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.RNAInteractionColourScheme;
  64 import jalview.schemes.StrandColourScheme;
  65 import jalview.schemes.TCoffeeColourScheme;
  66 import jalview.schemes.TaylorColourScheme;
  67 import jalview.schemes.TurnColourScheme;
  68 import jalview.schemes.ZappoColourScheme;
  69 import jalview.structure.StructureSelectionManager;
  70 import jalview.structures.models.AAStructureBindingModel;
  71 import jalview.util.MappingUtils;
  72 import jalview.util.MessageManager;
  73 import jalview.viewmodel.AlignmentViewport;
  74
  75 import java.awt.BorderLayout;
  76 import java.awt.Canvas;
  77 import java.awt.CheckboxMenuItem;
  78 import java.awt.Color;
  79 import java.awt.Font;
  80 import java.awt.FontMetrics;
  81 import java.awt.Frame;
  82 import java.awt.Graphics;
  83 import java.awt.Label;
  84 import java.awt.Menu;
  85 import java.awt.MenuBar;
  86 import java.awt.MenuItem;
  87 import java.awt.event.ActionEvent;
  88 import java.awt.event.ActionListener;
  89 import java.awt.event.FocusEvent;
  90 import java.awt.event.FocusListener;
  91 import java.awt.event.ItemEvent;
  92 import java.awt.event.ItemListener;
  93 import java.awt.event.KeyEvent;
  94 import java.awt.event.KeyListener;
  95 import java.awt.event.WindowAdapter;
  96 import java.awt.event.WindowEvent;
  97 import java.io.IOException;
  98 import java.net.URL;
  99 import java.net.URLEncoder;
 100 import java.util.Arrays;
 101 import java.util.Deque;
 102 import java.util.HashMap;
 103 import java.util.Hashtable;
 104 import java.util.List;
 105 import java.util.Map;
 106 import java.util.StringTokenizer;
 107 import java.util.Vector;
 108
 109 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 110         ItemListener, KeyListener, AlignViewControllerGuiI
 111 {
 112   public AlignViewControllerI avc;
 113
 114   public AlignmentPanel alignPanel;
 115
 116   public AlignViewport viewport;
 117
 118   // width and height may be overridden by applet parameters
 119   int frameWidth = 700;
 120
 121   int frameHeight = 500;
 122
 123   String jalviewServletURL;
 124
 125   /*
 126    * Flag for showing autocalculated consensus above or below other consensus
 127    * rows
 128    */
 129   private boolean showAutoCalculatedAbove;
 130
 131   private SequenceAnnotationOrder annotationSortOrder;
 132
 133   /**
 134    * Constructor that creates the frame and adds it to the display.
 135    *
 136    * @param al
 137    * @param applet
 138    * @param title
 139    * @param embedded
 140    */
 141   public AlignFrame(AlignmentI al, JalviewLite applet,
 142           String title, boolean embedded)
 143   {
 144     this(al, applet, title, embedded, true);
 145   }
 146
 147   /**
 148    * Constructor that optionally allows the frame to be displayed or only
 149    * created.
 150    *
 151    * @param al
 152    * @param applet
 153    * @param title
 154    * @param embedded
 155    * @param addToDisplay
 156    */
 157   public AlignFrame(AlignmentI al, JalviewLite applet,
 158           String title, boolean embedded, boolean addToDisplay)
 159   {
 160     this(al, null, null, applet, title, embedded, addToDisplay);
 161   }
 162
 163   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 164           ColumnSelection columnSelection, JalviewLite applet,
 165           String title, boolean embedded)
 166   {
 167     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 168   }
 169
 170   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 171           ColumnSelection columnSelection, JalviewLite applet,
 172           String title, boolean embedded, boolean addToDisplay)
 173   {
 174     if (applet != null)
 175     {
 176       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 177     }
 178
 179     try
 180     {
 181       jbInit();
 182     } catch (Exception ex)
 183     {
 184       ex.printStackTrace();
 185     }
 186     // need to get window geometry before we calculate alignment layout
 187     if (applet != null)
 188     {
 189       String param;
 190       try
 191       {
 192         param = applet.getParameter("windowWidth");
 193         if (param != null)
 194         {
 195           int width = Integer.parseInt(param);
 196           frameWidth = width;
 197         }
 198         param = applet.getParameter("windowHeight");
 199         if (param != null)
 200         {
 201           int height = Integer.parseInt(param);
 202           frameHeight = height;
 203         }
 204       } catch (Exception ex)
 205       {
 206       }
 207     }
 208     viewport = new AlignViewport(al, applet);
 209
 210     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 211     {
 212       viewport.hideSequence(hiddenSeqs);
 213     }
 214     if (columnSelection != null)
 215     {
 216       viewport.setColumnSelection(columnSelection);
 217     }
 218
 219     alignPanel = new AlignmentPanel(this, viewport);
 220     avc = new jalview.controller.AlignViewController(this, viewport,
 221             alignPanel);
 222     viewport.updateConservation(alignPanel);
 223     viewport.updateConsensus(alignPanel);
 224
 225     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 226     followMouseOverFlag.setState(viewport.isFollowHighlight());
 227     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 228     showGroupConservation.setState(viewport.isShowGroupConservation());
 229     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 230     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 231     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 232     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 233     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 234     showAlignmentAnnotations.setState(viewport.isShowAnnotation());
 235     showSequenceAnnotations.setState(viewport.isShowAnnotation());
 236
 237     seqLimits.setState(viewport.getShowJVSuffix());
 238
 239     if (applet != null)
 240     {
 241       String param = applet.getParameter("sortBy");
 242       if (param != null)
 243       {
 244         if (param.equalsIgnoreCase("Id"))
 245         {
 246           sortIDMenuItem_actionPerformed();
 247         }
 248         else if (param.equalsIgnoreCase("Pairwise Identity"))
 249         {
 250           sortPairwiseMenuItem_actionPerformed();
 251         }
 252         else if (param.equalsIgnoreCase("Length"))
 253         {
 254           sortLengthMenuItem_actionPerformed();
 255         }
 256       }
 257
 258       param = applet.getParameter("wrap");
 259       if (param != null)
 260       {
 261         if (param.equalsIgnoreCase("true"))
 262         {
 263           wrapMenuItem.setState(true);
 264           wrapMenuItem_actionPerformed();
 265         }
 266       }
 267       param = applet.getParameter("centrecolumnlabels");
 268       if (param != null)
 269       {
 270         centreColumnLabelFlag.setState(true);
 271         centreColumnLabelFlag_stateChanged();
 272       }
 273
 274     }
 275     if (viewport.getAlignment().isNucleotide())
 276     {
 277       viewport.updateStrucConsensus(alignPanel);
 278       if (viewport.getAlignment().hasRNAStructure())
 279       {
 280         RNAHelixColour.setEnabled(true);
 281       }
 282       else
 283       {
 284         RNAHelixColour.setEnabled(false);
 285       }
 286     }
 287     else
 288     {
 289       RNAHelixColour.setEnabled(false);
 290       purinePyrimidineColour.setEnabled(false);
 291     }
 292     // Some JVMS send keyevents to Top frame or lowest panel,
 293     // Havent worked out why yet. So add to both this frame and seqCanvas for
 294     // now
 295     this.addKeyListener(this);
 296     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 297     alignPanel.idPanel.idCanvas.addKeyListener(this);
 298     alignPanel.scalePanel.addKeyListener(this);
 299     alignPanel.annotationPanel.addKeyListener(this);
 300     alignPanel.annotationPanelHolder.addKeyListener(this);
 301     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 302     alignPanel.alabels.addKeyListener(this);
 303
 304     if (addToDisplay)
 305     {
 306       addToDisplay(embedded);
 307     }
 308   }
 309
 310   /**
 311    * @param embedded
 312    */
 313   public void addToDisplay(boolean embedded)
 314   {
 315     createAlignFrameWindow(embedded);
 316     validate();
 317     alignPanel.adjustAnnotationHeight();
 318     alignPanel.paintAlignment(true);
 319   }
 320
 321   public AlignViewport getAlignViewport()
 322   {
 323     return viewport;
 324   }
 325
 326   public SeqCanvas getSeqcanvas()
 327   {
 328     return alignPanel.seqPanel.seqCanvas;
 329   }
 330
 331   /**
 332    * Load a features file onto the alignment
 333    *
 334    * @param file
 335    *          file URL, content, or other resolvable path
 336    * @param type
 337    *          is protocol for accessing data referred to by file
 338    */
 339
 340   public boolean parseFeaturesFile(String file, String type)
 341   {
 342     return parseFeaturesFile(file, type, true);
 343   }
 344
 345   /**
 346    * Load a features file onto the alignment
 347    *
 348    * @param file
 349    *          file URL, content, or other resolvable path
 350    * @param type
 351    *          is protocol for accessing data referred to by file
 352    * @param autoenabledisplay
 353    *          when true, display features flag will be automatically enabled if
 354    *          features are loaded
 355    * @return true if data parsed as a features file
 356    */
 357   public boolean parseFeaturesFile(String file, String type,
 358           boolean autoenabledisplay)
 359   {
 360     // TODO: test if importing a features file onto an alignment which already
 361     // has features with links overwrites the original links.
 362
 363     Hashtable featureLinks = new Hashtable();
 364     boolean featuresFile = false;
 365     try
 366     {
 367       featuresFile = new jalview.io.FeaturesFile(file, type)
 368               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 369                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 370                       true, viewport.applet.getDefaultParameter(
 371                               "relaxedidmatch", false));
 372     } catch (Exception ex)
 373     {
 374       ex.printStackTrace();
 375     }
 376
 377     if (featuresFile)
 378     {
 379       if (featureLinks.size() > 0)
 380       {
 381         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 382       }
 383       if (autoenabledisplay)
 384       {
 385         viewport.setShowSequenceFeatures(true);
 386         sequenceFeatures.setState(true);
 387       }
 388       if (alignPanel.seqPanel.seqCanvas.fr != null)
 389       {
 390         // update the min/max ranges where necessary
 391         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 392       }
 393       if (viewport.featureSettings != null)
 394       {
 395         viewport.featureSettings.refreshTable();
 396       }
 397       alignPanel.paintAlignment(true);
 398       statusBar.setText(MessageManager
 399               .getString("label.successfully_added_features_alignment"));
 400     }
 401     return featuresFile;
 402   }
 403
 404   @Override
 405   public void keyPressed(KeyEvent evt)
 406   {
 407     if (viewport.cursorMode
 408             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 409                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 410                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 411             && Character.isDigit(evt.getKeyChar()))
 412     {
 413       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 414     }
 415
 416     switch (evt.getKeyCode())
 417     {
 418     case 27: // escape key
 419       deselectAllSequenceMenuItem_actionPerformed();
 420
 421       alignPanel.alabels.cancelDrag();
 422       break;
 423     case KeyEvent.VK_X:
 424       if (evt.isControlDown() || evt.isMetaDown())
 425       {
 426         cut_actionPerformed();
 427       }
 428       break;
 429     case KeyEvent.VK_C:
 430       if (viewport.cursorMode && !evt.isControlDown())
 431       {
 432         alignPanel.seqPanel.setCursorColumn();
 433       }
 434       if (evt.isControlDown() || evt.isMetaDown())
 435       {
 436         copy_actionPerformed();
 437       }
 438       break;
 439     case KeyEvent.VK_V:
 440       if (evt.isControlDown())
 441       {
 442         paste(evt.isShiftDown());
 443       }
 444       break;
 445     case KeyEvent.VK_A:
 446       if (evt.isControlDown() || evt.isMetaDown())
 447       {
 448         selectAllSequenceMenuItem_actionPerformed();
 449       }
 450       break;
 451     case KeyEvent.VK_DOWN:
 452       if (viewport.cursorMode)
 453       {
 454         alignPanel.seqPanel.moveCursor(0, 1);
 455       }
 456       else
 457       {
 458         moveSelectedSequences(false);
 459       }
 460       break;
 461
 462     case KeyEvent.VK_UP:
 463       if (viewport.cursorMode)
 464       {
 465         alignPanel.seqPanel.moveCursor(0, -1);
 466       }
 467       else
 468       {
 469         moveSelectedSequences(true);
 470       }
 471       break;
 472
 473     case KeyEvent.VK_LEFT:
 474       if (evt.isAltDown() || !viewport.cursorMode)
 475       {
 476         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 477       }
 478       else
 479       {
 480         alignPanel.seqPanel.moveCursor(-1, 0);
 481       }
 482       break;
 483
 484     case KeyEvent.VK_RIGHT:
 485       if (evt.isAltDown() || !viewport.cursorMode)
 486       {
 487         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 488       }
 489       else
 490       {
 491         alignPanel.seqPanel.moveCursor(1, 0);
 492       }
 493       break;
 494
 495     case KeyEvent.VK_SPACE:
 496       if (viewport.cursorMode)
 497       {
 498         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 499                 || evt.isShiftDown() || evt.isAltDown());
 500       }
 501       break;
 502
 503     case KeyEvent.VK_DELETE:
 504     case KeyEvent.VK_BACK_SPACE:
 505       if (viewport.cursorMode)
 506       {
 507         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 508                 || evt.isShiftDown() || evt.isAltDown());
 509       }
 510       else
 511       {
 512         cut_actionPerformed();
 513         alignPanel.seqPanel.seqCanvas.repaint();
 514       }
 515       break;
 516
 517     case KeyEvent.VK_S:
 518       if (viewport.cursorMode)
 519       {
 520         alignPanel.seqPanel.setCursorRow();
 521       }
 522       break;
 523     case KeyEvent.VK_P:
 524       if (viewport.cursorMode)
 525       {
 526         alignPanel.seqPanel.setCursorPosition();
 527       }
 528       break;
 529
 530     case KeyEvent.VK_ENTER:
 531     case KeyEvent.VK_COMMA:
 532       if (viewport.cursorMode)
 533       {
 534         alignPanel.seqPanel.setCursorRowAndColumn();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_Q:
 539       if (viewport.cursorMode)
 540       {
 541         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 542       }
 543       break;
 544     case KeyEvent.VK_M:
 545       if (viewport.cursorMode)
 546       {
 547         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 548       }
 549       break;
 550
 551     case KeyEvent.VK_F2:
 552       viewport.cursorMode = !viewport.cursorMode;
 553       statusBar.setText(MessageManager.formatMessage(
 554               "label.keyboard_editing_mode", new String[]
 555               { (viewport.cursorMode ? "on" : "off") }));
 556       if (viewport.cursorMode)
 557       {
 558         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 559         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 560       }
 561       break;
 562
 563     case KeyEvent.VK_F:
 564       if (evt.isControlDown())
 565       {
 566         findMenuItem_actionPerformed();
 567       }
 568       break;
 569
 570     case KeyEvent.VK_H:
 571     {
 572       boolean toggleSeqs = !evt.isControlDown();
 573       boolean toggleCols = !evt.isShiftDown();
 574       toggleHiddenRegions(toggleSeqs, toggleCols);
 575       break;
 576     }
 577
 578     case KeyEvent.VK_PAGE_UP:
 579       if (viewport.getWrapAlignment())
 580       {
 581         alignPanel.scrollUp(true);
 582       }
 583       else
 584       {
 585         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 586                 - viewport.endSeq + viewport.startSeq);
 587       }
 588       break;
 589
 590     case KeyEvent.VK_PAGE_DOWN:
 591       if (viewport.getWrapAlignment())
 592       {
 593         alignPanel.scrollUp(false);
 594       }
 595       else
 596       {
 597         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 598                 + viewport.endSeq - viewport.startSeq);
 599       }
 600       break;
 601
 602     case KeyEvent.VK_Z:
 603       if (evt.isControlDown())
 604       {
 605         undoMenuItem_actionPerformed();
 606       }
 607       break;
 608
 609     case KeyEvent.VK_Y:
 610       if (evt.isControlDown())
 611       {
 612         redoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_L:
 617       if (evt.isControlDown())
 618       {
 619         trimAlignment(true);
 620       }
 621       break;
 622
 623     case KeyEvent.VK_R:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(false);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_E:
 631       if (evt.isControlDown())
 632       {
 633         if (evt.isShiftDown())
 634         {
 635           this.removeAllGapsMenuItem_actionPerformed();
 636         }
 637         else
 638         {
 639           removeGappedColumnMenuItem_actionPerformed();
 640         }
 641       }
 642       break;
 643     case KeyEvent.VK_I:
 644       if (evt.isControlDown())
 645       {
 646         if (evt.isAltDown())
 647         {
 648           invertColSel_actionPerformed();
 649         }
 650         else
 651         {
 652           invertSequenceMenuItem_actionPerformed();
 653         }
 654       }
 655       break;
 656
 657     case KeyEvent.VK_G:
 658       if (evt.isControlDown())
 659       {
 660         if (evt.isShiftDown())
 661         {
 662           this.unGroup_actionPerformed();
 663         }
 664         else
 665         {
 666           this.createGroup_actionPerformed();
 667         }
 668       }
 669       break;
 670
 671     case KeyEvent.VK_U:
 672       if (evt.isControlDown())
 673       {
 674         this.deleteGroups_actionPerformed();
 675       }
 676       break;
 677
 678     case KeyEvent.VK_T:
 679       if (evt.isControlDown())
 680       {
 681         newView(null);
 682       }
 683       break;
 684
 685     }
 686     alignPanel.paintAlignment(true);
 687   }
 688
 689   /**
 690    * called by key handler and the hide all/show all menu items
 691    *
 692    * @param toggleSeqs
 693    * @param toggleCols
 694    */
 695   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 696   {
 697     boolean hide = false;
 698     SequenceGroup sg = viewport.getSelectionGroup();
 699     if (!toggleSeqs && !toggleCols)
 700     {
 701       // Hide everything by the current selection - this is a hack - we do the
 702       // invert and then hide
 703       // first check that there will be visible columns after the invert.
 704       if ((viewport.getColumnSelection() != null
 705               && viewport.getColumnSelection().getSelected() != null && viewport
 706               .getColumnSelection().getSelected().size() > 0)
 707               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 708                       .getEndRes()))
 709       {
 710         // now invert the sequence set, if required - empty selection implies
 711         // that no hiding is required.
 712         if (sg != null)
 713         {
 714           invertSequenceMenuItem_actionPerformed();
 715           sg = viewport.getSelectionGroup();
 716           toggleSeqs = true;
 717
 718         }
 719         viewport.expandColSelection(sg, true);
 720         // finally invert the column selection and get the new sequence
 721         // selection and indicate it should be hidden.
 722         invertColSel_actionPerformed();
 723         toggleCols = true;
 724       }
 725     }
 726
 727     if (toggleSeqs)
 728     {
 729       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 730       {
 731         hide = true;
 732         viewport.hideAllSelectedSeqs();
 733       }
 734       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 735               .size() > 0))
 736       {
 737         viewport.showAllHiddenSeqs();
 738       }
 739     }
 740
 741     if (toggleCols)
 742     {
 743       if (viewport.getColumnSelection().getSelected().size() > 0)
 744       {
 745         viewport.hideSelectedColumns();
 746         if (!toggleSeqs)
 747         {
 748           viewport.setSelectionGroup(sg);
 749         }
 750       }
 751       else if (!hide)
 752       {
 753         viewport.showAllHiddenColumns();
 754       }
 755     }
 756   }
 757
 758   @Override
 759   public void keyReleased(KeyEvent evt)
 760   {
 761   }
 762
 763   @Override
 764   public void keyTyped(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void itemStateChanged(ItemEvent evt)
 770   {
 771     final Object source = evt.getSource();
 772     if (source == displayNonconservedMenuItem)
 773     {
 774       displayNonconservedMenuItem_actionPerformed();
 775     }
 776     else if (source == colourTextMenuItem)
 777     {
 778       colourTextMenuItem_actionPerformed();
 779     }
 780     else if (source == wrapMenuItem)
 781     {
 782       wrapMenuItem_actionPerformed();
 783     }
 784     else if (source == scaleAbove)
 785     {
 786       viewport.setScaleAboveWrapped(scaleAbove.getState());
 787     }
 788     else if (source == scaleLeft)
 789     {
 790       viewport.setScaleLeftWrapped(scaleLeft.getState());
 791     }
 792     else if (source == scaleRight)
 793     {
 794       viewport.setScaleRightWrapped(scaleRight.getState());
 795     }
 796     else if (source == seqLimits)
 797     {
 798       seqLimits_itemStateChanged();
 799     }
 800     else if (source == viewBoxesMenuItem)
 801     {
 802       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 803     }
 804     else if (source == viewTextMenuItem)
 805     {
 806       viewport.setShowText(viewTextMenuItem.getState());
 807     }
 808     else if (source == renderGapsMenuItem)
 809     {
 810       viewport.setRenderGaps(renderGapsMenuItem.getState());
 811     }
 812     else if (source == annotationPanelMenuItem)
 813     {
 814       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 815       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 816     }
 817     else if (source == sequenceFeatures)
 818     {
 819       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 820       alignPanel.seqPanel.seqCanvas.repaint();
 821     }
 822     else if (source == showAlignmentAnnotations)
 823     {
 824       setAnnotationsVisibility();
 825     }
 826     else if (source == showSequenceAnnotations)
 827     {
 828       setAnnotationsVisibility();
 829     }
 830     else if (source == sortAnnBySequence)
 831     {
 832       boolean newState = sortAnnBySequence.getState();
 833       sortAnnByLabel.setState(false);
 834       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 835               : SequenceAnnotationOrder.NONE);
 836       setViewportAnnotationOrder();
 837     }
 838     else if (source == sortAnnByLabel)
 839     {
 840       boolean newState = sortAnnByLabel.getState();
 841       sortAnnBySequence.setState(false);
 842       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 843               : SequenceAnnotationOrder.NONE);
 844       setViewportAnnotationOrder();
 845     }
 846     else if (source == showAutoFirst)
 847     {
 848       showAutoLast.setState(!showAutoFirst.getState());
 849       setShowAutoCalculatedAbove(showAutoFirst.getState());
 850       setViewportAnnotationOrder();
 851     }
 852     else if (source == showAutoLast)
 853     {
 854       showAutoFirst.setState(!showAutoLast.getState());
 855       setShowAutoCalculatedAbove(showAutoFirst.getState());
 856       setViewportAnnotationOrder();
 857     }
 858     else if (source == conservationMenuItem)
 859     {
 860       conservationMenuItem_actionPerformed();
 861     }
 862     else if (source == abovePIDThreshold)
 863     {
 864       abovePIDThreshold_actionPerformed();
 865     }
 866     else if (source == applyToAllGroups)
 867     {
 868       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 869     }
 870     else if (source == autoCalculate)
 871     {
 872       viewport.autoCalculateConsensus = autoCalculate.getState();
 873     }
 874     else if (source == sortByTree)
 875     {
 876       viewport.sortByTree = sortByTree.getState();
 877     }
 878     else if (source == this.centreColumnLabelFlag)
 879     {
 880       centreColumnLabelFlag_stateChanged();
 881     }
 882     else if (source == this.followMouseOverFlag)
 883     {
 884       mouseOverFlag_stateChanged();
 885     }
 886     else if (source == showGroupConsensus)
 887     {
 888       showGroupConsensus_actionPerformed();
 889     }
 890     else if (source == showGroupConservation)
 891     {
 892       showGroupConservation_actionPerformed();
 893     }
 894     else if (source == showSequenceLogo)
 895     {
 896       showSequenceLogo_actionPerformed();
 897     }
 898     else if (source == normSequenceLogo)
 899     {
 900       normSequenceLogo_actionPerformed();
 901     }
 902     else if (source == showConsensusHistogram)
 903     {
 904       showConsensusHistogram_actionPerformed();
 905     }
 906     else if (source == applyAutoAnnotationSettings)
 907     {
 908       applyAutoAnnotationSettings_actionPerformed();
 909     }
 910     alignPanel.paintAlignment(true);
 911   }
 912
 913   /**
 914    * Set the visibility state of sequence-related and/or alignment-related
 915    * annotations depending on checkbox selections. Repaint after calling.
 916    *
 917    * @param visible
 918    */
 919   private void setAnnotationsVisibility()
 920   {
 921     boolean showForAlignment = showAlignmentAnnotations.getState();
 922     boolean showForSequences = showSequenceAnnotations.getState();
 923     for (AlignmentAnnotation aa : alignPanel.getAlignment()
 924             .getAlignmentAnnotation())
 925     {
 926       boolean visible = (aa.sequenceRef == null ? showForAlignment
 927               : showForSequences);
 928         aa.visible = visible;
 929     }
 930     alignPanel.validateAnnotationDimensions(false);
 931   }
 932
 933   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 934   {
 935     this.annotationSortOrder = order;
 936   }
 937
 938   /**
 939    * Set flags on the viewport that control annotation ordering
 940    */
 941   private void setViewportAnnotationOrder()
 942   {
 943     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 944     this.alignPanel.av
 945             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 946   }
 947
 948   private void setShowAutoCalculatedAbove(boolean showAbove)
 949   {
 950     this.showAutoCalculatedAbove = showAbove;
 951   }
 952
 953   private void mouseOverFlag_stateChanged()
 954   {
 955     viewport.setFollowHighlight(followMouseOverFlag.getState());
 956     // TODO: could kick the scrollTo mechanism to reset view for current
 957     // searchresults.
 958   }
 959
 960   private void centreColumnLabelFlag_stateChanged()
 961   {
 962     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 963     this.alignPanel.annotationPanel.repaint();
 964   }
 965
 966   @Override
 967   public void actionPerformed(ActionEvent evt)
 968   {
 969     Object source = evt.getSource();
 970
 971     if (source == inputText)
 972     {
 973       inputText_actionPerformed();
 974     }
 975     else if (source == loadTree)
 976     {
 977       loadTree_actionPerformed();
 978     }
 979     else if (source == loadApplication)
 980     {
 981       launchFullApplication();
 982     }
 983     else if (source == loadAnnotations)
 984     {
 985       loadAnnotations();
 986     }
 987     else if (source == outputAnnotations)
 988     {
 989       outputAnnotations(true);
 990     }
 991     else if (source == outputFeatures)
 992     {
 993       outputFeatures(true, "Jalview");
 994     }
 995     else if (source == closeMenuItem)
 996     {
 997       closeMenuItem_actionPerformed();
 998     }
 999     else if (source == copy)
1000     {
1001       copy_actionPerformed();
1002     }
1003     else if (source == undoMenuItem)
1004     {
1005       undoMenuItem_actionPerformed();
1006     }
1007     else if (source == redoMenuItem)
1008     {
1009       redoMenuItem_actionPerformed();
1010     }
1011     else if (source == inputText)
1012     {
1013       inputText_actionPerformed();
1014     }
1015     else if (source == closeMenuItem)
1016     {
1017       closeMenuItem_actionPerformed();
1018     }
1019     else if (source == undoMenuItem)
1020     {
1021       undoMenuItem_actionPerformed();
1022     }
1023     else if (source == redoMenuItem)
1024     {
1025       redoMenuItem_actionPerformed();
1026     }
1027     else if (source == copy)
1028     {
1029       copy_actionPerformed();
1030     }
1031     else if (source == pasteNew)
1032     {
1033       pasteNew_actionPerformed();
1034     }
1035     else if (source == pasteThis)
1036     {
1037       pasteThis_actionPerformed();
1038     }
1039     else if (source == cut)
1040     {
1041       cut_actionPerformed();
1042     }
1043     else if (source == delete)
1044     {
1045       delete_actionPerformed();
1046     }
1047     else if (source == grpsFromSelection)
1048     {
1049       makeGrpsFromSelection_actionPerformed();
1050     }
1051     else if (source == deleteGroups)
1052     {
1053       deleteGroups_actionPerformed();
1054     }
1055     else if (source == selectAllSequenceMenuItem)
1056     {
1057       selectAllSequenceMenuItem_actionPerformed();
1058     }
1059     else if (source == deselectAllSequenceMenuItem)
1060     {
1061       deselectAllSequenceMenuItem_actionPerformed();
1062     }
1063     else if (source == invertSequenceMenuItem)
1064     {
1065       invertSequenceMenuItem_actionPerformed();
1066     }
1067     else if (source == invertColSel)
1068     {
1069       viewport.invertColumnSelection();
1070       alignPanel.paintAlignment(true);
1071     }
1072     else if (source == remove2LeftMenuItem)
1073     {
1074       trimAlignment(true);
1075     }
1076     else if (source == remove2RightMenuItem)
1077     {
1078       trimAlignment(false);
1079     }
1080     else if (source == removeGappedColumnMenuItem)
1081     {
1082       removeGappedColumnMenuItem_actionPerformed();
1083     }
1084     else if (source == removeAllGapsMenuItem)
1085     {
1086       removeAllGapsMenuItem_actionPerformed();
1087     }
1088     else if (source == findMenuItem)
1089     {
1090       findMenuItem_actionPerformed();
1091     }
1092     else if (source == font)
1093     {
1094       new FontChooser(alignPanel);
1095     }
1096     else if (source == newView)
1097     {
1098       newView(null);
1099     }
1100     else if (source == showColumns)
1101     {
1102       viewport.showAllHiddenColumns();
1103       alignPanel.paintAlignment(true);
1104     }
1105     else if (source == showSeqs)
1106     {
1107       viewport.showAllHiddenSeqs();
1108       alignPanel.paintAlignment(true);
1109     }
1110     else if (source == hideColumns)
1111     {
1112       viewport.hideSelectedColumns();
1113       alignPanel.paintAlignment(true);
1114     }
1115     else if (source == hideSequences
1116             && viewport.getSelectionGroup() != null)
1117     {
1118       viewport.hideAllSelectedSeqs();
1119       alignPanel.paintAlignment(true);
1120     }
1121     else if (source == hideAllButSelection)
1122     {
1123       toggleHiddenRegions(false, false);
1124       alignPanel.paintAlignment(true);
1125     }
1126     else if (source == hideAllSelection)
1127     {
1128       SequenceGroup sg = viewport.getSelectionGroup();
1129       viewport.expandColSelection(sg, false);
1130       viewport.hideAllSelectedSeqs();
1131       viewport.hideSelectedColumns();
1132       alignPanel.paintAlignment(true);
1133     }
1134     else if (source == showAllHidden)
1135     {
1136       viewport.showAllHiddenColumns();
1137       viewport.showAllHiddenSeqs();
1138       alignPanel.paintAlignment(true);
1139     }
1140     else if (source == showGroupConsensus)
1141     {
1142       showGroupConsensus_actionPerformed();
1143     }
1144     else if (source == showGroupConservation)
1145     {
1146       showGroupConservation_actionPerformed();
1147     }
1148     else if (source == showSequenceLogo)
1149     {
1150       showSequenceLogo_actionPerformed();
1151     }
1152     else if (source == normSequenceLogo)
1153     {
1154       normSequenceLogo_actionPerformed();
1155     }
1156     else if (source == showConsensusHistogram)
1157     {
1158       showConsensusHistogram_actionPerformed();
1159     }
1160     else if (source == applyAutoAnnotationSettings)
1161     {
1162       applyAutoAnnotationSettings_actionPerformed();
1163     }
1164     else if (source == featureSettings)
1165     {
1166       new FeatureSettings(alignPanel);
1167     }
1168     else if (source == alProperties)
1169     {
1170       StringBuffer contents = new jalview.io.AlignmentProperties(
1171               viewport.getAlignment()).formatAsString();
1172       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1173       cap.setText(contents.toString());
1174       Frame frame = new Frame();
1175       frame.add(cap);
1176       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1177               "label.alignment_properties", new String[]
1178               { getTitle() }), 400, 250);
1179     }
1180     else if (source == overviewMenuItem)
1181     {
1182       overviewMenuItem_actionPerformed();
1183     }
1184     else if (source == noColourmenuItem)
1185     {
1186       changeColour(null);
1187     }
1188     else if (source == clustalColour)
1189     {
1190       abovePIDThreshold.setState(false);
1191       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1192     }
1193     else if (source == zappoColour)
1194     {
1195       changeColour(new ZappoColourScheme());
1196     }
1197     else if (source == taylorColour)
1198     {
1199       changeColour(new TaylorColourScheme());
1200     }
1201     else if (source == hydrophobicityColour)
1202     {
1203       changeColour(new HydrophobicColourScheme());
1204     }
1205     else if (source == helixColour)
1206     {
1207       changeColour(new HelixColourScheme());
1208     }
1209     else if (source == strandColour)
1210     {
1211       changeColour(new StrandColourScheme());
1212     }
1213     else if (source == turnColour)
1214     {
1215       changeColour(new TurnColourScheme());
1216     }
1217     else if (source == buriedColour)
1218     {
1219       changeColour(new BuriedColourScheme());
1220     }
1221     else if (source == nucleotideColour)
1222     {
1223       changeColour(new NucleotideColourScheme());
1224     }
1225     else if (source == purinePyrimidineColour)
1226     {
1227       changeColour(new PurinePyrimidineColourScheme());
1228     }
1229     else if (source == RNAInteractionColour)
1230     {
1231       changeColour(new RNAInteractionColourScheme());
1232     }
1233     else if (source == RNAHelixColour)
1234     {
1235       new RNAHelicesColourChooser(viewport, alignPanel);
1236     }
1237     else if (source == modifyPID)
1238     {
1239       modifyPID_actionPerformed();
1240     }
1241     else if (source == modifyConservation)
1242     {
1243       modifyConservation_actionPerformed();
1244     }
1245     else if (source == userDefinedColour)
1246     {
1247       new UserDefinedColours(alignPanel, null);
1248     }
1249     else if (source == PIDColour)
1250     {
1251       changeColour(new PIDColourScheme());
1252     }
1253     else if (source == BLOSUM62Colour)
1254     {
1255       changeColour(new Blosum62ColourScheme());
1256     }
1257     else if (source == tcoffeeColour)
1258     {
1259       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1260     }
1261     else if (source == annotationColour)
1262     {
1263       new AnnotationColourChooser(viewport, alignPanel);
1264     }
1265     else if (source == annotationColumnSelection)
1266     {
1267       new AnnotationColumnChooser(viewport, alignPanel);
1268     }
1269     else if (source == sortPairwiseMenuItem)
1270     {
1271       sortPairwiseMenuItem_actionPerformed();
1272     }
1273     else if (source == sortIDMenuItem)
1274     {
1275       sortIDMenuItem_actionPerformed();
1276     }
1277     else if (source == sortLengthMenuItem)
1278     {
1279       sortLengthMenuItem_actionPerformed();
1280     }
1281     else if (source == sortGroupMenuItem)
1282     {
1283       sortGroupMenuItem_actionPerformed();
1284     }
1285     else if (source == removeRedundancyMenuItem)
1286     {
1287       removeRedundancyMenuItem_actionPerformed();
1288     }
1289     else if (source == pairwiseAlignmentMenuItem)
1290     {
1291       pairwiseAlignmentMenuItem_actionPerformed();
1292     }
1293     else if (source == PCAMenuItem)
1294     {
1295       PCAMenuItem_actionPerformed();
1296     }
1297     else if (source == averageDistanceTreeMenuItem)
1298     {
1299       averageDistanceTreeMenuItem_actionPerformed();
1300     }
1301     else if (source == neighbourTreeMenuItem)
1302     {
1303       neighbourTreeMenuItem_actionPerformed();
1304     }
1305     else if (source == njTreeBlosumMenuItem)
1306     {
1307       njTreeBlosumMenuItem_actionPerformed();
1308     }
1309     else if (source == avDistanceTreeBlosumMenuItem)
1310     {
1311       avTreeBlosumMenuItem_actionPerformed();
1312     }
1313     else if (source == documentation)
1314     {
1315       documentation_actionPerformed();
1316     }
1317     else if (source == about)
1318     {
1319       about_actionPerformed();
1320     }
1321
1322   }
1323
1324   public void inputText_actionPerformed()
1325   {
1326     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1327     Frame frame = new Frame();
1328     frame.add(cap);
1329     jalview.bin.JalviewLite.addFrame(frame,
1330             MessageManager.getString("label.input_cut_paste"), 500, 500);
1331   }
1332
1333   protected void outputText_actionPerformed(ActionEvent e)
1334   {
1335     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1336     Frame frame = new Frame();
1337     frame.add(cap);
1338     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1339             "label.alignment_output_command", new Object[]
1340             { e.getActionCommand() }), 600, 500);
1341
1342     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1343     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1344             e.getActionCommand(), viewport.getAlignment(),
1345             viewport.getShowJVSuffix()));
1346   }
1347
1348   public void loadAnnotations()
1349   {
1350     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1351     cap.setText(MessageManager
1352             .getString("label.paste_features_annotations_Tcoffee_here"));
1353     cap.setAnnotationImport();
1354     Frame frame = new Frame();
1355     frame.add(cap);
1356     jalview.bin.JalviewLite.addFrame(frame,
1357             MessageManager.getString("action.paste_annotations"), 400, 300);
1358
1359   }
1360
1361   public String outputAnnotations(boolean displayTextbox)
1362   {
1363     String annotation = new AnnotationFile()
1364             .printAnnotationsForView(viewport);
1365
1366     if (displayTextbox)
1367     {
1368       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1369       Frame frame = new Frame();
1370       frame.add(cap);
1371       jalview.bin.JalviewLite.addFrame(frame,
1372               MessageManager.getString("label.annotations"), 600, 500);
1373       cap.setText(annotation);
1374     }
1375
1376     return annotation;
1377   }
1378
1379   private Map<String,Object> getDisplayedFeatureCols()
1380   {
1381     if (alignPanel.getFeatureRenderer() != null
1382             && viewport.getFeaturesDisplayed()!= null)
1383     {
1384       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1385
1386     }
1387     return null;
1388   }
1389
1390   public String outputFeatures(boolean displayTextbox, String format)
1391   {
1392     String features;
1393     if (format.equalsIgnoreCase("Jalview"))
1394     {
1395       features = new FeaturesFile().printJalviewFormat(viewport
1396               .getAlignment().getSequencesArray(),
1397               getDisplayedFeatureCols());
1398     }
1399     else
1400     {
1401       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1402               .getSequencesArray(), getDisplayedFeatureCols());
1403     }
1404
1405     if (displayTextbox)
1406     {
1407       boolean frimport = false;
1408       if (features == null || features.equals("No Features Visible"))
1409       {
1410         features = "# No features visible - paste some and import them here.";
1411         frimport = true;
1412       }
1413
1414       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1415       if (frimport)
1416       {
1417         cap.setAnnotationImport();
1418       }
1419       Frame frame = new Frame();
1420       frame.add(cap);
1421       jalview.bin.JalviewLite.addFrame(frame,
1422               MessageManager.getString("label.features"), 600, 500);
1423       cap.setText(features);
1424     }
1425     else
1426     {
1427       if (features == null)
1428       {
1429         features = "";
1430       }
1431     }
1432
1433     return features;
1434   }
1435
1436   void launchFullApplication()
1437   {
1438     StringBuffer url = new StringBuffer(jalviewServletURL);
1439
1440     // allow servlet parameters to be passed in applet parameter
1441     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1442             : "?";
1443     url.append(firstSep);
1444
1445     url.append("open="
1446             + appendProtocol(viewport.applet.getParameter("file")));
1447
1448     if (viewport.applet.getParameter("features") != null)
1449     {
1450       url.append("&features=");
1451       url.append(appendProtocol(viewport.applet.getParameter("features")));
1452     }
1453
1454     if (viewport.applet.getParameter("annotations") != null)
1455     {
1456       url.append("&annotations=");
1457       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1458     }
1459
1460     if (viewport.applet.getParameter("jnetfile") != null)
1461     {
1462       url.append("&annotations=");
1463       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1464     }
1465
1466     if (viewport.applet.getParameter("defaultColour") != null)
1467     {
1468       url.append("&colour="
1469               + removeWhiteSpace(viewport.applet
1470                       .getParameter("defaultColour")));
1471     }
1472
1473     if (viewport.applet.getParameter("userDefinedColour") != null)
1474     {
1475       url.append("&colour="
1476               + removeWhiteSpace(viewport.applet
1477                       .getParameter("userDefinedColour")));
1478     }
1479     if (viewport.applet.getParameter("tree") != null)
1480     {
1481       url.append("&tree="
1482               + appendProtocol(viewport.applet.getParameter("tree")));
1483     }
1484     if (viewport.applet.getParameter("treeFile") != null)
1485     {
1486       url.append("&tree="
1487               + appendProtocol(viewport.applet.getParameter("treeFile")));
1488     }
1489
1490     showURL(url.toString(), "FULL_APP");
1491   }
1492
1493   String removeWhiteSpace(String colour)
1494   {
1495     StringBuffer sb = new StringBuffer();
1496     for (int i = 0; i < colour.length(); i++)
1497     {
1498       if (Character.isWhitespace(colour.charAt(i)))
1499       {
1500         sb.append("%20");
1501       }
1502       else
1503       {
1504         sb.append(colour.charAt(i));
1505       }
1506     }
1507
1508     return sb.toString();
1509   }
1510
1511   String appendProtocol(String url)
1512   {
1513     try
1514     {
1515       new URL(url);
1516       url = URLEncoder.encode(url);
1517     }
1518     /*
1519      * When we finally deprecate 1.1 compatibility, we can start to use
1520      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1521      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1522      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1523      * ex.printStackTrace(); }
1524      */
1525     catch (java.net.MalformedURLException ex)
1526     {
1527       url = viewport.applet.getCodeBase() + url;
1528     }
1529     return url;
1530   }
1531
1532   public void closeMenuItem_actionPerformed()
1533   {
1534     PaintRefresher.RemoveComponent(alignPanel);
1535     if (alignPanel.seqPanel != null
1536             && alignPanel.seqPanel.seqCanvas != null)
1537     {
1538       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1539     }
1540     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1541     {
1542       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1543     }
1544
1545     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1546     {
1547       System.exit(0);
1548     }
1549     else
1550     {
1551     }
1552     viewport = null;
1553     alignPanel = null;
1554     this.dispose();
1555   }
1556
1557   /**
1558    * TODO: JAL-1104
1559    */
1560   void updateEditMenuBar()
1561   {
1562
1563     if (viewport.getHistoryList().size() > 0)
1564     {
1565       undoMenuItem.setEnabled(true);
1566       CommandI command = viewport.getHistoryList().peek();
1567       undoMenuItem.setLabel(MessageManager.formatMessage(
1568               "label.undo_command", new Object[]
1569               { command.getDescription() }));
1570     }
1571     else
1572     {
1573       undoMenuItem.setEnabled(false);
1574       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1575     }
1576
1577     if (viewport.getRedoList().size() > 0)
1578     {
1579       redoMenuItem.setEnabled(true);
1580
1581       CommandI command = viewport.getRedoList().peek();
1582       redoMenuItem.setLabel(MessageManager.formatMessage(
1583               "label.redo_command", new Object[]
1584               { command.getDescription() }));
1585     }
1586     else
1587     {
1588       redoMenuItem.setEnabled(false);
1589       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1590     }
1591   }
1592
1593   /**
1594    * TODO: JAL-1104
1595    */
1596   @Override
1597   public void addHistoryItem(CommandI command)
1598   {
1599     if (command.getSize() > 0)
1600     {
1601       viewport.addToHistoryList(command);
1602       viewport.clearRedoList();
1603       updateEditMenuBar();
1604       viewport.updateHiddenColumns();
1605     }
1606   }
1607
1608   /**
1609    * TODO: JAL-1104 DOCUMENT ME!
1610    *
1611    * @param e
1612    *          DOCUMENT ME!
1613    */
1614   protected void undoMenuItem_actionPerformed()
1615   {
1616     if (viewport.getHistoryList().isEmpty())
1617     {
1618       return;
1619     }
1620
1621     CommandI command = viewport.getHistoryList().pop();
1622     viewport.addToRedoList(command);
1623     command.undoCommand(null);
1624
1625     AlignmentViewport originalSource = getOriginatingSource(command);
1626     // JBPNote Test
1627     if (originalSource != viewport)
1628     {
1629       System.err
1630               .println("Warning: Viewport object mismatch whilst undoing");
1631     }
1632     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1633                                           // viewport.getColumnSelection().getHiddenColumns()
1634                                           // != null;
1635     updateEditMenuBar();
1636     originalSource.firePropertyChange("alignment", null, originalSource
1637             .getAlignment().getSequences());
1638   }
1639
1640   /**
1641    * TODO: JAL-1104 DOCUMENT ME!
1642    *
1643    * @param e
1644    *          DOCUMENT ME!
1645    */
1646   protected void redoMenuItem_actionPerformed()
1647   {
1648     if (viewport.getRedoList().isEmpty())
1649     {
1650       return;
1651     }
1652
1653     CommandI command = viewport.getRedoList().pop();
1654     viewport.addToHistoryList(command);
1655     command.doCommand(null);
1656
1657     AlignmentViewport originalSource = getOriginatingSource(command);
1658     // JBPNote Test
1659     if (originalSource != viewport)
1660     {
1661       System.err
1662               .println("Warning: Viewport object mismatch whilst re-doing");
1663     }
1664     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1665                                           // viewport.getColumnSelection().getHiddenColumns()
1666                                           // != null;
1667
1668     updateEditMenuBar();
1669     originalSource.firePropertyChange("alignment", null, originalSource
1670             .getAlignment().getSequences());
1671   }
1672
1673   AlignmentViewport getOriginatingSource(CommandI command)
1674   {
1675     AlignmentViewport originalSource = null;
1676     // For sequence removal and addition, we need to fire
1677     // the property change event FROM the viewport where the
1678     // original alignment was altered
1679     AlignmentI al = null;
1680     if (command instanceof EditCommand)
1681     {
1682       EditCommand editCommand = (EditCommand) command;
1683       al = editCommand.getAlignment();
1684       Vector comps = (Vector) PaintRefresher.components.get(viewport
1685               .getSequenceSetId());
1686       for (int i = 0; i < comps.size(); i++)
1687       {
1688         if (comps.elementAt(i) instanceof AlignmentPanel)
1689         {
1690           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1691           {
1692             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1693             break;
1694           }
1695         }
1696       }
1697     }
1698
1699     if (originalSource == null)
1700     {
1701       // The original view is closed, we must validate
1702       // the current view against the closed view first
1703       if (al != null)
1704       {
1705         PaintRefresher.validateSequences(al, viewport.getAlignment());
1706       }
1707
1708       originalSource = viewport;
1709     }
1710
1711     return originalSource;
1712   }
1713
1714   /**
1715    * Move the currently selected sequences up or down one position in the
1716    * alignment
1717    *
1718    * @param up
1719    */
1720   public void moveSelectedSequences(boolean up)
1721   {
1722     SequenceGroup sg = viewport.getSelectionGroup();
1723     if (sg == null)
1724     {
1725       return;
1726     }
1727     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1728             up ? null : viewport.getHiddenRepSequences(), up);
1729     alignPanel.paintAlignment(true);
1730
1731     /*
1732      * Also move cDNA/protein complement sequences
1733      */
1734     AlignViewportI complement = viewport.getCodingComplement();
1735     if (complement != null)
1736     {
1737       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1738               viewport, complement);
1739       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1740               up ? null : complement.getHiddenRepSequences(), up);
1741       // TODO need to trigger a repaint of the complementary panel - how?
1742       // would prefer to handle in SplitFrame but it is not overriding key
1743       // listener chiz
1744     }
1745   }
1746
1747   synchronized void slideSequences(boolean right, int size)
1748   {
1749     List<SequenceI> sg = new Vector<SequenceI>();
1750     if (viewport.cursorMode)
1751     {
1752       sg.add(viewport.getAlignment().getSequenceAt(
1753               alignPanel.seqPanel.seqCanvas.cursorY));
1754     }
1755     else if (viewport.getSelectionGroup() != null
1756             && viewport.getSelectionGroup().getSize() != viewport
1757                     .getAlignment().getHeight())
1758     {
1759       sg = viewport.getSelectionGroup().getSequences(
1760               viewport.getHiddenRepSequences());
1761     }
1762
1763     if (sg.size() < 1)
1764     {
1765       return;
1766     }
1767
1768     Vector<SequenceI> invertGroup = new Vector();
1769
1770     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1771     {
1772       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1773       {
1774         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1775       }
1776     }
1777
1778     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1779
1780     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1781             .size()]);
1782     for (int i = 0; i < invertGroup.size(); i++)
1783     {
1784       seqs2[i] = invertGroup.elementAt(i);
1785     }
1786
1787     SlideSequencesCommand ssc;
1788     if (right)
1789     {
1790       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1791               size, viewport.getGapCharacter());
1792     }
1793     else
1794     {
1795       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1796               size, viewport.getGapCharacter());
1797     }
1798
1799     int groupAdjustment = 0;
1800     if (ssc.getGapsInsertedBegin() && right)
1801     {
1802       if (viewport.cursorMode)
1803       {
1804         alignPanel.seqPanel.moveCursor(size, 0);
1805       }
1806       else
1807       {
1808         groupAdjustment = size;
1809       }
1810     }
1811     else if (!ssc.getGapsInsertedBegin() && !right)
1812     {
1813       if (viewport.cursorMode)
1814       {
1815         alignPanel.seqPanel.moveCursor(-size, 0);
1816       }
1817       else
1818       {
1819         groupAdjustment = -size;
1820       }
1821     }
1822
1823     if (groupAdjustment != 0)
1824     {
1825       viewport.getSelectionGroup().setStartRes(
1826               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1827       viewport.getSelectionGroup().setEndRes(
1828               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1829     }
1830
1831     boolean appendHistoryItem = false;
1832     Deque<CommandI> historyList = viewport.getHistoryList();
1833     if (historyList != null && historyList.size() > 0
1834             && historyList.peek() instanceof SlideSequencesCommand)
1835     {
1836       appendHistoryItem = ssc
1837               .appendSlideCommand((SlideSequencesCommand) historyList
1838                       .peek());
1839     }
1840
1841     if (!appendHistoryItem)
1842     {
1843       addHistoryItem(ssc);
1844     }
1845
1846     repaint();
1847   }
1848
1849   static StringBuffer copiedSequences;
1850
1851   static Vector copiedHiddenColumns;
1852
1853   protected void copy_actionPerformed()
1854   {
1855     if (viewport.getSelectionGroup() == null)
1856     {
1857       return;
1858     }
1859
1860     SequenceGroup sg = viewport.getSelectionGroup();
1861     copiedSequences = new StringBuffer();
1862     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1863     for (int i = 0; i < sg.getSize(); i++)
1864     {
1865       SequenceI seq = sg.getSequenceAt(i);
1866       int index = viewport.getAlignment().findIndex(seq);
1867       orderedSeqs.put(index, seq);
1868     }
1869
1870     int index = 0, startRes, endRes;
1871     char ch;
1872
1873     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1874     {
1875       copiedHiddenColumns = new Vector();
1876       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1877       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1878       {
1879         copiedHiddenColumns.addElement(new int[]
1880         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1881       }
1882     }
1883     else
1884     {
1885       copiedHiddenColumns = null;
1886     }
1887
1888     for (int i = 0; i < sg.getSize(); i++)
1889     {
1890       SequenceI seq = null;
1891
1892       while (seq == null)
1893       {
1894         if (orderedSeqs.containsKey(index))
1895         {
1896           seq = orderedSeqs.get(index);
1897           index++;
1898           break;
1899         }
1900         else
1901         {
1902           index++;
1903         }
1904       }
1905
1906       // FIND START RES
1907       // Returns residue following index if gap
1908       startRes = seq.findPosition(sg.getStartRes());
1909
1910       // FIND END RES
1911       // Need to find the residue preceeding index if gap
1912       endRes = 0;
1913
1914       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1915       {
1916         ch = seq.getCharAt(j);
1917         if (!jalview.util.Comparison.isGap((ch)))
1918         {
1919           endRes++;
1920         }
1921       }
1922
1923       if (endRes > 0)
1924       {
1925         endRes += seq.getStart() - 1;
1926       }
1927
1928       copiedSequences.append(seq.getName()
1929               + "\t"
1930               + startRes
1931               + "\t"
1932               + endRes
1933               + "\t"
1934               + seq.getSequenceAsString(sg.getStartRes(),
1935                       sg.getEndRes() + 1) + "\n");
1936     }
1937
1938   }
1939
1940   protected void pasteNew_actionPerformed()
1941   {
1942     paste(true);
1943   }
1944
1945   protected void pasteThis_actionPerformed()
1946   {
1947     paste(false);
1948   }
1949
1950   void paste(boolean newAlignment)
1951   {
1952     try
1953     {
1954
1955       if (copiedSequences == null)
1956       {
1957         return;
1958       }
1959
1960       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1961       Vector seqs = new Vector();
1962       while (st.hasMoreElements())
1963       {
1964         String name = st.nextToken();
1965         int start = Integer.parseInt(st.nextToken());
1966         int end = Integer.parseInt(st.nextToken());
1967         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1968       }
1969       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1970       for (int i = 0; i < seqs.size(); i++)
1971       {
1972         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1973       }
1974
1975       if (newAlignment)
1976       {
1977         String newtitle = MessageManager.getString("label.copied_sequences");
1978         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1979         {
1980           newtitle = getTitle();
1981         }
1982         else
1983         {
1984           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1985         }
1986         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1987                 viewport.applet, newtitle, false);
1988         if (copiedHiddenColumns != null)
1989         {
1990           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1991           {
1992             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1993             af.viewport.hideColumns(region[0], region[1]);
1994           }
1995         }
1996
1997         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
1998                 frameHeight);
1999       }
2000       else
2001       {
2002         addSequences(newSeqs);
2003       }
2004
2005     } catch (Exception ex)
2006     {
2007     } // could be anything being pasted in here
2008
2009   }
2010
2011   void addSequences(SequenceI[] seqs)
2012   {
2013     for (int i = 0; i < seqs.length; i++)
2014     {
2015       viewport.getAlignment().addSequence(seqs[i]);
2016     }
2017
2018     // !newAlignment
2019     addHistoryItem(new EditCommand(
2020             MessageManager.getString("label.add_sequences"), Action.PASTE,
2021             seqs, 0, viewport.getAlignment().getWidth(),
2022             viewport.getAlignment()));
2023
2024     viewport.setEndSeq(viewport.getAlignment().getHeight());
2025     viewport.getAlignment().getWidth();
2026     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2027             .getSequences());
2028
2029   }
2030
2031   protected void cut_actionPerformed()
2032   {
2033     copy_actionPerformed();
2034     delete_actionPerformed();
2035   }
2036
2037   protected void delete_actionPerformed()
2038   {
2039
2040     SequenceGroup sg = viewport.getSelectionGroup();
2041     if (sg == null)
2042     {
2043       return;
2044     }
2045
2046     Vector seqs = new Vector();
2047     SequenceI seq;
2048     for (int i = 0; i < sg.getSize(); i++)
2049     {
2050       seq = sg.getSequenceAt(i);
2051       seqs.addElement(seq);
2052     }
2053
2054     // If the cut affects all sequences, remove highlighted columns
2055     if (sg.getSize() == viewport.getAlignment().getHeight())
2056     {
2057       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2058               sg.getEndRes() + 1);
2059     }
2060
2061     SequenceI[] cut = new SequenceI[seqs.size()];
2062     for (int i = 0; i < seqs.size(); i++)
2063     {
2064       cut[i] = (SequenceI) seqs.elementAt(i);
2065     }
2066
2067     /*
2068      * //ADD HISTORY ITEM
2069      */
2070     addHistoryItem(new EditCommand(
2071             MessageManager.getString("label.cut_sequences"), Action.CUT,
2072             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2073             viewport.getAlignment()));
2074
2075     viewport.setSelectionGroup(null);
2076     viewport.getAlignment().deleteGroup(sg);
2077
2078     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2079             .getSequences());
2080
2081     if (viewport.getAlignment().getHeight() < 1)
2082     {
2083       this.setVisible(false);
2084     }
2085     viewport.sendSelection();
2086   }
2087
2088   /**
2089    * group consensus toggled
2090    *
2091    */
2092   protected void showGroupConsensus_actionPerformed()
2093   {
2094     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2095     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2096
2097   }
2098
2099   /**
2100    * group conservation toggled.
2101    */
2102   protected void showGroupConservation_actionPerformed()
2103   {
2104     viewport.setShowGroupConservation(showGroupConservation.getState());
2105     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2106   }
2107
2108   /*
2109    * (non-Javadoc)
2110    *
2111    * @see
2112    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2113    * .event.ActionEvent)
2114    */
2115   protected void showConsensusHistogram_actionPerformed()
2116   {
2117     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2118     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2119   }
2120
2121   /*
2122    * (non-Javadoc)
2123    *
2124    * @see
2125    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2126    * .event.ActionEvent)
2127    */
2128   protected void showSequenceLogo_actionPerformed()
2129   {
2130     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2131     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2132   }
2133
2134   protected void normSequenceLogo_actionPerformed()
2135   {
2136     showSequenceLogo.setState(true);
2137     viewport.setShowSequenceLogo(true);
2138     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2139     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2140   }
2141
2142   protected void applyAutoAnnotationSettings_actionPerformed()
2143   {
2144     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145   }
2146
2147   protected void makeGrpsFromSelection_actionPerformed()
2148   {
2149     if (avc.makeGroupsFromSelection())
2150     {
2151       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2152       alignPanel.updateAnnotation();
2153       alignPanel.paintAlignment(true);
2154     }
2155   }
2156
2157   protected void createGroup_actionPerformed()
2158   {
2159     avc.createGroup();
2160   }
2161
2162   protected void unGroup_actionPerformed()
2163   {
2164     if (avc.unGroup())
2165     {
2166       alignPanel.alignmentChanged();
2167     }
2168   }
2169
2170   protected void deleteGroups_actionPerformed()
2171   {
2172     if (avc.deleteGroups())
2173     {
2174       alignPanel.alignmentChanged();
2175     }
2176   }
2177
2178   public void selectAllSequenceMenuItem_actionPerformed()
2179   {
2180     SequenceGroup sg = new SequenceGroup();
2181     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2182     {
2183       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2184     }
2185     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2186     viewport.setSelectionGroup(sg);
2187     alignPanel.paintAlignment(true);
2188     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2189     viewport.sendSelection();
2190   }
2191
2192   public void deselectAllSequenceMenuItem_actionPerformed()
2193   {
2194     if (viewport.cursorMode)
2195     {
2196       alignPanel.seqPanel.keyboardNo1 = null;
2197       alignPanel.seqPanel.keyboardNo2 = null;
2198     }
2199     viewport.setSelectionGroup(null);
2200     viewport.getColumnSelection().clear();
2201     viewport.setSelectionGroup(null);
2202     alignPanel.idPanel.idCanvas.searchResults = null;
2203     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2204     alignPanel.paintAlignment(true);
2205     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2206     viewport.sendSelection();
2207   }
2208
2209   public void invertSequenceMenuItem_actionPerformed()
2210   {
2211     SequenceGroup sg = viewport.getSelectionGroup();
2212     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2213     {
2214       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2215     }
2216
2217     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2218     viewport.sendSelection();
2219   }
2220
2221   public void invertColSel_actionPerformed()
2222   {
2223     viewport.invertColumnSelection();
2224     alignPanel.paintAlignment(true);
2225     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2226     viewport.sendSelection();
2227   }
2228
2229   void trimAlignment(boolean trimLeft)
2230   {
2231     ColumnSelection colSel = viewport.getColumnSelection();
2232     int column;
2233
2234     if (colSel.size() > 0)
2235     {
2236       if (trimLeft)
2237       {
2238         column = colSel.getMin();
2239       }
2240       else
2241       {
2242         column = colSel.getMax();
2243       }
2244
2245       SequenceI[] seqs;
2246       if (viewport.getSelectionGroup() != null)
2247       {
2248         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2249                 viewport.getHiddenRepSequences());
2250       }
2251       else
2252       {
2253         seqs = viewport.getAlignment().getSequencesArray();
2254       }
2255
2256       TrimRegionCommand trimRegion;
2257       if (trimLeft)
2258       {
2259         trimRegion = new TrimRegionCommand("Remove Left",
2260                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2261                 viewport.getAlignment(), viewport.getColumnSelection(),
2262                 viewport.getSelectionGroup());
2263         viewport.setStartRes(0);
2264       }
2265       else
2266       {
2267         trimRegion = new TrimRegionCommand("Remove Right",
2268                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2269                 viewport.getAlignment(), viewport.getColumnSelection(),
2270                 viewport.getSelectionGroup());
2271       }
2272
2273       statusBar.setText(MessageManager.formatMessage(
2274               "label.removed_columns", new String[]
2275               { Integer.valueOf(trimRegion.getSize()).toString() }));
2276       addHistoryItem(trimRegion);
2277
2278       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2279       {
2280         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2281                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2282         {
2283           viewport.getAlignment().deleteGroup(sg);
2284         }
2285       }
2286
2287       viewport.firePropertyChange("alignment", null, viewport
2288               .getAlignment().getSequences());
2289     }
2290   }
2291
2292   public void removeGappedColumnMenuItem_actionPerformed()
2293   {
2294     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2295
2296     SequenceI[] seqs;
2297     if (viewport.getSelectionGroup() != null)
2298     {
2299       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2300               viewport.getHiddenRepSequences());
2301       start = viewport.getSelectionGroup().getStartRes();
2302       end = viewport.getSelectionGroup().getEndRes();
2303     }
2304     else
2305     {
2306       seqs = viewport.getAlignment().getSequencesArray();
2307     }
2308
2309     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2310             "Remove Gapped Columns", seqs, start, end,
2311             viewport.getAlignment());
2312
2313     addHistoryItem(removeGapCols);
2314
2315     statusBar.setText(MessageManager.formatMessage(
2316             "label.removed_empty_columns", new String[]
2317             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2318
2319     // This is to maintain viewport position on first residue
2320     // of first sequence
2321     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2322     int startRes = seq.findPosition(viewport.startRes);
2323     // ShiftList shifts;
2324     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2325     // edit.alColumnChanges=shifts.getInverse();
2326     // if (viewport.hasHiddenColumns)
2327     // viewport.getColumnSelection().compensateForEdits(shifts);
2328     viewport.setStartRes(seq.findIndex(startRes) - 1);
2329     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2330             .getSequences());
2331
2332   }
2333
2334   public void removeAllGapsMenuItem_actionPerformed()
2335   {
2336     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2337
2338     SequenceI[] seqs;
2339     if (viewport.getSelectionGroup() != null)
2340     {
2341       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2342               viewport.getHiddenRepSequences());
2343       start = viewport.getSelectionGroup().getStartRes();
2344       end = viewport.getSelectionGroup().getEndRes();
2345     }
2346     else
2347     {
2348       seqs = viewport.getAlignment().getSequencesArray();
2349     }
2350
2351     // This is to maintain viewport position on first residue
2352     // of first sequence
2353     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2354     int startRes = seq.findPosition(viewport.startRes);
2355
2356     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2357             viewport.getAlignment()));
2358
2359     viewport.setStartRes(seq.findIndex(startRes) - 1);
2360
2361     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2362             .getSequences());
2363
2364   }
2365
2366   public void findMenuItem_actionPerformed()
2367   {
2368     new Finder(alignPanel);
2369   }
2370
2371   /**
2372    * create a new view derived from the current view
2373    *
2374    * @param viewtitle
2375    * @return frame for the new view
2376    */
2377   public AlignFrame newView(String viewtitle)
2378   {
2379     AlignmentI newal;
2380     if (viewport.hasHiddenRows())
2381     {
2382       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2383               .getFullAlignment().getSequencesArray());
2384     }
2385     else
2386     {
2387       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2388     }
2389
2390     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2391     {
2392       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2393       {
2394         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2395         {
2396           newal.addAnnotation(viewport.getAlignment()
2397                   .getAlignmentAnnotation()[i]);
2398         }
2399       }
2400     }
2401
2402     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2403
2404     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2405     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2406     PaintRefresher.Register(newaf.alignPanel,
2407             newaf.alignPanel.av.getSequenceSetId());
2408
2409     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2410             newaf.alignPanel.av.getSequenceSetId());
2411     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2412             newaf.alignPanel.av.getSequenceSetId());
2413
2414     Vector comps = (Vector) PaintRefresher.components.get(viewport
2415             .getSequenceSetId());
2416     int viewSize = -1;
2417     for (int i = 0; i < comps.size(); i++)
2418     {
2419       if (comps.elementAt(i) instanceof AlignmentPanel)
2420       {
2421         viewSize++;
2422       }
2423     }
2424
2425     String title = new String(this.getTitle());
2426     if (viewtitle != null)
2427     {
2428       title = viewtitle + " ( " + title + ")";
2429     }
2430     else
2431     {
2432       if (title.indexOf("(View") > -1)
2433       {
2434         title = title.substring(0, title.indexOf("(View"));
2435       }
2436       title += "(View " + viewSize + ")";
2437     }
2438
2439     newaf.setTitle(title.toString());
2440
2441     newaf.viewport.setHistoryList(viewport.getHistoryList());
2442     newaf.viewport.setRedoList(viewport.getRedoList());
2443     return newaf;
2444   }
2445
2446   /**
2447    *
2448    * @return list of feature groups on the view
2449    */
2450   public String[] getFeatureGroups()
2451   {
2452     FeatureRenderer fr = null;
2453     if (alignPanel != null
2454             && (fr = alignPanel.getFeatureRenderer()) != null)
2455     {
2456       List<String> gps = fr.getFeatureGroups();
2457       String[] _gps = gps.toArray(new String[gps.size()]);
2458       return _gps;
2459     }
2460     return null;
2461   }
2462
2463   /**
2464    * get sequence feature groups that are hidden or shown
2465    *
2466    * @param visible
2467    *          true is visible
2468    * @return list
2469    */
2470   public String[] getFeatureGroupsOfState(boolean visible)
2471   {
2472     FeatureRenderer fr = null;
2473     if (alignPanel != null
2474             && (fr = alignPanel.getFeatureRenderer()) != null)
2475     {
2476       List<String> gps = fr.getGroups(visible);
2477       String[] _gps = gps.toArray(new String[gps.size()]);
2478       return _gps;
2479     }
2480     return null;
2481   }
2482
2483   /**
2484    * Change the display state for the given feature groups
2485    *
2486    * @param groups
2487    *          list of group strings
2488    * @param state
2489    *          visible or invisible
2490    */
2491   public void setFeatureGroupState(String[] groups, boolean state)
2492   {
2493     FeatureRenderer fr = null;
2494     this.sequenceFeatures.setState(true);
2495     viewport.setShowSequenceFeatures(true);
2496     if (alignPanel != null
2497             && (fr = alignPanel.getFeatureRenderer()) != null)
2498     {
2499
2500       fr.setGroupVisibility(Arrays.asList(groups), state);
2501       alignPanel.seqPanel.seqCanvas.repaint();
2502       if (alignPanel.overviewPanel != null)
2503       {
2504         alignPanel.overviewPanel.updateOverviewImage();
2505       }
2506     }
2507   }
2508
2509   public void seqLimits_itemStateChanged()
2510   {
2511     viewport.setShowJVSuffix(seqLimits.getState());
2512     alignPanel.fontChanged();
2513     alignPanel.paintAlignment(true);
2514   }
2515
2516   protected void colourTextMenuItem_actionPerformed()
2517   {
2518     viewport.setColourText(colourTextMenuItem.getState());
2519     alignPanel.paintAlignment(true);
2520   }
2521
2522   protected void displayNonconservedMenuItem_actionPerformed()
2523   {
2524     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2525     alignPanel.paintAlignment(true);
2526   }
2527
2528   protected void wrapMenuItem_actionPerformed()
2529   {
2530     viewport.setWrapAlignment(wrapMenuItem.getState());
2531     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2532     scaleAbove.setEnabled(wrapMenuItem.getState());
2533     scaleLeft.setEnabled(wrapMenuItem.getState());
2534     scaleRight.setEnabled(wrapMenuItem.getState());
2535     alignPanel.paintAlignment(true);
2536   }
2537
2538   public void overviewMenuItem_actionPerformed()
2539   {
2540     if (alignPanel.overviewPanel != null)
2541     {
2542       return;
2543     }
2544
2545     Frame frame = new Frame();
2546     OverviewPanel overview = new OverviewPanel(alignPanel);
2547     frame.add(overview);
2548     // +50 must allow for applet frame window
2549     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2550             "label.overview_params", new String[]
2551             { this.getTitle() }), overview.getPreferredSize().width,
2552             overview.getPreferredSize().height + 50);
2553
2554     frame.pack();
2555     final AlignmentPanel ap = alignPanel;
2556     frame.addWindowListener(new WindowAdapter()
2557     {
2558       @Override
2559       public void windowClosing(WindowEvent e)
2560       {
2561         if (ap != null)
2562         {
2563           ap.setOverviewPanel(null);
2564         }
2565       };
2566     });
2567
2568     alignPanel.setOverviewPanel(overview);
2569
2570   }
2571
2572   public void changeColour(ColourSchemeI cs)
2573   {
2574     int threshold = 0;
2575
2576     if (cs != null)
2577     {
2578       if (viewport.getAbovePIDThreshold())
2579       {
2580         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2581                 cs, "Background"));
2582       }
2583
2584       if (viewport.getConservationSelected())
2585       {
2586         cs.setConservationApplied(true);
2587         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2588                 cs, "Background"));
2589       }
2590       else
2591       {
2592         cs.setConservationApplied(false);
2593       }
2594     }
2595     viewport.setGlobalColourScheme(cs);
2596
2597     if (alignPanel.getOverviewPanel() != null)
2598     {
2599       alignPanel.getOverviewPanel().updateOverviewImage();
2600     }
2601
2602     jalview.structure.StructureSelectionManager
2603             .getStructureSelectionManager(viewport.applet)
2604             .sequenceColoursChanged(alignPanel);
2605
2606     alignPanel.paintAlignment(true);
2607   }
2608
2609   protected void modifyPID_actionPerformed()
2610   {
2611     if (viewport.getAbovePIDThreshold()
2612             && viewport.getGlobalColourScheme() != null)
2613     {
2614       SliderPanel.setPIDSliderSource(alignPanel,
2615               viewport.getGlobalColourScheme(), "Background");
2616       SliderPanel.showPIDSlider();
2617     }
2618   }
2619
2620   protected void modifyConservation_actionPerformed()
2621   {
2622     if (viewport.getConservationSelected()
2623             && viewport.getGlobalColourScheme() != null)
2624     {
2625       SliderPanel.setConservationSlider(alignPanel,
2626               viewport.getGlobalColourScheme(), "Background");
2627       SliderPanel.showConservationSlider();
2628     }
2629   }
2630
2631   protected void conservationMenuItem_actionPerformed()
2632   {
2633     viewport.setConservationSelected(conservationMenuItem.getState());
2634
2635     viewport.setAbovePIDThreshold(false);
2636     abovePIDThreshold.setState(false);
2637
2638     changeColour(viewport.getGlobalColourScheme());
2639
2640     modifyConservation_actionPerformed();
2641   }
2642
2643   public void abovePIDThreshold_actionPerformed()
2644   {
2645     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2646
2647     conservationMenuItem.setState(false);
2648     viewport.setConservationSelected(false);
2649
2650     changeColour(viewport.getGlobalColourScheme());
2651
2652     modifyPID_actionPerformed();
2653   }
2654
2655   public void sortPairwiseMenuItem_actionPerformed()
2656   {
2657     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2658     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2659             .getAlignment().getSequenceAt(0), null);
2660
2661     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2662             viewport.getAlignment()));
2663     alignPanel.paintAlignment(true);
2664   }
2665
2666   public void sortIDMenuItem_actionPerformed()
2667   {
2668     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2669     AlignmentSorter.sortByID(viewport.getAlignment());
2670     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2671             viewport.getAlignment()));
2672     alignPanel.paintAlignment(true);
2673   }
2674
2675   public void sortLengthMenuItem_actionPerformed()
2676   {
2677     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2678     AlignmentSorter.sortByLength(viewport.getAlignment());
2679     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2680             viewport.getAlignment()));
2681     alignPanel.paintAlignment(true);
2682   }
2683
2684   public void sortGroupMenuItem_actionPerformed()
2685   {
2686     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2687     AlignmentSorter.sortByGroup(viewport.getAlignment());
2688     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2689             viewport.getAlignment()));
2690     alignPanel.paintAlignment(true);
2691
2692   }
2693
2694   public void removeRedundancyMenuItem_actionPerformed()
2695   {
2696     new RedundancyPanel(alignPanel);
2697   }
2698
2699   public void pairwiseAlignmentMenuItem_actionPerformed()
2700   {
2701     if (viewport.getSelectionGroup() != null
2702             && viewport.getSelectionGroup().getSize() > 1)
2703     {
2704       Frame frame = new Frame();
2705       frame.add(new PairwiseAlignPanel(alignPanel));
2706       jalview.bin.JalviewLite.addFrame(frame,
2707               MessageManager.getString("action.pairwise_alignment"), 600,
2708               500);
2709     }
2710   }
2711
2712   public void PCAMenuItem_actionPerformed()
2713   {
2714     // are the sequences aligned?
2715     if (!viewport.getAlignment().isAligned(false))
2716     {
2717       SequenceI current;
2718       int Width = viewport.getAlignment().getWidth();
2719
2720       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2721       {
2722         current = viewport.getAlignment().getSequenceAt(i);
2723
2724         if (current.getLength() < Width)
2725         {
2726           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2727         }
2728       }
2729       alignPanel.paintAlignment(true);
2730     }
2731
2732     if ((viewport.getSelectionGroup() != null
2733             && viewport.getSelectionGroup().getSize() < 4 && viewport
2734             .getSelectionGroup().getSize() > 0)
2735             || viewport.getAlignment().getHeight() < 4)
2736     {
2737       return;
2738     }
2739
2740     try
2741     {
2742       new PCAPanel(viewport);
2743     } catch (java.lang.OutOfMemoryError ex)
2744     {
2745     }
2746
2747   }
2748
2749   public void averageDistanceTreeMenuItem_actionPerformed()
2750   {
2751     NewTreePanel("AV", "PID", "Average distance tree using PID");
2752   }
2753
2754   public void neighbourTreeMenuItem_actionPerformed()
2755   {
2756     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2757   }
2758
2759   protected void njTreeBlosumMenuItem_actionPerformed()
2760   {
2761     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2762   }
2763
2764   protected void avTreeBlosumMenuItem_actionPerformed()
2765   {
2766     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2767   }
2768
2769   void NewTreePanel(String type, String pwType, String title)
2770   {
2771     // are the sequences aligned?
2772     if (!viewport.getAlignment().isAligned(false))
2773     {
2774       SequenceI current;
2775       int Width = viewport.getAlignment().getWidth();
2776
2777       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2778       {
2779         current = viewport.getAlignment().getSequenceAt(i);
2780
2781         if (current.getLength() < Width)
2782         {
2783           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2784         }
2785       }
2786       alignPanel.paintAlignment(true);
2787
2788     }
2789
2790     if ((viewport.getSelectionGroup() != null && viewport
2791             .getSelectionGroup().getSize() > 1)
2792             || (viewport.getAlignment().getHeight() > 1))
2793     {
2794       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2795
2796       addTreeMenuItem(tp, title);
2797
2798       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2799     }
2800   }
2801
2802   void loadTree_actionPerformed()
2803   {
2804     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2805     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2806     cap.setTreeImport();
2807     Frame frame = new Frame();
2808     frame.add(cap);
2809     jalview.bin.JalviewLite.addFrame(frame,
2810             MessageManager.getString("label.paste_newick_file"), 400, 300);
2811   }
2812
2813   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2814   {
2815     TreePanel tp = new TreePanel(alignPanel, treeFile,
2816             MessageManager.getString("label.load_tree_from_file"), tree);
2817     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2818     addTreeMenuItem(tp, treeFile);
2819   }
2820
2821   /**
2822    * sort the alignment using the given treePanel
2823    *
2824    * @param treePanel
2825    *          tree used to sort view
2826    * @param title
2827    *          string used for undo event name
2828    */
2829   public void sortByTree(TreePanel treePanel, String title)
2830   {
2831     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2832     AlignmentSorter
2833             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2834     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2835     // HistoryItem.SORT));
2836     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2837             "label.order_by_params", new String[]
2838             { title }), oldOrder, viewport.getAlignment()));
2839     alignPanel.paintAlignment(true);
2840   }
2841
2842   /**
2843    * Do any automatic reordering of the alignment and add the necessary bits to
2844    * the menu structure for the new tree
2845    *
2846    * @param treePanel
2847    * @param title
2848    */
2849   protected void addTreeMenuItem(final TreePanel treePanel,
2850           final String title)
2851   {
2852     final MenuItem item = new MenuItem(title);
2853     sortByTreeMenu.add(item);
2854     item.addActionListener(new java.awt.event.ActionListener()
2855     {
2856       @Override
2857       public void actionPerformed(ActionEvent evt)
2858       {
2859         sortByTree(treePanel, title); // treePanel.getTitle());
2860       }
2861     });
2862
2863     treePanel.addWindowListener(new WindowAdapter()
2864     {
2865       @Override
2866       public void windowOpened(WindowEvent e)
2867       {
2868         if (viewport.sortByTree)
2869         {
2870           sortByTree(treePanel, title);
2871         }
2872         super.windowOpened(e);
2873       }
2874
2875       @Override
2876       public void windowClosing(WindowEvent e)
2877       {
2878         sortByTreeMenu.remove(item);
2879       };
2880     });
2881   }
2882
2883   public boolean sortBy(AlignmentOrder alorder, String undoname)
2884   {
2885     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2886     if (viewport.applet.debug)
2887     {
2888       System.err.println("Sorting " + alorder.getOrder().size()
2889               + " in alignment '" + getTitle() + "'");
2890     }
2891     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2892     if (undoname != null)
2893     {
2894       addHistoryItem(new OrderCommand(undoname, oldOrder,
2895               viewport.getAlignment()));
2896     }
2897     alignPanel.paintAlignment(true);
2898     return true;
2899   }
2900
2901   protected void documentation_actionPerformed()
2902   {
2903     alignPanel.av.applet.openJalviewHelpUrl();
2904   }
2905
2906   protected void about_actionPerformed()
2907   {
2908
2909     class AboutPanel extends Canvas
2910     {
2911       String version;
2912
2913       String builddate;
2914
2915       public AboutPanel(String version, String builddate)
2916       {
2917         this.version = version;
2918         this.builddate = builddate;
2919       }
2920
2921       @Override
2922       public void paint(Graphics g)
2923       {
2924         g.setColor(Color.white);
2925         g.fillRect(0, 0, getSize().width, getSize().height);
2926         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2927         FontMetrics fm = g.getFontMetrics();
2928         int fh = fm.getHeight();
2929         int y = 5, x = 7;
2930         g.setColor(Color.black);
2931         // TODO: update this text for each release or centrally store it for
2932         // lite and application
2933         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2934         g.drawString(MessageManager.formatMessage(
2935                 "label.jalviewLite_release", new String[]
2936                 { version }), x, y += fh);
2937         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2938         g.drawString(MessageManager.formatMessage(
2939                 "label.jaview_build_date", new String[]
2940                 { builddate }), x, y += fh);
2941         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2942         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2943                 x, y += fh * 1.5);
2944         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2945                 x + 50, y += fh + 8);
2946         g.drawString(
2947                 MessageManager.getString("label.jalview_dev_managers"), x,
2948                 y += fh);
2949         g.drawString(MessageManager
2950                 .getString("label.jalview_distribution_lists"), x, y += fh);
2951         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2952                 x, y += fh + 8);
2953         g.drawString(
2954                 MessageManager.getString("label.jalview_cite_1_authors"),
2955                 x, y += fh);
2956         g.drawString(
2957                 MessageManager.getString("label.jalview_cite_1_title"), x,
2958                 y += fh);
2959         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2960                 x, y += fh);
2961       }
2962     }
2963
2964     Frame frame = new Frame();
2965     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2966             .getBuildDate()));
2967     jalview.bin.JalviewLite.addFrame(frame,
2968             MessageManager.getString("label.jalview"), 580, 220);
2969
2970   }
2971
2972   public void showURL(String url, String target)
2973   {
2974     if (viewport.applet == null)
2975     {
2976       System.out.println("Not running as applet - no browser available.");
2977     }
2978     else
2979     {
2980       viewport.applet.showURL(url, target);
2981     }
2982   }
2983
2984   // ////////////////////////////////////////////////////////////////////////////////
2985   // JBuilder Graphics here
2986
2987   MenuBar alignFrameMenuBar = new MenuBar();
2988
2989   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2990
2991   MenuItem loadApplication = new MenuItem(
2992           MessageManager.getString("label.view_full_application"));
2993
2994   MenuItem loadTree = new MenuItem(
2995           MessageManager.getString("label.load_associated_tree"));
2996
2997   MenuItem loadAnnotations = new MenuItem(
2998           MessageManager.getString("label.load_features_annotations"));
2999
3000   MenuItem outputFeatures = new MenuItem(
3001           MessageManager.getString("label.export_features").concat("..."));
3002
3003   MenuItem outputAnnotations = new MenuItem(
3004           MessageManager.getString("label.export_annotations").concat("..."));
3005
3006   MenuItem closeMenuItem = new MenuItem(
3007           MessageManager.getString("action.close"));
3008
3009   MenuItem selectAllSequenceMenuItem = new MenuItem(
3010           MessageManager.getString("action.select_all"));
3011
3012   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3013           MessageManager.getString("action.deselect_all"));
3014
3015   MenuItem invertSequenceMenuItem = new MenuItem(
3016           MessageManager.getString("action.invert_selection"));
3017
3018   MenuItem remove2LeftMenuItem = new MenuItem();
3019
3020   MenuItem remove2RightMenuItem = new MenuItem();
3021
3022   MenuItem removeGappedColumnMenuItem = new MenuItem();
3023
3024   MenuItem removeAllGapsMenuItem = new MenuItem();
3025
3026   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3027
3028   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3029
3030   MenuItem sortPairwiseMenuItem = new MenuItem();
3031
3032   MenuItem sortIDMenuItem = new MenuItem();
3033
3034   MenuItem sortLengthMenuItem = new MenuItem();
3035
3036   MenuItem sortGroupMenuItem = new MenuItem();
3037
3038   MenuItem removeRedundancyMenuItem = new MenuItem();
3039
3040   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3041
3042   MenuItem PCAMenuItem = new MenuItem();
3043
3044   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3045
3046   MenuItem neighbourTreeMenuItem = new MenuItem();
3047
3048   BorderLayout borderLayout1 = new BorderLayout();
3049
3050   public Label statusBar = new Label();
3051
3052   MenuItem clustalColour = new MenuItem();
3053
3054   MenuItem zappoColour = new MenuItem();
3055
3056   MenuItem taylorColour = new MenuItem();
3057
3058   MenuItem hydrophobicityColour = new MenuItem();
3059
3060   MenuItem helixColour = new MenuItem();
3061
3062   MenuItem strandColour = new MenuItem();
3063
3064   MenuItem turnColour = new MenuItem();
3065
3066   MenuItem buriedColour = new MenuItem();
3067
3068   MenuItem purinePyrimidineColour = new MenuItem();
3069
3070   MenuItem RNAInteractionColour = new MenuItem();
3071
3072   MenuItem RNAHelixColour = new MenuItem();
3073
3074   MenuItem userDefinedColour = new MenuItem();
3075
3076   MenuItem PIDColour = new MenuItem();
3077
3078   MenuItem BLOSUM62Colour = new MenuItem();
3079
3080   MenuItem tcoffeeColour = new MenuItem();
3081
3082   MenuItem njTreeBlosumMenuItem = new MenuItem();
3083
3084   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3085
3086   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3087
3088   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3089
3090   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3091
3092   MenuItem alProperties = new MenuItem(
3093           MessageManager.getString("label.alignment_props"));
3094
3095   MenuItem overviewMenuItem = new MenuItem();
3096
3097   MenuItem undoMenuItem = new MenuItem();
3098
3099   MenuItem redoMenuItem = new MenuItem();
3100
3101   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3102
3103   MenuItem noColourmenuItem = new MenuItem();
3104
3105   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3106
3107   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3108
3109   MenuItem findMenuItem = new MenuItem();
3110
3111   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3112
3113   MenuItem nucleotideColour = new MenuItem();
3114
3115   MenuItem deleteGroups = new MenuItem();
3116
3117   MenuItem grpsFromSelection = new MenuItem();
3118
3119   MenuItem createGroup = new MenuItem();
3120
3121   MenuItem unGroup = new MenuItem();
3122
3123   MenuItem delete = new MenuItem();
3124
3125   MenuItem copy = new MenuItem();
3126
3127   MenuItem cut = new MenuItem();
3128
3129   Menu pasteMenu = new Menu();
3130
3131   MenuItem pasteNew = new MenuItem();
3132
3133   MenuItem pasteThis = new MenuItem();
3134
3135   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3136
3137   MenuItem font = new MenuItem();
3138
3139   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3140
3141   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3142
3143   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3144
3145   MenuItem modifyPID = new MenuItem();
3146
3147   MenuItem modifyConservation = new MenuItem();
3148
3149   CheckboxMenuItem autoCalculate = null;
3150
3151   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3152           "Sort Alignment With New Tree", true);
3153
3154   Menu sortByTreeMenu = new Menu();
3155
3156   MenuItem inputText = new MenuItem();
3157
3158   MenuItem documentation = new MenuItem();
3159
3160   MenuItem about = new MenuItem();
3161
3162   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3163
3164   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3165
3166   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3167
3168   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3169
3170   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3171
3172   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3173
3174   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3175
3176   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3177
3178   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3179
3180   /**
3181    * Initialise menus and other items
3182    *
3183    * @throws Exception
3184    */
3185   private void jbInit() throws Exception
3186   {
3187     setMenuBar(alignFrameMenuBar);
3188
3189     /*
3190      * Configure File menu items and actions
3191      */
3192     inputText
3193             .setLabel(MessageManager.getString("label.input_from_textbox"));
3194     inputText.addActionListener(this);
3195     Menu outputTextboxMenu = new Menu(
3196             MessageManager.getString("label.out_to_textbox"));
3197     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3198     {
3199
3200       MenuItem item = new MenuItem(
3201               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3202
3203       item.addActionListener(new java.awt.event.ActionListener()
3204       {
3205         @Override
3206         public void actionPerformed(ActionEvent e)
3207         {
3208           outputText_actionPerformed(e);
3209         }
3210       });
3211
3212       outputTextboxMenu.add(item);
3213     }
3214     closeMenuItem.addActionListener(this);
3215     loadApplication.addActionListener(this);
3216     loadTree.addActionListener(this);
3217     loadAnnotations.addActionListener(this);
3218     outputFeatures.addActionListener(this);
3219     outputAnnotations.addActionListener(this);
3220
3221     /*
3222      * Configure Edit menu items and actions
3223      */
3224     undoMenuItem.setEnabled(false);
3225     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3226     undoMenuItem.addActionListener(this);
3227     redoMenuItem.setEnabled(false);
3228     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3229     redoMenuItem.addActionListener(this);
3230     copy.setLabel(MessageManager.getString("action.copy"));
3231     copy.addActionListener(this);
3232     cut.setLabel(MessageManager.getString("action.cut"));
3233     cut.addActionListener(this);
3234     delete.setLabel(MessageManager.getString("action.delete"));
3235     delete.addActionListener(this);
3236     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3237     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3238     pasteNew.addActionListener(this);
3239     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3240     pasteThis.addActionListener(this);
3241     remove2LeftMenuItem.setLabel(MessageManager
3242             .getString("action.remove_left"));
3243     remove2LeftMenuItem.addActionListener(this);
3244     remove2RightMenuItem.setLabel(MessageManager
3245             .getString("action.remove_right"));
3246     remove2RightMenuItem.addActionListener(this);
3247     removeGappedColumnMenuItem.setLabel(MessageManager
3248             .getString("action.remove_empty_columns"));
3249     removeGappedColumnMenuItem.addActionListener(this);
3250     removeAllGapsMenuItem.setLabel(MessageManager
3251             .getString("action.remove_all_gaps"));
3252     removeAllGapsMenuItem.addActionListener(this);
3253     removeRedundancyMenuItem.setLabel(MessageManager.getString(
3254             "action.remove_redundancy").concat("..."));
3255     removeRedundancyMenuItem.addActionListener(this);
3256
3257     /*
3258      * Configure Select menu items and actions
3259      */
3260     findMenuItem.setLabel(MessageManager.getString("action.find"));
3261     findMenuItem.addActionListener(this);
3262     selectAllSequenceMenuItem.addActionListener(this);
3263     deselectAllSequenceMenuItem.addActionListener(this);
3264     invertSequenceMenuItem.setLabel(MessageManager
3265             .getString("action.invert_sequence_selection"));
3266     invertSequenceMenuItem.addActionListener(this);
3267     invertColSel.setLabel(MessageManager
3268             .getString("action.invert_column_selection"));
3269     invertColSel.addActionListener(this);
3270     deleteGroups.setLabel(MessageManager
3271             .getString("action.undefine_groups"));
3272     deleteGroups.addActionListener(this);
3273     grpsFromSelection.setLabel(MessageManager
3274             .getString("action.make_groups_selection"));
3275     grpsFromSelection.addActionListener(this);
3276     createGroup.setLabel(MessageManager.getString("action.create_group"));
3277     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3278     annotationColumnSelection.setLabel("Select by Annotation");
3279     annotationColumnSelection.addActionListener(this);
3280
3281     /*
3282      * Configure View menu items and actions
3283      */
3284     newView.setLabel(MessageManager.getString("action.new_view"));
3285     newView.addActionListener(this);
3286     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3287     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3288     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3289     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3290     hideColumns
3291             .setLabel(MessageManager.getString("label.selected_columns"));
3292     hideSequences.setLabel(MessageManager
3293             .getString("label.selected_sequences"));
3294     hideAllButSelection.setLabel(MessageManager
3295             .getString("label.all_but_selected_region"));
3296     hideAllSelection.setLabel(MessageManager
3297             .getString("label.selected_region"));
3298     showAllHidden.setLabel(MessageManager
3299             .getString("label.all_sequences_columns"));
3300     showColumns.addActionListener(this);
3301     showSeqs.addActionListener(this);
3302     hideColumns.addActionListener(this);
3303     hideSequences.addActionListener(this);
3304     hideAllButSelection.addActionListener(this);
3305     hideAllSelection.addActionListener(this);
3306     showAllHidden.addActionListener(this);
3307     featureSettings.setLabel(MessageManager
3308             .getString("label.feature_settings"));
3309     featureSettings.addActionListener(this);
3310     sequenceFeatures.setLabel(MessageManager
3311             .getString("label.show_sequence_features"));
3312     sequenceFeatures.addItemListener(this);
3313     sequenceFeatures.setState(false);
3314     followMouseOverFlag.setLabel(MessageManager
3315             .getString("label.automatic_scrolling"));
3316     followMouseOverFlag.addItemListener(this);
3317     alProperties.addActionListener(this);
3318     overviewMenuItem.setLabel(MessageManager
3319             .getString("label.overview_window"));
3320     overviewMenuItem.addActionListener(this);
3321
3322     /*
3323      * Configure Annotations menu items and actions
3324      */
3325     annotationPanelMenuItem.setLabel(MessageManager
3326             .getString("label.show_annotations"));
3327     annotationPanelMenuItem.addItemListener(this);
3328     showGroupConsensus.setLabel(MessageManager
3329             .getString("label.group_consensus"));
3330     showGroupConservation.setLabel(MessageManager
3331             .getString("label.group_conservation"));
3332     showConsensusHistogram.setLabel(MessageManager
3333             .getString("label.show_consensus_histogram"));
3334     showSequenceLogo.setLabel(MessageManager
3335             .getString("label.show_consensus_logo"));
3336     normSequenceLogo.setLabel(MessageManager
3337             .getString("label.norm_consensus_logo"));
3338     applyAutoAnnotationSettings.setLabel(MessageManager
3339             .getString("label.apply_all_groups"));
3340     applyAutoAnnotationSettings.setState(true);
3341     Menu autoAnnMenu = new Menu(
3342             MessageManager.getString("label.autocalculated_annotation"));
3343     showGroupConsensus.addItemListener(this);
3344     showGroupConservation.addItemListener(this);
3345     showConsensusHistogram.addItemListener(this);
3346     showSequenceLogo.addItemListener(this);
3347     normSequenceLogo.addItemListener(this);
3348     applyAutoAnnotationSettings.addItemListener(this);
3349     showAlignmentAnnotations = new CheckboxMenuItem(
3350             MessageManager.getString("label.show_all_al_annotations"));
3351     showSequenceAnnotations = new CheckboxMenuItem(
3352             MessageManager.getString("label.show_all_seq_annotations"));
3353     sortAnnBySequence = new CheckboxMenuItem(
3354             MessageManager.getString("label.sort_annotations_by_sequence"));
3355     sortAnnByLabel = new CheckboxMenuItem(
3356             MessageManager.getString("label.sort_annotations_by_label"));
3357     showAutoFirst = new CheckboxMenuItem(
3358             MessageManager.getString("label.show_first"));
3359     showAutoLast = new CheckboxMenuItem(
3360             MessageManager.getString("label.show_last"));
3361     showAlignmentAnnotations.addItemListener(this);
3362     showSequenceAnnotations.addItemListener(this);
3363     sortAnnBySequence.addItemListener(this);
3364     sortAnnByLabel.addItemListener(this);
3365     showAutoFirst.addItemListener(this);
3366     showAutoLast.addItemListener(this);
3367
3368     /*
3369      * Configure Format menu items and actions
3370      */
3371     font.setLabel(MessageManager.getString("action.font"));
3372     font.addActionListener(this);
3373     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3374     scaleAbove.setState(true);
3375     scaleAbove.setEnabled(false);
3376     scaleAbove.addItemListener(this);
3377     scaleLeft.setEnabled(false);
3378     scaleLeft.setState(true);
3379     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3380     scaleLeft.addItemListener(this);
3381     scaleRight.setEnabled(false);
3382     scaleRight.setState(true);
3383     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3384     scaleRight.addItemListener(this);
3385     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3386     viewBoxesMenuItem.setState(true);
3387     viewBoxesMenuItem.addItemListener(this);
3388     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3389     viewTextMenuItem.setState(true);
3390     viewTextMenuItem.addItemListener(this);
3391     colourTextMenuItem.setLabel(MessageManager
3392             .getString("label.colour_text"));
3393     colourTextMenuItem.addItemListener(this);
3394     displayNonconservedMenuItem.setLabel(MessageManager
3395             .getString("label.show_non_conversed"));
3396     displayNonconservedMenuItem.addItemListener(this);
3397     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3398     wrapMenuItem.addItemListener(this);
3399     renderGapsMenuItem.setLabel(MessageManager
3400             .getString("action.show_gaps"));
3401     renderGapsMenuItem.setState(true);
3402     renderGapsMenuItem.addItemListener(this);
3403     centreColumnLabelFlag.setLabel(MessageManager
3404             .getString("label.centre_column_labels"));
3405     centreColumnLabelFlag.addItemListener(this);
3406     seqLimits.setState(true);
3407     seqLimits.setLabel(MessageManager
3408             .getString("label.show_sequence_limits"));
3409     seqLimits.addItemListener(this);
3410
3411     /*
3412      * Configure Colour menu items and actions
3413      */
3414     applyToAllGroups.setLabel(MessageManager
3415             .getString("label.apply_colour_to_all_groups"));
3416     applyToAllGroups.setState(true);
3417     applyToAllGroups.addItemListener(this);
3418     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3419     clustalColour.addActionListener(this);
3420     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3421     zappoColour.addActionListener(this);
3422     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3423     taylorColour.addActionListener(this);
3424     hydrophobicityColour.setLabel(MessageManager
3425             .getString("label.hydrophobicity"));
3426     hydrophobicityColour.addActionListener(this);
3427     helixColour
3428             .setLabel(MessageManager.getString("label.helix_propensity"));
3429     helixColour.addActionListener(this);
3430     strandColour.setLabel(MessageManager
3431             .getString("label.strand_propensity"));
3432     strandColour.addActionListener(this);
3433     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3434     turnColour.addActionListener(this);
3435     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3436     buriedColour.addActionListener(this);
3437     purinePyrimidineColour.setLabel(MessageManager
3438             .getString("label.purine_pyrimidine"));
3439     purinePyrimidineColour.addActionListener(this);
3440     RNAInteractionColour.setLabel(MessageManager
3441             .getString("label.rna_interaction"));
3442     RNAInteractionColour.addActionListener(this);
3443     RNAHelixColour.setLabel(MessageManager
3444             .getString("action.by_rna_helixes"));
3445     RNAHelixColour.addActionListener(this);
3446     userDefinedColour.setLabel(MessageManager
3447             .getString("action.user_defined"));
3448     userDefinedColour.addActionListener(this);
3449     PIDColour.setLabel(MessageManager
3450             .getString("label.percentage_identity"));
3451     PIDColour.addActionListener(this);
3452     BLOSUM62Colour.setLabel(MessageManager
3453             .getString("label.blosum62_score"));
3454     BLOSUM62Colour.addActionListener(this);
3455     tcoffeeColour
3456             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3457     // it will be enabled only if a score file is provided
3458     tcoffeeColour.setEnabled(false);
3459     tcoffeeColour.addActionListener(this);
3460     conservationMenuItem.setLabel(MessageManager
3461             .getString("action.by_conservation"));
3462     conservationMenuItem.addItemListener(this);
3463     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3464     noColourmenuItem.addActionListener(this);
3465     abovePIDThreshold.setLabel(MessageManager
3466             .getString("label.above_identity_threshold"));
3467     abovePIDThreshold.addItemListener(this);
3468     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3469     nucleotideColour.addActionListener(this);
3470     modifyPID.setLabel(MessageManager
3471             .getString("label.modify_identity_thereshold"));
3472     modifyPID.addActionListener(this);
3473     modifyConservation.setLabel(MessageManager
3474             .getString("label.modify_conservation_thereshold"));
3475     modifyConservation.addActionListener(this);
3476     annotationColour.setLabel(MessageManager
3477             .getString("action.by_annotation"));
3478     annotationColour.addActionListener(this);
3479
3480     /*
3481      * Configure Calculate menu items and actions
3482      */
3483     sortPairwiseMenuItem.setLabel(MessageManager
3484             .getString("action.by_pairwise_id"));
3485     sortPairwiseMenuItem.addActionListener(this);
3486     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3487     sortIDMenuItem.addActionListener(this);
3488     sortLengthMenuItem.setLabel(MessageManager
3489             .getString("action.by_length"));
3490     sortLengthMenuItem.addActionListener(this);
3491     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3492     sortGroupMenuItem.addActionListener(this);
3493     pairwiseAlignmentMenuItem.setLabel(MessageManager
3494             .getString("action.pairwise_alignment"));
3495     pairwiseAlignmentMenuItem.addActionListener(this);
3496     PCAMenuItem.setLabel(MessageManager
3497             .getString("label.principal_component_analysis"));
3498     PCAMenuItem.addActionListener(this);
3499     autoCalculate = new CheckboxMenuItem(
3500             MessageManager.getString("label.autocalculate_consensus"), true);
3501     averageDistanceTreeMenuItem.setLabel(MessageManager
3502             .getString("label.average_distance_identity"));
3503     averageDistanceTreeMenuItem.addActionListener(this);
3504     neighbourTreeMenuItem.setLabel(MessageManager
3505             .getString("label.neighbour_joining_identity"));
3506     neighbourTreeMenuItem.addActionListener(this);
3507     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3508             .getString("label.average_distance_bloslum62"));
3509     avDistanceTreeBlosumMenuItem.addActionListener(this);
3510     njTreeBlosumMenuItem.setLabel(MessageManager
3511             .getString("label.neighbour_blosum62"));
3512     njTreeBlosumMenuItem.addActionListener(this);
3513     sortByTreeMenu.setLabel(MessageManager
3514             .getString("action.by_tree_order"));
3515     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3516     Menu calculateTreeMenu = new Menu(
3517             MessageManager.getString("action.calculate_tree"));
3518     autoCalculate.addItemListener(this);
3519     sortByTree.addItemListener(this);
3520
3521     /*
3522      * Configure Help menu items and actions
3523      */
3524     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3525     documentation.setLabel(MessageManager.getString("label.documentation"));
3526     documentation.addActionListener(this);
3527     about.setLabel(MessageManager.getString("label.about"));
3528     about.addActionListener(this);
3529
3530     /*
3531      * Add top level menus to frame
3532      */
3533     alignFrameMenuBar.add(fileMenu);
3534     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3535     alignFrameMenuBar.add(editMenu);
3536     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3537     alignFrameMenuBar.add(selectMenu);
3538     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3539     alignFrameMenuBar.add(viewMenu);
3540     Menu annotationsMenu = new Menu(
3541             MessageManager.getString("action.annotations"));
3542     alignFrameMenuBar.add(annotationsMenu);
3543     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3544     alignFrameMenuBar.add(formatMenu);
3545     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3546     alignFrameMenuBar.add(colourMenu);
3547     Menu calculateMenu = new Menu(
3548             MessageManager.getString("action.calculate"));
3549     alignFrameMenuBar.add(calculateMenu);
3550     alignFrameMenuBar.add(helpMenu);
3551
3552     /*
3553      * File menu
3554      */
3555     fileMenu.add(inputText);
3556     fileMenu.add(loadTree);
3557     fileMenu.add(loadAnnotations);
3558     fileMenu.addSeparator();
3559     fileMenu.add(outputTextboxMenu);
3560     fileMenu.add(outputFeatures);
3561     fileMenu.add(outputAnnotations);
3562     if (jalviewServletURL != null)
3563     {
3564       fileMenu.add(loadApplication);
3565     }
3566     fileMenu.addSeparator();
3567     fileMenu.add(closeMenuItem);
3568
3569     /*
3570      * Edit menu
3571      */
3572     editMenu.add(undoMenuItem);
3573     editMenu.add(redoMenuItem);
3574     editMenu.add(cut);
3575     editMenu.add(copy);
3576     pasteMenu.add(pasteNew);
3577     pasteMenu.add(pasteThis);
3578     editMenu.add(pasteMenu);
3579     editMenu.add(delete);
3580     editMenu.addSeparator();
3581     editMenu.add(remove2LeftMenuItem);
3582     editMenu.add(remove2RightMenuItem);
3583     editMenu.add(removeGappedColumnMenuItem);
3584     editMenu.add(removeAllGapsMenuItem);
3585     editMenu.add(removeRedundancyMenuItem);
3586
3587     /*
3588      * Select menu
3589      */
3590     selectMenu.add(findMenuItem);
3591     selectMenu.addSeparator();
3592     selectMenu.add(selectAllSequenceMenuItem);
3593     selectMenu.add(deselectAllSequenceMenuItem);
3594     selectMenu.add(invertSequenceMenuItem);
3595     selectMenu.add(invertColSel);
3596     selectMenu.add(createGroup);
3597     selectMenu.add(unGroup);
3598     selectMenu.add(grpsFromSelection);
3599     selectMenu.add(deleteGroups);
3600     selectMenu.add(annotationColumnSelection);
3601
3602     /*
3603      * View menu
3604      */
3605     viewMenu.add(newView);
3606     viewMenu.addSeparator();
3607     showMenu.add(showColumns);
3608     showMenu.add(showSeqs);
3609     showMenu.add(showAllHidden);
3610     viewMenu.add(showMenu);
3611     hideMenu.add(hideColumns);
3612     hideMenu.add(hideSequences);
3613     hideMenu.add(hideAllSelection);
3614     hideMenu.add(hideAllButSelection);
3615     viewMenu.add(hideMenu);
3616     viewMenu.addSeparator();
3617     viewMenu.add(followMouseOverFlag);
3618     viewMenu.addSeparator();
3619     viewMenu.add(sequenceFeatures);
3620     viewMenu.add(featureSettings);
3621     viewMenu.addSeparator();
3622     viewMenu.add(alProperties);
3623     viewMenu.addSeparator();
3624     viewMenu.add(overviewMenuItem);
3625
3626     /*
3627      * Annotations menu
3628      */
3629     annotationsMenu.add(annotationPanelMenuItem);
3630     annotationsMenu.addSeparator();
3631     annotationsMenu.add(showAlignmentAnnotations);
3632     annotationsMenu.add(showSequenceAnnotations);
3633     annotationsMenu.add(sortAnnBySequence);
3634     annotationsMenu.add(sortAnnByLabel);
3635     annotationsMenu.addSeparator();
3636     autoAnnMenu.add(showAutoFirst);
3637     autoAnnMenu.add(showAutoLast);
3638     autoAnnMenu.addSeparator();
3639     autoAnnMenu.add(applyAutoAnnotationSettings);
3640     autoAnnMenu.add(showConsensusHistogram);
3641     autoAnnMenu.add(showSequenceLogo);
3642     autoAnnMenu.add(normSequenceLogo);
3643     autoAnnMenu.addSeparator();
3644     autoAnnMenu.add(showGroupConservation);
3645     autoAnnMenu.add(showGroupConsensus);
3646     annotationsMenu.add(autoAnnMenu);
3647
3648     /*
3649      * Format menu
3650      */
3651     formatMenu.add(font);
3652     formatMenu.add(seqLimits);
3653     formatMenu.add(wrapMenuItem);
3654     formatMenu.add(scaleAbove);
3655     formatMenu.add(scaleLeft);
3656     formatMenu.add(scaleRight);
3657     formatMenu.add(viewBoxesMenuItem);
3658     formatMenu.add(viewTextMenuItem);
3659     formatMenu.add(colourTextMenuItem);
3660     formatMenu.add(displayNonconservedMenuItem);
3661     formatMenu.add(renderGapsMenuItem);
3662     formatMenu.add(centreColumnLabelFlag);
3663
3664     /*
3665      * Colour menu
3666      */
3667     colourMenu.add(applyToAllGroups);
3668     colourMenu.addSeparator();
3669     colourMenu.add(noColourmenuItem);
3670     colourMenu.add(clustalColour);
3671     colourMenu.add(BLOSUM62Colour);
3672     colourMenu.add(PIDColour);
3673     colourMenu.add(zappoColour);
3674     colourMenu.add(taylorColour);
3675     colourMenu.add(hydrophobicityColour);
3676     colourMenu.add(helixColour);
3677     colourMenu.add(strandColour);
3678     colourMenu.add(turnColour);
3679     colourMenu.add(buriedColour);
3680     colourMenu.add(nucleotideColour);
3681     colourMenu.add(purinePyrimidineColour);
3682     // colourMenu.add(RNAInteractionColour);
3683     colourMenu.add(tcoffeeColour);
3684     colourMenu.add(userDefinedColour);
3685     colourMenu.addSeparator();
3686     colourMenu.add(conservationMenuItem);
3687     colourMenu.add(modifyConservation);
3688     colourMenu.add(abovePIDThreshold);
3689     colourMenu.add(modifyPID);
3690     colourMenu.add(annotationColour);
3691     colourMenu.add(RNAHelixColour);
3692
3693     /*
3694      * Calculate menu
3695      */
3696     sortMenu.add(sortIDMenuItem);
3697     sortMenu.add(sortLengthMenuItem);
3698     sortMenu.add(sortByTreeMenu);
3699     sortMenu.add(sortGroupMenuItem);
3700     sortMenu.add(sortPairwiseMenuItem);
3701     calculateMenu.add(sortMenu);
3702     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3703     calculateTreeMenu.add(neighbourTreeMenuItem);
3704     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3705     calculateTreeMenu.add(njTreeBlosumMenuItem);
3706     calculateMenu.add(calculateTreeMenu);
3707     calculateMenu.addSeparator();
3708     calculateMenu.add(pairwiseAlignmentMenuItem);
3709     calculateMenu.add(PCAMenuItem);
3710     calculateMenu.add(autoCalculate);
3711     calculateMenu.add(sortByTree);
3712
3713     /*
3714      * Help menu
3715      */
3716     helpMenu.add(documentation);
3717     helpMenu.add(about);
3718
3719     /*
3720      * Status bar
3721      */
3722     statusBar.setBackground(Color.white);
3723     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3724     statusBar.setText(MessageManager.getString("label.status_bar"));
3725     this.add(statusBar, BorderLayout.SOUTH);
3726   }
3727
3728   public void setStatus(String string)
3729   {
3730     statusBar.setText(string);
3731   };
3732
3733   MenuItem featureSettings = new MenuItem();
3734
3735   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3736
3737   MenuItem annotationColour = new MenuItem();
3738
3739   MenuItem annotationColumnSelection = new MenuItem();
3740
3741   MenuItem invertColSel = new MenuItem();
3742
3743   MenuItem showColumns = new MenuItem();
3744
3745   MenuItem showSeqs = new MenuItem();
3746
3747   MenuItem hideColumns = new MenuItem();
3748
3749   MenuItem hideSequences = new MenuItem();
3750
3751   MenuItem hideAllButSelection = new MenuItem();
3752
3753   MenuItem hideAllSelection = new MenuItem();
3754
3755   MenuItem showAllHidden = new MenuItem();
3756
3757   MenuItem newView = new MenuItem();
3758
3759   private CheckboxMenuItem showAlignmentAnnotations;
3760
3761   private CheckboxMenuItem showSequenceAnnotations;
3762
3763   private CheckboxMenuItem sortAnnBySequence;
3764
3765   private CheckboxMenuItem sortAnnByLabel;
3766
3767   private CheckboxMenuItem showAutoFirst;
3768
3769   private CheckboxMenuItem showAutoLast;
3770
3771   private SplitFrame splitFrame;
3772
3773   /**
3774    * Attach the alignFrame panels after embedding menus, if necessary. This used
3775    * to be called setEmbedded, but is now creates the dropdown menus in a
3776    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3777    *
3778    * @param reallyEmbedded
3779    *          true to attach the view to the applet area on the page rather than
3780    *          in a new window
3781    */
3782   public void createAlignFrameWindow(boolean reallyEmbedded)
3783   {
3784     if (reallyEmbedded)
3785     {
3786       embedAlignFrameInApplet(viewport.applet);
3787     }
3788     else
3789     {
3790       // //////
3791       // test and embed menu bar if necessary.
3792       //
3793       if (embedMenuIfNeeded(alignPanel))
3794       {
3795         /*
3796          * adjust for status bar height too. ? pointless as overridden by layout
3797          * manager
3798          */
3799         alignPanel.setSize(getSize().width,
3800                 getSize().height - statusBar.getHeight());
3801       }
3802       add(statusBar, BorderLayout.SOUTH);
3803       add(alignPanel, BorderLayout.CENTER);
3804       // and register with the applet so it can pass external API calls to us
3805       jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3806               frameWidth,
3807               frameHeight);
3808     }
3809   }
3810
3811   /**
3812    * Add the components of this AlignFrame to the applet container.
3813    *
3814    * @param theApplet
3815    */
3816   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3817   {
3818     // ////
3819     // Explicitly build the embedded menu panel for the on-page applet
3820     //
3821     // view cannot be closed if its actually on the page
3822     fileMenu.remove(closeMenuItem);
3823     fileMenu.remove(3); // Remove Separator
3824     // construct embedded menu, using default font
3825     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3826     // and actually add the components to the applet area
3827     theApplet.setLayout(new BorderLayout());
3828     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3829     theApplet.add(statusBar, BorderLayout.SOUTH);
3830     // TODO should size be left to the layout manager?
3831     alignPanel.setSize(theApplet.getSize().width,
3832             theApplet.getSize().height - embeddedMenu.getHeight()
3833                     - statusBar.getHeight());
3834     theApplet.add(alignPanel, BorderLayout.CENTER);
3835     final AlignFrame me = this;
3836     theApplet.addFocusListener(new FocusListener()
3837     {
3838
3839       @Override
3840       public void focusLost(FocusEvent e)
3841       {
3842         if (theApplet.currentAlignFrame == me)
3843         {
3844           theApplet.currentAlignFrame = null;
3845         }
3846       }
3847
3848       @Override
3849       public void focusGained(FocusEvent e)
3850       {
3851         theApplet.currentAlignFrame = me;
3852       }
3853     });
3854     theApplet.validate();
3855   }
3856
3857   /**
3858    * create a new binding between structures in an existing jmol viewer instance
3859    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3860    * this does not open a new Jmol window, or modify the display of the
3861    * structures in the original jmol window. Note This method doesn't work
3862    * without an additional javascript library to exchange messages between the
3863    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3864    *
3865    * @param viewer
3866    *          JmolViewer instance
3867    * @param sequenceIds
3868    *          - sequence Ids to search for associations
3869    */
3870   public SequenceStructureBinding addStructureViewInstance(
3871           Object jmolviewer, String[] sequenceIds)
3872   {
3873     org.jmol.api.JmolViewer viewer = null;
3874     try
3875     {
3876       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3877     } catch (ClassCastException ex)
3878     {
3879       System.err.println("Unsupported viewer object :"
3880               + jmolviewer.getClass());
3881     }
3882     if (viewer == null)
3883     {
3884       System.err.println("Can't use this object as a structure viewer:"
3885               + jmolviewer.getClass());
3886       return null;
3887     }
3888     SequenceI[] seqs = null;
3889     if (sequenceIds == null || sequenceIds.length == 0)
3890     {
3891       seqs = viewport.getAlignment().getSequencesArray();
3892     }
3893     else
3894     {
3895       Vector sqi = new Vector();
3896       AlignmentI al = viewport.getAlignment();
3897       for (int sid = 0; sid < sequenceIds.length; sid++)
3898       {
3899         SequenceI sq = al.findName(sequenceIds[sid]);
3900         if (sq != null)
3901         {
3902           sqi.addElement(sq);
3903         }
3904       }
3905       if (sqi.size() > 0)
3906       {
3907         seqs = new SequenceI[sqi.size()];
3908         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3909         {
3910           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3911         }
3912       }
3913       else
3914       {
3915         return null;
3916       }
3917     }
3918     AAStructureBindingModel jmv = null;
3919     // TODO: search for a jmv that involves viewer
3920     if (jmv == null)
3921     { // create a new viewer/jalview binding.
3922       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3923       { seqs });
3924     }
3925     return jmv;
3926
3927   }
3928
3929   /**
3930    * bind a pdb file to a sequence in the current view
3931    *
3932    * @param sequenceId
3933    *          - sequenceId within the dataset.
3934    * @param pdbEntryString
3935    *          - the short name for the PDB file
3936    * @param pdbFile
3937    *          - pdb file - either a URL or a valid PDB file.
3938    * @return true if binding was as success TODO: consider making an exception
3939    *         structure for indicating when PDB parsing or sequenceId location
3940    *         fails.
3941    */
3942   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3943           String pdbFile)
3944   {
3945     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3946     boolean needtoadd = false;
3947     if (toaddpdb != null)
3948     {
3949       Vector pdbe = toaddpdb.getPDBId();
3950       PDBEntry pdbentry = null;
3951       if (pdbe != null && pdbe.size() > 0)
3952       {
3953         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3954         {
3955           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3956           if (!pdbentry.getId().equals(pdbEntryString)
3957                   && !pdbentry.getFile().equals(pdbFile))
3958           {
3959             pdbentry = null;
3960           }
3961           else
3962           {
3963             continue;
3964           }
3965         }
3966       }
3967       if (pdbentry == null)
3968       {
3969         pdbentry = new PDBEntry();
3970         pdbentry.setId(pdbEntryString);
3971         pdbentry.setFile(pdbFile);
3972         needtoadd = true; // add this new entry to sequence.
3973       }
3974       // resolve data source
3975       // TODO: this code should be a refactored to an io package
3976       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3977       if (protocol == null)
3978       {
3979         return false;
3980       }
3981       if (needtoadd)
3982       {
3983         // make a note of the access mode and add
3984         if (pdbentry.getProperty() == null)
3985         {
3986           pdbentry.setProperty(new Hashtable());
3987         }
3988         pdbentry.getProperty().put("protocol", protocol);
3989         toaddpdb.addPDBId(pdbentry);
3990         alignPanel.getStructureSelectionManager()
3991                 .registerPDBEntry(pdbentry);
3992       }
3993     }
3994     return true;
3995   }
3996
3997   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3998   {
3999     if (seqs != null)
4000     {
4001       Vector sequences = new Vector();
4002       for (int i = 0; i < seqs.length; i++)
4003       {
4004         if (seqs[i] != null)
4005         {
4006           sequences.addElement(new Object[]
4007           { seqs[i], (chains != null) ? chains[i] : null });
4008         }
4009       }
4010       seqs = new SequenceI[sequences.size()];
4011       chains = new String[sequences.size()];
4012       for (int i = 0, isize = sequences.size(); i < isize; i++)
4013       {
4014         Object[] oj = (Object[]) sequences.elementAt(i);
4015
4016         seqs[i] = (SequenceI) oj[0];
4017         chains[i] = (String) oj[1];
4018       }
4019     }
4020     return new Object[]
4021     { seqs, chains };
4022
4023   }
4024
4025   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4026           SequenceI[] seqs, String[] chains, String protocol)
4027   {
4028     // Scrub any null sequences from the array
4029     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4030     seqs = (SequenceI[]) sqch[0];
4031     chains = (String[]) sqch[1];
4032     if (seqs == null || seqs.length == 0)
4033     {
4034       System.err
4035               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4036     }
4037     if (protocol == null || protocol.trim().length() == 0
4038             || protocol.equals("null"))
4039     {
4040       protocol = (String) pdb.getProperty().get("protocol");
4041       if (protocol == null)
4042       {
4043         System.err.println("Couldn't work out protocol to open structure: "
4044                 + pdb.getId());
4045         return;
4046       }
4047     }
4048     if (applet.useXtrnalSviewer)
4049     {
4050       // register the association(s) and quit, don't create any windows.
4051       if (StructureSelectionManager.getStructureSelectionManager(applet)
4052               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4053       {
4054         System.err.println("Failed to map " + pdb.getFile() + " ("
4055                 + protocol + ") to any sequences");
4056       }
4057       return;
4058     }
4059     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4060     {
4061       // can only do alignments with Jmol
4062       // find the last jmol window assigned to this alignment
4063       jalview.appletgui.AppletJmol ajm = null, tajm;
4064       Vector jmols = applet
4065               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4066       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4067       {
4068         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4069         if (tajm.ap.alignFrame == this)
4070         {
4071           ajm = tajm;
4072           break;
4073         }
4074       }
4075       if (ajm != null)
4076       {
4077         System.err
4078                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4079         // try and add the pdb structure
4080         // ajm.addS
4081         ajm = null;
4082       }
4083     }
4084     // otherwise, create a new window
4085     if (applet.jmolAvailable)
4086     {
4087       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4088               protocol);
4089       applet.lastFrameX += 40;
4090       applet.lastFrameY += 40;
4091     }
4092     else
4093     {
4094       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4095     }
4096
4097   }
4098
4099   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4100           SequenceI[][] seqs, String[][] chains, String[] protocols)
4101   {
4102     // TODO Auto-generated method stub
4103     System.err.println("Aligned Structure View: Not yet implemented.");
4104   }
4105
4106   /**
4107    * modify the current selection, providing the user has not made a selection
4108    * already.
4109    *
4110    * @param sel
4111    *          - sequences from this alignment
4112    * @param csel
4113    *          - columns to be selected on the alignment
4114    */
4115   public void select(SequenceGroup sel, ColumnSelection csel)
4116   {
4117     alignPanel.seqPanel.selection(sel, csel, null);
4118   }
4119
4120   public void scrollTo(int row, int column)
4121   {
4122     alignPanel.seqPanel.scrollTo(row, column);
4123   }
4124
4125   public void scrollToRow(int row)
4126   {
4127     alignPanel.seqPanel.scrollToRow(row);
4128   }
4129
4130   public void scrollToColumn(int column)
4131   {
4132     alignPanel.seqPanel.scrollToColumn(column);
4133   }
4134
4135   /**
4136    * @return the alignments unique ID.
4137    */
4138   public String getSequenceSetId()
4139   {
4140     return viewport.getSequenceSetId();
4141   }
4142
4143   /**
4144    * Load the (T-Coffee) score file from the specified url
4145    *
4146    * @param source
4147    *          File/URL/T-COFFEE score file contents
4148    * @throws IOException
4149    * @return true if alignment was annotated with data from source
4150    */
4151   public boolean loadScoreFile(String source) throws IOException
4152   {
4153
4154     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4155             AppletFormatAdapter.checkProtocol(source));
4156     if (!file.isValid())
4157     {
4158       // TODO: raise dialog for gui
4159       System.err.println("Problems parsing T-Coffee scores: "
4160               + file.getWarningMessage());
4161       System.err.println("Origin was:\n" + source);
4162       return false;
4163     }
4164
4165     /*
4166      * check that the score matrix matches the alignment dimensions
4167      */
4168     AlignmentI aln;
4169     if ((aln = viewport.getAlignment()) != null
4170             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4171                     .getWidth()))
4172     {
4173       // TODO: raise a dialog box here rather than bomb out.
4174       System.err
4175               .println("The scores matrix does not match the alignment dimensions");
4176
4177     }
4178
4179     // TODO add parameter to indicate if matching should be done
4180     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4181     {
4182       alignPanel.fontChanged();
4183       tcoffeeColour.setEnabled(true);
4184       // switch to this color
4185       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4186       return true;
4187     }
4188     else
4189     {
4190       System.err.println("Problems resolving T-Coffee scores:");
4191       if (file.getWarningMessage() != null)
4192       {
4193         System.err.println(file.getWarningMessage());
4194       }
4195     }
4196     return false;
4197   }
4198
4199   public SplitFrame getSplitFrame()
4200   {
4201     return this.splitFrame;
4202   }
4203
4204   public void setSplitFrame(SplitFrame sf)
4205   {
4206     this.splitFrame = sf;
4207   }
4208
4209     // may not need this
4210   @Override
4211   public void setShowSeqFeatures(boolean b)
4212   {
4213     // showSeqFeatures.setSelected(b);
4214     viewport.setShowSequenceFeatures(b);
4215
4216   }
4217
4218   @Override
4219   public void setMenusForViewport()
4220   {
4221     // setMenusFromViewport(viewport);
4222
4223   }
4224   @Override
4225   public void refreshFeatureUI(boolean enableIfNecessary)
4226   {
4227     if (enableIfNecessary)
4228     {
4229       sequenceFeatures.setState(true);
4230       alignPanel.av.setShowSequenceFeatures(true);
4231     }
4232   }
4233
4234   @Override
4235   public FeatureSettingsControllerI getFeatureSettingsUI()
4236   {
4237     return alignPanel.av.featureSettings;
4238   }
4239
4240 }