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