src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsControllerI;
  30 import jalview.api.SequenceStructureBinding;
  31 import jalview.bin.JalviewLite;
  32 import jalview.commands.CommandI;
  33 import jalview.commands.EditCommand;
  34 import jalview.commands.EditCommand.Action;
  35 import jalview.commands.OrderCommand;
  36 import jalview.commands.RemoveGapColCommand;
  37 import jalview.commands.RemoveGapsCommand;
  38 import jalview.commands.SlideSequencesCommand;
  39 import jalview.commands.TrimRegionCommand;
  40 import jalview.datamodel.Alignment;
  41 import jalview.datamodel.AlignmentAnnotation;
  42 import jalview.datamodel.AlignmentI;
  43 import jalview.datamodel.AlignmentOrder;
  44 import jalview.datamodel.ColumnSelection;
  45 import jalview.datamodel.PDBEntry;
  46 import jalview.datamodel.Sequence;
  47 import jalview.datamodel.SequenceGroup;
  48 import jalview.datamodel.SequenceI;
  49 import jalview.io.AnnotationFile;
  50 import jalview.io.AppletFormatAdapter;
  51 import jalview.io.FeaturesFile;
  52 import jalview.io.TCoffeeScoreFile;
  53 import jalview.schemes.Blosum62ColourScheme;
  54 import jalview.schemes.BuriedColourScheme;
  55 import jalview.schemes.ClustalxColourScheme;
  56 import jalview.schemes.ColourSchemeI;
  57 import jalview.schemes.HelixColourScheme;
  58 import jalview.schemes.HydrophobicColourScheme;
  59 import jalview.schemes.NucleotideColourScheme;
  60 import jalview.schemes.PIDColourScheme;
  61 import jalview.schemes.PurinePyrimidineColourScheme;
  62 import jalview.schemes.RNAHelicesColourChooser;
  63 import jalview.schemes.StrandColourScheme;
  64 import jalview.schemes.TCoffeeColourScheme;
  65 import jalview.schemes.TaylorColourScheme;
  66 import jalview.schemes.TurnColourScheme;
  67 import jalview.schemes.ZappoColourScheme;
  68 import jalview.structure.StructureSelectionManager;
  69 import jalview.structures.models.AAStructureBindingModel;
  70 import jalview.util.MappingUtils;
  71 import jalview.util.MessageManager;
  72 import jalview.viewmodel.AlignmentViewport;
  73
  74 import java.awt.BorderLayout;
  75 import java.awt.Canvas;
  76 import java.awt.CheckboxMenuItem;
  77 import java.awt.Color;
  78 import java.awt.Font;
  79 import java.awt.FontMetrics;
  80 import java.awt.Frame;
  81 import java.awt.Graphics;
  82 import java.awt.Label;
  83 import java.awt.Menu;
  84 import java.awt.MenuBar;
  85 import java.awt.MenuItem;
  86 import java.awt.event.ActionEvent;
  87 import java.awt.event.ActionListener;
  88 import java.awt.event.FocusEvent;
  89 import java.awt.event.FocusListener;
  90 import java.awt.event.ItemEvent;
  91 import java.awt.event.ItemListener;
  92 import java.awt.event.KeyEvent;
  93 import java.awt.event.KeyListener;
  94 import java.awt.event.WindowAdapter;
  95 import java.awt.event.WindowEvent;
  96 import java.io.IOException;
  97 import java.net.URL;
  98 import java.net.URLEncoder;
  99 import java.util.Arrays;
 100 import java.util.Deque;
 101 import java.util.HashMap;
 102 import java.util.Hashtable;
 103 import java.util.List;
 104 import java.util.Map;
 105 import java.util.StringTokenizer;
 106 import java.util.Vector;
 107
 108 import org.jmol.viewer.Viewer;
 109
 110 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 111         ItemListener, KeyListener, AlignViewControllerGuiI
 112 {
 113   public AlignViewControllerI avc;
 114
 115   public AlignmentPanel alignPanel;
 116
 117   public AlignViewport viewport;
 118
 119   // width and height may be overridden by applet parameters
 120   int frameWidth = 700;
 121
 122   int frameHeight = 500;
 123
 124   String jalviewServletURL;
 125
 126   /*
 127    * Flag for showing autocalculated consensus above or below other consensus
 128    * rows
 129    */
 130   private boolean showAutoCalculatedAbove;
 131
 132   private SequenceAnnotationOrder annotationSortOrder;
 133
 134   /**
 135    * Constructor that creates the frame and adds it to the display.
 136    *
 137    * @param al
 138    * @param applet
 139    * @param title
 140    * @param embedded
 141    */
 142   public AlignFrame(AlignmentI al, JalviewLite applet,
 143           String title, boolean embedded)
 144   {
 145     this(al, applet, title, embedded, true);
 146   }
 147
 148   /**
 149    * Constructor that optionally allows the frame to be displayed or only
 150    * created.
 151    *
 152    * @param al
 153    * @param applet
 154    * @param title
 155    * @param embedded
 156    * @param addToDisplay
 157    */
 158   public AlignFrame(AlignmentI al, JalviewLite applet,
 159           String title, boolean embedded, boolean addToDisplay)
 160   {
 161     this(al, null, null, applet, title, embedded, addToDisplay);
 162   }
 163
 164   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 165           ColumnSelection columnSelection, JalviewLite applet,
 166           String title, boolean embedded)
 167   {
 168     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 169   }
 170
 171   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 172           ColumnSelection columnSelection, JalviewLite applet,
 173           String title, boolean embedded, boolean addToDisplay)
 174   {
 175     if (applet != null)
 176     {
 177       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 178     }
 179
 180     try
 181     {
 182       jbInit();
 183     } catch (Exception ex)
 184     {
 185       ex.printStackTrace();
 186     }
 187     // need to get window geometry before we calculate alignment layout
 188     if (applet != null)
 189     {
 190       String param;
 191       try
 192       {
 193         param = applet.getParameter("windowWidth");
 194         if (param != null)
 195         {
 196           int width = Integer.parseInt(param);
 197           frameWidth = width;
 198         }
 199         param = applet.getParameter("windowHeight");
 200         if (param != null)
 201         {
 202           int height = Integer.parseInt(param);
 203           frameHeight = height;
 204         }
 205       } catch (Exception ex)
 206       {
 207       }
 208     }
 209     viewport = new AlignViewport(al, applet);
 210
 211     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 212     {
 213       viewport.hideSequence(hiddenSeqs);
 214     }
 215     if (columnSelection != null)
 216     {
 217       viewport.setColumnSelection(columnSelection);
 218     }
 219
 220     alignPanel = new AlignmentPanel(this, viewport);
 221     avc = new jalview.controller.AlignViewController(this, viewport,
 222             alignPanel);
 223     viewport.updateConservation(alignPanel);
 224     viewport.updateConsensus(alignPanel);
 225
 226     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 227     followMouseOverFlag.setState(viewport.isFollowHighlight());
 228     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 229     showGroupConservation.setState(viewport.isShowGroupConservation());
 230     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 231     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 232     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 233     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 234     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 235     showAlignmentAnnotations.setState(viewport.isShowAnnotation());
 236     showSequenceAnnotations.setState(viewport.isShowAnnotation());
 237
 238     seqLimits.setState(viewport.getShowJVSuffix());
 239
 240     if (applet != null)
 241     {
 242       String param = applet.getParameter("sortBy");
 243       if (param != null)
 244       {
 245         if (param.equalsIgnoreCase("Id"))
 246         {
 247           sortIDMenuItem_actionPerformed();
 248         }
 249         else if (param.equalsIgnoreCase("Pairwise Identity"))
 250         {
 251           sortPairwiseMenuItem_actionPerformed();
 252         }
 253         else if (param.equalsIgnoreCase("Length"))
 254         {
 255           sortLengthMenuItem_actionPerformed();
 256         }
 257       }
 258
 259       param = applet.getParameter("wrap");
 260       if (param != null)
 261       {
 262         if (param.equalsIgnoreCase("true"))
 263         {
 264           wrapMenuItem.setState(true);
 265           wrapMenuItem_actionPerformed();
 266         }
 267       }
 268       param = applet.getParameter("centrecolumnlabels");
 269       if (param != null)
 270       {
 271         centreColumnLabelFlag.setState(true);
 272         centreColumnLabelFlag_stateChanged();
 273       }
 274
 275     }
 276     if (viewport.getAlignment().isNucleotide())
 277     {
 278       viewport.updateStrucConsensus(alignPanel);
 279       if (viewport.getAlignment().hasRNAStructure())
 280       {
 281         RNAHelixColour.setEnabled(true);
 282       }
 283       else
 284       {
 285         RNAHelixColour.setEnabled(false);
 286       }
 287     }
 288     else
 289     {
 290       RNAHelixColour.setEnabled(false);
 291       purinePyrimidineColour.setEnabled(false);
 292     }
 293     // Some JVMS send keyevents to Top frame or lowest panel,
 294     // Havent worked out why yet. So add to both this frame and seqCanvas for
 295     // now
 296     this.addKeyListener(this);
 297     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 298     alignPanel.idPanel.idCanvas.addKeyListener(this);
 299     alignPanel.scalePanel.addKeyListener(this);
 300     alignPanel.annotationPanel.addKeyListener(this);
 301     alignPanel.annotationPanelHolder.addKeyListener(this);
 302     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 303     alignPanel.alabels.addKeyListener(this);
 304
 305     if (addToDisplay)
 306     {
 307       addToDisplay(embedded);
 308     }
 309   }
 310
 311   /**
 312    * @param embedded
 313    */
 314   public void addToDisplay(boolean embedded)
 315   {
 316     createAlignFrameWindow(embedded);
 317     validate();
 318     alignPanel.adjustAnnotationHeight();
 319     alignPanel.paintAlignment(true);
 320   }
 321
 322   public AlignViewport getAlignViewport()
 323   {
 324     return viewport;
 325   }
 326
 327   public SeqCanvas getSeqcanvas()
 328   {
 329     return alignPanel.seqPanel.seqCanvas;
 330   }
 331
 332   /**
 333    * Load a features file onto the alignment
 334    *
 335    * @param file
 336    *          file URL, content, or other resolvable path
 337    * @param type
 338    *          is protocol for accessing data referred to by file
 339    */
 340
 341   public boolean parseFeaturesFile(String file, String type)
 342   {
 343     return parseFeaturesFile(file, type, true);
 344   }
 345
 346   /**
 347    * Load a features file onto the alignment
 348    *
 349    * @param file
 350    *          file URL, content, or other resolvable path
 351    * @param type
 352    *          is protocol for accessing data referred to by file
 353    * @param autoenabledisplay
 354    *          when true, display features flag will be automatically enabled if
 355    *          features are loaded
 356    * @return true if data parsed as a features file
 357    */
 358   public boolean parseFeaturesFile(String file, String type,
 359           boolean autoenabledisplay)
 360   {
 361     // TODO: test if importing a features file onto an alignment which already
 362     // has features with links overwrites the original links.
 363
 364     Hashtable featureLinks = new Hashtable();
 365     boolean featuresFile = false;
 366     try
 367     {
 368       featuresFile = new jalview.io.FeaturesFile(file, type)
 369               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 370                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 371                       true, viewport.applet.getDefaultParameter(
 372                               "relaxedidmatch", false));
 373     } catch (Exception ex)
 374     {
 375       ex.printStackTrace();
 376     }
 377
 378     if (featuresFile)
 379     {
 380       if (featureLinks.size() > 0)
 381       {
 382         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 383       }
 384       if (autoenabledisplay)
 385       {
 386         viewport.setShowSequenceFeatures(true);
 387         sequenceFeatures.setState(true);
 388       }
 389       if (alignPanel.seqPanel.seqCanvas.fr != null)
 390       {
 391         // update the min/max ranges where necessary
 392         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 393       }
 394       if (viewport.featureSettings != null)
 395       {
 396         viewport.featureSettings.refreshTable();
 397       }
 398       alignPanel.paintAlignment(true);
 399       statusBar.setText(MessageManager
 400               .getString("label.successfully_added_features_alignment"));
 401     }
 402     return featuresFile;
 403   }
 404
 405   @Override
 406   public void keyPressed(KeyEvent evt)
 407   {
 408     if (viewport.cursorMode
 409             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 410                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 411                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 412             && Character.isDigit(evt.getKeyChar()))
 413     {
 414       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 415     }
 416
 417     switch (evt.getKeyCode())
 418     {
 419     case 27: // escape key
 420       deselectAllSequenceMenuItem_actionPerformed();
 421
 422       alignPanel.alabels.cancelDrag();
 423       break;
 424     case KeyEvent.VK_X:
 425       if (evt.isControlDown() || evt.isMetaDown())
 426       {
 427         cut_actionPerformed();
 428       }
 429       break;
 430     case KeyEvent.VK_C:
 431       if (viewport.cursorMode && !evt.isControlDown())
 432       {
 433         alignPanel.seqPanel.setCursorColumn();
 434       }
 435       if (evt.isControlDown() || evt.isMetaDown())
 436       {
 437         copy_actionPerformed();
 438       }
 439       break;
 440     case KeyEvent.VK_V:
 441       if (evt.isControlDown())
 442       {
 443         paste(evt.isShiftDown());
 444       }
 445       break;
 446     case KeyEvent.VK_A:
 447       if (evt.isControlDown() || evt.isMetaDown())
 448       {
 449         selectAllSequenceMenuItem_actionPerformed();
 450       }
 451       break;
 452     case KeyEvent.VK_DOWN:
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.moveCursor(0, 1);
 456       }
 457       else
 458       {
 459         moveSelectedSequences(false);
 460       }
 461       break;
 462
 463     case KeyEvent.VK_UP:
 464       if (viewport.cursorMode)
 465       {
 466         alignPanel.seqPanel.moveCursor(0, -1);
 467       }
 468       else
 469       {
 470         moveSelectedSequences(true);
 471       }
 472       break;
 473
 474     case KeyEvent.VK_LEFT:
 475       if (evt.isAltDown() || !viewport.cursorMode)
 476       {
 477         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 478       }
 479       else
 480       {
 481         alignPanel.seqPanel.moveCursor(-1, 0);
 482       }
 483       break;
 484
 485     case KeyEvent.VK_RIGHT:
 486       if (evt.isAltDown() || !viewport.cursorMode)
 487       {
 488         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 489       }
 490       else
 491       {
 492         alignPanel.seqPanel.moveCursor(1, 0);
 493       }
 494       break;
 495
 496     case KeyEvent.VK_SPACE:
 497       if (viewport.cursorMode)
 498       {
 499         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 500                 || evt.isShiftDown() || evt.isAltDown());
 501       }
 502       break;
 503
 504     case KeyEvent.VK_DELETE:
 505     case KeyEvent.VK_BACK_SPACE:
 506       if (viewport.cursorMode)
 507       {
 508         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 509                 || evt.isShiftDown() || evt.isAltDown());
 510       }
 511       else
 512       {
 513         cut_actionPerformed();
 514         alignPanel.seqPanel.seqCanvas.repaint();
 515       }
 516       break;
 517
 518     case KeyEvent.VK_S:
 519       if (viewport.cursorMode)
 520       {
 521         alignPanel.seqPanel.setCursorRow();
 522       }
 523       break;
 524     case KeyEvent.VK_P:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorPosition();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_ENTER:
 532     case KeyEvent.VK_COMMA:
 533       if (viewport.cursorMode)
 534       {
 535         alignPanel.seqPanel.setCursorRowAndColumn();
 536       }
 537       break;
 538
 539     case KeyEvent.VK_Q:
 540       if (viewport.cursorMode)
 541       {
 542         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 543       }
 544       break;
 545     case KeyEvent.VK_M:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_F2:
 553       viewport.cursorMode = !viewport.cursorMode;
 554       statusBar.setText(MessageManager.formatMessage(
 555               "label.keyboard_editing_mode", new String[]
 556               { (viewport.cursorMode ? "on" : "off") }));
 557       if (viewport.cursorMode)
 558       {
 559         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 560         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 561       }
 562       break;
 563
 564     case KeyEvent.VK_F:
 565       if (evt.isControlDown())
 566       {
 567         findMenuItem_actionPerformed();
 568       }
 569       break;
 570
 571     case KeyEvent.VK_H:
 572     {
 573       boolean toggleSeqs = !evt.isControlDown();
 574       boolean toggleCols = !evt.isShiftDown();
 575       toggleHiddenRegions(toggleSeqs, toggleCols);
 576       break;
 577     }
 578
 579     case KeyEvent.VK_PAGE_UP:
 580       if (viewport.getWrapAlignment())
 581       {
 582         alignPanel.scrollUp(true);
 583       }
 584       else
 585       {
 586         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 587                 - viewport.endSeq + viewport.startSeq);
 588       }
 589       break;
 590
 591     case KeyEvent.VK_PAGE_DOWN:
 592       if (viewport.getWrapAlignment())
 593       {
 594         alignPanel.scrollUp(false);
 595       }
 596       else
 597       {
 598         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 599                 + viewport.endSeq - viewport.startSeq);
 600       }
 601       break;
 602
 603     case KeyEvent.VK_Z:
 604       if (evt.isControlDown())
 605       {
 606         undoMenuItem_actionPerformed();
 607       }
 608       break;
 609
 610     case KeyEvent.VK_Y:
 611       if (evt.isControlDown())
 612       {
 613         redoMenuItem_actionPerformed();
 614       }
 615       break;
 616
 617     case KeyEvent.VK_L:
 618       if (evt.isControlDown())
 619       {
 620         trimAlignment(true);
 621       }
 622       break;
 623
 624     case KeyEvent.VK_R:
 625       if (evt.isControlDown())
 626       {
 627         trimAlignment(false);
 628       }
 629       break;
 630
 631     case KeyEvent.VK_E:
 632       if (evt.isControlDown())
 633       {
 634         if (evt.isShiftDown())
 635         {
 636           this.removeAllGapsMenuItem_actionPerformed();
 637         }
 638         else
 639         {
 640           removeGappedColumnMenuItem_actionPerformed();
 641         }
 642       }
 643       break;
 644     case KeyEvent.VK_I:
 645       if (evt.isControlDown())
 646       {
 647         if (evt.isAltDown())
 648         {
 649           invertColSel_actionPerformed();
 650         }
 651         else
 652         {
 653           invertSequenceMenuItem_actionPerformed();
 654         }
 655       }
 656       break;
 657
 658     case KeyEvent.VK_G:
 659       if (evt.isControlDown())
 660       {
 661         if (evt.isShiftDown())
 662         {
 663           this.unGroup_actionPerformed();
 664         }
 665         else
 666         {
 667           this.createGroup_actionPerformed();
 668         }
 669       }
 670       break;
 671
 672     case KeyEvent.VK_U:
 673       if (evt.isControlDown())
 674       {
 675         this.deleteGroups_actionPerformed();
 676       }
 677       break;
 678
 679     case KeyEvent.VK_T:
 680       if (evt.isControlDown())
 681       {
 682         newView(null);
 683       }
 684       break;
 685
 686     }
 687     alignPanel.paintAlignment(true);
 688   }
 689
 690   /**
 691    * called by key handler and the hide all/show all menu items
 692    *
 693    * @param toggleSeqs
 694    * @param toggleCols
 695    */
 696   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 697   {
 698     boolean hide = false;
 699     SequenceGroup sg = viewport.getSelectionGroup();
 700     if (!toggleSeqs && !toggleCols)
 701     {
 702       // Hide everything by the current selection - this is a hack - we do the
 703       // invert and then hide
 704       // first check that there will be visible columns after the invert.
 705       if ((viewport.getColumnSelection() != null
 706               && viewport.getColumnSelection().getSelected() != null && viewport
 707               .getColumnSelection().getSelected().size() > 0)
 708               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 709                       .getEndRes()))
 710       {
 711         // now invert the sequence set, if required - empty selection implies
 712         // that no hiding is required.
 713         if (sg != null)
 714         {
 715           invertSequenceMenuItem_actionPerformed();
 716           sg = viewport.getSelectionGroup();
 717           toggleSeqs = true;
 718
 719         }
 720         viewport.expandColSelection(sg, true);
 721         // finally invert the column selection and get the new sequence
 722         // selection and indicate it should be hidden.
 723         invertColSel_actionPerformed();
 724         toggleCols = true;
 725       }
 726     }
 727
 728     if (toggleSeqs)
 729     {
 730       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 731       {
 732         hide = true;
 733         viewport.hideAllSelectedSeqs();
 734       }
 735       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 736               .size() > 0))
 737       {
 738         viewport.showAllHiddenSeqs();
 739       }
 740     }
 741
 742     if (toggleCols)
 743     {
 744       if (viewport.getColumnSelection().getSelected().size() > 0)
 745       {
 746         viewport.hideSelectedColumns();
 747         if (!toggleSeqs)
 748         {
 749           viewport.setSelectionGroup(sg);
 750         }
 751       }
 752       else if (!hide)
 753       {
 754         viewport.showAllHiddenColumns();
 755       }
 756     }
 757   }
 758
 759   @Override
 760   public void keyReleased(KeyEvent evt)
 761   {
 762   }
 763
 764   @Override
 765   public void keyTyped(KeyEvent evt)
 766   {
 767   }
 768
 769   @Override
 770   public void itemStateChanged(ItemEvent evt)
 771   {
 772     final Object source = evt.getSource();
 773     if (source == displayNonconservedMenuItem)
 774     {
 775       displayNonconservedMenuItem_actionPerformed();
 776     }
 777     else if (source == colourTextMenuItem)
 778     {
 779       colourTextMenuItem_actionPerformed();
 780     }
 781     else if (source == wrapMenuItem)
 782     {
 783       wrapMenuItem_actionPerformed();
 784     }
 785     else if (source == scaleAbove)
 786     {
 787       viewport.setScaleAboveWrapped(scaleAbove.getState());
 788     }
 789     else if (source == scaleLeft)
 790     {
 791       viewport.setScaleLeftWrapped(scaleLeft.getState());
 792     }
 793     else if (source == scaleRight)
 794     {
 795       viewport.setScaleRightWrapped(scaleRight.getState());
 796     }
 797     else if (source == seqLimits)
 798     {
 799       seqLimits_itemStateChanged();
 800     }
 801     else if (source == viewBoxesMenuItem)
 802     {
 803       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 804     }
 805     else if (source == viewTextMenuItem)
 806     {
 807       viewport.setShowText(viewTextMenuItem.getState());
 808     }
 809     else if (source == renderGapsMenuItem)
 810     {
 811       viewport.setRenderGaps(renderGapsMenuItem.getState());
 812     }
 813     else if (source == annotationPanelMenuItem)
 814     {
 815       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 816       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 817     }
 818     else if (source == sequenceFeatures)
 819     {
 820       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 821       alignPanel.seqPanel.seqCanvas.repaint();
 822     }
 823     else if (source == showAlignmentAnnotations)
 824     {
 825       setAnnotationsVisibility();
 826     }
 827     else if (source == showSequenceAnnotations)
 828     {
 829       setAnnotationsVisibility();
 830     }
 831     else if (source == sortAnnBySequence)
 832     {
 833       boolean newState = sortAnnBySequence.getState();
 834       sortAnnByLabel.setState(false);
 835       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 836               : SequenceAnnotationOrder.NONE);
 837       setViewportAnnotationOrder();
 838     }
 839     else if (source == sortAnnByLabel)
 840     {
 841       boolean newState = sortAnnByLabel.getState();
 842       sortAnnBySequence.setState(false);
 843       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 844               : SequenceAnnotationOrder.NONE);
 845       setViewportAnnotationOrder();
 846     }
 847     else if (source == showAutoFirst)
 848     {
 849       showAutoLast.setState(!showAutoFirst.getState());
 850       setShowAutoCalculatedAbove(showAutoFirst.getState());
 851       setViewportAnnotationOrder();
 852     }
 853     else if (source == showAutoLast)
 854     {
 855       showAutoFirst.setState(!showAutoLast.getState());
 856       setShowAutoCalculatedAbove(showAutoFirst.getState());
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == conservationMenuItem)
 860     {
 861       conservationMenuItem_actionPerformed();
 862     }
 863     else if (source == abovePIDThreshold)
 864     {
 865       abovePIDThreshold_actionPerformed();
 866     }
 867     else if (source == applyToAllGroups)
 868     {
 869       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 870     }
 871     else if (source == autoCalculate)
 872     {
 873       viewport.autoCalculateConsensus = autoCalculate.getState();
 874     }
 875     else if (source == sortByTree)
 876     {
 877       viewport.sortByTree = sortByTree.getState();
 878     }
 879     else if (source == this.centreColumnLabelFlag)
 880     {
 881       centreColumnLabelFlag_stateChanged();
 882     }
 883     else if (source == this.followMouseOverFlag)
 884     {
 885       mouseOverFlag_stateChanged();
 886     }
 887     else if (source == showGroupConsensus)
 888     {
 889       showGroupConsensus_actionPerformed();
 890     }
 891     else if (source == showGroupConservation)
 892     {
 893       showGroupConservation_actionPerformed();
 894     }
 895     else if (source == showSequenceLogo)
 896     {
 897       showSequenceLogo_actionPerformed();
 898     }
 899     else if (source == normSequenceLogo)
 900     {
 901       normSequenceLogo_actionPerformed();
 902     }
 903     else if (source == showConsensusHistogram)
 904     {
 905       showConsensusHistogram_actionPerformed();
 906     }
 907     else if (source == applyAutoAnnotationSettings)
 908     {
 909       applyAutoAnnotationSettings_actionPerformed();
 910     }
 911     alignPanel.paintAlignment(true);
 912   }
 913
 914   /**
 915    * Set the visibility state of sequence-related and/or alignment-related
 916    * annotations depending on checkbox selections. Repaint after calling.
 917    *
 918    * @param visible
 919    */
 920   private void setAnnotationsVisibility()
 921   {
 922     boolean showForAlignment = showAlignmentAnnotations.getState();
 923     boolean showForSequences = showSequenceAnnotations.getState();
 924     for (AlignmentAnnotation aa : alignPanel.getAlignment()
 925             .getAlignmentAnnotation())
 926     {
 927       boolean visible = (aa.sequenceRef == null ? showForAlignment
 928               : showForSequences);
 929         aa.visible = visible;
 930     }
 931     alignPanel.validateAnnotationDimensions(true);
 932     validate();
 933     repaint();
 934   }
 935
 936   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 937   {
 938     this.annotationSortOrder = order;
 939   }
 940
 941   /**
 942    * Set flags on the viewport that control annotation ordering
 943    */
 944   private void setViewportAnnotationOrder()
 945   {
 946     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 947     this.alignPanel.av
 948             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 949   }
 950
 951   private void setShowAutoCalculatedAbove(boolean showAbove)
 952   {
 953     this.showAutoCalculatedAbove = showAbove;
 954   }
 955
 956   private void mouseOverFlag_stateChanged()
 957   {
 958     viewport.setFollowHighlight(followMouseOverFlag.getState());
 959     // TODO: could kick the scrollTo mechanism to reset view for current
 960     // searchresults.
 961   }
 962
 963   private void centreColumnLabelFlag_stateChanged()
 964   {
 965     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 966     this.alignPanel.annotationPanel.repaint();
 967   }
 968
 969   @Override
 970   public void actionPerformed(ActionEvent evt)
 971   {
 972     viewport.applet.currentAlignFrame = this;
 973
 974     Object source = evt.getSource();
 975
 976     if (source == inputText)
 977     {
 978       inputText_actionPerformed();
 979     }
 980     else if (source == loadTree)
 981     {
 982       loadTree_actionPerformed();
 983     }
 984     else if (source == loadApplication)
 985     {
 986       launchFullApplication();
 987     }
 988     else if (source == loadAnnotations)
 989     {
 990       loadAnnotations();
 991     }
 992     else if (source == outputAnnotations)
 993     {
 994       outputAnnotations(true);
 995     }
 996     else if (source == outputFeatures)
 997     {
 998       outputFeatures(true, "Jalview");
 999     }
1000     else if (source == closeMenuItem)
1001     {
1002       closeMenuItem_actionPerformed();
1003     }
1004     else if (source == copy)
1005     {
1006       copy_actionPerformed();
1007     }
1008     else if (source == undoMenuItem)
1009     {
1010       undoMenuItem_actionPerformed();
1011     }
1012     else if (source == redoMenuItem)
1013     {
1014       redoMenuItem_actionPerformed();
1015     }
1016     else if (source == inputText)
1017     {
1018       inputText_actionPerformed();
1019     }
1020     else if (source == closeMenuItem)
1021     {
1022       closeMenuItem_actionPerformed();
1023     }
1024     else if (source == undoMenuItem)
1025     {
1026       undoMenuItem_actionPerformed();
1027     }
1028     else if (source == redoMenuItem)
1029     {
1030       redoMenuItem_actionPerformed();
1031     }
1032     else if (source == copy)
1033     {
1034       copy_actionPerformed();
1035     }
1036     else if (source == pasteNew)
1037     {
1038       pasteNew_actionPerformed();
1039     }
1040     else if (source == pasteThis)
1041     {
1042       pasteThis_actionPerformed();
1043     }
1044     else if (source == cut)
1045     {
1046       cut_actionPerformed();
1047     }
1048     else if (source == delete)
1049     {
1050       delete_actionPerformed();
1051     }
1052     else if (source == grpsFromSelection)
1053     {
1054       makeGrpsFromSelection_actionPerformed();
1055     }
1056     else if (source == deleteGroups)
1057     {
1058       deleteGroups_actionPerformed();
1059     }
1060     else if (source == selectAllSequenceMenuItem)
1061     {
1062       selectAllSequenceMenuItem_actionPerformed();
1063     }
1064     else if (source == deselectAllSequenceMenuItem)
1065     {
1066       deselectAllSequenceMenuItem_actionPerformed();
1067     }
1068     else if (source == invertSequenceMenuItem)
1069     {
1070       invertSequenceMenuItem_actionPerformed();
1071     }
1072     else if (source == invertColSel)
1073     {
1074       viewport.invertColumnSelection();
1075       alignPanel.paintAlignment(true);
1076     }
1077     else if (source == remove2LeftMenuItem)
1078     {
1079       trimAlignment(true);
1080     }
1081     else if (source == remove2RightMenuItem)
1082     {
1083       trimAlignment(false);
1084     }
1085     else if (source == removeGappedColumnMenuItem)
1086     {
1087       removeGappedColumnMenuItem_actionPerformed();
1088     }
1089     else if (source == removeAllGapsMenuItem)
1090     {
1091       removeAllGapsMenuItem_actionPerformed();
1092     }
1093     else if (source == findMenuItem)
1094     {
1095       findMenuItem_actionPerformed();
1096     }
1097     else if (source == font)
1098     {
1099       new FontChooser(alignPanel);
1100     }
1101     else if (source == newView)
1102     {
1103       newView(null);
1104     }
1105     else if (source == showColumns)
1106     {
1107       viewport.showAllHiddenColumns();
1108       alignPanel.paintAlignment(true);
1109     }
1110     else if (source == showSeqs)
1111     {
1112       viewport.showAllHiddenSeqs();
1113       alignPanel.paintAlignment(true);
1114     }
1115     else if (source == hideColumns)
1116     {
1117       viewport.hideSelectedColumns();
1118       alignPanel.paintAlignment(true);
1119     }
1120     else if (source == hideSequences
1121             && viewport.getSelectionGroup() != null)
1122     {
1123       viewport.hideAllSelectedSeqs();
1124       alignPanel.paintAlignment(true);
1125     }
1126     else if (source == hideAllButSelection)
1127     {
1128       toggleHiddenRegions(false, false);
1129       alignPanel.paintAlignment(true);
1130     }
1131     else if (source == hideAllSelection)
1132     {
1133       SequenceGroup sg = viewport.getSelectionGroup();
1134       viewport.expandColSelection(sg, false);
1135       viewport.hideAllSelectedSeqs();
1136       viewport.hideSelectedColumns();
1137       alignPanel.paintAlignment(true);
1138     }
1139     else if (source == showAllHidden)
1140     {
1141       viewport.showAllHiddenColumns();
1142       viewport.showAllHiddenSeqs();
1143       alignPanel.paintAlignment(true);
1144     }
1145     else if (source == showGroupConsensus)
1146     {
1147       showGroupConsensus_actionPerformed();
1148     }
1149     else if (source == showGroupConservation)
1150     {
1151       showGroupConservation_actionPerformed();
1152     }
1153     else if (source == showSequenceLogo)
1154     {
1155       showSequenceLogo_actionPerformed();
1156     }
1157     else if (source == normSequenceLogo)
1158     {
1159       normSequenceLogo_actionPerformed();
1160     }
1161     else if (source == showConsensusHistogram)
1162     {
1163       showConsensusHistogram_actionPerformed();
1164     }
1165     else if (source == applyAutoAnnotationSettings)
1166     {
1167       applyAutoAnnotationSettings_actionPerformed();
1168     }
1169     else if (source == featureSettings)
1170     {
1171       new FeatureSettings(alignPanel);
1172     }
1173     else if (source == alProperties)
1174     {
1175       StringBuffer contents = new jalview.io.AlignmentProperties(
1176               viewport.getAlignment()).formatAsString();
1177       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1178       cap.setText(contents.toString());
1179       Frame frame = new Frame();
1180       frame.add(cap);
1181       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1182               "label.alignment_properties", new String[]
1183               { getTitle() }), 400, 250);
1184     }
1185     else if (source == overviewMenuItem)
1186     {
1187       overviewMenuItem_actionPerformed();
1188     }
1189     else if (source == noColourmenuItem)
1190     {
1191       changeColour(null);
1192     }
1193     else if (source == clustalColour)
1194     {
1195       abovePIDThreshold.setState(false);
1196       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1197     }
1198     else if (source == zappoColour)
1199     {
1200       changeColour(new ZappoColourScheme());
1201     }
1202     else if (source == taylorColour)
1203     {
1204       changeColour(new TaylorColourScheme());
1205     }
1206     else if (source == hydrophobicityColour)
1207     {
1208       changeColour(new HydrophobicColourScheme());
1209     }
1210     else if (source == helixColour)
1211     {
1212       changeColour(new HelixColourScheme());
1213     }
1214     else if (source == strandColour)
1215     {
1216       changeColour(new StrandColourScheme());
1217     }
1218     else if (source == turnColour)
1219     {
1220       changeColour(new TurnColourScheme());
1221     }
1222     else if (source == buriedColour)
1223     {
1224       changeColour(new BuriedColourScheme());
1225     }
1226     else if (source == nucleotideColour)
1227     {
1228       changeColour(new NucleotideColourScheme());
1229     }
1230     else if (source == purinePyrimidineColour)
1231     {
1232       changeColour(new PurinePyrimidineColourScheme());
1233     }
1234     // else if (source == RNAInteractionColour)
1235     // {
1236     // changeColour(new RNAInteractionColourScheme());
1237     // }
1238     else if (source == RNAHelixColour)
1239     {
1240       new RNAHelicesColourChooser(viewport, alignPanel);
1241     }
1242     else if (source == modifyPID)
1243     {
1244       modifyPID_actionPerformed();
1245     }
1246     else if (source == modifyConservation)
1247     {
1248       modifyConservation_actionPerformed();
1249     }
1250     else if (source == userDefinedColour)
1251     {
1252       new UserDefinedColours(alignPanel, null);
1253     }
1254     else if (source == PIDColour)
1255     {
1256       changeColour(new PIDColourScheme());
1257     }
1258     else if (source == BLOSUM62Colour)
1259     {
1260       changeColour(new Blosum62ColourScheme());
1261     }
1262     else if (source == tcoffeeColour)
1263     {
1264       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1265     }
1266     else if (source == annotationColour)
1267     {
1268       new AnnotationColourChooser(viewport, alignPanel);
1269     }
1270     else if (source == annotationColumnSelection)
1271     {
1272       new AnnotationColumnChooser(viewport, alignPanel);
1273     }
1274     else if (source == sortPairwiseMenuItem)
1275     {
1276       sortPairwiseMenuItem_actionPerformed();
1277     }
1278     else if (source == sortIDMenuItem)
1279     {
1280       sortIDMenuItem_actionPerformed();
1281     }
1282     else if (source == sortLengthMenuItem)
1283     {
1284       sortLengthMenuItem_actionPerformed();
1285     }
1286     else if (source == sortGroupMenuItem)
1287     {
1288       sortGroupMenuItem_actionPerformed();
1289     }
1290     else if (source == removeRedundancyMenuItem)
1291     {
1292       removeRedundancyMenuItem_actionPerformed();
1293     }
1294     else if (source == pairwiseAlignmentMenuItem)
1295     {
1296       pairwiseAlignmentMenuItem_actionPerformed();
1297     }
1298     else if (source == PCAMenuItem)
1299     {
1300       PCAMenuItem_actionPerformed();
1301     }
1302     else if (source == averageDistanceTreeMenuItem)
1303     {
1304       averageDistanceTreeMenuItem_actionPerformed();
1305     }
1306     else if (source == neighbourTreeMenuItem)
1307     {
1308       neighbourTreeMenuItem_actionPerformed();
1309     }
1310     else if (source == njTreeBlosumMenuItem)
1311     {
1312       njTreeBlosumMenuItem_actionPerformed();
1313     }
1314     else if (source == avDistanceTreeBlosumMenuItem)
1315     {
1316       avTreeBlosumMenuItem_actionPerformed();
1317     }
1318     else if (source == documentation)
1319     {
1320       documentation_actionPerformed();
1321     }
1322     else if (source == about)
1323     {
1324       about_actionPerformed();
1325     }
1326
1327   }
1328
1329   public void inputText_actionPerformed()
1330   {
1331     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1332     Frame frame = new Frame();
1333     frame.add(cap);
1334     jalview.bin.JalviewLite.addFrame(frame,
1335             MessageManager.getString("label.input_cut_paste"), 500, 500);
1336   }
1337
1338   protected void outputText_actionPerformed(ActionEvent e)
1339   {
1340     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1341     Frame frame = new Frame();
1342     frame.add(cap);
1343     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1344             "label.alignment_output_command", new Object[]
1345             { e.getActionCommand() }), 600, 500);
1346
1347     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1348     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1349             e.getActionCommand(), viewport.getAlignment(),
1350             viewport.getShowJVSuffix()));
1351   }
1352
1353   public void loadAnnotations()
1354   {
1355     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1356     cap.setText(MessageManager
1357             .getString("label.paste_features_annotations_Tcoffee_here"));
1358     cap.setAnnotationImport();
1359     Frame frame = new Frame();
1360     frame.add(cap);
1361     jalview.bin.JalviewLite.addFrame(frame,
1362             MessageManager.getString("action.paste_annotations"), 400, 300);
1363
1364   }
1365
1366   public String outputAnnotations(boolean displayTextbox)
1367   {
1368     String annotation = new AnnotationFile()
1369             .printAnnotationsForView(viewport);
1370
1371     if (displayTextbox)
1372     {
1373       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1374       Frame frame = new Frame();
1375       frame.add(cap);
1376       jalview.bin.JalviewLite.addFrame(frame,
1377               MessageManager.getString("label.annotations"), 600, 500);
1378       cap.setText(annotation);
1379     }
1380
1381     return annotation;
1382   }
1383
1384   private Map<String,Object> getDisplayedFeatureCols()
1385   {
1386     if (alignPanel.getFeatureRenderer() != null
1387             && viewport.getFeaturesDisplayed()!= null)
1388     {
1389       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1390
1391     }
1392     return null;
1393   }
1394
1395   public String outputFeatures(boolean displayTextbox, String format)
1396   {
1397     String features;
1398     if (format.equalsIgnoreCase("Jalview"))
1399     {
1400       features = new FeaturesFile().printJalviewFormat(viewport
1401               .getAlignment().getSequencesArray(),
1402               getDisplayedFeatureCols());
1403     }
1404     else
1405     {
1406       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1407               .getSequencesArray(), getDisplayedFeatureCols());
1408     }
1409
1410     if (displayTextbox)
1411     {
1412       boolean frimport = false;
1413       if (features == null || features.equals("No Features Visible"))
1414       {
1415         features = "# No features visible - paste some and import them here.";
1416         frimport = true;
1417       }
1418
1419       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1420       if (frimport)
1421       {
1422         cap.setAnnotationImport();
1423       }
1424       Frame frame = new Frame();
1425       frame.add(cap);
1426       jalview.bin.JalviewLite.addFrame(frame,
1427               MessageManager.getString("label.features"), 600, 500);
1428       cap.setText(features);
1429     }
1430     else
1431     {
1432       if (features == null)
1433       {
1434         features = "";
1435       }
1436     }
1437
1438     return features;
1439   }
1440
1441   void launchFullApplication()
1442   {
1443     StringBuffer url = new StringBuffer(jalviewServletURL);
1444
1445     // allow servlet parameters to be passed in applet parameter
1446     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1447             : "?";
1448     url.append(firstSep);
1449
1450     url.append("open="
1451             + appendProtocol(viewport.applet.getParameter("file")));
1452
1453     if (viewport.applet.getParameter("features") != null)
1454     {
1455       url.append("&features=");
1456       url.append(appendProtocol(viewport.applet.getParameter("features")));
1457     }
1458
1459     if (viewport.applet.getParameter("annotations") != null)
1460     {
1461       url.append("&annotations=");
1462       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1463     }
1464
1465     if (viewport.applet.getParameter("jnetfile") != null)
1466     {
1467       url.append("&annotations=");
1468       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1469     }
1470
1471     if (viewport.applet.getParameter("defaultColour") != null)
1472     {
1473       url.append("&colour="
1474               + removeWhiteSpace(viewport.applet
1475                       .getParameter("defaultColour")));
1476     }
1477
1478     if (viewport.applet.getParameter("userDefinedColour") != null)
1479     {
1480       url.append("&colour="
1481               + removeWhiteSpace(viewport.applet
1482                       .getParameter("userDefinedColour")));
1483     }
1484     if (viewport.applet.getParameter("tree") != null)
1485     {
1486       url.append("&tree="
1487               + appendProtocol(viewport.applet.getParameter("tree")));
1488     }
1489     if (viewport.applet.getParameter("treeFile") != null)
1490     {
1491       url.append("&tree="
1492               + appendProtocol(viewport.applet.getParameter("treeFile")));
1493     }
1494
1495     showURL(url.toString(), "FULL_APP");
1496   }
1497
1498   String removeWhiteSpace(String colour)
1499   {
1500     StringBuffer sb = new StringBuffer();
1501     for (int i = 0; i < colour.length(); i++)
1502     {
1503       if (Character.isWhitespace(colour.charAt(i)))
1504       {
1505         sb.append("%20");
1506       }
1507       else
1508       {
1509         sb.append(colour.charAt(i));
1510       }
1511     }
1512
1513     return sb.toString();
1514   }
1515
1516   String appendProtocol(String url)
1517   {
1518     try
1519     {
1520       new URL(url);
1521       url = URLEncoder.encode(url);
1522     }
1523     /*
1524      * When we finally deprecate 1.1 compatibility, we can start to use
1525      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1526      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1527      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1528      * ex.printStackTrace(); }
1529      */
1530     catch (java.net.MalformedURLException ex)
1531     {
1532       url = viewport.applet.getCodeBase() + url;
1533     }
1534     return url;
1535   }
1536
1537   public void closeMenuItem_actionPerformed()
1538   {
1539     PaintRefresher.RemoveComponent(alignPanel);
1540     if (alignPanel.seqPanel != null
1541             && alignPanel.seqPanel.seqCanvas != null)
1542     {
1543       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1544     }
1545     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1546     {
1547       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1548     }
1549
1550     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1551     {
1552       System.exit(0);
1553     }
1554     else
1555     {
1556     }
1557     viewport = null;
1558     alignPanel = null;
1559     this.dispose();
1560   }
1561
1562   /**
1563    * TODO: JAL-1104
1564    */
1565   void updateEditMenuBar()
1566   {
1567
1568     if (viewport.getHistoryList().size() > 0)
1569     {
1570       undoMenuItem.setEnabled(true);
1571       CommandI command = viewport.getHistoryList().peek();
1572       undoMenuItem.setLabel(MessageManager.formatMessage(
1573               "label.undo_command", new Object[]
1574               { command.getDescription() }));
1575     }
1576     else
1577     {
1578       undoMenuItem.setEnabled(false);
1579       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1580     }
1581
1582     if (viewport.getRedoList().size() > 0)
1583     {
1584       redoMenuItem.setEnabled(true);
1585
1586       CommandI command = viewport.getRedoList().peek();
1587       redoMenuItem.setLabel(MessageManager.formatMessage(
1588               "label.redo_command", new Object[]
1589               { command.getDescription() }));
1590     }
1591     else
1592     {
1593       redoMenuItem.setEnabled(false);
1594       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1595     }
1596   }
1597
1598   /**
1599    * TODO: JAL-1104
1600    */
1601   @Override
1602   public void addHistoryItem(CommandI command)
1603   {
1604     if (command.getSize() > 0)
1605     {
1606       viewport.addToHistoryList(command);
1607       viewport.clearRedoList();
1608       updateEditMenuBar();
1609       viewport.updateHiddenColumns();
1610     }
1611   }
1612
1613   /**
1614    * TODO: JAL-1104 DOCUMENT ME!
1615    *
1616    * @param e
1617    *          DOCUMENT ME!
1618    */
1619   protected void undoMenuItem_actionPerformed()
1620   {
1621     if (viewport.getHistoryList().isEmpty())
1622     {
1623       return;
1624     }
1625
1626     CommandI command = viewport.getHistoryList().pop();
1627     viewport.addToRedoList(command);
1628     command.undoCommand(null);
1629
1630     AlignmentViewport originalSource = getOriginatingSource(command);
1631     // JBPNote Test
1632     if (originalSource != viewport)
1633     {
1634       System.err
1635               .println("Warning: Viewport object mismatch whilst undoing");
1636     }
1637     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1638                                           // viewport.getColumnSelection().getHiddenColumns()
1639                                           // != null;
1640     updateEditMenuBar();
1641     originalSource.firePropertyChange("alignment", null, originalSource
1642             .getAlignment().getSequences());
1643   }
1644
1645   /**
1646    * TODO: JAL-1104 DOCUMENT ME!
1647    *
1648    * @param e
1649    *          DOCUMENT ME!
1650    */
1651   protected void redoMenuItem_actionPerformed()
1652   {
1653     if (viewport.getRedoList().isEmpty())
1654     {
1655       return;
1656     }
1657
1658     CommandI command = viewport.getRedoList().pop();
1659     viewport.addToHistoryList(command);
1660     command.doCommand(null);
1661
1662     AlignmentViewport originalSource = getOriginatingSource(command);
1663     // JBPNote Test
1664     if (originalSource != viewport)
1665     {
1666       System.err
1667               .println("Warning: Viewport object mismatch whilst re-doing");
1668     }
1669     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1670                                           // viewport.getColumnSelection().getHiddenColumns()
1671                                           // != null;
1672
1673     updateEditMenuBar();
1674     originalSource.firePropertyChange("alignment", null, originalSource
1675             .getAlignment().getSequences());
1676   }
1677
1678   AlignmentViewport getOriginatingSource(CommandI command)
1679   {
1680     AlignmentViewport originalSource = null;
1681     // For sequence removal and addition, we need to fire
1682     // the property change event FROM the viewport where the
1683     // original alignment was altered
1684     AlignmentI al = null;
1685     if (command instanceof EditCommand)
1686     {
1687       EditCommand editCommand = (EditCommand) command;
1688       al = editCommand.getAlignment();
1689       Vector comps = (Vector) PaintRefresher.components.get(viewport
1690               .getSequenceSetId());
1691       for (int i = 0; i < comps.size(); i++)
1692       {
1693         if (comps.elementAt(i) instanceof AlignmentPanel)
1694         {
1695           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1696           {
1697             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1698             break;
1699           }
1700         }
1701       }
1702     }
1703
1704     if (originalSource == null)
1705     {
1706       // The original view is closed, we must validate
1707       // the current view against the closed view first
1708       if (al != null)
1709       {
1710         PaintRefresher.validateSequences(al, viewport.getAlignment());
1711       }
1712
1713       originalSource = viewport;
1714     }
1715
1716     return originalSource;
1717   }
1718
1719   /**
1720    * Move the currently selected sequences up or down one position in the
1721    * alignment
1722    *
1723    * @param up
1724    */
1725   public void moveSelectedSequences(boolean up)
1726   {
1727     SequenceGroup sg = viewport.getSelectionGroup();
1728     if (sg == null)
1729     {
1730       return;
1731     }
1732     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1733             up ? null : viewport.getHiddenRepSequences(), up);
1734     alignPanel.paintAlignment(true);
1735
1736     /*
1737      * Also move cDNA/protein complement sequences
1738      */
1739     AlignViewportI complement = viewport.getCodingComplement();
1740     if (complement != null)
1741     {
1742       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1743               viewport, complement);
1744       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1745               up ? null : complement.getHiddenRepSequences(), up);
1746       // TODO need to trigger a repaint of the complementary panel - how?
1747       // would prefer to handle in SplitFrame but it is not overriding key
1748       // listener chiz
1749     }
1750   }
1751
1752   synchronized void slideSequences(boolean right, int size)
1753   {
1754     List<SequenceI> sg = new Vector<SequenceI>();
1755     if (viewport.cursorMode)
1756     {
1757       sg.add(viewport.getAlignment().getSequenceAt(
1758               alignPanel.seqPanel.seqCanvas.cursorY));
1759     }
1760     else if (viewport.getSelectionGroup() != null
1761             && viewport.getSelectionGroup().getSize() != viewport
1762                     .getAlignment().getHeight())
1763     {
1764       sg = viewport.getSelectionGroup().getSequences(
1765               viewport.getHiddenRepSequences());
1766     }
1767
1768     if (sg.size() < 1)
1769     {
1770       return;
1771     }
1772
1773     Vector<SequenceI> invertGroup = new Vector();
1774
1775     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1776     {
1777       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1778       {
1779         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1780       }
1781     }
1782
1783     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1784
1785     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1786             .size()]);
1787     for (int i = 0; i < invertGroup.size(); i++)
1788     {
1789       seqs2[i] = invertGroup.elementAt(i);
1790     }
1791
1792     SlideSequencesCommand ssc;
1793     if (right)
1794     {
1795       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1796               size, viewport.getGapCharacter());
1797     }
1798     else
1799     {
1800       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1801               size, viewport.getGapCharacter());
1802     }
1803
1804     int groupAdjustment = 0;
1805     if (ssc.getGapsInsertedBegin() && right)
1806     {
1807       if (viewport.cursorMode)
1808       {
1809         alignPanel.seqPanel.moveCursor(size, 0);
1810       }
1811       else
1812       {
1813         groupAdjustment = size;
1814       }
1815     }
1816     else if (!ssc.getGapsInsertedBegin() && !right)
1817     {
1818       if (viewport.cursorMode)
1819       {
1820         alignPanel.seqPanel.moveCursor(-size, 0);
1821       }
1822       else
1823       {
1824         groupAdjustment = -size;
1825       }
1826     }
1827
1828     if (groupAdjustment != 0)
1829     {
1830       viewport.getSelectionGroup().setStartRes(
1831               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1832       viewport.getSelectionGroup().setEndRes(
1833               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1834     }
1835
1836     boolean appendHistoryItem = false;
1837     Deque<CommandI> historyList = viewport.getHistoryList();
1838     if (historyList != null && historyList.size() > 0
1839             && historyList.peek() instanceof SlideSequencesCommand)
1840     {
1841       appendHistoryItem = ssc
1842               .appendSlideCommand((SlideSequencesCommand) historyList
1843                       .peek());
1844     }
1845
1846     if (!appendHistoryItem)
1847     {
1848       addHistoryItem(ssc);
1849     }
1850
1851     repaint();
1852   }
1853
1854   static StringBuffer copiedSequences;
1855
1856   static Vector copiedHiddenColumns;
1857
1858   protected void copy_actionPerformed()
1859   {
1860     if (viewport.getSelectionGroup() == null)
1861     {
1862       return;
1863     }
1864
1865     SequenceGroup sg = viewport.getSelectionGroup();
1866     copiedSequences = new StringBuffer();
1867     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1868     for (int i = 0; i < sg.getSize(); i++)
1869     {
1870       SequenceI seq = sg.getSequenceAt(i);
1871       int index = viewport.getAlignment().findIndex(seq);
1872       orderedSeqs.put(index, seq);
1873     }
1874
1875     int index = 0, startRes, endRes;
1876     char ch;
1877
1878     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1879     {
1880       copiedHiddenColumns = new Vector();
1881       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1882       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1883       {
1884         copiedHiddenColumns.addElement(new int[]
1885         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1886       }
1887     }
1888     else
1889     {
1890       copiedHiddenColumns = null;
1891     }
1892
1893     for (int i = 0; i < sg.getSize(); i++)
1894     {
1895       SequenceI seq = null;
1896
1897       while (seq == null)
1898       {
1899         if (orderedSeqs.containsKey(index))
1900         {
1901           seq = orderedSeqs.get(index);
1902           index++;
1903           break;
1904         }
1905         else
1906         {
1907           index++;
1908         }
1909       }
1910
1911       // FIND START RES
1912       // Returns residue following index if gap
1913       startRes = seq.findPosition(sg.getStartRes());
1914
1915       // FIND END RES
1916       // Need to find the residue preceeding index if gap
1917       endRes = 0;
1918
1919       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1920       {
1921         ch = seq.getCharAt(j);
1922         if (!jalview.util.Comparison.isGap((ch)))
1923         {
1924           endRes++;
1925         }
1926       }
1927
1928       if (endRes > 0)
1929       {
1930         endRes += seq.getStart() - 1;
1931       }
1932
1933       copiedSequences.append(seq.getName()
1934               + "\t"
1935               + startRes
1936               + "\t"
1937               + endRes
1938               + "\t"
1939               + seq.getSequenceAsString(sg.getStartRes(),
1940                       sg.getEndRes() + 1) + "\n");
1941     }
1942
1943   }
1944
1945   protected void pasteNew_actionPerformed()
1946   {
1947     paste(true);
1948   }
1949
1950   protected void pasteThis_actionPerformed()
1951   {
1952     paste(false);
1953   }
1954
1955   void paste(boolean newAlignment)
1956   {
1957     try
1958     {
1959
1960       if (copiedSequences == null)
1961       {
1962         return;
1963       }
1964
1965       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1966       Vector seqs = new Vector();
1967       while (st.hasMoreElements())
1968       {
1969         String name = st.nextToken();
1970         int start = Integer.parseInt(st.nextToken());
1971         int end = Integer.parseInt(st.nextToken());
1972         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1973       }
1974       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1975       for (int i = 0; i < seqs.size(); i++)
1976       {
1977         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1978       }
1979
1980       if (newAlignment)
1981       {
1982         String newtitle = MessageManager.getString("label.copied_sequences");
1983         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1984         {
1985           newtitle = getTitle();
1986         }
1987         else
1988         {
1989           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1990         }
1991         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1992                 viewport.applet, newtitle, false);
1993         if (copiedHiddenColumns != null)
1994         {
1995           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1996           {
1997             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1998             af.viewport.hideColumns(region[0], region[1]);
1999           }
2000         }
2001
2002         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2003                 frameHeight);
2004       }
2005       else
2006       {
2007         addSequences(newSeqs);
2008       }
2009
2010     } catch (Exception ex)
2011     {
2012     } // could be anything being pasted in here
2013
2014   }
2015
2016   void addSequences(SequenceI[] seqs)
2017   {
2018     for (int i = 0; i < seqs.length; i++)
2019     {
2020       viewport.getAlignment().addSequence(seqs[i]);
2021     }
2022
2023     // !newAlignment
2024     addHistoryItem(new EditCommand(
2025             MessageManager.getString("label.add_sequences"), Action.PASTE,
2026             seqs, 0, viewport.getAlignment().getWidth(),
2027             viewport.getAlignment()));
2028
2029     viewport.setEndSeq(viewport.getAlignment().getHeight());
2030     viewport.getAlignment().getWidth();
2031     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2032             .getSequences());
2033
2034   }
2035
2036   protected void cut_actionPerformed()
2037   {
2038     copy_actionPerformed();
2039     delete_actionPerformed();
2040   }
2041
2042   protected void delete_actionPerformed()
2043   {
2044
2045     SequenceGroup sg = viewport.getSelectionGroup();
2046     if (sg == null)
2047     {
2048       return;
2049     }
2050
2051     Vector seqs = new Vector();
2052     SequenceI seq;
2053     for (int i = 0; i < sg.getSize(); i++)
2054     {
2055       seq = sg.getSequenceAt(i);
2056       seqs.addElement(seq);
2057     }
2058
2059     // If the cut affects all sequences, remove highlighted columns
2060     if (sg.getSize() == viewport.getAlignment().getHeight())
2061     {
2062       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2063               sg.getEndRes() + 1);
2064     }
2065
2066     SequenceI[] cut = new SequenceI[seqs.size()];
2067     for (int i = 0; i < seqs.size(); i++)
2068     {
2069       cut[i] = (SequenceI) seqs.elementAt(i);
2070     }
2071
2072     /*
2073      * //ADD HISTORY ITEM
2074      */
2075     addHistoryItem(new EditCommand(
2076             MessageManager.getString("label.cut_sequences"), Action.CUT,
2077             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2078             viewport.getAlignment()));
2079
2080     viewport.setSelectionGroup(null);
2081     viewport.getAlignment().deleteGroup(sg);
2082
2083     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2084             .getSequences());
2085
2086     if (viewport.getAlignment().getHeight() < 1)
2087     {
2088       this.setVisible(false);
2089     }
2090     viewport.sendSelection();
2091   }
2092
2093   /**
2094    * group consensus toggled
2095    *
2096    */
2097   protected void showGroupConsensus_actionPerformed()
2098   {
2099     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2100     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2101
2102   }
2103
2104   /**
2105    * group conservation toggled.
2106    */
2107   protected void showGroupConservation_actionPerformed()
2108   {
2109     viewport.setShowGroupConservation(showGroupConservation.getState());
2110     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2111   }
2112
2113   /*
2114    * (non-Javadoc)
2115    *
2116    * @see
2117    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2118    * .event.ActionEvent)
2119    */
2120   protected void showConsensusHistogram_actionPerformed()
2121   {
2122     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2123     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2124   }
2125
2126   /*
2127    * (non-Javadoc)
2128    *
2129    * @see
2130    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2131    * .event.ActionEvent)
2132    */
2133   protected void showSequenceLogo_actionPerformed()
2134   {
2135     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2136     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2137   }
2138
2139   protected void normSequenceLogo_actionPerformed()
2140   {
2141     showSequenceLogo.setState(true);
2142     viewport.setShowSequenceLogo(true);
2143     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2144     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145   }
2146
2147   protected void applyAutoAnnotationSettings_actionPerformed()
2148   {
2149     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2150   }
2151
2152   protected void makeGrpsFromSelection_actionPerformed()
2153   {
2154     if (avc.makeGroupsFromSelection())
2155     {
2156       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2157       alignPanel.updateAnnotation();
2158       alignPanel.paintAlignment(true);
2159     }
2160   }
2161
2162   protected void createGroup_actionPerformed()
2163   {
2164     avc.createGroup();
2165   }
2166
2167   protected void unGroup_actionPerformed()
2168   {
2169     if (avc.unGroup())
2170     {
2171       alignPanel.alignmentChanged();
2172     }
2173   }
2174
2175   protected void deleteGroups_actionPerformed()
2176   {
2177     if (avc.deleteGroups())
2178     {
2179       alignPanel.alignmentChanged();
2180     }
2181   }
2182
2183   public void selectAllSequenceMenuItem_actionPerformed()
2184   {
2185     SequenceGroup sg = new SequenceGroup();
2186     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2187     {
2188       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2189     }
2190     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2191     viewport.setSelectionGroup(sg);
2192     alignPanel.paintAlignment(true);
2193     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2194     viewport.sendSelection();
2195   }
2196
2197   public void deselectAllSequenceMenuItem_actionPerformed()
2198   {
2199     if (viewport.cursorMode)
2200     {
2201       alignPanel.seqPanel.keyboardNo1 = null;
2202       alignPanel.seqPanel.keyboardNo2 = null;
2203     }
2204     viewport.setSelectionGroup(null);
2205     viewport.getColumnSelection().clear();
2206     viewport.setSelectionGroup(null);
2207     alignPanel.idPanel.idCanvas.searchResults = null;
2208     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2209     alignPanel.paintAlignment(true);
2210     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2211     viewport.sendSelection();
2212   }
2213
2214   public void invertSequenceMenuItem_actionPerformed()
2215   {
2216     SequenceGroup sg = viewport.getSelectionGroup();
2217     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2218     {
2219       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2220     }
2221
2222     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2223     viewport.sendSelection();
2224   }
2225
2226   public void invertColSel_actionPerformed()
2227   {
2228     viewport.invertColumnSelection();
2229     alignPanel.paintAlignment(true);
2230     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2231     viewport.sendSelection();
2232   }
2233
2234   void trimAlignment(boolean trimLeft)
2235   {
2236     ColumnSelection colSel = viewport.getColumnSelection();
2237     int column;
2238
2239     if (colSel.size() > 0)
2240     {
2241       if (trimLeft)
2242       {
2243         column = colSel.getMin();
2244       }
2245       else
2246       {
2247         column = colSel.getMax();
2248       }
2249
2250       SequenceI[] seqs;
2251       if (viewport.getSelectionGroup() != null)
2252       {
2253         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2254                 viewport.getHiddenRepSequences());
2255       }
2256       else
2257       {
2258         seqs = viewport.getAlignment().getSequencesArray();
2259       }
2260
2261       TrimRegionCommand trimRegion;
2262       if (trimLeft)
2263       {
2264         trimRegion = new TrimRegionCommand("Remove Left",
2265                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2266                 viewport.getAlignment(), viewport.getColumnSelection(),
2267                 viewport.getSelectionGroup());
2268         viewport.setStartRes(0);
2269       }
2270       else
2271       {
2272         trimRegion = new TrimRegionCommand("Remove Right",
2273                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2274                 viewport.getAlignment(), viewport.getColumnSelection(),
2275                 viewport.getSelectionGroup());
2276       }
2277
2278       statusBar.setText(MessageManager.formatMessage(
2279               "label.removed_columns", new String[]
2280               { Integer.valueOf(trimRegion.getSize()).toString() }));
2281       addHistoryItem(trimRegion);
2282
2283       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2284       {
2285         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2286                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2287         {
2288           viewport.getAlignment().deleteGroup(sg);
2289         }
2290       }
2291
2292       viewport.firePropertyChange("alignment", null, viewport
2293               .getAlignment().getSequences());
2294     }
2295   }
2296
2297   public void removeGappedColumnMenuItem_actionPerformed()
2298   {
2299     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2300
2301     SequenceI[] seqs;
2302     if (viewport.getSelectionGroup() != null)
2303     {
2304       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2305               viewport.getHiddenRepSequences());
2306       start = viewport.getSelectionGroup().getStartRes();
2307       end = viewport.getSelectionGroup().getEndRes();
2308     }
2309     else
2310     {
2311       seqs = viewport.getAlignment().getSequencesArray();
2312     }
2313
2314     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2315             "Remove Gapped Columns", seqs, start, end,
2316             viewport.getAlignment());
2317
2318     addHistoryItem(removeGapCols);
2319
2320     statusBar.setText(MessageManager.formatMessage(
2321             "label.removed_empty_columns", new String[]
2322             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2323
2324     // This is to maintain viewport position on first residue
2325     // of first sequence
2326     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2327     int startRes = seq.findPosition(viewport.startRes);
2328     // ShiftList shifts;
2329     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2330     // edit.alColumnChanges=shifts.getInverse();
2331     // if (viewport.hasHiddenColumns)
2332     // viewport.getColumnSelection().compensateForEdits(shifts);
2333     viewport.setStartRes(seq.findIndex(startRes) - 1);
2334     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2335             .getSequences());
2336
2337   }
2338
2339   public void removeAllGapsMenuItem_actionPerformed()
2340   {
2341     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2342
2343     SequenceI[] seqs;
2344     if (viewport.getSelectionGroup() != null)
2345     {
2346       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2347               viewport.getHiddenRepSequences());
2348       start = viewport.getSelectionGroup().getStartRes();
2349       end = viewport.getSelectionGroup().getEndRes();
2350     }
2351     else
2352     {
2353       seqs = viewport.getAlignment().getSequencesArray();
2354     }
2355
2356     // This is to maintain viewport position on first residue
2357     // of first sequence
2358     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2359     int startRes = seq.findPosition(viewport.startRes);
2360
2361     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2362             viewport.getAlignment()));
2363
2364     viewport.setStartRes(seq.findIndex(startRes) - 1);
2365
2366     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2367             .getSequences());
2368
2369   }
2370
2371   public void findMenuItem_actionPerformed()
2372   {
2373     new Finder(alignPanel);
2374   }
2375
2376   /**
2377    * create a new view derived from the current view
2378    *
2379    * @param viewtitle
2380    * @return frame for the new view
2381    */
2382   public AlignFrame newView(String viewtitle)
2383   {
2384     AlignmentI newal;
2385     if (viewport.hasHiddenRows())
2386     {
2387       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2388               .getFullAlignment().getSequencesArray());
2389     }
2390     else
2391     {
2392       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2393     }
2394
2395     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2396     {
2397       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2398       {
2399         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2400         {
2401           newal.addAnnotation(viewport.getAlignment()
2402                   .getAlignmentAnnotation()[i]);
2403         }
2404       }
2405     }
2406
2407     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2408
2409     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2410     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2411     PaintRefresher.Register(newaf.alignPanel,
2412             newaf.alignPanel.av.getSequenceSetId());
2413
2414     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2415             newaf.alignPanel.av.getSequenceSetId());
2416     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2417             newaf.alignPanel.av.getSequenceSetId());
2418
2419     Vector comps = (Vector) PaintRefresher.components.get(viewport
2420             .getSequenceSetId());
2421     int viewSize = -1;
2422     for (int i = 0; i < comps.size(); i++)
2423     {
2424       if (comps.elementAt(i) instanceof AlignmentPanel)
2425       {
2426         viewSize++;
2427       }
2428     }
2429
2430     String title = new String(this.getTitle());
2431     if (viewtitle != null)
2432     {
2433       title = viewtitle + " ( " + title + ")";
2434     }
2435     else
2436     {
2437       if (title.indexOf("(View") > -1)
2438       {
2439         title = title.substring(0, title.indexOf("(View"));
2440       }
2441       title += "(View " + viewSize + ")";
2442     }
2443
2444     newaf.setTitle(title.toString());
2445
2446     newaf.viewport.setHistoryList(viewport.getHistoryList());
2447     newaf.viewport.setRedoList(viewport.getRedoList());
2448     return newaf;
2449   }
2450
2451   /**
2452    *
2453    * @return list of feature groups on the view
2454    */
2455   public String[] getFeatureGroups()
2456   {
2457     FeatureRenderer fr = null;
2458     if (alignPanel != null
2459             && (fr = alignPanel.getFeatureRenderer()) != null)
2460     {
2461       List<String> gps = fr.getFeatureGroups();
2462       String[] _gps = gps.toArray(new String[gps.size()]);
2463       return _gps;
2464     }
2465     return null;
2466   }
2467
2468   /**
2469    * get sequence feature groups that are hidden or shown
2470    *
2471    * @param visible
2472    *          true is visible
2473    * @return list
2474    */
2475   public String[] getFeatureGroupsOfState(boolean visible)
2476   {
2477     FeatureRenderer fr = null;
2478     if (alignPanel != null
2479             && (fr = alignPanel.getFeatureRenderer()) != null)
2480     {
2481       List<String> gps = fr.getGroups(visible);
2482       String[] _gps = gps.toArray(new String[gps.size()]);
2483       return _gps;
2484     }
2485     return null;
2486   }
2487
2488   /**
2489    * Change the display state for the given feature groups
2490    *
2491    * @param groups
2492    *          list of group strings
2493    * @param state
2494    *          visible or invisible
2495    */
2496   public void setFeatureGroupState(String[] groups, boolean state)
2497   {
2498     FeatureRenderer fr = null;
2499     this.sequenceFeatures.setState(true);
2500     viewport.setShowSequenceFeatures(true);
2501     if (alignPanel != null
2502             && (fr = alignPanel.getFeatureRenderer()) != null)
2503     {
2504
2505       fr.setGroupVisibility(Arrays.asList(groups), state);
2506       alignPanel.seqPanel.seqCanvas.repaint();
2507       if (alignPanel.overviewPanel != null)
2508       {
2509         alignPanel.overviewPanel.updateOverviewImage();
2510       }
2511     }
2512   }
2513
2514   public void seqLimits_itemStateChanged()
2515   {
2516     viewport.setShowJVSuffix(seqLimits.getState());
2517     alignPanel.fontChanged();
2518     alignPanel.paintAlignment(true);
2519   }
2520
2521   protected void colourTextMenuItem_actionPerformed()
2522   {
2523     viewport.setColourText(colourTextMenuItem.getState());
2524     alignPanel.paintAlignment(true);
2525   }
2526
2527   protected void displayNonconservedMenuItem_actionPerformed()
2528   {
2529     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2530     alignPanel.paintAlignment(true);
2531   }
2532
2533   protected void wrapMenuItem_actionPerformed()
2534   {
2535     viewport.setWrapAlignment(wrapMenuItem.getState());
2536     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2537     scaleAbove.setEnabled(wrapMenuItem.getState());
2538     scaleLeft.setEnabled(wrapMenuItem.getState());
2539     scaleRight.setEnabled(wrapMenuItem.getState());
2540     alignPanel.paintAlignment(true);
2541   }
2542
2543   public void overviewMenuItem_actionPerformed()
2544   {
2545     if (alignPanel.overviewPanel != null)
2546     {
2547       return;
2548     }
2549
2550     Frame frame = new Frame();
2551     OverviewPanel overview = new OverviewPanel(alignPanel);
2552     frame.add(overview);
2553     // +50 must allow for applet frame window
2554     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2555             "label.overview_params", new String[]
2556             { this.getTitle() }), overview.getPreferredSize().width,
2557             overview.getPreferredSize().height + 50);
2558
2559     frame.pack();
2560     final AlignmentPanel ap = alignPanel;
2561     frame.addWindowListener(new WindowAdapter()
2562     {
2563       @Override
2564       public void windowClosing(WindowEvent e)
2565       {
2566         if (ap != null)
2567         {
2568           ap.setOverviewPanel(null);
2569         }
2570       };
2571     });
2572
2573     alignPanel.setOverviewPanel(overview);
2574
2575   }
2576
2577   public void changeColour(ColourSchemeI cs)
2578   {
2579
2580     if (cs != null)
2581     {
2582       if (viewport.getAbovePIDThreshold())
2583       {
2584         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2585                 cs, "Background"));
2586       }
2587
2588       if (viewport.getConservationSelected())
2589       {
2590         cs.setConservationApplied(true);
2591         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2592                 cs, "Background"));
2593       }
2594       else
2595       {
2596         cs.setConservationApplied(false);
2597       }
2598     }
2599     viewport.setGlobalColourScheme(cs);
2600
2601     alignPanel.paintAlignment(true);
2602   }
2603
2604   protected void modifyPID_actionPerformed()
2605   {
2606     if (viewport.getAbovePIDThreshold()
2607             && viewport.getGlobalColourScheme() != null)
2608     {
2609       SliderPanel.setPIDSliderSource(alignPanel,
2610               viewport.getGlobalColourScheme(), "Background");
2611       SliderPanel.showPIDSlider();
2612     }
2613   }
2614
2615   protected void modifyConservation_actionPerformed()
2616   {
2617     if (viewport.getConservationSelected()
2618             && viewport.getGlobalColourScheme() != null)
2619     {
2620       SliderPanel.setConservationSlider(alignPanel,
2621               viewport.getGlobalColourScheme(), "Background");
2622       SliderPanel.showConservationSlider();
2623     }
2624   }
2625
2626   protected void conservationMenuItem_actionPerformed()
2627   {
2628     viewport.setConservationSelected(conservationMenuItem.getState());
2629
2630     viewport.setAbovePIDThreshold(false);
2631     abovePIDThreshold.setState(false);
2632
2633     changeColour(viewport.getGlobalColourScheme());
2634
2635     modifyConservation_actionPerformed();
2636   }
2637
2638   public void abovePIDThreshold_actionPerformed()
2639   {
2640     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2641
2642     conservationMenuItem.setState(false);
2643     viewport.setConservationSelected(false);
2644
2645     changeColour(viewport.getGlobalColourScheme());
2646
2647     modifyPID_actionPerformed();
2648   }
2649
2650   public void sortPairwiseMenuItem_actionPerformed()
2651   {
2652     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2653     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2654             .getAlignment().getSequenceAt(0), null);
2655
2656     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2657             viewport.getAlignment()));
2658     alignPanel.paintAlignment(true);
2659   }
2660
2661   public void sortIDMenuItem_actionPerformed()
2662   {
2663     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2664     AlignmentSorter.sortByID(viewport.getAlignment());
2665     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2666             viewport.getAlignment()));
2667     alignPanel.paintAlignment(true);
2668   }
2669
2670   public void sortLengthMenuItem_actionPerformed()
2671   {
2672     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2673     AlignmentSorter.sortByLength(viewport.getAlignment());
2674     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2675             viewport.getAlignment()));
2676     alignPanel.paintAlignment(true);
2677   }
2678
2679   public void sortGroupMenuItem_actionPerformed()
2680   {
2681     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2682     AlignmentSorter.sortByGroup(viewport.getAlignment());
2683     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2684             viewport.getAlignment()));
2685     alignPanel.paintAlignment(true);
2686
2687   }
2688
2689   public void removeRedundancyMenuItem_actionPerformed()
2690   {
2691     new RedundancyPanel(alignPanel);
2692   }
2693
2694   public void pairwiseAlignmentMenuItem_actionPerformed()
2695   {
2696     if (viewport.getSelectionGroup() != null
2697             && viewport.getSelectionGroup().getSize() > 1)
2698     {
2699       Frame frame = new Frame();
2700       frame.add(new PairwiseAlignPanel(alignPanel));
2701       jalview.bin.JalviewLite.addFrame(frame,
2702               MessageManager.getString("action.pairwise_alignment"), 600,
2703               500);
2704     }
2705   }
2706
2707   public void PCAMenuItem_actionPerformed()
2708   {
2709     // are the sequences aligned?
2710     if (!viewport.getAlignment().isAligned(false))
2711     {
2712       SequenceI current;
2713       int Width = viewport.getAlignment().getWidth();
2714
2715       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2716       {
2717         current = viewport.getAlignment().getSequenceAt(i);
2718
2719         if (current.getLength() < Width)
2720         {
2721           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2722         }
2723       }
2724       alignPanel.paintAlignment(true);
2725     }
2726
2727     if ((viewport.getSelectionGroup() != null
2728             && viewport.getSelectionGroup().getSize() < 4 && viewport
2729             .getSelectionGroup().getSize() > 0)
2730             || viewport.getAlignment().getHeight() < 4)
2731     {
2732       return;
2733     }
2734
2735     try
2736     {
2737       new PCAPanel(viewport);
2738     } catch (java.lang.OutOfMemoryError ex)
2739     {
2740     }
2741
2742   }
2743
2744   public void averageDistanceTreeMenuItem_actionPerformed()
2745   {
2746     NewTreePanel("AV", "PID", "Average distance tree using PID");
2747   }
2748
2749   public void neighbourTreeMenuItem_actionPerformed()
2750   {
2751     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2752   }
2753
2754   protected void njTreeBlosumMenuItem_actionPerformed()
2755   {
2756     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2757   }
2758
2759   protected void avTreeBlosumMenuItem_actionPerformed()
2760   {
2761     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2762   }
2763
2764   void NewTreePanel(String type, String pwType, String title)
2765   {
2766     // are the sequences aligned?
2767     if (!viewport.getAlignment().isAligned(false))
2768     {
2769       SequenceI current;
2770       int Width = viewport.getAlignment().getWidth();
2771
2772       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2773       {
2774         current = viewport.getAlignment().getSequenceAt(i);
2775
2776         if (current.getLength() < Width)
2777         {
2778           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2779         }
2780       }
2781       alignPanel.paintAlignment(true);
2782
2783     }
2784
2785     if ((viewport.getSelectionGroup() != null && viewport
2786             .getSelectionGroup().getSize() > 1)
2787             || (viewport.getAlignment().getHeight() > 1))
2788     {
2789       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2790
2791       addTreeMenuItem(tp, title);
2792
2793       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2794     }
2795   }
2796
2797   void loadTree_actionPerformed()
2798   {
2799     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2800     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2801     cap.setTreeImport();
2802     Frame frame = new Frame();
2803     frame.add(cap);
2804     jalview.bin.JalviewLite.addFrame(frame,
2805             MessageManager.getString("label.paste_newick_file"), 400, 300);
2806   }
2807
2808   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2809   {
2810     TreePanel tp = new TreePanel(alignPanel, treeFile,
2811             MessageManager.getString("label.load_tree_from_file"), tree);
2812     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2813     addTreeMenuItem(tp, treeFile);
2814   }
2815
2816   /**
2817    * sort the alignment using the given treePanel
2818    *
2819    * @param treePanel
2820    *          tree used to sort view
2821    * @param title
2822    *          string used for undo event name
2823    */
2824   public void sortByTree(TreePanel treePanel, String title)
2825   {
2826     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2827     AlignmentSorter
2828             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2829     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2830     // HistoryItem.SORT));
2831     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2832             "label.order_by_params", new String[]
2833             { title }), oldOrder, viewport.getAlignment()));
2834     alignPanel.paintAlignment(true);
2835   }
2836
2837   /**
2838    * Do any automatic reordering of the alignment and add the necessary bits to
2839    * the menu structure for the new tree
2840    *
2841    * @param treePanel
2842    * @param title
2843    */
2844   protected void addTreeMenuItem(final TreePanel treePanel,
2845           final String title)
2846   {
2847     final MenuItem item = new MenuItem(title);
2848     sortByTreeMenu.add(item);
2849     item.addActionListener(new java.awt.event.ActionListener()
2850     {
2851       @Override
2852       public void actionPerformed(ActionEvent evt)
2853       {
2854         sortByTree(treePanel, title); // treePanel.getTitle());
2855       }
2856     });
2857
2858     treePanel.addWindowListener(new WindowAdapter()
2859     {
2860       @Override
2861       public void windowOpened(WindowEvent e)
2862       {
2863         if (viewport.sortByTree)
2864         {
2865           sortByTree(treePanel, title);
2866         }
2867         super.windowOpened(e);
2868       }
2869
2870       @Override
2871       public void windowClosing(WindowEvent e)
2872       {
2873         sortByTreeMenu.remove(item);
2874       };
2875     });
2876   }
2877
2878   public boolean sortBy(AlignmentOrder alorder, String undoname)
2879   {
2880     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2881     if (viewport.applet.debug)
2882     {
2883       System.err.println("Sorting " + alorder.getOrder().size()
2884               + " in alignment '" + getTitle() + "'");
2885     }
2886     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2887     if (undoname != null)
2888     {
2889       addHistoryItem(new OrderCommand(undoname, oldOrder,
2890               viewport.getAlignment()));
2891     }
2892     alignPanel.paintAlignment(true);
2893     return true;
2894   }
2895
2896   protected void documentation_actionPerformed()
2897   {
2898     alignPanel.av.applet.openJalviewHelpUrl();
2899   }
2900
2901   protected void about_actionPerformed()
2902   {
2903
2904     class AboutPanel extends Canvas
2905     {
2906       String version;
2907
2908       String builddate;
2909
2910       public AboutPanel(String version, String builddate)
2911       {
2912         this.version = version;
2913         this.builddate = builddate;
2914       }
2915
2916       @Override
2917       public void paint(Graphics g)
2918       {
2919         g.setColor(Color.white);
2920         g.fillRect(0, 0, getSize().width, getSize().height);
2921         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2922         FontMetrics fm = g.getFontMetrics();
2923         int fh = fm.getHeight();
2924         int y = 5, x = 7;
2925         g.setColor(Color.black);
2926         // TODO: update this text for each release or centrally store it for
2927         // lite and application
2928         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2929         g.drawString(MessageManager.formatMessage(
2930                 "label.jalviewLite_release", new String[]
2931                 { version }), x, y += fh);
2932         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2933         g.drawString(MessageManager.formatMessage(
2934                 "label.jaview_build_date", new String[]
2935                 { builddate }), x, y += fh);
2936         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2937         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2938                 x, y += fh * 1.5);
2939         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2940                 x + 50, y += fh + 8);
2941         g.drawString(
2942                 MessageManager.getString("label.jalview_dev_managers"), x,
2943                 y += fh);
2944         g.drawString(MessageManager
2945                 .getString("label.jalview_distribution_lists"), x, y += fh);
2946         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2947                 x, y += fh + 8);
2948         g.drawString(
2949                 MessageManager.getString("label.jalview_cite_1_authors"),
2950                 x, y += fh);
2951         g.drawString(
2952                 MessageManager.getString("label.jalview_cite_1_title"), x,
2953                 y += fh);
2954         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2955                 x, y += fh);
2956       }
2957     }
2958
2959     Frame frame = new Frame();
2960     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2961             .getBuildDate()));
2962     jalview.bin.JalviewLite.addFrame(frame,
2963             MessageManager.getString("label.jalview"), 580, 220);
2964
2965   }
2966
2967   public void showURL(String url, String target)
2968   {
2969     if (viewport.applet == null)
2970     {
2971       System.out.println("Not running as applet - no browser available.");
2972     }
2973     else
2974     {
2975       viewport.applet.showURL(url, target);
2976     }
2977   }
2978
2979   // ////////////////////////////////////////////////////////////////////////////////
2980   // JBuilder Graphics here
2981
2982   MenuBar alignFrameMenuBar = new MenuBar();
2983
2984   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2985
2986   MenuItem loadApplication = new MenuItem(
2987           MessageManager.getString("label.view_full_application"));
2988
2989   MenuItem loadTree = new MenuItem(
2990           MessageManager.getString("label.load_associated_tree"));
2991
2992   MenuItem loadAnnotations = new MenuItem(
2993           MessageManager.getString("label.load_features_annotations"));
2994
2995   MenuItem outputFeatures = new MenuItem(
2996           MessageManager.getString("label.export_features"));
2997
2998   MenuItem outputAnnotations = new MenuItem(
2999           MessageManager.getString("label.export_annotations"));
3000
3001   MenuItem closeMenuItem = new MenuItem(
3002           MessageManager.getString("action.close"));
3003
3004   MenuItem selectAllSequenceMenuItem = new MenuItem(
3005           MessageManager.getString("action.select_all"));
3006
3007   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3008           MessageManager.getString("action.deselect_all"));
3009
3010   MenuItem invertSequenceMenuItem = new MenuItem(
3011           MessageManager.getString("action.invert_selection"));
3012
3013   MenuItem remove2LeftMenuItem = new MenuItem();
3014
3015   MenuItem remove2RightMenuItem = new MenuItem();
3016
3017   MenuItem removeGappedColumnMenuItem = new MenuItem();
3018
3019   MenuItem removeAllGapsMenuItem = new MenuItem();
3020
3021   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3022
3023   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3024
3025   MenuItem sortPairwiseMenuItem = new MenuItem();
3026
3027   MenuItem sortIDMenuItem = new MenuItem();
3028
3029   MenuItem sortLengthMenuItem = new MenuItem();
3030
3031   MenuItem sortGroupMenuItem = new MenuItem();
3032
3033   MenuItem removeRedundancyMenuItem = new MenuItem();
3034
3035   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3036
3037   MenuItem PCAMenuItem = new MenuItem();
3038
3039   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3040
3041   MenuItem neighbourTreeMenuItem = new MenuItem();
3042
3043   BorderLayout borderLayout1 = new BorderLayout();
3044
3045   public Label statusBar = new Label();
3046
3047   MenuItem clustalColour = new MenuItem();
3048
3049   MenuItem zappoColour = new MenuItem();
3050
3051   MenuItem taylorColour = new MenuItem();
3052
3053   MenuItem hydrophobicityColour = new MenuItem();
3054
3055   MenuItem helixColour = new MenuItem();
3056
3057   MenuItem strandColour = new MenuItem();
3058
3059   MenuItem turnColour = new MenuItem();
3060
3061   MenuItem buriedColour = new MenuItem();
3062
3063   MenuItem purinePyrimidineColour = new MenuItem();
3064
3065   // MenuItem RNAInteractionColour = new MenuItem();
3066
3067   MenuItem RNAHelixColour = new MenuItem();
3068
3069   MenuItem userDefinedColour = new MenuItem();
3070
3071   MenuItem PIDColour = new MenuItem();
3072
3073   MenuItem BLOSUM62Colour = new MenuItem();
3074
3075   MenuItem tcoffeeColour = new MenuItem();
3076
3077   MenuItem njTreeBlosumMenuItem = new MenuItem();
3078
3079   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3080
3081   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3082
3083   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3084
3085   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3086
3087   MenuItem alProperties = new MenuItem(
3088           MessageManager.getString("label.alignment_props"));
3089
3090   MenuItem overviewMenuItem = new MenuItem();
3091
3092   MenuItem undoMenuItem = new MenuItem();
3093
3094   MenuItem redoMenuItem = new MenuItem();
3095
3096   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3097
3098   MenuItem noColourmenuItem = new MenuItem();
3099
3100   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3101
3102   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3103
3104   MenuItem findMenuItem = new MenuItem();
3105
3106   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3107
3108   MenuItem nucleotideColour = new MenuItem();
3109
3110   MenuItem deleteGroups = new MenuItem();
3111
3112   MenuItem grpsFromSelection = new MenuItem();
3113
3114   MenuItem createGroup = new MenuItem();
3115
3116   MenuItem unGroup = new MenuItem();
3117
3118   MenuItem delete = new MenuItem();
3119
3120   MenuItem copy = new MenuItem();
3121
3122   MenuItem cut = new MenuItem();
3123
3124   Menu pasteMenu = new Menu();
3125
3126   MenuItem pasteNew = new MenuItem();
3127
3128   MenuItem pasteThis = new MenuItem();
3129
3130   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3131
3132   MenuItem font = new MenuItem();
3133
3134   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3135
3136   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3137
3138   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3139
3140   MenuItem modifyPID = new MenuItem();
3141
3142   MenuItem modifyConservation = new MenuItem();
3143
3144   CheckboxMenuItem autoCalculate = null;
3145
3146   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3147           "Sort Alignment With New Tree", true);
3148
3149   Menu sortByTreeMenu = new Menu();
3150
3151   MenuItem inputText = new MenuItem();
3152
3153   MenuItem documentation = new MenuItem();
3154
3155   MenuItem about = new MenuItem();
3156
3157   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3158
3159   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3160
3161   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3162
3163   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3164
3165   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3166
3167   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3168
3169   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3170
3171   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3174
3175   /**
3176    * Initialise menus and other items
3177    *
3178    * @throws Exception
3179    */
3180   private void jbInit() throws Exception
3181   {
3182     setMenuBar(alignFrameMenuBar);
3183
3184     /*
3185      * Configure File menu items and actions
3186      */
3187     inputText
3188             .setLabel(MessageManager.getString("label.input_from_textbox"));
3189     inputText.addActionListener(this);
3190     Menu outputTextboxMenu = new Menu(
3191             MessageManager.getString("label.out_to_textbox"));
3192     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3193     {
3194
3195       MenuItem item = new MenuItem(
3196               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3197
3198       item.addActionListener(new java.awt.event.ActionListener()
3199       {
3200         @Override
3201         public void actionPerformed(ActionEvent e)
3202         {
3203           outputText_actionPerformed(e);
3204         }
3205       });
3206
3207       outputTextboxMenu.add(item);
3208     }
3209     closeMenuItem.addActionListener(this);
3210     loadApplication.addActionListener(this);
3211     loadTree.addActionListener(this);
3212     loadAnnotations.addActionListener(this);
3213     outputFeatures.addActionListener(this);
3214     outputAnnotations.addActionListener(this);
3215
3216     /*
3217      * Configure Edit menu items and actions
3218      */
3219     undoMenuItem.setEnabled(false);
3220     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3221     undoMenuItem.addActionListener(this);
3222     redoMenuItem.setEnabled(false);
3223     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3224     redoMenuItem.addActionListener(this);
3225     copy.setLabel(MessageManager.getString("action.copy"));
3226     copy.addActionListener(this);
3227     cut.setLabel(MessageManager.getString("action.cut"));
3228     cut.addActionListener(this);
3229     delete.setLabel(MessageManager.getString("action.delete"));
3230     delete.addActionListener(this);
3231     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3232     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3233     pasteNew.addActionListener(this);
3234     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3235     pasteThis.addActionListener(this);
3236     remove2LeftMenuItem.setLabel(MessageManager
3237             .getString("action.remove_left"));
3238     remove2LeftMenuItem.addActionListener(this);
3239     remove2RightMenuItem.setLabel(MessageManager
3240             .getString("action.remove_right"));
3241     remove2RightMenuItem.addActionListener(this);
3242     removeGappedColumnMenuItem.setLabel(MessageManager
3243             .getString("action.remove_empty_columns"));
3244     removeGappedColumnMenuItem.addActionListener(this);
3245     removeAllGapsMenuItem.setLabel(MessageManager
3246             .getString("action.remove_all_gaps"));
3247     removeAllGapsMenuItem.addActionListener(this);
3248     removeRedundancyMenuItem.setLabel(MessageManager
3249             .getString("action.remove_redundancy"));
3250     removeRedundancyMenuItem.addActionListener(this);
3251
3252     /*
3253      * Configure Select menu items and actions
3254      */
3255     findMenuItem.setLabel(MessageManager.getString("action.find"));
3256     findMenuItem.addActionListener(this);
3257     selectAllSequenceMenuItem.addActionListener(this);
3258     deselectAllSequenceMenuItem.addActionListener(this);
3259     invertSequenceMenuItem.setLabel(MessageManager
3260             .getString("action.invert_sequence_selection"));
3261     invertSequenceMenuItem.addActionListener(this);
3262     invertColSel.setLabel(MessageManager
3263             .getString("action.invert_column_selection"));
3264     invertColSel.addActionListener(this);
3265     deleteGroups.setLabel(MessageManager
3266             .getString("action.undefine_groups"));
3267     deleteGroups.addActionListener(this);
3268     grpsFromSelection.setLabel(MessageManager
3269             .getString("action.make_groups_selection"));
3270     grpsFromSelection.addActionListener(this);
3271     createGroup.setLabel(MessageManager.getString("action.create_group"));
3272     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3273     annotationColumnSelection.setLabel(MessageManager
3274             .getString("action.select_by_annotation"));
3275     annotationColumnSelection.addActionListener(this);
3276
3277     /*
3278      * Configure View menu items and actions
3279      */
3280     newView.setLabel(MessageManager.getString("action.new_view"));
3281     newView.addActionListener(this);
3282     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3283     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3284     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3285     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3286     hideColumns
3287             .setLabel(MessageManager.getString("label.selected_columns"));
3288     hideSequences.setLabel(MessageManager
3289             .getString("label.selected_sequences"));
3290     hideAllButSelection.setLabel(MessageManager
3291             .getString("label.all_but_selected_region"));
3292     hideAllSelection.setLabel(MessageManager
3293             .getString("label.selected_region"));
3294     showAllHidden.setLabel(MessageManager
3295             .getString("label.all_sequences_columns"));
3296     showColumns.addActionListener(this);
3297     showSeqs.addActionListener(this);
3298     hideColumns.addActionListener(this);
3299     hideSequences.addActionListener(this);
3300     hideAllButSelection.addActionListener(this);
3301     hideAllSelection.addActionListener(this);
3302     showAllHidden.addActionListener(this);
3303     featureSettings.setLabel(MessageManager
3304             .getString("action.feature_settings"));
3305     featureSettings.addActionListener(this);
3306     sequenceFeatures.setLabel(MessageManager
3307             .getString("label.show_sequence_features"));
3308     sequenceFeatures.addItemListener(this);
3309     sequenceFeatures.setState(false);
3310     followMouseOverFlag.setLabel(MessageManager
3311             .getString("label.automatic_scrolling"));
3312     followMouseOverFlag.addItemListener(this);
3313     alProperties.addActionListener(this);
3314     overviewMenuItem.setLabel(MessageManager
3315             .getString("label.overview_window"));
3316     overviewMenuItem.addActionListener(this);
3317
3318     /*
3319      * Configure Annotations menu items and actions
3320      */
3321     annotationPanelMenuItem.setLabel(MessageManager
3322             .getString("label.show_annotations"));
3323     annotationPanelMenuItem.addItemListener(this);
3324     showGroupConsensus.setLabel(MessageManager
3325             .getString("label.group_consensus"));
3326     showGroupConservation.setLabel(MessageManager
3327             .getString("label.group_conservation"));
3328     showConsensusHistogram.setLabel(MessageManager
3329             .getString("label.show_consensus_histogram"));
3330     showSequenceLogo.setLabel(MessageManager
3331             .getString("label.show_consensus_logo"));
3332     normSequenceLogo.setLabel(MessageManager
3333             .getString("label.norm_consensus_logo"));
3334     applyAutoAnnotationSettings.setLabel(MessageManager
3335             .getString("label.apply_all_groups"));
3336     applyAutoAnnotationSettings.setState(true);
3337     Menu autoAnnMenu = new Menu(
3338             MessageManager.getString("label.autocalculated_annotation"));
3339     showGroupConsensus.addItemListener(this);
3340     showGroupConservation.addItemListener(this);
3341     showConsensusHistogram.addItemListener(this);
3342     showSequenceLogo.addItemListener(this);
3343     normSequenceLogo.addItemListener(this);
3344     applyAutoAnnotationSettings.addItemListener(this);
3345     showAlignmentAnnotations = new CheckboxMenuItem(
3346             MessageManager.getString("label.show_all_al_annotations"));
3347     showSequenceAnnotations = new CheckboxMenuItem(
3348             MessageManager.getString("label.show_all_seq_annotations"));
3349     sortAnnBySequence = new CheckboxMenuItem(
3350             MessageManager.getString("label.sort_annotations_by_sequence"));
3351     sortAnnByLabel = new CheckboxMenuItem(
3352             MessageManager.getString("label.sort_annotations_by_label"));
3353     showAutoFirst = new CheckboxMenuItem(
3354             MessageManager.getString("label.show_first"));
3355     showAutoLast = new CheckboxMenuItem(
3356             MessageManager.getString("label.show_last"));
3357     showAlignmentAnnotations.addItemListener(this);
3358     showSequenceAnnotations.addItemListener(this);
3359     sortAnnBySequence.addItemListener(this);
3360     sortAnnByLabel.addItemListener(this);
3361     showAutoFirst.addItemListener(this);
3362     showAutoLast.addItemListener(this);
3363
3364     /*
3365      * Configure Format menu items and actions
3366      */
3367     font.setLabel(MessageManager.getString("action.font"));
3368     font.addActionListener(this);
3369     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3370     scaleAbove.setState(true);
3371     scaleAbove.setEnabled(false);
3372     scaleAbove.addItemListener(this);
3373     scaleLeft.setEnabled(false);
3374     scaleLeft.setState(true);
3375     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3376     scaleLeft.addItemListener(this);
3377     scaleRight.setEnabled(false);
3378     scaleRight.setState(true);
3379     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3380     scaleRight.addItemListener(this);
3381     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3382     viewBoxesMenuItem.setState(true);
3383     viewBoxesMenuItem.addItemListener(this);
3384     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3385     viewTextMenuItem.setState(true);
3386     viewTextMenuItem.addItemListener(this);
3387     colourTextMenuItem.setLabel(MessageManager
3388             .getString("label.colour_text"));
3389     colourTextMenuItem.addItemListener(this);
3390     displayNonconservedMenuItem.setLabel(MessageManager
3391             .getString("label.show_non_conversed"));
3392     displayNonconservedMenuItem.addItemListener(this);
3393     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3394     wrapMenuItem.addItemListener(this);
3395     renderGapsMenuItem.setLabel(MessageManager
3396             .getString("action.show_gaps"));
3397     renderGapsMenuItem.setState(true);
3398     renderGapsMenuItem.addItemListener(this);
3399     centreColumnLabelFlag.setLabel(MessageManager
3400             .getString("label.centre_column_labels"));
3401     centreColumnLabelFlag.addItemListener(this);
3402     seqLimits.setState(true);
3403     seqLimits.setLabel(MessageManager
3404             .getString("label.show_sequence_limits"));
3405     seqLimits.addItemListener(this);
3406
3407     /*
3408      * Configure Colour menu items and actions
3409      */
3410     applyToAllGroups.setLabel(MessageManager
3411             .getString("label.apply_colour_to_all_groups"));
3412     applyToAllGroups.setState(true);
3413     applyToAllGroups.addItemListener(this);
3414     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3415     clustalColour.addActionListener(this);
3416     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3417     zappoColour.addActionListener(this);
3418     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3419     taylorColour.addActionListener(this);
3420     hydrophobicityColour.setLabel(MessageManager
3421             .getString("label.hydrophobicity"));
3422     hydrophobicityColour.addActionListener(this);
3423     helixColour
3424             .setLabel(MessageManager.getString("label.helix_propensity"));
3425     helixColour.addActionListener(this);
3426     strandColour.setLabel(MessageManager
3427             .getString("label.strand_propensity"));
3428     strandColour.addActionListener(this);
3429     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3430     turnColour.addActionListener(this);
3431     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3432     buriedColour.addActionListener(this);
3433     purinePyrimidineColour.setLabel(MessageManager
3434             .getString("label.purine_pyrimidine"));
3435     purinePyrimidineColour.addActionListener(this);
3436     // RNAInteractionColour.setLabel(MessageManager
3437     // .getString("label.rna_interaction"));
3438     // RNAInteractionColour.addActionListener(this);
3439     RNAHelixColour.setLabel(MessageManager
3440             .getString("action.by_rna_helixes"));
3441     RNAHelixColour.addActionListener(this);
3442     userDefinedColour.setLabel(MessageManager
3443             .getString("action.user_defined"));
3444     userDefinedColour.addActionListener(this);
3445     PIDColour.setLabel(MessageManager
3446             .getString("label.percentage_identity"));
3447     PIDColour.addActionListener(this);
3448     BLOSUM62Colour.setLabel(MessageManager
3449             .getString("label.blosum62_score"));
3450     BLOSUM62Colour.addActionListener(this);
3451     tcoffeeColour
3452             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3453     // it will be enabled only if a score file is provided
3454     tcoffeeColour.setEnabled(false);
3455     tcoffeeColour.addActionListener(this);
3456     conservationMenuItem.setLabel(MessageManager
3457             .getString("action.by_conservation"));
3458     conservationMenuItem.addItemListener(this);
3459     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3460     noColourmenuItem.addActionListener(this);
3461     abovePIDThreshold.setLabel(MessageManager
3462             .getString("label.above_identity_threshold"));
3463     abovePIDThreshold.addItemListener(this);
3464     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3465     nucleotideColour.addActionListener(this);
3466     modifyPID.setLabel(MessageManager
3467             .getString("label.modify_identity_thereshold"));
3468     modifyPID.addActionListener(this);
3469     modifyConservation.setLabel(MessageManager
3470             .getString("label.modify_conservation_thereshold"));
3471     modifyConservation.addActionListener(this);
3472     annotationColour.setLabel(MessageManager
3473             .getString("action.by_annotation"));
3474     annotationColour.addActionListener(this);
3475
3476     /*
3477      * Configure Calculate menu items and actions
3478      */
3479     sortPairwiseMenuItem.setLabel(MessageManager
3480             .getString("action.by_pairwise_id"));
3481     sortPairwiseMenuItem.addActionListener(this);
3482     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3483     sortIDMenuItem.addActionListener(this);
3484     sortLengthMenuItem.setLabel(MessageManager
3485             .getString("action.by_length"));
3486     sortLengthMenuItem.addActionListener(this);
3487     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3488     sortGroupMenuItem.addActionListener(this);
3489     pairwiseAlignmentMenuItem.setLabel(MessageManager
3490             .getString("action.pairwise_alignment"));
3491     pairwiseAlignmentMenuItem.addActionListener(this);
3492     PCAMenuItem.setLabel(MessageManager
3493             .getString("label.principal_component_analysis"));
3494     PCAMenuItem.addActionListener(this);
3495     autoCalculate = new CheckboxMenuItem(
3496             MessageManager.getString("label.autocalculate_consensus"), true);
3497     averageDistanceTreeMenuItem.setLabel(MessageManager
3498             .getString("label.average_distance_identity"));
3499     averageDistanceTreeMenuItem.addActionListener(this);
3500     neighbourTreeMenuItem.setLabel(MessageManager
3501             .getString("label.neighbour_joining_identity"));
3502     neighbourTreeMenuItem.addActionListener(this);
3503     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3504             .getString("label.average_distance_bloslum62"));
3505     avDistanceTreeBlosumMenuItem.addActionListener(this);
3506     njTreeBlosumMenuItem.setLabel(MessageManager
3507             .getString("label.neighbour_blosum62"));
3508     njTreeBlosumMenuItem.addActionListener(this);
3509     sortByTreeMenu.setLabel(MessageManager
3510             .getString("action.by_tree_order"));
3511     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3512     Menu calculateTreeMenu = new Menu(
3513             MessageManager.getString("action.calculate_tree"));
3514     autoCalculate.addItemListener(this);
3515     sortByTree.addItemListener(this);
3516
3517     /*
3518      * Configure Help menu items and actions
3519      */
3520     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3521     documentation.setLabel(MessageManager.getString("label.documentation"));
3522     documentation.addActionListener(this);
3523     about.setLabel(MessageManager.getString("label.about"));
3524     about.addActionListener(this);
3525
3526     /*
3527      * Add top level menus to frame
3528      */
3529     alignFrameMenuBar.add(fileMenu);
3530     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3531     alignFrameMenuBar.add(editMenu);
3532     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3533     alignFrameMenuBar.add(selectMenu);
3534     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3535     alignFrameMenuBar.add(viewMenu);
3536     Menu annotationsMenu = new Menu(
3537             MessageManager.getString("action.annotations"));
3538     alignFrameMenuBar.add(annotationsMenu);
3539     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3540     alignFrameMenuBar.add(formatMenu);
3541     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3542     alignFrameMenuBar.add(colourMenu);
3543     Menu calculateMenu = new Menu(
3544             MessageManager.getString("action.calculate"));
3545     alignFrameMenuBar.add(calculateMenu);
3546     alignFrameMenuBar.add(helpMenu);
3547
3548     /*
3549      * File menu
3550      */
3551     fileMenu.add(inputText);
3552     fileMenu.add(loadTree);
3553     fileMenu.add(loadAnnotations);
3554     fileMenu.addSeparator();
3555     fileMenu.add(outputTextboxMenu);
3556     fileMenu.add(outputFeatures);
3557     fileMenu.add(outputAnnotations);
3558     if (jalviewServletURL != null)
3559     {
3560       fileMenu.add(loadApplication);
3561     }
3562     fileMenu.addSeparator();
3563     fileMenu.add(closeMenuItem);
3564
3565     /*
3566      * Edit menu
3567      */
3568     editMenu.add(undoMenuItem);
3569     editMenu.add(redoMenuItem);
3570     editMenu.add(cut);
3571     editMenu.add(copy);
3572     pasteMenu.add(pasteNew);
3573     pasteMenu.add(pasteThis);
3574     editMenu.add(pasteMenu);
3575     editMenu.add(delete);
3576     editMenu.addSeparator();
3577     editMenu.add(remove2LeftMenuItem);
3578     editMenu.add(remove2RightMenuItem);
3579     editMenu.add(removeGappedColumnMenuItem);
3580     editMenu.add(removeAllGapsMenuItem);
3581     editMenu.add(removeRedundancyMenuItem);
3582
3583     /*
3584      * Select menu
3585      */
3586     selectMenu.add(findMenuItem);
3587     selectMenu.addSeparator();
3588     selectMenu.add(selectAllSequenceMenuItem);
3589     selectMenu.add(deselectAllSequenceMenuItem);
3590     selectMenu.add(invertSequenceMenuItem);
3591     selectMenu.add(invertColSel);
3592     selectMenu.add(createGroup);
3593     selectMenu.add(unGroup);
3594     selectMenu.add(grpsFromSelection);
3595     selectMenu.add(deleteGroups);
3596     selectMenu.add(annotationColumnSelection);
3597
3598     /*
3599      * View menu
3600      */
3601     viewMenu.add(newView);
3602     viewMenu.addSeparator();
3603     showMenu.add(showColumns);
3604     showMenu.add(showSeqs);
3605     showMenu.add(showAllHidden);
3606     viewMenu.add(showMenu);
3607     hideMenu.add(hideColumns);
3608     hideMenu.add(hideSequences);
3609     hideMenu.add(hideAllSelection);
3610     hideMenu.add(hideAllButSelection);
3611     viewMenu.add(hideMenu);
3612     viewMenu.addSeparator();
3613     viewMenu.add(followMouseOverFlag);
3614     viewMenu.addSeparator();
3615     viewMenu.add(sequenceFeatures);
3616     viewMenu.add(featureSettings);
3617     viewMenu.addSeparator();
3618     viewMenu.add(alProperties);
3619     viewMenu.addSeparator();
3620     viewMenu.add(overviewMenuItem);
3621
3622     /*
3623      * Annotations menu
3624      */
3625     annotationsMenu.add(annotationPanelMenuItem);
3626     annotationsMenu.addSeparator();
3627     annotationsMenu.add(showAlignmentAnnotations);
3628     annotationsMenu.add(showSequenceAnnotations);
3629     annotationsMenu.add(sortAnnBySequence);
3630     annotationsMenu.add(sortAnnByLabel);
3631     annotationsMenu.addSeparator();
3632     autoAnnMenu.add(showAutoFirst);
3633     autoAnnMenu.add(showAutoLast);
3634     autoAnnMenu.addSeparator();
3635     autoAnnMenu.add(applyAutoAnnotationSettings);
3636     autoAnnMenu.add(showConsensusHistogram);
3637     autoAnnMenu.add(showSequenceLogo);
3638     autoAnnMenu.add(normSequenceLogo);
3639     autoAnnMenu.addSeparator();
3640     autoAnnMenu.add(showGroupConservation);
3641     autoAnnMenu.add(showGroupConsensus);
3642     annotationsMenu.add(autoAnnMenu);
3643
3644     /*
3645      * Format menu
3646      */
3647     formatMenu.add(font);
3648     formatMenu.add(seqLimits);
3649     formatMenu.add(wrapMenuItem);
3650     formatMenu.add(scaleAbove);
3651     formatMenu.add(scaleLeft);
3652     formatMenu.add(scaleRight);
3653     formatMenu.add(viewBoxesMenuItem);
3654     formatMenu.add(viewTextMenuItem);
3655     formatMenu.add(colourTextMenuItem);
3656     formatMenu.add(displayNonconservedMenuItem);
3657     formatMenu.add(renderGapsMenuItem);
3658     formatMenu.add(centreColumnLabelFlag);
3659
3660     /*
3661      * Colour menu
3662      */
3663     colourMenu.add(applyToAllGroups);
3664     colourMenu.addSeparator();
3665     colourMenu.add(noColourmenuItem);
3666     colourMenu.add(clustalColour);
3667     colourMenu.add(BLOSUM62Colour);
3668     colourMenu.add(PIDColour);
3669     colourMenu.add(zappoColour);
3670     colourMenu.add(taylorColour);
3671     colourMenu.add(hydrophobicityColour);
3672     colourMenu.add(helixColour);
3673     colourMenu.add(strandColour);
3674     colourMenu.add(turnColour);
3675     colourMenu.add(buriedColour);
3676     colourMenu.add(nucleotideColour);
3677     colourMenu.add(purinePyrimidineColour);
3678     // colourMenu.add(RNAInteractionColour);
3679     colourMenu.add(tcoffeeColour);
3680     colourMenu.add(userDefinedColour);
3681     colourMenu.addSeparator();
3682     colourMenu.add(conservationMenuItem);
3683     colourMenu.add(modifyConservation);
3684     colourMenu.add(abovePIDThreshold);
3685     colourMenu.add(modifyPID);
3686     colourMenu.add(annotationColour);
3687     colourMenu.add(RNAHelixColour);
3688
3689     /*
3690      * Calculate menu
3691      */
3692     sortMenu.add(sortIDMenuItem);
3693     sortMenu.add(sortLengthMenuItem);
3694     sortMenu.add(sortByTreeMenu);
3695     sortMenu.add(sortGroupMenuItem);
3696     sortMenu.add(sortPairwiseMenuItem);
3697     calculateMenu.add(sortMenu);
3698     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3699     calculateTreeMenu.add(neighbourTreeMenuItem);
3700     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3701     calculateTreeMenu.add(njTreeBlosumMenuItem);
3702     calculateMenu.add(calculateTreeMenu);
3703     calculateMenu.addSeparator();
3704     calculateMenu.add(pairwiseAlignmentMenuItem);
3705     calculateMenu.add(PCAMenuItem);
3706     calculateMenu.add(autoCalculate);
3707     calculateMenu.add(sortByTree);
3708
3709     /*
3710      * Help menu
3711      */
3712     helpMenu.add(documentation);
3713     helpMenu.add(about);
3714
3715     /*
3716      * Status bar
3717      */
3718     statusBar.setBackground(Color.white);
3719     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3720     statusBar.setText(MessageManager.getString("label.status_bar"));
3721     this.add(statusBar, BorderLayout.SOUTH);
3722   }
3723
3724   public void setStatus(String string)
3725   {
3726     statusBar.setText(string);
3727   };
3728
3729   MenuItem featureSettings = new MenuItem();
3730
3731   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3732
3733   MenuItem annotationColour = new MenuItem();
3734
3735   MenuItem annotationColumnSelection = new MenuItem();
3736
3737   MenuItem invertColSel = new MenuItem();
3738
3739   MenuItem showColumns = new MenuItem();
3740
3741   MenuItem showSeqs = new MenuItem();
3742
3743   MenuItem hideColumns = new MenuItem();
3744
3745   MenuItem hideSequences = new MenuItem();
3746
3747   MenuItem hideAllButSelection = new MenuItem();
3748
3749   MenuItem hideAllSelection = new MenuItem();
3750
3751   MenuItem showAllHidden = new MenuItem();
3752
3753   MenuItem newView = new MenuItem();
3754
3755   private CheckboxMenuItem showAlignmentAnnotations;
3756
3757   private CheckboxMenuItem showSequenceAnnotations;
3758
3759   private CheckboxMenuItem sortAnnBySequence;
3760
3761   private CheckboxMenuItem sortAnnByLabel;
3762
3763   private CheckboxMenuItem showAutoFirst;
3764
3765   private CheckboxMenuItem showAutoLast;
3766
3767   private SplitFrame splitFrame;
3768
3769   /**
3770    * Attach the alignFrame panels after embedding menus, if necessary. This used
3771    * to be called setEmbedded, but is now creates the dropdown menus in a
3772    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3773    *
3774    * @param reallyEmbedded
3775    *          true to attach the view to the applet area on the page rather than
3776    *          in a new window
3777    */
3778   public void createAlignFrameWindow(boolean reallyEmbedded)
3779   {
3780     if (reallyEmbedded)
3781     {
3782       embedAlignFrameInApplet(viewport.applet);
3783     }
3784     else
3785     {
3786       // //////
3787       // test and embed menu bar if necessary.
3788       //
3789       if (embedMenuIfNeeded(alignPanel))
3790       {
3791         /*
3792          * adjust for status bar height too. ? pointless as overridden by layout
3793          * manager
3794          */
3795         alignPanel.setSize(getSize().width,
3796                 getSize().height - statusBar.getHeight());
3797       }
3798       add(statusBar, BorderLayout.SOUTH);
3799       add(alignPanel, BorderLayout.CENTER);
3800       // and register with the applet so it can pass external API calls to us
3801       jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3802               frameWidth,
3803               frameHeight);
3804     }
3805   }
3806
3807   /**
3808    * Add the components of this AlignFrame to the applet container.
3809    *
3810    * @param theApplet
3811    */
3812   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3813   {
3814     // ////
3815     // Explicitly build the embedded menu panel for the on-page applet
3816     //
3817     // view cannot be closed if its actually on the page
3818     fileMenu.remove(closeMenuItem);
3819     fileMenu.remove(3); // Remove Separator
3820     // construct embedded menu, using default font
3821     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3822     // and actually add the components to the applet area
3823     theApplet.setLayout(new BorderLayout());
3824     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3825     theApplet.add(statusBar, BorderLayout.SOUTH);
3826     // TODO should size be left to the layout manager?
3827     alignPanel.setSize(theApplet.getSize().width,
3828             theApplet.getSize().height - embeddedMenu.getHeight()
3829                     - statusBar.getHeight());
3830     theApplet.add(alignPanel, BorderLayout.CENTER);
3831     final AlignFrame me = this;
3832     theApplet.addFocusListener(new FocusListener()
3833     {
3834
3835       @Override
3836       public void focusLost(FocusEvent e)
3837       {
3838         if (theApplet.currentAlignFrame == me)
3839         {
3840           theApplet.currentAlignFrame = null;
3841         }
3842       }
3843
3844       @Override
3845       public void focusGained(FocusEvent e)
3846       {
3847         theApplet.currentAlignFrame = me;
3848       }
3849     });
3850     theApplet.validate();
3851   }
3852
3853   /**
3854    * create a new binding between structures in an existing jmol viewer instance
3855    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3856    * this does not open a new Jmol window, or modify the display of the
3857    * structures in the original jmol window. Note This method doesn't work
3858    * without an additional javascript library to exchange messages between the
3859    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3860    *
3861    * @param viewer
3862    *          JmolViewer instance
3863    * @param sequenceIds
3864    *          - sequence Ids to search for associations
3865    */
3866   public SequenceStructureBinding addStructureViewInstance(
3867           Object jmolviewer, String[] sequenceIds)
3868   {
3869     Viewer viewer = null;
3870     try
3871     {
3872       viewer = (Viewer) jmolviewer;
3873     } catch (ClassCastException ex)
3874     {
3875       System.err.println("Unsupported viewer object :"
3876               + jmolviewer.getClass());
3877     }
3878     if (viewer == null)
3879     {
3880       System.err.println("Can't use this object as a structure viewer:"
3881               + jmolviewer.getClass());
3882       return null;
3883     }
3884     SequenceI[] seqs = null;
3885     if (sequenceIds == null || sequenceIds.length == 0)
3886     {
3887       seqs = viewport.getAlignment().getSequencesArray();
3888     }
3889     else
3890     {
3891       Vector sqi = new Vector();
3892       AlignmentI al = viewport.getAlignment();
3893       for (int sid = 0; sid < sequenceIds.length; sid++)
3894       {
3895         SequenceI sq = al.findName(sequenceIds[sid]);
3896         if (sq != null)
3897         {
3898           sqi.addElement(sq);
3899         }
3900       }
3901       if (sqi.size() > 0)
3902       {
3903         seqs = new SequenceI[sqi.size()];
3904         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3905         {
3906           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3907         }
3908       }
3909       else
3910       {
3911         return null;
3912       }
3913     }
3914     AAStructureBindingModel jmv = null;
3915     // TODO: search for a jmv that involves viewer
3916     if (jmv == null)
3917     { // create a new viewer/jalview binding.
3918       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3919       { seqs });
3920     }
3921     return jmv;
3922
3923   }
3924
3925   /**
3926    * bind a pdb file to a sequence in the current view
3927    *
3928    * @param sequenceId
3929    *          - sequenceId within the dataset.
3930    * @param pdbEntryString
3931    *          - the short name for the PDB file
3932    * @param pdbFile
3933    *          - pdb file - either a URL or a valid PDB file.
3934    * @return true if binding was as success TODO: consider making an exception
3935    *         structure for indicating when PDB parsing or sequenceId location
3936    *         fails.
3937    */
3938   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3939           String pdbFile)
3940   {
3941     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3942     boolean needtoadd = false;
3943     if (toaddpdb != null)
3944     {
3945       Vector pdbe = toaddpdb.getAllPDBEntries();
3946       PDBEntry pdbentry = null;
3947       if (pdbe != null && pdbe.size() > 0)
3948       {
3949         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3950         {
3951           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3952           if (!pdbentry.getId().equals(pdbEntryString)
3953                   && !pdbentry.getFile().equals(pdbFile))
3954           {
3955             pdbentry = null;
3956           }
3957           else
3958           {
3959             continue;
3960           }
3961         }
3962       }
3963       if (pdbentry == null)
3964       {
3965         pdbentry = new PDBEntry();
3966         pdbentry.setId(pdbEntryString);
3967         pdbentry.setFile(pdbFile);
3968         needtoadd = true; // add this new entry to sequence.
3969       }
3970       // resolve data source
3971       // TODO: this code should be a refactored to an io package
3972       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3973       if (protocol == null)
3974       {
3975         return false;
3976       }
3977       if (needtoadd)
3978       {
3979         // make a note of the access mode and add
3980         if (pdbentry.getProperty() == null)
3981         {
3982           pdbentry.setProperty(new Hashtable());
3983         }
3984         pdbentry.getProperty().put("protocol", protocol);
3985         toaddpdb.addPDBId(pdbentry);
3986         alignPanel.getStructureSelectionManager()
3987                 .registerPDBEntry(pdbentry);
3988       }
3989     }
3990     return true;
3991   }
3992
3993   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3994   {
3995     if (seqs != null)
3996     {
3997       Vector sequences = new Vector();
3998       for (int i = 0; i < seqs.length; i++)
3999       {
4000         if (seqs[i] != null)
4001         {
4002           sequences.addElement(new Object[]
4003           { seqs[i], (chains != null) ? chains[i] : null });
4004         }
4005       }
4006       seqs = new SequenceI[sequences.size()];
4007       chains = new String[sequences.size()];
4008       for (int i = 0, isize = sequences.size(); i < isize; i++)
4009       {
4010         Object[] oj = (Object[]) sequences.elementAt(i);
4011
4012         seqs[i] = (SequenceI) oj[0];
4013         chains[i] = (String) oj[1];
4014       }
4015     }
4016     return new Object[]
4017     { seqs, chains };
4018
4019   }
4020
4021   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4022           SequenceI[] seqs, String[] chains, String protocol)
4023   {
4024     // Scrub any null sequences from the array
4025     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4026     seqs = (SequenceI[]) sqch[0];
4027     chains = (String[]) sqch[1];
4028     if (seqs == null || seqs.length == 0)
4029     {
4030       System.err
4031               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4032     }
4033     if (protocol == null || protocol.trim().length() == 0
4034             || protocol.equals("null"))
4035     {
4036       protocol = (String) pdb.getProperty().get("protocol");
4037       if (protocol == null)
4038       {
4039         System.err.println("Couldn't work out protocol to open structure: "
4040                 + pdb.getId());
4041         return;
4042       }
4043     }
4044     if (applet.useXtrnalSviewer)
4045     {
4046       // register the association(s) and quit, don't create any windows.
4047       if (StructureSelectionManager.getStructureSelectionManager(applet)
4048               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4049       {
4050         System.err.println("Failed to map " + pdb.getFile() + " ("
4051                 + protocol + ") to any sequences");
4052       }
4053       return;
4054     }
4055     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4056     {
4057       // can only do alignments with Jmol
4058       // find the last jmol window assigned to this alignment
4059       jalview.appletgui.AppletJmol ajm = null, tajm;
4060       Vector jmols = applet
4061               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4062       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4063       {
4064         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4065         if (tajm.ap.alignFrame == this)
4066         {
4067           ajm = tajm;
4068           break;
4069         }
4070       }
4071       if (ajm != null)
4072       {
4073         System.err
4074                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4075         // try and add the pdb structure
4076         // ajm.addS
4077         ajm = null;
4078       }
4079     }
4080     // otherwise, create a new window
4081     if (applet.jmolAvailable)
4082     {
4083       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4084               protocol);
4085       applet.lastFrameX += 40;
4086       applet.lastFrameY += 40;
4087     }
4088     else
4089     {
4090       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4091     }
4092
4093   }
4094
4095   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4096           SequenceI[][] seqs, String[][] chains, String[] protocols)
4097   {
4098     // TODO Auto-generated method stub
4099     System.err.println("Aligned Structure View: Not yet implemented.");
4100   }
4101
4102   /**
4103    * modify the current selection, providing the user has not made a selection
4104    * already.
4105    *
4106    * @param sel
4107    *          - sequences from this alignment
4108    * @param csel
4109    *          - columns to be selected on the alignment
4110    */
4111   public void select(SequenceGroup sel, ColumnSelection csel)
4112   {
4113     alignPanel.seqPanel.selection(sel, csel, null);
4114   }
4115
4116   public void scrollTo(int row, int column)
4117   {
4118     alignPanel.seqPanel.scrollTo(row, column);
4119   }
4120
4121   public void scrollToRow(int row)
4122   {
4123     alignPanel.seqPanel.scrollToRow(row);
4124   }
4125
4126   public void scrollToColumn(int column)
4127   {
4128     alignPanel.seqPanel.scrollToColumn(column);
4129   }
4130
4131   /**
4132    * @return the alignments unique ID.
4133    */
4134   public String getSequenceSetId()
4135   {
4136     return viewport.getSequenceSetId();
4137   }
4138
4139   /**
4140    * Load the (T-Coffee) score file from the specified url
4141    *
4142    * @param source
4143    *          File/URL/T-COFFEE score file contents
4144    * @throws IOException
4145    * @return true if alignment was annotated with data from source
4146    */
4147   public boolean loadScoreFile(String source) throws IOException
4148   {
4149
4150     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4151             AppletFormatAdapter.checkProtocol(source));
4152     if (!file.isValid())
4153     {
4154       // TODO: raise dialog for gui
4155       System.err.println("Problems parsing T-Coffee scores: "
4156               + file.getWarningMessage());
4157       System.err.println("Origin was:\n" + source);
4158       return false;
4159     }
4160
4161     /*
4162      * check that the score matrix matches the alignment dimensions
4163      */
4164     AlignmentI aln;
4165     if ((aln = viewport.getAlignment()) != null
4166             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4167                     .getWidth()))
4168     {
4169       // TODO: raise a dialog box here rather than bomb out.
4170       System.err
4171               .println("The scores matrix does not match the alignment dimensions");
4172
4173     }
4174
4175     // TODO add parameter to indicate if matching should be done
4176     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4177     {
4178       alignPanel.fontChanged();
4179       tcoffeeColour.setEnabled(true);
4180       // switch to this color
4181       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4182       return true;
4183     }
4184     else
4185     {
4186       System.err.println("Problems resolving T-Coffee scores:");
4187       if (file.getWarningMessage() != null)
4188       {
4189         System.err.println(file.getWarningMessage());
4190       }
4191     }
4192     return false;
4193   }
4194
4195   public SplitFrame getSplitFrame()
4196   {
4197     return this.splitFrame;
4198   }
4199
4200   public void setSplitFrame(SplitFrame sf)
4201   {
4202     this.splitFrame = sf;
4203   }
4204
4205     // may not need this
4206   @Override
4207   public void setShowSeqFeatures(boolean b)
4208   {
4209     // showSeqFeatures.setSelected(b);
4210     viewport.setShowSequenceFeatures(b);
4211
4212   }
4213
4214   @Override
4215   public void setMenusForViewport()
4216   {
4217     // setMenusFromViewport(viewport);
4218
4219   }
4220   @Override
4221   public void refreshFeatureUI(boolean enableIfNecessary)
4222   {
4223     if (enableIfNecessary)
4224     {
4225       sequenceFeatures.setState(true);
4226       alignPanel.av.setShowSequenceFeatures(true);
4227     }
4228   }
4229
4230   @Override
4231   public FeatureSettingsControllerI getFeatureSettingsUI()
4232   {
4233     return alignPanel.av.featureSettings;
4234   }
4235
4236 }