src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Canvas;
  25 import java.awt.CheckboxMenuItem;
  26 import java.awt.Color;
  27 import java.awt.Font;
  28 import java.awt.FontMetrics;
  29 import java.awt.Frame;
  30 import java.awt.Graphics;
  31 import java.awt.Label;
  32 import java.awt.Menu;
  33 import java.awt.MenuBar;
  34 import java.awt.MenuItem;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.awt.event.FocusEvent;
  38 import java.awt.event.FocusListener;
  39 import java.awt.event.ItemEvent;
  40 import java.awt.event.ItemListener;
  41 import java.awt.event.KeyEvent;
  42 import java.awt.event.KeyListener;
  43 import java.awt.event.WindowAdapter;
  44 import java.awt.event.WindowEvent;
  45 import java.io.IOException;
  46 import java.net.URL;
  47 import java.net.URLEncoder;
  48 import java.util.Arrays;
  49 import java.util.Deque;
  50 import java.util.HashMap;
  51 import java.util.Hashtable;
  52 import java.util.List;
  53 import java.util.Map;
  54 import java.util.StringTokenizer;
  55 import java.util.Vector;
  56
  57 import jalview.analysis.AlignmentSorter;
  58 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  59 import jalview.api.AlignViewControllerGuiI;
  60 import jalview.api.AlignViewControllerI;
  61 import jalview.api.AlignViewportI;
  62 import jalview.api.FeatureRenderer;
  63 import jalview.api.SequenceStructureBinding;
  64 import jalview.bin.JalviewLite;
  65 import jalview.commands.CommandI;
  66 import jalview.commands.EditCommand;
  67 import jalview.commands.EditCommand.Action;
  68 import jalview.commands.OrderCommand;
  69 import jalview.commands.RemoveGapColCommand;
  70 import jalview.commands.RemoveGapsCommand;
  71 import jalview.commands.SlideSequencesCommand;
  72 import jalview.commands.TrimRegionCommand;
  73 import jalview.datamodel.Alignment;
  74 import jalview.datamodel.AlignmentAnnotation;
  75 import jalview.datamodel.AlignmentI;
  76 import jalview.datamodel.AlignmentOrder;
  77 import jalview.datamodel.ColumnSelection;
  78 import jalview.datamodel.PDBEntry;
  79 import jalview.datamodel.Sequence;
  80 import jalview.datamodel.SequenceGroup;
  81 import jalview.datamodel.SequenceI;
  82 import jalview.io.AnnotationFile;
  83 import jalview.io.AppletFormatAdapter;
  84 import jalview.io.FeaturesFile;
  85 import jalview.io.TCoffeeScoreFile;
  86 import jalview.schemes.Blosum62ColourScheme;
  87 import jalview.schemes.BuriedColourScheme;
  88 import jalview.schemes.ClustalxColourScheme;
  89 import jalview.schemes.ColourSchemeI;
  90 import jalview.schemes.HelixColourScheme;
  91 import jalview.schemes.HydrophobicColourScheme;
  92 import jalview.schemes.NucleotideColourScheme;
  93 import jalview.schemes.PIDColourScheme;
  94 import jalview.schemes.PurinePyrimidineColourScheme;
  95 import jalview.schemes.RNAHelicesColourChooser;
  96 import jalview.schemes.RNAInteractionColourScheme;
  97 import jalview.schemes.StrandColourScheme;
  98 import jalview.schemes.TCoffeeColourScheme;
  99 import jalview.schemes.TaylorColourScheme;
 100 import jalview.schemes.TurnColourScheme;
 101 import jalview.schemes.ZappoColourScheme;
 102 import jalview.structure.StructureSelectionManager;
 103 import jalview.structures.models.AAStructureBindingModel;
 104 import jalview.util.MappingUtils;
 105 import jalview.util.MessageManager;
 106 import jalview.viewmodel.AlignmentViewport;
 107
 108 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 109         ItemListener, KeyListener, AlignViewControllerGuiI
 110 {
 111   public AlignViewControllerI avc;
 112
 113   public AlignmentPanel alignPanel;
 114
 115   public AlignViewport viewport;
 116
 117   // width and height may be overridden by applet parameters
 118   int frameWidth = 700;
 119
 120   int frameHeight = 500;
 121
 122   String jalviewServletURL;
 123
 124   /*
 125    * Flag for showing autocalculated consensus above or below other consensus
 126    * rows
 127    */
 128   private boolean showAutoCalculatedAbove;
 129
 130   private SequenceAnnotationOrder annotationSortOrder;
 131
 132   /**
 133    * Constructor that creates the frame and adds it to the display.
 134    *
 135    * @param al
 136    * @param applet
 137    * @param title
 138    * @param embedded
 139    */
 140   public AlignFrame(AlignmentI al, JalviewLite applet,
 141           String title, boolean embedded)
 142   {
 143     this(al, applet, title, embedded, true);
 144   }
 145
 146   /**
 147    * Constructor that optionally allows the frame to be displayed or only
 148    * created.
 149    *
 150    * @param al
 151    * @param applet
 152    * @param title
 153    * @param embedded
 154    * @param addToDisplay
 155    */
 156   public AlignFrame(AlignmentI al, JalviewLite applet,
 157           String title, boolean embedded, boolean addToDisplay)
 158   {
 159     this(al, null, null, applet, title, embedded, addToDisplay);
 160   }
 161
 162   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 163           ColumnSelection columnSelection, JalviewLite applet,
 164           String title, boolean embedded)
 165   {
 166     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 167   }
 168
 169   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 170           ColumnSelection columnSelection, JalviewLite applet,
 171           String title, boolean embedded, boolean addToDisplay)
 172   {
 173     if (applet != null)
 174     {
 175       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 176     }
 177
 178     try
 179     {
 180       jbInit();
 181     } catch (Exception ex)
 182     {
 183       ex.printStackTrace();
 184     }
 185     // need to get window geometry before we calculate alignment layout
 186     if (applet != null)
 187     {
 188       String param;
 189       try
 190       {
 191         param = applet.getParameter("windowWidth");
 192         if (param != null)
 193         {
 194           int width = Integer.parseInt(param);
 195           frameWidth = width;
 196         }
 197         param = applet.getParameter("windowHeight");
 198         if (param != null)
 199         {
 200           int height = Integer.parseInt(param);
 201           frameHeight = height;
 202         }
 203       } catch (Exception ex)
 204       {
 205       }
 206     }
 207     viewport = new AlignViewport(al, applet);
 208
 209     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 210     {
 211       viewport.hideSequence(hiddenSeqs);
 212       viewport.setHasHiddenRows(true);
 213     }
 214     if (columnSelection != null)
 215     {
 216       viewport.setColumnSelection(columnSelection);
 217     }
 218
 219     alignPanel = new AlignmentPanel(this, viewport);
 220     avc = new jalview.controller.AlignViewController(this, viewport,
 221             alignPanel);
 222     viewport.updateConservation(alignPanel);
 223     viewport.updateConsensus(alignPanel);
 224
 225     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 226     followMouseOverFlag.setState(viewport.isFollowHighlight());
 227     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 228     showGroupConservation.setState(viewport.isShowGroupConservation());
 229     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 230     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 231     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 232     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 233     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 234     showAlignmentAnnotations.setState(viewport.isShowAnnotation());
 235     showSequenceAnnotations.setState(viewport.isShowAnnotation());
 236
 237     seqLimits.setState(viewport.getShowJVSuffix());
 238
 239     if (applet != null)
 240     {
 241       String param = applet.getParameter("sortBy");
 242       if (param != null)
 243       {
 244         if (param.equalsIgnoreCase("Id"))
 245         {
 246           sortIDMenuItem_actionPerformed();
 247         }
 248         else if (param.equalsIgnoreCase("Pairwise Identity"))
 249         {
 250           sortPairwiseMenuItem_actionPerformed();
 251         }
 252         else if (param.equalsIgnoreCase("Length"))
 253         {
 254           sortLengthMenuItem_actionPerformed();
 255         }
 256       }
 257
 258       param = applet.getParameter("wrap");
 259       if (param != null)
 260       {
 261         if (param.equalsIgnoreCase("true"))
 262         {
 263           wrapMenuItem.setState(true);
 264           wrapMenuItem_actionPerformed();
 265         }
 266       }
 267       param = applet.getParameter("centrecolumnlabels");
 268       if (param != null)
 269       {
 270         centreColumnLabelFlag.setState(true);
 271         centreColumnLabelFlag_stateChanged();
 272       }
 273
 274     }
 275     if (viewport.getAlignment().isNucleotide())
 276     {
 277       viewport.updateStrucConsensus(alignPanel);
 278       if (viewport.getAlignment().hasRNAStructure())
 279       {
 280         RNAHelixColour.setEnabled(true);
 281       }
 282       else
 283       {
 284         RNAHelixColour.setEnabled(false);
 285       }
 286     }
 287     else
 288     {
 289       RNAHelixColour.setEnabled(false);
 290       purinePyrimidineColour.setEnabled(false);
 291     }
 292     // Some JVMS send keyevents to Top frame or lowest panel,
 293     // Havent worked out why yet. So add to both this frame and seqCanvas for
 294     // now
 295     this.addKeyListener(this);
 296     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 297     alignPanel.idPanel.idCanvas.addKeyListener(this);
 298     alignPanel.scalePanel.addKeyListener(this);
 299     alignPanel.annotationPanel.addKeyListener(this);
 300     alignPanel.annotationPanelHolder.addKeyListener(this);
 301     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 302     alignPanel.alabels.addKeyListener(this);
 303
 304     if (addToDisplay)
 305     {
 306       addToDisplay(embedded);
 307     }
 308   }
 309
 310   /**
 311    * @param embedded
 312    */
 313   public void addToDisplay(boolean embedded)
 314   {
 315     createAlignFrameWindow(embedded);
 316     validate();
 317     alignPanel.adjustAnnotationHeight();
 318     alignPanel.paintAlignment(true);
 319   }
 320
 321   public AlignViewport getAlignViewport()
 322   {
 323     return viewport;
 324   }
 325
 326   public SeqCanvas getSeqcanvas()
 327   {
 328     return alignPanel.seqPanel.seqCanvas;
 329   }
 330
 331   /**
 332    * Load a features file onto the alignment
 333    *
 334    * @param file
 335    *          file URL, content, or other resolvable path
 336    * @param type
 337    *          is protocol for accessing data referred to by file
 338    */
 339
 340   public boolean parseFeaturesFile(String file, String type)
 341   {
 342     return parseFeaturesFile(file, type, true);
 343   }
 344
 345   /**
 346    * Load a features file onto the alignment
 347    *
 348    * @param file
 349    *          file URL, content, or other resolvable path
 350    * @param type
 351    *          is protocol for accessing data referred to by file
 352    * @param autoenabledisplay
 353    *          when true, display features flag will be automatically enabled if
 354    *          features are loaded
 355    * @return true if data parsed as a features file
 356    */
 357   public boolean parseFeaturesFile(String file, String type,
 358           boolean autoenabledisplay)
 359   {
 360     // TODO: test if importing a features file onto an alignment which already
 361     // has features with links overwrites the original links.
 362
 363     Hashtable featureLinks = new Hashtable();
 364     boolean featuresFile = false;
 365     try
 366     {
 367       featuresFile = new jalview.io.FeaturesFile(file, type)
 368               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 369                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 370                       true, viewport.applet.getDefaultParameter(
 371                               "relaxedidmatch", false));
 372     } catch (Exception ex)
 373     {
 374       ex.printStackTrace();
 375     }
 376
 377     if (featuresFile)
 378     {
 379       if (featureLinks.size() > 0)
 380       {
 381         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 382       }
 383       if (autoenabledisplay)
 384       {
 385         viewport.setShowSequenceFeatures(true);
 386         sequenceFeatures.setState(true);
 387       }
 388       if (alignPanel.seqPanel.seqCanvas.fr != null)
 389       {
 390         // update the min/max ranges where necessary
 391         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 392       }
 393       if (viewport.featureSettings != null)
 394       {
 395         viewport.featureSettings.refreshTable();
 396       }
 397       alignPanel.paintAlignment(true);
 398       statusBar.setText(MessageManager
 399               .getString("label.successfully_added_features_alignment"));
 400     }
 401     return featuresFile;
 402   }
 403
 404   @Override
 405   public void keyPressed(KeyEvent evt)
 406   {
 407     if (viewport.cursorMode
 408             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 409                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 410                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 411             && Character.isDigit(evt.getKeyChar()))
 412     {
 413       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 414     }
 415
 416     switch (evt.getKeyCode())
 417     {
 418     case 27: // escape key
 419       deselectAllSequenceMenuItem_actionPerformed();
 420
 421       alignPanel.alabels.cancelDrag();
 422       break;
 423     case KeyEvent.VK_X:
 424       if (evt.isControlDown() || evt.isMetaDown())
 425       {
 426         cut_actionPerformed();
 427       }
 428       break;
 429     case KeyEvent.VK_C:
 430       if (viewport.cursorMode && !evt.isControlDown())
 431       {
 432         alignPanel.seqPanel.setCursorColumn();
 433       }
 434       if (evt.isControlDown() || evt.isMetaDown())
 435       {
 436         copy_actionPerformed();
 437       }
 438       break;
 439     case KeyEvent.VK_V:
 440       if (evt.isControlDown())
 441       {
 442         paste(evt.isShiftDown());
 443       }
 444       break;
 445     case KeyEvent.VK_A:
 446       if (evt.isControlDown() || evt.isMetaDown())
 447       {
 448         selectAllSequenceMenuItem_actionPerformed();
 449       }
 450       break;
 451     case KeyEvent.VK_DOWN:
 452       if (viewport.cursorMode)
 453       {
 454         alignPanel.seqPanel.moveCursor(0, 1);
 455       }
 456       else
 457       {
 458         moveSelectedSequences(false);
 459       }
 460       break;
 461
 462     case KeyEvent.VK_UP:
 463       if (viewport.cursorMode)
 464       {
 465         alignPanel.seqPanel.moveCursor(0, -1);
 466       }
 467       else
 468       {
 469         moveSelectedSequences(true);
 470       }
 471       break;
 472
 473     case KeyEvent.VK_LEFT:
 474       if (evt.isAltDown() || !viewport.cursorMode)
 475       {
 476         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 477       }
 478       else
 479       {
 480         alignPanel.seqPanel.moveCursor(-1, 0);
 481       }
 482       break;
 483
 484     case KeyEvent.VK_RIGHT:
 485       if (evt.isAltDown() || !viewport.cursorMode)
 486       {
 487         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 488       }
 489       else
 490       {
 491         alignPanel.seqPanel.moveCursor(1, 0);
 492       }
 493       break;
 494
 495     case KeyEvent.VK_SPACE:
 496       if (viewport.cursorMode)
 497       {
 498         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 499                 || evt.isShiftDown() || evt.isAltDown());
 500       }
 501       break;
 502
 503     case KeyEvent.VK_DELETE:
 504     case KeyEvent.VK_BACK_SPACE:
 505       if (viewport.cursorMode)
 506       {
 507         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 508                 || evt.isShiftDown() || evt.isAltDown());
 509       }
 510       else
 511       {
 512         cut_actionPerformed();
 513         alignPanel.seqPanel.seqCanvas.repaint();
 514       }
 515       break;
 516
 517     case KeyEvent.VK_S:
 518       if (viewport.cursorMode)
 519       {
 520         alignPanel.seqPanel.setCursorRow();
 521       }
 522       break;
 523     case KeyEvent.VK_P:
 524       if (viewport.cursorMode)
 525       {
 526         alignPanel.seqPanel.setCursorPosition();
 527       }
 528       break;
 529
 530     case KeyEvent.VK_ENTER:
 531     case KeyEvent.VK_COMMA:
 532       if (viewport.cursorMode)
 533       {
 534         alignPanel.seqPanel.setCursorRowAndColumn();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_Q:
 539       if (viewport.cursorMode)
 540       {
 541         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 542       }
 543       break;
 544     case KeyEvent.VK_M:
 545       if (viewport.cursorMode)
 546       {
 547         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 548       }
 549       break;
 550
 551     case KeyEvent.VK_F2:
 552       viewport.cursorMode = !viewport.cursorMode;
 553       statusBar.setText(MessageManager.formatMessage(
 554               "label.keyboard_editing_mode", new String[]
 555               { (viewport.cursorMode ? "on" : "off") }));
 556       if (viewport.cursorMode)
 557       {
 558         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 559         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 560       }
 561       break;
 562
 563     case KeyEvent.VK_F:
 564       if (evt.isControlDown())
 565       {
 566         findMenuItem_actionPerformed();
 567       }
 568       break;
 569
 570     case KeyEvent.VK_H:
 571     {
 572       boolean toggleSeqs = !evt.isControlDown();
 573       boolean toggleCols = !evt.isShiftDown();
 574       toggleHiddenRegions(toggleSeqs, toggleCols);
 575       break;
 576     }
 577
 578     case KeyEvent.VK_PAGE_UP:
 579       if (viewport.getWrapAlignment())
 580       {
 581         alignPanel.scrollUp(true);
 582       }
 583       else
 584       {
 585         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 586                 - viewport.endSeq + viewport.startSeq);
 587       }
 588       break;
 589
 590     case KeyEvent.VK_PAGE_DOWN:
 591       if (viewport.getWrapAlignment())
 592       {
 593         alignPanel.scrollUp(false);
 594       }
 595       else
 596       {
 597         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 598                 + viewport.endSeq - viewport.startSeq);
 599       }
 600       break;
 601
 602     case KeyEvent.VK_Z:
 603       if (evt.isControlDown())
 604       {
 605         undoMenuItem_actionPerformed();
 606       }
 607       break;
 608
 609     case KeyEvent.VK_Y:
 610       if (evt.isControlDown())
 611       {
 612         redoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_L:
 617       if (evt.isControlDown())
 618       {
 619         trimAlignment(true);
 620       }
 621       break;
 622
 623     case KeyEvent.VK_R:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(false);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_E:
 631       if (evt.isControlDown())
 632       {
 633         if (evt.isShiftDown())
 634         {
 635           this.removeAllGapsMenuItem_actionPerformed();
 636         }
 637         else
 638         {
 639           removeGappedColumnMenuItem_actionPerformed();
 640         }
 641       }
 642       break;
 643     case KeyEvent.VK_I:
 644       if (evt.isControlDown())
 645       {
 646         if (evt.isAltDown())
 647         {
 648           invertColSel_actionPerformed();
 649         }
 650         else
 651         {
 652           invertSequenceMenuItem_actionPerformed();
 653         }
 654       }
 655       break;
 656
 657     case KeyEvent.VK_G:
 658       if (evt.isControlDown())
 659       {
 660         if (evt.isShiftDown())
 661         {
 662           this.unGroup_actionPerformed();
 663         }
 664         else
 665         {
 666           this.createGroup_actionPerformed();
 667         }
 668       }
 669       break;
 670
 671     case KeyEvent.VK_U:
 672       if (evt.isControlDown())
 673       {
 674         this.deleteGroups_actionPerformed();
 675       }
 676       break;
 677
 678     case KeyEvent.VK_T:
 679       if (evt.isControlDown())
 680       {
 681         newView(null);
 682       }
 683       break;
 684
 685     }
 686     alignPanel.paintAlignment(true);
 687   }
 688
 689   /**
 690    * called by key handler and the hide all/show all menu items
 691    *
 692    * @param toggleSeqs
 693    * @param toggleCols
 694    */
 695   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 696   {
 697     boolean hide = false;
 698     SequenceGroup sg = viewport.getSelectionGroup();
 699     if (!toggleSeqs && !toggleCols)
 700     {
 701       // Hide everything by the current selection - this is a hack - we do the
 702       // invert and then hide
 703       // first check that there will be visible columns after the invert.
 704       if ((viewport.getColumnSelection() != null
 705               && viewport.getColumnSelection().getSelected() != null && viewport
 706               .getColumnSelection().getSelected().size() > 0)
 707               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 708                       .getEndRes()))
 709       {
 710         // now invert the sequence set, if required - empty selection implies
 711         // that no hiding is required.
 712         if (sg != null)
 713         {
 714           invertSequenceMenuItem_actionPerformed();
 715           sg = viewport.getSelectionGroup();
 716           toggleSeqs = true;
 717
 718         }
 719         viewport.expandColSelection(sg, true);
 720         // finally invert the column selection and get the new sequence
 721         // selection and indicate it should be hidden.
 722         invertColSel_actionPerformed();
 723         toggleCols = true;
 724       }
 725     }
 726
 727     if (toggleSeqs)
 728     {
 729       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 730       {
 731         hide = true;
 732         viewport.hideAllSelectedSeqs();
 733       }
 734       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 735               .size() > 0))
 736       {
 737         viewport.showAllHiddenSeqs();
 738       }
 739     }
 740
 741     if (toggleCols)
 742     {
 743       if (viewport.getColumnSelection().getSelected().size() > 0)
 744       {
 745         viewport.hideSelectedColumns();
 746         if (!toggleSeqs)
 747         {
 748           viewport.setSelectionGroup(sg);
 749         }
 750       }
 751       else if (!hide)
 752       {
 753         viewport.showAllHiddenColumns();
 754       }
 755     }
 756   }
 757
 758   @Override
 759   public void keyReleased(KeyEvent evt)
 760   {
 761   }
 762
 763   @Override
 764   public void keyTyped(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void itemStateChanged(ItemEvent evt)
 770   {
 771     final Object source = evt.getSource();
 772     if (source == displayNonconservedMenuItem)
 773     {
 774       displayNonconservedMenuItem_actionPerformed();
 775     }
 776     else if (source == colourTextMenuItem)
 777     {
 778       colourTextMenuItem_actionPerformed();
 779     }
 780     else if (source == wrapMenuItem)
 781     {
 782       wrapMenuItem_actionPerformed();
 783     }
 784     else if (source == scaleAbove)
 785     {
 786       viewport.setScaleAboveWrapped(scaleAbove.getState());
 787     }
 788     else if (source == scaleLeft)
 789     {
 790       viewport.setScaleLeftWrapped(scaleLeft.getState());
 791     }
 792     else if (source == scaleRight)
 793     {
 794       viewport.setScaleRightWrapped(scaleRight.getState());
 795     }
 796     else if (source == seqLimits)
 797     {
 798       seqLimits_itemStateChanged();
 799     }
 800     else if (source == viewBoxesMenuItem)
 801     {
 802       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 803     }
 804     else if (source == viewTextMenuItem)
 805     {
 806       viewport.setShowText(viewTextMenuItem.getState());
 807     }
 808     else if (source == renderGapsMenuItem)
 809     {
 810       viewport.setRenderGaps(renderGapsMenuItem.getState());
 811     }
 812     else if (source == annotationPanelMenuItem)
 813     {
 814       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 815       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 816     }
 817     else if (source == sequenceFeatures)
 818     {
 819       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 820       alignPanel.seqPanel.seqCanvas.repaint();
 821     }
 822     else if (source == showAlignmentAnnotations)
 823     {
 824       setAnnotationsVisibility();
 825     }
 826     else if (source == showSequenceAnnotations)
 827     {
 828       setAnnotationsVisibility();
 829     }
 830     else if (source == sortAnnBySequence)
 831     {
 832       boolean newState = sortAnnBySequence.getState();
 833       sortAnnByLabel.setState(false);
 834       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 835               : SequenceAnnotationOrder.NONE);
 836       setViewportAnnotationOrder();
 837     }
 838     else if (source == sortAnnByLabel)
 839     {
 840       boolean newState = sortAnnByLabel.getState();
 841       sortAnnBySequence.setState(false);
 842       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 843               : SequenceAnnotationOrder.NONE);
 844       setViewportAnnotationOrder();
 845     }
 846     else if (source == showAutoFirst)
 847     {
 848       showAutoLast.setState(!showAutoFirst.getState());
 849       setShowAutoCalculatedAbove(showAutoFirst.getState());
 850       setViewportAnnotationOrder();
 851     }
 852     else if (source == showAutoLast)
 853     {
 854       showAutoFirst.setState(!showAutoLast.getState());
 855       setShowAutoCalculatedAbove(showAutoFirst.getState());
 856       setViewportAnnotationOrder();
 857     }
 858     else if (source == conservationMenuItem)
 859     {
 860       conservationMenuItem_actionPerformed();
 861     }
 862     else if (source == abovePIDThreshold)
 863     {
 864       abovePIDThreshold_actionPerformed();
 865     }
 866     else if (source == applyToAllGroups)
 867     {
 868       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 869     }
 870     else if (source == autoCalculate)
 871     {
 872       viewport.autoCalculateConsensus = autoCalculate.getState();
 873     }
 874     else if (source == sortByTree)
 875     {
 876       viewport.sortByTree = sortByTree.getState();
 877     }
 878     else if (source == this.centreColumnLabelFlag)
 879     {
 880       centreColumnLabelFlag_stateChanged();
 881     }
 882     else if (source == this.followMouseOverFlag)
 883     {
 884       mouseOverFlag_stateChanged();
 885     }
 886     else if (source == showGroupConsensus)
 887     {
 888       showGroupConsensus_actionPerformed();
 889     }
 890     else if (source == showGroupConservation)
 891     {
 892       showGroupConservation_actionPerformed();
 893     }
 894     else if (source == showSequenceLogo)
 895     {
 896       showSequenceLogo_actionPerformed();
 897     }
 898     else if (source == normSequenceLogo)
 899     {
 900       normSequenceLogo_actionPerformed();
 901     }
 902     else if (source == showConsensusHistogram)
 903     {
 904       showConsensusHistogram_actionPerformed();
 905     }
 906     else if (source == applyAutoAnnotationSettings)
 907     {
 908       applyAutoAnnotationSettings_actionPerformed();
 909     }
 910     alignPanel.paintAlignment(true);
 911   }
 912
 913   /**
 914    * Set the visibility state of sequence-related and/or alignment-related
 915    * annotations depending on checkbox selections. Repaint after calling.
 916    *
 917    * @param visible
 918    */
 919   private void setAnnotationsVisibility()
 920   {
 921     boolean showForAlignment = showAlignmentAnnotations.getState();
 922     boolean showForSequences = showSequenceAnnotations.getState();
 923     for (AlignmentAnnotation aa : alignPanel.getAlignment()
 924             .getAlignmentAnnotation())
 925     {
 926       boolean visible = (aa.sequenceRef == null ? showForAlignment
 927               : showForSequences);
 928         aa.visible = visible;
 929     }
 930     alignPanel.validateAnnotationDimensions(false);
 931   }
 932
 933   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 934   {
 935     this.annotationSortOrder = order;
 936   }
 937
 938   /**
 939    * Set flags on the viewport that control annotation ordering
 940    */
 941   private void setViewportAnnotationOrder()
 942   {
 943     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 944     this.alignPanel.av
 945             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 946   }
 947
 948   private void setShowAutoCalculatedAbove(boolean showAbove)
 949   {
 950     this.showAutoCalculatedAbove = showAbove;
 951   }
 952
 953   private void mouseOverFlag_stateChanged()
 954   {
 955     viewport.setFollowHighlight(followMouseOverFlag.getState());
 956     // TODO: could kick the scrollTo mechanism to reset view for current
 957     // searchresults.
 958   }
 959
 960   private void centreColumnLabelFlag_stateChanged()
 961   {
 962     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 963     this.alignPanel.annotationPanel.repaint();
 964   }
 965
 966   @Override
 967   public void actionPerformed(ActionEvent evt)
 968   {
 969     Object source = evt.getSource();
 970
 971     if (source == inputText)
 972     {
 973       inputText_actionPerformed();
 974     }
 975     else if (source == loadTree)
 976     {
 977       loadTree_actionPerformed();
 978     }
 979     else if (source == loadApplication)
 980     {
 981       launchFullApplication();
 982     }
 983     else if (source == loadAnnotations)
 984     {
 985       loadAnnotations();
 986     }
 987     else if (source == outputAnnotations)
 988     {
 989       outputAnnotations(true);
 990     }
 991     else if (source == outputFeatures)
 992     {
 993       outputFeatures(true, "Jalview");
 994     }
 995     else if (source == closeMenuItem)
 996     {
 997       closeMenuItem_actionPerformed();
 998     }
 999     else if (source == copy)
1000     {
1001       copy_actionPerformed();
1002     }
1003     else if (source == undoMenuItem)
1004     {
1005       undoMenuItem_actionPerformed();
1006     }
1007     else if (source == redoMenuItem)
1008     {
1009       redoMenuItem_actionPerformed();
1010     }
1011     else if (source == inputText)
1012     {
1013       inputText_actionPerformed();
1014     }
1015     else if (source == closeMenuItem)
1016     {
1017       closeMenuItem_actionPerformed();
1018     }
1019     else if (source == undoMenuItem)
1020     {
1021       undoMenuItem_actionPerformed();
1022     }
1023     else if (source == redoMenuItem)
1024     {
1025       redoMenuItem_actionPerformed();
1026     }
1027     else if (source == copy)
1028     {
1029       copy_actionPerformed();
1030     }
1031     else if (source == pasteNew)
1032     {
1033       pasteNew_actionPerformed();
1034     }
1035     else if (source == pasteThis)
1036     {
1037       pasteThis_actionPerformed();
1038     }
1039     else if (source == cut)
1040     {
1041       cut_actionPerformed();
1042     }
1043     else if (source == delete)
1044     {
1045       delete_actionPerformed();
1046     }
1047     else if (source == grpsFromSelection)
1048     {
1049       makeGrpsFromSelection_actionPerformed();
1050     }
1051     else if (source == deleteGroups)
1052     {
1053       deleteGroups_actionPerformed();
1054     }
1055     else if (source == selectAllSequenceMenuItem)
1056     {
1057       selectAllSequenceMenuItem_actionPerformed();
1058     }
1059     else if (source == deselectAllSequenceMenuItem)
1060     {
1061       deselectAllSequenceMenuItem_actionPerformed();
1062     }
1063     else if (source == invertSequenceMenuItem)
1064     {
1065       invertSequenceMenuItem_actionPerformed();
1066     }
1067     else if (source == invertColSel)
1068     {
1069       viewport.invertColumnSelection();
1070       alignPanel.paintAlignment(true);
1071     }
1072     else if (source == remove2LeftMenuItem)
1073     {
1074       trimAlignment(true);
1075     }
1076     else if (source == remove2RightMenuItem)
1077     {
1078       trimAlignment(false);
1079     }
1080     else if (source == removeGappedColumnMenuItem)
1081     {
1082       removeGappedColumnMenuItem_actionPerformed();
1083     }
1084     else if (source == removeAllGapsMenuItem)
1085     {
1086       removeAllGapsMenuItem_actionPerformed();
1087     }
1088     else if (source == findMenuItem)
1089     {
1090       findMenuItem_actionPerformed();
1091     }
1092     else if (source == font)
1093     {
1094       new FontChooser(alignPanel);
1095     }
1096     else if (source == newView)
1097     {
1098       newView(null);
1099     }
1100     else if (source == showColumns)
1101     {
1102       viewport.showAllHiddenColumns();
1103       alignPanel.paintAlignment(true);
1104     }
1105     else if (source == showSeqs)
1106     {
1107       viewport.showAllHiddenSeqs();
1108       alignPanel.paintAlignment(true);
1109     }
1110     else if (source == hideColumns)
1111     {
1112       viewport.hideSelectedColumns();
1113       alignPanel.paintAlignment(true);
1114     }
1115     else if (source == hideSequences
1116             && viewport.getSelectionGroup() != null)
1117     {
1118       viewport.hideAllSelectedSeqs();
1119       alignPanel.paintAlignment(true);
1120     }
1121     else if (source == hideAllButSelection)
1122     {
1123       toggleHiddenRegions(false, false);
1124       alignPanel.paintAlignment(true);
1125     }
1126     else if (source == hideAllSelection)
1127     {
1128       SequenceGroup sg = viewport.getSelectionGroup();
1129       viewport.expandColSelection(sg, false);
1130       viewport.hideAllSelectedSeqs();
1131       viewport.hideSelectedColumns();
1132       alignPanel.paintAlignment(true);
1133     }
1134     else if (source == showAllHidden)
1135     {
1136       viewport.showAllHiddenColumns();
1137       viewport.showAllHiddenSeqs();
1138       alignPanel.paintAlignment(true);
1139     }
1140     else if (source == showGroupConsensus)
1141     {
1142       showGroupConsensus_actionPerformed();
1143     }
1144     else if (source == showGroupConservation)
1145     {
1146       showGroupConservation_actionPerformed();
1147     }
1148     else if (source == showSequenceLogo)
1149     {
1150       showSequenceLogo_actionPerformed();
1151     }
1152     else if (source == normSequenceLogo)
1153     {
1154       normSequenceLogo_actionPerformed();
1155     }
1156     else if (source == showConsensusHistogram)
1157     {
1158       showConsensusHistogram_actionPerformed();
1159     }
1160     else if (source == applyAutoAnnotationSettings)
1161     {
1162       applyAutoAnnotationSettings_actionPerformed();
1163     }
1164     else if (source == featureSettings)
1165     {
1166       new FeatureSettings(alignPanel);
1167     }
1168     else if (source == alProperties)
1169     {
1170       StringBuffer contents = new jalview.io.AlignmentProperties(
1171               viewport.getAlignment()).formatAsString();
1172       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1173       cap.setText(contents.toString());
1174       Frame frame = new Frame();
1175       frame.add(cap);
1176       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1177               "label.alignment_properties", new String[]
1178               { getTitle() }), 400, 250);
1179     }
1180     else if (source == overviewMenuItem)
1181     {
1182       overviewMenuItem_actionPerformed();
1183     }
1184     else if (source == noColourmenuItem)
1185     {
1186       changeColour(null);
1187     }
1188     else if (source == clustalColour)
1189     {
1190       abovePIDThreshold.setState(false);
1191       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1192     }
1193     else if (source == zappoColour)
1194     {
1195       changeColour(new ZappoColourScheme());
1196     }
1197     else if (source == taylorColour)
1198     {
1199       changeColour(new TaylorColourScheme());
1200     }
1201     else if (source == hydrophobicityColour)
1202     {
1203       changeColour(new HydrophobicColourScheme());
1204     }
1205     else if (source == helixColour)
1206     {
1207       changeColour(new HelixColourScheme());
1208     }
1209     else if (source == strandColour)
1210     {
1211       changeColour(new StrandColourScheme());
1212     }
1213     else if (source == turnColour)
1214     {
1215       changeColour(new TurnColourScheme());
1216     }
1217     else if (source == buriedColour)
1218     {
1219       changeColour(new BuriedColourScheme());
1220     }
1221     else if (source == nucleotideColour)
1222     {
1223       changeColour(new NucleotideColourScheme());
1224     }
1225     else if (source == purinePyrimidineColour)
1226     {
1227       changeColour(new PurinePyrimidineColourScheme());
1228     }
1229     else if (source == RNAInteractionColour)
1230     {
1231       changeColour(new RNAInteractionColourScheme());
1232     }
1233     else if (source == RNAHelixColour)
1234     {
1235       new RNAHelicesColourChooser(viewport, alignPanel);
1236     }
1237     else if (source == modifyPID)
1238     {
1239       modifyPID_actionPerformed();
1240     }
1241     else if (source == modifyConservation)
1242     {
1243       modifyConservation_actionPerformed();
1244     }
1245     else if (source == userDefinedColour)
1246     {
1247       new UserDefinedColours(alignPanel, null);
1248     }
1249     else if (source == PIDColour)
1250     {
1251       changeColour(new PIDColourScheme());
1252     }
1253     else if (source == BLOSUM62Colour)
1254     {
1255       changeColour(new Blosum62ColourScheme());
1256     }
1257     else if (source == tcoffeeColour)
1258     {
1259       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1260     }
1261     else if (source == annotationColour)
1262     {
1263       new AnnotationColourChooser(viewport, alignPanel);
1264     }
1265     else if (source == annotationColumnSelection)
1266     {
1267       new AnnotationColumnChooser(viewport, alignPanel);
1268     }
1269     else if (source == sortPairwiseMenuItem)
1270     {
1271       sortPairwiseMenuItem_actionPerformed();
1272     }
1273     else if (source == sortIDMenuItem)
1274     {
1275       sortIDMenuItem_actionPerformed();
1276     }
1277     else if (source == sortLengthMenuItem)
1278     {
1279       sortLengthMenuItem_actionPerformed();
1280     }
1281     else if (source == sortGroupMenuItem)
1282     {
1283       sortGroupMenuItem_actionPerformed();
1284     }
1285     else if (source == removeRedundancyMenuItem)
1286     {
1287       removeRedundancyMenuItem_actionPerformed();
1288     }
1289     else if (source == pairwiseAlignmentMenuItem)
1290     {
1291       pairwiseAlignmentMenuItem_actionPerformed();
1292     }
1293     else if (source == PCAMenuItem)
1294     {
1295       PCAMenuItem_actionPerformed();
1296     }
1297     else if (source == averageDistanceTreeMenuItem)
1298     {
1299       averageDistanceTreeMenuItem_actionPerformed();
1300     }
1301     else if (source == neighbourTreeMenuItem)
1302     {
1303       neighbourTreeMenuItem_actionPerformed();
1304     }
1305     else if (source == njTreeBlosumMenuItem)
1306     {
1307       njTreeBlosumMenuItem_actionPerformed();
1308     }
1309     else if (source == avDistanceTreeBlosumMenuItem)
1310     {
1311       avTreeBlosumMenuItem_actionPerformed();
1312     }
1313     else if (source == documentation)
1314     {
1315       documentation_actionPerformed();
1316     }
1317     else if (source == about)
1318     {
1319       about_actionPerformed();
1320     }
1321
1322   }
1323
1324   public void inputText_actionPerformed()
1325   {
1326     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1327     Frame frame = new Frame();
1328     frame.add(cap);
1329     jalview.bin.JalviewLite.addFrame(frame,
1330             MessageManager.getString("label.input_cut_paste"), 500, 500);
1331   }
1332
1333   protected void outputText_actionPerformed(ActionEvent e)
1334   {
1335     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1336     Frame frame = new Frame();
1337     frame.add(cap);
1338     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1339             "label.alignment_output_command", new Object[]
1340             { e.getActionCommand() }), 600, 500);
1341
1342     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1343     viewport.setFeatureRenderer(fr);
1344     cap.setText(new AppletFormatAdapter(viewport).formatSequences(
1345             e.getActionCommand(), viewport.getAlignment(),
1346             viewport.getShowJVSuffix()));
1347   }
1348
1349   public void loadAnnotations()
1350   {
1351     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352     cap.setText(MessageManager
1353             .getString("label.paste_features_annotations_Tcoffee_here"));
1354     cap.setAnnotationImport();
1355     Frame frame = new Frame();
1356     frame.add(cap);
1357     jalview.bin.JalviewLite.addFrame(frame,
1358             MessageManager.getString("action.paste_annotations"), 400, 300);
1359
1360   }
1361
1362   public String outputAnnotations(boolean displayTextbox)
1363   {
1364     String annotation = new AnnotationFile()
1365             .printAnnotationsForView(viewport);
1366
1367     if (displayTextbox)
1368     {
1369       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1370       Frame frame = new Frame();
1371       frame.add(cap);
1372       jalview.bin.JalviewLite.addFrame(frame,
1373               MessageManager.getString("label.annotations"), 600, 500);
1374       cap.setText(annotation);
1375     }
1376
1377     return annotation;
1378   }
1379
1380   private Map<String,Object> getDisplayedFeatureCols()
1381   {
1382     if (alignPanel.getFeatureRenderer() != null
1383             && viewport.getFeaturesDisplayed()!= null)
1384     {
1385       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1386
1387     }
1388     return null;
1389   }
1390
1391   public String outputFeatures(boolean displayTextbox, String format)
1392   {
1393     String features;
1394     if (format.equalsIgnoreCase("Jalview"))
1395     {
1396       features = new FeaturesFile().printJalviewFormat(viewport
1397               .getAlignment().getSequencesArray(),
1398               getDisplayedFeatureCols());
1399     }
1400     else
1401     {
1402       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1403               .getSequencesArray(), getDisplayedFeatureCols());
1404     }
1405
1406     if (displayTextbox)
1407     {
1408       boolean frimport = false;
1409       if (features == null || features.equals("No Features Visible"))
1410       {
1411         features = "# No features visible - paste some and import them here.";
1412         frimport = true;
1413       }
1414
1415       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1416       if (frimport)
1417       {
1418         cap.setAnnotationImport();
1419       }
1420       Frame frame = new Frame();
1421       frame.add(cap);
1422       jalview.bin.JalviewLite.addFrame(frame,
1423               MessageManager.getString("label.features"), 600, 500);
1424       cap.setText(features);
1425     }
1426     else
1427     {
1428       if (features == null)
1429       {
1430         features = "";
1431       }
1432     }
1433
1434     return features;
1435   }
1436
1437   void launchFullApplication()
1438   {
1439     StringBuffer url = new StringBuffer(jalviewServletURL);
1440
1441     // allow servlet parameters to be passed in applet parameter
1442     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1443             : "?";
1444     url.append(firstSep);
1445
1446     url.append("open="
1447             + appendProtocol(viewport.applet.getParameter("file")));
1448
1449     if (viewport.applet.getParameter("features") != null)
1450     {
1451       url.append("&features=");
1452       url.append(appendProtocol(viewport.applet.getParameter("features")));
1453     }
1454
1455     if (viewport.applet.getParameter("annotations") != null)
1456     {
1457       url.append("&annotations=");
1458       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1459     }
1460
1461     if (viewport.applet.getParameter("jnetfile") != null)
1462     {
1463       url.append("&annotations=");
1464       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1465     }
1466
1467     if (viewport.applet.getParameter("defaultColour") != null)
1468     {
1469       url.append("&colour="
1470               + removeWhiteSpace(viewport.applet
1471                       .getParameter("defaultColour")));
1472     }
1473
1474     if (viewport.applet.getParameter("userDefinedColour") != null)
1475     {
1476       url.append("&colour="
1477               + removeWhiteSpace(viewport.applet
1478                       .getParameter("userDefinedColour")));
1479     }
1480     if (viewport.applet.getParameter("tree") != null)
1481     {
1482       url.append("&tree="
1483               + appendProtocol(viewport.applet.getParameter("tree")));
1484     }
1485     if (viewport.applet.getParameter("treeFile") != null)
1486     {
1487       url.append("&tree="
1488               + appendProtocol(viewport.applet.getParameter("treeFile")));
1489     }
1490
1491     showURL(url.toString(), "FULL_APP");
1492   }
1493
1494   String removeWhiteSpace(String colour)
1495   {
1496     StringBuffer sb = new StringBuffer();
1497     for (int i = 0; i < colour.length(); i++)
1498     {
1499       if (Character.isWhitespace(colour.charAt(i)))
1500       {
1501         sb.append("%20");
1502       }
1503       else
1504       {
1505         sb.append(colour.charAt(i));
1506       }
1507     }
1508
1509     return sb.toString();
1510   }
1511
1512   String appendProtocol(String url)
1513   {
1514     try
1515     {
1516       new URL(url);
1517       url = URLEncoder.encode(url);
1518     }
1519     /*
1520      * When we finally deprecate 1.1 compatibility, we can start to use
1521      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1522      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1523      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1524      * ex.printStackTrace(); }
1525      */
1526     catch (java.net.MalformedURLException ex)
1527     {
1528       url = viewport.applet.getCodeBase() + url;
1529     }
1530     return url;
1531   }
1532
1533   public void closeMenuItem_actionPerformed()
1534   {
1535     PaintRefresher.RemoveComponent(alignPanel);
1536     if (alignPanel.seqPanel != null
1537             && alignPanel.seqPanel.seqCanvas != null)
1538     {
1539       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1540     }
1541     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1542     {
1543       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1544     }
1545
1546     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1547     {
1548       System.exit(0);
1549     }
1550     else
1551     {
1552     }
1553     viewport = null;
1554     alignPanel = null;
1555     this.dispose();
1556   }
1557
1558   /**
1559    * TODO: JAL-1104
1560    */
1561   void updateEditMenuBar()
1562   {
1563
1564     if (viewport.getHistoryList().size() > 0)
1565     {
1566       undoMenuItem.setEnabled(true);
1567       CommandI command = viewport.getHistoryList().peek();
1568       undoMenuItem.setLabel(MessageManager.formatMessage(
1569               "label.undo_command", new Object[]
1570               { command.getDescription() }));
1571     }
1572     else
1573     {
1574       undoMenuItem.setEnabled(false);
1575       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1576     }
1577
1578     if (viewport.getRedoList().size() > 0)
1579     {
1580       redoMenuItem.setEnabled(true);
1581
1582       CommandI command = viewport.getRedoList().peek();
1583       redoMenuItem.setLabel(MessageManager.formatMessage(
1584               "label.redo_command", new Object[]
1585               { command.getDescription() }));
1586     }
1587     else
1588     {
1589       redoMenuItem.setEnabled(false);
1590       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1591     }
1592   }
1593
1594   /**
1595    * TODO: JAL-1104
1596    */
1597   @Override
1598   public void addHistoryItem(CommandI command)
1599   {
1600     if (command.getSize() > 0)
1601     {
1602       viewport.addToHistoryList(command);
1603       viewport.clearRedoList();
1604       updateEditMenuBar();
1605       viewport.updateHiddenColumns();
1606     }
1607   }
1608
1609   /**
1610    * TODO: JAL-1104 DOCUMENT ME!
1611    *
1612    * @param e
1613    *          DOCUMENT ME!
1614    */
1615   protected void undoMenuItem_actionPerformed()
1616   {
1617     if (viewport.getHistoryList().isEmpty())
1618     {
1619       return;
1620     }
1621
1622     CommandI command = viewport.getHistoryList().pop();
1623     viewport.addToRedoList(command);
1624     command.undoCommand(null);
1625
1626     AlignmentViewport originalSource = getOriginatingSource(command);
1627     // JBPNote Test
1628     if (originalSource != viewport)
1629     {
1630       System.err
1631               .println("Warning: Viewport object mismatch whilst undoing");
1632     }
1633     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1634                                           // viewport.getColumnSelection().getHiddenColumns()
1635                                           // != null;
1636     updateEditMenuBar();
1637     originalSource.firePropertyChange("alignment", null, originalSource
1638             .getAlignment().getSequences());
1639   }
1640
1641   /**
1642    * TODO: JAL-1104 DOCUMENT ME!
1643    *
1644    * @param e
1645    *          DOCUMENT ME!
1646    */
1647   protected void redoMenuItem_actionPerformed()
1648   {
1649     if (viewport.getRedoList().isEmpty())
1650     {
1651       return;
1652     }
1653
1654     CommandI command = viewport.getRedoList().pop();
1655     viewport.addToHistoryList(command);
1656     command.doCommand(null);
1657
1658     AlignmentViewport originalSource = getOriginatingSource(command);
1659     // JBPNote Test
1660     if (originalSource != viewport)
1661     {
1662       System.err
1663               .println("Warning: Viewport object mismatch whilst re-doing");
1664     }
1665     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1666                                           // viewport.getColumnSelection().getHiddenColumns()
1667                                           // != null;
1668
1669     updateEditMenuBar();
1670     originalSource.firePropertyChange("alignment", null, originalSource
1671             .getAlignment().getSequences());
1672   }
1673
1674   AlignmentViewport getOriginatingSource(CommandI command)
1675   {
1676     AlignmentViewport originalSource = null;
1677     // For sequence removal and addition, we need to fire
1678     // the property change event FROM the viewport where the
1679     // original alignment was altered
1680     AlignmentI al = null;
1681     if (command instanceof EditCommand)
1682     {
1683       EditCommand editCommand = (EditCommand) command;
1684       al = editCommand.getAlignment();
1685       Vector comps = (Vector) PaintRefresher.components.get(viewport
1686               .getSequenceSetId());
1687       for (int i = 0; i < comps.size(); i++)
1688       {
1689         if (comps.elementAt(i) instanceof AlignmentPanel)
1690         {
1691           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1692           {
1693             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1694             break;
1695           }
1696         }
1697       }
1698     }
1699
1700     if (originalSource == null)
1701     {
1702       // The original view is closed, we must validate
1703       // the current view against the closed view first
1704       if (al != null)
1705       {
1706         PaintRefresher.validateSequences(al, viewport.getAlignment());
1707       }
1708
1709       originalSource = viewport;
1710     }
1711
1712     return originalSource;
1713   }
1714
1715   /**
1716    * Move the currently selected sequences up or down one position in the
1717    * alignment
1718    *
1719    * @param up
1720    */
1721   public void moveSelectedSequences(boolean up)
1722   {
1723     SequenceGroup sg = viewport.getSelectionGroup();
1724     if (sg == null)
1725     {
1726       return;
1727     }
1728     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1729             up ? null : viewport.getHiddenRepSequences(), up);
1730     alignPanel.paintAlignment(true);
1731
1732     /*
1733      * Also move cDNA/protein complement sequences
1734      */
1735     AlignViewportI complement = viewport.getCodingComplement();
1736     if (complement != null)
1737     {
1738       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1739               viewport, complement);
1740       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1741               up ? null : complement.getHiddenRepSequences(), up);
1742       // TODO need to trigger a repaint of the complementary panel - how?
1743       // would prefer to handle in SplitFrame but it is not overriding key
1744       // listener chiz
1745     }
1746   }
1747
1748   synchronized void slideSequences(boolean right, int size)
1749   {
1750     List<SequenceI> sg = new Vector<SequenceI>();
1751     if (viewport.cursorMode)
1752     {
1753       sg.add(viewport.getAlignment().getSequenceAt(
1754               alignPanel.seqPanel.seqCanvas.cursorY));
1755     }
1756     else if (viewport.getSelectionGroup() != null
1757             && viewport.getSelectionGroup().getSize() != viewport
1758                     .getAlignment().getHeight())
1759     {
1760       sg = viewport.getSelectionGroup().getSequences(
1761               viewport.getHiddenRepSequences());
1762     }
1763
1764     if (sg.size() < 1)
1765     {
1766       return;
1767     }
1768
1769     Vector<SequenceI> invertGroup = new Vector();
1770
1771     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1772     {
1773       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1774       {
1775         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1776       }
1777     }
1778
1779     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1780
1781     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1782             .size()]);
1783     for (int i = 0; i < invertGroup.size(); i++)
1784     {
1785       seqs2[i] = invertGroup.elementAt(i);
1786     }
1787
1788     SlideSequencesCommand ssc;
1789     if (right)
1790     {
1791       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1792               size, viewport.getGapCharacter());
1793     }
1794     else
1795     {
1796       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1797               size, viewport.getGapCharacter());
1798     }
1799
1800     int groupAdjustment = 0;
1801     if (ssc.getGapsInsertedBegin() && right)
1802     {
1803       if (viewport.cursorMode)
1804       {
1805         alignPanel.seqPanel.moveCursor(size, 0);
1806       }
1807       else
1808       {
1809         groupAdjustment = size;
1810       }
1811     }
1812     else if (!ssc.getGapsInsertedBegin() && !right)
1813     {
1814       if (viewport.cursorMode)
1815       {
1816         alignPanel.seqPanel.moveCursor(-size, 0);
1817       }
1818       else
1819       {
1820         groupAdjustment = -size;
1821       }
1822     }
1823
1824     if (groupAdjustment != 0)
1825     {
1826       viewport.getSelectionGroup().setStartRes(
1827               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1828       viewport.getSelectionGroup().setEndRes(
1829               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1830     }
1831
1832     boolean appendHistoryItem = false;
1833     Deque<CommandI> historyList = viewport.getHistoryList();
1834     if (historyList != null && historyList.size() > 0
1835             && historyList.peek() instanceof SlideSequencesCommand)
1836     {
1837       appendHistoryItem = ssc
1838               .appendSlideCommand((SlideSequencesCommand) historyList
1839                       .peek());
1840     }
1841
1842     if (!appendHistoryItem)
1843     {
1844       addHistoryItem(ssc);
1845     }
1846
1847     repaint();
1848   }
1849
1850   static StringBuffer copiedSequences;
1851
1852   static Vector copiedHiddenColumns;
1853
1854   protected void copy_actionPerformed()
1855   {
1856     if (viewport.getSelectionGroup() == null)
1857     {
1858       return;
1859     }
1860
1861     SequenceGroup sg = viewport.getSelectionGroup();
1862     copiedSequences = new StringBuffer();
1863     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1864     for (int i = 0; i < sg.getSize(); i++)
1865     {
1866       SequenceI seq = sg.getSequenceAt(i);
1867       int index = viewport.getAlignment().findIndex(seq);
1868       orderedSeqs.put(index, seq);
1869     }
1870
1871     int index = 0, startRes, endRes;
1872     char ch;
1873
1874     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1875     {
1876       copiedHiddenColumns = new Vector();
1877       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1878       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1879       {
1880         copiedHiddenColumns.addElement(new int[]
1881         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1882       }
1883     }
1884     else
1885     {
1886       copiedHiddenColumns = null;
1887     }
1888
1889     for (int i = 0; i < sg.getSize(); i++)
1890     {
1891       SequenceI seq = null;
1892
1893       while (seq == null)
1894       {
1895         if (orderedSeqs.containsKey(index))
1896         {
1897           seq = orderedSeqs.get(index);
1898           index++;
1899           break;
1900         }
1901         else
1902         {
1903           index++;
1904         }
1905       }
1906
1907       // FIND START RES
1908       // Returns residue following index if gap
1909       startRes = seq.findPosition(sg.getStartRes());
1910
1911       // FIND END RES
1912       // Need to find the residue preceeding index if gap
1913       endRes = 0;
1914
1915       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1916       {
1917         ch = seq.getCharAt(j);
1918         if (!jalview.util.Comparison.isGap((ch)))
1919         {
1920           endRes++;
1921         }
1922       }
1923
1924       if (endRes > 0)
1925       {
1926         endRes += seq.getStart() - 1;
1927       }
1928
1929       copiedSequences.append(seq.getName()
1930               + "\t"
1931               + startRes
1932               + "\t"
1933               + endRes
1934               + "\t"
1935               + seq.getSequenceAsString(sg.getStartRes(),
1936                       sg.getEndRes() + 1) + "\n");
1937     }
1938
1939   }
1940
1941   protected void pasteNew_actionPerformed()
1942   {
1943     paste(true);
1944   }
1945
1946   protected void pasteThis_actionPerformed()
1947   {
1948     paste(false);
1949   }
1950
1951   void paste(boolean newAlignment)
1952   {
1953     try
1954     {
1955
1956       if (copiedSequences == null)
1957       {
1958         return;
1959       }
1960
1961       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1962       Vector seqs = new Vector();
1963       while (st.hasMoreElements())
1964       {
1965         String name = st.nextToken();
1966         int start = Integer.parseInt(st.nextToken());
1967         int end = Integer.parseInt(st.nextToken());
1968         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1969       }
1970       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1971       for (int i = 0; i < seqs.size(); i++)
1972       {
1973         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1974       }
1975
1976       if (newAlignment)
1977       {
1978         String newtitle = MessageManager.getString("label.copied_sequences");
1979         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1980         {
1981           newtitle = getTitle();
1982         }
1983         else
1984         {
1985           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1986         }
1987         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1988                 viewport.applet, newtitle, false);
1989         if (copiedHiddenColumns != null)
1990         {
1991           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1992           {
1993             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1994             af.viewport.hideColumns(region[0], region[1]);
1995           }
1996         }
1997
1998         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
1999                 frameHeight);
2000       }
2001       else
2002       {
2003         addSequences(newSeqs);
2004       }
2005
2006     } catch (Exception ex)
2007     {
2008     } // could be anything being pasted in here
2009
2010   }
2011
2012   void addSequences(SequenceI[] seqs)
2013   {
2014     for (int i = 0; i < seqs.length; i++)
2015     {
2016       viewport.getAlignment().addSequence(seqs[i]);
2017     }
2018
2019     // !newAlignment
2020     addHistoryItem(new EditCommand(
2021             MessageManager.getString("label.add_sequences"), Action.PASTE,
2022             seqs, 0, viewport.getAlignment().getWidth(),
2023             viewport.getAlignment()));
2024
2025     viewport.setEndSeq(viewport.getAlignment().getHeight());
2026     viewport.getAlignment().getWidth();
2027     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2028             .getSequences());
2029
2030   }
2031
2032   protected void cut_actionPerformed()
2033   {
2034     copy_actionPerformed();
2035     delete_actionPerformed();
2036   }
2037
2038   protected void delete_actionPerformed()
2039   {
2040
2041     SequenceGroup sg = viewport.getSelectionGroup();
2042     if (sg == null)
2043     {
2044       return;
2045     }
2046
2047     Vector seqs = new Vector();
2048     SequenceI seq;
2049     for (int i = 0; i < sg.getSize(); i++)
2050     {
2051       seq = sg.getSequenceAt(i);
2052       seqs.addElement(seq);
2053     }
2054
2055     // If the cut affects all sequences, remove highlighted columns
2056     if (sg.getSize() == viewport.getAlignment().getHeight())
2057     {
2058       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2059               sg.getEndRes() + 1);
2060     }
2061
2062     SequenceI[] cut = new SequenceI[seqs.size()];
2063     for (int i = 0; i < seqs.size(); i++)
2064     {
2065       cut[i] = (SequenceI) seqs.elementAt(i);
2066     }
2067
2068     /*
2069      * //ADD HISTORY ITEM
2070      */
2071     addHistoryItem(new EditCommand(
2072             MessageManager.getString("label.cut_sequences"), Action.CUT,
2073             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2074             viewport.getAlignment()));
2075
2076     viewport.setSelectionGroup(null);
2077     viewport.getAlignment().deleteGroup(sg);
2078
2079     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2080             .getSequences());
2081
2082     if (viewport.getAlignment().getHeight() < 1)
2083     {
2084       this.setVisible(false);
2085     }
2086     viewport.sendSelection();
2087   }
2088
2089   /**
2090    * group consensus toggled
2091    *
2092    */
2093   protected void showGroupConsensus_actionPerformed()
2094   {
2095     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2096     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2097
2098   }
2099
2100   /**
2101    * group conservation toggled.
2102    */
2103   protected void showGroupConservation_actionPerformed()
2104   {
2105     viewport.setShowGroupConservation(showGroupConservation.getState());
2106     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2107   }
2108
2109   /*
2110    * (non-Javadoc)
2111    *
2112    * @see
2113    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2114    * .event.ActionEvent)
2115    */
2116   protected void showConsensusHistogram_actionPerformed()
2117   {
2118     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2119     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2120   }
2121
2122   /*
2123    * (non-Javadoc)
2124    *
2125    * @see
2126    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2127    * .event.ActionEvent)
2128    */
2129   protected void showSequenceLogo_actionPerformed()
2130   {
2131     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2132     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2133   }
2134
2135   protected void normSequenceLogo_actionPerformed()
2136   {
2137     showSequenceLogo.setState(true);
2138     viewport.setShowSequenceLogo(true);
2139     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2140     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2141   }
2142
2143   protected void applyAutoAnnotationSettings_actionPerformed()
2144   {
2145     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2146   }
2147
2148   protected void makeGrpsFromSelection_actionPerformed()
2149   {
2150     if (avc.makeGroupsFromSelection())
2151     {
2152       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2153       alignPanel.updateAnnotation();
2154       alignPanel.paintAlignment(true);
2155     }
2156   }
2157
2158   protected void createGroup_actionPerformed()
2159   {
2160     avc.createGroup();
2161   }
2162
2163   protected void unGroup_actionPerformed()
2164   {
2165     if (avc.unGroup())
2166     {
2167       alignPanel.alignmentChanged();
2168     }
2169   }
2170
2171   protected void deleteGroups_actionPerformed()
2172   {
2173     if (avc.deleteGroups())
2174     {
2175       alignPanel.alignmentChanged();
2176     }
2177   }
2178
2179   public void selectAllSequenceMenuItem_actionPerformed()
2180   {
2181     SequenceGroup sg = new SequenceGroup();
2182     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2183     {
2184       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2185     }
2186     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2187     viewport.setSelectionGroup(sg);
2188     alignPanel.paintAlignment(true);
2189     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2190     viewport.sendSelection();
2191   }
2192
2193   public void deselectAllSequenceMenuItem_actionPerformed()
2194   {
2195     if (viewport.cursorMode)
2196     {
2197       alignPanel.seqPanel.keyboardNo1 = null;
2198       alignPanel.seqPanel.keyboardNo2 = null;
2199     }
2200     viewport.setSelectionGroup(null);
2201     viewport.getColumnSelection().clear();
2202     viewport.setSelectionGroup(null);
2203     alignPanel.idPanel.idCanvas.searchResults = null;
2204     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2205     alignPanel.paintAlignment(true);
2206     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2207     viewport.sendSelection();
2208   }
2209
2210   public void invertSequenceMenuItem_actionPerformed()
2211   {
2212     SequenceGroup sg = viewport.getSelectionGroup();
2213     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2214     {
2215       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2216     }
2217
2218     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2219     viewport.sendSelection();
2220   }
2221
2222   public void invertColSel_actionPerformed()
2223   {
2224     viewport.invertColumnSelection();
2225     alignPanel.paintAlignment(true);
2226     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2227     viewport.sendSelection();
2228   }
2229
2230   void trimAlignment(boolean trimLeft)
2231   {
2232     ColumnSelection colSel = viewport.getColumnSelection();
2233     int column;
2234
2235     if (colSel.size() > 0)
2236     {
2237       if (trimLeft)
2238       {
2239         column = colSel.getMin();
2240       }
2241       else
2242       {
2243         column = colSel.getMax();
2244       }
2245
2246       SequenceI[] seqs;
2247       if (viewport.getSelectionGroup() != null)
2248       {
2249         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2250                 viewport.getHiddenRepSequences());
2251       }
2252       else
2253       {
2254         seqs = viewport.getAlignment().getSequencesArray();
2255       }
2256
2257       TrimRegionCommand trimRegion;
2258       if (trimLeft)
2259       {
2260         trimRegion = new TrimRegionCommand("Remove Left",
2261                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2262                 viewport.getAlignment(), viewport.getColumnSelection(),
2263                 viewport.getSelectionGroup());
2264         viewport.setStartRes(0);
2265       }
2266       else
2267       {
2268         trimRegion = new TrimRegionCommand("Remove Right",
2269                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2270                 viewport.getAlignment(), viewport.getColumnSelection(),
2271                 viewport.getSelectionGroup());
2272       }
2273
2274       statusBar.setText(MessageManager.formatMessage(
2275               "label.removed_columns", new String[]
2276               { Integer.valueOf(trimRegion.getSize()).toString() }));
2277       addHistoryItem(trimRegion);
2278
2279       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2280       {
2281         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2282                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2283         {
2284           viewport.getAlignment().deleteGroup(sg);
2285         }
2286       }
2287
2288       viewport.firePropertyChange("alignment", null, viewport
2289               .getAlignment().getSequences());
2290     }
2291   }
2292
2293   public void removeGappedColumnMenuItem_actionPerformed()
2294   {
2295     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2296
2297     SequenceI[] seqs;
2298     if (viewport.getSelectionGroup() != null)
2299     {
2300       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2301               viewport.getHiddenRepSequences());
2302       start = viewport.getSelectionGroup().getStartRes();
2303       end = viewport.getSelectionGroup().getEndRes();
2304     }
2305     else
2306     {
2307       seqs = viewport.getAlignment().getSequencesArray();
2308     }
2309
2310     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2311             "Remove Gapped Columns", seqs, start, end,
2312             viewport.getAlignment());
2313
2314     addHistoryItem(removeGapCols);
2315
2316     statusBar.setText(MessageManager.formatMessage(
2317             "label.removed_empty_columns", new String[]
2318             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2319
2320     // This is to maintain viewport position on first residue
2321     // of first sequence
2322     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2323     int startRes = seq.findPosition(viewport.startRes);
2324     // ShiftList shifts;
2325     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2326     // edit.alColumnChanges=shifts.getInverse();
2327     // if (viewport.hasHiddenColumns)
2328     // viewport.getColumnSelection().compensateForEdits(shifts);
2329     viewport.setStartRes(seq.findIndex(startRes) - 1);
2330     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2331             .getSequences());
2332
2333   }
2334
2335   public void removeAllGapsMenuItem_actionPerformed()
2336   {
2337     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2338
2339     SequenceI[] seqs;
2340     if (viewport.getSelectionGroup() != null)
2341     {
2342       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2343               viewport.getHiddenRepSequences());
2344       start = viewport.getSelectionGroup().getStartRes();
2345       end = viewport.getSelectionGroup().getEndRes();
2346     }
2347     else
2348     {
2349       seqs = viewport.getAlignment().getSequencesArray();
2350     }
2351
2352     // This is to maintain viewport position on first residue
2353     // of first sequence
2354     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2355     int startRes = seq.findPosition(viewport.startRes);
2356
2357     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2358             viewport.getAlignment()));
2359
2360     viewport.setStartRes(seq.findIndex(startRes) - 1);
2361
2362     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2363             .getSequences());
2364
2365   }
2366
2367   public void findMenuItem_actionPerformed()
2368   {
2369     new Finder(alignPanel);
2370   }
2371
2372   /**
2373    * create a new view derived from the current view
2374    *
2375    * @param viewtitle
2376    * @return frame for the new view
2377    */
2378   public AlignFrame newView(String viewtitle)
2379   {
2380     AlignmentI newal;
2381     if (viewport.hasHiddenRows())
2382     {
2383       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2384               .getFullAlignment().getSequencesArray());
2385     }
2386     else
2387     {
2388       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2389     }
2390
2391     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2392     {
2393       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2394       {
2395         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2396         {
2397           newal.addAnnotation(viewport.getAlignment()
2398                   .getAlignmentAnnotation()[i]);
2399         }
2400       }
2401     }
2402
2403     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2404
2405     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2406     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2407     PaintRefresher.Register(newaf.alignPanel,
2408             newaf.alignPanel.av.getSequenceSetId());
2409
2410     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2411             newaf.alignPanel.av.getSequenceSetId());
2412     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2413             newaf.alignPanel.av.getSequenceSetId());
2414
2415     Vector comps = (Vector) PaintRefresher.components.get(viewport
2416             .getSequenceSetId());
2417     int viewSize = -1;
2418     for (int i = 0; i < comps.size(); i++)
2419     {
2420       if (comps.elementAt(i) instanceof AlignmentPanel)
2421       {
2422         viewSize++;
2423       }
2424     }
2425
2426     String title = new String(this.getTitle());
2427     if (viewtitle != null)
2428     {
2429       title = viewtitle + " ( " + title + ")";
2430     }
2431     else
2432     {
2433       if (title.indexOf("(View") > -1)
2434       {
2435         title = title.substring(0, title.indexOf("(View"));
2436       }
2437       title += "(View " + viewSize + ")";
2438     }
2439
2440     newaf.setTitle(title.toString());
2441
2442     newaf.viewport.setHistoryList(viewport.getHistoryList());
2443     newaf.viewport.setRedoList(viewport.getRedoList());
2444     return newaf;
2445   }
2446
2447   /**
2448    *
2449    * @return list of feature groups on the view
2450    */
2451   public String[] getFeatureGroups()
2452   {
2453     FeatureRenderer fr = null;
2454     if (alignPanel != null
2455             && (fr = alignPanel.getFeatureRenderer()) != null)
2456     {
2457       List<String> gps = fr.getFeatureGroups();
2458       String[] _gps = gps.toArray(new String[gps.size()]);
2459       return _gps;
2460     }
2461     return null;
2462   }
2463
2464   /**
2465    * get sequence feature groups that are hidden or shown
2466    *
2467    * @param visible
2468    *          true is visible
2469    * @return list
2470    */
2471   public String[] getFeatureGroupsOfState(boolean visible)
2472   {
2473     FeatureRenderer fr = null;
2474     if (alignPanel != null
2475             && (fr = alignPanel.getFeatureRenderer()) != null)
2476     {
2477       List<String> gps = fr.getGroups(visible);
2478       String[] _gps = gps.toArray(new String[gps.size()]);
2479       return _gps;
2480     }
2481     return null;
2482   }
2483
2484   /**
2485    * Change the display state for the given feature groups
2486    *
2487    * @param groups
2488    *          list of group strings
2489    * @param state
2490    *          visible or invisible
2491    */
2492   public void setFeatureGroupState(String[] groups, boolean state)
2493   {
2494     FeatureRenderer fr = null;
2495     this.sequenceFeatures.setState(true);
2496     viewport.setShowSequenceFeatures(true);
2497     if (alignPanel != null
2498             && (fr = alignPanel.getFeatureRenderer()) != null)
2499     {
2500
2501       fr.setGroupVisibility(Arrays.asList(groups), state);
2502       alignPanel.seqPanel.seqCanvas.repaint();
2503       if (alignPanel.overviewPanel != null)
2504       {
2505         alignPanel.overviewPanel.updateOverviewImage();
2506       }
2507     }
2508   }
2509
2510   public void seqLimits_itemStateChanged()
2511   {
2512     viewport.setShowJVSuffix(seqLimits.getState());
2513     alignPanel.fontChanged();
2514     alignPanel.paintAlignment(true);
2515   }
2516
2517   protected void colourTextMenuItem_actionPerformed()
2518   {
2519     viewport.setColourText(colourTextMenuItem.getState());
2520     alignPanel.paintAlignment(true);
2521   }
2522
2523   protected void displayNonconservedMenuItem_actionPerformed()
2524   {
2525     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2526     alignPanel.paintAlignment(true);
2527   }
2528
2529   protected void wrapMenuItem_actionPerformed()
2530   {
2531     viewport.setWrapAlignment(wrapMenuItem.getState());
2532     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2533     scaleAbove.setEnabled(wrapMenuItem.getState());
2534     scaleLeft.setEnabled(wrapMenuItem.getState());
2535     scaleRight.setEnabled(wrapMenuItem.getState());
2536     alignPanel.paintAlignment(true);
2537   }
2538
2539   public void overviewMenuItem_actionPerformed()
2540   {
2541     if (alignPanel.overviewPanel != null)
2542     {
2543       return;
2544     }
2545
2546     Frame frame = new Frame();
2547     OverviewPanel overview = new OverviewPanel(alignPanel);
2548     frame.add(overview);
2549     // +50 must allow for applet frame window
2550     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2551             "label.overview_params", new String[]
2552             { this.getTitle() }), overview.getPreferredSize().width,
2553             overview.getPreferredSize().height + 50);
2554
2555     frame.pack();
2556     final AlignmentPanel ap = alignPanel;
2557     frame.addWindowListener(new WindowAdapter()
2558     {
2559       @Override
2560       public void windowClosing(WindowEvent e)
2561       {
2562         if (ap != null)
2563         {
2564           ap.setOverviewPanel(null);
2565         }
2566       };
2567     });
2568
2569     alignPanel.setOverviewPanel(overview);
2570
2571   }
2572
2573   public void changeColour(ColourSchemeI cs)
2574   {
2575     int threshold = 0;
2576
2577     if (cs != null)
2578     {
2579       if (viewport.getAbovePIDThreshold())
2580       {
2581         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2582                 cs, "Background"));
2583       }
2584
2585       if (viewport.getConservationSelected())
2586       {
2587         cs.setConservationApplied(true);
2588         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2589                 cs, "Background"));
2590       }
2591       else
2592       {
2593         cs.setConservationApplied(false);
2594       }
2595     }
2596     viewport.setGlobalColourScheme(cs);
2597
2598     if (alignPanel.getOverviewPanel() != null)
2599     {
2600       alignPanel.getOverviewPanel().updateOverviewImage();
2601     }
2602
2603     jalview.structure.StructureSelectionManager
2604             .getStructureSelectionManager(viewport.applet)
2605             .sequenceColoursChanged(alignPanel);
2606
2607     alignPanel.paintAlignment(true);
2608   }
2609
2610   protected void modifyPID_actionPerformed()
2611   {
2612     if (viewport.getAbovePIDThreshold()
2613             && viewport.getGlobalColourScheme() != null)
2614     {
2615       SliderPanel.setPIDSliderSource(alignPanel,
2616               viewport.getGlobalColourScheme(), "Background");
2617       SliderPanel.showPIDSlider();
2618     }
2619   }
2620
2621   protected void modifyConservation_actionPerformed()
2622   {
2623     if (viewport.getConservationSelected()
2624             && viewport.getGlobalColourScheme() != null)
2625     {
2626       SliderPanel.setConservationSlider(alignPanel,
2627               viewport.getGlobalColourScheme(), "Background");
2628       SliderPanel.showConservationSlider();
2629     }
2630   }
2631
2632   protected void conservationMenuItem_actionPerformed()
2633   {
2634     viewport.setConservationSelected(conservationMenuItem.getState());
2635
2636     viewport.setAbovePIDThreshold(false);
2637     abovePIDThreshold.setState(false);
2638
2639     changeColour(viewport.getGlobalColourScheme());
2640
2641     modifyConservation_actionPerformed();
2642   }
2643
2644   public void abovePIDThreshold_actionPerformed()
2645   {
2646     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2647
2648     conservationMenuItem.setState(false);
2649     viewport.setConservationSelected(false);
2650
2651     changeColour(viewport.getGlobalColourScheme());
2652
2653     modifyPID_actionPerformed();
2654   }
2655
2656   public void sortPairwiseMenuItem_actionPerformed()
2657   {
2658     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2659     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2660             .getAlignment().getSequenceAt(0), null);
2661
2662     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2663             viewport.getAlignment()));
2664     alignPanel.paintAlignment(true);
2665   }
2666
2667   public void sortIDMenuItem_actionPerformed()
2668   {
2669     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2670     AlignmentSorter.sortByID(viewport.getAlignment());
2671     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2672             viewport.getAlignment()));
2673     alignPanel.paintAlignment(true);
2674   }
2675
2676   public void sortLengthMenuItem_actionPerformed()
2677   {
2678     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2679     AlignmentSorter.sortByLength(viewport.getAlignment());
2680     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2681             viewport.getAlignment()));
2682     alignPanel.paintAlignment(true);
2683   }
2684
2685   public void sortGroupMenuItem_actionPerformed()
2686   {
2687     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2688     AlignmentSorter.sortByGroup(viewport.getAlignment());
2689     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2690             viewport.getAlignment()));
2691     alignPanel.paintAlignment(true);
2692
2693   }
2694
2695   public void removeRedundancyMenuItem_actionPerformed()
2696   {
2697     new RedundancyPanel(alignPanel);
2698   }
2699
2700   public void pairwiseAlignmentMenuItem_actionPerformed()
2701   {
2702     if (viewport.getSelectionGroup() != null
2703             && viewport.getSelectionGroup().getSize() > 1)
2704     {
2705       Frame frame = new Frame();
2706       frame.add(new PairwiseAlignPanel(alignPanel));
2707       jalview.bin.JalviewLite.addFrame(frame,
2708               MessageManager.getString("action.pairwise_alignment"), 600,
2709               500);
2710     }
2711   }
2712
2713   public void PCAMenuItem_actionPerformed()
2714   {
2715     // are the sequences aligned?
2716     if (!viewport.getAlignment().isAligned(false))
2717     {
2718       SequenceI current;
2719       int Width = viewport.getAlignment().getWidth();
2720
2721       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2722       {
2723         current = viewport.getAlignment().getSequenceAt(i);
2724
2725         if (current.getLength() < Width)
2726         {
2727           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2728         }
2729       }
2730       alignPanel.paintAlignment(true);
2731     }
2732
2733     if ((viewport.getSelectionGroup() != null
2734             && viewport.getSelectionGroup().getSize() < 4 && viewport
2735             .getSelectionGroup().getSize() > 0)
2736             || viewport.getAlignment().getHeight() < 4)
2737     {
2738       return;
2739     }
2740
2741     try
2742     {
2743       new PCAPanel(viewport);
2744     } catch (java.lang.OutOfMemoryError ex)
2745     {
2746     }
2747
2748   }
2749
2750   public void averageDistanceTreeMenuItem_actionPerformed()
2751   {
2752     NewTreePanel("AV", "PID", "Average distance tree using PID");
2753   }
2754
2755   public void neighbourTreeMenuItem_actionPerformed()
2756   {
2757     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2758   }
2759
2760   protected void njTreeBlosumMenuItem_actionPerformed()
2761   {
2762     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2763   }
2764
2765   protected void avTreeBlosumMenuItem_actionPerformed()
2766   {
2767     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2768   }
2769
2770   void NewTreePanel(String type, String pwType, String title)
2771   {
2772     // are the sequences aligned?
2773     if (!viewport.getAlignment().isAligned(false))
2774     {
2775       SequenceI current;
2776       int Width = viewport.getAlignment().getWidth();
2777
2778       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2779       {
2780         current = viewport.getAlignment().getSequenceAt(i);
2781
2782         if (current.getLength() < Width)
2783         {
2784           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2785         }
2786       }
2787       alignPanel.paintAlignment(true);
2788
2789     }
2790
2791     if ((viewport.getSelectionGroup() != null && viewport
2792             .getSelectionGroup().getSize() > 1)
2793             || (viewport.getAlignment().getHeight() > 1))
2794     {
2795       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2796
2797       addTreeMenuItem(tp, title);
2798
2799       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2800     }
2801   }
2802
2803   void loadTree_actionPerformed()
2804   {
2805     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2806     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2807     cap.setTreeImport();
2808     Frame frame = new Frame();
2809     frame.add(cap);
2810     jalview.bin.JalviewLite.addFrame(frame,
2811             MessageManager.getString("label.paste_newick_file"), 400, 300);
2812   }
2813
2814   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2815   {
2816     TreePanel tp = new TreePanel(alignPanel, treeFile,
2817             MessageManager.getString("label.load_tree_from_file"), tree);
2818     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2819     addTreeMenuItem(tp, treeFile);
2820   }
2821
2822   /**
2823    * sort the alignment using the given treePanel
2824    *
2825    * @param treePanel
2826    *          tree used to sort view
2827    * @param title
2828    *          string used for undo event name
2829    */
2830   public void sortByTree(TreePanel treePanel, String title)
2831   {
2832     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2833     AlignmentSorter
2834             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2835     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2836     // HistoryItem.SORT));
2837     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2838             "label.order_by_params", new String[]
2839             { title }), oldOrder, viewport.getAlignment()));
2840     alignPanel.paintAlignment(true);
2841   }
2842
2843   /**
2844    * Do any automatic reordering of the alignment and add the necessary bits to
2845    * the menu structure for the new tree
2846    *
2847    * @param treePanel
2848    * @param title
2849    */
2850   protected void addTreeMenuItem(final TreePanel treePanel,
2851           final String title)
2852   {
2853     final MenuItem item = new MenuItem(title);
2854     sortByTreeMenu.add(item);
2855     item.addActionListener(new java.awt.event.ActionListener()
2856     {
2857       @Override
2858       public void actionPerformed(ActionEvent evt)
2859       {
2860         sortByTree(treePanel, title); // treePanel.getTitle());
2861       }
2862     });
2863
2864     treePanel.addWindowListener(new WindowAdapter()
2865     {
2866       @Override
2867       public void windowOpened(WindowEvent e)
2868       {
2869         if (viewport.sortByTree)
2870         {
2871           sortByTree(treePanel, title);
2872         }
2873         super.windowOpened(e);
2874       }
2875
2876       @Override
2877       public void windowClosing(WindowEvent e)
2878       {
2879         sortByTreeMenu.remove(item);
2880       };
2881     });
2882   }
2883
2884   public boolean sortBy(AlignmentOrder alorder, String undoname)
2885   {
2886     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2887     if (viewport.applet.debug)
2888     {
2889       System.err.println("Sorting " + alorder.getOrder().size()
2890               + " in alignment '" + getTitle() + "'");
2891     }
2892     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2893     if (undoname != null)
2894     {
2895       addHistoryItem(new OrderCommand(undoname, oldOrder,
2896               viewport.getAlignment()));
2897     }
2898     alignPanel.paintAlignment(true);
2899     return true;
2900   }
2901
2902   protected void documentation_actionPerformed()
2903   {
2904     alignPanel.av.applet.openJalviewHelpUrl();
2905   }
2906
2907   protected void about_actionPerformed()
2908   {
2909
2910     class AboutPanel extends Canvas
2911     {
2912       String version;
2913
2914       String builddate;
2915
2916       public AboutPanel(String version, String builddate)
2917       {
2918         this.version = version;
2919         this.builddate = builddate;
2920       }
2921
2922       @Override
2923       public void paint(Graphics g)
2924       {
2925         g.setColor(Color.white);
2926         g.fillRect(0, 0, getSize().width, getSize().height);
2927         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2928         FontMetrics fm = g.getFontMetrics();
2929         int fh = fm.getHeight();
2930         int y = 5, x = 7;
2931         g.setColor(Color.black);
2932         // TODO: update this text for each release or centrally store it for
2933         // lite and application
2934         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2935         g.drawString(MessageManager.formatMessage(
2936                 "label.jalviewLite_release", new String[]
2937                 { version }), x, y += fh);
2938         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2939         g.drawString(MessageManager.formatMessage(
2940                 "label.jaview_build_date", new String[]
2941                 { builddate }), x, y += fh);
2942         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2943         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2944                 x, y += fh * 1.5);
2945         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2946                 x + 50, y += fh + 8);
2947         g.drawString(
2948                 MessageManager.getString("label.jalview_dev_managers"), x,
2949                 y += fh);
2950         g.drawString(MessageManager
2951                 .getString("label.jalview_distribution_lists"), x, y += fh);
2952         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2953                 x, y += fh + 8);
2954         g.drawString(
2955                 MessageManager.getString("label.jalview_cite_1_authors"),
2956                 x, y += fh);
2957         g.drawString(
2958                 MessageManager.getString("label.jalview_cite_1_title"), x,
2959                 y += fh);
2960         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2961                 x, y += fh);
2962       }
2963     }
2964
2965     Frame frame = new Frame();
2966     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2967             .getBuildDate()));
2968     jalview.bin.JalviewLite.addFrame(frame,
2969             MessageManager.getString("label.jalview"), 580, 220);
2970
2971   }
2972
2973   public void showURL(String url, String target)
2974   {
2975     if (viewport.applet == null)
2976     {
2977       System.out.println("Not running as applet - no browser available.");
2978     }
2979     else
2980     {
2981       viewport.applet.showURL(url, target);
2982     }
2983   }
2984
2985   // ////////////////////////////////////////////////////////////////////////////////
2986   // JBuilder Graphics here
2987
2988   MenuBar alignFrameMenuBar = new MenuBar();
2989
2990   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2991
2992   MenuItem loadApplication = new MenuItem(
2993           MessageManager.getString("label.view_full_application"));
2994
2995   MenuItem loadTree = new MenuItem(
2996           MessageManager.getString("label.load_associated_tree"));
2997
2998   MenuItem loadAnnotations = new MenuItem(
2999           MessageManager.getString("label.load_features_annotations"));
3000
3001   MenuItem outputFeatures = new MenuItem(
3002           MessageManager.getString("label.export_features").concat("..."));
3003
3004   MenuItem outputAnnotations = new MenuItem(
3005           MessageManager.getString("label.export_annotations").concat("..."));
3006
3007   MenuItem closeMenuItem = new MenuItem(
3008           MessageManager.getString("action.close"));
3009
3010   MenuItem selectAllSequenceMenuItem = new MenuItem(
3011           MessageManager.getString("action.select_all"));
3012
3013   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3014           MessageManager.getString("action.deselect_all"));
3015
3016   MenuItem invertSequenceMenuItem = new MenuItem(
3017           MessageManager.getString("action.invert_selection"));
3018
3019   MenuItem remove2LeftMenuItem = new MenuItem();
3020
3021   MenuItem remove2RightMenuItem = new MenuItem();
3022
3023   MenuItem removeGappedColumnMenuItem = new MenuItem();
3024
3025   MenuItem removeAllGapsMenuItem = new MenuItem();
3026
3027   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3028
3029   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3030
3031   MenuItem sortPairwiseMenuItem = new MenuItem();
3032
3033   MenuItem sortIDMenuItem = new MenuItem();
3034
3035   MenuItem sortLengthMenuItem = new MenuItem();
3036
3037   MenuItem sortGroupMenuItem = new MenuItem();
3038
3039   MenuItem removeRedundancyMenuItem = new MenuItem();
3040
3041   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3042
3043   MenuItem PCAMenuItem = new MenuItem();
3044
3045   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3046
3047   MenuItem neighbourTreeMenuItem = new MenuItem();
3048
3049   BorderLayout borderLayout1 = new BorderLayout();
3050
3051   public Label statusBar = new Label();
3052
3053   MenuItem clustalColour = new MenuItem();
3054
3055   MenuItem zappoColour = new MenuItem();
3056
3057   MenuItem taylorColour = new MenuItem();
3058
3059   MenuItem hydrophobicityColour = new MenuItem();
3060
3061   MenuItem helixColour = new MenuItem();
3062
3063   MenuItem strandColour = new MenuItem();
3064
3065   MenuItem turnColour = new MenuItem();
3066
3067   MenuItem buriedColour = new MenuItem();
3068
3069   MenuItem purinePyrimidineColour = new MenuItem();
3070
3071   MenuItem RNAInteractionColour = new MenuItem();
3072
3073   MenuItem RNAHelixColour = new MenuItem();
3074
3075   MenuItem userDefinedColour = new MenuItem();
3076
3077   MenuItem PIDColour = new MenuItem();
3078
3079   MenuItem BLOSUM62Colour = new MenuItem();
3080
3081   MenuItem tcoffeeColour = new MenuItem();
3082
3083   MenuItem njTreeBlosumMenuItem = new MenuItem();
3084
3085   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3086
3087   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3088
3089   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3090
3091   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3092
3093   MenuItem alProperties = new MenuItem(
3094           MessageManager.getString("label.alignment_props"));
3095
3096   MenuItem overviewMenuItem = new MenuItem();
3097
3098   MenuItem undoMenuItem = new MenuItem();
3099
3100   MenuItem redoMenuItem = new MenuItem();
3101
3102   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3103
3104   MenuItem noColourmenuItem = new MenuItem();
3105
3106   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3107
3108   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3109
3110   MenuItem findMenuItem = new MenuItem();
3111
3112   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3113
3114   MenuItem nucleotideColour = new MenuItem();
3115
3116   MenuItem deleteGroups = new MenuItem();
3117
3118   MenuItem grpsFromSelection = new MenuItem();
3119
3120   MenuItem createGroup = new MenuItem();
3121
3122   MenuItem unGroup = new MenuItem();
3123
3124   MenuItem delete = new MenuItem();
3125
3126   MenuItem copy = new MenuItem();
3127
3128   MenuItem cut = new MenuItem();
3129
3130   Menu pasteMenu = new Menu();
3131
3132   MenuItem pasteNew = new MenuItem();
3133
3134   MenuItem pasteThis = new MenuItem();
3135
3136   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3137
3138   MenuItem font = new MenuItem();
3139
3140   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3141
3142   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3143
3144   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3145
3146   MenuItem modifyPID = new MenuItem();
3147
3148   MenuItem modifyConservation = new MenuItem();
3149
3150   CheckboxMenuItem autoCalculate = null;
3151
3152   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3153           "Sort Alignment With New Tree", true);
3154
3155   Menu sortByTreeMenu = new Menu();
3156
3157   MenuItem inputText = new MenuItem();
3158
3159   MenuItem documentation = new MenuItem();
3160
3161   MenuItem about = new MenuItem();
3162
3163   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3164
3165   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3166
3167   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3168
3169   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3170
3171   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3174
3175   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3176
3177   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3178
3179   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3180
3181   /**
3182    * Initialise menus and other items
3183    *
3184    * @throws Exception
3185    */
3186   private void jbInit() throws Exception
3187   {
3188     setMenuBar(alignFrameMenuBar);
3189
3190     /*
3191      * Configure File menu items and actions
3192      */
3193     inputText
3194             .setLabel(MessageManager.getString("label.input_from_textbox"));
3195     inputText.addActionListener(this);
3196     Menu outputTextboxMenu = new Menu(
3197             MessageManager.getString("label.out_to_textbox"));
3198     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3199     {
3200
3201       MenuItem item = new MenuItem(
3202               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3203
3204       item.addActionListener(new java.awt.event.ActionListener()
3205       {
3206         @Override
3207         public void actionPerformed(ActionEvent e)
3208         {
3209           outputText_actionPerformed(e);
3210         }
3211       });
3212
3213       outputTextboxMenu.add(item);
3214     }
3215     closeMenuItem.addActionListener(this);
3216     loadApplication.addActionListener(this);
3217     loadTree.addActionListener(this);
3218     loadAnnotations.addActionListener(this);
3219     outputFeatures.addActionListener(this);
3220     outputAnnotations.addActionListener(this);
3221
3222     /*
3223      * Configure Edit menu items and actions
3224      */
3225     undoMenuItem.setEnabled(false);
3226     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3227     undoMenuItem.addActionListener(this);
3228     redoMenuItem.setEnabled(false);
3229     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3230     redoMenuItem.addActionListener(this);
3231     copy.setLabel(MessageManager.getString("action.copy"));
3232     copy.addActionListener(this);
3233     cut.setLabel(MessageManager.getString("action.cut"));
3234     cut.addActionListener(this);
3235     delete.setLabel(MessageManager.getString("action.delete"));
3236     delete.addActionListener(this);
3237     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3238     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3239     pasteNew.addActionListener(this);
3240     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3241     pasteThis.addActionListener(this);
3242     remove2LeftMenuItem.setLabel(MessageManager
3243             .getString("action.remove_left"));
3244     remove2LeftMenuItem.addActionListener(this);
3245     remove2RightMenuItem.setLabel(MessageManager
3246             .getString("action.remove_right"));
3247     remove2RightMenuItem.addActionListener(this);
3248     removeGappedColumnMenuItem.setLabel(MessageManager
3249             .getString("action.remove_empty_columns"));
3250     removeGappedColumnMenuItem.addActionListener(this);
3251     removeAllGapsMenuItem.setLabel(MessageManager
3252             .getString("action.remove_all_gaps"));
3253     removeAllGapsMenuItem.addActionListener(this);
3254     removeRedundancyMenuItem.setLabel(MessageManager.getString(
3255             "action.remove_redundancy").concat("..."));
3256     removeRedundancyMenuItem.addActionListener(this);
3257
3258     /*
3259      * Configure Select menu items and actions
3260      */
3261     findMenuItem.setLabel(MessageManager.getString("action.find"));
3262     findMenuItem.addActionListener(this);
3263     selectAllSequenceMenuItem.addActionListener(this);
3264     deselectAllSequenceMenuItem.addActionListener(this);
3265     invertSequenceMenuItem.setLabel(MessageManager
3266             .getString("action.invert_sequence_selection"));
3267     invertSequenceMenuItem.addActionListener(this);
3268     invertColSel.setLabel(MessageManager
3269             .getString("action.invert_column_selection"));
3270     invertColSel.addActionListener(this);
3271     deleteGroups.setLabel(MessageManager
3272             .getString("action.undefine_groups"));
3273     deleteGroups.addActionListener(this);
3274     grpsFromSelection.setLabel(MessageManager
3275             .getString("action.make_groups_selection"));
3276     grpsFromSelection.addActionListener(this);
3277     createGroup.setLabel(MessageManager.getString("action.create_group"));
3278     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3279     annotationColumnSelection.setLabel("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("label.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(),
3807               frameWidth,
3808               frameHeight);
3809     }
3810   }
3811
3812   /**
3813    * Add the components of this AlignFrame to the applet container.
3814    *
3815    * @param theApplet
3816    */
3817   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3818   {
3819     // ////
3820     // Explicitly build the embedded menu panel for the on-page applet
3821     //
3822     // view cannot be closed if its actually on the page
3823     fileMenu.remove(closeMenuItem);
3824     fileMenu.remove(3); // Remove Separator
3825     // construct embedded menu, using default font
3826     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3827     // and actually add the components to the applet area
3828     theApplet.setLayout(new BorderLayout());
3829     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3830     theApplet.add(statusBar, BorderLayout.SOUTH);
3831     // TODO should size be left to the layout manager?
3832     alignPanel.setSize(theApplet.getSize().width,
3833             theApplet.getSize().height - embeddedMenu.getHeight()
3834                     - statusBar.getHeight());
3835     theApplet.add(alignPanel, BorderLayout.CENTER);
3836     final AlignFrame me = this;
3837     theApplet.addFocusListener(new FocusListener()
3838     {
3839
3840       @Override
3841       public void focusLost(FocusEvent e)
3842       {
3843         if (theApplet.currentAlignFrame == me)
3844         {
3845           theApplet.currentAlignFrame = null;
3846         }
3847       }
3848
3849       @Override
3850       public void focusGained(FocusEvent e)
3851       {
3852         theApplet.currentAlignFrame = me;
3853       }
3854     });
3855     theApplet.validate();
3856   }
3857
3858   /**
3859    * create a new binding between structures in an existing jmol viewer instance
3860    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3861    * this does not open a new Jmol window, or modify the display of the
3862    * structures in the original jmol window. Note This method doesn't work
3863    * without an additional javascript library to exchange messages between the
3864    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3865    *
3866    * @param viewer
3867    *          JmolViewer instance
3868    * @param sequenceIds
3869    *          - sequence Ids to search for associations
3870    */
3871   public SequenceStructureBinding addStructureViewInstance(
3872           Object jmolviewer, String[] sequenceIds)
3873   {
3874     org.jmol.api.JmolViewer viewer = null;
3875     try
3876     {
3877       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3878     } catch (ClassCastException ex)
3879     {
3880       System.err.println("Unsupported viewer object :"
3881               + jmolviewer.getClass());
3882     }
3883     if (viewer == null)
3884     {
3885       System.err.println("Can't use this object as a structure viewer:"
3886               + jmolviewer.getClass());
3887       return null;
3888     }
3889     SequenceI[] seqs = null;
3890     if (sequenceIds == null || sequenceIds.length == 0)
3891     {
3892       seqs = viewport.getAlignment().getSequencesArray();
3893     }
3894     else
3895     {
3896       Vector sqi = new Vector();
3897       AlignmentI al = viewport.getAlignment();
3898       for (int sid = 0; sid < sequenceIds.length; sid++)
3899       {
3900         SequenceI sq = al.findName(sequenceIds[sid]);
3901         if (sq != null)
3902         {
3903           sqi.addElement(sq);
3904         }
3905       }
3906       if (sqi.size() > 0)
3907       {
3908         seqs = new SequenceI[sqi.size()];
3909         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3910         {
3911           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3912         }
3913       }
3914       else
3915       {
3916         return null;
3917       }
3918     }
3919     AAStructureBindingModel jmv = null;
3920     // TODO: search for a jmv that involves viewer
3921     if (jmv == null)
3922     { // create a new viewer/jalview binding.
3923       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3924       { seqs });
3925     }
3926     return jmv;
3927
3928   }
3929
3930   /**
3931    * bind a pdb file to a sequence in the current view
3932    *
3933    * @param sequenceId
3934    *          - sequenceId within the dataset.
3935    * @param pdbEntryString
3936    *          - the short name for the PDB file
3937    * @param pdbFile
3938    *          - pdb file - either a URL or a valid PDB file.
3939    * @return true if binding was as success TODO: consider making an exception
3940    *         structure for indicating when PDB parsing or sequenceId location
3941    *         fails.
3942    */
3943   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3944           String pdbFile)
3945   {
3946     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3947     boolean needtoadd = false;
3948     if (toaddpdb != null)
3949     {
3950       Vector pdbe = toaddpdb.getPDBId();
3951       PDBEntry pdbentry = null;
3952       if (pdbe != null && pdbe.size() > 0)
3953       {
3954         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3955         {
3956           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3957           if (!pdbentry.getId().equals(pdbEntryString)
3958                   && !pdbentry.getFile().equals(pdbFile))
3959           {
3960             pdbentry = null;
3961           }
3962           else
3963           {
3964             continue;
3965           }
3966         }
3967       }
3968       if (pdbentry == null)
3969       {
3970         pdbentry = new PDBEntry();
3971         pdbentry.setId(pdbEntryString);
3972         pdbentry.setFile(pdbFile);
3973         needtoadd = true; // add this new entry to sequence.
3974       }
3975       // resolve data source
3976       // TODO: this code should be a refactored to an io package
3977       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3978       if (protocol == null)
3979       {
3980         return false;
3981       }
3982       if (needtoadd)
3983       {
3984         // make a note of the access mode and add
3985         if (pdbentry.getProperty() == null)
3986         {
3987           pdbentry.setProperty(new Hashtable());
3988         }
3989         pdbentry.getProperty().put("protocol", protocol);
3990         toaddpdb.addPDBId(pdbentry);
3991         alignPanel.getStructureSelectionManager()
3992                 .registerPDBEntry(pdbentry);
3993       }
3994     }
3995     return true;
3996   }
3997
3998   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3999   {
4000     if (seqs != null)
4001     {
4002       Vector sequences = new Vector();
4003       for (int i = 0; i < seqs.length; i++)
4004       {
4005         if (seqs[i] != null)
4006         {
4007           sequences.addElement(new Object[]
4008           { seqs[i], (chains != null) ? chains[i] : null });
4009         }
4010       }
4011       seqs = new SequenceI[sequences.size()];
4012       chains = new String[sequences.size()];
4013       for (int i = 0, isize = sequences.size(); i < isize; i++)
4014       {
4015         Object[] oj = (Object[]) sequences.elementAt(i);
4016
4017         seqs[i] = (SequenceI) oj[0];
4018         chains[i] = (String) oj[1];
4019       }
4020     }
4021     return new Object[]
4022     { seqs, chains };
4023
4024   }
4025
4026   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4027           SequenceI[] seqs, String[] chains, String protocol)
4028   {
4029     // Scrub any null sequences from the array
4030     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4031     seqs = (SequenceI[]) sqch[0];
4032     chains = (String[]) sqch[1];
4033     if (seqs == null || seqs.length == 0)
4034     {
4035       System.err
4036               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4037     }
4038     if (protocol == null || protocol.trim().length() == 0
4039             || protocol.equals("null"))
4040     {
4041       protocol = (String) pdb.getProperty().get("protocol");
4042       if (protocol == null)
4043       {
4044         System.err.println("Couldn't work out protocol to open structure: "
4045                 + pdb.getId());
4046         return;
4047       }
4048     }
4049     if (applet.useXtrnalSviewer)
4050     {
4051       // register the association(s) and quit, don't create any windows.
4052       if (StructureSelectionManager.getStructureSelectionManager(applet)
4053               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4054       {
4055         System.err.println("Failed to map " + pdb.getFile() + " ("
4056                 + protocol + ") to any sequences");
4057       }
4058       return;
4059     }
4060     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4061     {
4062       // can only do alignments with Jmol
4063       // find the last jmol window assigned to this alignment
4064       jalview.appletgui.AppletJmol ajm = null, tajm;
4065       Vector jmols = applet
4066               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4067       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4068       {
4069         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4070         if (tajm.ap.alignFrame == this)
4071         {
4072           ajm = tajm;
4073           break;
4074         }
4075       }
4076       if (ajm != null)
4077       {
4078         System.err
4079                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4080         // try and add the pdb structure
4081         // ajm.addS
4082         ajm = null;
4083       }
4084     }
4085     // otherwise, create a new window
4086     if (applet.jmolAvailable)
4087     {
4088       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4089               protocol);
4090       applet.lastFrameX += 40;
4091       applet.lastFrameY += 40;
4092     }
4093     else
4094     {
4095       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4096     }
4097
4098   }
4099
4100   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4101           SequenceI[][] seqs, String[][] chains, String[] protocols)
4102   {
4103     // TODO Auto-generated method stub
4104     System.err.println("Aligned Structure View: Not yet implemented.");
4105   }
4106
4107   /**
4108    * modify the current selection, providing the user has not made a selection
4109    * already.
4110    *
4111    * @param sel
4112    *          - sequences from this alignment
4113    * @param csel
4114    *          - columns to be selected on the alignment
4115    */
4116   public void select(SequenceGroup sel, ColumnSelection csel)
4117   {
4118     alignPanel.seqPanel.selection(sel, csel, null);
4119   }
4120
4121   public void scrollTo(int row, int column)
4122   {
4123     alignPanel.seqPanel.scrollTo(row, column);
4124   }
4125
4126   public void scrollToRow(int row)
4127   {
4128     alignPanel.seqPanel.scrollToRow(row);
4129   }
4130
4131   public void scrollToColumn(int column)
4132   {
4133     alignPanel.seqPanel.scrollToColumn(column);
4134   }
4135
4136   /**
4137    * @return the alignments unique ID.
4138    */
4139   public String getSequenceSetId()
4140   {
4141     return viewport.getSequenceSetId();
4142   }
4143
4144   /**
4145    * Load the (T-Coffee) score file from the specified url
4146    *
4147    * @param source
4148    *          File/URL/T-COFFEE score file contents
4149    * @throws IOException
4150    * @return true if alignment was annotated with data from source
4151    */
4152   public boolean loadScoreFile(String source) throws IOException
4153   {
4154
4155     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4156             AppletFormatAdapter.checkProtocol(source));
4157     if (!file.isValid())
4158     {
4159       // TODO: raise dialog for gui
4160       System.err.println("Problems parsing T-Coffee scores: "
4161               + file.getWarningMessage());
4162       System.err.println("Origin was:\n" + source);
4163       return false;
4164     }
4165
4166     /*
4167      * check that the score matrix matches the alignment dimensions
4168      */
4169     AlignmentI aln;
4170     if ((aln = viewport.getAlignment()) != null
4171             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4172                     .getWidth()))
4173     {
4174       // TODO: raise a dialog box here rather than bomb out.
4175       System.err
4176               .println("The scores matrix does not match the alignment dimensions");
4177
4178     }
4179
4180     // TODO add parameter to indicate if matching should be done
4181     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4182     {
4183       alignPanel.fontChanged();
4184       tcoffeeColour.setEnabled(true);
4185       // switch to this color
4186       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4187       return true;
4188     }
4189     else
4190     {
4191       System.err.println("Problems resolving T-Coffee scores:");
4192       if (file.getWarningMessage() != null)
4193       {
4194         System.err.println(file.getWarningMessage());
4195       }
4196     }
4197     return false;
4198   }
4199
4200   public SplitFrame getSplitFrame()
4201   {
4202     return this.splitFrame;
4203   }
4204
4205   public void setSplitFrame(SplitFrame sf)
4206   {
4207     this.splitFrame = sf;
4208   }
4209 }