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.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.TCoffeeScoreFile;
  56 import jalview.schemes.Blosum62ColourScheme;
  57 import jalview.schemes.BuriedColourScheme;
  58 import jalview.schemes.ClustalxColourScheme;
  59 import jalview.schemes.ColourSchemeI;
  60 import jalview.schemes.HelixColourScheme;
  61 import jalview.schemes.HydrophobicColourScheme;
  62 import jalview.schemes.NucleotideColourScheme;
  63 import jalview.schemes.PIDColourScheme;
  64 import jalview.schemes.PurinePyrimidineColourScheme;
  65 import jalview.schemes.RNAHelicesColour;
  66 import jalview.schemes.StrandColourScheme;
  67 import jalview.schemes.TCoffeeColourScheme;
  68 import jalview.schemes.TaylorColourScheme;
  69 import jalview.schemes.TurnColourScheme;
  70 import jalview.schemes.ZappoColourScheme;
  71 import jalview.structure.StructureSelectionManager;
  72 import jalview.structures.models.AAStructureBindingModel;
  73 import jalview.util.MappingUtils;
  74 import jalview.util.MessageManager;
  75 import jalview.viewmodel.AlignmentViewport;
  76
  77 import java.awt.BorderLayout;
  78 import java.awt.Canvas;
  79 import java.awt.CheckboxMenuItem;
  80 import java.awt.Color;
  81 import java.awt.FlowLayout;
  82 import java.awt.Font;
  83 import java.awt.FontMetrics;
  84 import java.awt.Frame;
  85 import java.awt.Graphics;
  86 import java.awt.Label;
  87 import java.awt.Menu;
  88 import java.awt.MenuBar;
  89 import java.awt.MenuItem;
  90 import java.awt.Panel;
  91 import java.awt.event.ActionEvent;
  92 import java.awt.event.ActionListener;
  93 import java.awt.event.FocusEvent;
  94 import java.awt.event.FocusListener;
  95 import java.awt.event.ItemEvent;
  96 import java.awt.event.ItemListener;
  97 import java.awt.event.KeyEvent;
  98 import java.awt.event.KeyListener;
  99 import java.awt.event.WindowAdapter;
 100 import java.awt.event.WindowEvent;
 101 import java.io.IOException;
 102 import java.net.URL;
 103 import java.net.URLEncoder;
 104 import java.util.Arrays;
 105 import java.util.Deque;
 106 import java.util.HashMap;
 107 import java.util.List;
 108 import java.util.Map;
 109 import java.util.StringTokenizer;
 110 import java.util.Vector;
 111
 112 import org.jmol.viewer.Viewer;
 113
 114 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 115         ItemListener, KeyListener, AlignViewControllerGuiI
 116 {
 117   public AlignViewControllerI avc;
 118
 119   public AlignmentPanel alignPanel;
 120
 121   public AlignViewport viewport;
 122
 123   // width and height may be overridden by applet parameters
 124   int frameWidth = 700;
 125
 126   int frameHeight = 500;
 127
 128   String jalviewServletURL;
 129
 130   /*
 131    * Flag for showing autocalculated consensus above or below other consensus
 132    * rows
 133    */
 134   private boolean showAutoCalculatedAbove;
 135
 136   private SequenceAnnotationOrder annotationSortOrder;
 137
 138   /**
 139    * Constructor that creates the frame and adds it to the display.
 140    *
 141    * @param al
 142    * @param applet
 143    * @param title
 144    * @param embedded
 145    */
 146   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 147           boolean embedded)
 148   {
 149     this(al, applet, title, embedded, true);
 150   }
 151
 152   /**
 153    * Constructor that optionally allows the frame to be displayed or only
 154    * created.
 155    *
 156    * @param al
 157    * @param applet
 158    * @param title
 159    * @param embedded
 160    * @param addToDisplay
 161    */
 162   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 163           boolean embedded, boolean addToDisplay)
 164   {
 165     this(al, null, null, applet, title, embedded, addToDisplay);
 166   }
 167
 168   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 169           ColumnSelection columnSelection, JalviewLite applet,
 170           String title, boolean embedded)
 171   {
 172     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           ColumnSelection columnSelection, JalviewLite applet,
 177           String title, boolean embedded, boolean addToDisplay)
 178   {
 179     if (applet != null)
 180     {
 181       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception ex)
 188     {
 189       ex.printStackTrace();
 190     }
 191     // need to get window geometry before we calculate alignment layout
 192     if (applet != null)
 193     {
 194       String param;
 195       try
 196       {
 197         param = applet.getParameter("windowWidth");
 198         if (param != null)
 199         {
 200           int width = Integer.parseInt(param);
 201           frameWidth = width;
 202         }
 203         param = applet.getParameter("windowHeight");
 204         if (param != null)
 205         {
 206           int height = Integer.parseInt(param);
 207           frameHeight = height;
 208         }
 209       } catch (Exception ex)
 210       {
 211       }
 212     }
 213     viewport = new AlignViewport(al, applet);
 214
 215     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 216     {
 217       viewport.hideSequence(hiddenSeqs);
 218     }
 219     if (columnSelection != null)
 220     {
 221       viewport.setColumnSelection(columnSelection);
 222     }
 223     viewport.setScaleAboveWrapped(scaleAbove.getState());
 224
 225     alignPanel = new AlignmentPanel(this, viewport);
 226     avc = new jalview.controller.AlignViewController(this, viewport,
 227             alignPanel);
 228     viewport.updateConservation(alignPanel);
 229     viewport.updateConsensus(alignPanel);
 230
 231     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 232     followMouseOverFlag.setState(viewport.isFollowHighlight());
 233     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 234     showGroupConservation.setState(viewport.isShowGroupConservation());
 235     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 236     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 237     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 238     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 239     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 240     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 242     showAlignmentAnnotations.setState(true);
 243     showSequenceAnnotations.setState(false);
 244
 245     seqLimits.setState(viewport.getShowJVSuffix());
 246
 247     if (applet != null)
 248     {
 249       String param = applet.getParameter("sortBy");
 250       if (param != null)
 251       {
 252         if (param.equalsIgnoreCase("Id"))
 253         {
 254           sortIDMenuItem_actionPerformed();
 255         }
 256         else if (param.equalsIgnoreCase("Pairwise Identity"))
 257         {
 258           sortPairwiseMenuItem_actionPerformed();
 259         }
 260         else if (param.equalsIgnoreCase("Length"))
 261         {
 262           sortLengthMenuItem_actionPerformed();
 263         }
 264       }
 265
 266       param = applet.getParameter("wrap");
 267       if (param != null)
 268       {
 269         if (param.equalsIgnoreCase("true"))
 270         {
 271           wrapMenuItem.setState(true);
 272           wrapMenuItem_actionPerformed();
 273         }
 274       }
 275       param = applet.getParameter("centrecolumnlabels");
 276       if (param != null)
 277       {
 278         centreColumnLabelFlag.setState(true);
 279         centreColumnLabelFlag_stateChanged();
 280       }
 281
 282     }
 283     if (viewport.getAlignment().isNucleotide())
 284     {
 285       viewport.updateStrucConsensus(alignPanel);
 286       if (viewport.getAlignment().hasRNAStructure())
 287       {
 288         RNAHelixColour.setEnabled(true);
 289       }
 290       else
 291       {
 292         RNAHelixColour.setEnabled(false);
 293       }
 294     }
 295     else
 296     {
 297       RNAHelixColour.setEnabled(false);
 298       purinePyrimidineColour.setEnabled(false);
 299       nucleotideColour.setEnabled(false);
 300     }
 301     // Some JVMS send keyevents to Top frame or lowest panel,
 302     // Havent worked out why yet. So add to both this frame and seqCanvas for
 303     // now
 304     this.addKeyListener(this);
 305     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 306     alignPanel.idPanel.idCanvas.addKeyListener(this);
 307     alignPanel.scalePanel.addKeyListener(this);
 308     alignPanel.annotationPanel.addKeyListener(this);
 309     alignPanel.annotationPanelHolder.addKeyListener(this);
 310     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 311     alignPanel.alabels.addKeyListener(this);
 312
 313     setAnnotationsVisibility();
 314
 315     if (addToDisplay)
 316     {
 317       addToDisplay(embedded);
 318     }
 319   }
 320
 321   /**
 322    * @param embedded
 323    */
 324   public void addToDisplay(boolean embedded)
 325   {
 326     createAlignFrameWindow(embedded);
 327     validate();
 328     alignPanel.adjustAnnotationHeight();
 329     alignPanel.paintAlignment(true);
 330   }
 331
 332   public AlignViewport getAlignViewport()
 333   {
 334     return viewport;
 335   }
 336
 337   public SeqCanvas getSeqcanvas()
 338   {
 339     return alignPanel.seqPanel.seqCanvas;
 340   }
 341
 342   /**
 343    * Load a features file onto the alignment
 344    *
 345    * @param file
 346    *          file URL, content, or other resolvable path
 347    * @param type
 348    *          is protocol for accessing data referred to by file
 349    */
 350
 351   public boolean parseFeaturesFile(String file, DataSourceType type)
 352   {
 353     return parseFeaturesFile(file, type, true);
 354   }
 355
 356   /**
 357    * Load a features file onto the alignment
 358    *
 359    * @param file
 360    *          file URL, content, or other resolvable path
 361    * @param sourceType
 362    *          is protocol for accessing data referred to by file
 363    * @param autoenabledisplay
 364    *          when true, display features flag will be automatically enabled if
 365    *          features are loaded
 366    * @return true if data parsed as a features file
 367    */
 368   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 369           boolean autoenabledisplay)
 370   {
 371     boolean featuresFile = false;
 372     try
 373     {
 374       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 375               .getFeatureRenderer().getFeatureColours();
 376       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 377               "relaxedidmatch", false);
 378       featuresFile = new FeaturesFile(file, sourceType).parse(
 379               viewport.getAlignment(), colours, true, relaxedIdMatching);
 380     } catch (Exception ex)
 381     {
 382       ex.printStackTrace();
 383     }
 384
 385     if (featuresFile)
 386     {
 387       if (autoenabledisplay)
 388       {
 389         viewport.setShowSequenceFeatures(true);
 390         sequenceFeatures.setState(true);
 391       }
 392       if (alignPanel.seqPanel.seqCanvas.fr != null)
 393       {
 394         // update the min/max ranges where necessary
 395         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 396       }
 397       if (viewport.featureSettings != null)
 398       {
 399         viewport.featureSettings.refreshTable();
 400       }
 401       alignPanel.paintAlignment(true);
 402       statusBar.setText(MessageManager
 403               .getString("label.successfully_added_features_alignment"));
 404     }
 405     return featuresFile;
 406   }
 407
 408   @Override
 409   public void keyPressed(KeyEvent evt)
 410   {
 411     if (viewport.cursorMode
 412             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 413                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 414                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 415             && Character.isDigit(evt.getKeyChar()))
 416     {
 417       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 418     }
 419
 420     switch (evt.getKeyCode())
 421     {
 422     case 27: // escape key
 423       deselectAllSequenceMenuItem_actionPerformed();
 424
 425       alignPanel.alabels.cancelDrag();
 426       break;
 427     case KeyEvent.VK_X:
 428       if (evt.isControlDown() || evt.isMetaDown())
 429       {
 430         cut_actionPerformed();
 431       }
 432       break;
 433     case KeyEvent.VK_C:
 434       if (viewport.cursorMode && !evt.isControlDown())
 435       {
 436         alignPanel.seqPanel.setCursorColumn();
 437       }
 438       if (evt.isControlDown() || evt.isMetaDown())
 439       {
 440         copy_actionPerformed();
 441       }
 442       break;
 443     case KeyEvent.VK_V:
 444       if (evt.isControlDown())
 445       {
 446         paste(evt.isShiftDown());
 447       }
 448       break;
 449     case KeyEvent.VK_A:
 450       if (evt.isControlDown() || evt.isMetaDown())
 451       {
 452         selectAllSequenceMenuItem_actionPerformed();
 453       }
 454       break;
 455     case KeyEvent.VK_DOWN:
 456       if (viewport.cursorMode)
 457       {
 458         alignPanel.seqPanel.moveCursor(0, 1);
 459       }
 460       else
 461       {
 462         moveSelectedSequences(false);
 463       }
 464       break;
 465
 466     case KeyEvent.VK_UP:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.moveCursor(0, -1);
 470       }
 471       else
 472       {
 473         moveSelectedSequences(true);
 474       }
 475       break;
 476
 477     case KeyEvent.VK_LEFT:
 478       if (evt.isAltDown() || !viewport.cursorMode)
 479       {
 480         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 481       }
 482       else
 483       {
 484         alignPanel.seqPanel.moveCursor(-1, 0);
 485       }
 486       break;
 487
 488     case KeyEvent.VK_RIGHT:
 489       if (evt.isAltDown() || !viewport.cursorMode)
 490       {
 491         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 492       }
 493       else
 494       {
 495         alignPanel.seqPanel.moveCursor(1, 0);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_SPACE:
 500       if (viewport.cursorMode)
 501       {
 502         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 503                 || evt.isShiftDown() || evt.isAltDown());
 504       }
 505       break;
 506
 507     case KeyEvent.VK_DELETE:
 508     case KeyEvent.VK_BACK_SPACE:
 509       if (viewport.cursorMode)
 510       {
 511         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 512                 || evt.isShiftDown() || evt.isAltDown());
 513       }
 514       else
 515       {
 516         cut_actionPerformed();
 517         alignPanel.seqPanel.seqCanvas.repaint();
 518       }
 519       break;
 520
 521     case KeyEvent.VK_S:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.setCursorRow();
 525       }
 526       break;
 527     case KeyEvent.VK_P:
 528       if (viewport.cursorMode)
 529       {
 530         alignPanel.seqPanel.setCursorPosition();
 531       }
 532       break;
 533
 534     case KeyEvent.VK_ENTER:
 535     case KeyEvent.VK_COMMA:
 536       if (viewport.cursorMode)
 537       {
 538         alignPanel.seqPanel.setCursorRowAndColumn();
 539       }
 540       break;
 541
 542     case KeyEvent.VK_Q:
 543       if (viewport.cursorMode)
 544       {
 545         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 546       }
 547       break;
 548     case KeyEvent.VK_M:
 549       if (viewport.cursorMode)
 550       {
 551         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 552       }
 553       break;
 554
 555     case KeyEvent.VK_F2:
 556       viewport.cursorMode = !viewport.cursorMode;
 557       statusBar.setText(MessageManager.formatMessage(
 558               "label.keyboard_editing_mode",
 559               new String[] { (viewport.cursorMode ? "on" : "off") }));
 560       if (viewport.cursorMode)
 561       {
 562         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 563         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 564       }
 565       break;
 566
 567     case KeyEvent.VK_F:
 568       if (evt.isControlDown())
 569       {
 570         findMenuItem_actionPerformed();
 571       }
 572       break;
 573
 574     case KeyEvent.VK_H:
 575     {
 576       boolean toggleSeqs = !evt.isControlDown();
 577       boolean toggleCols = !evt.isShiftDown();
 578       toggleHiddenRegions(toggleSeqs, toggleCols);
 579       break;
 580     }
 581
 582     case KeyEvent.VK_PAGE_UP:
 583       if (viewport.getWrapAlignment())
 584       {
 585         alignPanel.scrollUp(true);
 586       }
 587       else
 588       {
 589         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 590                 - viewport.endSeq + viewport.startSeq);
 591       }
 592       break;
 593
 594     case KeyEvent.VK_PAGE_DOWN:
 595       if (viewport.getWrapAlignment())
 596       {
 597         alignPanel.scrollUp(false);
 598       }
 599       else
 600       {
 601         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 602                 + viewport.endSeq - viewport.startSeq);
 603       }
 604       break;
 605
 606     case KeyEvent.VK_Z:
 607       if (evt.isControlDown())
 608       {
 609         undoMenuItem_actionPerformed();
 610       }
 611       break;
 612
 613     case KeyEvent.VK_Y:
 614       if (evt.isControlDown())
 615       {
 616         redoMenuItem_actionPerformed();
 617       }
 618       break;
 619
 620     case KeyEvent.VK_L:
 621       if (evt.isControlDown())
 622       {
 623         trimAlignment(true);
 624       }
 625       break;
 626
 627     case KeyEvent.VK_R:
 628       if (evt.isControlDown())
 629       {
 630         trimAlignment(false);
 631       }
 632       break;
 633
 634     case KeyEvent.VK_E:
 635       if (evt.isControlDown())
 636       {
 637         if (evt.isShiftDown())
 638         {
 639           this.removeAllGapsMenuItem_actionPerformed();
 640         }
 641         else
 642         {
 643           removeGappedColumnMenuItem_actionPerformed();
 644         }
 645       }
 646       break;
 647     case KeyEvent.VK_I:
 648       if (evt.isControlDown())
 649       {
 650         if (evt.isAltDown())
 651         {
 652           invertColSel_actionPerformed();
 653         }
 654         else
 655         {
 656           invertSequenceMenuItem_actionPerformed();
 657         }
 658       }
 659       break;
 660
 661     case KeyEvent.VK_G:
 662       if (evt.isControlDown())
 663       {
 664         if (evt.isShiftDown())
 665         {
 666           this.unGroup_actionPerformed();
 667         }
 668         else
 669         {
 670           this.createGroup_actionPerformed();
 671         }
 672       }
 673       break;
 674
 675     case KeyEvent.VK_U:
 676       if (evt.isControlDown())
 677       {
 678         this.deleteGroups_actionPerformed();
 679       }
 680       break;
 681
 682     case KeyEvent.VK_T:
 683       if (evt.isControlDown())
 684       {
 685         newView(null);
 686       }
 687       break;
 688
 689     }
 690     alignPanel.paintAlignment(true);
 691   }
 692
 693   /**
 694    * called by key handler and the hide all/show all menu items
 695    *
 696    * @param toggleSeqs
 697    * @param toggleCols
 698    */
 699   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 700   {
 701     boolean hide = false;
 702     SequenceGroup sg = viewport.getSelectionGroup();
 703     if (!toggleSeqs && !toggleCols)
 704     {
 705       // Hide everything by the current selection - this is a hack - we do the
 706       // invert and then hide
 707       // first check that there will be visible columns after the invert.
 708       if (viewport.hasSelectedColumns()
 709               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 710                       .getEndRes()))
 711       {
 712         // now invert the sequence set, if required - empty selection implies
 713         // that no hiding is required.
 714         if (sg != null)
 715         {
 716           invertSequenceMenuItem_actionPerformed();
 717           sg = viewport.getSelectionGroup();
 718           toggleSeqs = true;
 719
 720         }
 721         viewport.expandColSelection(sg, true);
 722         // finally invert the column selection and get the new sequence
 723         // selection and indicate it should be hidden.
 724         invertColSel_actionPerformed();
 725         toggleCols = true;
 726       }
 727     }
 728
 729     if (toggleSeqs)
 730     {
 731       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 732       {
 733         hide = true;
 734         viewport.hideAllSelectedSeqs();
 735       }
 736       else if (!(toggleCols && viewport.hasSelectedColumns()))
 737       {
 738         viewport.showAllHiddenSeqs();
 739       }
 740     }
 741
 742     if (toggleCols)
 743     {
 744       if (viewport.hasSelectedColumns())
 745       {
 746         viewport.hideSelectedColumns();
 747         if (!toggleSeqs)
 748         {
 749           viewport.setSelectionGroup(sg);
 750         }
 751       }
 752       else if (!hide)
 753       {
 754         viewport.showAllHiddenColumns();
 755       }
 756       viewport.sendSelection();
 757     }
 758   }
 759
 760   @Override
 761   public void keyReleased(KeyEvent evt)
 762   {
 763   }
 764
 765   @Override
 766   public void keyTyped(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void itemStateChanged(ItemEvent evt)
 772   {
 773     final Object source = evt.getSource();
 774     if (source == displayNonconservedMenuItem)
 775     {
 776       displayNonconservedMenuItem_actionPerformed();
 777     }
 778     else if (source == colourTextMenuItem)
 779     {
 780       colourTextMenuItem_actionPerformed();
 781     }
 782     else if (source == wrapMenuItem)
 783     {
 784       wrapMenuItem_actionPerformed();
 785     }
 786     else if (source == scaleAbove)
 787     {
 788       viewport.setScaleAboveWrapped(scaleAbove.getState());
 789     }
 790     else if (source == scaleLeft)
 791     {
 792       viewport.setScaleLeftWrapped(scaleLeft.getState());
 793     }
 794     else if (source == scaleRight)
 795     {
 796       viewport.setScaleRightWrapped(scaleRight.getState());
 797     }
 798     else if (source == seqLimits)
 799     {
 800       seqLimits_itemStateChanged();
 801     }
 802     else if (source == viewBoxesMenuItem)
 803     {
 804       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 805     }
 806     else if (source == viewTextMenuItem)
 807     {
 808       viewport.setShowText(viewTextMenuItem.getState());
 809     }
 810     else if (source == renderGapsMenuItem)
 811     {
 812       viewport.setRenderGaps(renderGapsMenuItem.getState());
 813     }
 814     else if (source == annotationPanelMenuItem)
 815     {
 816       boolean showAnnotations = annotationPanelMenuItem.getState();
 817       showAlignmentAnnotations.setEnabled(showAnnotations);
 818       showSequenceAnnotations.setEnabled(showAnnotations);
 819       viewport.setShowAnnotation(showAnnotations);
 820       alignPanel.setAnnotationVisible(showAnnotations);
 821     }
 822     else if (source == sequenceFeatures)
 823     {
 824       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 825       alignPanel.seqPanel.seqCanvas.repaint();
 826     }
 827     else if (source == showAlignmentAnnotations)
 828     {
 829       setAnnotationsVisibility();
 830     }
 831     else if (source == showSequenceAnnotations)
 832     {
 833       setAnnotationsVisibility();
 834     }
 835     else if (source == sortAnnBySequence)
 836     {
 837       boolean newState = sortAnnBySequence.getState();
 838       sortAnnByLabel.setState(false);
 839       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 840               : SequenceAnnotationOrder.NONE);
 841       setViewportAnnotationOrder();
 842     }
 843     else if (source == sortAnnByLabel)
 844     {
 845       boolean newState = sortAnnByLabel.getState();
 846       sortAnnBySequence.setState(false);
 847       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 848               : SequenceAnnotationOrder.NONE);
 849       setViewportAnnotationOrder();
 850     }
 851     else if (source == showAutoFirst)
 852     {
 853       showAutoLast.setState(!showAutoFirst.getState());
 854       setShowAutoCalculatedAbove(showAutoFirst.getState());
 855       setViewportAnnotationOrder();
 856     }
 857     else if (source == showAutoLast)
 858     {
 859       showAutoFirst.setState(!showAutoLast.getState());
 860       setShowAutoCalculatedAbove(showAutoFirst.getState());
 861       setViewportAnnotationOrder();
 862     }
 863     else if (source == conservationMenuItem)
 864     {
 865       conservationMenuItem_actionPerformed();
 866     }
 867     else if (source == abovePIDThreshold)
 868     {
 869       abovePIDThreshold_actionPerformed();
 870     }
 871     else if (source == applyToAllGroups)
 872     {
 873       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 874     }
 875     else if (source == autoCalculate)
 876     {
 877       viewport.autoCalculateConsensus = autoCalculate.getState();
 878     }
 879     else if (source == sortByTree)
 880     {
 881       viewport.sortByTree = sortByTree.getState();
 882     }
 883     else if (source == this.centreColumnLabelFlag)
 884     {
 885       centreColumnLabelFlag_stateChanged();
 886     }
 887     else if (source == this.followMouseOverFlag)
 888     {
 889       mouseOverFlag_stateChanged();
 890     }
 891     else if (source == showGroupConsensus)
 892     {
 893       showGroupConsensus_actionPerformed();
 894     }
 895     else if (source == showGroupConservation)
 896     {
 897       showGroupConservation_actionPerformed();
 898     }
 899     else if (source == showSequenceLogo)
 900     {
 901       showSequenceLogo_actionPerformed();
 902     }
 903     else if (source == normSequenceLogo)
 904     {
 905       normSequenceLogo_actionPerformed();
 906     }
 907     else if (source == showConsensusHistogram)
 908     {
 909       showConsensusHistogram_actionPerformed();
 910     }
 911     else if (source == applyAutoAnnotationSettings)
 912     {
 913       applyAutoAnnotationSettings_actionPerformed();
 914     }
 915     alignPanel.paintAlignment(true);
 916   }
 917
 918   /**
 919    * Set the visibility state of sequence-related and/or alignment-related
 920    * annotations depending on checkbox selections, and repaint.
 921    *
 922    * @param visible
 923    */
 924   private void setAnnotationsVisibility()
 925   {
 926     boolean showForAlignment = showAlignmentAnnotations.getState();
 927     boolean showForSequences = showSequenceAnnotations.getState();
 928     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 929     {
 930       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 931               .getAlignmentAnnotation())
 932       {
 933         boolean visible = (aa.sequenceRef == null ? showForAlignment
 934                 : showForSequences);
 935         aa.visible = visible;
 936       }
 937     }
 938     alignPanel.validateAnnotationDimensions(true);
 939     validate();
 940     repaint();
 941   }
 942
 943   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 944   {
 945     this.annotationSortOrder = order;
 946   }
 947
 948   /**
 949    * Set flags on the viewport that control annotation ordering
 950    */
 951   private void setViewportAnnotationOrder()
 952   {
 953     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 954     this.alignPanel.av
 955             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 956   }
 957
 958   private void setShowAutoCalculatedAbove(boolean showAbove)
 959   {
 960     this.showAutoCalculatedAbove = showAbove;
 961   }
 962
 963   private void mouseOverFlag_stateChanged()
 964   {
 965     viewport.setFollowHighlight(followMouseOverFlag.getState());
 966     // TODO: could kick the scrollTo mechanism to reset view for current
 967     // searchresults.
 968   }
 969
 970   private void centreColumnLabelFlag_stateChanged()
 971   {
 972     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 973     this.alignPanel.annotationPanel.repaint();
 974   }
 975
 976   @Override
 977   public void actionPerformed(ActionEvent evt)
 978   {
 979     viewport.applet.currentAlignFrame = this;
 980
 981     Object source = evt.getSource();
 982
 983     if (source == inputText)
 984     {
 985       inputText_actionPerformed();
 986     }
 987     else if (source == loadTree)
 988     {
 989       loadTree_actionPerformed();
 990     }
 991     else if (source == loadApplication)
 992     {
 993       launchFullApplication();
 994     }
 995     else if (source == loadAnnotations)
 996     {
 997       loadAnnotations();
 998     }
 999     else if (source == outputAnnotations)
1000     {
1001       outputAnnotations(true);
1002     }
1003     else if (source == outputFeatures)
1004     {
1005       outputFeatures(true, "Jalview");
1006     }
1007     else if (source == closeMenuItem)
1008     {
1009       closeMenuItem_actionPerformed();
1010     }
1011     else if (source == copy)
1012     {
1013       copy_actionPerformed();
1014     }
1015     else if (source == undoMenuItem)
1016     {
1017       undoMenuItem_actionPerformed();
1018     }
1019     else if (source == redoMenuItem)
1020     {
1021       redoMenuItem_actionPerformed();
1022     }
1023     else if (source == inputText)
1024     {
1025       inputText_actionPerformed();
1026     }
1027     else if (source == closeMenuItem)
1028     {
1029       closeMenuItem_actionPerformed();
1030     }
1031     else if (source == undoMenuItem)
1032     {
1033       undoMenuItem_actionPerformed();
1034     }
1035     else if (source == redoMenuItem)
1036     {
1037       redoMenuItem_actionPerformed();
1038     }
1039     else if (source == copy)
1040     {
1041       copy_actionPerformed();
1042     }
1043     else if (source == pasteNew)
1044     {
1045       pasteNew_actionPerformed();
1046     }
1047     else if (source == pasteThis)
1048     {
1049       pasteThis_actionPerformed();
1050     }
1051     else if (source == cut)
1052     {
1053       cut_actionPerformed();
1054     }
1055     else if (source == delete)
1056     {
1057       delete_actionPerformed();
1058     }
1059     else if (source == grpsFromSelection)
1060     {
1061       makeGrpsFromSelection_actionPerformed();
1062     }
1063     else if (source == deleteGroups)
1064     {
1065       deleteGroups_actionPerformed();
1066     }
1067     else if (source == selectAllSequenceMenuItem)
1068     {
1069       selectAllSequenceMenuItem_actionPerformed();
1070     }
1071     else if (source == deselectAllSequenceMenuItem)
1072     {
1073       deselectAllSequenceMenuItem_actionPerformed();
1074     }
1075     else if (source == invertSequenceMenuItem)
1076     {
1077       invertSequenceMenuItem_actionPerformed();
1078       // uncomment to slave sequence selections in split frame
1079       // viewport.sendSelection();
1080     }
1081     else if (source == invertColSel)
1082     {
1083       viewport.invertColumnSelection();
1084       alignPanel.paintAlignment(true);
1085       viewport.sendSelection();
1086     }
1087     else if (source == remove2LeftMenuItem)
1088     {
1089       trimAlignment(true);
1090     }
1091     else if (source == remove2RightMenuItem)
1092     {
1093       trimAlignment(false);
1094     }
1095     else if (source == removeGappedColumnMenuItem)
1096     {
1097       removeGappedColumnMenuItem_actionPerformed();
1098     }
1099     else if (source == removeAllGapsMenuItem)
1100     {
1101       removeAllGapsMenuItem_actionPerformed();
1102     }
1103     else if (source == findMenuItem)
1104     {
1105       findMenuItem_actionPerformed();
1106     }
1107     else if (source == font)
1108     {
1109       new FontChooser(alignPanel);
1110     }
1111     else if (source == newView)
1112     {
1113       newView(null);
1114     }
1115     else if (source == showColumns)
1116     {
1117       viewport.showAllHiddenColumns();
1118       alignPanel.paintAlignment(true);
1119       viewport.sendSelection();
1120     }
1121     else if (source == showSeqs)
1122     {
1123       viewport.showAllHiddenSeqs();
1124       alignPanel.paintAlignment(true);
1125       // uncomment if we want to slave sequence selections in split frame
1126       // viewport.sendSelection();
1127     }
1128     else if (source == hideColumns)
1129     {
1130       viewport.hideSelectedColumns();
1131       alignPanel.paintAlignment(true);
1132       viewport.sendSelection();
1133     }
1134     else if (source == hideSequences
1135             && viewport.getSelectionGroup() != null)
1136     {
1137       viewport.hideAllSelectedSeqs();
1138       alignPanel.paintAlignment(true);
1139       // uncomment if we want to slave sequence selections in split frame
1140       // viewport.sendSelection();
1141     }
1142     else if (source == hideAllButSelection)
1143     {
1144       toggleHiddenRegions(false, false);
1145       alignPanel.paintAlignment(true);
1146       viewport.sendSelection();
1147     }
1148     else if (source == hideAllSelection)
1149     {
1150       SequenceGroup sg = viewport.getSelectionGroup();
1151       viewport.expandColSelection(sg, false);
1152       viewport.hideAllSelectedSeqs();
1153       viewport.hideSelectedColumns();
1154       alignPanel.paintAlignment(true);
1155       viewport.sendSelection();
1156     }
1157     else if (source == showAllHidden)
1158     {
1159       viewport.showAllHiddenColumns();
1160       viewport.showAllHiddenSeqs();
1161       alignPanel.paintAlignment(true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == showGroupConsensus)
1165     {
1166       showGroupConsensus_actionPerformed();
1167     }
1168     else if (source == showGroupConservation)
1169     {
1170       showGroupConservation_actionPerformed();
1171     }
1172     else if (source == showSequenceLogo)
1173     {
1174       showSequenceLogo_actionPerformed();
1175     }
1176     else if (source == normSequenceLogo)
1177     {
1178       normSequenceLogo_actionPerformed();
1179     }
1180     else if (source == showConsensusHistogram)
1181     {
1182       showConsensusHistogram_actionPerformed();
1183     }
1184     else if (source == applyAutoAnnotationSettings)
1185     {
1186       applyAutoAnnotationSettings_actionPerformed();
1187     }
1188     else if (source == featureSettings)
1189     {
1190       new FeatureSettings(alignPanel);
1191     }
1192     else if (source == alProperties)
1193     {
1194       StringBuffer contents = new jalview.io.AlignmentProperties(
1195               viewport.getAlignment()).formatAsString();
1196       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1197       cap.setText(contents.toString());
1198       Frame frame = new Frame();
1199       frame.add(cap);
1200       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1201               "label.alignment_properties", new String[] { getTitle() }),
1202               400, 250);
1203     }
1204     else if (source == overviewMenuItem)
1205     {
1206       overviewMenuItem_actionPerformed();
1207     }
1208     else if (source == noColourmenuItem)
1209     {
1210       changeColour(null);
1211     }
1212     else if (source == clustalColour)
1213     {
1214       abovePIDThreshold.setState(false);
1215       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1216     }
1217     else if (source == zappoColour)
1218     {
1219       changeColour(new ZappoColourScheme());
1220     }
1221     else if (source == taylorColour)
1222     {
1223       changeColour(new TaylorColourScheme());
1224     }
1225     else if (source == hydrophobicityColour)
1226     {
1227       changeColour(new HydrophobicColourScheme());
1228     }
1229     else if (source == helixColour)
1230     {
1231       changeColour(new HelixColourScheme());
1232     }
1233     else if (source == strandColour)
1234     {
1235       changeColour(new StrandColourScheme());
1236     }
1237     else if (source == turnColour)
1238     {
1239       changeColour(new TurnColourScheme());
1240     }
1241     else if (source == buriedColour)
1242     {
1243       changeColour(new BuriedColourScheme());
1244     }
1245     else if (source == nucleotideColour)
1246     {
1247       changeColour(new NucleotideColourScheme());
1248     }
1249     else if (source == purinePyrimidineColour)
1250     {
1251       changeColour(new PurinePyrimidineColourScheme());
1252     }
1253     // else if (source == RNAInteractionColour)
1254     // {
1255     // changeColour(new RNAInteractionColourScheme());
1256     // }
1257     else if (source == RNAHelixColour)
1258     {
1259       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1260       // new RNAHelicesColourChooser(viewport, alignPanel);
1261     }
1262     else if (source == modifyPID)
1263     {
1264       modifyPID_actionPerformed();
1265     }
1266     else if (source == modifyConservation)
1267     {
1268       modifyConservation_actionPerformed();
1269     }
1270     else if (source == userDefinedColour)
1271     {
1272       new UserDefinedColours(alignPanel, null);
1273     }
1274     else if (source == PIDColour)
1275     {
1276       changeColour(new PIDColourScheme());
1277     }
1278     else if (source == BLOSUM62Colour)
1279     {
1280       changeColour(new Blosum62ColourScheme());
1281     }
1282     else if (source == tcoffeeColour)
1283     {
1284       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1285     }
1286     else if (source == annotationColour)
1287     {
1288       new AnnotationColourChooser(viewport, alignPanel);
1289     }
1290     else if (source == annotationColumnSelection)
1291     {
1292       new AnnotationColumnChooser(viewport, alignPanel);
1293     }
1294     else if (source == sortPairwiseMenuItem)
1295     {
1296       sortPairwiseMenuItem_actionPerformed();
1297     }
1298     else if (source == sortIDMenuItem)
1299     {
1300       sortIDMenuItem_actionPerformed();
1301     }
1302     else if (source == sortLengthMenuItem)
1303     {
1304       sortLengthMenuItem_actionPerformed();
1305     }
1306     else if (source == sortGroupMenuItem)
1307     {
1308       sortGroupMenuItem_actionPerformed();
1309     }
1310     else if (source == removeRedundancyMenuItem)
1311     {
1312       removeRedundancyMenuItem_actionPerformed();
1313     }
1314     else if (source == pairwiseAlignmentMenuItem)
1315     {
1316       pairwiseAlignmentMenuItem_actionPerformed();
1317     }
1318     else if (source == PCAMenuItem)
1319     {
1320       PCAMenuItem_actionPerformed();
1321     }
1322     else if (source == averageDistanceTreeMenuItem)
1323     {
1324       averageDistanceTreeMenuItem_actionPerformed();
1325     }
1326     else if (source == neighbourTreeMenuItem)
1327     {
1328       neighbourTreeMenuItem_actionPerformed();
1329     }
1330     else if (source == njTreeBlosumMenuItem)
1331     {
1332       njTreeBlosumMenuItem_actionPerformed();
1333     }
1334     else if (source == avDistanceTreeBlosumMenuItem)
1335     {
1336       avTreeBlosumMenuItem_actionPerformed();
1337     }
1338     else if (source == documentation)
1339     {
1340       documentation_actionPerformed();
1341     }
1342     else if (source == about)
1343     {
1344       about_actionPerformed();
1345     }
1346
1347   }
1348
1349   public void inputText_actionPerformed()
1350   {
1351     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352     Frame frame = new Frame();
1353     frame.add(cap);
1354     jalview.bin.JalviewLite.addFrame(frame,
1355             MessageManager.getString("label.input_cut_paste"), 500, 500);
1356   }
1357
1358   protected void outputText_actionPerformed(ActionEvent e)
1359   {
1360     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1361     Frame frame = new Frame();
1362     frame.add(cap);
1363     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1364             "label.alignment_output_command",
1365             new Object[] { e.getActionCommand() }), 600, 500);
1366
1367     FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1368     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1369             fileFormat, viewport.getAlignment(),
1370             viewport.getShowJVSuffix()));
1371   }
1372
1373   public void loadAnnotations()
1374   {
1375     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376     cap.setText(MessageManager
1377             .getString("label.paste_features_annotations_Tcoffee_here"));
1378     cap.setAnnotationImport();
1379     Frame frame = new Frame();
1380     frame.add(cap);
1381     jalview.bin.JalviewLite.addFrame(frame,
1382             MessageManager.getString("action.paste_annotations"), 400, 300);
1383
1384   }
1385
1386   public String outputAnnotations(boolean displayTextbox)
1387   {
1388     String annotation = new AnnotationFile()
1389             .printAnnotationsForView(viewport);
1390
1391     if (displayTextbox)
1392     {
1393       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1394       Frame frame = new Frame();
1395       frame.add(cap);
1396       jalview.bin.JalviewLite.addFrame(frame,
1397               MessageManager.getString("label.annotations"), 600, 500);
1398       cap.setText(annotation);
1399     }
1400
1401     return annotation;
1402   }
1403
1404   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1405   {
1406     if (alignPanel.getFeatureRenderer() != null
1407             && viewport.getFeaturesDisplayed() != null)
1408     {
1409       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1410
1411     }
1412     return null;
1413   }
1414
1415   public String outputFeatures(boolean displayTextbox, String format)
1416   {
1417     String features;
1418     FeaturesFile formatter = new FeaturesFile();
1419     if (format.equalsIgnoreCase("Jalview"))
1420     {
1421       features = formatter.printJalviewFormat(viewport.getAlignment()
1422               .getSequencesArray(), getDisplayedFeatureCols());
1423     }
1424     else
1425     {
1426       features = formatter.printGffFormat(viewport.getAlignment()
1427               .getSequencesArray(), getDisplayedFeatureCols());
1428     }
1429
1430     if (displayTextbox)
1431     {
1432       boolean frimport = false;
1433       if (features == null || features.equals("No Features Visible"))
1434       {
1435         features = "# No features visible - paste some and import them here.";
1436         frimport = true;
1437       }
1438
1439       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1440       if (frimport)
1441       {
1442         cap.setAnnotationImport();
1443       }
1444       Frame frame = new Frame();
1445       frame.add(cap);
1446       jalview.bin.JalviewLite.addFrame(frame,
1447               MessageManager.getString("label.features"), 600, 500);
1448       cap.setText(features);
1449     }
1450     else
1451     {
1452       if (features == null)
1453       {
1454         features = "";
1455       }
1456     }
1457
1458     return features;
1459   }
1460
1461   void launchFullApplication()
1462   {
1463     StringBuffer url = new StringBuffer(jalviewServletURL);
1464
1465     // allow servlet parameters to be passed in applet parameter
1466     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1467             : "?";
1468     url.append(firstSep);
1469
1470     url.append("open="
1471             + appendProtocol(viewport.applet.getParameter("file")));
1472
1473     if (viewport.applet.getParameter("features") != null)
1474     {
1475       url.append("&features=");
1476       url.append(appendProtocol(viewport.applet.getParameter("features")));
1477     }
1478
1479     if (viewport.applet.getParameter("annotations") != null)
1480     {
1481       url.append("&annotations=");
1482       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1483     }
1484
1485     if (viewport.applet.getParameter("jnetfile") != null
1486             || viewport.applet.getParameter("jpredfile") != null)
1487     {
1488       url.append("&annotations=");
1489       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1490               .getParameter("jnetfile") : viewport.applet
1491               .getParameter("jpredfile")));
1492     }
1493
1494     if (viewport.applet.getParameter("defaultColour") != null)
1495     {
1496       url.append("&colour="
1497               + removeWhiteSpace(viewport.applet
1498                       .getParameter("defaultColour")));
1499     }
1500
1501     if (viewport.applet.getParameter("userDefinedColour") != null)
1502     {
1503       url.append("&colour="
1504               + removeWhiteSpace(viewport.applet
1505                       .getParameter("userDefinedColour")));
1506     }
1507     if (viewport.applet.getParameter("tree") != null)
1508     {
1509       url.append("&tree="
1510               + appendProtocol(viewport.applet.getParameter("tree")));
1511     }
1512     if (viewport.applet.getParameter("treeFile") != null)
1513     {
1514       url.append("&tree="
1515               + appendProtocol(viewport.applet.getParameter("treeFile")));
1516     }
1517
1518     showURL(url.toString(), "FULL_APP");
1519   }
1520
1521   String removeWhiteSpace(String colour)
1522   {
1523     StringBuffer sb = new StringBuffer();
1524     for (int i = 0; i < colour.length(); i++)
1525     {
1526       if (Character.isWhitespace(colour.charAt(i)))
1527       {
1528         sb.append("%20");
1529       }
1530       else
1531       {
1532         sb.append(colour.charAt(i));
1533       }
1534     }
1535
1536     return sb.toString();
1537   }
1538
1539   String appendProtocol(String url)
1540   {
1541     try
1542     {
1543       new URL(url);
1544       url = URLEncoder.encode(url);
1545     }
1546     /*
1547      * When we finally deprecate 1.1 compatibility, we can start to use
1548      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1549      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1550      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1551      * ex.printStackTrace(); }
1552      */
1553     catch (java.net.MalformedURLException ex)
1554     {
1555       url = viewport.applet.getCodeBase() + url;
1556     }
1557     return url;
1558   }
1559
1560   public void closeMenuItem_actionPerformed()
1561   {
1562     PaintRefresher.RemoveComponent(alignPanel);
1563     if (alignPanel.seqPanel != null
1564             && alignPanel.seqPanel.seqCanvas != null)
1565     {
1566       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1567     }
1568     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1569     {
1570       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1571     }
1572
1573     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1574     {
1575       System.exit(0);
1576     }
1577     else
1578     {
1579     }
1580     viewport = null;
1581     alignPanel = null;
1582     this.dispose();
1583   }
1584
1585   /**
1586    * TODO: JAL-1104
1587    */
1588   void updateEditMenuBar()
1589   {
1590
1591     if (viewport.getHistoryList().size() > 0)
1592     {
1593       undoMenuItem.setEnabled(true);
1594       CommandI command = viewport.getHistoryList().peek();
1595       undoMenuItem.setLabel(MessageManager.formatMessage(
1596               "label.undo_command",
1597               new Object[] { command.getDescription() }));
1598     }
1599     else
1600     {
1601       undoMenuItem.setEnabled(false);
1602       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1603     }
1604
1605     if (viewport.getRedoList().size() > 0)
1606     {
1607       redoMenuItem.setEnabled(true);
1608
1609       CommandI command = viewport.getRedoList().peek();
1610       redoMenuItem.setLabel(MessageManager.formatMessage(
1611               "label.redo_command",
1612               new Object[] { command.getDescription() }));
1613     }
1614     else
1615     {
1616       redoMenuItem.setEnabled(false);
1617       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1618     }
1619   }
1620
1621   /**
1622    * TODO: JAL-1104
1623    */
1624   @Override
1625   public void addHistoryItem(CommandI command)
1626   {
1627     if (command.getSize() > 0)
1628     {
1629       viewport.addToHistoryList(command);
1630       viewport.clearRedoList();
1631       updateEditMenuBar();
1632       viewport.updateHiddenColumns();
1633     }
1634   }
1635
1636   /**
1637    * TODO: JAL-1104 DOCUMENT ME!
1638    *
1639    * @param e
1640    *          DOCUMENT ME!
1641    */
1642   protected void undoMenuItem_actionPerformed()
1643   {
1644     if (viewport.getHistoryList().isEmpty())
1645     {
1646       return;
1647     }
1648
1649     CommandI command = viewport.getHistoryList().pop();
1650     viewport.addToRedoList(command);
1651     command.undoCommand(null);
1652
1653     AlignmentViewport originalSource = getOriginatingSource(command);
1654     // JBPNote Test
1655     if (originalSource != viewport)
1656     {
1657       System.err
1658               .println("Warning: Viewport object mismatch whilst undoing");
1659     }
1660     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1661                                           // viewport.getColumnSelection().getHiddenColumns()
1662                                           // != null;
1663     updateEditMenuBar();
1664     originalSource.firePropertyChange("alignment", null, originalSource
1665             .getAlignment().getSequences());
1666   }
1667
1668   /**
1669    * TODO: JAL-1104 DOCUMENT ME!
1670    *
1671    * @param e
1672    *          DOCUMENT ME!
1673    */
1674   protected void redoMenuItem_actionPerformed()
1675   {
1676     if (viewport.getRedoList().isEmpty())
1677     {
1678       return;
1679     }
1680
1681     CommandI command = viewport.getRedoList().pop();
1682     viewport.addToHistoryList(command);
1683     command.doCommand(null);
1684
1685     AlignmentViewport originalSource = getOriginatingSource(command);
1686     // JBPNote Test
1687     if (originalSource != viewport)
1688     {
1689       System.err
1690               .println("Warning: Viewport object mismatch whilst re-doing");
1691     }
1692     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1693                                           // viewport.getColumnSelection().getHiddenColumns()
1694                                           // != null;
1695
1696     updateEditMenuBar();
1697     originalSource.firePropertyChange("alignment", null, originalSource
1698             .getAlignment().getSequences());
1699   }
1700
1701   AlignmentViewport getOriginatingSource(CommandI command)
1702   {
1703     AlignmentViewport originalSource = null;
1704     // For sequence removal and addition, we need to fire
1705     // the property change event FROM the viewport where the
1706     // original alignment was altered
1707     AlignmentI al = null;
1708     if (command instanceof EditCommand)
1709     {
1710       EditCommand editCommand = (EditCommand) command;
1711       al = editCommand.getAlignment();
1712       Vector comps = (Vector) PaintRefresher.components.get(viewport
1713               .getSequenceSetId());
1714       for (int i = 0; i < comps.size(); i++)
1715       {
1716         if (comps.elementAt(i) instanceof AlignmentPanel)
1717         {
1718           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1719           {
1720             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1721             break;
1722           }
1723         }
1724       }
1725     }
1726
1727     if (originalSource == null)
1728     {
1729       // The original view is closed, we must validate
1730       // the current view against the closed view first
1731       if (al != null)
1732       {
1733         PaintRefresher.validateSequences(al, viewport.getAlignment());
1734       }
1735
1736       originalSource = viewport;
1737     }
1738
1739     return originalSource;
1740   }
1741
1742   /**
1743    * Move the currently selected sequences up or down one position in the
1744    * alignment
1745    *
1746    * @param up
1747    */
1748   public void moveSelectedSequences(boolean up)
1749   {
1750     SequenceGroup sg = viewport.getSelectionGroup();
1751     if (sg == null)
1752     {
1753       return;
1754     }
1755     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1756             up ? null : viewport.getHiddenRepSequences(), up);
1757     alignPanel.paintAlignment(true);
1758
1759     /*
1760      * Also move cDNA/protein complement sequences
1761      */
1762     AlignViewportI complement = viewport.getCodingComplement();
1763     if (complement != null)
1764     {
1765       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1766               viewport, complement);
1767       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1768               up ? null : complement.getHiddenRepSequences(), up);
1769       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1770     }
1771   }
1772
1773   synchronized void slideSequences(boolean right, int size)
1774   {
1775     List<SequenceI> sg = new Vector<SequenceI>();
1776     if (viewport.cursorMode)
1777     {
1778       sg.add(viewport.getAlignment().getSequenceAt(
1779               alignPanel.seqPanel.seqCanvas.cursorY));
1780     }
1781     else if (viewport.getSelectionGroup() != null
1782             && viewport.getSelectionGroup().getSize() != viewport
1783                     .getAlignment().getHeight())
1784     {
1785       sg = viewport.getSelectionGroup().getSequences(
1786               viewport.getHiddenRepSequences());
1787     }
1788
1789     if (sg.size() < 1)
1790     {
1791       return;
1792     }
1793
1794     Vector<SequenceI> invertGroup = new Vector();
1795
1796     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1797     {
1798       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1799       {
1800         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1801       }
1802     }
1803
1804     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1805
1806     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1807             .size()]);
1808     for (int i = 0; i < invertGroup.size(); i++)
1809     {
1810       seqs2[i] = invertGroup.elementAt(i);
1811     }
1812
1813     SlideSequencesCommand ssc;
1814     if (right)
1815     {
1816       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1817               size, viewport.getGapCharacter());
1818     }
1819     else
1820     {
1821       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1822               size, viewport.getGapCharacter());
1823     }
1824
1825     int groupAdjustment = 0;
1826     if (ssc.getGapsInsertedBegin() && right)
1827     {
1828       if (viewport.cursorMode)
1829       {
1830         alignPanel.seqPanel.moveCursor(size, 0);
1831       }
1832       else
1833       {
1834         groupAdjustment = size;
1835       }
1836     }
1837     else if (!ssc.getGapsInsertedBegin() && !right)
1838     {
1839       if (viewport.cursorMode)
1840       {
1841         alignPanel.seqPanel.moveCursor(-size, 0);
1842       }
1843       else
1844       {
1845         groupAdjustment = -size;
1846       }
1847     }
1848
1849     if (groupAdjustment != 0)
1850     {
1851       viewport.getSelectionGroup().setStartRes(
1852               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1853       viewport.getSelectionGroup().setEndRes(
1854               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1855     }
1856
1857     boolean appendHistoryItem = false;
1858     Deque<CommandI> historyList = viewport.getHistoryList();
1859     if (historyList != null && historyList.size() > 0
1860             && historyList.peek() instanceof SlideSequencesCommand)
1861     {
1862       appendHistoryItem = ssc
1863               .appendSlideCommand((SlideSequencesCommand) historyList
1864                       .peek());
1865     }
1866
1867     if (!appendHistoryItem)
1868     {
1869       addHistoryItem(ssc);
1870     }
1871
1872     repaint();
1873   }
1874
1875   static StringBuffer copiedSequences;
1876
1877   static Vector copiedHiddenColumns;
1878
1879   protected void copy_actionPerformed()
1880   {
1881     if (viewport.getSelectionGroup() == null)
1882     {
1883       return;
1884     }
1885
1886     SequenceGroup sg = viewport.getSelectionGroup();
1887     copiedSequences = new StringBuffer();
1888     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1889     for (int i = 0; i < sg.getSize(); i++)
1890     {
1891       SequenceI seq = sg.getSequenceAt(i);
1892       int index = viewport.getAlignment().findIndex(seq);
1893       orderedSeqs.put(index, seq);
1894     }
1895
1896     int index = 0, startRes, endRes;
1897     char ch;
1898
1899     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1900     {
1901       copiedHiddenColumns = new Vector();
1902       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1903       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1904       {
1905         copiedHiddenColumns.addElement(new int[] {
1906             region[0] - hiddenOffset, region[1] - hiddenOffset });
1907       }
1908     }
1909     else
1910     {
1911       copiedHiddenColumns = null;
1912     }
1913
1914     for (int i = 0; i < sg.getSize(); i++)
1915     {
1916       SequenceI seq = null;
1917
1918       while (seq == null)
1919       {
1920         if (orderedSeqs.containsKey(index))
1921         {
1922           seq = orderedSeqs.get(index);
1923           index++;
1924           break;
1925         }
1926         else
1927         {
1928           index++;
1929         }
1930       }
1931
1932       // FIND START RES
1933       // Returns residue following index if gap
1934       startRes = seq.findPosition(sg.getStartRes());
1935
1936       // FIND END RES
1937       // Need to find the residue preceeding index if gap
1938       endRes = 0;
1939
1940       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1941       {
1942         ch = seq.getCharAt(j);
1943         if (!jalview.util.Comparison.isGap((ch)))
1944         {
1945           endRes++;
1946         }
1947       }
1948
1949       if (endRes > 0)
1950       {
1951         endRes += seq.getStart() - 1;
1952       }
1953
1954       copiedSequences.append(seq.getName()
1955               + "\t"
1956               + startRes
1957               + "\t"
1958               + endRes
1959               + "\t"
1960               + seq.getSequenceAsString(sg.getStartRes(),
1961                       sg.getEndRes() + 1) + "\n");
1962     }
1963
1964   }
1965
1966   protected void pasteNew_actionPerformed()
1967   {
1968     paste(true);
1969   }
1970
1971   protected void pasteThis_actionPerformed()
1972   {
1973     paste(false);
1974   }
1975
1976   void paste(boolean newAlignment)
1977   {
1978     try
1979     {
1980
1981       if (copiedSequences == null)
1982       {
1983         return;
1984       }
1985
1986       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1987       Vector seqs = new Vector();
1988       while (st.hasMoreElements())
1989       {
1990         String name = st.nextToken();
1991         int start = Integer.parseInt(st.nextToken());
1992         int end = Integer.parseInt(st.nextToken());
1993         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1994       }
1995       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1996       for (int i = 0; i < seqs.size(); i++)
1997       {
1998         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1999       }
2000
2001       if (newAlignment)
2002       {
2003         String newtitle = MessageManager
2004                 .getString("label.copied_sequences");
2005         if (getTitle().startsWith(
2006                 MessageManager.getString("label.copied_sequences")))
2007         {
2008           newtitle = getTitle();
2009         }
2010         else
2011         {
2012           newtitle = newtitle.concat(MessageManager.formatMessage(
2013                   "label.from_msname", new String[] { getTitle() }));
2014         }
2015         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2016                 viewport.applet, newtitle, false);
2017         if (copiedHiddenColumns != null)
2018         {
2019           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2020           {
2021             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2022             af.viewport.hideColumns(region[0], region[1]);
2023           }
2024         }
2025
2026         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2027                 frameHeight);
2028       }
2029       else
2030       {
2031         addSequences(newSeqs);
2032       }
2033
2034     } catch (Exception ex)
2035     {
2036     } // could be anything being pasted in here
2037
2038   }
2039
2040   void addSequences(SequenceI[] seqs)
2041   {
2042     for (int i = 0; i < seqs.length; i++)
2043     {
2044       viewport.getAlignment().addSequence(seqs[i]);
2045     }
2046
2047     // !newAlignment
2048     addHistoryItem(new EditCommand(
2049             MessageManager.getString("label.add_sequences"), Action.PASTE,
2050             seqs, 0, viewport.getAlignment().getWidth(),
2051             viewport.getAlignment()));
2052
2053     viewport.setEndSeq(viewport.getAlignment().getHeight());
2054     viewport.getAlignment().getWidth();
2055     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2056             .getSequences());
2057
2058   }
2059
2060   protected void cut_actionPerformed()
2061   {
2062     copy_actionPerformed();
2063     delete_actionPerformed();
2064   }
2065
2066   protected void delete_actionPerformed()
2067   {
2068
2069     SequenceGroup sg = viewport.getSelectionGroup();
2070     if (sg == null)
2071     {
2072       return;
2073     }
2074
2075     Vector seqs = new Vector();
2076     SequenceI seq;
2077     for (int i = 0; i < sg.getSize(); i++)
2078     {
2079       seq = sg.getSequenceAt(i);
2080       seqs.addElement(seq);
2081     }
2082
2083     /*
2084      * If the cut affects all sequences, warn, remove highlighted columns
2085      */
2086     if (sg.getSize() == viewport.getAlignment().getHeight())
2087     {
2088       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2089               .getAlignment().getWidth()) ? true : false;
2090       if (isEntireAlignWidth)
2091       {
2092         String title = MessageManager.getString("label.delete_all");
2093         Panel infoPanel = new Panel();
2094         infoPanel.setLayout(new FlowLayout());
2095         infoPanel
2096                 .add(new Label(MessageManager.getString("warn.delete_all")));
2097
2098         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2099         dialog.setMainPanel(infoPanel);
2100         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2101         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2102         dialog.setVisible(true);
2103
2104         if (!dialog.accept)
2105         {
2106           return;
2107         }
2108       }
2109       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2110               sg.getEndRes() + 1);
2111     }
2112
2113     SequenceI[] cut = new SequenceI[seqs.size()];
2114     for (int i = 0; i < seqs.size(); i++)
2115     {
2116       cut[i] = (SequenceI) seqs.elementAt(i);
2117     }
2118
2119     /*
2120      * //ADD HISTORY ITEM
2121      */
2122     addHistoryItem(new EditCommand(
2123             MessageManager.getString("label.cut_sequences"), Action.CUT,
2124             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2125             viewport.getAlignment()));
2126
2127     viewport.setSelectionGroup(null);
2128     viewport.getAlignment().deleteGroup(sg);
2129
2130     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2131             .getSequences());
2132
2133     if (viewport.getAlignment().getHeight() < 1)
2134     {
2135       this.setVisible(false);
2136     }
2137     viewport.sendSelection();
2138   }
2139
2140   /**
2141    * group consensus toggled
2142    *
2143    */
2144   protected void showGroupConsensus_actionPerformed()
2145   {
2146     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2147     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2148
2149   }
2150
2151   /**
2152    * group conservation toggled.
2153    */
2154   protected void showGroupConservation_actionPerformed()
2155   {
2156     viewport.setShowGroupConservation(showGroupConservation.getState());
2157     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2158   }
2159
2160   /*
2161    * (non-Javadoc)
2162    *
2163    * @see
2164    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2165    * .event.ActionEvent)
2166    */
2167   protected void showConsensusHistogram_actionPerformed()
2168   {
2169     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2170     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2171   }
2172
2173   /*
2174    * (non-Javadoc)
2175    *
2176    * @see
2177    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2178    * .event.ActionEvent)
2179    */
2180   protected void showSequenceLogo_actionPerformed()
2181   {
2182     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2183     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184   }
2185
2186   protected void normSequenceLogo_actionPerformed()
2187   {
2188     showSequenceLogo.setState(true);
2189     viewport.setShowSequenceLogo(true);
2190     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2191     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192   }
2193
2194   protected void applyAutoAnnotationSettings_actionPerformed()
2195   {
2196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197   }
2198
2199   protected void makeGrpsFromSelection_actionPerformed()
2200   {
2201     if (avc.makeGroupsFromSelection())
2202     {
2203       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2204       alignPanel.updateAnnotation();
2205       alignPanel.paintAlignment(true);
2206     }
2207   }
2208
2209   protected void createGroup_actionPerformed()
2210   {
2211     avc.createGroup();
2212   }
2213
2214   protected void unGroup_actionPerformed()
2215   {
2216     if (avc.unGroup())
2217     {
2218       alignPanel.alignmentChanged();
2219     }
2220   }
2221
2222   protected void deleteGroups_actionPerformed()
2223   {
2224     if (avc.deleteGroups())
2225     {
2226       alignPanel.alignmentChanged();
2227     }
2228   }
2229
2230   public void selectAllSequenceMenuItem_actionPerformed()
2231   {
2232     SequenceGroup sg = new SequenceGroup();
2233     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2234     {
2235       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2236     }
2237     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2238     viewport.setSelectionGroup(sg);
2239     // JAL-2034 - should delegate to
2240     // alignPanel to decide if overview needs
2241     // updating.
2242     alignPanel.paintAlignment(false);
2243     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2244     viewport.sendSelection();
2245   }
2246
2247   public void deselectAllSequenceMenuItem_actionPerformed()
2248   {
2249     if (viewport.cursorMode)
2250     {
2251       alignPanel.seqPanel.keyboardNo1 = null;
2252       alignPanel.seqPanel.keyboardNo2 = null;
2253     }
2254     viewport.setSelectionGroup(null);
2255     viewport.getColumnSelection().clear();
2256     viewport.setSelectionGroup(null);
2257     alignPanel.idPanel.idCanvas.searchResults = null;
2258     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2259     // JAL-2034 - should delegate to
2260     // alignPanel to decide if overview needs
2261     // updating.
2262     alignPanel.paintAlignment(false);
2263     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2264     viewport.sendSelection();
2265   }
2266
2267   public void invertSequenceMenuItem_actionPerformed()
2268   {
2269     SequenceGroup sg = viewport.getSelectionGroup();
2270     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2271     {
2272       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2273     }
2274
2275     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2276     viewport.sendSelection();
2277   }
2278
2279   public void invertColSel_actionPerformed()
2280   {
2281     viewport.invertColumnSelection();
2282     alignPanel.paintAlignment(true);
2283     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2284     viewport.sendSelection();
2285   }
2286
2287   void trimAlignment(boolean trimLeft)
2288   {
2289     ColumnSelection colSel = viewport.getColumnSelection();
2290     int column;
2291
2292     if (!colSel.isEmpty())
2293     {
2294       if (trimLeft)
2295       {
2296         column = colSel.getMin();
2297       }
2298       else
2299       {
2300         column = colSel.getMax();
2301       }
2302
2303       SequenceI[] seqs;
2304       if (viewport.getSelectionGroup() != null)
2305       {
2306         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2307                 viewport.getHiddenRepSequences());
2308       }
2309       else
2310       {
2311         seqs = viewport.getAlignment().getSequencesArray();
2312       }
2313
2314       TrimRegionCommand trimRegion;
2315       if (trimLeft)
2316       {
2317         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2318                 column, viewport.getAlignment());
2319         viewport.setStartRes(0);
2320       }
2321       else
2322       {
2323         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2324                 column, viewport.getAlignment());
2325       }
2326
2327       statusBar.setText(MessageManager.formatMessage(
2328               "label.removed_columns",
2329               new String[] { Integer.valueOf(trimRegion.getSize())
2330                       .toString() }));
2331       addHistoryItem(trimRegion);
2332
2333       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2334       {
2335         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2336                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2337         {
2338           viewport.getAlignment().deleteGroup(sg);
2339         }
2340       }
2341
2342       viewport.firePropertyChange("alignment", null, viewport
2343               .getAlignment().getSequences());
2344     }
2345   }
2346
2347   public void removeGappedColumnMenuItem_actionPerformed()
2348   {
2349     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2350
2351     SequenceI[] seqs;
2352     if (viewport.getSelectionGroup() != null)
2353     {
2354       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2355               viewport.getHiddenRepSequences());
2356       start = viewport.getSelectionGroup().getStartRes();
2357       end = viewport.getSelectionGroup().getEndRes();
2358     }
2359     else
2360     {
2361       seqs = viewport.getAlignment().getSequencesArray();
2362     }
2363
2364     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2365             "Remove Gapped Columns", seqs, start, end,
2366             viewport.getAlignment());
2367
2368     addHistoryItem(removeGapCols);
2369
2370     statusBar.setText(MessageManager.formatMessage(
2371             "label.removed_empty_columns",
2372             new String[] { Integer.valueOf(removeGapCols.getSize())
2373                     .toString() }));
2374
2375     // This is to maintain viewport position on first residue
2376     // of first sequence
2377     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2378     int startRes = seq.findPosition(viewport.startRes);
2379     // ShiftList shifts;
2380     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2381     // edit.alColumnChanges=shifts.getInverse();
2382     // if (viewport.hasHiddenColumns)
2383     // viewport.getColumnSelection().compensateForEdits(shifts);
2384     viewport.setStartRes(seq.findIndex(startRes) - 1);
2385     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386             .getSequences());
2387
2388   }
2389
2390   public void removeAllGapsMenuItem_actionPerformed()
2391   {
2392     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2393
2394     SequenceI[] seqs;
2395     if (viewport.getSelectionGroup() != null)
2396     {
2397       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2398               viewport.getHiddenRepSequences());
2399       start = viewport.getSelectionGroup().getStartRes();
2400       end = viewport.getSelectionGroup().getEndRes();
2401     }
2402     else
2403     {
2404       seqs = viewport.getAlignment().getSequencesArray();
2405     }
2406
2407     // This is to maintain viewport position on first residue
2408     // of first sequence
2409     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2410     int startRes = seq.findPosition(viewport.startRes);
2411
2412     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2413             viewport.getAlignment()));
2414
2415     viewport.setStartRes(seq.findIndex(startRes) - 1);
2416
2417     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2418             .getSequences());
2419
2420   }
2421
2422   public void findMenuItem_actionPerformed()
2423   {
2424     new Finder(alignPanel);
2425   }
2426
2427   /**
2428    * create a new view derived from the current view
2429    *
2430    * @param viewtitle
2431    * @return frame for the new view
2432    */
2433   public AlignFrame newView(String viewtitle)
2434   {
2435     AlignmentI newal;
2436     if (viewport.hasHiddenRows())
2437     {
2438       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2439               .getFullAlignment().getSequencesArray());
2440     }
2441     else
2442     {
2443       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2444     }
2445
2446     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2447     {
2448       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2449       {
2450         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2451         {
2452           newal.addAnnotation(viewport.getAlignment()
2453                   .getAlignmentAnnotation()[i]);
2454         }
2455       }
2456     }
2457
2458     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2459
2460     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2461     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2462     PaintRefresher.Register(newaf.alignPanel,
2463             newaf.alignPanel.av.getSequenceSetId());
2464
2465     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2466             newaf.alignPanel.av.getSequenceSetId());
2467     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2468             newaf.alignPanel.av.getSequenceSetId());
2469
2470     Vector comps = (Vector) PaintRefresher.components.get(viewport
2471             .getSequenceSetId());
2472     int viewSize = -1;
2473     for (int i = 0; i < comps.size(); i++)
2474     {
2475       if (comps.elementAt(i) instanceof AlignmentPanel)
2476       {
2477         viewSize++;
2478       }
2479     }
2480
2481     String title = new String(this.getTitle());
2482     if (viewtitle != null)
2483     {
2484       title = viewtitle + " ( " + title + ")";
2485     }
2486     else
2487     {
2488       if (title.indexOf("(View") > -1)
2489       {
2490         title = title.substring(0, title.indexOf("(View"));
2491       }
2492       title += "(View " + viewSize + ")";
2493     }
2494
2495     newaf.setTitle(title.toString());
2496
2497     newaf.viewport.setHistoryList(viewport.getHistoryList());
2498     newaf.viewport.setRedoList(viewport.getRedoList());
2499     return newaf;
2500   }
2501
2502   /**
2503    *
2504    * @return list of feature groups on the view
2505    */
2506   public String[] getFeatureGroups()
2507   {
2508     FeatureRenderer fr = null;
2509     if (alignPanel != null
2510             && (fr = alignPanel.getFeatureRenderer()) != null)
2511     {
2512       List<String> gps = fr.getFeatureGroups();
2513       String[] _gps = gps.toArray(new String[gps.size()]);
2514       return _gps;
2515     }
2516     return null;
2517   }
2518
2519   /**
2520    * get sequence feature groups that are hidden or shown
2521    *
2522    * @param visible
2523    *          true is visible
2524    * @return list
2525    */
2526   public String[] getFeatureGroupsOfState(boolean visible)
2527   {
2528     FeatureRenderer fr = null;
2529     if (alignPanel != null
2530             && (fr = alignPanel.getFeatureRenderer()) != null)
2531     {
2532       List<String> gps = fr.getGroups(visible);
2533       String[] _gps = gps.toArray(new String[gps.size()]);
2534       return _gps;
2535     }
2536     return null;
2537   }
2538
2539   /**
2540    * Change the display state for the given feature groups
2541    *
2542    * @param groups
2543    *          list of group strings
2544    * @param state
2545    *          visible or invisible
2546    */
2547   public void setFeatureGroupState(String[] groups, boolean state)
2548   {
2549     FeatureRenderer fr = null;
2550     this.sequenceFeatures.setState(true);
2551     viewport.setShowSequenceFeatures(true);
2552     if (alignPanel != null
2553             && (fr = alignPanel.getFeatureRenderer()) != null)
2554     {
2555
2556       fr.setGroupVisibility(Arrays.asList(groups), state);
2557       alignPanel.seqPanel.seqCanvas.repaint();
2558       if (alignPanel.overviewPanel != null)
2559       {
2560         alignPanel.overviewPanel.updateOverviewImage();
2561       }
2562     }
2563   }
2564
2565   public void seqLimits_itemStateChanged()
2566   {
2567     viewport.setShowJVSuffix(seqLimits.getState());
2568     alignPanel.fontChanged();
2569     alignPanel.paintAlignment(true);
2570   }
2571
2572   protected void colourTextMenuItem_actionPerformed()
2573   {
2574     viewport.setColourText(colourTextMenuItem.getState());
2575     alignPanel.paintAlignment(true);
2576   }
2577
2578   protected void displayNonconservedMenuItem_actionPerformed()
2579   {
2580     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2581     alignPanel.paintAlignment(true);
2582   }
2583
2584   protected void wrapMenuItem_actionPerformed()
2585   {
2586     viewport.setWrapAlignment(wrapMenuItem.getState());
2587     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2588     scaleAbove.setEnabled(wrapMenuItem.getState());
2589     scaleLeft.setEnabled(wrapMenuItem.getState());
2590     scaleRight.setEnabled(wrapMenuItem.getState());
2591     alignPanel.paintAlignment(true);
2592   }
2593
2594   public void overviewMenuItem_actionPerformed()
2595   {
2596     if (alignPanel.overviewPanel != null)
2597     {
2598       return;
2599     }
2600
2601     Frame frame = new Frame();
2602     OverviewPanel overview = new OverviewPanel(alignPanel);
2603     frame.add(overview);
2604     // +50 must allow for applet frame window
2605     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2606             "label.overview_params", new String[] { this.getTitle() }),
2607             overview.getPreferredSize().width,
2608             overview.getPreferredSize().height + 50);
2609
2610     frame.pack();
2611     final AlignmentPanel ap = alignPanel;
2612     frame.addWindowListener(new WindowAdapter()
2613     {
2614       @Override
2615       public void windowClosing(WindowEvent e)
2616       {
2617         if (ap != null)
2618         {
2619           ap.setOverviewPanel(null);
2620         }
2621       };
2622     });
2623
2624     alignPanel.setOverviewPanel(overview);
2625
2626   }
2627
2628   @Override
2629   public void changeColour(ColourSchemeI cs)
2630   {
2631     // FIXME threshold, conservation, increment belong inside
2632     // AlignmentColourScheme and/or ViewStyleI, not ColourSchemeI
2633     if (cs != null)
2634     {
2635       if (viewport.getAbovePIDThreshold())
2636       {
2637         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2638                 viewport.getViewportColourScheme(), "Background"));
2639       }
2640
2641       if (viewport.getConservationSelected())
2642       {
2643         // cs.setConservationApplied(true);
2644         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2645                 viewport.getViewportColourScheme(), "Background"));
2646       }
2647       // else
2648       // {
2649       // cs.setConservationApplied(false);
2650       // }
2651     }
2652     viewport.setGlobalColourScheme(cs);
2653     viewport.getViewportColourScheme().setConservationApplied(
2654             viewport.getConservationSelected());
2655
2656     alignPanel.paintAlignment(true);
2657   }
2658
2659   protected void modifyPID_actionPerformed()
2660   {
2661     if (viewport.getAbovePIDThreshold()
2662             && viewport.getGlobalColourScheme() != null)
2663     {
2664       SliderPanel.setPIDSliderSource(alignPanel,
2665               viewport.getViewportColourScheme(), "Background");
2666       SliderPanel.showPIDSlider();
2667     }
2668   }
2669
2670   protected void modifyConservation_actionPerformed()
2671   {
2672     if (viewport.getConservationSelected()
2673             && viewport.getGlobalColourScheme() != null)
2674     {
2675       SliderPanel.setConservationSlider(alignPanel,
2676               viewport.getViewportColourScheme(), "Background");
2677       SliderPanel.showConservationSlider();
2678     }
2679   }
2680
2681   protected void conservationMenuItem_actionPerformed()
2682   {
2683     viewport.setConservationSelected(conservationMenuItem.getState());
2684
2685     viewport.setAbovePIDThreshold(false);
2686     abovePIDThreshold.setState(false);
2687
2688     changeColour(viewport.getGlobalColourScheme());
2689
2690     modifyConservation_actionPerformed();
2691   }
2692
2693   public void abovePIDThreshold_actionPerformed()
2694   {
2695     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2696
2697     conservationMenuItem.setState(false);
2698     viewport.setConservationSelected(false);
2699
2700     changeColour(viewport.getGlobalColourScheme());
2701
2702     modifyPID_actionPerformed();
2703   }
2704
2705   public void sortPairwiseMenuItem_actionPerformed()
2706   {
2707     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2708     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2709             .getAlignment().getSequenceAt(0), null);
2710
2711     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2712             viewport.getAlignment()));
2713     alignPanel.paintAlignment(true);
2714   }
2715
2716   public void sortIDMenuItem_actionPerformed()
2717   {
2718     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2719     AlignmentSorter.sortByID(viewport.getAlignment());
2720     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2721             viewport.getAlignment()));
2722     alignPanel.paintAlignment(true);
2723   }
2724
2725   public void sortLengthMenuItem_actionPerformed()
2726   {
2727     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2728     AlignmentSorter.sortByLength(viewport.getAlignment());
2729     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2730             viewport.getAlignment()));
2731     alignPanel.paintAlignment(true);
2732   }
2733
2734   public void sortGroupMenuItem_actionPerformed()
2735   {
2736     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2737     AlignmentSorter.sortByGroup(viewport.getAlignment());
2738     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2739             viewport.getAlignment()));
2740     alignPanel.paintAlignment(true);
2741
2742   }
2743
2744   public void removeRedundancyMenuItem_actionPerformed()
2745   {
2746     new RedundancyPanel(alignPanel);
2747   }
2748
2749   public void pairwiseAlignmentMenuItem_actionPerformed()
2750   {
2751     if (viewport.getSelectionGroup() != null
2752             && viewport.getSelectionGroup().getSize() > 1)
2753     {
2754       Frame frame = new Frame();
2755       frame.add(new PairwiseAlignPanel(alignPanel));
2756       jalview.bin.JalviewLite.addFrame(frame,
2757               MessageManager.getString("action.pairwise_alignment"), 600,
2758               500);
2759     }
2760   }
2761
2762   public void PCAMenuItem_actionPerformed()
2763   {
2764     // are the sequences aligned?
2765     if (!viewport.getAlignment().isAligned(false))
2766     {
2767       SequenceI current;
2768       int Width = viewport.getAlignment().getWidth();
2769
2770       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2771       {
2772         current = viewport.getAlignment().getSequenceAt(i);
2773
2774         if (current.getLength() < Width)
2775         {
2776           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2777         }
2778       }
2779       alignPanel.paintAlignment(true);
2780     }
2781
2782     if ((viewport.getSelectionGroup() != null
2783             && viewport.getSelectionGroup().getSize() < 4 && viewport
2784             .getSelectionGroup().getSize() > 0)
2785             || viewport.getAlignment().getHeight() < 4)
2786     {
2787       return;
2788     }
2789
2790     try
2791     {
2792       new PCAPanel(viewport);
2793     } catch (java.lang.OutOfMemoryError ex)
2794     {
2795     }
2796
2797   }
2798
2799   public void averageDistanceTreeMenuItem_actionPerformed()
2800   {
2801     NewTreePanel("AV", "PID", "Average distance tree using PID");
2802   }
2803
2804   public void neighbourTreeMenuItem_actionPerformed()
2805   {
2806     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2807   }
2808
2809   protected void njTreeBlosumMenuItem_actionPerformed()
2810   {
2811     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2812   }
2813
2814   protected void avTreeBlosumMenuItem_actionPerformed()
2815   {
2816     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2817   }
2818
2819   void NewTreePanel(String type, String pwType, String title)
2820   {
2821     // are the sequences aligned?
2822     if (!viewport.getAlignment().isAligned(false))
2823     {
2824       SequenceI current;
2825       int Width = viewport.getAlignment().getWidth();
2826
2827       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2828       {
2829         current = viewport.getAlignment().getSequenceAt(i);
2830
2831         if (current.getLength() < Width)
2832         {
2833           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2834         }
2835       }
2836       alignPanel.paintAlignment(true);
2837
2838     }
2839
2840     if ((viewport.getSelectionGroup() != null && viewport
2841             .getSelectionGroup().getSize() > 1)
2842             || (viewport.getAlignment().getHeight() > 1))
2843     {
2844       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2845
2846       addTreeMenuItem(tp, title);
2847
2848       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2849     }
2850   }
2851
2852   void loadTree_actionPerformed()
2853   {
2854     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2855     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2856     cap.setTreeImport();
2857     Frame frame = new Frame();
2858     frame.add(cap);
2859     jalview.bin.JalviewLite.addFrame(frame,
2860             MessageManager.getString("label.paste_newick_file"), 400, 300);
2861   }
2862
2863   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2864   {
2865     TreePanel tp = new TreePanel(alignPanel, treeFile,
2866             MessageManager.getString("label.load_tree_from_file"), tree);
2867     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2868     addTreeMenuItem(tp, treeFile);
2869   }
2870
2871   /**
2872    * sort the alignment using the given treePanel
2873    *
2874    * @param treePanel
2875    *          tree used to sort view
2876    * @param title
2877    *          string used for undo event name
2878    */
2879   public void sortByTree(TreePanel treePanel, String title)
2880   {
2881     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2882     AlignmentSorter
2883             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2884     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2885     // HistoryItem.SORT));
2886     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2887             "label.order_by_params", new String[] { title }), oldOrder,
2888             viewport.getAlignment()));
2889     alignPanel.paintAlignment(true);
2890   }
2891
2892   /**
2893    * Do any automatic reordering of the alignment and add the necessary bits to
2894    * the menu structure for the new tree
2895    *
2896    * @param treePanel
2897    * @param title
2898    */
2899   protected void addTreeMenuItem(final TreePanel treePanel,
2900           final String title)
2901   {
2902     final MenuItem item = new MenuItem(title);
2903     sortByTreeMenu.add(item);
2904     item.addActionListener(new java.awt.event.ActionListener()
2905     {
2906       @Override
2907       public void actionPerformed(ActionEvent evt)
2908       {
2909         sortByTree(treePanel, title); // treePanel.getTitle());
2910       }
2911     });
2912
2913     treePanel.addWindowListener(new WindowAdapter()
2914     {
2915       @Override
2916       public void windowOpened(WindowEvent e)
2917       {
2918         if (viewport.sortByTree)
2919         {
2920           sortByTree(treePanel, title);
2921         }
2922         super.windowOpened(e);
2923       }
2924
2925       @Override
2926       public void windowClosing(WindowEvent e)
2927       {
2928         sortByTreeMenu.remove(item);
2929       };
2930     });
2931   }
2932
2933   public boolean sortBy(AlignmentOrder alorder, String undoname)
2934   {
2935     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2936     if (viewport.applet.debug)
2937     {
2938       System.err.println("Sorting " + alorder.getOrder().size()
2939               + " in alignment '" + getTitle() + "'");
2940     }
2941     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2942     if (undoname != null)
2943     {
2944       addHistoryItem(new OrderCommand(undoname, oldOrder,
2945               viewport.getAlignment()));
2946     }
2947     alignPanel.paintAlignment(true);
2948     return true;
2949   }
2950
2951   protected void documentation_actionPerformed()
2952   {
2953     alignPanel.av.applet.openJalviewHelpUrl();
2954   }
2955
2956   protected void about_actionPerformed()
2957   {
2958
2959     class AboutPanel extends Canvas
2960     {
2961       String version;
2962
2963       String builddate;
2964
2965       public AboutPanel(String version, String builddate)
2966       {
2967         this.version = version;
2968         this.builddate = builddate;
2969       }
2970
2971       @Override
2972       public void paint(Graphics g)
2973       {
2974         g.setColor(Color.white);
2975         g.fillRect(0, 0, getSize().width, getSize().height);
2976         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2977         FontMetrics fm = g.getFontMetrics();
2978         int fh = fm.getHeight();
2979         int y = 5, x = 7;
2980         g.setColor(Color.black);
2981         // TODO: update this text for each release or centrally store it for
2982         // lite and application
2983         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2984         g.drawString(MessageManager.formatMessage(
2985                 "label.jalviewLite_release", new String[] { version }), x,
2986                 y += fh);
2987         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2988         g.drawString(MessageManager.formatMessage(
2989                 "label.jaview_build_date", new String[] { builddate }), x,
2990                 y += fh);
2991         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2992         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2993                 x, y += fh * 1.5);
2994         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2995                 x + 50, y += fh + 8);
2996         g.drawString(
2997                 MessageManager.getString("label.jalview_dev_managers"), x,
2998                 y += fh);
2999         g.drawString(MessageManager
3000                 .getString("label.jalview_distribution_lists"), x, y += fh);
3001         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3002                 x, y += fh + 8);
3003         g.drawString(
3004                 MessageManager.getString("label.jalview_cite_1_authors"),
3005                 x, y += fh);
3006         g.drawString(
3007                 MessageManager.getString("label.jalview_cite_1_title"), x,
3008                 y += fh);
3009         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3010                 x, y += fh);
3011       }
3012     }
3013
3014     Frame frame = new Frame();
3015     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3016             .getBuildDate()));
3017     jalview.bin.JalviewLite.addFrame(frame,
3018             MessageManager.getString("label.jalview"), 580, 220);
3019
3020   }
3021
3022   public void showURL(String url, String target)
3023   {
3024     if (viewport.applet == null)
3025     {
3026       System.out.println("Not running as applet - no browser available.");
3027     }
3028     else
3029     {
3030       viewport.applet.showURL(url, target);
3031     }
3032   }
3033
3034   // ////////////////////////////////////////////////////////////////////////////////
3035   // JBuilder Graphics here
3036
3037   MenuBar alignFrameMenuBar = new MenuBar();
3038
3039   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3040
3041   MenuItem loadApplication = new MenuItem(
3042           MessageManager.getString("label.view_full_application"));
3043
3044   MenuItem loadTree = new MenuItem(
3045           MessageManager.getString("label.load_associated_tree"));
3046
3047   MenuItem loadAnnotations = new MenuItem(
3048           MessageManager.getString("label.load_features_annotations"));
3049
3050   MenuItem outputFeatures = new MenuItem(
3051           MessageManager.getString("label.export_features"));
3052
3053   MenuItem outputAnnotations = new MenuItem(
3054           MessageManager.getString("label.export_annotations"));
3055
3056   MenuItem closeMenuItem = new MenuItem(
3057           MessageManager.getString("action.close"));
3058
3059   MenuItem selectAllSequenceMenuItem = new MenuItem(
3060           MessageManager.getString("action.select_all"));
3061
3062   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3063           MessageManager.getString("action.deselect_all"));
3064
3065   MenuItem invertSequenceMenuItem = new MenuItem(
3066           MessageManager.getString("action.invert_selection"));
3067
3068   MenuItem remove2LeftMenuItem = new MenuItem();
3069
3070   MenuItem remove2RightMenuItem = new MenuItem();
3071
3072   MenuItem removeGappedColumnMenuItem = new MenuItem();
3073
3074   MenuItem removeAllGapsMenuItem = new MenuItem();
3075
3076   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3077
3078   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3079
3080   MenuItem sortPairwiseMenuItem = new MenuItem();
3081
3082   MenuItem sortIDMenuItem = new MenuItem();
3083
3084   MenuItem sortLengthMenuItem = new MenuItem();
3085
3086   MenuItem sortGroupMenuItem = new MenuItem();
3087
3088   MenuItem removeRedundancyMenuItem = new MenuItem();
3089
3090   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3091
3092   MenuItem PCAMenuItem = new MenuItem();
3093
3094   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3095
3096   MenuItem neighbourTreeMenuItem = new MenuItem();
3097
3098   BorderLayout borderLayout1 = new BorderLayout();
3099
3100   public Label statusBar = new Label();
3101
3102   MenuItem clustalColour = new MenuItem();
3103
3104   MenuItem zappoColour = new MenuItem();
3105
3106   MenuItem taylorColour = new MenuItem();
3107
3108   MenuItem hydrophobicityColour = new MenuItem();
3109
3110   MenuItem helixColour = new MenuItem();
3111
3112   MenuItem strandColour = new MenuItem();
3113
3114   MenuItem turnColour = new MenuItem();
3115
3116   MenuItem buriedColour = new MenuItem();
3117
3118   MenuItem purinePyrimidineColour = new MenuItem();
3119
3120   // MenuItem RNAInteractionColour = new MenuItem();
3121
3122   MenuItem RNAHelixColour = new MenuItem();
3123
3124   MenuItem userDefinedColour = new MenuItem();
3125
3126   MenuItem PIDColour = new MenuItem();
3127
3128   MenuItem BLOSUM62Colour = new MenuItem();
3129
3130   MenuItem tcoffeeColour = new MenuItem();
3131
3132   MenuItem njTreeBlosumMenuItem = new MenuItem();
3133
3134   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3135
3136   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3137
3138   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3139
3140   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3141
3142   MenuItem alProperties = new MenuItem(
3143           MessageManager.getString("label.alignment_props"));
3144
3145   MenuItem overviewMenuItem = new MenuItem();
3146
3147   MenuItem undoMenuItem = new MenuItem();
3148
3149   MenuItem redoMenuItem = new MenuItem();
3150
3151   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3152
3153   MenuItem noColourmenuItem = new MenuItem();
3154
3155   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3156
3157   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3158
3159   MenuItem findMenuItem = new MenuItem();
3160
3161   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3162
3163   MenuItem nucleotideColour = new MenuItem();
3164
3165   MenuItem deleteGroups = new MenuItem();
3166
3167   MenuItem grpsFromSelection = new MenuItem();
3168
3169   MenuItem createGroup = new MenuItem();
3170
3171   MenuItem unGroup = new MenuItem();
3172
3173   MenuItem delete = new MenuItem();
3174
3175   MenuItem copy = new MenuItem();
3176
3177   MenuItem cut = new MenuItem();
3178
3179   Menu pasteMenu = new Menu();
3180
3181   MenuItem pasteNew = new MenuItem();
3182
3183   MenuItem pasteThis = new MenuItem();
3184
3185   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3186
3187   MenuItem font = new MenuItem();
3188
3189   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3190
3191   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3192
3193   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3194
3195   MenuItem modifyPID = new MenuItem();
3196
3197   MenuItem modifyConservation = new MenuItem();
3198
3199   CheckboxMenuItem autoCalculate = null;
3200
3201   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3202           "Sort Alignment With New Tree", true);
3203
3204   Menu sortByTreeMenu = new Menu();
3205
3206   MenuItem inputText = new MenuItem();
3207
3208   MenuItem documentation = new MenuItem();
3209
3210   MenuItem about = new MenuItem();
3211
3212   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3213
3214   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3215
3216   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3217
3218   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3219
3220   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3221
3222   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3223
3224   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3225
3226   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3227
3228   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3229
3230   /**
3231    * Initialise menus and other items
3232    *
3233    * @throws Exception
3234    */
3235   private void jbInit() throws Exception
3236   {
3237     setMenuBar(alignFrameMenuBar);
3238
3239     /*
3240      * Configure File menu items and actions
3241      */
3242     inputText
3243             .setLabel(MessageManager.getString("label.input_from_textbox"));
3244     inputText.addActionListener(this);
3245     Menu outputTextboxMenu = new Menu(
3246             MessageManager.getString("label.out_to_textbox"));
3247     for (String ff : FileFormat.getWritableFormats(true))
3248     {
3249       MenuItem item = new MenuItem(ff);
3250
3251       item.addActionListener(new java.awt.event.ActionListener()
3252       {
3253         @Override
3254         public void actionPerformed(ActionEvent e)
3255         {
3256           outputText_actionPerformed(e);
3257         }
3258       });
3259
3260       outputTextboxMenu.add(item);
3261     }
3262     closeMenuItem.addActionListener(this);
3263     loadApplication.addActionListener(this);
3264     loadTree.addActionListener(this);
3265     loadAnnotations.addActionListener(this);
3266     outputFeatures.addActionListener(this);
3267     outputAnnotations.addActionListener(this);
3268
3269     /*
3270      * Configure Edit menu items and actions
3271      */
3272     undoMenuItem.setEnabled(false);
3273     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3274     undoMenuItem.addActionListener(this);
3275     redoMenuItem.setEnabled(false);
3276     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3277     redoMenuItem.addActionListener(this);
3278     copy.setLabel(MessageManager.getString("action.copy"));
3279     copy.addActionListener(this);
3280     cut.setLabel(MessageManager.getString("action.cut"));
3281     cut.addActionListener(this);
3282     delete.setLabel(MessageManager.getString("action.delete"));
3283     delete.addActionListener(this);
3284     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3285     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3286     pasteNew.addActionListener(this);
3287     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3288     pasteThis.addActionListener(this);
3289     remove2LeftMenuItem.setLabel(MessageManager
3290             .getString("action.remove_left"));
3291     remove2LeftMenuItem.addActionListener(this);
3292     remove2RightMenuItem.setLabel(MessageManager
3293             .getString("action.remove_right"));
3294     remove2RightMenuItem.addActionListener(this);
3295     removeGappedColumnMenuItem.setLabel(MessageManager
3296             .getString("action.remove_empty_columns"));
3297     removeGappedColumnMenuItem.addActionListener(this);
3298     removeAllGapsMenuItem.setLabel(MessageManager
3299             .getString("action.remove_all_gaps"));
3300     removeAllGapsMenuItem.addActionListener(this);
3301     removeRedundancyMenuItem.setLabel(MessageManager
3302             .getString("action.remove_redundancy"));
3303     removeRedundancyMenuItem.addActionListener(this);
3304
3305     /*
3306      * Configure Select menu items and actions
3307      */
3308     findMenuItem.setLabel(MessageManager.getString("action.find"));
3309     findMenuItem.addActionListener(this);
3310     selectAllSequenceMenuItem.addActionListener(this);
3311     deselectAllSequenceMenuItem.addActionListener(this);
3312     invertSequenceMenuItem.setLabel(MessageManager
3313             .getString("action.invert_sequence_selection"));
3314     invertSequenceMenuItem.addActionListener(this);
3315     invertColSel.setLabel(MessageManager
3316             .getString("action.invert_column_selection"));
3317     invertColSel.addActionListener(this);
3318     deleteGroups.setLabel(MessageManager
3319             .getString("action.undefine_groups"));
3320     deleteGroups.addActionListener(this);
3321     grpsFromSelection.setLabel(MessageManager
3322             .getString("action.make_groups_selection"));
3323     grpsFromSelection.addActionListener(this);
3324     createGroup.setLabel(MessageManager.getString("action.create_group"));
3325     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3326     annotationColumnSelection.setLabel(MessageManager
3327             .getString("action.select_by_annotation"));
3328     annotationColumnSelection.addActionListener(this);
3329
3330     /*
3331      * Configure View menu items and actions
3332      */
3333     newView.setLabel(MessageManager.getString("action.new_view"));
3334     newView.addActionListener(this);
3335     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3336     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3337     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3338     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3339     hideColumns
3340             .setLabel(MessageManager.getString("label.selected_columns"));
3341     hideSequences.setLabel(MessageManager
3342             .getString("label.selected_sequences"));
3343     hideAllButSelection.setLabel(MessageManager
3344             .getString("label.all_but_selected_region"));
3345     hideAllSelection.setLabel(MessageManager
3346             .getString("label.selected_region"));
3347     showAllHidden.setLabel(MessageManager
3348             .getString("label.all_sequences_columns"));
3349     showColumns.addActionListener(this);
3350     showSeqs.addActionListener(this);
3351     hideColumns.addActionListener(this);
3352     hideSequences.addActionListener(this);
3353     hideAllButSelection.addActionListener(this);
3354     hideAllSelection.addActionListener(this);
3355     showAllHidden.addActionListener(this);
3356     featureSettings.setLabel(MessageManager
3357             .getString("action.feature_settings"));
3358     featureSettings.addActionListener(this);
3359     sequenceFeatures.setLabel(MessageManager
3360             .getString("label.show_sequence_features"));
3361     sequenceFeatures.addItemListener(this);
3362     sequenceFeatures.setState(false);
3363     followMouseOverFlag.setLabel(MessageManager
3364             .getString("label.automatic_scrolling"));
3365     followMouseOverFlag.addItemListener(this);
3366     alProperties.addActionListener(this);
3367     overviewMenuItem.setLabel(MessageManager
3368             .getString("label.overview_window"));
3369     overviewMenuItem.addActionListener(this);
3370
3371     /*
3372      * Configure Annotations menu items and actions
3373      */
3374     annotationPanelMenuItem.setLabel(MessageManager
3375             .getString("label.show_annotations"));
3376     annotationPanelMenuItem.addItemListener(this);
3377     showGroupConsensus.setLabel(MessageManager
3378             .getString("label.group_consensus"));
3379     showGroupConservation.setLabel(MessageManager
3380             .getString("label.group_conservation"));
3381     showConsensusHistogram.setLabel(MessageManager
3382             .getString("label.show_consensus_histogram"));
3383     showSequenceLogo.setLabel(MessageManager
3384             .getString("label.show_consensus_logo"));
3385     normSequenceLogo.setLabel(MessageManager
3386             .getString("label.norm_consensus_logo"));
3387     applyAutoAnnotationSettings.setLabel(MessageManager
3388             .getString("label.apply_all_groups"));
3389     applyAutoAnnotationSettings.setState(true);
3390     Menu autoAnnMenu = new Menu(
3391             MessageManager.getString("label.autocalculated_annotation"));
3392     showGroupConsensus.addItemListener(this);
3393     showGroupConservation.addItemListener(this);
3394     showConsensusHistogram.addItemListener(this);
3395     showSequenceLogo.addItemListener(this);
3396     normSequenceLogo.addItemListener(this);
3397     applyAutoAnnotationSettings.addItemListener(this);
3398     showAlignmentAnnotations = new CheckboxMenuItem(
3399             MessageManager.getString("label.show_all_al_annotations"));
3400     showSequenceAnnotations = new CheckboxMenuItem(
3401             MessageManager.getString("label.show_all_seq_annotations"));
3402     sortAnnBySequence = new CheckboxMenuItem(
3403             MessageManager.getString("label.sort_annotations_by_sequence"));
3404     sortAnnByLabel = new CheckboxMenuItem(
3405             MessageManager.getString("label.sort_annotations_by_label"));
3406     showAutoFirst = new CheckboxMenuItem(
3407             MessageManager.getString("label.show_first"));
3408     showAutoFirst.setState(false); // pending applet parameter
3409     setShowAutoCalculatedAbove(showAutoFirst.getState());
3410     showAutoLast = new CheckboxMenuItem(
3411             MessageManager.getString("label.show_last"));
3412     showAutoLast.setState(!showAutoFirst.getState());
3413     showAlignmentAnnotations.addItemListener(this);
3414     showSequenceAnnotations.addItemListener(this);
3415     sortAnnBySequence.addItemListener(this);
3416     sortAnnByLabel.addItemListener(this);
3417     showAutoFirst.addItemListener(this);
3418     showAutoLast.addItemListener(this);
3419
3420     /*
3421      * Configure Format menu items and actions
3422      */
3423     font.setLabel(MessageManager.getString("action.font"));
3424     font.addActionListener(this);
3425     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3426     scaleAbove.setState(true);
3427     scaleAbove.setEnabled(false);
3428     scaleAbove.addItemListener(this);
3429     scaleLeft.setEnabled(false);
3430     scaleLeft.setState(true);
3431     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3432     scaleLeft.addItemListener(this);
3433     scaleRight.setEnabled(false);
3434     scaleRight.setState(true);
3435     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3436     scaleRight.addItemListener(this);
3437     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3438     viewBoxesMenuItem.setState(true);
3439     viewBoxesMenuItem.addItemListener(this);
3440     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3441     viewTextMenuItem.setState(true);
3442     viewTextMenuItem.addItemListener(this);
3443     colourTextMenuItem.setLabel(MessageManager
3444             .getString("label.colour_text"));
3445     colourTextMenuItem.addItemListener(this);
3446     displayNonconservedMenuItem.setLabel(MessageManager
3447             .getString("label.show_non_conserved"));
3448     displayNonconservedMenuItem.addItemListener(this);
3449     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3450     wrapMenuItem.addItemListener(this);
3451     renderGapsMenuItem.setLabel(MessageManager
3452             .getString("action.show_gaps"));
3453     renderGapsMenuItem.setState(true);
3454     renderGapsMenuItem.addItemListener(this);
3455     centreColumnLabelFlag.setLabel(MessageManager
3456             .getString("label.centre_column_labels"));
3457     centreColumnLabelFlag.addItemListener(this);
3458     seqLimits.setState(true);
3459     seqLimits.setLabel(MessageManager
3460             .getString("label.show_sequence_limits"));
3461     seqLimits.addItemListener(this);
3462
3463     /*
3464      * Configure Colour menu items and actions
3465      */
3466     applyToAllGroups.setLabel(MessageManager
3467             .getString("label.apply_colour_to_all_groups"));
3468     applyToAllGroups.setState(true);
3469     applyToAllGroups.addItemListener(this);
3470     clustalColour.setLabel(MessageManager
3471             .getString("label.colourScheme_clustal"));
3472     clustalColour.addActionListener(this);
3473     zappoColour.setLabel(MessageManager
3474             .getString("label.colourScheme_zappo"));
3475     zappoColour.addActionListener(this);
3476     taylorColour.setLabel(MessageManager
3477             .getString("label.colourScheme_taylor"));
3478     taylorColour.addActionListener(this);
3479     hydrophobicityColour.setLabel(MessageManager
3480             .getString("label.colourScheme_hydrophobic"));
3481     hydrophobicityColour.addActionListener(this);
3482     helixColour.setLabel(MessageManager
3483             .getString("label.colourScheme_helix_propensity"));
3484     helixColour.addActionListener(this);
3485     strandColour.setLabel(MessageManager
3486             .getString("label.colourScheme_strand_propensity"));
3487     strandColour.addActionListener(this);
3488     turnColour.setLabel(MessageManager
3489             .getString("label.colourScheme_turn_propensity"));
3490     turnColour.addActionListener(this);
3491     buriedColour.setLabel(MessageManager
3492             .getString("label.colourScheme_buried_index"));
3493     buriedColour.addActionListener(this);
3494     purinePyrimidineColour.setLabel(MessageManager
3495             .getString("label.colourScheme_purine/pyrimidine"));
3496     purinePyrimidineColour.addActionListener(this);
3497     // RNAInteractionColour.setLabel(MessageManager
3498     // .getString("label.rna_interaction"));
3499     // RNAInteractionColour.addActionListener(this);
3500     RNAHelixColour.setLabel(MessageManager
3501             .getString("label.colourScheme_rna_helices"));
3502     RNAHelixColour.addActionListener(this);
3503     userDefinedColour.setLabel(MessageManager
3504             .getString("action.user_defined"));
3505     userDefinedColour.addActionListener(this);
3506     PIDColour.setLabel(MessageManager
3507             .getString("label.colourScheme_%_identity"));
3508     PIDColour.addActionListener(this);
3509     BLOSUM62Colour.setLabel(MessageManager
3510             .getString("label.colourScheme_blosum62"));
3511     BLOSUM62Colour.addActionListener(this);
3512     tcoffeeColour.setLabel(MessageManager
3513             .getString("label.colourScheme_t-coffee_scores"));
3514     // it will be enabled only if a score file is provided
3515     tcoffeeColour.setEnabled(false);
3516     tcoffeeColour.addActionListener(this);
3517     conservationMenuItem.setLabel(MessageManager
3518             .getString("action.by_conservation"));
3519     conservationMenuItem.addItemListener(this);
3520     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3521     noColourmenuItem.addActionListener(this);
3522     abovePIDThreshold.setLabel(MessageManager
3523             .getString("label.above_identity_threshold"));
3524     abovePIDThreshold.addItemListener(this);
3525     nucleotideColour.setLabel(MessageManager
3526             .getString("label.colourScheme_nucleotide"));
3527     nucleotideColour.addActionListener(this);
3528     modifyPID.setLabel(MessageManager
3529             .getString("label.modify_identity_threshold"));
3530     modifyPID.addActionListener(this);
3531     modifyConservation.setLabel(MessageManager
3532             .getString("label.modify_conservation_threshold"));
3533     modifyConservation.addActionListener(this);
3534     annotationColour.setLabel(MessageManager
3535             .getString("action.by_annotation"));
3536     annotationColour.addActionListener(this);
3537
3538     /*
3539      * Configure Calculate menu items and actions
3540      */
3541     sortPairwiseMenuItem.setLabel(MessageManager
3542             .getString("action.by_pairwise_id"));
3543     sortPairwiseMenuItem.addActionListener(this);
3544     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3545     sortIDMenuItem.addActionListener(this);
3546     sortLengthMenuItem.setLabel(MessageManager
3547             .getString("action.by_length"));
3548     sortLengthMenuItem.addActionListener(this);
3549     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3550     sortGroupMenuItem.addActionListener(this);
3551     pairwiseAlignmentMenuItem.setLabel(MessageManager
3552             .getString("action.pairwise_alignment"));
3553     pairwiseAlignmentMenuItem.addActionListener(this);
3554     PCAMenuItem.setLabel(MessageManager
3555             .getString("label.principal_component_analysis"));
3556     PCAMenuItem.addActionListener(this);
3557     autoCalculate = new CheckboxMenuItem(
3558             MessageManager.getString("label.autocalculate_consensus"), true);
3559     averageDistanceTreeMenuItem.setLabel(MessageManager
3560             .getString("label.average_distance_identity"));
3561     averageDistanceTreeMenuItem.addActionListener(this);
3562     neighbourTreeMenuItem.setLabel(MessageManager
3563             .getString("label.neighbour_joining_identity"));
3564     neighbourTreeMenuItem.addActionListener(this);
3565     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3566             .getString("label.average_distance_blosum62"));
3567     avDistanceTreeBlosumMenuItem.addActionListener(this);
3568     njTreeBlosumMenuItem.setLabel(MessageManager
3569             .getString("label.neighbour_blosum62"));
3570     njTreeBlosumMenuItem.addActionListener(this);
3571     sortByTreeMenu.setLabel(MessageManager
3572             .getString("action.by_tree_order"));
3573     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3574     Menu calculateTreeMenu = new Menu(
3575             MessageManager.getString("action.calculate_tree"));
3576     autoCalculate.addItemListener(this);
3577     sortByTree.addItemListener(this);
3578
3579     /*
3580      * Configure Help menu items and actions
3581      */
3582     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3583     documentation.setLabel(MessageManager.getString("label.documentation"));
3584     documentation.addActionListener(this);
3585     about.setLabel(MessageManager.getString("label.about"));
3586     about.addActionListener(this);
3587
3588     /*
3589      * Add top level menus to frame
3590      */
3591     alignFrameMenuBar.add(fileMenu);
3592     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3593     alignFrameMenuBar.add(editMenu);
3594     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3595     alignFrameMenuBar.add(selectMenu);
3596     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3597     alignFrameMenuBar.add(viewMenu);
3598     Menu annotationsMenu = new Menu(
3599             MessageManager.getString("action.annotations"));
3600     alignFrameMenuBar.add(annotationsMenu);
3601     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3602     alignFrameMenuBar.add(formatMenu);
3603     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3604     alignFrameMenuBar.add(colourMenu);
3605     Menu calculateMenu = new Menu(
3606             MessageManager.getString("action.calculate"));
3607     alignFrameMenuBar.add(calculateMenu);
3608     alignFrameMenuBar.add(helpMenu);
3609
3610     /*
3611      * File menu
3612      */
3613     fileMenu.add(inputText);
3614     fileMenu.add(loadTree);
3615     fileMenu.add(loadAnnotations);
3616     fileMenu.addSeparator();
3617     fileMenu.add(outputTextboxMenu);
3618     fileMenu.add(outputFeatures);
3619     fileMenu.add(outputAnnotations);
3620     if (jalviewServletURL != null)
3621     {
3622       fileMenu.add(loadApplication);
3623     }
3624     fileMenu.addSeparator();
3625     fileMenu.add(closeMenuItem);
3626
3627     /*
3628      * Edit menu
3629      */
3630     editMenu.add(undoMenuItem);
3631     editMenu.add(redoMenuItem);
3632     editMenu.add(cut);
3633     editMenu.add(copy);
3634     pasteMenu.add(pasteNew);
3635     pasteMenu.add(pasteThis);
3636     editMenu.add(pasteMenu);
3637     editMenu.add(delete);
3638     editMenu.addSeparator();
3639     editMenu.add(remove2LeftMenuItem);
3640     editMenu.add(remove2RightMenuItem);
3641     editMenu.add(removeGappedColumnMenuItem);
3642     editMenu.add(removeAllGapsMenuItem);
3643     editMenu.add(removeRedundancyMenuItem);
3644
3645     /*
3646      * Select menu
3647      */
3648     selectMenu.add(findMenuItem);
3649     selectMenu.addSeparator();
3650     selectMenu.add(selectAllSequenceMenuItem);
3651     selectMenu.add(deselectAllSequenceMenuItem);
3652     selectMenu.add(invertSequenceMenuItem);
3653     selectMenu.add(invertColSel);
3654     selectMenu.add(createGroup);
3655     selectMenu.add(unGroup);
3656     selectMenu.add(grpsFromSelection);
3657     selectMenu.add(deleteGroups);
3658     selectMenu.add(annotationColumnSelection);
3659
3660     /*
3661      * View menu
3662      */
3663     viewMenu.add(newView);
3664     viewMenu.addSeparator();
3665     showMenu.add(showColumns);
3666     showMenu.add(showSeqs);
3667     showMenu.add(showAllHidden);
3668     viewMenu.add(showMenu);
3669     hideMenu.add(hideColumns);
3670     hideMenu.add(hideSequences);
3671     hideMenu.add(hideAllSelection);
3672     hideMenu.add(hideAllButSelection);
3673     viewMenu.add(hideMenu);
3674     viewMenu.addSeparator();
3675     viewMenu.add(followMouseOverFlag);
3676     viewMenu.addSeparator();
3677     viewMenu.add(sequenceFeatures);
3678     viewMenu.add(featureSettings);
3679     viewMenu.addSeparator();
3680     viewMenu.add(alProperties);
3681     viewMenu.addSeparator();
3682     viewMenu.add(overviewMenuItem);
3683
3684     /*
3685      * Annotations menu
3686      */
3687     annotationsMenu.add(annotationPanelMenuItem);
3688     annotationsMenu.addSeparator();
3689     annotationsMenu.add(showAlignmentAnnotations);
3690     annotationsMenu.add(showSequenceAnnotations);
3691     annotationsMenu.add(sortAnnBySequence);
3692     annotationsMenu.add(sortAnnByLabel);
3693     annotationsMenu.addSeparator();
3694     autoAnnMenu.add(showAutoFirst);
3695     autoAnnMenu.add(showAutoLast);
3696     autoAnnMenu.addSeparator();
3697     autoAnnMenu.add(applyAutoAnnotationSettings);
3698     autoAnnMenu.add(showConsensusHistogram);
3699     autoAnnMenu.add(showSequenceLogo);
3700     autoAnnMenu.add(normSequenceLogo);
3701     autoAnnMenu.addSeparator();
3702     autoAnnMenu.add(showGroupConservation);
3703     autoAnnMenu.add(showGroupConsensus);
3704     annotationsMenu.add(autoAnnMenu);
3705
3706     /*
3707      * Format menu
3708      */
3709     formatMenu.add(font);
3710     formatMenu.add(seqLimits);
3711     formatMenu.add(wrapMenuItem);
3712     formatMenu.add(scaleAbove);
3713     formatMenu.add(scaleLeft);
3714     formatMenu.add(scaleRight);
3715     formatMenu.add(viewBoxesMenuItem);
3716     formatMenu.add(viewTextMenuItem);
3717     formatMenu.add(colourTextMenuItem);
3718     formatMenu.add(displayNonconservedMenuItem);
3719     formatMenu.add(renderGapsMenuItem);
3720     formatMenu.add(centreColumnLabelFlag);
3721
3722     /*
3723      * Colour menu
3724      */
3725     colourMenu.add(applyToAllGroups);
3726     colourMenu.addSeparator();
3727     colourMenu.add(noColourmenuItem);
3728     colourMenu.add(clustalColour);
3729     colourMenu.add(BLOSUM62Colour);
3730     colourMenu.add(PIDColour);
3731     colourMenu.add(zappoColour);
3732     colourMenu.add(taylorColour);
3733     colourMenu.add(hydrophobicityColour);
3734     colourMenu.add(helixColour);
3735     colourMenu.add(strandColour);
3736     colourMenu.add(turnColour);
3737     colourMenu.add(buriedColour);
3738     colourMenu.add(nucleotideColour);
3739     colourMenu.add(purinePyrimidineColour);
3740     // colourMenu.add(RNAInteractionColour);
3741     colourMenu.add(tcoffeeColour);
3742     colourMenu.add(userDefinedColour);
3743     colourMenu.addSeparator();
3744     colourMenu.add(conservationMenuItem);
3745     colourMenu.add(modifyConservation);
3746     colourMenu.add(abovePIDThreshold);
3747     colourMenu.add(modifyPID);
3748     colourMenu.add(annotationColour);
3749     colourMenu.add(RNAHelixColour);
3750
3751     /*
3752      * Calculate menu
3753      */
3754     sortMenu.add(sortIDMenuItem);
3755     sortMenu.add(sortLengthMenuItem);
3756     sortMenu.add(sortByTreeMenu);
3757     sortMenu.add(sortGroupMenuItem);
3758     sortMenu.add(sortPairwiseMenuItem);
3759     calculateMenu.add(sortMenu);
3760     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3761     calculateTreeMenu.add(neighbourTreeMenuItem);
3762     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3763     calculateTreeMenu.add(njTreeBlosumMenuItem);
3764     calculateMenu.add(calculateTreeMenu);
3765     calculateMenu.addSeparator();
3766     calculateMenu.add(pairwiseAlignmentMenuItem);
3767     calculateMenu.add(PCAMenuItem);
3768     calculateMenu.add(autoCalculate);
3769     calculateMenu.add(sortByTree);
3770
3771     /*
3772      * Help menu
3773      */
3774     helpMenu.add(documentation);
3775     helpMenu.add(about);
3776
3777     /*
3778      * Status bar
3779      */
3780     statusBar.setBackground(Color.white);
3781     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3782     statusBar.setText(MessageManager.getString("label.status_bar"));
3783     this.add(statusBar, BorderLayout.SOUTH);
3784   }
3785
3786   @Override
3787   public void setStatus(String string)
3788   {
3789     statusBar.setText(string);
3790   };
3791
3792   MenuItem featureSettings = new MenuItem();
3793
3794   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3795
3796   MenuItem annotationColour = new MenuItem();
3797
3798   MenuItem annotationColumnSelection = new MenuItem();
3799
3800   MenuItem invertColSel = new MenuItem();
3801
3802   MenuItem showColumns = new MenuItem();
3803
3804   MenuItem showSeqs = new MenuItem();
3805
3806   MenuItem hideColumns = new MenuItem();
3807
3808   MenuItem hideSequences = new MenuItem();
3809
3810   MenuItem hideAllButSelection = new MenuItem();
3811
3812   MenuItem hideAllSelection = new MenuItem();
3813
3814   MenuItem showAllHidden = new MenuItem();
3815
3816   MenuItem newView = new MenuItem();
3817
3818   private CheckboxMenuItem showAlignmentAnnotations;
3819
3820   private CheckboxMenuItem showSequenceAnnotations;
3821
3822   private CheckboxMenuItem sortAnnBySequence;
3823
3824   private CheckboxMenuItem sortAnnByLabel;
3825
3826   private CheckboxMenuItem showAutoFirst;
3827
3828   private CheckboxMenuItem showAutoLast;
3829
3830   private SplitFrame splitFrame;
3831
3832   /**
3833    * Attach the alignFrame panels after embedding menus, if necessary. This used
3834    * to be called setEmbedded, but is now creates the dropdown menus in a
3835    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3836    *
3837    * @param reallyEmbedded
3838    *          true to attach the view to the applet area on the page rather than
3839    *          in a new window
3840    */
3841   public void createAlignFrameWindow(boolean reallyEmbedded)
3842   {
3843     if (reallyEmbedded)
3844     {
3845       embedAlignFrameInApplet(viewport.applet);
3846     }
3847     else
3848     {
3849       // //////
3850       // test and embed menu bar if necessary.
3851       //
3852       if (embedMenuIfNeeded(alignPanel))
3853       {
3854         /*
3855          * adjust for status bar height too. ? pointless as overridden by layout
3856          * manager
3857          */
3858         alignPanel.setSize(getSize().width,
3859                 getSize().height - statusBar.getHeight());
3860       }
3861       add(statusBar, BorderLayout.SOUTH);
3862       add(alignPanel, BorderLayout.CENTER);
3863       // and register with the applet so it can pass external API calls to us
3864       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3865               frameHeight);
3866     }
3867   }
3868
3869   /**
3870    * Add the components of this AlignFrame to the applet container.
3871    *
3872    * @param theApplet
3873    */
3874   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3875   {
3876     // ////
3877     // Explicitly build the embedded menu panel for the on-page applet
3878     //
3879     // view cannot be closed if its actually on the page
3880     fileMenu.remove(closeMenuItem);
3881     fileMenu.remove(3); // Remove Separator
3882     // construct embedded menu, using default font
3883     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3884     // and actually add the components to the applet area
3885     theApplet.setLayout(new BorderLayout());
3886     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3887     theApplet.add(statusBar, BorderLayout.SOUTH);
3888     // TODO should size be left to the layout manager?
3889     alignPanel.setSize(theApplet.getSize().width,
3890             theApplet.getSize().height - embeddedMenu.getHeight()
3891                     - statusBar.getHeight());
3892     theApplet.add(alignPanel, BorderLayout.CENTER);
3893     final AlignFrame me = this;
3894     theApplet.addFocusListener(new FocusListener()
3895     {
3896
3897       @Override
3898       public void focusLost(FocusEvent e)
3899       {
3900         if (theApplet.currentAlignFrame == me)
3901         {
3902           theApplet.currentAlignFrame = null;
3903         }
3904       }
3905
3906       @Override
3907       public void focusGained(FocusEvent e)
3908       {
3909         theApplet.currentAlignFrame = me;
3910       }
3911     });
3912     theApplet.validate();
3913   }
3914
3915   /**
3916    * create a new binding between structures in an existing jmol viewer instance
3917    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3918    * this does not open a new Jmol window, or modify the display of the
3919    * structures in the original jmol window. Note This method doesn't work
3920    * without an additional javascript library to exchange messages between the
3921    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3922    *
3923    * @param viewer
3924    *          JmolViewer instance
3925    * @param sequenceIds
3926    *          - sequence Ids to search for associations
3927    */
3928   public SequenceStructureBinding addStructureViewInstance(
3929           Object jmolviewer, String[] sequenceIds)
3930   {
3931     Viewer viewer = null;
3932     try
3933     {
3934       viewer = (Viewer) jmolviewer;
3935     } catch (ClassCastException ex)
3936     {
3937       System.err.println("Unsupported viewer object :"
3938               + jmolviewer.getClass());
3939     }
3940     if (viewer == null)
3941     {
3942       System.err.println("Can't use this object as a structure viewer:"
3943               + jmolviewer.getClass());
3944       return null;
3945     }
3946     SequenceI[] seqs = null;
3947     if (sequenceIds == null || sequenceIds.length == 0)
3948     {
3949       seqs = viewport.getAlignment().getSequencesArray();
3950     }
3951     else
3952     {
3953       Vector sqi = new Vector();
3954       AlignmentI al = viewport.getAlignment();
3955       for (int sid = 0; sid < sequenceIds.length; sid++)
3956       {
3957         SequenceI sq = al.findName(sequenceIds[sid]);
3958         if (sq != null)
3959         {
3960           sqi.addElement(sq);
3961         }
3962       }
3963       if (sqi.size() > 0)
3964       {
3965         seqs = new SequenceI[sqi.size()];
3966         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3967         {
3968           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3969         }
3970       }
3971       else
3972       {
3973         return null;
3974       }
3975     }
3976     AAStructureBindingModel jmv = null;
3977     // TODO: search for a jmv that involves viewer
3978     if (jmv == null)
3979     { // create a new viewer/jalview binding.
3980       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3981     }
3982     return jmv;
3983
3984   }
3985
3986   /**
3987    * bind a pdb file to a sequence in the current view
3988    *
3989    * @param sequenceId
3990    *          - sequenceId within the dataset.
3991    * @param pdbEntryString
3992    *          - the short name for the PDB file
3993    * @param pdbFile
3994    *          - pdb file - either a URL or a valid PDB file.
3995    * @return true if binding was as success TODO: consider making an exception
3996    *         structure for indicating when PDB parsing or sequenceId location
3997    *         fails.
3998    */
3999   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4000           String pdbFile)
4001   {
4002     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4003     boolean needtoadd = false;
4004     if (toaddpdb != null)
4005     {
4006       Vector pdbe = toaddpdb.getAllPDBEntries();
4007       PDBEntry pdbentry = null;
4008       if (pdbe != null && pdbe.size() > 0)
4009       {
4010         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4011         {
4012           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4013           if (!pdbentry.getId().equals(pdbEntryString)
4014                   && !pdbentry.getFile().equals(pdbFile))
4015           {
4016             pdbentry = null;
4017           }
4018           else
4019           {
4020             continue;
4021           }
4022         }
4023       }
4024       if (pdbentry == null)
4025       {
4026         pdbentry = new PDBEntry();
4027         pdbentry.setId(pdbEntryString);
4028         pdbentry.setFile(pdbFile);
4029         needtoadd = true; // add this new entry to sequence.
4030       }
4031       // resolve data source
4032       // TODO: this code should be a refactored to an io package
4033       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4034               pdbFile, FileFormat.PDB);
4035       if (protocol == null)
4036       {
4037         return false;
4038       }
4039       if (needtoadd)
4040       {
4041         pdbentry.setProperty("protocol", protocol);
4042         toaddpdb.addPDBId(pdbentry);
4043         alignPanel.getStructureSelectionManager()
4044                 .registerPDBEntry(pdbentry);
4045       }
4046     }
4047     return true;
4048   }
4049
4050   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4051   {
4052     if (seqs != null)
4053     {
4054       Vector sequences = new Vector();
4055       for (int i = 0; i < seqs.length; i++)
4056       {
4057         if (seqs[i] != null)
4058         {
4059           sequences.addElement(new Object[] { seqs[i],
4060               (chains != null) ? chains[i] : null });
4061         }
4062       }
4063       seqs = new SequenceI[sequences.size()];
4064       chains = new String[sequences.size()];
4065       for (int i = 0, isize = sequences.size(); i < isize; i++)
4066       {
4067         Object[] oj = (Object[]) sequences.elementAt(i);
4068
4069         seqs[i] = (SequenceI) oj[0];
4070         chains[i] = (String) oj[1];
4071       }
4072     }
4073     return new Object[] { seqs, chains };
4074
4075   }
4076
4077   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4078           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4079   {
4080     // Scrub any null sequences from the array
4081     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4082     seqs = (SequenceI[]) sqch[0];
4083     chains = (String[]) sqch[1];
4084     if (seqs == null || seqs.length == 0)
4085     {
4086       System.err
4087               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4088     }
4089     if (protocol == null)
4090     {
4091       String sourceType = (String) pdb.getProperty("protocol");
4092       try
4093       {
4094         protocol = DataSourceType.valueOf(sourceType);
4095       } catch (IllegalArgumentException e)
4096       {
4097         // ignore
4098       }
4099       if (protocol == null)
4100       {
4101         System.err.println("Couldn't work out protocol to open structure: "
4102                 + pdb.getId());
4103         return;
4104       }
4105     }
4106     if (applet.useXtrnalSviewer)
4107     {
4108       // register the association(s) and quit, don't create any windows.
4109       if (StructureSelectionManager.getStructureSelectionManager(applet)
4110               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4111       {
4112         System.err.println("Failed to map " + pdb.getFile() + " ("
4113                 + protocol + ") to any sequences");
4114       }
4115       return;
4116     }
4117     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4118     {
4119       // can only do alignments with Jmol
4120       // find the last jmol window assigned to this alignment
4121       AppletJmol ajm = null, tajm;
4122       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4123       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4124       {
4125         tajm = (AppletJmol) jmols.elementAt(i);
4126         if (tajm.ap.alignFrame == this)
4127         {
4128           ajm = tajm;
4129           break;
4130         }
4131       }
4132       if (ajm != null)
4133       {
4134         System.err
4135                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4136         // try and add the pdb structure
4137         // ajm.addS
4138         ajm = null;
4139       }
4140     }
4141     // otherwise, create a new window
4142     if (applet.jmolAvailable)
4143     {
4144       new AppletJmol(pdb, seqs, chains, alignPanel,
4145               protocol);
4146       applet.lastFrameX += 40;
4147       applet.lastFrameY += 40;
4148     }
4149     else
4150     {
4151       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4152     }
4153
4154   }
4155
4156   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4157           SequenceI[][] seqs, String[][] chains, String[] protocols)
4158   {
4159     // TODO Auto-generated method stub
4160     System.err.println("Aligned Structure View: Not yet implemented.");
4161   }
4162
4163   /**
4164    * modify the current selection, providing the user has not made a selection
4165    * already.
4166    *
4167    * @param sel
4168    *          - sequences from this alignment
4169    * @param csel
4170    *          - columns to be selected on the alignment
4171    */
4172   public void select(SequenceGroup sel, ColumnSelection csel)
4173   {
4174     alignPanel.seqPanel.selection(sel, csel, null);
4175   }
4176
4177   public void scrollTo(int row, int column)
4178   {
4179     alignPanel.seqPanel.scrollTo(row, column);
4180   }
4181
4182   public void scrollToRow(int row)
4183   {
4184     alignPanel.seqPanel.scrollToRow(row);
4185   }
4186
4187   public void scrollToColumn(int column)
4188   {
4189     alignPanel.seqPanel.scrollToColumn(column);
4190   }
4191
4192   /**
4193    * @return the alignments unique ID.
4194    */
4195   public String getSequenceSetId()
4196   {
4197     return viewport.getSequenceSetId();
4198   }
4199
4200   /**
4201    * Load the (T-Coffee) score file from the specified url
4202    *
4203    * @param source
4204    *          File/URL/T-COFFEE score file contents
4205    * @throws IOException
4206    * @return true if alignment was annotated with data from source
4207    */
4208   public boolean loadScoreFile(String source) throws IOException
4209   {
4210
4211     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4212             AppletFormatAdapter.checkProtocol(source));
4213     if (!file.isValid())
4214     {
4215       // TODO: raise dialog for gui
4216       System.err.println("Problems parsing T-Coffee scores: "
4217               + file.getWarningMessage());
4218       System.err.println("Origin was:\n" + source);
4219       return false;
4220     }
4221
4222     /*
4223      * check that the score matrix matches the alignment dimensions
4224      */
4225     AlignmentI aln;
4226     if ((aln = viewport.getAlignment()) != null
4227             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4228                     .getWidth()))
4229     {
4230       // TODO: raise a dialog box here rather than bomb out.
4231       System.err
4232               .println("The scores matrix does not match the alignment dimensions");
4233
4234     }
4235
4236     // TODO add parameter to indicate if matching should be done
4237     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4238     {
4239       alignPanel.fontChanged();
4240       tcoffeeColour.setEnabled(true);
4241       // switch to this color
4242       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4243       return true;
4244     }
4245     else
4246     {
4247       System.err.println("Problems resolving T-Coffee scores:");
4248       if (file.getWarningMessage() != null)
4249       {
4250         System.err.println(file.getWarningMessage());
4251       }
4252     }
4253     return false;
4254   }
4255
4256   public SplitFrame getSplitFrame()
4257   {
4258     return this.splitFrame;
4259   }
4260
4261   public void setSplitFrame(SplitFrame sf)
4262   {
4263     this.splitFrame = sf;
4264   }
4265
4266   // may not need this
4267   @Override
4268   public void setShowSeqFeatures(boolean b)
4269   {
4270     // showSeqFeatures.setSelected(b);
4271     viewport.setShowSequenceFeatures(b);
4272
4273   }
4274
4275   @Override
4276   public void setMenusForViewport()
4277   {
4278     // setMenusFromViewport(viewport);
4279
4280   }
4281
4282   @Override
4283   public void refreshFeatureUI(boolean enableIfNecessary)
4284   {
4285     if (enableIfNecessary)
4286     {
4287       sequenceFeatures.setState(true);
4288       alignPanel.av.setShowSequenceFeatures(true);
4289     }
4290   }
4291
4292   @Override
4293   public FeatureSettingsControllerI getFeatureSettingsUI()
4294   {
4295     return alignPanel.av.featureSettings;
4296   }
4297
4298 }