 949   }
 950
 951   private void setShowAutoCalculatedAbove(boolean showAbove)
 952   {
 953     this.showAutoCalculatedAbove = showAbove;
 954   }
 955
 956   private void mouseOverFlag_stateChanged()
 957   {
 958     viewport.setFollowHighlight(followMouseOverFlag.getState());
 959     // TODO: could kick the scrollTo mechanism to reset view for current
 960     // searchresults.
 961   }
 962
 963   private void centreColumnLabelFlag_stateChanged()
 964   {
 965     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 966     this.alignPanel.annotationPanel.repaint();
 967   }
 968
 969   @Override
 970   public void actionPerformed(ActionEvent evt)
 971   {
 972     viewport.applet.currentAlignFrame = this;
 973
 974     Object source = evt.getSource();
 975
 976     if (source == inputText)
 977     {
 978       inputText_actionPerformed();
 979     }
 980     else if (source == loadTree)
 981     {
 982       loadTree_actionPerformed();
 983     }
 984     else if (source == loadApplication)
 985     {
 986       launchFullApplication();
 987     }
 988     else if (source == loadAnnotations)
 989     {
 990       loadAnnotations();
 991     }
 992     else if (source == outputAnnotations)
 993     {
 994       outputAnnotations(true);
 995     }
 996     else if (source == outputFeatures)
 997     {
 998       outputFeatures(true, "Jalview");
 999     }
1000     else if (source == closeMenuItem)
1001     {
1002       closeMenuItem_actionPerformed();
1003     }
1004     else if (source == copy)
1005     {
1006       copy_actionPerformed();
1007     }
1008     else if (source == undoMenuItem)
1009     {
1010       undoMenuItem_actionPerformed();
1011     }
1012     else if (source == redoMenuItem)
1013     {
1014       redoMenuItem_actionPerformed();
1015     }
1016     else if (source == inputText)
1017     {
1018       inputText_actionPerformed();
1019     }
1020     else if (source == closeMenuItem)
1021     {
1022       closeMenuItem_actionPerformed();
1023     }
1024     else if (source == undoMenuItem)
1025     {
1026       undoMenuItem_actionPerformed();
1027     }
1028     else if (source == redoMenuItem)
1029     {
1030       redoMenuItem_actionPerformed();
1031     }
1032     else if (source == copy)
1033     {
1034       copy_actionPerformed();
1035     }
1036     else if (source == pasteNew)
1037     {
1038       pasteNew_actionPerformed();
1039     }
1040     else if (source == pasteThis)
1041     {
1042       pasteThis_actionPerformed();
1043     }
1044     else if (source == cut)
1045     {
1046       cut_actionPerformed();
1047     }
1048     else if (source == delete)
1049     {
1050       delete_actionPerformed();
1051     }
1052     else if (source == grpsFromSelection)
1053     {
1054       makeGrpsFromSelection_actionPerformed();
1055     }
1056     else if (source == deleteGroups)
1057     {
1058       deleteGroups_actionPerformed();
1059     }
1060     else if (source == selectAllSequenceMenuItem)
1061     {
1062       selectAllSequenceMenuItem_actionPerformed();
1063     }
1064     else if (source == deselectAllSequenceMenuItem)
1065     {
1066       deselectAllSequenceMenuItem_actionPerformed();
1067     }
1068     else if (source == invertSequenceMenuItem)
1069     {
1070       invertSequenceMenuItem_actionPerformed();
1071     }
1072     else if (source == invertColSel)
1073     {
1074       viewport.invertColumnSelection();
1075       alignPanel.paintAlignment(true);
1076     }
1077     else if (source == remove2LeftMenuItem)
1078     {
1079       trimAlignment(true);
1080     }
1081     else if (source == remove2RightMenuItem)
1082     {
1083       trimAlignment(false);
1084     }
1085     else if (source == removeGappedColumnMenuItem)
1086     {
1087       removeGappedColumnMenuItem_actionPerformed();
1088     }
1089     else if (source == removeAllGapsMenuItem)
1090     {
1091       removeAllGapsMenuItem_actionPerformed();
1092     }
1093     else if (source == findMenuItem)
1094     {
1095       findMenuItem_actionPerformed();
1096     }
1097     else if (source == font)
1098     {
1099       new FontChooser(alignPanel);
1100     }
1101     else if (source == newView)
1102     {
1103       newView(null);
1104     }
1105     else if (source == showColumns)
1106     {
1107       viewport.showAllHiddenColumns();
1108       alignPanel.paintAlignment(true);
1109     }
1110     else if (source == showSeqs)
1111     {
1112       viewport.showAllHiddenSeqs();
1113       alignPanel.paintAlignment(true);
1114     }
1115     else if (source == hideColumns)
1116     {
1117       viewport.hideSelectedColumns();
1118       alignPanel.paintAlignment(true);
1119     }
1120     else if (source == hideSequences
1121             && viewport.getSelectionGroup() != null)
1122     {
1123       viewport.hideAllSelectedSeqs();
1124       alignPanel.paintAlignment(true);
1125     }
1126     else if (source == hideAllButSelection)
1127     {
1128       toggleHiddenRegions(false, false);
1129       alignPanel.paintAlignment(true);
1130     }
1131     else if (source == hideAllSelection)
1132     {
1133       SequenceGroup sg = viewport.getSelectionGroup();
1134       viewport.expandColSelection(sg, false);
1135       viewport.hideAllSelectedSeqs();
1136       viewport.hideSelectedColumns();
1137       alignPanel.paintAlignment(true);
1138     }
1139     else if (source == showAllHidden)
1140     {
1141       viewport.showAllHiddenColumns();
1142       viewport.showAllHiddenSeqs();
1143       alignPanel.paintAlignment(true);
1144     }
1145     else if (source == showGroupConsensus)
1146     {
1147       showGroupConsensus_actionPerformed();
1148     }
1149     else if (source == showGroupConservation)
1150     {
1151       showGroupConservation_actionPerformed();
1152     }
1153     else if (source == showSequenceLogo)
1154     {
1155       showSequenceLogo_actionPerformed();
1156     }
1157     else if (source == normSequenceLogo)
1158     {
1159       normSequenceLogo_actionPerformed();
1160     }
1161     else if (source == showConsensusHistogram)
1162     {
1163       showConsensusHistogram_actionPerformed();
1164     }
1165     else if (source == applyAutoAnnotationSettings)
1166     {
1167       applyAutoAnnotationSettings_actionPerformed();
1168     }
1169     else if (source == featureSettings)
1170     {
1171       new FeatureSettings(alignPanel);
1172     }
1173     else if (source == alProperties)
1174     {
1175       StringBuffer contents = new jalview.io.AlignmentProperties(
1176               viewport.getAlignment()).formatAsString();
1177       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1178       cap.setText(contents.toString());
1179       Frame frame = new Frame();
1180       frame.add(cap);
1181       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1182               "label.alignment_properties", new String[] { getTitle() }),
1183               400, 250);
1184     }
1185     else if (source == overviewMenuItem)
1186     {
1187       overviewMenuItem_actionPerformed();
1188     }
1189     else if (source == noColourmenuItem)
1190     {
1191       changeColour(null);
1192     }
1193     else if (source == clustalColour)
1194     {
1195       abovePIDThreshold.setState(false);
1196       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1197     }
1198     else if (source == zappoColour)
1199     {
1200       changeColour(new ZappoColourScheme());
1201     }
1202     else if (source == taylorColour)
1203     {
1204       changeColour(new TaylorColourScheme());
1205     }
1206     else if (source == hydrophobicityColour)
1207     {
1208       changeColour(new HydrophobicColourScheme());
1209     }
1210     else if (source == helixColour)
1211     {
1212       changeColour(new HelixColourScheme());
1213     }
1214     else if (source == strandColour)
1215     {
1216       changeColour(new StrandColourScheme());
1217     }
1218     else if (source == turnColour)
1219     {
1220       changeColour(new TurnColourScheme());
1221     }
1222     else if (source == buriedColour)
1223     {
1224       changeColour(new BuriedColourScheme());
1225     }
1226     else if (source == nucleotideColour)
1227     {
1228       changeColour(new NucleotideColourScheme());
1229     }
1230     else if (source == purinePyrimidineColour)
1231     {
1232       changeColour(new PurinePyrimidineColourScheme());
1233     }
1234     // else if (source == RNAInteractionColour)
1235     // {
1236     // changeColour(new RNAInteractionColourScheme());
1237     // }
1238     else if (source == RNAHelixColour)
1239     {
1240       new RNAHelicesColourChooser(viewport, alignPanel);
1241     }
1242     else if (source == modifyPID)
1243     {
1244       modifyPID_actionPerformed();
1245     }
1246     else if (source == modifyConservation)
1247     {
1248       modifyConservation_actionPerformed();
1249     }
1250     else if (source == userDefinedColour)
1251     {
1252       new UserDefinedColours(alignPanel, null);
1253     }
1254     else if (source == PIDColour)
1255     {
1256       changeColour(new PIDColourScheme());
1257     }
1258     else if (source == BLOSUM62Colour)
1259     {
1260       changeColour(new Blosum62ColourScheme());
1261     }
1262     else if (source == tcoffeeColour)
1263     {
1264       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1265     }
1266     else if (source == annotationColour)
1267     {
1268       new AnnotationColourChooser(viewport, alignPanel);
1269     }
1270     else if (source == annotationColumnSelection)
1271     {
1272       new AnnotationColumnChooser(viewport, alignPanel);
1273     }
1274     else if (source == sortPairwiseMenuItem)
1275     {
1276       sortPairwiseMenuItem_actionPerformed();
1277     }
1278     else if (source == sortIDMenuItem)
1279     {
1280       sortIDMenuItem_actionPerformed();
1281     }
1282     else if (source == sortLengthMenuItem)
1283     {
1284       sortLengthMenuItem_actionPerformed();
1285     }
1286     else if (source == sortGroupMenuItem)
1287     {
1288       sortGroupMenuItem_actionPerformed();
1289     }
1290     else if (source == removeRedundancyMenuItem)
1291     {
1292       removeRedundancyMenuItem_actionPerformed();
1293     }
1294     else if (source == pairwiseAlignmentMenuItem)
1295     {
1296       pairwiseAlignmentMenuItem_actionPerformed();
1297     }
1298     else if (source == PCAMenuItem)
1299     {
1300       PCAMenuItem_actionPerformed();
1301     }
1302     else if (source == averageDistanceTreeMenuItem)
1303     {
1304       averageDistanceTreeMenuItem_actionPerformed();
1305     }
1306     else if (source == neighbourTreeMenuItem)
1307     {
1308       neighbourTreeMenuItem_actionPerformed();
1309     }
1310     else if (source == njTreeBlosumMenuItem)
1311     {
1312       njTreeBlosumMenuItem_actionPerformed();
1313     }
1314     else if (source == avDistanceTreeBlosumMenuItem)
1315     {
1316       avTreeBlosumMenuItem_actionPerformed();
1317     }
1318     else if (source == documentation)
1319     {
1320       documentation_actionPerformed();
1321     }
1322     else if (source == about)
1323     {
1324       about_actionPerformed();
1325     }
1326
1327   }
1328
1329   public void inputText_actionPerformed()
1330   {
1331     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1332     Frame frame = new Frame();
1333     frame.add(cap);
1334     jalview.bin.JalviewLite.addFrame(frame,
1335             MessageManager.getString("label.input_cut_paste"), 500, 500);
1336   }
1337
1338   protected void outputText_actionPerformed(ActionEvent e)
1339   {
1340     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1341     Frame frame = new Frame();
1342     frame.add(cap);
1343     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1344             "label.alignment_output_command",
1345             new Object[] { e.getActionCommand() }), 600, 500);
1346
1347     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1348     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1349             e.getActionCommand(), viewport.getAlignment(),
1350             viewport.getShowJVSuffix()));
1351   }
1352
1353   public void loadAnnotations()
1354   {
1355     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1356     cap.setText(MessageManager
1357             .getString("label.paste_features_annotations_Tcoffee_here"));
1358     cap.setAnnotationImport();
1359     Frame frame = new Frame();
1360     frame.add(cap);
1361     jalview.bin.JalviewLite.addFrame(frame,
1362             MessageManager.getString("action.paste_annotations"), 400, 300);
1363
1364   }
1365
1366   public String outputAnnotations(boolean displayTextbox)
1367   {
1368     String annotation = new AnnotationFile()
1369             .printAnnotationsForView(viewport);
1370
1371     if (displayTextbox)
1372     {
1373       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1374       Frame frame = new Frame();
1375       frame.add(cap);
1376       jalview.bin.JalviewLite.addFrame(frame,
1377               MessageManager.getString("label.annotations"), 600, 500);
1378       cap.setText(annotation);
1379     }
1380
1381     return annotation;
1382   }
1383
1384   private Map<String, Object> getDisplayedFeatureCols()
1385   {
1386     if (alignPanel.getFeatureRenderer() != null
1387             && viewport.getFeaturesDisplayed() != null)
1388     {
1389       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1390
1391     }
1392     return null;
1393   }
1394
1395   public String outputFeatures(boolean displayTextbox, String format)
1396   {
1397     String features;
1398     if (format.equalsIgnoreCase("Jalview"))
1399     {
1400       features = new FeaturesFile().printJalviewFormat(viewport
1401               .getAlignment().getSequencesArray(),
1402               getDisplayedFeatureCols());
1403     }
1404     else
1405     {
1406       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1407               .getSequencesArray(), getDisplayedFeatureCols());
1408     }
1409
1410     if (displayTextbox)
1411     {
1412       boolean frimport = false;
1413       if (features == null || features.equals("No Features Visible"))
1414       {
1415         features = "# No features visible - paste some and import them here.";
1416         frimport = true;
1417       }
1418
1419       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1420       if (frimport)
1421       {
1422         cap.setAnnotationImport();
1423       }
1424       Frame frame = new Frame();
1425       frame.add(cap);
1426       jalview.bin.JalviewLite.addFrame(frame,
1427               MessageManager.getString("label.features"), 600, 500);
1428       cap.setText(features);
1429     }
1430     else
1431     {
1432       if (features == null)
1433       {
1434         features = "";
1435       }
1436     }
1437
1438     return features;
1439   }
1440
1441   void launchFullApplication()
1442   {
1443     StringBuffer url = new StringBuffer(jalviewServletURL);
1444
1445     // allow servlet parameters to be passed in applet parameter
1446     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1447             : "?";
1448     url.append(firstSep);
1449
1450     url.append("open="
1451             + appendProtocol(viewport.applet.getParameter("file")));
1452
1453     if (viewport.applet.getParameter("features") != null)
1454     {
1455       url.append("&features=");
1456       url.append(appendProtocol(viewport.applet.getParameter("features")));
1457     }
1458
1459     if (viewport.applet.getParameter("annotations") != null)
1460     {
1461       url.append("&annotations=");
1462       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1463     }
1464
1465     if (viewport.applet.getParameter("jnetfile") != null)
1466     {
1467       url.append("&annotations=");
1468       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1469     }
1470
1471     if (viewport.applet.getParameter("defaultColour") != null)
1472     {
1473       url.append("&colour="
1474               + removeWhiteSpace(viewport.applet
1475                       .getParameter("defaultColour")));
1476     }
1477
1478     if (viewport.applet.getParameter("userDefinedColour") != null)
1479     {
1480       url.append("&colour="
1481               + removeWhiteSpace(viewport.applet
1482                       .getParameter("userDefinedColour")));
1483     }
1484     if (viewport.applet.getParameter("tree") != null)
1485     {
1486       url.append("&tree="
1487               + appendProtocol(viewport.applet.getParameter("tree")));
1488     }
1489     if (viewport.applet.getParameter("treeFile") != null)
1490     {
1491       url.append("&tree="
1492               + appendProtocol(viewport.applet.getParameter("treeFile")));
1493     }
1494
1495     showURL(url.toString(), "FULL_APP");
1496   }
1497
1498   String removeWhiteSpace(String colour)
1499   {
1500     StringBuffer sb = new StringBuffer();
1501     for (int i = 0; i < colour.length(); i++)
1502     {
1503       if (Character.isWhitespace(colour.charAt(i)))
1504       {
1505         sb.append("%20");
1506       }
1507       else
1508       {
1509         sb.append(colour.charAt(i));
1510       }
1511     }
1512
1513     return sb.toString();
1514   }
1515
1516   String appendProtocol(String url)
1517   {
1518     try
1519     {
1520       new URL(url);
1521       url = URLEncoder.encode(url);
1522     }
1523     /*
1524      * When we finally deprecate 1.1 compatibility, we can start to use
1525      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1526      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1527      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1528      * ex.printStackTrace(); }
1529      */
1530     catch (java.net.MalformedURLException ex)
1531     {
1532       url = viewport.applet.getCodeBase() + url;
1533     }
1534     return url;
1535   }
1536
1537   public void closeMenuItem_actionPerformed()
1538   {
1539     PaintRefresher.RemoveComponent(alignPanel);
1540     if (alignPanel.seqPanel != null
1541             && alignPanel.seqPanel.seqCanvas != null)
1542     {
1543       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1544     }
1545     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1546     {
1547       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1548     }
1549
1550     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1551     {
1552       System.exit(0);
1553     }
1554     else
1555     {
1556     }
1557     viewport = null;
1558     alignPanel = null;
1559     this.dispose();
1560   }
1561
1562   /**
1563    * TODO: JAL-1104
1564    */
1565   void updateEditMenuBar()
1566   {
1567
1568     if (viewport.getHistoryList().size() > 0)
1569     {
1570       undoMenuItem.setEnabled(true);
1571       CommandI command = viewport.getHistoryList().peek();
1572       undoMenuItem.setLabel(MessageManager.formatMessage(
1573               "label.undo_command",
1574               new Object[] { command.getDescription() }));
1575     }
1576     else
1577     {
1578       undoMenuItem.setEnabled(false);
1579       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1580     }
1581
1582     if (viewport.getRedoList().size() > 0)
1583     {
1584       redoMenuItem.setEnabled(true);
1585
1586       CommandI command = viewport.getRedoList().peek();
1587       redoMenuItem.setLabel(MessageManager.formatMessage(
1588               "label.redo_command",
1589               new Object[] { command.getDescription() }));
1590     }
1591     else
1592     {
1593       redoMenuItem.setEnabled(false);
1594       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1595     }
1596   }
1597
1598   /**
1599    * TODO: JAL-1104
1600    */
1601   @Override
1602   public void addHistoryItem(CommandI command)
1603   {
1604     if (command.getSize() > 0)
1605     {
1606       viewport.addToHistoryList(command);
1607       viewport.clearRedoList();
1608       updateEditMenuBar();
1609       viewport.updateHiddenColumns();
1610     }
1611   }
1612
1613   /**
1614    * TODO: JAL-1104 DOCUMENT ME!
1615    *
1616    * @param e
1617    *          DOCUMENT ME!
1618    */
1619   protected void undoMenuItem_actionPerformed()
1620   {
1621     if (viewport.getHistoryList().isEmpty())
1622     {
1623       return;
1624     }
1625
1626     CommandI command = viewport.getHistoryList().pop();
1627     viewport.addToRedoList(command);
1628     command.undoCommand(null);
1629
1630     AlignmentViewport originalSource = getOriginatingSource(command);
1631     // JBPNote Test
1632     if (originalSource != viewport)
1633     {
1634       System.err
1635               .println("Warning: Viewport object mismatch whilst undoing");
1636     }
1637     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1638                                           // viewport.getColumnSelection().getHiddenColumns()
1639                                           // != null;
1640     updateEditMenuBar();
1641     originalSource.firePropertyChange("alignment", null, originalSource
1642             .getAlignment().getSequences());
1643   }
1644
1645   /**
1646    * TODO: JAL-1104 DOCUMENT ME!
1647    *
1648    * @param e
1649    *          DOCUMENT ME!
1650    */
1651   protected void redoMenuItem_actionPerformed()
1652   {
1653     if (viewport.getRedoList().isEmpty())
1654     {
1655       return;
1656     }
1657
1658     CommandI command = viewport.getRedoList().pop();
1659     viewport.addToHistoryList(command);
1660     command.doCommand(null);
1661
1662     AlignmentViewport originalSource = getOriginatingSource(command);
1663     // JBPNote Test
1664     if (originalSource != viewport)
1665     {
1666       System.err
1667               .println("Warning: Viewport object mismatch whilst re-doing");
1668     }
1669     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1670                                           // viewport.getColumnSelection().getHiddenColumns()
1671                                           // != null;
1672
1673     updateEditMenuBar();
1674     originalSource.firePropertyChange("alignment", null, originalSource
1675             .getAlignment().getSequences());
1676   }
1677
1678   AlignmentViewport getOriginatingSource(CommandI command)
1679   {
1680     AlignmentViewport originalSource = null;
1681     // For sequence removal and addition, we need to fire
1682     // the property change event FROM the viewport where the
1683     // original alignment was altered
1684     AlignmentI al = null;
1685     if (command instanceof EditCommand)
1686     {
1687       EditCommand editCommand = (EditCommand) command;
1688       al = editCommand.getAlignment();
1689       Vector comps = (Vector) PaintRefresher.components.get(viewport
1690               .getSequenceSetId());
1691       for (int i = 0; i < comps.size(); i++)
1692       {
1693         if (comps.elementAt(i) instanceof AlignmentPanel)
1694         {
1695           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1696           {
1697             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1698             break;
1699           }
1700         }
1701       }
1702     }
1703
1704     if (originalSource == null)
1705     {
1706       // The original view is closed, we must validate
1707       // the current view against the closed view first
1708       if (al != null)
1709       {
1710         PaintRefresher.validateSequences(al, viewport.getAlignment());
1711       }
1712
1713       originalSource = viewport;
1714     }
1715
1716     return originalSource;
1717   }
1718
1719   /**
1720    * Move the currently selected sequences up or down one position in the
1721    * alignment
1722    *
1723    * @param up
1724    */
1725   public void moveSelectedSequences(boolean up)
1726   {
1727     SequenceGroup sg = viewport.getSelectionGroup();
1728     if (sg == null)
1729     {
1730       return;
1731     }
1732     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1733             up ? null : viewport.getHiddenRepSequences(), up);
1734     alignPanel.paintAlignment(true);
1735
1736     /*
1737      * Also move cDNA/protein complement sequences
1738      */
1739     AlignViewportI complement = viewport.getCodingComplement();
1740     if (complement != null)
1741     {
1742       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1743               viewport, complement);
1744       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1745               up ? null : complement.getHiddenRepSequences(), up);
1746       // TODO need to trigger a repaint of the complementary panel - how?
1747       // would prefer to handle in SplitFrame but it is not overriding key
1748       // listener chiz
1749     }
1750   }
1751
1752   synchronized void slideSequences(boolean right, int size)
1753   {
1754     List<SequenceI> sg = new Vector<SequenceI>();
1755     if (viewport.cursorMode)
1756     {
1757       sg.add(viewport.getAlignment().getSequenceAt(
1758               alignPanel.seqPanel.seqCanvas.cursorY));
1759     }
1760     else if (viewport.getSelectionGroup() != null
1761             && viewport.getSelectionGroup().getSize() != viewport
1762                     .getAlignment().getHeight())
1763     {
1764       sg = viewport.getSelectionGroup().getSequences(
1765               viewport.getHiddenRepSequences());
1766     }
1767
1768     if (sg.size() < 1)
1769     {
1770       return;
1771     }
1772
1773     Vector<SequenceI> invertGroup = new Vector();
1774
1775     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1776     {
1777       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1778       {
1779         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1780       }
1781     }
1782
1783     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1784
1785     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1786             .size()]);
1787     for (int i = 0; i < invertGroup.size(); i++)
1788     {
1789       seqs2[i] = invertGroup.elementAt(i);
1790     }
1791
1792     SlideSequencesCommand ssc;
1793     if (right)
1794     {
1795       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1796               size, viewport.getGapCharacter());
1797     }
1798     else
1799     {
1800       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1801               size, viewport.getGapCharacter());
1802     }
1803
1804     int groupAdjustment = 0;
1805     if (ssc.getGapsInsertedBegin() && right)
1806     {
1807       if (viewport.cursorMode)
1808       {
1809         alignPanel.seqPanel.moveCursor(size, 0);
1810       }
1811       else
1812       {
1813         groupAdjustment = size;
1814       }
1815     }
1816     else if (!ssc.getGapsInsertedBegin() && !right)
1817     {
1818       if (viewport.cursorMode)
1819       {
1820         alignPanel.seqPanel.moveCursor(-size, 0);
1821       }
1822       else
1823       {
1824         groupAdjustment = -size;
1825       }
1826     }
1827
1828     if (groupAdjustment != 0)
1829     {
1830       viewport.getSelectionGroup().setStartRes(
1831               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1832       viewport.getSelectionGroup().setEndRes(
1833               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1834     }
1835
1836     boolean appendHistoryItem = false;
1837     Deque<CommandI> historyList = viewport.getHistoryList();
1838     if (historyList != null && historyList.size() > 0
1839             && historyList.peek() instanceof SlideSequencesCommand)
1840     {
1841       appendHistoryItem = ssc
1842               .appendSlideCommand((SlideSequencesCommand) historyList
1843                       .peek());
1844     }
1845
1846     if (!appendHistoryItem)
1847     {
1848       addHistoryItem(ssc);
1849     }
1850
1851     repaint();
1852   }
1853
1854   static StringBuffer copiedSequences;
1855
1856   static Vector copiedHiddenColumns;
1857
1858   protected void copy_actionPerformed()
1859   {
1860     if (viewport.getSelectionGroup() == null)
1861     {
1862       return;
1863     }
1864
1865     SequenceGroup sg = viewport.getSelectionGroup();
1866     copiedSequences = new StringBuffer();
1867     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1868     for (int i = 0; i < sg.getSize(); i++)
1869     {
1870       SequenceI seq = sg.getSequenceAt(i);
1871       int index = viewport.getAlignment().findIndex(seq);
1872       orderedSeqs.put(index, seq);
1873     }
1874
1875     int index = 0, startRes, endRes;
1876     char ch;
1877
1878     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1879     {
1880       copiedHiddenColumns = new Vector();
1881       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1882       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1883       {
1884         copiedHiddenColumns.addElement(new int[] {
1885             region[0] - hiddenOffset, region[1] - hiddenOffset });
1886       }
1887     }
1888     else
1889     {
1890       copiedHiddenColumns = null;
1891     }
1892
1893     for (int i = 0; i < sg.getSize(); i++)
1894     {
1895       SequenceI seq = null;
1896
1897       while (seq == null)
1898       {
1899         if (orderedSeqs.containsKey(index))
1900         {
1901           seq = orderedSeqs.get(index);
1902           index++;
1903           break;
1904         }
1905         else
1906         {
1907           index++;
1908         }
1909       }
1910
1911       // FIND START RES
1912       // Returns residue following index if gap
1913       startRes = seq.findPosition(sg.getStartRes());
1914
1915       // FIND END RES
1916       // Need to find the residue preceeding index if gap
1917       endRes = 0;
1918
1919       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1920       {
1921         ch = seq.getCharAt(j);
1922         if (!jalview.util.Comparison.isGap((ch)))
1923         {
1924           endRes++;
1925         }
1926       }
1927
1928       if (endRes > 0)
1929       {
1930         endRes += seq.getStart() - 1;
1931       }
1932
1933       copiedSequences.append(seq.getName()
1934               + "\t"
1935               + startRes
1936               + "\t"
1937               + endRes
1938               + "\t"
1939               + seq.getSequenceAsString(sg.getStartRes(),
1940                       sg.getEndRes() + 1) + "\n");
1941     }
1942
1943   }
1944
1945   protected void pasteNew_actionPerformed()
1946   {
1947     paste(true);
1948   }
1949
1950   protected void pasteThis_actionPerformed()
1951   {
1952     paste(false);
1953   }
1954
1955   void paste(boolean newAlignment)
1956   {
1957     try
1958     {
1959
1960       if (copiedSequences == null)
1961       {
1962         return;
1963       }
1964
1965       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1966       Vector seqs = new Vector();
1967       while (st.hasMoreElements())
1968       {
1969         String name = st.nextToken();
1970         int start = Integer.parseInt(st.nextToken());
1971         int end = Integer.parseInt(st.nextToken());
1972         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1973       }
1974       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1975       for (int i = 0; i < seqs.size(); i++)
1976       {
1977         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1978       }
1979
1980       if (newAlignment)
1981       {
1982         String newtitle = MessageManager
1983                 .getString("label.copied_sequences");
1984         if (getTitle().startsWith(
1985                 MessageManager.getString("label.copied_sequences")))
1986         {
1987           newtitle = getTitle();
1988         }
1989         else
1990         {
1991           newtitle = newtitle.concat(MessageManager.formatMessage(
1992                   "label.from_msname", new String[] { getTitle() }));
1993         }
1994         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1995                 viewport.applet, newtitle, false);
1996         if (copiedHiddenColumns != null)
1997         {
1998           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1999           {
2000             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2001             af.viewport.hideColumns(region[0], region[1]);
2002           }
2003         }
2004
2005         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2006                 frameHeight);
2007       }
2008       else
2009       {
2010         addSequences(newSeqs);
2011       }
2012
2013     } catch (Exception ex)
2014     {
2015     } // could be anything being pasted in here
2016
2017   }
2018
2019   void addSequences(SequenceI[] seqs)
2020   {
2021     for (int i = 0; i < seqs.length; i++)
2022     {
2023       viewport.getAlignment().addSequence(seqs[i]);
2024     }
2025
2026     // !newAlignment
2027     addHistoryItem(new EditCommand(
2028             MessageManager.getString("label.add_sequences"), Action.PASTE,
2029             seqs, 0, viewport.getAlignment().getWidth(),
2030             viewport.getAlignment()));
2031
2032     viewport.setEndSeq(viewport.getAlignment().getHeight());
2033     viewport.getAlignment().getWidth();
2034     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2035             .getSequences());
2036
2037   }
2038
2039   protected void cut_actionPerformed()
2040   {
2041     copy_actionPerformed();
2042     delete_actionPerformed();
2043   }
2044
2045   protected void delete_actionPerformed()
2046   {
2047
2048     SequenceGroup sg = viewport.getSelectionGroup();
2049     if (sg == null)
2050     {
2051       return;
2052     }
2053
2054     Vector seqs = new Vector();
2055     SequenceI seq;
2056     for (int i = 0; i < sg.getSize(); i++)
2057     {
2058       seq = sg.getSequenceAt(i);
2059       seqs.addElement(seq);
2060     }
2061
2062     // If the cut affects all sequences, remove highlighted columns
2063     if (sg.getSize() == viewport.getAlignment().getHeight())
2064     {
2065       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2066               sg.getEndRes() + 1);
2067     }
2068
2069     SequenceI[] cut = new SequenceI[seqs.size()];
2070     for (int i = 0; i < seqs.size(); i++)
2071     {
2072       cut[i] = (SequenceI) seqs.elementAt(i);
2073     }
2074
2075     /*
2076      * //ADD HISTORY ITEM
2077      */
2078     addHistoryItem(new EditCommand(
2079             MessageManager.getString("label.cut_sequences"), Action.CUT,
2080             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2081             viewport.getAlignment()));
2082
2083     viewport.setSelectionGroup(null);
2084     viewport.getAlignment().deleteGroup(sg);
2085
2086     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2087             .getSequences());
2088
2089     if (viewport.getAlignment().getHeight() < 1)
2090     {
2091       this.setVisible(false);
2092     }
2093     viewport.sendSelection();
2094   }
2095
2096   /**
2097    * group consensus toggled
2098    *
2099    */
2100   protected void showGroupConsensus_actionPerformed()
2101   {
2102     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2103     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2104
2105   }
2106
2107   /**
2108    * group conservation toggled.
2109    */
2110   protected void showGroupConservation_actionPerformed()
2111   {
2112     viewport.setShowGroupConservation(showGroupConservation.getState());
2113     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2114   }
2115
2116   /*
2117    * (non-Javadoc)
2118    *
2119    * @see
2120    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2121    * .event.ActionEvent)
2122    */
2123   protected void showConsensusHistogram_actionPerformed()
2124   {
2125     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2126     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2127   }
2128
2129   /*
2130    * (non-Javadoc)
2131    *
2132    * @see
2133    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2134    * .event.ActionEvent)
2135    */
2136   protected void showSequenceLogo_actionPerformed()
2137   {
2138     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2139     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2140   }
2141
2142   protected void normSequenceLogo_actionPerformed()
2143   {
2144     showSequenceLogo.setState(true);
2145     viewport.setShowSequenceLogo(true);
2146     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2147     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2148   }
2149
2150   protected void applyAutoAnnotationSettings_actionPerformed()
2151   {
2152     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2153   }
2154
2155   protected void makeGrpsFromSelection_actionPerformed()
2156   {
2157     if (avc.makeGroupsFromSelection())
2158     {
2159       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2160       alignPanel.updateAnnotation();
2161       alignPanel.paintAlignment(true);
2162     }
2163   }
2164
2165   protected void createGroup_actionPerformed()
2166   {
2167     avc.createGroup();
2168   }
2169
2170   protected void unGroup_actionPerformed()
2171   {
2172     if (avc.unGroup())
2173     {
2174       alignPanel.alignmentChanged();
2175     }
2176   }
2177
2178   protected void deleteGroups_actionPerformed()
2179   {
2180     if (avc.deleteGroups())
2181     {
2182       alignPanel.alignmentChanged();
2183     }
2184   }
2185
2186   public void selectAllSequenceMenuItem_actionPerformed()
2187   {
2188     SequenceGroup sg = new SequenceGroup();
2189     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2190     {
2191       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2192     }
2193     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2194     viewport.setSelectionGroup(sg);
2195     alignPanel.paintAlignment(true);
2196     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2197     viewport.sendSelection();
2198   }
2199
2200   public void deselectAllSequenceMenuItem_actionPerformed()
2201   {
2202     if (viewport.cursorMode)
2203     {
2204       alignPanel.seqPanel.keyboardNo1 = null;
2205       alignPanel.seqPanel.keyboardNo2 = null;
2206     }
2207     viewport.setSelectionGroup(null);
2208     viewport.getColumnSelection().clear();
2209     viewport.setSelectionGroup(null);
2210     alignPanel.idPanel.idCanvas.searchResults = null;
2211     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2212     alignPanel.paintAlignment(true);
2213     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2214     viewport.sendSelection();
2215   }
2216
2217   public void invertSequenceMenuItem_actionPerformed()
2218   {
2219     SequenceGroup sg = viewport.getSelectionGroup();
2220     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2221     {
2222       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2223     }
2224
2225     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2226     viewport.sendSelection();
2227   }
2228
2229   public void invertColSel_actionPerformed()
2230   {
2231     viewport.invertColumnSelection();
2232     alignPanel.paintAlignment(true);
2233     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2234     viewport.sendSelection();
2235   }
2236
2237   void trimAlignment(boolean trimLeft)
2238   {
2239     ColumnSelection colSel = viewport.getColumnSelection();
2240     int column;
2241
2242     if (colSel.size() > 0)
2243     {
2244       if (trimLeft)
2245       {
2246         column = colSel.getMin();
2247       }
2248       else
2249       {
2250         column = colSel.getMax();
2251       }
2252
2253       SequenceI[] seqs;
2254       if (viewport.getSelectionGroup() != null)
2255       {
2256         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2257                 viewport.getHiddenRepSequences());
2258       }
2259       else
2260       {
2261         seqs = viewport.getAlignment().getSequencesArray();
2262       }
2263
2264       TrimRegionCommand trimRegion;
2265       if (trimLeft)
2266       {
2267         trimRegion = new TrimRegionCommand("Remove Left",
2268                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2269                 viewport.getAlignment(), viewport.getColumnSelection(),
2270                 viewport.getSelectionGroup());
2271         viewport.setStartRes(0);
2272       }
2273       else
2274       {
2275         trimRegion = new TrimRegionCommand("Remove Right",
2276                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2277                 viewport.getAlignment(), viewport.getColumnSelection(),
2278                 viewport.getSelectionGroup());
2279       }
2280
2281       statusBar.setText(MessageManager.formatMessage(
2282               "label.removed_columns",
2283               new String[] { Integer.valueOf(trimRegion.getSize())
2284                       .toString() }));
2285       addHistoryItem(trimRegion);
2286
2287       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2288       {
2289         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2290                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2291         {
2292           viewport.getAlignment().deleteGroup(sg);
2293         }
2294       }
2295
2296       viewport.firePropertyChange("alignment", null, viewport
2297               .getAlignment().getSequences());
2298     }
2299   }
2300
2301   public void removeGappedColumnMenuItem_actionPerformed()
2302   {
2303     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2304
2305     SequenceI[] seqs;
2306     if (viewport.getSelectionGroup() != null)
2307     {
2308       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2309               viewport.getHiddenRepSequences());
2310       start = viewport.getSelectionGroup().getStartRes();
2311       end = viewport.getSelectionGroup().getEndRes();
2312     }
2313     else
2314     {
2315       seqs = viewport.getAlignment().getSequencesArray();
2316     }
2317
2318     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2319             "Remove Gapped Columns", seqs, start, end,
2320             viewport.getAlignment());
2321
2322     addHistoryItem(removeGapCols);
2323
2324     statusBar.setText(MessageManager.formatMessage(
2325             "label.removed_empty_columns",
2326             new String[] { Integer.valueOf(removeGapCols.getSize())
2327                     .toString() }));
2328
2329     // This is to maintain viewport position on first residue
2330     // of first sequence
2331     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2332     int startRes = seq.findPosition(viewport.startRes);
2333     // ShiftList shifts;
2334     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2335     // edit.alColumnChanges=shifts.getInverse();
2336     // if (viewport.hasHiddenColumns)
2337     // viewport.getColumnSelection().compensateForEdits(shifts);
2338     viewport.setStartRes(seq.findIndex(startRes) - 1);
2339     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2340             .getSequences());
2341
2342   }
2343
2344   public void removeAllGapsMenuItem_actionPerformed()
2345   {
2346     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2347
2348     SequenceI[] seqs;
2349     if (viewport.getSelectionGroup() != null)
2350     {
2351       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2352               viewport.getHiddenRepSequences());
2353       start = viewport.getSelectionGroup().getStartRes();
2354       end = viewport.getSelectionGroup().getEndRes();
2355     }
2356     else
2357     {
2358       seqs = viewport.getAlignment().getSequencesArray();
2359     }
2360
2361     // This is to maintain viewport position on first residue
2362     // of first sequence
2363     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2364     int startRes = seq.findPosition(viewport.startRes);
2365
2366     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2367             viewport.getAlignment()));
2368
2369     viewport.setStartRes(seq.findIndex(startRes) - 1);
2370
2371     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2372             .getSequences());
2373
2374   }
2375
2376   public void findMenuItem_actionPerformed()
2377   {
2378     new Finder(alignPanel);
2379   }
2380
2381   /**
2382    * create a new view derived from the current view
2383    *
2384    * @param viewtitle
2385    * @return frame for the new view
2386    */
2387   public AlignFrame newView(String viewtitle)
2388   {
2389     AlignmentI newal;
2390     if (viewport.hasHiddenRows())
2391     {
2392       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2393               .getFullAlignment().getSequencesArray());
2394     }
2395     else
2396     {
2397       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2398     }
2399
2400     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2401     {
2402       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2403       {
2404         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2405         {
2406           newal.addAnnotation(viewport.getAlignment()
2407                   .getAlignmentAnnotation()[i]);
2408         }
2409       }
2410     }
2411
2412     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2413
2414     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2415     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2416     PaintRefresher.Register(newaf.alignPanel,
2417             newaf.alignPanel.av.getSequenceSetId());
2418
2419     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2420             newaf.alignPanel.av.getSequenceSetId());
2421     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2422             newaf.alignPanel.av.getSequenceSetId());
2423
2424     Vector comps = (Vector) PaintRefresher.components.get(viewport
2425             .getSequenceSetId());
2426     int viewSize = -1;
2427     for (int i = 0; i < comps.size(); i++)
2428     {
2429       if (comps.elementAt(i) instanceof AlignmentPanel)
2430       {
2431         viewSize++;
2432       }
2433     }
2434
2435     String title = new String(this.getTitle());
2436     if (viewtitle != null)
2437     {
2438       title = viewtitle + " ( " + title + ")";
2439     }
2440     else
2441     {
2442       if (title.indexOf("(View") > -1)
2443       {
2444         title = title.substring(0, title.indexOf("(View"));
2445       }
2446       title += "(View " + viewSize + ")";
2447     }
2448
2449     newaf.setTitle(title.toString());
2450
2451     newaf.viewport.setHistoryList(viewport.getHistoryList());
2452     newaf.viewport.setRedoList(viewport.getRedoList());
2453     return newaf;
2454   }
2455
2456   /**
2457    *
2458    * @return list of feature groups on the view
2459    */
2460   public String[] getFeatureGroups()
2461   {
2462     FeatureRenderer fr = null;
2463     if (alignPanel != null
2464             && (fr = alignPanel.getFeatureRenderer()) != null)
2465     {
2466       List<String> gps = fr.getFeatureGroups();
2467       String[] _gps = gps.toArray(new String[gps.size()]);
2468       return _gps;
2469     }
2470     return null;
2471   }
2472
2473   /**
2474    * get sequence feature groups that are hidden or shown
2475    *
2476    * @param visible
2477    *          true is visible
2478    * @return list
2479    */
2480   public String[] getFeatureGroupsOfState(boolean visible)
2481   {
2482     FeatureRenderer fr = null;
2483     if (alignPanel != null
2484             && (fr = alignPanel.getFeatureRenderer()) != null)
2485     {
2486       List<String> gps = fr.getGroups(visible);
2487       String[] _gps = gps.toArray(new String[gps.size()]);
2488       return _gps;
2489     }
2490     return null;
2491   }
2492
2493   /**
2494    * Change the display state for the given feature groups
2495    *
2496    * @param groups
2497    *          list of group strings
2498    * @param state
2499    *          visible or invisible
2500    */
2501   public void setFeatureGroupState(String[] groups, boolean state)
2502   {
2503     FeatureRenderer fr = null;
2504     this.sequenceFeatures.setState(true);
2505     viewport.setShowSequenceFeatures(true);
2506     if (alignPanel != null
2507             && (fr = alignPanel.getFeatureRenderer()) != null)
2508     {
2509
2510       fr.setGroupVisibility(Arrays.asList(groups), state);
2511       alignPanel.seqPanel.seqCanvas.repaint();
2512       if (alignPanel.overviewPanel != null)
2513       {
2514         alignPanel.overviewPanel.updateOverviewImage();
2515       }
2516     }
2517   }
2518
2519   public void seqLimits_itemStateChanged()
2520   {
2521     viewport.setShowJVSuffix(seqLimits.getState());
2522     alignPanel.fontChanged();
2523     alignPanel.paintAlignment(true);
2524   }
2525
2526   protected void colourTextMenuItem_actionPerformed()
2527   {
2528     viewport.setColourText(colourTextMenuItem.getState());
2529     alignPanel.paintAlignment(true);
2530   }
2531
2532   protected void displayNonconservedMenuItem_actionPerformed()
2533   {
2534     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2535     alignPanel.paintAlignment(true);
2536   }
2537
2538   protected void wrapMenuItem_actionPerformed()
2539   {
2540     viewport.setWrapAlignment(wrapMenuItem.getState());
2541     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2542     scaleAbove.setEnabled(wrapMenuItem.getState());
2543     scaleLeft.setEnabled(wrapMenuItem.getState());
2544     scaleRight.setEnabled(wrapMenuItem.getState());
2545     alignPanel.paintAlignment(true);
2546   }
2547
2548   public void overviewMenuItem_actionPerformed()
2549   {
2550     if (alignPanel.overviewPanel != null)
2551     {
2552       return;
2553     }
2554
2555     Frame frame = new Frame();
2556     OverviewPanel overview = new OverviewPanel(alignPanel);
2557     frame.add(overview);
2558     // +50 must allow for applet frame window
2559     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2560             "label.overview_params", new String[] { this.getTitle() }),
2561             overview.getPreferredSize().width,
2562             overview.getPreferredSize().height + 50);
2563
2564     frame.pack();
2565     final AlignmentPanel ap = alignPanel;
2566     frame.addWindowListener(new WindowAdapter()
2567     {
2568       @Override
2569       public void windowClosing(WindowEvent e)
2570       {
2571         if (ap != null)
2572         {
2573           ap.setOverviewPanel(null);
2574         }
2575       };
2576     });
2577
2578     alignPanel.setOverviewPanel(overview);
2579
2580   }
2581
2582   public void changeColour(ColourSchemeI cs)
2583   {
2584
2585     if (cs != null)
2586     {
2587       if (viewport.getAbovePIDThreshold())
2588       {
2589         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2590                 cs, "Background"));
2591       }
2592
2593       if (viewport.getConservationSelected())
2594       {
2595         cs.setConservationApplied(true);
2596         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2597                 cs, "Background"));
2598       }
2599       else
2600       {
2601         cs.setConservationApplied(false);
2602       }
2603     }
2604     viewport.setGlobalColourScheme(cs);
2605
2606     alignPanel.paintAlignment(true);
2607   }
2608
2609   protected void modifyPID_actionPerformed()
2610   {
2611     if (viewport.getAbovePIDThreshold()
2612             && viewport.getGlobalColourScheme() != null)
2613     {
2614       SliderPanel.setPIDSliderSource(alignPanel,
2615               viewport.getGlobalColourScheme(), "Background");
2616       SliderPanel.showPIDSlider();
2617     }
2618   }
2619
2620   protected void modifyConservation_actionPerformed()
2621   {
2622     if (viewport.getConservationSelected()
2623             && viewport.getGlobalColourScheme() != null)
2624     {
2625       SliderPanel.setConservationSlider(alignPanel,
2626               viewport.getGlobalColourScheme(), "Background");
2627       SliderPanel.showConservationSlider();
2628     }
2629   }
2630
2631   protected void conservationMenuItem_actionPerformed()
2632   {
2633     viewport.setConservationSelected(conservationMenuItem.getState());
2634
2635     viewport.setAbovePIDThreshold(false);
2636     abovePIDThreshold.setState(false);
2637
2638     changeColour(viewport.getGlobalColourScheme());
2639
2640     modifyConservation_actionPerformed();
2641   }
2642
2643   public void abovePIDThreshold_actionPerformed()
2644   {
2645     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2646
2647     conservationMenuItem.setState(false);
2648     viewport.setConservationSelected(false);
2649
2650     changeColour(viewport.getGlobalColourScheme());
2651
2652     modifyPID_actionPerformed();
2653   }
2654
2655   public void sortPairwiseMenuItem_actionPerformed()
2656   {
2657     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2658     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2659             .getAlignment().getSequenceAt(0), null);
2660
2661     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2662             viewport.getAlignment()));
2663     alignPanel.paintAlignment(true);
2664   }
2665
2666   public void sortIDMenuItem_actionPerformed()
2667   {
2668     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2669     AlignmentSorter.sortByID(viewport.getAlignment());
2670     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2671             viewport.getAlignment()));
2672     alignPanel.paintAlignment(true);
2673   }
2674
2675   public void sortLengthMenuItem_actionPerformed()
2676   {
2677     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2678     AlignmentSorter.sortByLength(viewport.getAlignment());
2679     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2680             viewport.getAlignment()));
2681     alignPanel.paintAlignment(true);
2682   }
2683
2684   public void sortGroupMenuItem_actionPerformed()
2685   {
2686     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2687     AlignmentSorter.sortByGroup(viewport.getAlignment());
2688     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2689             viewport.getAlignment()));
2690     alignPanel.paintAlignment(true);
2691
2692   }
2693
2694   public void removeRedundancyMenuItem_actionPerformed()
2695   {
2696     new RedundancyPanel(alignPanel);
2697   }
2698
2699   public void pairwiseAlignmentMenuItem_actionPerformed()
2700   {
2701     if (viewport.getSelectionGroup() != null
2702             && viewport.getSelectionGroup().getSize() > 1)
2703     {
2704       Frame frame = new Frame();
2705       frame.add(new PairwiseAlignPanel(alignPanel));
2706       jalview.bin.JalviewLite.addFrame(frame,
2707               MessageManager.getString("action.pairwise_alignment"), 600,
2708               500);
2709     }
2710   }
2711
2712   public void PCAMenuItem_actionPerformed()
2713   {
2714     // are the sequences aligned?
2715     if (!viewport.getAlignment().isAligned(false))
2716     {
2717       SequenceI current;
2718       int Width = viewport.getAlignment().getWidth();
2719
2720       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2721       {
2722         current = viewport.getAlignment().getSequenceAt(i);
2723
2724         if (current.getLength() < Width)
2725         {
2726           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2727         }
2728       }
2729       alignPanel.paintAlignment(true);
2730     }
2731
2732     if ((viewport.getSelectionGroup() != null
2733             && viewport.getSelectionGroup().getSize() < 4 && viewport
2734             .getSelectionGroup().getSize() > 0)
2735             || viewport.getAlignment().getHeight() < 4)
2736     {
2737       return;
2738     }
2739
2740     try
2741     {
2742       new PCAPanel(viewport);
2743     } catch (java.lang.OutOfMemoryError ex)
2744     {
2745     }
2746
2747   }
2748
2749   public void averageDistanceTreeMenuItem_actionPerformed()
2750   {
2751     NewTreePanel("AV", "PID", "Average distance tree using PID");
2752   }
2753
2754   public void neighbourTreeMenuItem_actionPerformed()
2755   {
2756     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2757   }
2758
2759   protected void njTreeBlosumMenuItem_actionPerformed()
2760   {
2761     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2762   }
2763
2764   protected void avTreeBlosumMenuItem_actionPerformed()
2765   {
2766     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2767   }
2768
2769   void NewTreePanel(String type, String pwType, String title)
2770   {
2771     // are the sequences aligned?
2772     if (!viewport.getAlignment().isAligned(false))
2773     {
2774       SequenceI current;
2775       int Width = viewport.getAlignment().getWidth();
2776
2777       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2778       {
2779         current = viewport.getAlignment().getSequenceAt(i);
2780
2781         if (current.getLength() < Width)
2782         {
2783           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2784         }
2785       }
2786       alignPanel.paintAlignment(true);
2787
2788     }
2789
2790     if ((viewport.getSelectionGroup() != null && viewport
2791             .getSelectionGroup().getSize() > 1)
2792             || (viewport.getAlignment().getHeight() > 1))
2793     {
2794       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2795
2796       addTreeMenuItem(tp, title);
2797
2798       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2799     }
2800   }
2801
2802   void loadTree_actionPerformed()
2803   {
2804     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2805     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2806     cap.setTreeImport();
2807     Frame frame = new Frame();
2808     frame.add(cap);
2809     jalview.bin.JalviewLite.addFrame(frame,
2810             MessageManager.getString("label.paste_newick_file"), 400, 300);
2811   }
2812
2813   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2814   {
2815     TreePanel tp = new TreePanel(alignPanel, treeFile,
2816             MessageManager.getString("label.load_tree_from_file"), tree);
2817     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2818     addTreeMenuItem(tp, treeFile);
2819   }
2820
2821   /**
2822    * sort the alignment using the given treePanel
2823    *
2824    * @param treePanel
2825    *          tree used to sort view
2826    * @param title
2827    *          string used for undo event name
2828    */
2829   public void sortByTree(TreePanel treePanel, String title)
2830   {
2831     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2832     AlignmentSorter
2833             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2834     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2835     // HistoryItem.SORT));
2836     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2837             "label.order_by_params", new String[] { title }), oldOrder,
2838             viewport.getAlignment()));
2839     alignPanel.paintAlignment(true);
2840   }
2841
2842   /**
2843    * Do any automatic reordering of the alignment and add the necessary bits to
2844    * the menu structure for the new tree
2845    *
2846    * @param treePanel
2847    * @param title
2848    */
2849   protected void addTreeMenuItem(final TreePanel treePanel,
2850           final String title)
2851   {
2852     final MenuItem item = new MenuItem(title);
2853     sortByTreeMenu.add(item);
2854     item.addActionListener(new java.awt.event.ActionListener()
2855     {
2856       @Override
2857       public void actionPerformed(ActionEvent evt)
2858       {
2859         sortByTree(treePanel, title); // treePanel.getTitle());
2860       }
2861     });
2862
2863     treePanel.addWindowListener(new WindowAdapter()
2864     {
2865       @Override
2866       public void windowOpened(WindowEvent e)
2867       {
2868         if (viewport.sortByTree)
2869         {
2870           sortByTree(treePanel, title);
2871         }
2872         super.windowOpened(e);
2873       }
2874
2875       @Override
2876       public void windowClosing(WindowEvent e)
2877       {
2878         sortByTreeMenu.remove(item);
2879       };
2880     });
2881   }
2882
2883   public boolean sortBy(AlignmentOrder alorder, String undoname)
2884   {
2885     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2886     if (viewport.applet.debug)
2887     {
2888       System.err.println("Sorting " + alorder.getOrder().size()
2889               + " in alignment '" + getTitle() + "'");
2890     }
2891     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2892     if (undoname != null)
2893     {
2894       addHistoryItem(new OrderCommand(undoname, oldOrder,
2895               viewport.getAlignment()));
2896     }
2897     alignPanel.paintAlignment(true);
2898     return true;
2899   }
2900
2901   protected void documentation_actionPerformed()
2902   {
2903     alignPanel.av.applet.openJalviewHelpUrl();
2904   }
2905
2906   protected void about_actionPerformed()
2907   {
2908
2909     class AboutPanel extends Canvas
2910     {
2911       String version;
2912
2913       String builddate;
2914
2915       public AboutPanel(String version, String builddate)
2916       {
2917         this.version = version;
2918         this.builddate = builddate;
2919       }
2920
2921       @Override
2922       public void paint(Graphics g)
2923       {
2924         g.setColor(Color.white);
2925         g.fillRect(0, 0, getSize().width, getSize().height);
2926         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2927         FontMetrics fm = g.getFontMetrics();
2928         int fh = fm.getHeight();
2929         int y = 5, x = 7;
2930         g.setColor(Color.black);
2931         // TODO: update this text for each release or centrally store it for
2932         // lite and application
2933         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2934         g.drawString(MessageManager.formatMessage(
2935                 "label.jalviewLite_release", new String[] { version }), x,
2936                 y += fh);
2937         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2938         g.drawString(MessageManager.formatMessage(
2939                 "label.jaview_build_date", new String[] { builddate }), x,
2940                 y += fh);
2941         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2942         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2943                 x, y += fh * 1.5);
2944         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2945                 x + 50, y += fh + 8);
2946         g.drawString(
2947                 MessageManager.getString("label.jalview_dev_managers"), x,
2948                 y += fh);
2949         g.drawString(MessageManager
2950                 .getString("label.jalview_distribution_lists"), x, y += fh);
2951         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2952                 x, y += fh + 8);
2953         g.drawString(
2954                 MessageManager.getString("label.jalview_cite_1_authors"),
2955                 x, y += fh);
2956         g.drawString(
2957                 MessageManager.getString("label.jalview_cite_1_title"), x,
2958                 y += fh);
2959         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2960                 x, y += fh);
2961       }
2962     }
2963
2964     Frame frame = new Frame();
2965     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2966             .getBuildDate()));
2967     jalview.bin.JalviewLite.addFrame(frame,
2968             MessageManager.getString("label.jalview"), 580, 220);
2969
2970   }
2971
2972   public void showURL(String url, String target)
2973   {
2974     if (viewport.applet == null)
2975     {
2976       System.out.println("Not running as applet - no browser available.");
2977     }
2978     else
2979     {
2980       viewport.applet.showURL(url, target);
2981     }
2982   }
2983
2984   // ////////////////////////////////////////////////////////////////////////////////
2985   // JBuilder Graphics here
2986
2987   MenuBar alignFrameMenuBar = new MenuBar();
2988
2989   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2990
2991   MenuItem loadApplication = new MenuItem(
2992           MessageManager.getString("label.view_full_application"));
2993
2994   MenuItem loadTree = new MenuItem(
2995           MessageManager.getString("label.load_associated_tree"));
2996
2997   MenuItem loadAnnotations = new MenuItem(
2998           MessageManager.getString("label.load_features_annotations"));
2999
3000   MenuItem outputFeatures = new MenuItem(
3001           MessageManager.getString("label.export_features"));
3002
3003   MenuItem outputAnnotations = new MenuItem(
3004           MessageManager.getString("label.export_annotations"));
3005
3006   MenuItem closeMenuItem = new MenuItem(
3007           MessageManager.getString("action.close"));
3008
3009   MenuItem selectAllSequenceMenuItem = new MenuItem(
3010           MessageManager.getString("action.select_all"));
3011
3012   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3013           MessageManager.getString("action.deselect_all"));
3014
3015   MenuItem invertSequenceMenuItem = new MenuItem(
3016           MessageManager.getString("action.invert_selection"));
3017
3018   MenuItem remove2LeftMenuItem = new MenuItem();
3019
3020   MenuItem remove2RightMenuItem = new MenuItem();
3021
3022   MenuItem removeGappedColumnMenuItem = new MenuItem();
3023
3024   MenuItem removeAllGapsMenuItem = new MenuItem();
3025
3026   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3027
3028   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3029
3030   MenuItem sortPairwiseMenuItem = new MenuItem();
3031
3032   MenuItem sortIDMenuItem = new MenuItem();
3033
3034   MenuItem sortLengthMenuItem = new MenuItem();
3035
3036   MenuItem sortGroupMenuItem = new MenuItem();
3037
3038   MenuItem removeRedundancyMenuItem = new MenuItem();
3039
3040   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3041
3042   MenuItem PCAMenuItem = new MenuItem();
3043
3044   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3045
3046   MenuItem neighbourTreeMenuItem = new MenuItem();
3047
3048   BorderLayout borderLayout1 = new BorderLayout();
3049
3050   public Label statusBar = new Label();
3051
3052   MenuItem clustalColour = new MenuItem();
3053
3054   MenuItem zappoColour = new MenuItem();
3055
3056   MenuItem taylorColour = new MenuItem();
3057
3058   MenuItem hydrophobicityColour = new MenuItem();
3059
3060   MenuItem helixColour = new MenuItem();
3061
3062   MenuItem strandColour = new MenuItem();
3063
3064   MenuItem turnColour = new MenuItem();
3065
3066   MenuItem buriedColour = new MenuItem();
3067
3068   MenuItem purinePyrimidineColour = new MenuItem();
3069
3070   // MenuItem RNAInteractionColour = new MenuItem();
3071
3072   MenuItem RNAHelixColour = new MenuItem();
3073
3074   MenuItem userDefinedColour = new MenuItem();
3075
3076   MenuItem PIDColour = new MenuItem();
3077
3078   MenuItem BLOSUM62Colour = new MenuItem();
3079
3080   MenuItem tcoffeeColour = new MenuItem();
3081
3082   MenuItem njTreeBlosumMenuItem = new MenuItem();
3083
3084   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3085
3086   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3087
3088   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3089
3090   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3091
3092   MenuItem alProperties = new MenuItem(
3093           MessageManager.getString("label.alignment_props"));
3094
3095   MenuItem overviewMenuItem = new MenuItem();
3096
3097   MenuItem undoMenuItem = new MenuItem();
3098
3099   MenuItem redoMenuItem = new MenuItem();
3100
3101   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3102
3103   MenuItem noColourmenuItem = new MenuItem();
3104
3105   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3106
3107   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3108
3109   MenuItem findMenuItem = new MenuItem();
3110
3111   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3112
3113   MenuItem nucleotideColour = new MenuItem();
3114
3115   MenuItem deleteGroups = new MenuItem();
3116
3117   MenuItem grpsFromSelection = new MenuItem();
3118
3119   MenuItem createGroup = new MenuItem();
3120
3121   MenuItem unGroup = new MenuItem();
3122
3123   MenuItem delete = new MenuItem();
3124
3125   MenuItem copy = new MenuItem();
3126
3127   MenuItem cut = new MenuItem();
3128
3129   Menu pasteMenu = new Menu();
3130
3131   MenuItem pasteNew = new MenuItem();
3132
3133   MenuItem pasteThis = new MenuItem();
3134
3135   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3136
3137   MenuItem font = new MenuItem();
3138
3139   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3140
3141   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3142
3143   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3144
3145   MenuItem modifyPID = new MenuItem();
3146
3147   MenuItem modifyConservation = new MenuItem();
3148
3149   CheckboxMenuItem autoCalculate = null;
3150
3151   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3152           "Sort Alignment With New Tree", true);
3153
3154   Menu sortByTreeMenu = new Menu();
3155
3156   MenuItem inputText = new MenuItem();
3157
3158   MenuItem documentation = new MenuItem();
3159
3160   MenuItem about = new MenuItem();
3161
3162   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3163
3164   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3165
3166   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3167
3168   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3169
3170   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3171
3172   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3173
3174   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3175
3176   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3177
3178   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3179
3180   /**
3181    * Initialise menus and other items
3182    *
3183    * @throws Exception
3184    */
3185   private void jbInit() throws Exception
3186   {
3187     setMenuBar(alignFrameMenuBar);
3188
3189     /*
3190      * Configure File menu items and actions
3191      */
3192     inputText
3193             .setLabel(MessageManager.getString("label.input_from_textbox"));
3194     inputText.addActionListener(this);
3195     Menu outputTextboxMenu = new Menu(
3196             MessageManager.getString("label.out_to_textbox"));
3197     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3198     {
3199
3200       MenuItem item = new MenuItem(
3201               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3202
3203       item.addActionListener(new java.awt.event.ActionListener()
3204       {
3205         @Override
3206         public void actionPerformed(ActionEvent e)
3207         {
3208           outputText_actionPerformed(e);
3209         }
3210       });
3211
3212       outputTextboxMenu.add(item);
3213     }
3214     closeMenuItem.addActionListener(this);
3215     loadApplication.addActionListener(this);
3216     loadTree.addActionListener(this);
3217     loadAnnotations.addActionListener(this);
3218     outputFeatures.addActionListener(this);
3219     outputAnnotations.addActionListener(this);
3220
3221     /*
3222      * Configure Edit menu items and actions
3223      */
3224     undoMenuItem.setEnabled(false);
3225     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3226     undoMenuItem.addActionListener(this);
3227     redoMenuItem.setEnabled(false);
3228     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3229     redoMenuItem.addActionListener(this);
3230     copy.setLabel(MessageManager.getString("action.copy"));
3231     copy.addActionListener(this);
3232     cut.setLabel(MessageManager.getString("action.cut"));
3233     cut.addActionListener(this);
3234     delete.setLabel(MessageManager.getString("action.delete"));
3235     delete.addActionListener(this);
3236     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3237     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3238     pasteNew.addActionListener(this);
3239     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3240     pasteThis.addActionListener(this);
3241     remove2LeftMenuItem.setLabel(MessageManager
3242             .getString("action.remove_left"));
3243     remove2LeftMenuItem.addActionListener(this);
3244     remove2RightMenuItem.setLabel(MessageManager
3245             .getString("action.remove_right"));
3246     remove2RightMenuItem.addActionListener(this);
3247     removeGappedColumnMenuItem.setLabel(MessageManager
3248             .getString("action.remove_empty_columns"));
3249     removeGappedColumnMenuItem.addActionListener(this);
3250     removeAllGapsMenuItem.setLabel(MessageManager
3251             .getString("action.remove_all_gaps"));
3252     removeAllGapsMenuItem.addActionListener(this);
3253     removeRedundancyMenuItem.setLabel(MessageManager
3254             .getString("action.remove_redundancy"));
3255     removeRedundancyMenuItem.addActionListener(this);
3256
3257     /*
3258      * Configure Select menu items and actions
3259      */
3260     findMenuItem.setLabel(MessageManager.getString("action.find"));
3261     findMenuItem.addActionListener(this);
3262     selectAllSequenceMenuItem.addActionListener(this);
3263     deselectAllSequenceMenuItem.addActionListener(this);
3264     invertSequenceMenuItem.setLabel(MessageManager
3265             .getString("action.invert_sequence_selection"));
3266     invertSequenceMenuItem.addActionListener(this);
3267     invertColSel.setLabel(MessageManager
3268             .getString("action.invert_column_selection"));
3269     invertColSel.addActionListener(this);
3270     deleteGroups.setLabel(MessageManager
3271             .getString("action.undefine_groups"));
3272     deleteGroups.addActionListener(this);
3273     grpsFromSelection.setLabel(MessageManager
3274             .getString("action.make_groups_selection"));
3275     grpsFromSelection.addActionListener(this);
3276     createGroup.setLabel(MessageManager.getString("action.create_group"));
3277     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3278     annotationColumnSelection.setLabel(MessageManager
3279             .getString("action.select_by_annotation"));
3280     annotationColumnSelection.addActionListener(this);
3281
3282     /*
3283      * Configure View menu items and actions
3284      */
3285     newView.setLabel(MessageManager.getString("action.new_view"));
3286     newView.addActionListener(this);
3287     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3288     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3289     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3290     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3291     hideColumns
3292             .setLabel(MessageManager.getString("label.selected_columns"));
3293     hideSequences.setLabel(MessageManager
3294             .getString("label.selected_sequences"));
3295     hideAllButSelection.setLabel(MessageManager
3296             .getString("label.all_but_selected_region"));
3297     hideAllSelection.setLabel(MessageManager
3298             .getString("label.selected_region"));
3299     showAllHidden.setLabel(MessageManager
3300             .getString("label.all_sequences_columns"));
3301     showColumns.addActionListener(this);
3302     showSeqs.addActionListener(this);
3303     hideColumns.addActionListener(this);
3304     hideSequences.addActionListener(this);
3305     hideAllButSelection.addActionListener(this);
3306     hideAllSelection.addActionListener(this);
3307     showAllHidden.addActionListener(this);
3308     featureSettings.setLabel(MessageManager
3309             .getString("action.feature_settings"));
3310     featureSettings.addActionListener(this);
3311     sequenceFeatures.setLabel(MessageManager
3312             .getString("label.show_sequence_features"));
3313     sequenceFeatures.addItemListener(this);
3314     sequenceFeatures.setState(false);
3315     followMouseOverFlag.setLabel(MessageManager
3316             .getString("label.automatic_scrolling"));
3317     followMouseOverFlag.addItemListener(this);
3318     alProperties.addActionListener(this);
3319     overviewMenuItem.setLabel(MessageManager
3320             .getString("label.overview_window"));
3321     overviewMenuItem.addActionListener(this);
3322
3323     /*
3324      * Configure Annotations menu items and actions
3325      */
3326     annotationPanelMenuItem.setLabel(MessageManager
3327             .getString("label.show_annotations"));
3328     annotationPanelMenuItem.addItemListener(this);
3329     showGroupConsensus.setLabel(MessageManager
3330             .getString("label.group_consensus"));
3331     showGroupConservation.setLabel(MessageManager
3332             .getString("label.group_conservation"));
3333     showConsensusHistogram.setLabel(MessageManager
3334             .getString("label.show_consensus_histogram"));
3335     showSequenceLogo.setLabel(MessageManager
3336             .getString("label.show_consensus_logo"));
3337     normSequenceLogo.setLabel(MessageManager
3338             .getString("label.norm_consensus_logo"));
3339     applyAutoAnnotationSettings.setLabel(MessageManager
3340             .getString("label.apply_all_groups"));
3341     applyAutoAnnotationSettings.setState(true);
3342     Menu autoAnnMenu = new Menu(
3343             MessageManager.getString("label.autocalculated_annotation"));
3344     showGroupConsensus.addItemListener(this);
3345     showGroupConservation.addItemListener(this);
3346     showConsensusHistogram.addItemListener(this);
3347     showSequenceLogo.addItemListener(this);
3348     normSequenceLogo.addItemListener(this);
3349     applyAutoAnnotationSettings.addItemListener(this);
3350     showAlignmentAnnotations = new CheckboxMenuItem(
3351             MessageManager.getString("label.show_all_al_annotations"));
3352     showSequenceAnnotations = new CheckboxMenuItem(
3353             MessageManager.getString("label.show_all_seq_annotations"));
3354     sortAnnBySequence = new CheckboxMenuItem(
3355             MessageManager.getString("label.sort_annotations_by_sequence"));
3356     sortAnnByLabel = new CheckboxMenuItem(
3357             MessageManager.getString("label.sort_annotations_by_label"));
3358     showAutoFirst = new CheckboxMenuItem(
3359             MessageManager.getString("label.show_first"));
3360     showAutoLast = new CheckboxMenuItem(
3361             MessageManager.getString("label.show_last"));
3362     showAlignmentAnnotations.addItemListener(this);
3363     showSequenceAnnotations.addItemListener(this);
3364     sortAnnBySequence.addItemListener(this);
3365     sortAnnByLabel.addItemListener(this);
3366     showAutoFirst.addItemListener(this);
3367     showAutoLast.addItemListener(this);
3368
3369     /*
3370      * Configure Format menu items and actions
3371      */
3372     font.setLabel(MessageManager.getString("action.font"));
3373     font.addActionListener(this);
3374     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3375     scaleAbove.setState(true);
3376     scaleAbove.setEnabled(false);
3377     scaleAbove.addItemListener(this);
3378     scaleLeft.setEnabled(false);
3379     scaleLeft.setState(true);
3380     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3381     scaleLeft.addItemListener(this);
3382     scaleRight.setEnabled(false);
3383     scaleRight.setState(true);
3384     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3385     scaleRight.addItemListener(this);
3386     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3387     viewBoxesMenuItem.setState(true);
3388     viewBoxesMenuItem.addItemListener(this);
3389     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3390     viewTextMenuItem.setState(true);
3391     viewTextMenuItem.addItemListener(this);
3392     colourTextMenuItem.setLabel(MessageManager
3393             .getString("label.colour_text"));
3394     colourTextMenuItem.addItemListener(this);
3395     displayNonconservedMenuItem.setLabel(MessageManager
3396             .getString("label.show_non_conversed"));
3397     displayNonconservedMenuItem.addItemListener(this);
3398     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3399     wrapMenuItem.addItemListener(this);
3400     renderGapsMenuItem.setLabel(MessageManager
3401             .getString("action.show_gaps"));
3402     renderGapsMenuItem.setState(true);
3403     renderGapsMenuItem.addItemListener(this);
3404     centreColumnLabelFlag.setLabel(MessageManager
3405             .getString("label.centre_column_labels"));
3406     centreColumnLabelFlag.addItemListener(this);
3407     seqLimits.setState(true);
3408     seqLimits.setLabel(MessageManager
3409             .getString("label.show_sequence_limits"));
3410     seqLimits.addItemListener(this);
3411
3412     /*
3413      * Configure Colour menu items and actions
3414      */
3415     applyToAllGroups.setLabel(MessageManager
3416             .getString("label.apply_colour_to_all_groups"));
3417     applyToAllGroups.setState(true);
3418     applyToAllGroups.addItemListener(this);
3419     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3420     clustalColour.addActionListener(this);
3421     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3422     zappoColour.addActionListener(this);
3423     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3424     taylorColour.addActionListener(this);
3425     hydrophobicityColour.setLabel(MessageManager
3426             .getString("label.hydrophobicity"));
3427     hydrophobicityColour.addActionListener(this);
3428     helixColour
3429             .setLabel(MessageManager.getString("label.helix_propensity"));
3430     helixColour.addActionListener(this);
3431     strandColour.setLabel(MessageManager
3432             .getString("label.strand_propensity"));
3433     strandColour.addActionListener(this);
3434     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3435     turnColour.addActionListener(this);
3436     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3437     buriedColour.addActionListener(this);
3438     purinePyrimidineColour.setLabel(MessageManager
3439             .getString("label.purine_pyrimidine"));
3440     purinePyrimidineColour.addActionListener(this);
3441     // RNAInteractionColour.setLabel(MessageManager
3442     // .getString("label.rna_interaction"));
3443     // RNAInteractionColour.addActionListener(this);
3444     RNAHelixColour.setLabel(MessageManager
3445             .getString("action.by_rna_helixes"));
3446     RNAHelixColour.addActionListener(this);
3447     userDefinedColour.setLabel(MessageManager
3448             .getString("action.user_defined"));
3449     userDefinedColour.addActionListener(this);
3450     PIDColour.setLabel(MessageManager
3451             .getString("label.percentage_identity"));
3452     PIDColour.addActionListener(this);
3453     BLOSUM62Colour.setLabel(MessageManager
3454             .getString("label.blosum62_score"));
3455     BLOSUM62Colour.addActionListener(this);
3456     tcoffeeColour
3457             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3458     // it will be enabled only if a score file is provided
3459     tcoffeeColour.setEnabled(false);
3460     tcoffeeColour.addActionListener(this);
3461     conservationMenuItem.setLabel(MessageManager
3462             .getString("action.by_conservation"));
3463     conservationMenuItem.addItemListener(this);
3464     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3465     noColourmenuItem.addActionListener(this);
3466     abovePIDThreshold.setLabel(MessageManager
3467             .getString("label.above_identity_threshold"));
3468     abovePIDThreshold.addItemListener(this);
3469     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3470     nucleotideColour.addActionListener(this);
3471     modifyPID.setLabel(MessageManager
3472             .getString("label.modify_identity_thereshold"));
3473     modifyPID.addActionListener(this);
3474     modifyConservation.setLabel(MessageManager
3475             .getString("label.modify_conservation_thereshold"));
3476     modifyConservation.addActionListener(this);
3477     annotationColour.setLabel(MessageManager
3478             .getString("action.by_annotation"));
3479     annotationColour.addActionListener(this);
3480
3481     /*
3482      * Configure Calculate menu items and actions
3483      */
3484     sortPairwiseMenuItem.setLabel(MessageManager
3485             .getString("action.by_pairwise_id"));
3486     sortPairwiseMenuItem.addActionListener(this);
3487     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3488     sortIDMenuItem.addActionListener(this);
3489     sortLengthMenuItem.setLabel(MessageManager
3490             .getString("action.by_length"));
3491     sortLengthMenuItem.addActionListener(this);
3492     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3493     sortGroupMenuItem.addActionListener(this);
3494     pairwiseAlignmentMenuItem.setLabel(MessageManager
3495             .getString("action.pairwise_alignment"));
3496     pairwiseAlignmentMenuItem.addActionListener(this);
3497     PCAMenuItem.setLabel(MessageManager
3498             .getString("label.principal_component_analysis"));
3499     PCAMenuItem.addActionListener(this);
3500     autoCalculate = new CheckboxMenuItem(
3501             MessageManager.getString("label.autocalculate_consensus"), true);
3502     averageDistanceTreeMenuItem.setLabel(MessageManager
3503             .getString("label.average_distance_identity"));
3504     averageDistanceTreeMenuItem.addActionListener(this);
3505     neighbourTreeMenuItem.setLabel(MessageManager
3506             .getString("label.neighbour_joining_identity"));
3507     neighbourTreeMenuItem.addActionListener(this);
3508     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3509             .getString("label.average_distance_bloslum62"));
3510     avDistanceTreeBlosumMenuItem.addActionListener(this);
3511     njTreeBlosumMenuItem.setLabel(MessageManager
3512             .getString("label.neighbour_blosum62"));
3513     njTreeBlosumMenuItem.addActionListener(this);
3514     sortByTreeMenu.setLabel(MessageManager
3515             .getString("action.by_tree_order"));
3516     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3517     Menu calculateTreeMenu = new Menu(
3518             MessageManager.getString("action.calculate_tree"));
3519     autoCalculate.addItemListener(this);
3520     sortByTree.addItemListener(this);
3521
3522     /*
3523      * Configure Help menu items and actions
3524      */
3525     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3526     documentation.setLabel(MessageManager.getString("label.documentation"));
3527     documentation.addActionListener(this);
3528     about.setLabel(MessageManager.getString("label.about"));
3529     about.addActionListener(this);
3530
3531     /*
3532      * Add top level menus to frame
3533      */
3534     alignFrameMenuBar.add(fileMenu);
3535     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3536     alignFrameMenuBar.add(editMenu);
3537     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3538     alignFrameMenuBar.add(selectMenu);
3539     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3540     alignFrameMenuBar.add(viewMenu);
3541     Menu annotationsMenu = new Menu(
3542             MessageManager.getString("action.annotations"));
3543     alignFrameMenuBar.add(annotationsMenu);
3544     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3545     alignFrameMenuBar.add(formatMenu);
3546     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3547     alignFrameMenuBar.add(colourMenu);
3548     Menu calculateMenu = new Menu(
3549             MessageManager.getString("action.calculate"));
3550     alignFrameMenuBar.add(calculateMenu);
3551     alignFrameMenuBar.add(helpMenu);
3552
3553     /*
3554      * File menu
3555      */
3556     fileMenu.add(inputText);
3557     fileMenu.add(loadTree);
3558     fileMenu.add(loadAnnotations);
3559     fileMenu.addSeparator();
3560     fileMenu.add(outputTextboxMenu);
3561     fileMenu.add(outputFeatures);
3562     fileMenu.add(outputAnnotations);
3563     if (jalviewServletURL != null)
3564     {
3565       fileMenu.add(loadApplication);
3566     }
3567     fileMenu.addSeparator();
3568     fileMenu.add(closeMenuItem);
3569
3570     /*
3571      * Edit menu
3572      */
3573     editMenu.add(undoMenuItem);
3574     editMenu.add(redoMenuItem);
3575     editMenu.add(cut);
3576     editMenu.add(copy);
3577     pasteMenu.add(pasteNew);
3578     pasteMenu.add(pasteThis);
3579     editMenu.add(pasteMenu);
3580     editMenu.add(delete);
3581     editMenu.addSeparator();
3582     editMenu.add(remove2LeftMenuItem);
3583     editMenu.add(remove2RightMenuItem);
3584     editMenu.add(removeGappedColumnMenuItem);
3585     editMenu.add(removeAllGapsMenuItem);
3586     editMenu.add(removeRedundancyMenuItem);
3587
3588     /*
3589      * Select menu
3590      */
3591     selectMenu.add(findMenuItem);
3592     selectMenu.addSeparator();
3593     selectMenu.add(selectAllSequenceMenuItem);
3594     selectMenu.add(deselectAllSequenceMenuItem);
3595     selectMenu.add(invertSequenceMenuItem);
3596     selectMenu.add(invertColSel);
3597     selectMenu.add(createGroup);
3598     selectMenu.add(unGroup);
3599     selectMenu.add(grpsFromSelection);
3600     selectMenu.add(deleteGroups);
3601     selectMenu.add(annotationColumnSelection);
3602
3603     /*
3604      * View menu
3605      */
3606     viewMenu.add(newView);
3607     viewMenu.addSeparator();
3608     showMenu.add(showColumns);
3609     showMenu.add(showSeqs);
3610     showMenu.add(showAllHidden);
3611     viewMenu.add(showMenu);
3612     hideMenu.add(hideColumns);
3613     hideMenu.add(hideSequences);
3614     hideMenu.add(hideAllSelection);
3615     hideMenu.add(hideAllButSelection);
3616     viewMenu.add(hideMenu);
3617     viewMenu.addSeparator();
3618     viewMenu.add(followMouseOverFlag);
3619     viewMenu.addSeparator();
3620     viewMenu.add(sequenceFeatures);
3621     viewMenu.add(featureSettings);
3622     viewMenu.addSeparator();
3623     viewMenu.add(alProperties);
3624     viewMenu.addSeparator();
3625     viewMenu.add(overviewMenuItem);
3626
3627     /*
3628      * Annotations menu
3629      */
3630     annotationsMenu.add(annotationPanelMenuItem);
3631     annotationsMenu.addSeparator();
3632     annotationsMenu.add(showAlignmentAnnotations);
3633     annotationsMenu.add(showSequenceAnnotations);
3634     annotationsMenu.add(sortAnnBySequence);
3635     annotationsMenu.add(sortAnnByLabel);
3636     annotationsMenu.addSeparator();
3637     autoAnnMenu.add(showAutoFirst);
3638     autoAnnMenu.add(showAutoLast);
3639     autoAnnMenu.addSeparator();
3640     autoAnnMenu.add(applyAutoAnnotationSettings);
3641     autoAnnMenu.add(showConsensusHistogram);
3642     autoAnnMenu.add(showSequenceLogo);
3643     autoAnnMenu.add(normSequenceLogo);
3644     autoAnnMenu.addSeparator();
3645     autoAnnMenu.add(showGroupConservation);
3646     autoAnnMenu.add(showGroupConsensus);
3647     annotationsMenu.add(autoAnnMenu);
3648
3649     /*
3650      * Format menu
3651      */
3652     formatMenu.add(font);
3653     formatMenu.add(seqLimits);
3654     formatMenu.add(wrapMenuItem);
3655     formatMenu.add(scaleAbove);
3656     formatMenu.add(scaleLeft);
3657     formatMenu.add(scaleRight);
3658     formatMenu.add(viewBoxesMenuItem);
3659     formatMenu.add(viewTextMenuItem);
3660     formatMenu.add(colourTextMenuItem);
3661     formatMenu.add(displayNonconservedMenuItem);
3662     formatMenu.add(renderGapsMenuItem);
3663     formatMenu.add(centreColumnLabelFlag);
3664
3665     /*
3666      * Colour menu
3667      */
3668     colourMenu.add(applyToAllGroups);
3669     colourMenu.addSeparator();
3670     colourMenu.add(noColourmenuItem);
3671     colourMenu.add(clustalColour);
3672     colourMenu.add(BLOSUM62Colour);
3673     colourMenu.add(PIDColour);
3674     colourMenu.add(zappoColour);
3675     colourMenu.add(taylorColour);
3676     colourMenu.add(hydrophobicityColour);
3677     colourMenu.add(helixColour);
3678     colourMenu.add(strandColour);
3679     colourMenu.add(turnColour);
3680     colourMenu.add(buriedColour);
3681     colourMenu.add(nucleotideColour);
3682     colourMenu.add(purinePyrimidineColour);
3683     // colourMenu.add(RNAInteractionColour);
3684     colourMenu.add(tcoffeeColour);
3685     colourMenu.add(userDefinedColour);
3686     colourMenu.addSeparator();
3687     colourMenu.add(conservationMenuItem);
3688     colourMenu.add(modifyConservation);
3689     colourMenu.add(abovePIDThreshold);
3690     colourMenu.add(modifyPID);
3691     colourMenu.add(annotationColour);
3692     colourMenu.add(RNAHelixColour);
3693
3694     /*
3695      * Calculate menu
3696      */
3697     sortMenu.add(sortIDMenuItem);
3698     sortMenu.add(sortLengthMenuItem);
3699     sortMenu.add(sortByTreeMenu);
3700     sortMenu.add(sortGroupMenuItem);
3701     sortMenu.add(sortPairwiseMenuItem);
3702     calculateMenu.add(sortMenu);
3703     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3704     calculateTreeMenu.add(neighbourTreeMenuItem);
3705     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3706     calculateTreeMenu.add(njTreeBlosumMenuItem);
3707     calculateMenu.add(calculateTreeMenu);
3708     calculateMenu.addSeparator();
3709     calculateMenu.add(pairwiseAlignmentMenuItem);
3710     calculateMenu.add(PCAMenuItem);
3711     calculateMenu.add(autoCalculate);
3712     calculateMenu.add(sortByTree);
3713
3714     /*
3715      * Help menu
3716      */
3717     helpMenu.add(documentation);
3718     helpMenu.add(about);
3719
3720     /*
3721      * Status bar
3722      */
3723     statusBar.setBackground(Color.white);
3724     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3725     statusBar.setText(MessageManager.getString("label.status_bar"));
3726     this.add(statusBar, BorderLayout.SOUTH);
3727   }
3728
3729   public void setStatus(String string)
3730   {
3731     statusBar.setText(string);
3732   };
3733
3734   MenuItem featureSettings = new MenuItem();
3735
3736   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3737
3738   MenuItem annotationColour = new MenuItem();
3739
3740   MenuItem annotationColumnSelection = new MenuItem();
3741
3742   MenuItem invertColSel = new MenuItem();
3743
3744   MenuItem showColumns = new MenuItem();
3745
3746   MenuItem showSeqs = new MenuItem();
3747
3748   MenuItem hideColumns = new MenuItem();
3749
3750   MenuItem hideSequences = new MenuItem();
3751
3752   MenuItem hideAllButSelection = new MenuItem();
3753
3754   MenuItem hideAllSelection = new MenuItem();
3755
3756   MenuItem showAllHidden = new MenuItem();
3757
3758   MenuItem newView = new MenuItem();
3759
3760   private CheckboxMenuItem showAlignmentAnnotations;
3761
3762   private CheckboxMenuItem showSequenceAnnotations;
3763
3764   private CheckboxMenuItem sortAnnBySequence;
3765
3766   private CheckboxMenuItem sortAnnByLabel;
3767
3768   private CheckboxMenuItem showAutoFirst;
3769
3770   private CheckboxMenuItem showAutoLast;
3771
3772   private SplitFrame splitFrame;
3773
3774   /**
3775    * Attach the alignFrame panels after embedding menus, if necessary. This used
3776    * to be called setEmbedded, but is now creates the dropdown menus in a
3777    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3778    *
3779    * @param reallyEmbedded
3780    *          true to attach the view to the applet area on the page rather than
3781    *          in a new window
3782    */
3783   public void createAlignFrameWindow(boolean reallyEmbedded)
3784   {
3785     if (reallyEmbedded)
3786     {
3787       embedAlignFrameInApplet(viewport.applet);
3788     }
3789     else
3790     {
3791       // //////
3792       // test and embed menu bar if necessary.
3793       //
3794       if (embedMenuIfNeeded(alignPanel))
3795       {
3796         /*
3797          * adjust for status bar height too. ? pointless as overridden by layout
3798          * manager
3799          */
3800         alignPanel.setSize(getSize().width,
3801                 getSize().height - statusBar.getHeight());
3802       }
3803       add(statusBar, BorderLayout.SOUTH);
3804       add(alignPanel, BorderLayout.CENTER);
3805       // and register with the applet so it can pass external API calls to us
3806       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3807               frameHeight);
3808     }
3809   }
3810
3811   /**
3812    * Add the components of this AlignFrame to the applet container.
3813    *
3814    * @param theApplet
3815    */
3816   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3817   {
3818     // ////
3819     // Explicitly build the embedded menu panel for the on-page applet
3820     //
3821     // view cannot be closed if its actually on the page
3822     fileMenu.remove(closeMenuItem);
3823     fileMenu.remove(3); // Remove Separator
3824     // construct embedded menu, using default font
3825     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3826     // and actually add the components to the applet area
3827     theApplet.setLayout(new BorderLayout());
3828     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3829     theApplet.add(statusBar, BorderLayout.SOUTH);
3830     // TODO should size be left to the layout manager?
3831     alignPanel.setSize(theApplet.getSize().width,
3832             theApplet.getSize().height - embeddedMenu.getHeight()
3833                     - statusBar.getHeight());
3834     theApplet.add(alignPanel, BorderLayout.CENTER);
3835     final AlignFrame me = this;
3836     theApplet.addFocusListener(new FocusListener()
3837     {
3838
3839       @Override
3840       public void focusLost(FocusEvent e)
3841       {
3842         if (theApplet.currentAlignFrame == me)
3843         {
3844           theApplet.currentAlignFrame = null;
3845         }
3846       }
3847
3848       @Override
3849       public void focusGained(FocusEvent e)
3850       {
3851         theApplet.currentAlignFrame = me;
3852       }
3853     });
3854     theApplet.validate();
3855   }
3856
3857   /**
3858    * create a new binding between structures in an existing jmol viewer instance
3859    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3860    * this does not open a new Jmol window, or modify the display of the
3861    * structures in the original jmol window. Note This method doesn't work
3862    * without an additional javascript library to exchange messages between the
3863    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3864    *
3865    * @param viewer
3866    *          JmolViewer instance
3867    * @param sequenceIds
3868    *          - sequence Ids to search for associations
3869    */
3870   public SequenceStructureBinding addStructureViewInstance(
3871           Object jmolviewer, String[] sequenceIds)
3872   {
3873     Viewer viewer = null;
3874     try
3875     {
3876       viewer = (Viewer) jmolviewer;
3877     } catch (ClassCastException ex)
3878     {
3879       System.err.println("Unsupported viewer object :"
3880               + jmolviewer.getClass());
3881     }
3882     if (viewer == null)
3883     {
3884       System.err.println("Can't use this object as a structure viewer:"
3885               + jmolviewer.getClass());
3886       return null;
3887     }
3888     SequenceI[] seqs = null;
3889     if (sequenceIds == null || sequenceIds.length == 0)
3890     {
3891       seqs = viewport.getAlignment().getSequencesArray();
3892     }
3893     else
3894     {
3895       Vector sqi = new Vector();
3896       AlignmentI al = viewport.getAlignment();
3897       for (int sid = 0; sid < sequenceIds.length; sid++)
3898       {
3899         SequenceI sq = al.findName(sequenceIds[sid]);
3900         if (sq != null)
3901         {
3902           sqi.addElement(sq);
3903         }
3904       }
3905       if (sqi.size() > 0)
3906       {
3907         seqs = new SequenceI[sqi.size()];
3908         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3909         {
3910           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3911         }
3912       }
3913       else
3914       {
3915         return null;
3916       }
3917     }
3918     AAStructureBindingModel jmv = null;
3919     // TODO: search for a jmv that involves viewer
3920     if (jmv == null)
3921     { // create a new viewer/jalview binding.
3922       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3923     }
3924     return jmv;
3925
3926   }
3927
3928   /**
3929    * bind a pdb file to a sequence in the current view
3930    *
3931    * @param sequenceId
3932    *          - sequenceId within the dataset.
3933    * @param pdbEntryString
3934    *          - the short name for the PDB file
3935    * @param pdbFile
3936    *          - pdb file - either a URL or a valid PDB file.
3937    * @return true if binding was as success TODO: consider making an exception
3938    *         structure for indicating when PDB parsing or sequenceId location
3939    *         fails.
3940    */
3941   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3942           String pdbFile)
3943   {
3944     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3945     boolean needtoadd = false;
3946     if (toaddpdb != null)
3947     {
3948       Vector pdbe = toaddpdb.getAllPDBEntries();
3949       PDBEntry pdbentry = null;
3950       if (pdbe != null && pdbe.size() > 0)
3951       {
3952         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3953         {
3954           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3955           if (!pdbentry.getId().equals(pdbEntryString)
3956                   && !pdbentry.getFile().equals(pdbFile))
3957           {
3958             pdbentry = null;
3959           }
3960           else
3961           {
3962             continue;
3963           }
3964         }
3965       }
3966       if (pdbentry == null)
3967       {
3968         pdbentry = new PDBEntry();
3969         pdbentry.setId(pdbEntryString);
3970         pdbentry.setFile(pdbFile);
3971         needtoadd = true; // add this new entry to sequence.
3972       }
3973       // resolve data source
3974       // TODO: this code should be a refactored to an io package
3975       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3976       if (protocol == null)
3977       {
3978         return false;
3979       }
3980       if (needtoadd)
3981       {
3982         // make a note of the access mode and add
3983         if (pdbentry.getProperty() == null)
3984         {
3985           pdbentry.setProperty(new Hashtable());
3986         }
3987         pdbentry.getProperty().put("protocol", protocol);
3988         toaddpdb.addPDBId(pdbentry);
3989         alignPanel.getStructureSelectionManager()
3990                 .registerPDBEntry(pdbentry);
3991       }
3992     }
3993     return true;
3994   }
3995
3996   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3997   {
3998     if (seqs != null)
3999     {
4000       Vector sequences = new Vector();
4001       for (int i = 0; i < seqs.length; i++)
4002       {
4003         if (seqs[i] != null)
4004         {
4005           sequences.addElement(new Object[] { seqs[i],
4006               (chains != null) ? chains[i] : null });
4007         }
4008       }
4009       seqs = new SequenceI[sequences.size()];
4010       chains = new String[sequences.size()];
4011       for (int i = 0, isize = sequences.size(); i < isize; i++)
4012       {
4013         Object[] oj = (Object[]) sequences.elementAt(i);
4014
4015         seqs[i] = (SequenceI) oj[0];
4016         chains[i] = (String) oj[1];
4017       }
4018     }
4019     return new Object[] { seqs, chains };
4020
4021   }
4022
4023   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4024           SequenceI[] seqs, String[] chains, String protocol)
4025   {
4026     // Scrub any null sequences from the array
4027     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4028     seqs = (SequenceI[]) sqch[0];
4029     chains = (String[]) sqch[1];
4030     if (seqs == null || seqs.length == 0)
4031     {
4032       System.err
4033               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4034     }
4035     if (protocol == null || protocol.trim().length() == 0
4036             || protocol.equals("null"))
4037     {
4038       protocol = (String) pdb.getProperty().get("protocol");
4039       if (protocol == null)
4040       {
4041         System.err.println("Couldn't work out protocol to open structure: "
4042                 + pdb.getId());
4043         return;
4044       }
4045     }
4046     if (applet.useXtrnalSviewer)
4047     {
4048       // register the association(s) and quit, don't create any windows.
4049       if (StructureSelectionManager.getStructureSelectionManager(applet)
4050               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4051       {
4052         System.err.println("Failed to map " + pdb.getFile() + " ("
4053                 + protocol + ") to any sequences");
4054       }
4055       return;
4056     }
4057     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4058     {
4059       // can only do alignments with Jmol
4060       // find the last jmol window assigned to this alignment
4061       jalview.appletgui.AppletJmol ajm = null, tajm;
4062       Vector jmols = applet
4063               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4064       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4065       {
4066         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4067         if (tajm.ap.alignFrame == this)
4068         {
4069           ajm = tajm;
4070           break;
4071         }
4072       }
4073       if (ajm != null)
4074       {
4075         System.err
4076                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4077         // try and add the pdb structure
4078         // ajm.addS
4079         ajm = null;
4080       }
4081     }
4082     // otherwise, create a new window
4083     if (applet.jmolAvailable)
4084     {
4085       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4086               protocol);
4087       applet.lastFrameX += 40;
4088       applet.lastFrameY += 40;
4089     }
4090     else
4091     {
4092       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4093     }
4094
4095   }
4096
4097   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4098           SequenceI[][] seqs, String[][] chains, String[] protocols)
4099   {
4100     // TODO Auto-generated method stub
4101     System.err.println("Aligned Structure View: Not yet implemented.");
4102   }
4103
4104   /**
4105    * modify the current selection, providing the user has not made a selection
4106    * already.
4107    *
4108    * @param sel
4109    *          - sequences from this alignment
4110    * @param csel
4111    *          - columns to be selected on the alignment
4112    */
4113   public void select(SequenceGroup sel, ColumnSelection csel)
4114   {
4115     alignPanel.seqPanel.selection(sel, csel, null);
4116   }
4117
4118   public void scrollTo(int row, int column)
4119   {
4120     alignPanel.seqPanel.scrollTo(row, column);
4121   }
4122
4123   public void scrollToRow(int row)
4124   {
4125     alignPanel.seqPanel.scrollToRow(row);
4126   }
4127
4128   public void scrollToColumn(int column)
4129   {
4130     alignPanel.seqPanel.scrollToColumn(column);
4131   }
4132
4133   /**
4134    * @return the alignments unique ID.
4135    */
4136   public String getSequenceSetId()
4137   {
4138     return viewport.getSequenceSetId();
4139   }
4140
4141   /**
4142    * Load the (T-Coffee) score file from the specified url
4143    *
4144    * @param source
4145    *          File/URL/T-COFFEE score file contents
4146    * @throws IOException
4147    * @return true if alignment was annotated with data from source
4148    */
4149   public boolean loadScoreFile(String source) throws IOException
4150   {
4151
4152     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4153             AppletFormatAdapter.checkProtocol(source));
4154     if (!file.isValid())
4155     {
4156       // TODO: raise dialog for gui
4157       System.err.println("Problems parsing T-Coffee scores: "
4158               + file.getWarningMessage());
4159       System.err.println("Origin was:\n" + source);
4160       return false;
4161     }
4162
4163     /*
4164      * check that the score matrix matches the alignment dimensions
4165      */
4166     AlignmentI aln;
4167     if ((aln = viewport.getAlignment()) != null
4168             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4169                     .getWidth()))
4170     {
4171       // TODO: raise a dialog box here rather than bomb out.
4172       System.err
4173               .println("The scores matrix does not match the alignment dimensions");
4174
4175     }
4176
4177     // TODO add parameter to indicate if matching should be done
4178     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4179     {
4180       alignPanel.fontChanged();
4181       tcoffeeColour.setEnabled(true);
4182       // switch to this color
4183       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4184       return true;
4185     }
4186     else
4187     {
4188       System.err.println("Problems resolving T-Coffee scores:");
4189       if (file.getWarningMessage() != null)
4190       {
4191         System.err.println(file.getWarningMessage());
4192       }
4193     }
4194     return false;
4195   }
4196
4197   public SplitFrame getSplitFrame()
4198   {
4199     return this.splitFrame;
4200   }
4201
4202   public void setSplitFrame(SplitFrame sf)
4203   {
4204     this.splitFrame = sf;
4205   }
4206
4207   // may not need this
4208   @Override
4209   public void setShowSeqFeatures(boolean b)
4210   {
4211     // showSeqFeatures.setSelected(b);
4212     viewport.setShowSequenceFeatures(b);
4213
4214   }
4215
4216   @Override
4217   public void setMenusForViewport()
4218   {
4219     // setMenusFromViewport(viewport);
4220
4221   }
4222
4223   @Override
4224   public void refreshFeatureUI(boolean enableIfNecessary)
4225   {
4226     if (enableIfNecessary)
4227     {
4228       sequenceFeatures.setState(true);
4229       alignPanel.av.setShowSequenceFeatures(true);
4230     }
4231   }
4232
4233   @Override
4234   public FeatureSettingsControllerI getFeatureSettingsUI()
4235   {
4236     return alignPanel.av.featureSettings;
4237   }
4238
4239 }