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.FileFormatI;
  56 import jalview.io.FileFormats;
  57 import jalview.io.TCoffeeScoreFile;
  58 import jalview.schemes.Blosum62ColourScheme;
  59 import jalview.schemes.BuriedColourScheme;
  60 import jalview.schemes.ClustalxColourScheme;
  61 import jalview.schemes.ColourSchemeI;
  62 import jalview.schemes.HelixColourScheme;
  63 import jalview.schemes.HydrophobicColourScheme;
  64 import jalview.schemes.NucleotideColourScheme;
  65 import jalview.schemes.PIDColourScheme;
  66 import jalview.schemes.PurinePyrimidineColourScheme;
  67 import jalview.schemes.RNAHelicesColourChooser;
  68 import jalview.schemes.StrandColourScheme;
  69 import jalview.schemes.TCoffeeColourScheme;
  70 import jalview.schemes.TaylorColourScheme;
  71 import jalview.schemes.TurnColourScheme;
  72 import jalview.schemes.ZappoColourScheme;
  73 import jalview.structure.StructureSelectionManager;
  74 import jalview.structures.models.AAStructureBindingModel;
  75 import jalview.util.MappingUtils;
  76 import jalview.util.MessageManager;
  77 import jalview.viewmodel.AlignmentViewport;
  78
  79 import java.awt.BorderLayout;
  80 import java.awt.Canvas;
  81 import java.awt.CheckboxMenuItem;
  82 import java.awt.Color;
  83 import java.awt.FlowLayout;
  84 import java.awt.Font;
  85 import java.awt.FontMetrics;
  86 import java.awt.Frame;
  87 import java.awt.Graphics;
  88 import java.awt.Label;
  89 import java.awt.Menu;
  90 import java.awt.MenuBar;
  91 import java.awt.MenuItem;
  92 import java.awt.Panel;
  93 import java.awt.event.ActionEvent;
  94 import java.awt.event.ActionListener;
  95 import java.awt.event.FocusEvent;
  96 import java.awt.event.FocusListener;
  97 import java.awt.event.ItemEvent;
  98 import java.awt.event.ItemListener;
  99 import java.awt.event.KeyEvent;
 100 import java.awt.event.KeyListener;
 101 import java.awt.event.WindowAdapter;
 102 import java.awt.event.WindowEvent;
 103 import java.io.IOException;
 104 import java.net.URL;
 105 import java.net.URLEncoder;
 106 import java.util.Arrays;
 107 import java.util.Deque;
 108 import java.util.HashMap;
 109 import java.util.List;
 110 import java.util.Map;
 111 import java.util.StringTokenizer;
 112 import java.util.Vector;
 113
 114 import org.jmol.viewer.Viewer;
 115
 116 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 117         ItemListener, KeyListener, AlignViewControllerGuiI
 118 {
 119   public AlignViewControllerI avc;
 120
 121   public AlignmentPanel alignPanel;
 122
 123   public AlignViewport viewport;
 124
 125   // width and height may be overridden by applet parameters
 126   int frameWidth = 700;
 127
 128   int frameHeight = 500;
 129
 130   String jalviewServletURL;
 131
 132   /*
 133    * Flag for showing autocalculated consensus above or below other consensus
 134    * rows
 135    */
 136   private boolean showAutoCalculatedAbove;
 137
 138   private SequenceAnnotationOrder annotationSortOrder;
 139
 140   /**
 141    * Constructor that creates the frame and adds it to the display.
 142    *
 143    * @param al
 144    * @param applet
 145    * @param title
 146    * @param embedded
 147    */
 148   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 149           boolean embedded)
 150   {
 151     this(al, applet, title, embedded, true);
 152   }
 153
 154   /**
 155    * Constructor that optionally allows the frame to be displayed or only
 156    * created.
 157    *
 158    * @param al
 159    * @param applet
 160    * @param title
 161    * @param embedded
 162    * @param addToDisplay
 163    */
 164   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 165           boolean embedded, boolean addToDisplay)
 166   {
 167     this(al, null, null, applet, title, embedded, addToDisplay);
 168   }
 169
 170   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 171           ColumnSelection columnSelection, JalviewLite applet,
 172           String title, boolean embedded)
 173   {
 174     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 175   }
 176
 177   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 178           ColumnSelection columnSelection, JalviewLite applet,
 179           String title, boolean embedded, boolean addToDisplay)
 180   {
 181     if (applet != null)
 182     {
 183       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 184     }
 185
 186     try
 187     {
 188       jbInit();
 189     } catch (Exception ex)
 190     {
 191       ex.printStackTrace();
 192     }
 193     // need to get window geometry before we calculate alignment layout
 194     if (applet != null)
 195     {
 196       String param;
 197       try
 198       {
 199         param = applet.getParameter("windowWidth");
 200         if (param != null)
 201         {
 202           int width = Integer.parseInt(param);
 203           frameWidth = width;
 204         }
 205         param = applet.getParameter("windowHeight");
 206         if (param != null)
 207         {
 208           int height = Integer.parseInt(param);
 209           frameHeight = height;
 210         }
 211       } catch (Exception ex)
 212       {
 213       }
 214     }
 215     viewport = new AlignViewport(al, applet);
 216
 217     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 218     {
 219       viewport.hideSequence(hiddenSeqs);
 220     }
 221     if (columnSelection != null)
 222     {
 223       viewport.setColumnSelection(columnSelection);
 224     }
 225     viewport.setScaleAboveWrapped(scaleAbove.getState());
 226
 227     alignPanel = new AlignmentPanel(this, viewport);
 228     avc = new jalview.controller.AlignViewController(this, viewport,
 229             alignPanel);
 230     viewport.updateConservation(alignPanel);
 231     viewport.updateConsensus(alignPanel);
 232
 233     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 234     followMouseOverFlag.setState(viewport.isFollowHighlight());
 235     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 236     showGroupConservation.setState(viewport.isShowGroupConservation());
 237     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 238     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 239     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 240     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 241     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 242     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 243     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 244     showAlignmentAnnotations.setState(true);
 245     showSequenceAnnotations.setState(false);
 246
 247     seqLimits.setState(viewport.getShowJVSuffix());
 248
 249     if (applet != null)
 250     {
 251       String param = applet.getParameter("sortBy");
 252       if (param != null)
 253       {
 254         if (param.equalsIgnoreCase("Id"))
 255         {
 256           sortIDMenuItem_actionPerformed();
 257         }
 258         else if (param.equalsIgnoreCase("Pairwise Identity"))
 259         {
 260           sortPairwiseMenuItem_actionPerformed();
 261         }
 262         else if (param.equalsIgnoreCase("Length"))
 263         {
 264           sortLengthMenuItem_actionPerformed();
 265         }
 266       }
 267
 268       param = applet.getParameter("wrap");
 269       if (param != null)
 270       {
 271         if (param.equalsIgnoreCase("true"))
 272         {
 273           wrapMenuItem.setState(true);
 274           wrapMenuItem_actionPerformed();
 275         }
 276       }
 277       param = applet.getParameter("centrecolumnlabels");
 278       if (param != null)
 279       {
 280         centreColumnLabelFlag.setState(true);
 281         centreColumnLabelFlag_stateChanged();
 282       }
 283
 284     }
 285     if (viewport.getAlignment().isNucleotide())
 286     {
 287       viewport.updateStrucConsensus(alignPanel);
 288       if (viewport.getAlignment().hasRNAStructure())
 289       {
 290         RNAHelixColour.setEnabled(true);
 291       }
 292       else
 293       {
 294         RNAHelixColour.setEnabled(false);
 295       }
 296     }
 297     else
 298     {
 299       RNAHelixColour.setEnabled(false);
 300       purinePyrimidineColour.setEnabled(false);
 301     }
 302     // Some JVMS send keyevents to Top frame or lowest panel,
 303     // Havent worked out why yet. So add to both this frame and seqCanvas for
 304     // now
 305     this.addKeyListener(this);
 306     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 307     alignPanel.idPanel.idCanvas.addKeyListener(this);
 308     alignPanel.scalePanel.addKeyListener(this);
 309     alignPanel.annotationPanel.addKeyListener(this);
 310     alignPanel.annotationPanelHolder.addKeyListener(this);
 311     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 312     alignPanel.alabels.addKeyListener(this);
 313
 314     setAnnotationsVisibility();
 315
 316     if (addToDisplay)
 317     {
 318       addToDisplay(embedded);
 319     }
 320   }
 321
 322   /**
 323    * @param embedded
 324    */
 325   public void addToDisplay(boolean embedded)
 326   {
 327     createAlignFrameWindow(embedded);
 328     validate();
 329     alignPanel.adjustAnnotationHeight();
 330     alignPanel.paintAlignment(true);
 331   }
 332
 333   public AlignViewport getAlignViewport()
 334   {
 335     return viewport;
 336   }
 337
 338   public SeqCanvas getSeqcanvas()
 339   {
 340     return alignPanel.seqPanel.seqCanvas;
 341   }
 342
 343   /**
 344    * Load a features file onto the alignment
 345    *
 346    * @param file
 347    *          file URL, content, or other resolvable path
 348    * @param type
 349    *          is protocol for accessing data referred to by file
 350    */
 351
 352   public boolean parseFeaturesFile(String file, DataSourceType type)
 353   {
 354     return parseFeaturesFile(file, type, true);
 355   }
 356
 357   /**
 358    * Load a features file onto the alignment
 359    *
 360    * @param file
 361    *          file URL, content, or other resolvable path
 362    * @param sourceType
 363    *          is protocol for accessing data referred to by file
 364    * @param autoenabledisplay
 365    *          when true, display features flag will be automatically enabled if
 366    *          features are loaded
 367    * @return true if data parsed as a features file
 368    */
 369   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 370           boolean autoenabledisplay)
 371   {
 372     boolean featuresFile = false;
 373     try
 374     {
 375       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 376               .getFeatureRenderer().getFeatureColours();
 377       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 378               "relaxedidmatch", false);
 379       featuresFile = new FeaturesFile(file, sourceType).parse(
 380               viewport.getAlignment(), colours, true, relaxedIdMatching);
 381     } catch (Exception ex)
 382     {
 383       ex.printStackTrace();
 384     }
 385
 386     if (featuresFile)
 387     {
 388       if (autoenabledisplay)
 389       {
 390         viewport.setShowSequenceFeatures(true);
 391         sequenceFeatures.setState(true);
 392       }
 393       if (alignPanel.seqPanel.seqCanvas.fr != null)
 394       {
 395         // update the min/max ranges where necessary
 396         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 397       }
 398       if (viewport.featureSettings != null)
 399       {
 400         viewport.featureSettings.refreshTable();
 401       }
 402       alignPanel.paintAlignment(true);
 403       statusBar.setText(MessageManager
 404               .getString("label.successfully_added_features_alignment"));
 405     }
 406     return featuresFile;
 407   }
 408
 409   @Override
 410   public void keyPressed(KeyEvent evt)
 411   {
 412     if (viewport.cursorMode
 413             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 414                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 415                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 416             && Character.isDigit(evt.getKeyChar()))
 417     {
 418       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 419     }
 420
 421     switch (evt.getKeyCode())
 422     {
 423     case 27: // escape key
 424       deselectAllSequenceMenuItem_actionPerformed();
 425
 426       alignPanel.alabels.cancelDrag();
 427       break;
 428     case KeyEvent.VK_X:
 429       if (evt.isControlDown() || evt.isMetaDown())
 430       {
 431         cut_actionPerformed();
 432       }
 433       break;
 434     case KeyEvent.VK_C:
 435       if (viewport.cursorMode && !evt.isControlDown())
 436       {
 437         alignPanel.seqPanel.setCursorColumn();
 438       }
 439       if (evt.isControlDown() || evt.isMetaDown())
 440       {
 441         copy_actionPerformed();
 442       }
 443       break;
 444     case KeyEvent.VK_V:
 445       if (evt.isControlDown())
 446       {
 447         paste(evt.isShiftDown());
 448       }
 449       break;
 450     case KeyEvent.VK_A:
 451       if (evt.isControlDown() || evt.isMetaDown())
 452       {
 453         selectAllSequenceMenuItem_actionPerformed();
 454       }
 455       break;
 456     case KeyEvent.VK_DOWN:
 457       if (viewport.cursorMode)
 458       {
 459         alignPanel.seqPanel.moveCursor(0, 1);
 460       }
 461       else
 462       {
 463         moveSelectedSequences(false);
 464       }
 465       break;
 466
 467     case KeyEvent.VK_UP:
 468       if (viewport.cursorMode)
 469       {
 470         alignPanel.seqPanel.moveCursor(0, -1);
 471       }
 472       else
 473       {
 474         moveSelectedSequences(true);
 475       }
 476       break;
 477
 478     case KeyEvent.VK_LEFT:
 479       if (evt.isAltDown() || !viewport.cursorMode)
 480       {
 481         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 482       }
 483       else
 484       {
 485         alignPanel.seqPanel.moveCursor(-1, 0);
 486       }
 487       break;
 488
 489     case KeyEvent.VK_RIGHT:
 490       if (evt.isAltDown() || !viewport.cursorMode)
 491       {
 492         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 493       }
 494       else
 495       {
 496         alignPanel.seqPanel.moveCursor(1, 0);
 497       }
 498       break;
 499
 500     case KeyEvent.VK_SPACE:
 501       if (viewport.cursorMode)
 502       {
 503         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 504                 || evt.isShiftDown() || evt.isAltDown());
 505       }
 506       break;
 507
 508     case KeyEvent.VK_DELETE:
 509     case KeyEvent.VK_BACK_SPACE:
 510       if (viewport.cursorMode)
 511       {
 512         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 513                 || evt.isShiftDown() || evt.isAltDown());
 514       }
 515       else
 516       {
 517         cut_actionPerformed();
 518         alignPanel.seqPanel.seqCanvas.repaint();
 519       }
 520       break;
 521
 522     case KeyEvent.VK_S:
 523       if (viewport.cursorMode)
 524       {
 525         alignPanel.seqPanel.setCursorRow();
 526       }
 527       break;
 528     case KeyEvent.VK_P:
 529       if (viewport.cursorMode)
 530       {
 531         alignPanel.seqPanel.setCursorPosition();
 532       }
 533       break;
 534
 535     case KeyEvent.VK_ENTER:
 536     case KeyEvent.VK_COMMA:
 537       if (viewport.cursorMode)
 538       {
 539         alignPanel.seqPanel.setCursorRowAndColumn();
 540       }
 541       break;
 542
 543     case KeyEvent.VK_Q:
 544       if (viewport.cursorMode)
 545       {
 546         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 547       }
 548       break;
 549     case KeyEvent.VK_M:
 550       if (viewport.cursorMode)
 551       {
 552         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 553       }
 554       break;
 555
 556     case KeyEvent.VK_F2:
 557       viewport.cursorMode = !viewport.cursorMode;
 558       statusBar.setText(MessageManager.formatMessage(
 559               "label.keyboard_editing_mode",
 560               new String[] { (viewport.cursorMode ? "on" : "off") }));
 561       if (viewport.cursorMode)
 562       {
 563         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 564         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 565       }
 566       break;
 567
 568     case KeyEvent.VK_F:
 569       if (evt.isControlDown())
 570       {
 571         findMenuItem_actionPerformed();
 572       }
 573       break;
 574
 575     case KeyEvent.VK_H:
 576     {
 577       boolean toggleSeqs = !evt.isControlDown();
 578       boolean toggleCols = !evt.isShiftDown();
 579       toggleHiddenRegions(toggleSeqs, toggleCols);
 580       break;
 581     }
 582
 583     case KeyEvent.VK_PAGE_UP:
 584       if (viewport.getWrapAlignment())
 585       {
 586         alignPanel.scrollUp(true);
 587       }
 588       else
 589       {
 590         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 591                 - viewport.endSeq + viewport.startSeq);
 592       }
 593       break;
 594
 595     case KeyEvent.VK_PAGE_DOWN:
 596       if (viewport.getWrapAlignment())
 597       {
 598         alignPanel.scrollUp(false);
 599       }
 600       else
 601       {
 602         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 603                 + viewport.endSeq - viewport.startSeq);
 604       }
 605       break;
 606
 607     case KeyEvent.VK_Z:
 608       if (evt.isControlDown())
 609       {
 610         undoMenuItem_actionPerformed();
 611       }
 612       break;
 613
 614     case KeyEvent.VK_Y:
 615       if (evt.isControlDown())
 616       {
 617         redoMenuItem_actionPerformed();
 618       }
 619       break;
 620
 621     case KeyEvent.VK_L:
 622       if (evt.isControlDown())
 623       {
 624         trimAlignment(true);
 625       }
 626       break;
 627
 628     case KeyEvent.VK_R:
 629       if (evt.isControlDown())
 630       {
 631         trimAlignment(false);
 632       }
 633       break;
 634
 635     case KeyEvent.VK_E:
 636       if (evt.isControlDown())
 637       {
 638         if (evt.isShiftDown())
 639         {
 640           this.removeAllGapsMenuItem_actionPerformed();
 641         }
 642         else
 643         {
 644           removeGappedColumnMenuItem_actionPerformed();
 645         }
 646       }
 647       break;
 648     case KeyEvent.VK_I:
 649       if (evt.isControlDown())
 650       {
 651         if (evt.isAltDown())
 652         {
 653           invertColSel_actionPerformed();
 654         }
 655         else
 656         {
 657           invertSequenceMenuItem_actionPerformed();
 658         }
 659       }
 660       break;
 661
 662     case KeyEvent.VK_G:
 663       if (evt.isControlDown())
 664       {
 665         if (evt.isShiftDown())
 666         {
 667           this.unGroup_actionPerformed();
 668         }
 669         else
 670         {
 671           this.createGroup_actionPerformed();
 672         }
 673       }
 674       break;
 675
 676     case KeyEvent.VK_U:
 677       if (evt.isControlDown())
 678       {
 679         this.deleteGroups_actionPerformed();
 680       }
 681       break;
 682
 683     case KeyEvent.VK_T:
 684       if (evt.isControlDown())
 685       {
 686         newView(null);
 687       }
 688       break;
 689
 690     }
 691     alignPanel.paintAlignment(true);
 692   }
 693
 694   /**
 695    * called by key handler and the hide all/show all menu items
 696    *
 697    * @param toggleSeqs
 698    * @param toggleCols
 699    */
 700   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 701   {
 702     boolean hide = false;
 703     SequenceGroup sg = viewport.getSelectionGroup();
 704     if (!toggleSeqs && !toggleCols)
 705     {
 706       // Hide everything by the current selection - this is a hack - we do the
 707       // invert and then hide
 708       // first check that there will be visible columns after the invert.
 709       if (viewport.hasSelectedColumns()
 710               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 711                       .getEndRes()))
 712       {
 713         // now invert the sequence set, if required - empty selection implies
 714         // that no hiding is required.
 715         if (sg != null)
 716         {
 717           invertSequenceMenuItem_actionPerformed();
 718           sg = viewport.getSelectionGroup();
 719           toggleSeqs = true;
 720
 721         }
 722         viewport.expandColSelection(sg, true);
 723         // finally invert the column selection and get the new sequence
 724         // selection and indicate it should be hidden.
 725         invertColSel_actionPerformed();
 726         toggleCols = true;
 727       }
 728     }
 729
 730     if (toggleSeqs)
 731     {
 732       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 733       {
 734         hide = true;
 735         viewport.hideAllSelectedSeqs();
 736       }
 737       else if (!(toggleCols && viewport.hasSelectedColumns()))
 738       {
 739         viewport.showAllHiddenSeqs();
 740       }
 741     }
 742
 743     if (toggleCols)
 744     {
 745       if (viewport.hasSelectedColumns())
 746       {
 747         viewport.hideSelectedColumns();
 748         if (!toggleSeqs)
 749         {
 750           viewport.setSelectionGroup(sg);
 751         }
 752       }
 753       else if (!hide)
 754       {
 755         viewport.showAllHiddenColumns();
 756       }
 757       viewport.sendSelection();
 758     }
 759   }
 760
 761   @Override
 762   public void keyReleased(KeyEvent evt)
 763   {
 764   }
 765
 766   @Override
 767   public void keyTyped(KeyEvent evt)
 768   {
 769   }
 770
 771   @Override
 772   public void itemStateChanged(ItemEvent evt)
 773   {
 774     final Object source = evt.getSource();
 775     if (source == displayNonconservedMenuItem)
 776     {
 777       displayNonconservedMenuItem_actionPerformed();
 778     }
 779     else if (source == colourTextMenuItem)
 780     {
 781       colourTextMenuItem_actionPerformed();
 782     }
 783     else if (source == wrapMenuItem)
 784     {
 785       wrapMenuItem_actionPerformed();
 786     }
 787     else if (source == scaleAbove)
 788     {
 789       viewport.setScaleAboveWrapped(scaleAbove.getState());
 790     }
 791     else if (source == scaleLeft)
 792     {
 793       viewport.setScaleLeftWrapped(scaleLeft.getState());
 794     }
 795     else if (source == scaleRight)
 796     {
 797       viewport.setScaleRightWrapped(scaleRight.getState());
 798     }
 799     else if (source == seqLimits)
 800     {
 801       seqLimits_itemStateChanged();
 802     }
 803     else if (source == viewBoxesMenuItem)
 804     {
 805       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 806     }
 807     else if (source == viewTextMenuItem)
 808     {
 809       viewport.setShowText(viewTextMenuItem.getState());
 810     }
 811     else if (source == renderGapsMenuItem)
 812     {
 813       viewport.setRenderGaps(renderGapsMenuItem.getState());
 814     }
 815     else if (source == annotationPanelMenuItem)
 816     {
 817       boolean showAnnotations = annotationPanelMenuItem.getState();
 818       showAlignmentAnnotations.setEnabled(showAnnotations);
 819       showSequenceAnnotations.setEnabled(showAnnotations);
 820       viewport.setShowAnnotation(showAnnotations);
 821       alignPanel.setAnnotationVisible(showAnnotations);
 822     }
 823     else if (source == sequenceFeatures)
 824     {
 825       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 826       alignPanel.seqPanel.seqCanvas.repaint();
 827     }
 828     else if (source == showAlignmentAnnotations)
 829     {
 830       setAnnotationsVisibility();
 831     }
 832     else if (source == showSequenceAnnotations)
 833     {
 834       setAnnotationsVisibility();
 835     }
 836     else if (source == sortAnnBySequence)
 837     {
 838       boolean newState = sortAnnBySequence.getState();
 839       sortAnnByLabel.setState(false);
 840       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 841               : SequenceAnnotationOrder.NONE);
 842       setViewportAnnotationOrder();
 843     }
 844     else if (source == sortAnnByLabel)
 845     {
 846       boolean newState = sortAnnByLabel.getState();
 847       sortAnnBySequence.setState(false);
 848       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 849               : SequenceAnnotationOrder.NONE);
 850       setViewportAnnotationOrder();
 851     }
 852     else if (source == showAutoFirst)
 853     {
 854       showAutoLast.setState(!showAutoFirst.getState());
 855       setShowAutoCalculatedAbove(showAutoFirst.getState());
 856       setViewportAnnotationOrder();
 857     }
 858     else if (source == showAutoLast)
 859     {
 860       showAutoFirst.setState(!showAutoLast.getState());
 861       setShowAutoCalculatedAbove(showAutoFirst.getState());
 862       setViewportAnnotationOrder();
 863     }
 864     else if (source == conservationMenuItem)
 865     {
 866       conservationMenuItem_actionPerformed();
 867     }
 868     else if (source == abovePIDThreshold)
 869     {
 870       abovePIDThreshold_actionPerformed();
 871     }
 872     else if (source == applyToAllGroups)
 873     {
 874       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 875     }
 876     else if (source == autoCalculate)
 877     {
 878       viewport.autoCalculateConsensus = autoCalculate.getState();
 879     }
 880     else if (source == sortByTree)
 881     {
 882       viewport.sortByTree = sortByTree.getState();
 883     }
 884     else if (source == this.centreColumnLabelFlag)
 885     {
 886       centreColumnLabelFlag_stateChanged();
 887     }
 888     else if (source == this.followMouseOverFlag)
 889     {
 890       mouseOverFlag_stateChanged();
 891     }
 892     else if (source == showGroupConsensus)
 893     {
 894       showGroupConsensus_actionPerformed();
 895     }
 896     else if (source == showGroupConservation)
 897     {
 898       showGroupConservation_actionPerformed();
 899     }
 900     else if (source == showSequenceLogo)
 901     {
 902       showSequenceLogo_actionPerformed();
 903     }
 904     else if (source == normSequenceLogo)
 905     {
 906       normSequenceLogo_actionPerformed();
 907     }
 908     else if (source == showConsensusHistogram)
 909     {
 910       showConsensusHistogram_actionPerformed();
 911     }
 912     else if (source == applyAutoAnnotationSettings)
 913     {
 914       applyAutoAnnotationSettings_actionPerformed();
 915     }
 916     alignPanel.paintAlignment(true);
 917   }
 918
 919   /**
 920    * Set the visibility state of sequence-related and/or alignment-related
 921    * annotations depending on checkbox selections, and repaint.
 922    *
 923    * @param visible
 924    */
 925   private void setAnnotationsVisibility()
 926   {
 927     boolean showForAlignment = showAlignmentAnnotations.getState();
 928     boolean showForSequences = showSequenceAnnotations.getState();
 929     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 930     {
 931       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 932               .getAlignmentAnnotation())
 933       {
 934         boolean visible = (aa.sequenceRef == null ? showForAlignment
 935                 : showForSequences);
 936         aa.visible = visible;
 937       }
 938     }
 939     alignPanel.validateAnnotationDimensions(true);
 940     validate();
 941     repaint();
 942   }
 943
 944   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 945   {
 946     this.annotationSortOrder = order;
 947   }
 948
 949   /**
 950    * Set flags on the viewport that control annotation ordering
 951    */
 952   private void setViewportAnnotationOrder()
 953   {
 954     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 955     this.alignPanel.av
 956             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 957   }
 958
 959   private void setShowAutoCalculatedAbove(boolean showAbove)
 960   {
 961     this.showAutoCalculatedAbove = showAbove;
 962   }
 963
 964   private void mouseOverFlag_stateChanged()
 965   {
 966     viewport.setFollowHighlight(followMouseOverFlag.getState());
 967     // TODO: could kick the scrollTo mechanism to reset view for current
 968     // searchresults.
 969   }
 970
 971   private void centreColumnLabelFlag_stateChanged()
 972   {
 973     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 974     this.alignPanel.annotationPanel.repaint();
 975   }
 976
 977   @Override
 978   public void actionPerformed(ActionEvent evt)
 979   {
 980     viewport.applet.currentAlignFrame = this;
 981
 982     Object source = evt.getSource();
 983
 984     if (source == inputText)
 985     {
 986       inputText_actionPerformed();
 987     }
 988     else if (source == loadTree)
 989     {
 990       loadTree_actionPerformed();
 991     }
 992     else if (source == loadApplication)
 993     {
 994       launchFullApplication();
 995     }
 996     else if (source == loadAnnotations)
 997     {
 998       loadAnnotations();
 999     }
1000     else if (source == outputAnnotations)
1001     {
1002       outputAnnotations(true);
1003     }
1004     else if (source == outputFeatures)
1005     {
1006       outputFeatures(true, "Jalview");
1007     }
1008     else if (source == closeMenuItem)
1009     {
1010       closeMenuItem_actionPerformed();
1011     }
1012     else if (source == copy)
1013     {
1014       copy_actionPerformed();
1015     }
1016     else if (source == undoMenuItem)
1017     {
1018       undoMenuItem_actionPerformed();
1019     }
1020     else if (source == redoMenuItem)
1021     {
1022       redoMenuItem_actionPerformed();
1023     }
1024     else if (source == inputText)
1025     {
1026       inputText_actionPerformed();
1027     }
1028     else if (source == closeMenuItem)
1029     {
1030       closeMenuItem_actionPerformed();
1031     }
1032     else if (source == undoMenuItem)
1033     {
1034       undoMenuItem_actionPerformed();
1035     }
1036     else if (source == redoMenuItem)
1037     {
1038       redoMenuItem_actionPerformed();
1039     }
1040     else if (source == copy)
1041     {
1042       copy_actionPerformed();
1043     }
1044     else if (source == pasteNew)
1045     {
1046       pasteNew_actionPerformed();
1047     }
1048     else if (source == pasteThis)
1049     {
1050       pasteThis_actionPerformed();
1051     }
1052     else if (source == cut)
1053     {
1054       cut_actionPerformed();
1055     }
1056     else if (source == delete)
1057     {
1058       delete_actionPerformed();
1059     }
1060     else if (source == grpsFromSelection)
1061     {
1062       makeGrpsFromSelection_actionPerformed();
1063     }
1064     else if (source == deleteGroups)
1065     {
1066       deleteGroups_actionPerformed();
1067     }
1068     else if (source == selectAllSequenceMenuItem)
1069     {
1070       selectAllSequenceMenuItem_actionPerformed();
1071     }
1072     else if (source == deselectAllSequenceMenuItem)
1073     {
1074       deselectAllSequenceMenuItem_actionPerformed();
1075     }
1076     else if (source == invertSequenceMenuItem)
1077     {
1078       invertSequenceMenuItem_actionPerformed();
1079       // uncomment to slave sequence selections in split frame
1080       // viewport.sendSelection();
1081     }
1082     else if (source == invertColSel)
1083     {
1084       viewport.invertColumnSelection();
1085       alignPanel.paintAlignment(true);
1086       viewport.sendSelection();
1087     }
1088     else if (source == remove2LeftMenuItem)
1089     {
1090       trimAlignment(true);
1091     }
1092     else if (source == remove2RightMenuItem)
1093     {
1094       trimAlignment(false);
1095     }
1096     else if (source == removeGappedColumnMenuItem)
1097     {
1098       removeGappedColumnMenuItem_actionPerformed();
1099     }
1100     else if (source == removeAllGapsMenuItem)
1101     {
1102       removeAllGapsMenuItem_actionPerformed();
1103     }
1104     else if (source == findMenuItem)
1105     {
1106       findMenuItem_actionPerformed();
1107     }
1108     else if (source == font)
1109     {
1110       new FontChooser(alignPanel);
1111     }
1112     else if (source == newView)
1113     {
1114       newView(null);
1115     }
1116     else if (source == showColumns)
1117     {
1118       viewport.showAllHiddenColumns();
1119       alignPanel.paintAlignment(true);
1120       viewport.sendSelection();
1121     }
1122     else if (source == showSeqs)
1123     {
1124       viewport.showAllHiddenSeqs();
1125       alignPanel.paintAlignment(true);
1126       // uncomment if we want to slave sequence selections in split frame
1127       // viewport.sendSelection();
1128     }
1129     else if (source == hideColumns)
1130     {
1131       viewport.hideSelectedColumns();
1132       alignPanel.paintAlignment(true);
1133       viewport.sendSelection();
1134     }
1135     else if (source == hideSequences
1136             && viewport.getSelectionGroup() != null)
1137     {
1138       viewport.hideAllSelectedSeqs();
1139       alignPanel.paintAlignment(true);
1140       // uncomment if we want to slave sequence selections in split frame
1141       // viewport.sendSelection();
1142     }
1143     else if (source == hideAllButSelection)
1144     {
1145       toggleHiddenRegions(false, false);
1146       alignPanel.paintAlignment(true);
1147       viewport.sendSelection();
1148     }
1149     else if (source == hideAllSelection)
1150     {
1151       SequenceGroup sg = viewport.getSelectionGroup();
1152       viewport.expandColSelection(sg, false);
1153       viewport.hideAllSelectedSeqs();
1154       viewport.hideSelectedColumns();
1155       alignPanel.paintAlignment(true);
1156       viewport.sendSelection();
1157     }
1158     else if (source == showAllHidden)
1159     {
1160       viewport.showAllHiddenColumns();
1161       viewport.showAllHiddenSeqs();
1162       alignPanel.paintAlignment(true);
1163       viewport.sendSelection();
1164     }
1165     else if (source == showGroupConsensus)
1166     {
1167       showGroupConsensus_actionPerformed();
1168     }
1169     else if (source == showGroupConservation)
1170     {
1171       showGroupConservation_actionPerformed();
1172     }
1173     else if (source == showSequenceLogo)
1174     {
1175       showSequenceLogo_actionPerformed();
1176     }
1177     else if (source == normSequenceLogo)
1178     {
1179       normSequenceLogo_actionPerformed();
1180     }
1181     else if (source == showConsensusHistogram)
1182     {
1183       showConsensusHistogram_actionPerformed();
1184     }
1185     else if (source == applyAutoAnnotationSettings)
1186     {
1187       applyAutoAnnotationSettings_actionPerformed();
1188     }
1189     else if (source == featureSettings)
1190     {
1191       new FeatureSettings(alignPanel);
1192     }
1193     else if (source == alProperties)
1194     {
1195       StringBuffer contents = new jalview.io.AlignmentProperties(
1196               viewport.getAlignment()).formatAsString();
1197       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1198       cap.setText(contents.toString());
1199       Frame frame = new Frame();
1200       frame.add(cap);
1201       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1202               "label.alignment_properties", new String[] { getTitle() }),
1203               400, 250);
1204     }
1205     else if (source == overviewMenuItem)
1206     {
1207       overviewMenuItem_actionPerformed();
1208     }
1209     else if (source == noColourmenuItem)
1210     {
1211       changeColour(null);
1212     }
1213     else if (source == clustalColour)
1214     {
1215       abovePIDThreshold.setState(false);
1216       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1217     }
1218     else if (source == zappoColour)
1219     {
1220       changeColour(new ZappoColourScheme());
1221     }
1222     else if (source == taylorColour)
1223     {
1224       changeColour(new TaylorColourScheme());
1225     }
1226     else if (source == hydrophobicityColour)
1227     {
1228       changeColour(new HydrophobicColourScheme());
1229     }
1230     else if (source == helixColour)
1231     {
1232       changeColour(new HelixColourScheme());
1233     }
1234     else if (source == strandColour)
1235     {
1236       changeColour(new StrandColourScheme());
1237     }
1238     else if (source == turnColour)
1239     {
1240       changeColour(new TurnColourScheme());
1241     }
1242     else if (source == buriedColour)
1243     {
1244       changeColour(new BuriedColourScheme());
1245     }
1246     else if (source == nucleotideColour)
1247     {
1248       changeColour(new NucleotideColourScheme());
1249     }
1250     else if (source == purinePyrimidineColour)
1251     {
1252       changeColour(new PurinePyrimidineColourScheme());
1253     }
1254     // else if (source == RNAInteractionColour)
1255     // {
1256     // changeColour(new RNAInteractionColourScheme());
1257     // }
1258     else if (source == RNAHelixColour)
1259     {
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     FileFormatI fileFormat = FileFormats.getInstance().forName(
1368             e.getActionCommand());
1369     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1370             fileFormat, viewport.getAlignment(),
1371             viewport.getShowJVSuffix()));
1372   }
1373
1374   public void loadAnnotations()
1375   {
1376     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377     cap.setText(MessageManager
1378             .getString("label.paste_features_annotations_Tcoffee_here"));
1379     cap.setAnnotationImport();
1380     Frame frame = new Frame();
1381     frame.add(cap);
1382     jalview.bin.JalviewLite.addFrame(frame,
1383             MessageManager.getString("action.paste_annotations"), 400, 300);
1384
1385   }
1386
1387   public String outputAnnotations(boolean displayTextbox)
1388   {
1389     String annotation = new AnnotationFile()
1390             .printAnnotationsForView(viewport);
1391
1392     if (displayTextbox)
1393     {
1394       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1395       Frame frame = new Frame();
1396       frame.add(cap);
1397       jalview.bin.JalviewLite.addFrame(frame,
1398               MessageManager.getString("label.annotations"), 600, 500);
1399       cap.setText(annotation);
1400     }
1401
1402     return annotation;
1403   }
1404
1405   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1406   {
1407     if (alignPanel.getFeatureRenderer() != null
1408             && viewport.getFeaturesDisplayed() != null)
1409     {
1410       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1411
1412     }
1413     return null;
1414   }
1415
1416   public String outputFeatures(boolean displayTextbox, String format)
1417   {
1418     String features;
1419     FeaturesFile formatter = new FeaturesFile();
1420     if (format.equalsIgnoreCase("Jalview"))
1421     {
1422       features = formatter.printJalviewFormat(viewport.getAlignment()
1423               .getSequencesArray(), getDisplayedFeatureCols());
1424     }
1425     else
1426     {
1427       features = formatter.printGffFormat(viewport.getAlignment()
1428               .getSequencesArray(), getDisplayedFeatureCols());
1429     }
1430
1431     if (displayTextbox)
1432     {
1433       boolean frimport = false;
1434       if (features == null || features.equals("No Features Visible"))
1435       {
1436         features = "# No features visible - paste some and import them here.";
1437         frimport = true;
1438       }
1439
1440       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1441       if (frimport)
1442       {
1443         cap.setAnnotationImport();
1444       }
1445       Frame frame = new Frame();
1446       frame.add(cap);
1447       jalview.bin.JalviewLite.addFrame(frame,
1448               MessageManager.getString("label.features"), 600, 500);
1449       cap.setText(features);
1450     }
1451     else
1452     {
1453       if (features == null)
1454       {
1455         features = "";
1456       }
1457     }
1458
1459     return features;
1460   }
1461
1462   void launchFullApplication()
1463   {
1464     StringBuffer url = new StringBuffer(jalviewServletURL);
1465
1466     // allow servlet parameters to be passed in applet parameter
1467     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1468             : "?";
1469     url.append(firstSep);
1470
1471     url.append("open="
1472             + appendProtocol(viewport.applet.getParameter("file")));
1473
1474     if (viewport.applet.getParameter("features") != null)
1475     {
1476       url.append("&features=");
1477       url.append(appendProtocol(viewport.applet.getParameter("features")));
1478     }
1479
1480     if (viewport.applet.getParameter("annotations") != null)
1481     {
1482       url.append("&annotations=");
1483       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1484     }
1485
1486     if (viewport.applet.getParameter("jnetfile") != null
1487             || viewport.applet.getParameter("jpredfile") != null)
1488     {
1489       url.append("&annotations=");
1490       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1491               .getParameter("jnetfile") : viewport.applet
1492               .getParameter("jpredfile")));
1493     }
1494
1495     if (viewport.applet.getParameter("defaultColour") != null)
1496     {
1497       url.append("&colour="
1498               + removeWhiteSpace(viewport.applet
1499                       .getParameter("defaultColour")));
1500     }
1501
1502     if (viewport.applet.getParameter("userDefinedColour") != null)
1503     {
1504       url.append("&colour="
1505               + removeWhiteSpace(viewport.applet
1506                       .getParameter("userDefinedColour")));
1507     }
1508     if (viewport.applet.getParameter("tree") != null)
1509     {
1510       url.append("&tree="
1511               + appendProtocol(viewport.applet.getParameter("tree")));
1512     }
1513     if (viewport.applet.getParameter("treeFile") != null)
1514     {
1515       url.append("&tree="
1516               + appendProtocol(viewport.applet.getParameter("treeFile")));
1517     }
1518
1519     showURL(url.toString(), "FULL_APP");
1520   }
1521
1522   String removeWhiteSpace(String colour)
1523   {
1524     StringBuffer sb = new StringBuffer();
1525     for (int i = 0; i < colour.length(); i++)
1526     {
1527       if (Character.isWhitespace(colour.charAt(i)))
1528       {
1529         sb.append("%20");
1530       }
1531       else
1532       {
1533         sb.append(colour.charAt(i));
1534       }
1535     }
1536
1537     return sb.toString();
1538   }
1539
1540   String appendProtocol(String url)
1541   {
1542     try
1543     {
1544       new URL(url);
1545       url = URLEncoder.encode(url);
1546     }
1547     /*
1548      * When we finally deprecate 1.1 compatibility, we can start to use
1549      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1550      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1551      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1552      * ex.printStackTrace(); }
1553      */
1554     catch (java.net.MalformedURLException ex)
1555     {
1556       url = viewport.applet.getCodeBase() + url;
1557     }
1558     return url;
1559   }
1560
1561   public void closeMenuItem_actionPerformed()
1562   {
1563     PaintRefresher.RemoveComponent(alignPanel);
1564     if (alignPanel.seqPanel != null
1565             && alignPanel.seqPanel.seqCanvas != null)
1566     {
1567       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1568     }
1569     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1570     {
1571       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1572     }
1573
1574     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1575     {
1576       System.exit(0);
1577     }
1578     else
1579     {
1580     }
1581     viewport = null;
1582     alignPanel = null;
1583     this.dispose();
1584   }
1585
1586   /**
1587    * TODO: JAL-1104
1588    */
1589   void updateEditMenuBar()
1590   {
1591
1592     if (viewport.getHistoryList().size() > 0)
1593     {
1594       undoMenuItem.setEnabled(true);
1595       CommandI command = viewport.getHistoryList().peek();
1596       undoMenuItem.setLabel(MessageManager.formatMessage(
1597               "label.undo_command",
1598               new Object[] { command.getDescription() }));
1599     }
1600     else
1601     {
1602       undoMenuItem.setEnabled(false);
1603       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1604     }
1605
1606     if (viewport.getRedoList().size() > 0)
1607     {
1608       redoMenuItem.setEnabled(true);
1609
1610       CommandI command = viewport.getRedoList().peek();
1611       redoMenuItem.setLabel(MessageManager.formatMessage(
1612               "label.redo_command",
1613               new Object[] { command.getDescription() }));
1614     }
1615     else
1616     {
1617       redoMenuItem.setEnabled(false);
1618       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1619     }
1620   }
1621
1622   /**
1623    * TODO: JAL-1104
1624    */
1625   @Override
1626   public void addHistoryItem(CommandI command)
1627   {
1628     if (command.getSize() > 0)
1629     {
1630       viewport.addToHistoryList(command);
1631       viewport.clearRedoList();
1632       updateEditMenuBar();
1633       viewport.updateHiddenColumns();
1634     }
1635   }
1636
1637   /**
1638    * TODO: JAL-1104 DOCUMENT ME!
1639    *
1640    * @param e
1641    *          DOCUMENT ME!
1642    */
1643   protected void undoMenuItem_actionPerformed()
1644   {
1645     if (viewport.getHistoryList().isEmpty())
1646     {
1647       return;
1648     }
1649
1650     CommandI command = viewport.getHistoryList().pop();
1651     viewport.addToRedoList(command);
1652     command.undoCommand(null);
1653
1654     AlignmentViewport originalSource = getOriginatingSource(command);
1655     // JBPNote Test
1656     if (originalSource != viewport)
1657     {
1658       System.err
1659               .println("Warning: Viewport object mismatch whilst undoing");
1660     }
1661     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1662                                           // viewport.getColumnSelection().getHiddenColumns()
1663                                           // != null;
1664     updateEditMenuBar();
1665     originalSource.firePropertyChange("alignment", null, originalSource
1666             .getAlignment().getSequences());
1667   }
1668
1669   /**
1670    * TODO: JAL-1104 DOCUMENT ME!
1671    *
1672    * @param e
1673    *          DOCUMENT ME!
1674    */
1675   protected void redoMenuItem_actionPerformed()
1676   {
1677     if (viewport.getRedoList().isEmpty())
1678     {
1679       return;
1680     }
1681
1682     CommandI command = viewport.getRedoList().pop();
1683     viewport.addToHistoryList(command);
1684     command.doCommand(null);
1685
1686     AlignmentViewport originalSource = getOriginatingSource(command);
1687     // JBPNote Test
1688     if (originalSource != viewport)
1689     {
1690       System.err
1691               .println("Warning: Viewport object mismatch whilst re-doing");
1692     }
1693     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1694                                           // viewport.getColumnSelection().getHiddenColumns()
1695                                           // != null;
1696
1697     updateEditMenuBar();
1698     originalSource.firePropertyChange("alignment", null, originalSource
1699             .getAlignment().getSequences());
1700   }
1701
1702   AlignmentViewport getOriginatingSource(CommandI command)
1703   {
1704     AlignmentViewport originalSource = null;
1705     // For sequence removal and addition, we need to fire
1706     // the property change event FROM the viewport where the
1707     // original alignment was altered
1708     AlignmentI al = null;
1709     if (command instanceof EditCommand)
1710     {
1711       EditCommand editCommand = (EditCommand) command;
1712       al = editCommand.getAlignment();
1713       Vector comps = (Vector) PaintRefresher.components.get(viewport
1714               .getSequenceSetId());
1715       for (int i = 0; i < comps.size(); i++)
1716       {
1717         if (comps.elementAt(i) instanceof AlignmentPanel)
1718         {
1719           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1720           {
1721             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1722             break;
1723           }
1724         }
1725       }
1726     }
1727
1728     if (originalSource == null)
1729     {
1730       // The original view is closed, we must validate
1731       // the current view against the closed view first
1732       if (al != null)
1733       {
1734         PaintRefresher.validateSequences(al, viewport.getAlignment());
1735       }
1736
1737       originalSource = viewport;
1738     }
1739
1740     return originalSource;
1741   }
1742
1743   /**
1744    * Move the currently selected sequences up or down one position in the
1745    * alignment
1746    *
1747    * @param up
1748    */
1749   public void moveSelectedSequences(boolean up)
1750   {
1751     SequenceGroup sg = viewport.getSelectionGroup();
1752     if (sg == null)
1753     {
1754       return;
1755     }
1756     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1757             up ? null : viewport.getHiddenRepSequences(), up);
1758     alignPanel.paintAlignment(true);
1759
1760     /*
1761      * Also move cDNA/protein complement sequences
1762      */
1763     AlignViewportI complement = viewport.getCodingComplement();
1764     if (complement != null)
1765     {
1766       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1767               viewport, complement);
1768       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1769               up ? null : complement.getHiddenRepSequences(), up);
1770       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1771     }
1772   }
1773
1774   synchronized void slideSequences(boolean right, int size)
1775   {
1776     List<SequenceI> sg = new Vector<SequenceI>();
1777     if (viewport.cursorMode)
1778     {
1779       sg.add(viewport.getAlignment().getSequenceAt(
1780               alignPanel.seqPanel.seqCanvas.cursorY));
1781     }
1782     else if (viewport.getSelectionGroup() != null
1783             && viewport.getSelectionGroup().getSize() != viewport
1784                     .getAlignment().getHeight())
1785     {
1786       sg = viewport.getSelectionGroup().getSequences(
1787               viewport.getHiddenRepSequences());
1788     }
1789
1790     if (sg.size() < 1)
1791     {
1792       return;
1793     }
1794
1795     Vector<SequenceI> invertGroup = new Vector();
1796
1797     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1798     {
1799       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1800       {
1801         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1802       }
1803     }
1804
1805     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1806
1807     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1808             .size()]);
1809     for (int i = 0; i < invertGroup.size(); i++)
1810     {
1811       seqs2[i] = invertGroup.elementAt(i);
1812     }
1813
1814     SlideSequencesCommand ssc;
1815     if (right)
1816     {
1817       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1818               size, viewport.getGapCharacter());
1819     }
1820     else
1821     {
1822       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1823               size, viewport.getGapCharacter());
1824     }
1825
1826     int groupAdjustment = 0;
1827     if (ssc.getGapsInsertedBegin() && right)
1828     {
1829       if (viewport.cursorMode)
1830       {
1831         alignPanel.seqPanel.moveCursor(size, 0);
1832       }
1833       else
1834       {
1835         groupAdjustment = size;
1836       }
1837     }
1838     else if (!ssc.getGapsInsertedBegin() && !right)
1839     {
1840       if (viewport.cursorMode)
1841       {
1842         alignPanel.seqPanel.moveCursor(-size, 0);
1843       }
1844       else
1845       {
1846         groupAdjustment = -size;
1847       }
1848     }
1849
1850     if (groupAdjustment != 0)
1851     {
1852       viewport.getSelectionGroup().setStartRes(
1853               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1854       viewport.getSelectionGroup().setEndRes(
1855               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1856     }
1857
1858     boolean appendHistoryItem = false;
1859     Deque<CommandI> historyList = viewport.getHistoryList();
1860     if (historyList != null && historyList.size() > 0
1861             && historyList.peek() instanceof SlideSequencesCommand)
1862     {
1863       appendHistoryItem = ssc
1864               .appendSlideCommand((SlideSequencesCommand) historyList
1865                       .peek());
1866     }
1867
1868     if (!appendHistoryItem)
1869     {
1870       addHistoryItem(ssc);
1871     }
1872
1873     repaint();
1874   }
1875
1876   static StringBuffer copiedSequences;
1877
1878   static Vector copiedHiddenColumns;
1879
1880   protected void copy_actionPerformed()
1881   {
1882     if (viewport.getSelectionGroup() == null)
1883     {
1884       return;
1885     }
1886
1887     SequenceGroup sg = viewport.getSelectionGroup();
1888     copiedSequences = new StringBuffer();
1889     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1890     for (int i = 0; i < sg.getSize(); i++)
1891     {
1892       SequenceI seq = sg.getSequenceAt(i);
1893       int index = viewport.getAlignment().findIndex(seq);
1894       orderedSeqs.put(index, seq);
1895     }
1896
1897     int index = 0, startRes, endRes;
1898     char ch;
1899
1900     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1901     {
1902       copiedHiddenColumns = new Vector();
1903       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1904       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1905       {
1906         copiedHiddenColumns.addElement(new int[] {
1907             region[0] - hiddenOffset, region[1] - hiddenOffset });
1908       }
1909     }
1910     else
1911     {
1912       copiedHiddenColumns = null;
1913     }
1914
1915     for (int i = 0; i < sg.getSize(); i++)
1916     {
1917       SequenceI seq = null;
1918
1919       while (seq == null)
1920       {
1921         if (orderedSeqs.containsKey(index))
1922         {
1923           seq = orderedSeqs.get(index);
1924           index++;
1925           break;
1926         }
1927         else
1928         {
1929           index++;
1930         }
1931       }
1932
1933       // FIND START RES
1934       // Returns residue following index if gap
1935       startRes = seq.findPosition(sg.getStartRes());
1936
1937       // FIND END RES
1938       // Need to find the residue preceeding index if gap
1939       endRes = 0;
1940
1941       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1942       {
1943         ch = seq.getCharAt(j);
1944         if (!jalview.util.Comparison.isGap((ch)))
1945         {
1946           endRes++;
1947         }
1948       }
1949
1950       if (endRes > 0)
1951       {
1952         endRes += seq.getStart() - 1;
1953       }
1954
1955       copiedSequences.append(seq.getName()
1956               + "\t"
1957               + startRes
1958               + "\t"
1959               + endRes
1960               + "\t"
1961               + seq.getSequenceAsString(sg.getStartRes(),
1962                       sg.getEndRes() + 1) + "\n");
1963     }
1964
1965   }
1966
1967   protected void pasteNew_actionPerformed()
1968   {
1969     paste(true);
1970   }
1971
1972   protected void pasteThis_actionPerformed()
1973   {
1974     paste(false);
1975   }
1976
1977   void paste(boolean newAlignment)
1978   {
1979     try
1980     {
1981
1982       if (copiedSequences == null)
1983       {
1984         return;
1985       }
1986
1987       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1988       Vector seqs = new Vector();
1989       while (st.hasMoreElements())
1990       {
1991         String name = st.nextToken();
1992         int start = Integer.parseInt(st.nextToken());
1993         int end = Integer.parseInt(st.nextToken());
1994         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1995       }
1996       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1997       for (int i = 0; i < seqs.size(); i++)
1998       {
1999         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2000       }
2001
2002       if (newAlignment)
2003       {
2004         String newtitle = MessageManager
2005                 .getString("label.copied_sequences");
2006         if (getTitle().startsWith(
2007                 MessageManager.getString("label.copied_sequences")))
2008         {
2009           newtitle = getTitle();
2010         }
2011         else
2012         {
2013           newtitle = newtitle.concat(MessageManager.formatMessage(
2014                   "label.from_msname", new String[] { getTitle() }));
2015         }
2016         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2017                 viewport.applet, newtitle, false);
2018         if (copiedHiddenColumns != null)
2019         {
2020           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2021           {
2022             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2023             af.viewport.hideColumns(region[0], region[1]);
2024           }
2025         }
2026
2027         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2028                 frameHeight);
2029       }
2030       else
2031       {
2032         addSequences(newSeqs);
2033       }
2034
2035     } catch (Exception ex)
2036     {
2037     } // could be anything being pasted in here
2038
2039   }
2040
2041   void addSequences(SequenceI[] seqs)
2042   {
2043     for (int i = 0; i < seqs.length; i++)
2044     {
2045       viewport.getAlignment().addSequence(seqs[i]);
2046     }
2047
2048     // !newAlignment
2049     addHistoryItem(new EditCommand(
2050             MessageManager.getString("label.add_sequences"), Action.PASTE,
2051             seqs, 0, viewport.getAlignment().getWidth(),
2052             viewport.getAlignment()));
2053
2054     viewport.setEndSeq(viewport.getAlignment().getHeight());
2055     viewport.getAlignment().getWidth();
2056     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2057             .getSequences());
2058
2059   }
2060
2061   protected void cut_actionPerformed()
2062   {
2063     copy_actionPerformed();
2064     delete_actionPerformed();
2065   }
2066
2067   protected void delete_actionPerformed()
2068   {
2069
2070     SequenceGroup sg = viewport.getSelectionGroup();
2071     if (sg == null)
2072     {
2073       return;
2074     }
2075
2076     Vector seqs = new Vector();
2077     SequenceI seq;
2078     for (int i = 0; i < sg.getSize(); i++)
2079     {
2080       seq = sg.getSequenceAt(i);
2081       seqs.addElement(seq);
2082     }
2083
2084     /*
2085      * If the cut affects all sequences, warn, remove highlighted columns
2086      */
2087     if (sg.getSize() == viewport.getAlignment().getHeight())
2088     {
2089       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2090               .getAlignment().getWidth()) ? true : false;
2091       if (isEntireAlignWidth)
2092       {
2093         String title = MessageManager.getString("label.delete_all");
2094         Panel infoPanel = new Panel();
2095         infoPanel.setLayout(new FlowLayout());
2096         infoPanel
2097                 .add(new Label(MessageManager.getString("warn.delete_all")));
2098
2099         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2100         dialog.setMainPanel(infoPanel);
2101         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2102         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2103         dialog.setVisible(true);
2104
2105         if (!dialog.accept)
2106         {
2107           return;
2108         }
2109       }
2110       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2111               sg.getEndRes() + 1);
2112     }
2113
2114     SequenceI[] cut = new SequenceI[seqs.size()];
2115     for (int i = 0; i < seqs.size(); i++)
2116     {
2117       cut[i] = (SequenceI) seqs.elementAt(i);
2118     }
2119
2120     /*
2121      * //ADD HISTORY ITEM
2122      */
2123     addHistoryItem(new EditCommand(
2124             MessageManager.getString("label.cut_sequences"), Action.CUT,
2125             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2126             viewport.getAlignment()));
2127
2128     viewport.setSelectionGroup(null);
2129     viewport.getAlignment().deleteGroup(sg);
2130
2131     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2132             .getSequences());
2133
2134     if (viewport.getAlignment().getHeight() < 1)
2135     {
2136       this.setVisible(false);
2137     }
2138     viewport.sendSelection();
2139   }
2140
2141   /**
2142    * group consensus toggled
2143    *
2144    */
2145   protected void showGroupConsensus_actionPerformed()
2146   {
2147     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2148     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2149
2150   }
2151
2152   /**
2153    * group conservation toggled.
2154    */
2155   protected void showGroupConservation_actionPerformed()
2156   {
2157     viewport.setShowGroupConservation(showGroupConservation.getState());
2158     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2159   }
2160
2161   /*
2162    * (non-Javadoc)
2163    *
2164    * @see
2165    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2166    * .event.ActionEvent)
2167    */
2168   protected void showConsensusHistogram_actionPerformed()
2169   {
2170     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2171     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2172   }
2173
2174   /*
2175    * (non-Javadoc)
2176    *
2177    * @see
2178    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2179    * .event.ActionEvent)
2180    */
2181   protected void showSequenceLogo_actionPerformed()
2182   {
2183     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2184     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2185   }
2186
2187   protected void normSequenceLogo_actionPerformed()
2188   {
2189     showSequenceLogo.setState(true);
2190     viewport.setShowSequenceLogo(true);
2191     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2192     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2193   }
2194
2195   protected void applyAutoAnnotationSettings_actionPerformed()
2196   {
2197     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2198   }
2199
2200   protected void makeGrpsFromSelection_actionPerformed()
2201   {
2202     if (avc.makeGroupsFromSelection())
2203     {
2204       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2205       alignPanel.updateAnnotation();
2206       alignPanel.paintAlignment(true);
2207     }
2208   }
2209
2210   protected void createGroup_actionPerformed()
2211   {
2212     avc.createGroup();
2213   }
2214
2215   protected void unGroup_actionPerformed()
2216   {
2217     if (avc.unGroup())
2218     {
2219       alignPanel.alignmentChanged();
2220     }
2221   }
2222
2223   protected void deleteGroups_actionPerformed()
2224   {
2225     if (avc.deleteGroups())
2226     {
2227       alignPanel.alignmentChanged();
2228     }
2229   }
2230
2231   public void selectAllSequenceMenuItem_actionPerformed()
2232   {
2233     SequenceGroup sg = new SequenceGroup();
2234     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2235     {
2236       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2237     }
2238     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2239     viewport.setSelectionGroup(sg);
2240     // JAL-2034 - should delegate to
2241     // alignPanel to decide if overview needs
2242     // updating.
2243     alignPanel.paintAlignment(false);
2244     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2245     viewport.sendSelection();
2246   }
2247
2248   public void deselectAllSequenceMenuItem_actionPerformed()
2249   {
2250     if (viewport.cursorMode)
2251     {
2252       alignPanel.seqPanel.keyboardNo1 = null;
2253       alignPanel.seqPanel.keyboardNo2 = null;
2254     }
2255     viewport.setSelectionGroup(null);
2256     viewport.getColumnSelection().clear();
2257     viewport.setSelectionGroup(null);
2258     alignPanel.idPanel.idCanvas.searchResults = null;
2259     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2260     // JAL-2034 - should delegate to
2261     // alignPanel to decide if overview needs
2262     // updating.
2263     alignPanel.paintAlignment(false);
2264     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2265     viewport.sendSelection();
2266   }
2267
2268   public void invertSequenceMenuItem_actionPerformed()
2269   {
2270     SequenceGroup sg = viewport.getSelectionGroup();
2271     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2272     {
2273       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2274     }
2275
2276     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277     viewport.sendSelection();
2278   }
2279
2280   public void invertColSel_actionPerformed()
2281   {
2282     viewport.invertColumnSelection();
2283     alignPanel.paintAlignment(true);
2284     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2285     viewport.sendSelection();
2286   }
2287
2288   void trimAlignment(boolean trimLeft)
2289   {
2290     ColumnSelection colSel = viewport.getColumnSelection();
2291     int column;
2292
2293     if (!colSel.isEmpty())
2294     {
2295       if (trimLeft)
2296       {
2297         column = colSel.getMin();
2298       }
2299       else
2300       {
2301         column = colSel.getMax();
2302       }
2303
2304       SequenceI[] seqs;
2305       if (viewport.getSelectionGroup() != null)
2306       {
2307         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2308                 viewport.getHiddenRepSequences());
2309       }
2310       else
2311       {
2312         seqs = viewport.getAlignment().getSequencesArray();
2313       }
2314
2315       TrimRegionCommand trimRegion;
2316       if (trimLeft)
2317       {
2318         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2319                 column, viewport.getAlignment());
2320         viewport.setStartRes(0);
2321       }
2322       else
2323       {
2324         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2325                 column, viewport.getAlignment());
2326       }
2327
2328       statusBar.setText(MessageManager.formatMessage(
2329               "label.removed_columns",
2330               new String[] { Integer.valueOf(trimRegion.getSize())
2331                       .toString() }));
2332       addHistoryItem(trimRegion);
2333
2334       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2335       {
2336         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2337                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2338         {
2339           viewport.getAlignment().deleteGroup(sg);
2340         }
2341       }
2342
2343       viewport.firePropertyChange("alignment", null, viewport
2344               .getAlignment().getSequences());
2345     }
2346   }
2347
2348   public void removeGappedColumnMenuItem_actionPerformed()
2349   {
2350     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2351
2352     SequenceI[] seqs;
2353     if (viewport.getSelectionGroup() != null)
2354     {
2355       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2356               viewport.getHiddenRepSequences());
2357       start = viewport.getSelectionGroup().getStartRes();
2358       end = viewport.getSelectionGroup().getEndRes();
2359     }
2360     else
2361     {
2362       seqs = viewport.getAlignment().getSequencesArray();
2363     }
2364
2365     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2366             "Remove Gapped Columns", seqs, start, end,
2367             viewport.getAlignment());
2368
2369     addHistoryItem(removeGapCols);
2370
2371     statusBar.setText(MessageManager.formatMessage(
2372             "label.removed_empty_columns",
2373             new String[] { Integer.valueOf(removeGapCols.getSize())
2374                     .toString() }));
2375
2376     // This is to maintain viewport position on first residue
2377     // of first sequence
2378     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2379     int startRes = seq.findPosition(viewport.startRes);
2380     // ShiftList shifts;
2381     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2382     // edit.alColumnChanges=shifts.getInverse();
2383     // if (viewport.hasHiddenColumns)
2384     // viewport.getColumnSelection().compensateForEdits(shifts);
2385     viewport.setStartRes(seq.findIndex(startRes) - 1);
2386     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2387             .getSequences());
2388
2389   }
2390
2391   public void removeAllGapsMenuItem_actionPerformed()
2392   {
2393     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2394
2395     SequenceI[] seqs;
2396     if (viewport.getSelectionGroup() != null)
2397     {
2398       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2399               viewport.getHiddenRepSequences());
2400       start = viewport.getSelectionGroup().getStartRes();
2401       end = viewport.getSelectionGroup().getEndRes();
2402     }
2403     else
2404     {
2405       seqs = viewport.getAlignment().getSequencesArray();
2406     }
2407
2408     // This is to maintain viewport position on first residue
2409     // of first sequence
2410     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2411     int startRes = seq.findPosition(viewport.startRes);
2412
2413     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2414             viewport.getAlignment()));
2415
2416     viewport.setStartRes(seq.findIndex(startRes) - 1);
2417
2418     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2419             .getSequences());
2420
2421   }
2422
2423   public void findMenuItem_actionPerformed()
2424   {
2425     new Finder(alignPanel);
2426   }
2427
2428   /**
2429    * create a new view derived from the current view
2430    *
2431    * @param viewtitle
2432    * @return frame for the new view
2433    */
2434   public AlignFrame newView(String viewtitle)
2435   {
2436     AlignmentI newal;
2437     if (viewport.hasHiddenRows())
2438     {
2439       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2440               .getFullAlignment().getSequencesArray());
2441     }
2442     else
2443     {
2444       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2445     }
2446
2447     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2448     {
2449       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2450       {
2451         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2452         {
2453           newal.addAnnotation(viewport.getAlignment()
2454                   .getAlignmentAnnotation()[i]);
2455         }
2456       }
2457     }
2458
2459     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2460
2461     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2462     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2463     PaintRefresher.Register(newaf.alignPanel,
2464             newaf.alignPanel.av.getSequenceSetId());
2465
2466     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2467             newaf.alignPanel.av.getSequenceSetId());
2468     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2469             newaf.alignPanel.av.getSequenceSetId());
2470
2471     Vector comps = (Vector) PaintRefresher.components.get(viewport
2472             .getSequenceSetId());
2473     int viewSize = -1;
2474     for (int i = 0; i < comps.size(); i++)
2475     {
2476       if (comps.elementAt(i) instanceof AlignmentPanel)
2477       {
2478         viewSize++;
2479       }
2480     }
2481
2482     String title = new String(this.getTitle());
2483     if (viewtitle != null)
2484     {
2485       title = viewtitle + " ( " + title + ")";
2486     }
2487     else
2488     {
2489       if (title.indexOf("(View") > -1)
2490       {
2491         title = title.substring(0, title.indexOf("(View"));
2492       }
2493       title += "(View " + viewSize + ")";
2494     }
2495
2496     newaf.setTitle(title.toString());
2497
2498     newaf.viewport.setHistoryList(viewport.getHistoryList());
2499     newaf.viewport.setRedoList(viewport.getRedoList());
2500     return newaf;
2501   }
2502
2503   /**
2504    *
2505    * @return list of feature groups on the view
2506    */
2507   public String[] getFeatureGroups()
2508   {
2509     FeatureRenderer fr = null;
2510     if (alignPanel != null
2511             && (fr = alignPanel.getFeatureRenderer()) != null)
2512     {
2513       List<String> gps = fr.getFeatureGroups();
2514       String[] _gps = gps.toArray(new String[gps.size()]);
2515       return _gps;
2516     }
2517     return null;
2518   }
2519
2520   /**
2521    * get sequence feature groups that are hidden or shown
2522    *
2523    * @param visible
2524    *          true is visible
2525    * @return list
2526    */
2527   public String[] getFeatureGroupsOfState(boolean visible)
2528   {
2529     FeatureRenderer fr = null;
2530     if (alignPanel != null
2531             && (fr = alignPanel.getFeatureRenderer()) != null)
2532     {
2533       List<String> gps = fr.getGroups(visible);
2534       String[] _gps = gps.toArray(new String[gps.size()]);
2535       return _gps;
2536     }
2537     return null;
2538   }
2539
2540   /**
2541    * Change the display state for the given feature groups
2542    *
2543    * @param groups
2544    *          list of group strings
2545    * @param state
2546    *          visible or invisible
2547    */
2548   public void setFeatureGroupState(String[] groups, boolean state)
2549   {
2550     FeatureRenderer fr = null;
2551     this.sequenceFeatures.setState(true);
2552     viewport.setShowSequenceFeatures(true);
2553     if (alignPanel != null
2554             && (fr = alignPanel.getFeatureRenderer()) != null)
2555     {
2556
2557       fr.setGroupVisibility(Arrays.asList(groups), state);
2558       alignPanel.seqPanel.seqCanvas.repaint();
2559       if (alignPanel.overviewPanel != null)
2560       {
2561         alignPanel.overviewPanel.updateOverviewImage();
2562       }
2563     }
2564   }
2565
2566   public void seqLimits_itemStateChanged()
2567   {
2568     viewport.setShowJVSuffix(seqLimits.getState());
2569     alignPanel.fontChanged();
2570     alignPanel.paintAlignment(true);
2571   }
2572
2573   protected void colourTextMenuItem_actionPerformed()
2574   {
2575     viewport.setColourText(colourTextMenuItem.getState());
2576     alignPanel.paintAlignment(true);
2577   }
2578
2579   protected void displayNonconservedMenuItem_actionPerformed()
2580   {
2581     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2582     alignPanel.paintAlignment(true);
2583   }
2584
2585   protected void wrapMenuItem_actionPerformed()
2586   {
2587     viewport.setWrapAlignment(wrapMenuItem.getState());
2588     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2589     scaleAbove.setEnabled(wrapMenuItem.getState());
2590     scaleLeft.setEnabled(wrapMenuItem.getState());
2591     scaleRight.setEnabled(wrapMenuItem.getState());
2592     alignPanel.paintAlignment(true);
2593   }
2594
2595   public void overviewMenuItem_actionPerformed()
2596   {
2597     if (alignPanel.overviewPanel != null)
2598     {
2599       return;
2600     }
2601
2602     Frame frame = new Frame();
2603     OverviewPanel overview = new OverviewPanel(alignPanel);
2604     frame.add(overview);
2605     // +50 must allow for applet frame window
2606     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2607             "label.overview_params", new String[] { this.getTitle() }),
2608             overview.getPreferredSize().width,
2609             overview.getPreferredSize().height + 50);
2610
2611     frame.pack();
2612     final AlignmentPanel ap = alignPanel;
2613     frame.addWindowListener(new WindowAdapter()
2614     {
2615       @Override
2616       public void windowClosing(WindowEvent e)
2617       {
2618         if (ap != null)
2619         {
2620           ap.setOverviewPanel(null);
2621         }
2622       };
2623     });
2624
2625     alignPanel.setOverviewPanel(overview);
2626
2627   }
2628
2629   @Override
2630   public void changeColour(ColourSchemeI cs)
2631   {
2632
2633     if (cs != null)
2634     {
2635       if (viewport.getAbovePIDThreshold())
2636       {
2637         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2638                 cs, "Background"));
2639       }
2640
2641       if (viewport.getConservationSelected())
2642       {
2643         cs.setConservationApplied(true);
2644         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2645                 cs, "Background"));
2646       }
2647       else
2648       {
2649         cs.setConservationApplied(false);
2650       }
2651     }
2652     viewport.setGlobalColourScheme(cs);
2653
2654     alignPanel.paintAlignment(true);
2655   }
2656
2657   protected void modifyPID_actionPerformed()
2658   {
2659     if (viewport.getAbovePIDThreshold()
2660             && viewport.getGlobalColourScheme() != null)
2661     {
2662       SliderPanel.setPIDSliderSource(alignPanel,
2663               viewport.getGlobalColourScheme(), "Background");
2664       SliderPanel.showPIDSlider();
2665     }
2666   }
2667
2668   protected void modifyConservation_actionPerformed()
2669   {
2670     if (viewport.getConservationSelected()
2671             && viewport.getGlobalColourScheme() != null)
2672     {
2673       SliderPanel.setConservationSlider(alignPanel,
2674               viewport.getGlobalColourScheme(), "Background");
2675       SliderPanel.showConservationSlider();
2676     }
2677   }
2678
2679   protected void conservationMenuItem_actionPerformed()
2680   {
2681     boolean selected = conservationMenuItem.getState();
2682     modifyConservation.setEnabled(selected);
2683     viewport.setConservationSelected(selected);
2684
2685     // viewport.setAbovePIDThreshold(false);
2686     // abovePIDThreshold.setState(false);
2687
2688     changeColour(viewport.getGlobalColourScheme());
2689
2690     if (selected)
2691     {
2692       modifyConservation_actionPerformed();
2693     }
2694     else
2695     {
2696       SliderPanel.hideConservationSlider();
2697     }
2698   }
2699
2700   public void abovePIDThreshold_actionPerformed()
2701   {
2702     boolean selected = abovePIDThreshold.getState();
2703     modifyPID.setEnabled(selected);
2704     viewport.setAbovePIDThreshold(selected);
2705     // conservationMenuItem.setState(false);
2706     // viewport.setConservationSelected(false);
2707
2708     changeColour(viewport.getGlobalColourScheme());
2709
2710     if (selected)
2711     {
2712       modifyPID_actionPerformed();
2713     }
2714     else
2715     {
2716       SliderPanel.hidePIDSlider();
2717     }
2718   }
2719
2720   public void sortPairwiseMenuItem_actionPerformed()
2721   {
2722     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2724             .getAlignment().getSequenceAt(0), null);
2725
2726     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2727             viewport.getAlignment()));
2728     alignPanel.paintAlignment(true);
2729   }
2730
2731   public void sortIDMenuItem_actionPerformed()
2732   {
2733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734     AlignmentSorter.sortByID(viewport.getAlignment());
2735     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2736             viewport.getAlignment()));
2737     alignPanel.paintAlignment(true);
2738   }
2739
2740   public void sortLengthMenuItem_actionPerformed()
2741   {
2742     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2743     AlignmentSorter.sortByLength(viewport.getAlignment());
2744     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2745             viewport.getAlignment()));
2746     alignPanel.paintAlignment(true);
2747   }
2748
2749   public void sortGroupMenuItem_actionPerformed()
2750   {
2751     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752     AlignmentSorter.sortByGroup(viewport.getAlignment());
2753     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2754             viewport.getAlignment()));
2755     alignPanel.paintAlignment(true);
2756
2757   }
2758
2759   public void removeRedundancyMenuItem_actionPerformed()
2760   {
2761     new RedundancyPanel(alignPanel);
2762   }
2763
2764   public void pairwiseAlignmentMenuItem_actionPerformed()
2765   {
2766     if (viewport.getSelectionGroup() != null
2767             && viewport.getSelectionGroup().getSize() > 1)
2768     {
2769       Frame frame = new Frame();
2770       frame.add(new PairwiseAlignPanel(alignPanel));
2771       jalview.bin.JalviewLite.addFrame(frame,
2772               MessageManager.getString("action.pairwise_alignment"), 600,
2773               500);
2774     }
2775   }
2776
2777   public void PCAMenuItem_actionPerformed()
2778   {
2779     // are the sequences aligned?
2780     if (!viewport.getAlignment().isAligned(false))
2781     {
2782       SequenceI current;
2783       int Width = viewport.getAlignment().getWidth();
2784
2785       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2786       {
2787         current = viewport.getAlignment().getSequenceAt(i);
2788
2789         if (current.getLength() < Width)
2790         {
2791           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2792         }
2793       }
2794       alignPanel.paintAlignment(true);
2795     }
2796
2797     if ((viewport.getSelectionGroup() != null
2798             && viewport.getSelectionGroup().getSize() < 4 && viewport
2799             .getSelectionGroup().getSize() > 0)
2800             || viewport.getAlignment().getHeight() < 4)
2801     {
2802       return;
2803     }
2804
2805     try
2806     {
2807       new PCAPanel(viewport);
2808     } catch (java.lang.OutOfMemoryError ex)
2809     {
2810     }
2811
2812   }
2813
2814   public void averageDistanceTreeMenuItem_actionPerformed()
2815   {
2816     NewTreePanel("AV", "PID", "Average distance tree using PID");
2817   }
2818
2819   public void neighbourTreeMenuItem_actionPerformed()
2820   {
2821     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2822   }
2823
2824   protected void njTreeBlosumMenuItem_actionPerformed()
2825   {
2826     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2827   }
2828
2829   protected void avTreeBlosumMenuItem_actionPerformed()
2830   {
2831     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2832   }
2833
2834   void NewTreePanel(String type, String pwType, String title)
2835   {
2836     // are the sequences aligned?
2837     if (!viewport.getAlignment().isAligned(false))
2838     {
2839       SequenceI current;
2840       int Width = viewport.getAlignment().getWidth();
2841
2842       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2843       {
2844         current = viewport.getAlignment().getSequenceAt(i);
2845
2846         if (current.getLength() < Width)
2847         {
2848           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2849         }
2850       }
2851       alignPanel.paintAlignment(true);
2852
2853     }
2854
2855     if ((viewport.getSelectionGroup() != null && viewport
2856             .getSelectionGroup().getSize() > 1)
2857             || (viewport.getAlignment().getHeight() > 1))
2858     {
2859       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2860
2861       addTreeMenuItem(tp, title);
2862
2863       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2864     }
2865   }
2866
2867   void loadTree_actionPerformed()
2868   {
2869     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2870     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2871     cap.setTreeImport();
2872     Frame frame = new Frame();
2873     frame.add(cap);
2874     jalview.bin.JalviewLite.addFrame(frame,
2875             MessageManager.getString("label.paste_newick_file"), 400, 300);
2876   }
2877
2878   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2879   {
2880     TreePanel tp = new TreePanel(alignPanel, treeFile,
2881             MessageManager.getString("label.load_tree_from_file"), tree);
2882     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2883     addTreeMenuItem(tp, treeFile);
2884   }
2885
2886   /**
2887    * sort the alignment using the given treePanel
2888    *
2889    * @param treePanel
2890    *          tree used to sort view
2891    * @param title
2892    *          string used for undo event name
2893    */
2894   public void sortByTree(TreePanel treePanel, String title)
2895   {
2896     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2897     AlignmentSorter
2898             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2899     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2900     // HistoryItem.SORT));
2901     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2902             "label.order_by_params", new String[] { title }), oldOrder,
2903             viewport.getAlignment()));
2904     alignPanel.paintAlignment(true);
2905   }
2906
2907   /**
2908    * Do any automatic reordering of the alignment and add the necessary bits to
2909    * the menu structure for the new tree
2910    *
2911    * @param treePanel
2912    * @param title
2913    */
2914   protected void addTreeMenuItem(final TreePanel treePanel,
2915           final String title)
2916   {
2917     final MenuItem item = new MenuItem(title);
2918     sortByTreeMenu.add(item);
2919     item.addActionListener(new java.awt.event.ActionListener()
2920     {
2921       @Override
2922       public void actionPerformed(ActionEvent evt)
2923       {
2924         sortByTree(treePanel, title); // treePanel.getTitle());
2925       }
2926     });
2927
2928     treePanel.addWindowListener(new WindowAdapter()
2929     {
2930       @Override
2931       public void windowOpened(WindowEvent e)
2932       {
2933         if (viewport.sortByTree)
2934         {
2935           sortByTree(treePanel, title);
2936         }
2937         super.windowOpened(e);
2938       }
2939
2940       @Override
2941       public void windowClosing(WindowEvent e)
2942       {
2943         sortByTreeMenu.remove(item);
2944       };
2945     });
2946   }
2947
2948   public boolean sortBy(AlignmentOrder alorder, String undoname)
2949   {
2950     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2951     if (viewport.applet.debug)
2952     {
2953       System.err.println("Sorting " + alorder.getOrder().size()
2954               + " in alignment '" + getTitle() + "'");
2955     }
2956     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2957     if (undoname != null)
2958     {
2959       addHistoryItem(new OrderCommand(undoname, oldOrder,
2960               viewport.getAlignment()));
2961     }
2962     alignPanel.paintAlignment(true);
2963     return true;
2964   }
2965
2966   protected void documentation_actionPerformed()
2967   {
2968     alignPanel.av.applet.openJalviewHelpUrl();
2969   }
2970
2971   protected void about_actionPerformed()
2972   {
2973
2974     class AboutPanel extends Canvas
2975     {
2976       String version;
2977
2978       String builddate;
2979
2980       public AboutPanel(String version, String builddate)
2981       {
2982         this.version = version;
2983         this.builddate = builddate;
2984       }
2985
2986       @Override
2987       public void paint(Graphics g)
2988       {
2989         g.setColor(Color.white);
2990         g.fillRect(0, 0, getSize().width, getSize().height);
2991         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2992         FontMetrics fm = g.getFontMetrics();
2993         int fh = fm.getHeight();
2994         int y = 5, x = 7;
2995         g.setColor(Color.black);
2996         // TODO: update this text for each release or centrally store it for
2997         // lite and application
2998         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2999         g.drawString(MessageManager.formatMessage(
3000                 "label.jalviewLite_release", new String[] { version }), x,
3001                 y += fh);
3002         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3003         g.drawString(MessageManager.formatMessage(
3004                 "label.jaview_build_date", new String[] { builddate }), x,
3005                 y += fh);
3006         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3007         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3008                 x, y += fh * 1.5);
3009         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3010                 x + 50, y += fh + 8);
3011         g.drawString(
3012                 MessageManager.getString("label.jalview_dev_managers"), x,
3013                 y += fh);
3014         g.drawString(MessageManager
3015                 .getString("label.jalview_distribution_lists"), x, y += fh);
3016         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3017                 x, y += fh + 8);
3018         g.drawString(
3019                 MessageManager.getString("label.jalview_cite_1_authors"),
3020                 x, y += fh);
3021         g.drawString(
3022                 MessageManager.getString("label.jalview_cite_1_title"), x,
3023                 y += fh);
3024         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3025                 x, y += fh);
3026       }
3027     }
3028
3029     Frame frame = new Frame();
3030     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3031             .getBuildDate()));
3032     jalview.bin.JalviewLite.addFrame(frame,
3033             MessageManager.getString("label.jalview"), 580, 220);
3034
3035   }
3036
3037   public void showURL(String url, String target)
3038   {
3039     if (viewport.applet == null)
3040     {
3041       System.out.println("Not running as applet - no browser available.");
3042     }
3043     else
3044     {
3045       viewport.applet.showURL(url, target);
3046     }
3047   }
3048
3049   // ////////////////////////////////////////////////////////////////////////////////
3050   // JBuilder Graphics here
3051
3052   MenuBar alignFrameMenuBar = new MenuBar();
3053
3054   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3055
3056   MenuItem loadApplication = new MenuItem(
3057           MessageManager.getString("label.view_full_application"));
3058
3059   MenuItem loadTree = new MenuItem(
3060           MessageManager.getString("label.load_associated_tree"));
3061
3062   MenuItem loadAnnotations = new MenuItem(
3063           MessageManager.getString("label.load_features_annotations"));
3064
3065   MenuItem outputFeatures = new MenuItem(
3066           MessageManager.getString("label.export_features"));
3067
3068   MenuItem outputAnnotations = new MenuItem(
3069           MessageManager.getString("label.export_annotations"));
3070
3071   MenuItem closeMenuItem = new MenuItem(
3072           MessageManager.getString("action.close"));
3073
3074   MenuItem selectAllSequenceMenuItem = new MenuItem(
3075           MessageManager.getString("action.select_all"));
3076
3077   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3078           MessageManager.getString("action.deselect_all"));
3079
3080   MenuItem invertSequenceMenuItem = new MenuItem(
3081           MessageManager.getString("action.invert_selection"));
3082
3083   MenuItem remove2LeftMenuItem = new MenuItem();
3084
3085   MenuItem remove2RightMenuItem = new MenuItem();
3086
3087   MenuItem removeGappedColumnMenuItem = new MenuItem();
3088
3089   MenuItem removeAllGapsMenuItem = new MenuItem();
3090
3091   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3092
3093   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3094
3095   MenuItem sortPairwiseMenuItem = new MenuItem();
3096
3097   MenuItem sortIDMenuItem = new MenuItem();
3098
3099   MenuItem sortLengthMenuItem = new MenuItem();
3100
3101   MenuItem sortGroupMenuItem = new MenuItem();
3102
3103   MenuItem removeRedundancyMenuItem = new MenuItem();
3104
3105   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3106
3107   MenuItem PCAMenuItem = new MenuItem();
3108
3109   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3110
3111   MenuItem neighbourTreeMenuItem = new MenuItem();
3112
3113   BorderLayout borderLayout1 = new BorderLayout();
3114
3115   public Label statusBar = new Label();
3116
3117   MenuItem clustalColour = new MenuItem();
3118
3119   MenuItem zappoColour = new MenuItem();
3120
3121   MenuItem taylorColour = new MenuItem();
3122
3123   MenuItem hydrophobicityColour = new MenuItem();
3124
3125   MenuItem helixColour = new MenuItem();
3126
3127   MenuItem strandColour = new MenuItem();
3128
3129   MenuItem turnColour = new MenuItem();
3130
3131   MenuItem buriedColour = new MenuItem();
3132
3133   MenuItem purinePyrimidineColour = new MenuItem();
3134
3135   // MenuItem RNAInteractionColour = new MenuItem();
3136
3137   MenuItem RNAHelixColour = new MenuItem();
3138
3139   MenuItem userDefinedColour = new MenuItem();
3140
3141   MenuItem PIDColour = new MenuItem();
3142
3143   MenuItem BLOSUM62Colour = new MenuItem();
3144
3145   MenuItem tcoffeeColour = new MenuItem();
3146
3147   MenuItem njTreeBlosumMenuItem = new MenuItem();
3148
3149   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3150
3151   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3152
3153   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3154
3155   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3156
3157   MenuItem alProperties = new MenuItem(
3158           MessageManager.getString("label.alignment_props"));
3159
3160   MenuItem overviewMenuItem = new MenuItem();
3161
3162   MenuItem undoMenuItem = new MenuItem();
3163
3164   MenuItem redoMenuItem = new MenuItem();
3165
3166   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3167
3168   MenuItem noColourmenuItem = new MenuItem();
3169
3170   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3171
3172   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3173
3174   MenuItem findMenuItem = new MenuItem();
3175
3176   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3177
3178   MenuItem nucleotideColour = new MenuItem();
3179
3180   MenuItem deleteGroups = new MenuItem();
3181
3182   MenuItem grpsFromSelection = new MenuItem();
3183
3184   MenuItem createGroup = new MenuItem();
3185
3186   MenuItem unGroup = new MenuItem();
3187
3188   MenuItem delete = new MenuItem();
3189
3190   MenuItem copy = new MenuItem();
3191
3192   MenuItem cut = new MenuItem();
3193
3194   Menu pasteMenu = new Menu();
3195
3196   MenuItem pasteNew = new MenuItem();
3197
3198   MenuItem pasteThis = new MenuItem();
3199
3200   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3201
3202   MenuItem font = new MenuItem();
3203
3204   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3205
3206   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3209
3210   MenuItem modifyPID = new MenuItem();
3211
3212   MenuItem modifyConservation = new MenuItem();
3213
3214   CheckboxMenuItem autoCalculate = null;
3215
3216   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3217           "Sort Alignment With New Tree", true);
3218
3219   Menu sortByTreeMenu = new Menu();
3220
3221   MenuItem inputText = new MenuItem();
3222
3223   MenuItem documentation = new MenuItem();
3224
3225   MenuItem about = new MenuItem();
3226
3227   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3228
3229   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3230
3231   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3232
3233   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3234
3235   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3236
3237   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3238
3239   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3240
3241   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3242
3243   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3244
3245   /**
3246    * Initialise menus and other items
3247    *
3248    * @throws Exception
3249    */
3250   private void jbInit() throws Exception
3251   {
3252     setMenuBar(alignFrameMenuBar);
3253
3254     /*
3255      * Configure File menu items and actions
3256      */
3257     inputText
3258             .setLabel(MessageManager.getString("label.input_from_textbox"));
3259     inputText.addActionListener(this);
3260     Menu outputTextboxMenu = new Menu(
3261             MessageManager.getString("label.out_to_textbox"));
3262     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3263     {
3264       MenuItem item = new MenuItem(ff);
3265
3266       item.addActionListener(new java.awt.event.ActionListener()
3267       {
3268         @Override
3269         public void actionPerformed(ActionEvent e)
3270         {
3271           outputText_actionPerformed(e);
3272         }
3273       });
3274
3275       outputTextboxMenu.add(item);
3276     }
3277     closeMenuItem.addActionListener(this);
3278     loadApplication.addActionListener(this);
3279     loadTree.addActionListener(this);
3280     loadAnnotations.addActionListener(this);
3281     outputFeatures.addActionListener(this);
3282     outputAnnotations.addActionListener(this);
3283
3284     /*
3285      * Configure Edit menu items and actions
3286      */
3287     undoMenuItem.setEnabled(false);
3288     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3289     undoMenuItem.addActionListener(this);
3290     redoMenuItem.setEnabled(false);
3291     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3292     redoMenuItem.addActionListener(this);
3293     copy.setLabel(MessageManager.getString("action.copy"));
3294     copy.addActionListener(this);
3295     cut.setLabel(MessageManager.getString("action.cut"));
3296     cut.addActionListener(this);
3297     delete.setLabel(MessageManager.getString("action.delete"));
3298     delete.addActionListener(this);
3299     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3300     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3301     pasteNew.addActionListener(this);
3302     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3303     pasteThis.addActionListener(this);
3304     remove2LeftMenuItem.setLabel(MessageManager
3305             .getString("action.remove_left"));
3306     remove2LeftMenuItem.addActionListener(this);
3307     remove2RightMenuItem.setLabel(MessageManager
3308             .getString("action.remove_right"));
3309     remove2RightMenuItem.addActionListener(this);
3310     removeGappedColumnMenuItem.setLabel(MessageManager
3311             .getString("action.remove_empty_columns"));
3312     removeGappedColumnMenuItem.addActionListener(this);
3313     removeAllGapsMenuItem.setLabel(MessageManager
3314             .getString("action.remove_all_gaps"));
3315     removeAllGapsMenuItem.addActionListener(this);
3316     removeRedundancyMenuItem.setLabel(MessageManager
3317             .getString("action.remove_redundancy"));
3318     removeRedundancyMenuItem.addActionListener(this);
3319
3320     /*
3321      * Configure Select menu items and actions
3322      */
3323     findMenuItem.setLabel(MessageManager.getString("action.find"));
3324     findMenuItem.addActionListener(this);
3325     selectAllSequenceMenuItem.addActionListener(this);
3326     deselectAllSequenceMenuItem.addActionListener(this);
3327     invertSequenceMenuItem.setLabel(MessageManager
3328             .getString("action.invert_sequence_selection"));
3329     invertSequenceMenuItem.addActionListener(this);
3330     invertColSel.setLabel(MessageManager
3331             .getString("action.invert_column_selection"));
3332     invertColSel.addActionListener(this);
3333     deleteGroups.setLabel(MessageManager
3334             .getString("action.undefine_groups"));
3335     deleteGroups.addActionListener(this);
3336     grpsFromSelection.setLabel(MessageManager
3337             .getString("action.make_groups_selection"));
3338     grpsFromSelection.addActionListener(this);
3339     createGroup.setLabel(MessageManager.getString("action.create_group"));
3340     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3341     annotationColumnSelection.setLabel(MessageManager
3342             .getString("action.select_by_annotation"));
3343     annotationColumnSelection.addActionListener(this);
3344
3345     /*
3346      * Configure View menu items and actions
3347      */
3348     newView.setLabel(MessageManager.getString("action.new_view"));
3349     newView.addActionListener(this);
3350     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3351     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3352     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3353     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3354     hideColumns
3355             .setLabel(MessageManager.getString("label.selected_columns"));
3356     hideSequences.setLabel(MessageManager
3357             .getString("label.selected_sequences"));
3358     hideAllButSelection.setLabel(MessageManager
3359             .getString("label.all_but_selected_region"));
3360     hideAllSelection.setLabel(MessageManager
3361             .getString("label.selected_region"));
3362     showAllHidden.setLabel(MessageManager
3363             .getString("label.all_sequences_columns"));
3364     showColumns.addActionListener(this);
3365     showSeqs.addActionListener(this);
3366     hideColumns.addActionListener(this);
3367     hideSequences.addActionListener(this);
3368     hideAllButSelection.addActionListener(this);
3369     hideAllSelection.addActionListener(this);
3370     showAllHidden.addActionListener(this);
3371     featureSettings.setLabel(MessageManager
3372             .getString("action.feature_settings"));
3373     featureSettings.addActionListener(this);
3374     sequenceFeatures.setLabel(MessageManager
3375             .getString("label.show_sequence_features"));
3376     sequenceFeatures.addItemListener(this);
3377     sequenceFeatures.setState(false);
3378     followMouseOverFlag.setLabel(MessageManager
3379             .getString("label.automatic_scrolling"));
3380     followMouseOverFlag.addItemListener(this);
3381     alProperties.addActionListener(this);
3382     overviewMenuItem.setLabel(MessageManager
3383             .getString("label.overview_window"));
3384     overviewMenuItem.addActionListener(this);
3385
3386     /*
3387      * Configure Annotations menu items and actions
3388      */
3389     annotationPanelMenuItem.setLabel(MessageManager
3390             .getString("label.show_annotations"));
3391     annotationPanelMenuItem.addItemListener(this);
3392     showGroupConsensus.setLabel(MessageManager
3393             .getString("label.group_consensus"));
3394     showGroupConservation.setLabel(MessageManager
3395             .getString("label.group_conservation"));
3396     showConsensusHistogram.setLabel(MessageManager
3397             .getString("label.show_consensus_histogram"));
3398     showSequenceLogo.setLabel(MessageManager
3399             .getString("label.show_consensus_logo"));
3400     normSequenceLogo.setLabel(MessageManager
3401             .getString("label.norm_consensus_logo"));
3402     applyAutoAnnotationSettings.setLabel(MessageManager
3403             .getString("label.apply_all_groups"));
3404     applyAutoAnnotationSettings.setState(true);
3405     Menu autoAnnMenu = new Menu(
3406             MessageManager.getString("label.autocalculated_annotation"));
3407     showGroupConsensus.addItemListener(this);
3408     showGroupConservation.addItemListener(this);
3409     showConsensusHistogram.addItemListener(this);
3410     showSequenceLogo.addItemListener(this);
3411     normSequenceLogo.addItemListener(this);
3412     applyAutoAnnotationSettings.addItemListener(this);
3413     showAlignmentAnnotations = new CheckboxMenuItem(
3414             MessageManager.getString("label.show_all_al_annotations"));
3415     showSequenceAnnotations = new CheckboxMenuItem(
3416             MessageManager.getString("label.show_all_seq_annotations"));
3417     sortAnnBySequence = new CheckboxMenuItem(
3418             MessageManager.getString("label.sort_annotations_by_sequence"));
3419     sortAnnByLabel = new CheckboxMenuItem(
3420             MessageManager.getString("label.sort_annotations_by_label"));
3421     showAutoFirst = new CheckboxMenuItem(
3422             MessageManager.getString("label.show_first"));
3423     showAutoFirst.setState(false); // pending applet parameter
3424     setShowAutoCalculatedAbove(showAutoFirst.getState());
3425     showAutoLast = new CheckboxMenuItem(
3426             MessageManager.getString("label.show_last"));
3427     showAutoLast.setState(!showAutoFirst.getState());
3428     showAlignmentAnnotations.addItemListener(this);
3429     showSequenceAnnotations.addItemListener(this);
3430     sortAnnBySequence.addItemListener(this);
3431     sortAnnByLabel.addItemListener(this);
3432     showAutoFirst.addItemListener(this);
3433     showAutoLast.addItemListener(this);
3434
3435     /*
3436      * Configure Format menu items and actions
3437      */
3438     font.setLabel(MessageManager.getString("action.font"));
3439     font.addActionListener(this);
3440     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3441     scaleAbove.setState(true);
3442     scaleAbove.setEnabled(false);
3443     scaleAbove.addItemListener(this);
3444     scaleLeft.setEnabled(false);
3445     scaleLeft.setState(true);
3446     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3447     scaleLeft.addItemListener(this);
3448     scaleRight.setEnabled(false);
3449     scaleRight.setState(true);
3450     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3451     scaleRight.addItemListener(this);
3452     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3453     viewBoxesMenuItem.setState(true);
3454     viewBoxesMenuItem.addItemListener(this);
3455     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3456     viewTextMenuItem.setState(true);
3457     viewTextMenuItem.addItemListener(this);
3458     colourTextMenuItem.setLabel(MessageManager
3459             .getString("label.colour_text"));
3460     colourTextMenuItem.addItemListener(this);
3461     displayNonconservedMenuItem.setLabel(MessageManager
3462             .getString("label.show_non_conversed"));
3463     displayNonconservedMenuItem.addItemListener(this);
3464     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3465     wrapMenuItem.addItemListener(this);
3466     renderGapsMenuItem.setLabel(MessageManager
3467             .getString("action.show_gaps"));
3468     renderGapsMenuItem.setState(true);
3469     renderGapsMenuItem.addItemListener(this);
3470     centreColumnLabelFlag.setLabel(MessageManager
3471             .getString("label.centre_column_labels"));
3472     centreColumnLabelFlag.addItemListener(this);
3473     seqLimits.setState(true);
3474     seqLimits.setLabel(MessageManager
3475             .getString("label.show_sequence_limits"));
3476     seqLimits.addItemListener(this);
3477
3478     /*
3479      * Configure Colour menu items and actions
3480      */
3481     applyToAllGroups.setLabel(MessageManager
3482             .getString("label.apply_colour_to_all_groups"));
3483     applyToAllGroups.setState(true);
3484     applyToAllGroups.addItemListener(this);
3485     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3486     clustalColour.addActionListener(this);
3487     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3488     zappoColour.addActionListener(this);
3489     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3490     taylorColour.addActionListener(this);
3491     hydrophobicityColour.setLabel(MessageManager
3492             .getString("label.hydrophobicity"));
3493     hydrophobicityColour.addActionListener(this);
3494     helixColour
3495             .setLabel(MessageManager.getString("label.helix_propensity"));
3496     helixColour.addActionListener(this);
3497     strandColour.setLabel(MessageManager
3498             .getString("label.strand_propensity"));
3499     strandColour.addActionListener(this);
3500     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3501     turnColour.addActionListener(this);
3502     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3503     buriedColour.addActionListener(this);
3504     purinePyrimidineColour.setLabel(MessageManager
3505             .getString("label.purine_pyrimidine"));
3506     purinePyrimidineColour.addActionListener(this);
3507     // RNAInteractionColour.setLabel(MessageManager
3508     // .getString("label.rna_interaction"));
3509     // RNAInteractionColour.addActionListener(this);
3510     RNAHelixColour.setLabel(MessageManager
3511             .getString("action.by_rna_helixes"));
3512     RNAHelixColour.addActionListener(this);
3513     userDefinedColour.setLabel(MessageManager
3514             .getString("action.user_defined"));
3515     userDefinedColour.addActionListener(this);
3516     PIDColour.setLabel(MessageManager
3517             .getString("label.percentage_identity"));
3518     PIDColour.addActionListener(this);
3519     BLOSUM62Colour.setLabel(MessageManager
3520             .getString("label.blosum62_score"));
3521     BLOSUM62Colour.addActionListener(this);
3522     tcoffeeColour
3523             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3524     // it will be enabled only if a score file is provided
3525     tcoffeeColour.setEnabled(false);
3526     tcoffeeColour.addActionListener(this);
3527     conservationMenuItem.setLabel(MessageManager
3528             .getString("action.by_conservation"));
3529     conservationMenuItem.addItemListener(this);
3530     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3531     noColourmenuItem.addActionListener(this);
3532     abovePIDThreshold.setLabel(MessageManager
3533             .getString("label.above_identity_threshold"));
3534     abovePIDThreshold.addItemListener(this);
3535     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3536     nucleotideColour.addActionListener(this);
3537     modifyPID.setLabel(MessageManager
3538             .getString("label.modify_identity_threshold"));
3539     modifyPID.setEnabled(abovePIDThreshold.getState());
3540     modifyPID.addActionListener(this);
3541     modifyConservation.setLabel(MessageManager
3542             .getString("label.modify_conservation_threshold"));
3543     modifyConservation.setEnabled(conservationMenuItem.getState());
3544     modifyConservation.addActionListener(this);
3545     annotationColour.setLabel(MessageManager
3546             .getString("action.by_annotation"));
3547     annotationColour.addActionListener(this);
3548
3549     /*
3550      * Configure Calculate menu items and actions
3551      */
3552     sortPairwiseMenuItem.setLabel(MessageManager
3553             .getString("action.by_pairwise_id"));
3554     sortPairwiseMenuItem.addActionListener(this);
3555     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3556     sortIDMenuItem.addActionListener(this);
3557     sortLengthMenuItem.setLabel(MessageManager
3558             .getString("action.by_length"));
3559     sortLengthMenuItem.addActionListener(this);
3560     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3561     sortGroupMenuItem.addActionListener(this);
3562     pairwiseAlignmentMenuItem.setLabel(MessageManager
3563             .getString("action.pairwise_alignment"));
3564     pairwiseAlignmentMenuItem.addActionListener(this);
3565     PCAMenuItem.setLabel(MessageManager
3566             .getString("label.principal_component_analysis"));
3567     PCAMenuItem.addActionListener(this);
3568     autoCalculate = new CheckboxMenuItem(
3569             MessageManager.getString("label.autocalculate_consensus"), true);
3570     averageDistanceTreeMenuItem.setLabel(MessageManager
3571             .getString("label.average_distance_identity"));
3572     averageDistanceTreeMenuItem.addActionListener(this);
3573     neighbourTreeMenuItem.setLabel(MessageManager
3574             .getString("label.neighbour_joining_identity"));
3575     neighbourTreeMenuItem.addActionListener(this);
3576     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3577             .getString("label.average_distance_bloslum62"));
3578     avDistanceTreeBlosumMenuItem.addActionListener(this);
3579     njTreeBlosumMenuItem.setLabel(MessageManager
3580             .getString("label.neighbour_blosum62"));
3581     njTreeBlosumMenuItem.addActionListener(this);
3582     sortByTreeMenu.setLabel(MessageManager
3583             .getString("action.by_tree_order"));
3584     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3585     Menu calculateTreeMenu = new Menu(
3586             MessageManager.getString("action.calculate_tree"));
3587     autoCalculate.addItemListener(this);
3588     sortByTree.addItemListener(this);
3589
3590     /*
3591      * Configure Help menu items and actions
3592      */
3593     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3594     documentation.setLabel(MessageManager.getString("label.documentation"));
3595     documentation.addActionListener(this);
3596     about.setLabel(MessageManager.getString("label.about"));
3597     about.addActionListener(this);
3598
3599     /*
3600      * Add top level menus to frame
3601      */
3602     alignFrameMenuBar.add(fileMenu);
3603     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3604     alignFrameMenuBar.add(editMenu);
3605     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3606     alignFrameMenuBar.add(selectMenu);
3607     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3608     alignFrameMenuBar.add(viewMenu);
3609     Menu annotationsMenu = new Menu(
3610             MessageManager.getString("action.annotations"));
3611     alignFrameMenuBar.add(annotationsMenu);
3612     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3613     alignFrameMenuBar.add(formatMenu);
3614     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3615     alignFrameMenuBar.add(colourMenu);
3616     Menu calculateMenu = new Menu(
3617             MessageManager.getString("action.calculate"));
3618     alignFrameMenuBar.add(calculateMenu);
3619     alignFrameMenuBar.add(helpMenu);
3620
3621     /*
3622      * File menu
3623      */
3624     fileMenu.add(inputText);
3625     fileMenu.add(loadTree);
3626     fileMenu.add(loadAnnotations);
3627     fileMenu.addSeparator();
3628     fileMenu.add(outputTextboxMenu);
3629     fileMenu.add(outputFeatures);
3630     fileMenu.add(outputAnnotations);
3631     if (jalviewServletURL != null)
3632     {
3633       fileMenu.add(loadApplication);
3634     }
3635     fileMenu.addSeparator();
3636     fileMenu.add(closeMenuItem);
3637
3638     /*
3639      * Edit menu
3640      */
3641     editMenu.add(undoMenuItem);
3642     editMenu.add(redoMenuItem);
3643     editMenu.add(cut);
3644     editMenu.add(copy);
3645     pasteMenu.add(pasteNew);
3646     pasteMenu.add(pasteThis);
3647     editMenu.add(pasteMenu);
3648     editMenu.add(delete);
3649     editMenu.addSeparator();
3650     editMenu.add(remove2LeftMenuItem);
3651     editMenu.add(remove2RightMenuItem);
3652     editMenu.add(removeGappedColumnMenuItem);
3653     editMenu.add(removeAllGapsMenuItem);
3654     editMenu.add(removeRedundancyMenuItem);
3655
3656     /*
3657      * Select menu
3658      */
3659     selectMenu.add(findMenuItem);
3660     selectMenu.addSeparator();
3661     selectMenu.add(selectAllSequenceMenuItem);
3662     selectMenu.add(deselectAllSequenceMenuItem);
3663     selectMenu.add(invertSequenceMenuItem);
3664     selectMenu.add(invertColSel);
3665     selectMenu.add(createGroup);
3666     selectMenu.add(unGroup);
3667     selectMenu.add(grpsFromSelection);
3668     selectMenu.add(deleteGroups);
3669     selectMenu.add(annotationColumnSelection);
3670
3671     /*
3672      * View menu
3673      */
3674     viewMenu.add(newView);
3675     viewMenu.addSeparator();
3676     showMenu.add(showColumns);
3677     showMenu.add(showSeqs);
3678     showMenu.add(showAllHidden);
3679     viewMenu.add(showMenu);
3680     hideMenu.add(hideColumns);
3681     hideMenu.add(hideSequences);
3682     hideMenu.add(hideAllSelection);
3683     hideMenu.add(hideAllButSelection);
3684     viewMenu.add(hideMenu);
3685     viewMenu.addSeparator();
3686     viewMenu.add(followMouseOverFlag);
3687     viewMenu.addSeparator();
3688     viewMenu.add(sequenceFeatures);
3689     viewMenu.add(featureSettings);
3690     viewMenu.addSeparator();
3691     viewMenu.add(alProperties);
3692     viewMenu.addSeparator();
3693     viewMenu.add(overviewMenuItem);
3694
3695     /*
3696      * Annotations menu
3697      */
3698     annotationsMenu.add(annotationPanelMenuItem);
3699     annotationsMenu.addSeparator();
3700     annotationsMenu.add(showAlignmentAnnotations);
3701     annotationsMenu.add(showSequenceAnnotations);
3702     annotationsMenu.add(sortAnnBySequence);
3703     annotationsMenu.add(sortAnnByLabel);
3704     annotationsMenu.addSeparator();
3705     autoAnnMenu.add(showAutoFirst);
3706     autoAnnMenu.add(showAutoLast);
3707     autoAnnMenu.addSeparator();
3708     autoAnnMenu.add(applyAutoAnnotationSettings);
3709     autoAnnMenu.add(showConsensusHistogram);
3710     autoAnnMenu.add(showSequenceLogo);
3711     autoAnnMenu.add(normSequenceLogo);
3712     autoAnnMenu.addSeparator();
3713     autoAnnMenu.add(showGroupConservation);
3714     autoAnnMenu.add(showGroupConsensus);
3715     annotationsMenu.add(autoAnnMenu);
3716
3717     /*
3718      * Format menu
3719      */
3720     formatMenu.add(font);
3721     formatMenu.add(seqLimits);
3722     formatMenu.add(wrapMenuItem);
3723     formatMenu.add(scaleAbove);
3724     formatMenu.add(scaleLeft);
3725     formatMenu.add(scaleRight);
3726     formatMenu.add(viewBoxesMenuItem);
3727     formatMenu.add(viewTextMenuItem);
3728     formatMenu.add(colourTextMenuItem);
3729     formatMenu.add(displayNonconservedMenuItem);
3730     formatMenu.add(renderGapsMenuItem);
3731     formatMenu.add(centreColumnLabelFlag);
3732
3733     /*
3734      * Colour menu
3735      */
3736     colourMenu.add(applyToAllGroups);
3737     colourMenu.addSeparator();
3738     colourMenu.add(noColourmenuItem);
3739     colourMenu.add(clustalColour);
3740     colourMenu.add(BLOSUM62Colour);
3741     colourMenu.add(PIDColour);
3742     colourMenu.add(zappoColour);
3743     colourMenu.add(taylorColour);
3744     colourMenu.add(hydrophobicityColour);
3745     colourMenu.add(helixColour);
3746     colourMenu.add(strandColour);
3747     colourMenu.add(turnColour);
3748     colourMenu.add(buriedColour);
3749     colourMenu.add(nucleotideColour);
3750     colourMenu.add(purinePyrimidineColour);
3751     // colourMenu.add(RNAInteractionColour);
3752     colourMenu.add(tcoffeeColour);
3753     colourMenu.add(userDefinedColour);
3754     colourMenu.addSeparator();
3755     colourMenu.add(conservationMenuItem);
3756     colourMenu.add(modifyConservation);
3757     colourMenu.add(abovePIDThreshold);
3758     colourMenu.add(modifyPID);
3759     colourMenu.add(annotationColour);
3760     colourMenu.add(RNAHelixColour);
3761
3762     /*
3763      * Calculate menu
3764      */
3765     sortMenu.add(sortIDMenuItem);
3766     sortMenu.add(sortLengthMenuItem);
3767     sortMenu.add(sortByTreeMenu);
3768     sortMenu.add(sortGroupMenuItem);
3769     sortMenu.add(sortPairwiseMenuItem);
3770     calculateMenu.add(sortMenu);
3771     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3772     calculateTreeMenu.add(neighbourTreeMenuItem);
3773     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3774     calculateTreeMenu.add(njTreeBlosumMenuItem);
3775     calculateMenu.add(calculateTreeMenu);
3776     calculateMenu.addSeparator();
3777     calculateMenu.add(pairwiseAlignmentMenuItem);
3778     calculateMenu.add(PCAMenuItem);
3779     calculateMenu.add(autoCalculate);
3780     calculateMenu.add(sortByTree);
3781
3782     /*
3783      * Help menu
3784      */
3785     helpMenu.add(documentation);
3786     helpMenu.add(about);
3787
3788     /*
3789      * Status bar
3790      */
3791     statusBar.setBackground(Color.white);
3792     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3793     statusBar.setText(MessageManager.getString("label.status_bar"));
3794     this.add(statusBar, BorderLayout.SOUTH);
3795   }
3796
3797   @Override
3798   public void setStatus(String string)
3799   {
3800     statusBar.setText(string);
3801   };
3802
3803   MenuItem featureSettings = new MenuItem();
3804
3805   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3806
3807   MenuItem annotationColour = new MenuItem();
3808
3809   MenuItem annotationColumnSelection = new MenuItem();
3810
3811   MenuItem invertColSel = new MenuItem();
3812
3813   MenuItem showColumns = new MenuItem();
3814
3815   MenuItem showSeqs = new MenuItem();
3816
3817   MenuItem hideColumns = new MenuItem();
3818
3819   MenuItem hideSequences = new MenuItem();
3820
3821   MenuItem hideAllButSelection = new MenuItem();
3822
3823   MenuItem hideAllSelection = new MenuItem();
3824
3825   MenuItem showAllHidden = new MenuItem();
3826
3827   MenuItem newView = new MenuItem();
3828
3829   private CheckboxMenuItem showAlignmentAnnotations;
3830
3831   private CheckboxMenuItem showSequenceAnnotations;
3832
3833   private CheckboxMenuItem sortAnnBySequence;
3834
3835   private CheckboxMenuItem sortAnnByLabel;
3836
3837   private CheckboxMenuItem showAutoFirst;
3838
3839   private CheckboxMenuItem showAutoLast;
3840
3841   private SplitFrame splitFrame;
3842
3843   /**
3844    * Attach the alignFrame panels after embedding menus, if necessary. This used
3845    * to be called setEmbedded, but is now creates the dropdown menus in a
3846    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3847    *
3848    * @param reallyEmbedded
3849    *          true to attach the view to the applet area on the page rather than
3850    *          in a new window
3851    */
3852   public void createAlignFrameWindow(boolean reallyEmbedded)
3853   {
3854     if (reallyEmbedded)
3855     {
3856       embedAlignFrameInApplet(viewport.applet);
3857     }
3858     else
3859     {
3860       // //////
3861       // test and embed menu bar if necessary.
3862       //
3863       if (embedMenuIfNeeded(alignPanel))
3864       {
3865         /*
3866          * adjust for status bar height too. ? pointless as overridden by layout
3867          * manager
3868          */
3869         alignPanel.setSize(getSize().width,
3870                 getSize().height - statusBar.getHeight());
3871       }
3872       add(statusBar, BorderLayout.SOUTH);
3873       add(alignPanel, BorderLayout.CENTER);
3874       // and register with the applet so it can pass external API calls to us
3875       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3876               frameHeight);
3877     }
3878   }
3879
3880   /**
3881    * Add the components of this AlignFrame to the applet container.
3882    *
3883    * @param theApplet
3884    */
3885   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3886   {
3887     // ////
3888     // Explicitly build the embedded menu panel for the on-page applet
3889     //
3890     // view cannot be closed if its actually on the page
3891     fileMenu.remove(closeMenuItem);
3892     fileMenu.remove(3); // Remove Separator
3893     // construct embedded menu, using default font
3894     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3895     // and actually add the components to the applet area
3896     theApplet.setLayout(new BorderLayout());
3897     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3898     theApplet.add(statusBar, BorderLayout.SOUTH);
3899     // TODO should size be left to the layout manager?
3900     alignPanel.setSize(theApplet.getSize().width,
3901             theApplet.getSize().height - embeddedMenu.getHeight()
3902                     - statusBar.getHeight());
3903     theApplet.add(alignPanel, BorderLayout.CENTER);
3904     final AlignFrame me = this;
3905     theApplet.addFocusListener(new FocusListener()
3906     {
3907
3908       @Override
3909       public void focusLost(FocusEvent e)
3910       {
3911         if (theApplet.currentAlignFrame == me)
3912         {
3913           theApplet.currentAlignFrame = null;
3914         }
3915       }
3916
3917       @Override
3918       public void focusGained(FocusEvent e)
3919       {
3920         theApplet.currentAlignFrame = me;
3921       }
3922     });
3923     theApplet.validate();
3924   }
3925
3926   /**
3927    * create a new binding between structures in an existing jmol viewer instance
3928    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3929    * this does not open a new Jmol window, or modify the display of the
3930    * structures in the original jmol window. Note This method doesn't work
3931    * without an additional javascript library to exchange messages between the
3932    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3933    *
3934    * @param viewer
3935    *          JmolViewer instance
3936    * @param sequenceIds
3937    *          - sequence Ids to search for associations
3938    */
3939   public SequenceStructureBinding addStructureViewInstance(
3940           Object jmolviewer, String[] sequenceIds)
3941   {
3942     Viewer viewer = null;
3943     try
3944     {
3945       viewer = (Viewer) jmolviewer;
3946     } catch (ClassCastException ex)
3947     {
3948       System.err.println("Unsupported viewer object :"
3949               + jmolviewer.getClass());
3950     }
3951     if (viewer == null)
3952     {
3953       System.err.println("Can't use this object as a structure viewer:"
3954               + jmolviewer.getClass());
3955       return null;
3956     }
3957     SequenceI[] seqs = null;
3958     if (sequenceIds == null || sequenceIds.length == 0)
3959     {
3960       seqs = viewport.getAlignment().getSequencesArray();
3961     }
3962     else
3963     {
3964       Vector sqi = new Vector();
3965       AlignmentI al = viewport.getAlignment();
3966       for (int sid = 0; sid < sequenceIds.length; sid++)
3967       {
3968         SequenceI sq = al.findName(sequenceIds[sid]);
3969         if (sq != null)
3970         {
3971           sqi.addElement(sq);
3972         }
3973       }
3974       if (sqi.size() > 0)
3975       {
3976         seqs = new SequenceI[sqi.size()];
3977         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3978         {
3979           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3980         }
3981       }
3982       else
3983       {
3984         return null;
3985       }
3986     }
3987     AAStructureBindingModel jmv = null;
3988     // TODO: search for a jmv that involves viewer
3989     if (jmv == null)
3990     { // create a new viewer/jalview binding.
3991       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3992     }
3993     return jmv;
3994
3995   }
3996
3997   /**
3998    * bind a pdb file to a sequence in the current view
3999    *
4000    * @param sequenceId
4001    *          - sequenceId within the dataset.
4002    * @param pdbEntryString
4003    *          - the short name for the PDB file
4004    * @param pdbFile
4005    *          - pdb file - either a URL or a valid PDB file.
4006    * @return true if binding was as success TODO: consider making an exception
4007    *         structure for indicating when PDB parsing or sequenceId location
4008    *         fails.
4009    */
4010   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4011           String pdbFile)
4012   {
4013     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4014     boolean needtoadd = false;
4015     if (toaddpdb != null)
4016     {
4017       Vector pdbe = toaddpdb.getAllPDBEntries();
4018       PDBEntry pdbentry = null;
4019       if (pdbe != null && pdbe.size() > 0)
4020       {
4021         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4022         {
4023           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4024           if (!pdbentry.getId().equals(pdbEntryString)
4025                   && !pdbentry.getFile().equals(pdbFile))
4026           {
4027             pdbentry = null;
4028           }
4029           else
4030           {
4031             continue;
4032           }
4033         }
4034       }
4035       if (pdbentry == null)
4036       {
4037         pdbentry = new PDBEntry();
4038         pdbentry.setId(pdbEntryString);
4039         pdbentry.setFile(pdbFile);
4040         needtoadd = true; // add this new entry to sequence.
4041       }
4042       // resolve data source
4043       // TODO: this code should be a refactored to an io package
4044       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4045               pdbFile, FileFormat.PDB);
4046       if (protocol == null)
4047       {
4048         return false;
4049       }
4050       if (needtoadd)
4051       {
4052         pdbentry.setProperty("protocol", protocol);
4053         toaddpdb.addPDBId(pdbentry);
4054         alignPanel.getStructureSelectionManager()
4055                 .registerPDBEntry(pdbentry);
4056       }
4057     }
4058     return true;
4059   }
4060
4061   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4062   {
4063     if (seqs != null)
4064     {
4065       Vector sequences = new Vector();
4066       for (int i = 0; i < seqs.length; i++)
4067       {
4068         if (seqs[i] != null)
4069         {
4070           sequences.addElement(new Object[] { seqs[i],
4071               (chains != null) ? chains[i] : null });
4072         }
4073       }
4074       seqs = new SequenceI[sequences.size()];
4075       chains = new String[sequences.size()];
4076       for (int i = 0, isize = sequences.size(); i < isize; i++)
4077       {
4078         Object[] oj = (Object[]) sequences.elementAt(i);
4079
4080         seqs[i] = (SequenceI) oj[0];
4081         chains[i] = (String) oj[1];
4082       }
4083     }
4084     return new Object[] { seqs, chains };
4085
4086   }
4087
4088   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4089           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4090   {
4091     // Scrub any null sequences from the array
4092     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4093     seqs = (SequenceI[]) sqch[0];
4094     chains = (String[]) sqch[1];
4095     if (seqs == null || seqs.length == 0)
4096     {
4097       System.err
4098               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4099     }
4100     if (protocol == null)
4101     {
4102       String sourceType = (String) pdb.getProperty("protocol");
4103       try
4104       {
4105         protocol = DataSourceType.valueOf(sourceType);
4106       } catch (IllegalArgumentException e)
4107       {
4108         // ignore
4109       }
4110       if (protocol == null)
4111       {
4112         System.err.println("Couldn't work out protocol to open structure: "
4113                 + pdb.getId());
4114         return;
4115       }
4116     }
4117     if (applet.useXtrnalSviewer)
4118     {
4119       // register the association(s) and quit, don't create any windows.
4120       if (StructureSelectionManager.getStructureSelectionManager(applet)
4121               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4122       {
4123         System.err.println("Failed to map " + pdb.getFile() + " ("
4124                 + protocol + ") to any sequences");
4125       }
4126       return;
4127     }
4128     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4129     {
4130       // can only do alignments with Jmol
4131       // find the last jmol window assigned to this alignment
4132       AppletJmol ajm = null, tajm;
4133       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4134       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4135       {
4136         tajm = (AppletJmol) jmols.elementAt(i);
4137         if (tajm.ap.alignFrame == this)
4138         {
4139           ajm = tajm;
4140           break;
4141         }
4142       }
4143       if (ajm != null)
4144       {
4145         System.err
4146                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4147         // try and add the pdb structure
4148         // ajm.addS
4149         ajm = null;
4150       }
4151     }
4152     // otherwise, create a new window
4153     if (applet.jmolAvailable)
4154     {
4155       new AppletJmol(pdb, seqs, chains, alignPanel,
4156               protocol);
4157       applet.lastFrameX += 40;
4158       applet.lastFrameY += 40;
4159     }
4160     else
4161     {
4162       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4163     }
4164
4165   }
4166
4167   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4168           SequenceI[][] seqs, String[][] chains, String[] protocols)
4169   {
4170     // TODO Auto-generated method stub
4171     System.err.println("Aligned Structure View: Not yet implemented.");
4172   }
4173
4174   /**
4175    * modify the current selection, providing the user has not made a selection
4176    * already.
4177    *
4178    * @param sel
4179    *          - sequences from this alignment
4180    * @param csel
4181    *          - columns to be selected on the alignment
4182    */
4183   public void select(SequenceGroup sel, ColumnSelection csel)
4184   {
4185     alignPanel.seqPanel.selection(sel, csel, null);
4186   }
4187
4188   public void scrollTo(int row, int column)
4189   {
4190     alignPanel.seqPanel.scrollTo(row, column);
4191   }
4192
4193   public void scrollToRow(int row)
4194   {
4195     alignPanel.seqPanel.scrollToRow(row);
4196   }
4197
4198   public void scrollToColumn(int column)
4199   {
4200     alignPanel.seqPanel.scrollToColumn(column);
4201   }
4202
4203   /**
4204    * @return the alignments unique ID.
4205    */
4206   public String getSequenceSetId()
4207   {
4208     return viewport.getSequenceSetId();
4209   }
4210
4211   /**
4212    * Load the (T-Coffee) score file from the specified url
4213    *
4214    * @param source
4215    *          File/URL/T-COFFEE score file contents
4216    * @throws IOException
4217    * @return true if alignment was annotated with data from source
4218    */
4219   public boolean loadScoreFile(String source) throws IOException
4220   {
4221
4222     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4223             AppletFormatAdapter.checkProtocol(source));
4224     if (!file.isValid())
4225     {
4226       // TODO: raise dialog for gui
4227       System.err.println("Problems parsing T-Coffee scores: "
4228               + file.getWarningMessage());
4229       System.err.println("Origin was:\n" + source);
4230       return false;
4231     }
4232
4233     /*
4234      * check that the score matrix matches the alignment dimensions
4235      */
4236     AlignmentI aln;
4237     if ((aln = viewport.getAlignment()) != null
4238             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4239                     .getWidth()))
4240     {
4241       // TODO: raise a dialog box here rather than bomb out.
4242       System.err
4243               .println("The scores matrix does not match the alignment dimensions");
4244
4245     }
4246
4247     // TODO add parameter to indicate if matching should be done
4248     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4249     {
4250       alignPanel.fontChanged();
4251       tcoffeeColour.setEnabled(true);
4252       // switch to this color
4253       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4254       return true;
4255     }
4256     else
4257     {
4258       System.err.println("Problems resolving T-Coffee scores:");
4259       if (file.getWarningMessage() != null)
4260       {
4261         System.err.println(file.getWarningMessage());
4262       }
4263     }
4264     return false;
4265   }
4266
4267   public SplitFrame getSplitFrame()
4268   {
4269     return this.splitFrame;
4270   }
4271
4272   public void setSplitFrame(SplitFrame sf)
4273   {
4274     this.splitFrame = sf;
4275   }
4276
4277   // may not need this
4278   @Override
4279   public void setShowSeqFeatures(boolean b)
4280   {
4281     // showSeqFeatures.setSelected(b);
4282     viewport.setShowSequenceFeatures(b);
4283
4284   }
4285
4286   @Override
4287   public void setMenusForViewport()
4288   {
4289     // setMenusFromViewport(viewport);
4290
4291   }
4292
4293   @Override
4294   public void refreshFeatureUI(boolean enableIfNecessary)
4295   {
4296     if (enableIfNecessary)
4297     {
4298       sequenceFeatures.setState(true);
4299       alignPanel.av.setShowSequenceFeatures(true);
4300     }
4301   }
4302
4303   @Override
4304   public FeatureSettingsControllerI getFeatureSettingsUI()
4305   {
4306     return alignPanel.av.featureSettings;
4307   }
4308
4309 }