src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.TCoffeeScoreFile;
  56 import jalview.schemes.Blosum62ColourScheme;
  57 import jalview.schemes.BuriedColourScheme;
  58 import jalview.schemes.ClustalxColourScheme;
  59 import jalview.schemes.ColourSchemeI;
  60 import jalview.schemes.HelixColourScheme;
  61 import jalview.schemes.HydrophobicColourScheme;
  62 import jalview.schemes.NucleotideColourScheme;
  63 import jalview.schemes.PIDColourScheme;
  64 import jalview.schemes.PurinePyrimidineColourScheme;
  65 import jalview.schemes.RNAHelicesColour;
  66 import jalview.schemes.RNAHelicesColourChooser;
  67 import jalview.schemes.StrandColourScheme;
  68 import jalview.schemes.TCoffeeColourScheme;
  69 import jalview.schemes.TaylorColourScheme;
  70 import jalview.schemes.TurnColourScheme;
  71 import jalview.schemes.ZappoColourScheme;
  72 import jalview.structure.StructureSelectionManager;
  73 import jalview.structures.models.AAStructureBindingModel;
  74 import jalview.util.MappingUtils;
  75 import jalview.util.MessageManager;
  76 import jalview.viewmodel.AlignmentViewport;
  77
  78 import java.awt.BorderLayout;
  79 import java.awt.Canvas;
  80 import java.awt.CheckboxMenuItem;
  81 import java.awt.Color;
  82 import java.awt.FlowLayout;
  83 import java.awt.Font;
  84 import java.awt.FontMetrics;
  85 import java.awt.Frame;
  86 import java.awt.Graphics;
  87 import java.awt.Label;
  88 import java.awt.Menu;
  89 import java.awt.MenuBar;
  90 import java.awt.MenuItem;
  91 import java.awt.Panel;
  92 import java.awt.event.ActionEvent;
  93 import java.awt.event.ActionListener;
  94 import java.awt.event.FocusEvent;
  95 import java.awt.event.FocusListener;
  96 import java.awt.event.ItemEvent;
  97 import java.awt.event.ItemListener;
  98 import java.awt.event.KeyEvent;
  99 import java.awt.event.KeyListener;
 100 import java.awt.event.WindowAdapter;
 101 import java.awt.event.WindowEvent;
 102 import java.io.IOException;
 103 import java.net.URL;
 104 import java.net.URLEncoder;
 105 import java.util.Arrays;
 106 import java.util.Deque;
 107 import java.util.HashMap;
 108 import java.util.List;
 109 import java.util.Map;
 110 import java.util.StringTokenizer;
 111 import java.util.Vector;
 112
 113 import org.jmol.viewer.Viewer;
 114
 115 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 116         ItemListener, KeyListener, AlignViewControllerGuiI
 117 {
 118   public AlignViewControllerI avc;
 119
 120   public AlignmentPanel alignPanel;
 121
 122   public AlignViewport viewport;
 123
 124   // width and height may be overridden by applet parameters
 125   int frameWidth = 700;
 126
 127   int frameHeight = 500;
 128
 129   String jalviewServletURL;
 130
 131   /*
 132    * Flag for showing autocalculated consensus above or below other consensus
 133    * rows
 134    */
 135   private boolean showAutoCalculatedAbove;
 136
 137   private SequenceAnnotationOrder annotationSortOrder;
 138
 139   /**
 140    * Constructor that creates the frame and adds it to the display.
 141    *
 142    * @param al
 143    * @param applet
 144    * @param title
 145    * @param embedded
 146    */
 147   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 148           boolean embedded)
 149   {
 150     this(al, applet, title, embedded, true);
 151   }
 152
 153   /**
 154    * Constructor that optionally allows the frame to be displayed or only
 155    * created.
 156    *
 157    * @param al
 158    * @param applet
 159    * @param title
 160    * @param embedded
 161    * @param addToDisplay
 162    */
 163   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 164           boolean embedded, boolean addToDisplay)
 165   {
 166     this(al, null, null, applet, title, embedded, addToDisplay);
 167   }
 168
 169   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 170           ColumnSelection columnSelection, JalviewLite applet,
 171           String title, boolean embedded)
 172   {
 173     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 174   }
 175
 176   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 177           ColumnSelection columnSelection, JalviewLite applet,
 178           String title, boolean embedded, boolean addToDisplay)
 179   {
 180     if (applet != null)
 181     {
 182       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 183     }
 184
 185     try
 186     {
 187       jbInit();
 188     } catch (Exception ex)
 189     {
 190       ex.printStackTrace();
 191     }
 192     // need to get window geometry before we calculate alignment layout
 193     if (applet != null)
 194     {
 195       String param;
 196       try
 197       {
 198         param = applet.getParameter("windowWidth");
 199         if (param != null)
 200         {
 201           int width = Integer.parseInt(param);
 202           frameWidth = width;
 203         }
 204         param = applet.getParameter("windowHeight");
 205         if (param != null)
 206         {
 207           int height = Integer.parseInt(param);
 208           frameHeight = height;
 209         }
 210       } catch (Exception ex)
 211       {
 212       }
 213     }
 214     viewport = new AlignViewport(al, applet);
 215
 216     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 217     {
 218       viewport.hideSequence(hiddenSeqs);
 219     }
 220     if (columnSelection != null)
 221     {
 222       viewport.setColumnSelection(columnSelection);
 223     }
 224     viewport.setScaleAboveWrapped(scaleAbove.getState());
 225
 226     alignPanel = new AlignmentPanel(this, viewport);
 227     avc = new jalview.controller.AlignViewController(this, viewport,
 228             alignPanel);
 229     viewport.updateConservation(alignPanel);
 230     viewport.updateConsensus(alignPanel);
 231
 232     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 233     followMouseOverFlag.setState(viewport.isFollowHighlight());
 234     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 235     showGroupConservation.setState(viewport.isShowGroupConservation());
 236     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 237     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 238     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 239     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 240     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 241     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 242     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 243     showAlignmentAnnotations.setState(true);
 244     showSequenceAnnotations.setState(false);
 245
 246     seqLimits.setState(viewport.getShowJVSuffix());
 247
 248     if (applet != null)
 249     {
 250       String param = applet.getParameter("sortBy");
 251       if (param != null)
 252       {
 253         if (param.equalsIgnoreCase("Id"))
 254         {
 255           sortIDMenuItem_actionPerformed();
 256         }
 257         else if (param.equalsIgnoreCase("Pairwise Identity"))
 258         {
 259           sortPairwiseMenuItem_actionPerformed();
 260         }
 261         else if (param.equalsIgnoreCase("Length"))
 262         {
 263           sortLengthMenuItem_actionPerformed();
 264         }
 265       }
 266
 267       param = applet.getParameter("wrap");
 268       if (param != null)
 269       {
 270         if (param.equalsIgnoreCase("true"))
 271         {
 272           wrapMenuItem.setState(true);
 273           wrapMenuItem_actionPerformed();
 274         }
 275       }
 276       param = applet.getParameter("centrecolumnlabels");
 277       if (param != null)
 278       {
 279         centreColumnLabelFlag.setState(true);
 280         centreColumnLabelFlag_stateChanged();
 281       }
 282
 283     }
 284     if (viewport.getAlignment().isNucleotide())
 285     {
 286       viewport.updateStrucConsensus(alignPanel);
 287       if (viewport.getAlignment().hasRNAStructure())
 288       {
 289         RNAHelixColour.setEnabled(true);
 290       }
 291       else
 292       {
 293         RNAHelixColour.setEnabled(false);
 294       }
 295     }
 296     else
 297     {
 298       RNAHelixColour.setEnabled(false);
 299       purinePyrimidineColour.setEnabled(false);
 300       nucleotideColour.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       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1261       // new RNAHelicesColourChooser(viewport, alignPanel);
1262     }
1263     else if (source == modifyPID)
1264     {
1265       modifyPID_actionPerformed();
1266     }
1267     else if (source == modifyConservation)
1268     {
1269       modifyConservation_actionPerformed();
1270     }
1271     else if (source == userDefinedColour)
1272     {
1273       new UserDefinedColours(alignPanel, null);
1274     }
1275     else if (source == PIDColour)
1276     {
1277       changeColour(new PIDColourScheme());
1278     }
1279     else if (source == BLOSUM62Colour)
1280     {
1281       changeColour(new Blosum62ColourScheme());
1282     }
1283     else if (source == tcoffeeColour)
1284     {
1285       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1286     }
1287     else if (source == annotationColour)
1288     {
1289       new AnnotationColourChooser(viewport, alignPanel);
1290     }
1291     else if (source == annotationColumnSelection)
1292     {
1293       new AnnotationColumnChooser(viewport, alignPanel);
1294     }
1295     else if (source == sortPairwiseMenuItem)
1296     {
1297       sortPairwiseMenuItem_actionPerformed();
1298     }
1299     else if (source == sortIDMenuItem)
1300     {
1301       sortIDMenuItem_actionPerformed();
1302     }
1303     else if (source == sortLengthMenuItem)
1304     {
1305       sortLengthMenuItem_actionPerformed();
1306     }
1307     else if (source == sortGroupMenuItem)
1308     {
1309       sortGroupMenuItem_actionPerformed();
1310     }
1311     else if (source == removeRedundancyMenuItem)
1312     {
1313       removeRedundancyMenuItem_actionPerformed();
1314     }
1315     else if (source == pairwiseAlignmentMenuItem)
1316     {
1317       pairwiseAlignmentMenuItem_actionPerformed();
1318     }
1319     else if (source == PCAMenuItem)
1320     {
1321       PCAMenuItem_actionPerformed();
1322     }
1323     else if (source == averageDistanceTreeMenuItem)
1324     {
1325       averageDistanceTreeMenuItem_actionPerformed();
1326     }
1327     else if (source == neighbourTreeMenuItem)
1328     {
1329       neighbourTreeMenuItem_actionPerformed();
1330     }
1331     else if (source == njTreeBlosumMenuItem)
1332     {
1333       njTreeBlosumMenuItem_actionPerformed();
1334     }
1335     else if (source == avDistanceTreeBlosumMenuItem)
1336     {
1337       avTreeBlosumMenuItem_actionPerformed();
1338     }
1339     else if (source == documentation)
1340     {
1341       documentation_actionPerformed();
1342     }
1343     else if (source == about)
1344     {
1345       about_actionPerformed();
1346     }
1347
1348   }
1349
1350   public void inputText_actionPerformed()
1351   {
1352     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1353     Frame frame = new Frame();
1354     frame.add(cap);
1355     jalview.bin.JalviewLite.addFrame(frame,
1356             MessageManager.getString("label.input_cut_paste"), 500, 500);
1357   }
1358
1359   protected void outputText_actionPerformed(ActionEvent e)
1360   {
1361     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1362     Frame frame = new Frame();
1363     frame.add(cap);
1364     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1365             "label.alignment_output_command",
1366             new Object[] { e.getActionCommand() }), 600, 500);
1367
1368     FileFormat fileFormat = FileFormat.valueOf(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     {
1488       url.append("&annotations=");
1489       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1490     }
1491
1492     if (viewport.applet.getParameter("defaultColour") != null)
1493     {
1494       url.append("&colour="
1495               + removeWhiteSpace(viewport.applet
1496                       .getParameter("defaultColour")));
1497     }
1498
1499     if (viewport.applet.getParameter("userDefinedColour") != null)
1500     {
1501       url.append("&colour="
1502               + removeWhiteSpace(viewport.applet
1503                       .getParameter("userDefinedColour")));
1504     }
1505     if (viewport.applet.getParameter("tree") != null)
1506     {
1507       url.append("&tree="
1508               + appendProtocol(viewport.applet.getParameter("tree")));
1509     }
1510     if (viewport.applet.getParameter("treeFile") != null)
1511     {
1512       url.append("&tree="
1513               + appendProtocol(viewport.applet.getParameter("treeFile")));
1514     }
1515
1516     showURL(url.toString(), "FULL_APP");
1517   }
1518
1519   String removeWhiteSpace(String colour)
1520   {
1521     StringBuffer sb = new StringBuffer();
1522     for (int i = 0; i < colour.length(); i++)
1523     {
1524       if (Character.isWhitespace(colour.charAt(i)))
1525       {
1526         sb.append("%20");
1527       }
1528       else
1529       {
1530         sb.append(colour.charAt(i));
1531       }
1532     }
1533
1534     return sb.toString();
1535   }
1536
1537   String appendProtocol(String url)
1538   {
1539     try
1540     {
1541       new URL(url);
1542       url = URLEncoder.encode(url);
1543     }
1544     /*
1545      * When we finally deprecate 1.1 compatibility, we can start to use
1546      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1547      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1548      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1549      * ex.printStackTrace(); }
1550      */
1551     catch (java.net.MalformedURLException ex)
1552     {
1553       url = viewport.applet.getCodeBase() + url;
1554     }
1555     return url;
1556   }
1557
1558   public void closeMenuItem_actionPerformed()
1559   {
1560     PaintRefresher.RemoveComponent(alignPanel);
1561     if (alignPanel.seqPanel != null
1562             && alignPanel.seqPanel.seqCanvas != null)
1563     {
1564       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1565     }
1566     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1567     {
1568       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1569     }
1570
1571     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1572     {
1573       System.exit(0);
1574     }
1575     else
1576     {
1577     }
1578     viewport = null;
1579     alignPanel = null;
1580     this.dispose();
1581   }
1582
1583   /**
1584    * TODO: JAL-1104
1585    */
1586   void updateEditMenuBar()
1587   {
1588
1589     if (viewport.getHistoryList().size() > 0)
1590     {
1591       undoMenuItem.setEnabled(true);
1592       CommandI command = viewport.getHistoryList().peek();
1593       undoMenuItem.setLabel(MessageManager.formatMessage(
1594               "label.undo_command",
1595               new Object[] { command.getDescription() }));
1596     }
1597     else
1598     {
1599       undoMenuItem.setEnabled(false);
1600       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1601     }
1602
1603     if (viewport.getRedoList().size() > 0)
1604     {
1605       redoMenuItem.setEnabled(true);
1606
1607       CommandI command = viewport.getRedoList().peek();
1608       redoMenuItem.setLabel(MessageManager.formatMessage(
1609               "label.redo_command",
1610               new Object[] { command.getDescription() }));
1611     }
1612     else
1613     {
1614       redoMenuItem.setEnabled(false);
1615       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1616     }
1617   }
1618
1619   /**
1620    * TODO: JAL-1104
1621    */
1622   @Override
1623   public void addHistoryItem(CommandI command)
1624   {
1625     if (command.getSize() > 0)
1626     {
1627       viewport.addToHistoryList(command);
1628       viewport.clearRedoList();
1629       updateEditMenuBar();
1630       viewport.updateHiddenColumns();
1631     }
1632   }
1633
1634   /**
1635    * TODO: JAL-1104 DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   protected void undoMenuItem_actionPerformed()
1641   {
1642     if (viewport.getHistoryList().isEmpty())
1643     {
1644       return;
1645     }
1646
1647     CommandI command = viewport.getHistoryList().pop();
1648     viewport.addToRedoList(command);
1649     command.undoCommand(null);
1650
1651     AlignmentViewport originalSource = getOriginatingSource(command);
1652     // JBPNote Test
1653     if (originalSource != viewport)
1654     {
1655       System.err
1656               .println("Warning: Viewport object mismatch whilst undoing");
1657     }
1658     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1659                                           // viewport.getColumnSelection().getHiddenColumns()
1660                                           // != null;
1661     updateEditMenuBar();
1662     originalSource.firePropertyChange("alignment", null, originalSource
1663             .getAlignment().getSequences());
1664   }
1665
1666   /**
1667    * TODO: JAL-1104 DOCUMENT ME!
1668    *
1669    * @param e
1670    *          DOCUMENT ME!
1671    */
1672   protected void redoMenuItem_actionPerformed()
1673   {
1674     if (viewport.getRedoList().isEmpty())
1675     {
1676       return;
1677     }
1678
1679     CommandI command = viewport.getRedoList().pop();
1680     viewport.addToHistoryList(command);
1681     command.doCommand(null);
1682
1683     AlignmentViewport originalSource = getOriginatingSource(command);
1684     // JBPNote Test
1685     if (originalSource != viewport)
1686     {
1687       System.err
1688               .println("Warning: Viewport object mismatch whilst re-doing");
1689     }
1690     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1691                                           // viewport.getColumnSelection().getHiddenColumns()
1692                                           // != null;
1693
1694     updateEditMenuBar();
1695     originalSource.firePropertyChange("alignment", null, originalSource
1696             .getAlignment().getSequences());
1697   }
1698
1699   AlignmentViewport getOriginatingSource(CommandI command)
1700   {
1701     AlignmentViewport originalSource = null;
1702     // For sequence removal and addition, we need to fire
1703     // the property change event FROM the viewport where the
1704     // original alignment was altered
1705     AlignmentI al = null;
1706     if (command instanceof EditCommand)
1707     {
1708       EditCommand editCommand = (EditCommand) command;
1709       al = editCommand.getAlignment();
1710       Vector comps = (Vector) PaintRefresher.components.get(viewport
1711               .getSequenceSetId());
1712       for (int i = 0; i < comps.size(); i++)
1713       {
1714         if (comps.elementAt(i) instanceof AlignmentPanel)
1715         {
1716           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1717           {
1718             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1719             break;
1720           }
1721         }
1722       }
1723     }
1724
1725     if (originalSource == null)
1726     {
1727       // The original view is closed, we must validate
1728       // the current view against the closed view first
1729       if (al != null)
1730       {
1731         PaintRefresher.validateSequences(al, viewport.getAlignment());
1732       }
1733
1734       originalSource = viewport;
1735     }
1736
1737     return originalSource;
1738   }
1739
1740   /**
1741    * Move the currently selected sequences up or down one position in the
1742    * alignment
1743    *
1744    * @param up
1745    */
1746   public void moveSelectedSequences(boolean up)
1747   {
1748     SequenceGroup sg = viewport.getSelectionGroup();
1749     if (sg == null)
1750     {
1751       return;
1752     }
1753     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1754             up ? null : viewport.getHiddenRepSequences(), up);
1755     alignPanel.paintAlignment(true);
1756
1757     /*
1758      * Also move cDNA/protein complement sequences
1759      */
1760     AlignViewportI complement = viewport.getCodingComplement();
1761     if (complement != null)
1762     {
1763       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1764               viewport, complement);
1765       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1766               up ? null : complement.getHiddenRepSequences(), up);
1767       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1768     }
1769   }
1770
1771   synchronized void slideSequences(boolean right, int size)
1772   {
1773     List<SequenceI> sg = new Vector<SequenceI>();
1774     if (viewport.cursorMode)
1775     {
1776       sg.add(viewport.getAlignment().getSequenceAt(
1777               alignPanel.seqPanel.seqCanvas.cursorY));
1778     }
1779     else if (viewport.getSelectionGroup() != null
1780             && viewport.getSelectionGroup().getSize() != viewport
1781                     .getAlignment().getHeight())
1782     {
1783       sg = viewport.getSelectionGroup().getSequences(
1784               viewport.getHiddenRepSequences());
1785     }
1786
1787     if (sg.size() < 1)
1788     {
1789       return;
1790     }
1791
1792     Vector<SequenceI> invertGroup = new Vector();
1793
1794     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1795     {
1796       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1797       {
1798         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1799       }
1800     }
1801
1802     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1803
1804     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1805             .size()]);
1806     for (int i = 0; i < invertGroup.size(); i++)
1807     {
1808       seqs2[i] = invertGroup.elementAt(i);
1809     }
1810
1811     SlideSequencesCommand ssc;
1812     if (right)
1813     {
1814       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1815               size, viewport.getGapCharacter());
1816     }
1817     else
1818     {
1819       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1820               size, viewport.getGapCharacter());
1821     }
1822
1823     int groupAdjustment = 0;
1824     if (ssc.getGapsInsertedBegin() && right)
1825     {
1826       if (viewport.cursorMode)
1827       {
1828         alignPanel.seqPanel.moveCursor(size, 0);
1829       }
1830       else
1831       {
1832         groupAdjustment = size;
1833       }
1834     }
1835     else if (!ssc.getGapsInsertedBegin() && !right)
1836     {
1837       if (viewport.cursorMode)
1838       {
1839         alignPanel.seqPanel.moveCursor(-size, 0);
1840       }
1841       else
1842       {
1843         groupAdjustment = -size;
1844       }
1845     }
1846
1847     if (groupAdjustment != 0)
1848     {
1849       viewport.getSelectionGroup().setStartRes(
1850               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1851       viewport.getSelectionGroup().setEndRes(
1852               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1853     }
1854
1855     boolean appendHistoryItem = false;
1856     Deque<CommandI> historyList = viewport.getHistoryList();
1857     if (historyList != null && historyList.size() > 0
1858             && historyList.peek() instanceof SlideSequencesCommand)
1859     {
1860       appendHistoryItem = ssc
1861               .appendSlideCommand((SlideSequencesCommand) historyList
1862                       .peek());
1863     }
1864
1865     if (!appendHistoryItem)
1866     {
1867       addHistoryItem(ssc);
1868     }
1869
1870     repaint();
1871   }
1872
1873   static StringBuffer copiedSequences;
1874
1875   static Vector copiedHiddenColumns;
1876
1877   protected void copy_actionPerformed()
1878   {
1879     if (viewport.getSelectionGroup() == null)
1880     {
1881       return;
1882     }
1883
1884     SequenceGroup sg = viewport.getSelectionGroup();
1885     copiedSequences = new StringBuffer();
1886     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1887     for (int i = 0; i < sg.getSize(); i++)
1888     {
1889       SequenceI seq = sg.getSequenceAt(i);
1890       int index = viewport.getAlignment().findIndex(seq);
1891       orderedSeqs.put(index, seq);
1892     }
1893
1894     int index = 0, startRes, endRes;
1895     char ch;
1896
1897     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1898     {
1899       copiedHiddenColumns = new Vector();
1900       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1901       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1902       {
1903         copiedHiddenColumns.addElement(new int[] {
1904             region[0] - hiddenOffset, region[1] - hiddenOffset });
1905       }
1906     }
1907     else
1908     {
1909       copiedHiddenColumns = null;
1910     }
1911
1912     for (int i = 0; i < sg.getSize(); i++)
1913     {
1914       SequenceI seq = null;
1915
1916       while (seq == null)
1917       {
1918         if (orderedSeqs.containsKey(index))
1919         {
1920           seq = orderedSeqs.get(index);
1921           index++;
1922           break;
1923         }
1924         else
1925         {
1926           index++;
1927         }
1928       }
1929
1930       // FIND START RES
1931       // Returns residue following index if gap
1932       startRes = seq.findPosition(sg.getStartRes());
1933
1934       // FIND END RES
1935       // Need to find the residue preceeding index if gap
1936       endRes = 0;
1937
1938       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1939       {
1940         ch = seq.getCharAt(j);
1941         if (!jalview.util.Comparison.isGap((ch)))
1942         {
1943           endRes++;
1944         }
1945       }
1946
1947       if (endRes > 0)
1948       {
1949         endRes += seq.getStart() - 1;
1950       }
1951
1952       copiedSequences.append(seq.getName()
1953               + "\t"
1954               + startRes
1955               + "\t"
1956               + endRes
1957               + "\t"
1958               + seq.getSequenceAsString(sg.getStartRes(),
1959                       sg.getEndRes() + 1) + "\n");
1960     }
1961
1962   }
1963
1964   protected void pasteNew_actionPerformed()
1965   {
1966     paste(true);
1967   }
1968
1969   protected void pasteThis_actionPerformed()
1970   {
1971     paste(false);
1972   }
1973
1974   void paste(boolean newAlignment)
1975   {
1976     try
1977     {
1978
1979       if (copiedSequences == null)
1980       {
1981         return;
1982       }
1983
1984       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1985       Vector seqs = new Vector();
1986       while (st.hasMoreElements())
1987       {
1988         String name = st.nextToken();
1989         int start = Integer.parseInt(st.nextToken());
1990         int end = Integer.parseInt(st.nextToken());
1991         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1992       }
1993       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1994       for (int i = 0; i < seqs.size(); i++)
1995       {
1996         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1997       }
1998
1999       if (newAlignment)
2000       {
2001         String newtitle = MessageManager
2002                 .getString("label.copied_sequences");
2003         if (getTitle().startsWith(
2004                 MessageManager.getString("label.copied_sequences")))
2005         {
2006           newtitle = getTitle();
2007         }
2008         else
2009         {
2010           newtitle = newtitle.concat(MessageManager.formatMessage(
2011                   "label.from_msname", new String[] { getTitle() }));
2012         }
2013         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2014                 viewport.applet, newtitle, false);
2015         if (copiedHiddenColumns != null)
2016         {
2017           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2018           {
2019             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2020             af.viewport.hideColumns(region[0], region[1]);
2021           }
2022         }
2023
2024         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2025                 frameHeight);
2026       }
2027       else
2028       {
2029         addSequences(newSeqs);
2030       }
2031
2032     } catch (Exception ex)
2033     {
2034     } // could be anything being pasted in here
2035
2036   }
2037
2038   void addSequences(SequenceI[] seqs)
2039   {
2040     for (int i = 0; i < seqs.length; i++)
2041     {
2042       viewport.getAlignment().addSequence(seqs[i]);
2043     }
2044
2045     // !newAlignment
2046     addHistoryItem(new EditCommand(
2047             MessageManager.getString("label.add_sequences"), Action.PASTE,
2048             seqs, 0, viewport.getAlignment().getWidth(),
2049             viewport.getAlignment()));
2050
2051     viewport.setEndSeq(viewport.getAlignment().getHeight());
2052     viewport.getAlignment().getWidth();
2053     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2054             .getSequences());
2055
2056   }
2057
2058   protected void cut_actionPerformed()
2059   {
2060     copy_actionPerformed();
2061     delete_actionPerformed();
2062   }
2063
2064   protected void delete_actionPerformed()
2065   {
2066
2067     SequenceGroup sg = viewport.getSelectionGroup();
2068     if (sg == null)
2069     {
2070       return;
2071     }
2072
2073     Vector seqs = new Vector();
2074     SequenceI seq;
2075     for (int i = 0; i < sg.getSize(); i++)
2076     {
2077       seq = sg.getSequenceAt(i);
2078       seqs.addElement(seq);
2079     }
2080
2081     /*
2082      * If the cut affects all sequences, warn, remove highlighted columns
2083      */
2084     if (sg.getSize() == viewport.getAlignment().getHeight())
2085     {
2086       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2087               .getAlignment().getWidth()) ? true : false;
2088       if (isEntireAlignWidth)
2089       {
2090         String title = MessageManager.getString("label.delete_all");
2091         Panel infoPanel = new Panel();
2092         infoPanel.setLayout(new FlowLayout());
2093         infoPanel
2094                 .add(new Label(MessageManager.getString("warn.delete_all")));
2095
2096         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2097         dialog.setMainPanel(infoPanel);
2098         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2099         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2100         dialog.setVisible(true);
2101
2102         if (!dialog.accept)
2103         {
2104           return;
2105         }
2106       }
2107       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2108               sg.getEndRes() + 1);
2109     }
2110
2111     SequenceI[] cut = new SequenceI[seqs.size()];
2112     for (int i = 0; i < seqs.size(); i++)
2113     {
2114       cut[i] = (SequenceI) seqs.elementAt(i);
2115     }
2116
2117     /*
2118      * //ADD HISTORY ITEM
2119      */
2120     addHistoryItem(new EditCommand(
2121             MessageManager.getString("label.cut_sequences"), Action.CUT,
2122             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2123             viewport.getAlignment()));
2124
2125     viewport.setSelectionGroup(null);
2126     viewport.getAlignment().deleteGroup(sg);
2127
2128     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2129             .getSequences());
2130
2131     if (viewport.getAlignment().getHeight() < 1)
2132     {
2133       this.setVisible(false);
2134     }
2135     viewport.sendSelection();
2136   }
2137
2138   /**
2139    * group consensus toggled
2140    *
2141    */
2142   protected void showGroupConsensus_actionPerformed()
2143   {
2144     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2145     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2146
2147   }
2148
2149   /**
2150    * group conservation toggled.
2151    */
2152   protected void showGroupConservation_actionPerformed()
2153   {
2154     viewport.setShowGroupConservation(showGroupConservation.getState());
2155     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2156   }
2157
2158   /*
2159    * (non-Javadoc)
2160    *
2161    * @see
2162    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2163    * .event.ActionEvent)
2164    */
2165   protected void showConsensusHistogram_actionPerformed()
2166   {
2167     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2168     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2169   }
2170
2171   /*
2172    * (non-Javadoc)
2173    *
2174    * @see
2175    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2176    * .event.ActionEvent)
2177    */
2178   protected void showSequenceLogo_actionPerformed()
2179   {
2180     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2181     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2182   }
2183
2184   protected void normSequenceLogo_actionPerformed()
2185   {
2186     showSequenceLogo.setState(true);
2187     viewport.setShowSequenceLogo(true);
2188     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2189     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190   }
2191
2192   protected void applyAutoAnnotationSettings_actionPerformed()
2193   {
2194     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2195   }
2196
2197   protected void makeGrpsFromSelection_actionPerformed()
2198   {
2199     if (avc.makeGroupsFromSelection())
2200     {
2201       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2202       alignPanel.updateAnnotation();
2203       alignPanel.paintAlignment(true);
2204     }
2205   }
2206
2207   protected void createGroup_actionPerformed()
2208   {
2209     avc.createGroup();
2210   }
2211
2212   protected void unGroup_actionPerformed()
2213   {
2214     if (avc.unGroup())
2215     {
2216       alignPanel.alignmentChanged();
2217     }
2218   }
2219
2220   protected void deleteGroups_actionPerformed()
2221   {
2222     if (avc.deleteGroups())
2223     {
2224       alignPanel.alignmentChanged();
2225     }
2226   }
2227
2228   public void selectAllSequenceMenuItem_actionPerformed()
2229   {
2230     SequenceGroup sg = new SequenceGroup();
2231     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2232     {
2233       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2234     }
2235     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2236     viewport.setSelectionGroup(sg);
2237     // JAL-2034 - should delegate to
2238     // alignPanel to decide if overview needs
2239     // updating.
2240     alignPanel.paintAlignment(false);
2241     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2242     viewport.sendSelection();
2243   }
2244
2245   public void deselectAllSequenceMenuItem_actionPerformed()
2246   {
2247     if (viewport.cursorMode)
2248     {
2249       alignPanel.seqPanel.keyboardNo1 = null;
2250       alignPanel.seqPanel.keyboardNo2 = null;
2251     }
2252     viewport.setSelectionGroup(null);
2253     viewport.getColumnSelection().clear();
2254     viewport.setSelectionGroup(null);
2255     alignPanel.idPanel.idCanvas.searchResults = null;
2256     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2257     // JAL-2034 - should delegate to
2258     // alignPanel to decide if overview needs
2259     // updating.
2260     alignPanel.paintAlignment(false);
2261     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2262     viewport.sendSelection();
2263   }
2264
2265   public void invertSequenceMenuItem_actionPerformed()
2266   {
2267     SequenceGroup sg = viewport.getSelectionGroup();
2268     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2269     {
2270       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2271     }
2272
2273     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2274     viewport.sendSelection();
2275   }
2276
2277   public void invertColSel_actionPerformed()
2278   {
2279     viewport.invertColumnSelection();
2280     alignPanel.paintAlignment(true);
2281     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2282     viewport.sendSelection();
2283   }
2284
2285   void trimAlignment(boolean trimLeft)
2286   {
2287     ColumnSelection colSel = viewport.getColumnSelection();
2288     int column;
2289
2290     if (!colSel.isEmpty())
2291     {
2292       if (trimLeft)
2293       {
2294         column = colSel.getMin();
2295       }
2296       else
2297       {
2298         column = colSel.getMax();
2299       }
2300
2301       SequenceI[] seqs;
2302       if (viewport.getSelectionGroup() != null)
2303       {
2304         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2305                 viewport.getHiddenRepSequences());
2306       }
2307       else
2308       {
2309         seqs = viewport.getAlignment().getSequencesArray();
2310       }
2311
2312       TrimRegionCommand trimRegion;
2313       if (trimLeft)
2314       {
2315         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2316                 column, viewport.getAlignment());
2317         viewport.setStartRes(0);
2318       }
2319       else
2320       {
2321         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2322                 column, viewport.getAlignment());
2323       }
2324
2325       statusBar.setText(MessageManager.formatMessage(
2326               "label.removed_columns",
2327               new String[] { Integer.valueOf(trimRegion.getSize())
2328                       .toString() }));
2329       addHistoryItem(trimRegion);
2330
2331       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2332       {
2333         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2334                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2335         {
2336           viewport.getAlignment().deleteGroup(sg);
2337         }
2338       }
2339
2340       viewport.firePropertyChange("alignment", null, viewport
2341               .getAlignment().getSequences());
2342     }
2343   }
2344
2345   public void removeGappedColumnMenuItem_actionPerformed()
2346   {
2347     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2348
2349     SequenceI[] seqs;
2350     if (viewport.getSelectionGroup() != null)
2351     {
2352       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2353               viewport.getHiddenRepSequences());
2354       start = viewport.getSelectionGroup().getStartRes();
2355       end = viewport.getSelectionGroup().getEndRes();
2356     }
2357     else
2358     {
2359       seqs = viewport.getAlignment().getSequencesArray();
2360     }
2361
2362     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2363             "Remove Gapped Columns", seqs, start, end,
2364             viewport.getAlignment());
2365
2366     addHistoryItem(removeGapCols);
2367
2368     statusBar.setText(MessageManager.formatMessage(
2369             "label.removed_empty_columns",
2370             new String[] { Integer.valueOf(removeGapCols.getSize())
2371                     .toString() }));
2372
2373     // This is to maintain viewport position on first residue
2374     // of first sequence
2375     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2376     int startRes = seq.findPosition(viewport.startRes);
2377     // ShiftList shifts;
2378     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2379     // edit.alColumnChanges=shifts.getInverse();
2380     // if (viewport.hasHiddenColumns)
2381     // viewport.getColumnSelection().compensateForEdits(shifts);
2382     viewport.setStartRes(seq.findIndex(startRes) - 1);
2383     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2384             .getSequences());
2385
2386   }
2387
2388   public void removeAllGapsMenuItem_actionPerformed()
2389   {
2390     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2391
2392     SequenceI[] seqs;
2393     if (viewport.getSelectionGroup() != null)
2394     {
2395       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2396               viewport.getHiddenRepSequences());
2397       start = viewport.getSelectionGroup().getStartRes();
2398       end = viewport.getSelectionGroup().getEndRes();
2399     }
2400     else
2401     {
2402       seqs = viewport.getAlignment().getSequencesArray();
2403     }
2404
2405     // This is to maintain viewport position on first residue
2406     // of first sequence
2407     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2408     int startRes = seq.findPosition(viewport.startRes);
2409
2410     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2411             viewport.getAlignment()));
2412
2413     viewport.setStartRes(seq.findIndex(startRes) - 1);
2414
2415     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2416             .getSequences());
2417
2418   }
2419
2420   public void findMenuItem_actionPerformed()
2421   {
2422     new Finder(alignPanel);
2423   }
2424
2425   /**
2426    * create a new view derived from the current view
2427    *
2428    * @param viewtitle
2429    * @return frame for the new view
2430    */
2431   public AlignFrame newView(String viewtitle)
2432   {
2433     AlignmentI newal;
2434     if (viewport.hasHiddenRows())
2435     {
2436       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2437               .getFullAlignment().getSequencesArray());
2438     }
2439     else
2440     {
2441       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2442     }
2443
2444     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2445     {
2446       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2447       {
2448         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2449         {
2450           newal.addAnnotation(viewport.getAlignment()
2451                   .getAlignmentAnnotation()[i]);
2452         }
2453       }
2454     }
2455
2456     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2457
2458     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2459     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2460     PaintRefresher.Register(newaf.alignPanel,
2461             newaf.alignPanel.av.getSequenceSetId());
2462
2463     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2464             newaf.alignPanel.av.getSequenceSetId());
2465     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2466             newaf.alignPanel.av.getSequenceSetId());
2467
2468     Vector comps = (Vector) PaintRefresher.components.get(viewport
2469             .getSequenceSetId());
2470     int viewSize = -1;
2471     for (int i = 0; i < comps.size(); i++)
2472     {
2473       if (comps.elementAt(i) instanceof AlignmentPanel)
2474       {
2475         viewSize++;
2476       }
2477     }
2478
2479     String title = new String(this.getTitle());
2480     if (viewtitle != null)
2481     {
2482       title = viewtitle + " ( " + title + ")";
2483     }
2484     else
2485     {
2486       if (title.indexOf("(View") > -1)
2487       {
2488         title = title.substring(0, title.indexOf("(View"));
2489       }
2490       title += "(View " + viewSize + ")";
2491     }
2492
2493     newaf.setTitle(title.toString());
2494
2495     newaf.viewport.setHistoryList(viewport.getHistoryList());
2496     newaf.viewport.setRedoList(viewport.getRedoList());
2497     return newaf;
2498   }
2499
2500   /**
2501    *
2502    * @return list of feature groups on the view
2503    */
2504   public String[] getFeatureGroups()
2505   {
2506     FeatureRenderer fr = null;
2507     if (alignPanel != null
2508             && (fr = alignPanel.getFeatureRenderer()) != null)
2509     {
2510       List<String> gps = fr.getFeatureGroups();
2511       String[] _gps = gps.toArray(new String[gps.size()]);
2512       return _gps;
2513     }
2514     return null;
2515   }
2516
2517   /**
2518    * get sequence feature groups that are hidden or shown
2519    *
2520    * @param visible
2521    *          true is visible
2522    * @return list
2523    */
2524   public String[] getFeatureGroupsOfState(boolean visible)
2525   {
2526     FeatureRenderer fr = null;
2527     if (alignPanel != null
2528             && (fr = alignPanel.getFeatureRenderer()) != null)
2529     {
2530       List<String> gps = fr.getGroups(visible);
2531       String[] _gps = gps.toArray(new String[gps.size()]);
2532       return _gps;
2533     }
2534     return null;
2535   }
2536
2537   /**
2538    * Change the display state for the given feature groups
2539    *
2540    * @param groups
2541    *          list of group strings
2542    * @param state
2543    *          visible or invisible
2544    */
2545   public void setFeatureGroupState(String[] groups, boolean state)
2546   {
2547     FeatureRenderer fr = null;
2548     this.sequenceFeatures.setState(true);
2549     viewport.setShowSequenceFeatures(true);
2550     if (alignPanel != null
2551             && (fr = alignPanel.getFeatureRenderer()) != null)
2552     {
2553
2554       fr.setGroupVisibility(Arrays.asList(groups), state);
2555       alignPanel.seqPanel.seqCanvas.repaint();
2556       if (alignPanel.overviewPanel != null)
2557       {
2558         alignPanel.overviewPanel.updateOverviewImage();
2559       }
2560     }
2561   }
2562
2563   public void seqLimits_itemStateChanged()
2564   {
2565     viewport.setShowJVSuffix(seqLimits.getState());
2566     alignPanel.fontChanged();
2567     alignPanel.paintAlignment(true);
2568   }
2569
2570   protected void colourTextMenuItem_actionPerformed()
2571   {
2572     viewport.setColourText(colourTextMenuItem.getState());
2573     alignPanel.paintAlignment(true);
2574   }
2575
2576   protected void displayNonconservedMenuItem_actionPerformed()
2577   {
2578     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2579     alignPanel.paintAlignment(true);
2580   }
2581
2582   protected void wrapMenuItem_actionPerformed()
2583   {
2584     viewport.setWrapAlignment(wrapMenuItem.getState());
2585     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2586     scaleAbove.setEnabled(wrapMenuItem.getState());
2587     scaleLeft.setEnabled(wrapMenuItem.getState());
2588     scaleRight.setEnabled(wrapMenuItem.getState());
2589     alignPanel.paintAlignment(true);
2590   }
2591
2592   public void overviewMenuItem_actionPerformed()
2593   {
2594     if (alignPanel.overviewPanel != null)
2595     {
2596       return;
2597     }
2598
2599     Frame frame = new Frame();
2600     OverviewPanel overview = new OverviewPanel(alignPanel);
2601     frame.add(overview);
2602     // +50 must allow for applet frame window
2603     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2604             "label.overview_params", new String[] { this.getTitle() }),
2605             overview.getPreferredSize().width,
2606             overview.getPreferredSize().height + 50);
2607
2608     frame.pack();
2609     final AlignmentPanel ap = alignPanel;
2610     frame.addWindowListener(new WindowAdapter()
2611     {
2612       @Override
2613       public void windowClosing(WindowEvent e)
2614       {
2615         if (ap != null)
2616         {
2617           ap.setOverviewPanel(null);
2618         }
2619       };
2620     });
2621
2622     alignPanel.setOverviewPanel(overview);
2623
2624   }
2625
2626   @Override
2627   public void changeColour(ColourSchemeI cs)
2628   {
2629
2630     if (cs != null)
2631     {
2632       if (viewport.getAbovePIDThreshold())
2633       {
2634         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2635                 cs, "Background"));
2636       }
2637
2638       if (viewport.getConservationSelected())
2639       {
2640         cs.setConservationApplied(true);
2641         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2642                 cs, "Background"));
2643       }
2644       else
2645       {
2646         cs.setConservationApplied(false);
2647       }
2648     }
2649     viewport.setGlobalColourScheme(cs);
2650
2651     alignPanel.paintAlignment(true);
2652   }
2653
2654   protected void modifyPID_actionPerformed()
2655   {
2656     if (viewport.getAbovePIDThreshold()
2657             && viewport.getGlobalColourScheme() != null)
2658     {
2659       SliderPanel.setPIDSliderSource(alignPanel,
2660               viewport.getGlobalColourScheme(), "Background");
2661       SliderPanel.showPIDSlider();
2662     }
2663   }
2664
2665   protected void modifyConservation_actionPerformed()
2666   {
2667     if (viewport.getConservationSelected()
2668             && viewport.getGlobalColourScheme() != null)
2669     {
2670       SliderPanel.setConservationSlider(alignPanel,
2671               viewport.getGlobalColourScheme(), "Background");
2672       SliderPanel.showConservationSlider();
2673     }
2674   }
2675
2676   protected void conservationMenuItem_actionPerformed()
2677   {
2678     viewport.setConservationSelected(conservationMenuItem.getState());
2679
2680     viewport.setAbovePIDThreshold(false);
2681     abovePIDThreshold.setState(false);
2682
2683     changeColour(viewport.getGlobalColourScheme());
2684
2685     modifyConservation_actionPerformed();
2686   }
2687
2688   public void abovePIDThreshold_actionPerformed()
2689   {
2690     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2691
2692     conservationMenuItem.setState(false);
2693     viewport.setConservationSelected(false);
2694
2695     changeColour(viewport.getGlobalColourScheme());
2696
2697     modifyPID_actionPerformed();
2698   }
2699
2700   public void sortPairwiseMenuItem_actionPerformed()
2701   {
2702     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2703     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2704             .getAlignment().getSequenceAt(0), null);
2705
2706     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2707             viewport.getAlignment()));
2708     alignPanel.paintAlignment(true);
2709   }
2710
2711   public void sortIDMenuItem_actionPerformed()
2712   {
2713     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2714     AlignmentSorter.sortByID(viewport.getAlignment());
2715     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2716             viewport.getAlignment()));
2717     alignPanel.paintAlignment(true);
2718   }
2719
2720   public void sortLengthMenuItem_actionPerformed()
2721   {
2722     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723     AlignmentSorter.sortByLength(viewport.getAlignment());
2724     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2725             viewport.getAlignment()));
2726     alignPanel.paintAlignment(true);
2727   }
2728
2729   public void sortGroupMenuItem_actionPerformed()
2730   {
2731     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2732     AlignmentSorter.sortByGroup(viewport.getAlignment());
2733     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2734             viewport.getAlignment()));
2735     alignPanel.paintAlignment(true);
2736
2737   }
2738
2739   public void removeRedundancyMenuItem_actionPerformed()
2740   {
2741     new RedundancyPanel(alignPanel);
2742   }
2743
2744   public void pairwiseAlignmentMenuItem_actionPerformed()
2745   {
2746     if (viewport.getSelectionGroup() != null
2747             && viewport.getSelectionGroup().getSize() > 1)
2748     {
2749       Frame frame = new Frame();
2750       frame.add(new PairwiseAlignPanel(alignPanel));
2751       jalview.bin.JalviewLite.addFrame(frame,
2752               MessageManager.getString("action.pairwise_alignment"), 600,
2753               500);
2754     }
2755   }
2756
2757   public void PCAMenuItem_actionPerformed()
2758   {
2759     // are the sequences aligned?
2760     if (!viewport.getAlignment().isAligned(false))
2761     {
2762       SequenceI current;
2763       int Width = viewport.getAlignment().getWidth();
2764
2765       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2766       {
2767         current = viewport.getAlignment().getSequenceAt(i);
2768
2769         if (current.getLength() < Width)
2770         {
2771           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2772         }
2773       }
2774       alignPanel.paintAlignment(true);
2775     }
2776
2777     if ((viewport.getSelectionGroup() != null
2778             && viewport.getSelectionGroup().getSize() < 4 && viewport
2779             .getSelectionGroup().getSize() > 0)
2780             || viewport.getAlignment().getHeight() < 4)
2781     {
2782       return;
2783     }
2784
2785     try
2786     {
2787       new PCAPanel(viewport);
2788     } catch (java.lang.OutOfMemoryError ex)
2789     {
2790     }
2791
2792   }
2793
2794   public void averageDistanceTreeMenuItem_actionPerformed()
2795   {
2796     NewTreePanel("AV", "PID", "Average distance tree using PID");
2797   }
2798
2799   public void neighbourTreeMenuItem_actionPerformed()
2800   {
2801     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2802   }
2803
2804   protected void njTreeBlosumMenuItem_actionPerformed()
2805   {
2806     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2807   }
2808
2809   protected void avTreeBlosumMenuItem_actionPerformed()
2810   {
2811     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2812   }
2813
2814   void NewTreePanel(String type, String pwType, String title)
2815   {
2816     // are the sequences aligned?
2817     if (!viewport.getAlignment().isAligned(false))
2818     {
2819       SequenceI current;
2820       int Width = viewport.getAlignment().getWidth();
2821
2822       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2823       {
2824         current = viewport.getAlignment().getSequenceAt(i);
2825
2826         if (current.getLength() < Width)
2827         {
2828           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2829         }
2830       }
2831       alignPanel.paintAlignment(true);
2832
2833     }
2834
2835     if ((viewport.getSelectionGroup() != null && viewport
2836             .getSelectionGroup().getSize() > 1)
2837             || (viewport.getAlignment().getHeight() > 1))
2838     {
2839       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2840
2841       addTreeMenuItem(tp, title);
2842
2843       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2844     }
2845   }
2846
2847   void loadTree_actionPerformed()
2848   {
2849     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2850     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2851     cap.setTreeImport();
2852     Frame frame = new Frame();
2853     frame.add(cap);
2854     jalview.bin.JalviewLite.addFrame(frame,
2855             MessageManager.getString("label.paste_newick_file"), 400, 300);
2856   }
2857
2858   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2859   {
2860     TreePanel tp = new TreePanel(alignPanel, treeFile,
2861             MessageManager.getString("label.load_tree_from_file"), tree);
2862     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2863     addTreeMenuItem(tp, treeFile);
2864   }
2865
2866   /**
2867    * sort the alignment using the given treePanel
2868    *
2869    * @param treePanel
2870    *          tree used to sort view
2871    * @param title
2872    *          string used for undo event name
2873    */
2874   public void sortByTree(TreePanel treePanel, String title)
2875   {
2876     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2877     AlignmentSorter
2878             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2879     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2880     // HistoryItem.SORT));
2881     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2882             "label.order_by_params", new String[] { title }), oldOrder,
2883             viewport.getAlignment()));
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   /**
2888    * Do any automatic reordering of the alignment and add the necessary bits to
2889    * the menu structure for the new tree
2890    *
2891    * @param treePanel
2892    * @param title
2893    */
2894   protected void addTreeMenuItem(final TreePanel treePanel,
2895           final String title)
2896   {
2897     final MenuItem item = new MenuItem(title);
2898     sortByTreeMenu.add(item);
2899     item.addActionListener(new java.awt.event.ActionListener()
2900     {
2901       @Override
2902       public void actionPerformed(ActionEvent evt)
2903       {
2904         sortByTree(treePanel, title); // treePanel.getTitle());
2905       }
2906     });
2907
2908     treePanel.addWindowListener(new WindowAdapter()
2909     {
2910       @Override
2911       public void windowOpened(WindowEvent e)
2912       {
2913         if (viewport.sortByTree)
2914         {
2915           sortByTree(treePanel, title);
2916         }
2917         super.windowOpened(e);
2918       }
2919
2920       @Override
2921       public void windowClosing(WindowEvent e)
2922       {
2923         sortByTreeMenu.remove(item);
2924       };
2925     });
2926   }
2927
2928   public boolean sortBy(AlignmentOrder alorder, String undoname)
2929   {
2930     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2931     if (viewport.applet.debug)
2932     {
2933       System.err.println("Sorting " + alorder.getOrder().size()
2934               + " in alignment '" + getTitle() + "'");
2935     }
2936     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2937     if (undoname != null)
2938     {
2939       addHistoryItem(new OrderCommand(undoname, oldOrder,
2940               viewport.getAlignment()));
2941     }
2942     alignPanel.paintAlignment(true);
2943     return true;
2944   }
2945
2946   protected void documentation_actionPerformed()
2947   {
2948     alignPanel.av.applet.openJalviewHelpUrl();
2949   }
2950
2951   protected void about_actionPerformed()
2952   {
2953
2954     class AboutPanel extends Canvas
2955     {
2956       String version;
2957
2958       String builddate;
2959
2960       public AboutPanel(String version, String builddate)
2961       {
2962         this.version = version;
2963         this.builddate = builddate;
2964       }
2965
2966       @Override
2967       public void paint(Graphics g)
2968       {
2969         g.setColor(Color.white);
2970         g.fillRect(0, 0, getSize().width, getSize().height);
2971         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2972         FontMetrics fm = g.getFontMetrics();
2973         int fh = fm.getHeight();
2974         int y = 5, x = 7;
2975         g.setColor(Color.black);
2976         // TODO: update this text for each release or centrally store it for
2977         // lite and application
2978         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2979         g.drawString(MessageManager.formatMessage(
2980                 "label.jalviewLite_release", new String[] { version }), x,
2981                 y += fh);
2982         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2983         g.drawString(MessageManager.formatMessage(
2984                 "label.jaview_build_date", new String[] { builddate }), x,
2985                 y += fh);
2986         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2987         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2988                 x, y += fh * 1.5);
2989         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2990                 x + 50, y += fh + 8);
2991         g.drawString(
2992                 MessageManager.getString("label.jalview_dev_managers"), x,
2993                 y += fh);
2994         g.drawString(MessageManager
2995                 .getString("label.jalview_distribution_lists"), x, y += fh);
2996         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2997                 x, y += fh + 8);
2998         g.drawString(
2999                 MessageManager.getString("label.jalview_cite_1_authors"),
3000                 x, y += fh);
3001         g.drawString(
3002                 MessageManager.getString("label.jalview_cite_1_title"), x,
3003                 y += fh);
3004         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3005                 x, y += fh);
3006       }
3007     }
3008
3009     Frame frame = new Frame();
3010     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3011             .getBuildDate()));
3012     jalview.bin.JalviewLite.addFrame(frame,
3013             MessageManager.getString("label.jalview"), 580, 220);
3014
3015   }
3016
3017   public void showURL(String url, String target)
3018   {
3019     if (viewport.applet == null)
3020     {
3021       System.out.println("Not running as applet - no browser available.");
3022     }
3023     else
3024     {
3025       viewport.applet.showURL(url, target);
3026     }
3027   }
3028
3029   // ////////////////////////////////////////////////////////////////////////////////
3030   // JBuilder Graphics here
3031
3032   MenuBar alignFrameMenuBar = new MenuBar();
3033
3034   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3035
3036   MenuItem loadApplication = new MenuItem(
3037           MessageManager.getString("label.view_full_application"));
3038
3039   MenuItem loadTree = new MenuItem(
3040           MessageManager.getString("label.load_associated_tree"));
3041
3042   MenuItem loadAnnotations = new MenuItem(
3043           MessageManager.getString("label.load_features_annotations"));
3044
3045   MenuItem outputFeatures = new MenuItem(
3046           MessageManager.getString("label.export_features"));
3047
3048   MenuItem outputAnnotations = new MenuItem(
3049           MessageManager.getString("label.export_annotations"));
3050
3051   MenuItem closeMenuItem = new MenuItem(
3052           MessageManager.getString("action.close"));
3053
3054   MenuItem selectAllSequenceMenuItem = new MenuItem(
3055           MessageManager.getString("action.select_all"));
3056
3057   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3058           MessageManager.getString("action.deselect_all"));
3059
3060   MenuItem invertSequenceMenuItem = new MenuItem(
3061           MessageManager.getString("action.invert_selection"));
3062
3063   MenuItem remove2LeftMenuItem = new MenuItem();
3064
3065   MenuItem remove2RightMenuItem = new MenuItem();
3066
3067   MenuItem removeGappedColumnMenuItem = new MenuItem();
3068
3069   MenuItem removeAllGapsMenuItem = new MenuItem();
3070
3071   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3072
3073   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3074
3075   MenuItem sortPairwiseMenuItem = new MenuItem();
3076
3077   MenuItem sortIDMenuItem = new MenuItem();
3078
3079   MenuItem sortLengthMenuItem = new MenuItem();
3080
3081   MenuItem sortGroupMenuItem = new MenuItem();
3082
3083   MenuItem removeRedundancyMenuItem = new MenuItem();
3084
3085   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3086
3087   MenuItem PCAMenuItem = new MenuItem();
3088
3089   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3090
3091   MenuItem neighbourTreeMenuItem = new MenuItem();
3092
3093   BorderLayout borderLayout1 = new BorderLayout();
3094
3095   public Label statusBar = new Label();
3096
3097   MenuItem clustalColour = new MenuItem();
3098
3099   MenuItem zappoColour = new MenuItem();
3100
3101   MenuItem taylorColour = new MenuItem();
3102
3103   MenuItem hydrophobicityColour = new MenuItem();
3104
3105   MenuItem helixColour = new MenuItem();
3106
3107   MenuItem strandColour = new MenuItem();
3108
3109   MenuItem turnColour = new MenuItem();
3110
3111   MenuItem buriedColour = new MenuItem();
3112
3113   MenuItem purinePyrimidineColour = new MenuItem();
3114
3115   // MenuItem RNAInteractionColour = new MenuItem();
3116
3117   MenuItem RNAHelixColour = new MenuItem();
3118
3119   MenuItem userDefinedColour = new MenuItem();
3120
3121   MenuItem PIDColour = new MenuItem();
3122
3123   MenuItem BLOSUM62Colour = new MenuItem();
3124
3125   MenuItem tcoffeeColour = new MenuItem();
3126
3127   MenuItem njTreeBlosumMenuItem = new MenuItem();
3128
3129   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3130
3131   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3132
3133   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3134
3135   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3136
3137   MenuItem alProperties = new MenuItem(
3138           MessageManager.getString("label.alignment_props"));
3139
3140   MenuItem overviewMenuItem = new MenuItem();
3141
3142   MenuItem undoMenuItem = new MenuItem();
3143
3144   MenuItem redoMenuItem = new MenuItem();
3145
3146   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3147
3148   MenuItem noColourmenuItem = new MenuItem();
3149
3150   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3151
3152   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3153
3154   MenuItem findMenuItem = new MenuItem();
3155
3156   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3157
3158   MenuItem nucleotideColour = new MenuItem();
3159
3160   MenuItem deleteGroups = new MenuItem();
3161
3162   MenuItem grpsFromSelection = new MenuItem();
3163
3164   MenuItem createGroup = new MenuItem();
3165
3166   MenuItem unGroup = new MenuItem();
3167
3168   MenuItem delete = new MenuItem();
3169
3170   MenuItem copy = new MenuItem();
3171
3172   MenuItem cut = new MenuItem();
3173
3174   Menu pasteMenu = new Menu();
3175
3176   MenuItem pasteNew = new MenuItem();
3177
3178   MenuItem pasteThis = new MenuItem();
3179
3180   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3181
3182   MenuItem font = new MenuItem();
3183
3184   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3185
3186   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3187
3188   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3189
3190   MenuItem modifyPID = new MenuItem();
3191
3192   MenuItem modifyConservation = new MenuItem();
3193
3194   CheckboxMenuItem autoCalculate = null;
3195
3196   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3197           "Sort Alignment With New Tree", true);
3198
3199   Menu sortByTreeMenu = new Menu();
3200
3201   MenuItem inputText = new MenuItem();
3202
3203   MenuItem documentation = new MenuItem();
3204
3205   MenuItem about = new MenuItem();
3206
3207   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3208
3209   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3222
3223   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3224
3225   /**
3226    * Initialise menus and other items
3227    *
3228    * @throws Exception
3229    */
3230   private void jbInit() throws Exception
3231   {
3232     setMenuBar(alignFrameMenuBar);
3233
3234     /*
3235      * Configure File menu items and actions
3236      */
3237     inputText
3238             .setLabel(MessageManager.getString("label.input_from_textbox"));
3239     inputText.addActionListener(this);
3240     Menu outputTextboxMenu = new Menu(
3241             MessageManager.getString("label.out_to_textbox"));
3242     for (String ff : FileFormat.getWritableFormats(true))
3243     {
3244       MenuItem item = new MenuItem(ff);
3245
3246       item.addActionListener(new java.awt.event.ActionListener()
3247       {
3248         @Override
3249         public void actionPerformed(ActionEvent e)
3250         {
3251           outputText_actionPerformed(e);
3252         }
3253       });
3254
3255       outputTextboxMenu.add(item);
3256     }
3257     closeMenuItem.addActionListener(this);
3258     loadApplication.addActionListener(this);
3259     loadTree.addActionListener(this);
3260     loadAnnotations.addActionListener(this);
3261     outputFeatures.addActionListener(this);
3262     outputAnnotations.addActionListener(this);
3263
3264     /*
3265      * Configure Edit menu items and actions
3266      */
3267     undoMenuItem.setEnabled(false);
3268     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3269     undoMenuItem.addActionListener(this);
3270     redoMenuItem.setEnabled(false);
3271     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3272     redoMenuItem.addActionListener(this);
3273     copy.setLabel(MessageManager.getString("action.copy"));
3274     copy.addActionListener(this);
3275     cut.setLabel(MessageManager.getString("action.cut"));
3276     cut.addActionListener(this);
3277     delete.setLabel(MessageManager.getString("action.delete"));
3278     delete.addActionListener(this);
3279     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3280     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3281     pasteNew.addActionListener(this);
3282     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3283     pasteThis.addActionListener(this);
3284     remove2LeftMenuItem.setLabel(MessageManager
3285             .getString("action.remove_left"));
3286     remove2LeftMenuItem.addActionListener(this);
3287     remove2RightMenuItem.setLabel(MessageManager
3288             .getString("action.remove_right"));
3289     remove2RightMenuItem.addActionListener(this);
3290     removeGappedColumnMenuItem.setLabel(MessageManager
3291             .getString("action.remove_empty_columns"));
3292     removeGappedColumnMenuItem.addActionListener(this);
3293     removeAllGapsMenuItem.setLabel(MessageManager
3294             .getString("action.remove_all_gaps"));
3295     removeAllGapsMenuItem.addActionListener(this);
3296     removeRedundancyMenuItem.setLabel(MessageManager
3297             .getString("action.remove_redundancy"));
3298     removeRedundancyMenuItem.addActionListener(this);
3299
3300     /*
3301      * Configure Select menu items and actions
3302      */
3303     findMenuItem.setLabel(MessageManager.getString("action.find"));
3304     findMenuItem.addActionListener(this);
3305     selectAllSequenceMenuItem.addActionListener(this);
3306     deselectAllSequenceMenuItem.addActionListener(this);
3307     invertSequenceMenuItem.setLabel(MessageManager
3308             .getString("action.invert_sequence_selection"));
3309     invertSequenceMenuItem.addActionListener(this);
3310     invertColSel.setLabel(MessageManager
3311             .getString("action.invert_column_selection"));
3312     invertColSel.addActionListener(this);
3313     deleteGroups.setLabel(MessageManager
3314             .getString("action.undefine_groups"));
3315     deleteGroups.addActionListener(this);
3316     grpsFromSelection.setLabel(MessageManager
3317             .getString("action.make_groups_selection"));
3318     grpsFromSelection.addActionListener(this);
3319     createGroup.setLabel(MessageManager.getString("action.create_group"));
3320     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3321     annotationColumnSelection.setLabel(MessageManager
3322             .getString("action.select_by_annotation"));
3323     annotationColumnSelection.addActionListener(this);
3324
3325     /*
3326      * Configure View menu items and actions
3327      */
3328     newView.setLabel(MessageManager.getString("action.new_view"));
3329     newView.addActionListener(this);
3330     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3331     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3332     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3333     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3334     hideColumns
3335             .setLabel(MessageManager.getString("label.selected_columns"));
3336     hideSequences.setLabel(MessageManager
3337             .getString("label.selected_sequences"));
3338     hideAllButSelection.setLabel(MessageManager
3339             .getString("label.all_but_selected_region"));
3340     hideAllSelection.setLabel(MessageManager
3341             .getString("label.selected_region"));
3342     showAllHidden.setLabel(MessageManager
3343             .getString("label.all_sequences_columns"));
3344     showColumns.addActionListener(this);
3345     showSeqs.addActionListener(this);
3346     hideColumns.addActionListener(this);
3347     hideSequences.addActionListener(this);
3348     hideAllButSelection.addActionListener(this);
3349     hideAllSelection.addActionListener(this);
3350     showAllHidden.addActionListener(this);
3351     featureSettings.setLabel(MessageManager
3352             .getString("action.feature_settings"));
3353     featureSettings.addActionListener(this);
3354     sequenceFeatures.setLabel(MessageManager
3355             .getString("label.show_sequence_features"));
3356     sequenceFeatures.addItemListener(this);
3357     sequenceFeatures.setState(false);
3358     followMouseOverFlag.setLabel(MessageManager
3359             .getString("label.automatic_scrolling"));
3360     followMouseOverFlag.addItemListener(this);
3361     alProperties.addActionListener(this);
3362     overviewMenuItem.setLabel(MessageManager
3363             .getString("label.overview_window"));
3364     overviewMenuItem.addActionListener(this);
3365
3366     /*
3367      * Configure Annotations menu items and actions
3368      */
3369     annotationPanelMenuItem.setLabel(MessageManager
3370             .getString("label.show_annotations"));
3371     annotationPanelMenuItem.addItemListener(this);
3372     showGroupConsensus.setLabel(MessageManager
3373             .getString("label.group_consensus"));
3374     showGroupConservation.setLabel(MessageManager
3375             .getString("label.group_conservation"));
3376     showConsensusHistogram.setLabel(MessageManager
3377             .getString("label.show_consensus_histogram"));
3378     showSequenceLogo.setLabel(MessageManager
3379             .getString("label.show_consensus_logo"));
3380     normSequenceLogo.setLabel(MessageManager
3381             .getString("label.norm_consensus_logo"));
3382     applyAutoAnnotationSettings.setLabel(MessageManager
3383             .getString("label.apply_all_groups"));
3384     applyAutoAnnotationSettings.setState(true);
3385     Menu autoAnnMenu = new Menu(
3386             MessageManager.getString("label.autocalculated_annotation"));
3387     showGroupConsensus.addItemListener(this);
3388     showGroupConservation.addItemListener(this);
3389     showConsensusHistogram.addItemListener(this);
3390     showSequenceLogo.addItemListener(this);
3391     normSequenceLogo.addItemListener(this);
3392     applyAutoAnnotationSettings.addItemListener(this);
3393     showAlignmentAnnotations = new CheckboxMenuItem(
3394             MessageManager.getString("label.show_all_al_annotations"));
3395     showSequenceAnnotations = new CheckboxMenuItem(
3396             MessageManager.getString("label.show_all_seq_annotations"));
3397     sortAnnBySequence = new CheckboxMenuItem(
3398             MessageManager.getString("label.sort_annotations_by_sequence"));
3399     sortAnnByLabel = new CheckboxMenuItem(
3400             MessageManager.getString("label.sort_annotations_by_label"));
3401     showAutoFirst = new CheckboxMenuItem(
3402             MessageManager.getString("label.show_first"));
3403     showAutoFirst.setState(false); // pending applet parameter
3404     setShowAutoCalculatedAbove(showAutoFirst.getState());
3405     showAutoLast = new CheckboxMenuItem(
3406             MessageManager.getString("label.show_last"));
3407     showAutoLast.setState(!showAutoFirst.getState());
3408     showAlignmentAnnotations.addItemListener(this);
3409     showSequenceAnnotations.addItemListener(this);
3410     sortAnnBySequence.addItemListener(this);
3411     sortAnnByLabel.addItemListener(this);
3412     showAutoFirst.addItemListener(this);
3413     showAutoLast.addItemListener(this);
3414
3415     /*
3416      * Configure Format menu items and actions
3417      */
3418     font.setLabel(MessageManager.getString("action.font"));
3419     font.addActionListener(this);
3420     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3421     scaleAbove.setState(true);
3422     scaleAbove.setEnabled(false);
3423     scaleAbove.addItemListener(this);
3424     scaleLeft.setEnabled(false);
3425     scaleLeft.setState(true);
3426     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3427     scaleLeft.addItemListener(this);
3428     scaleRight.setEnabled(false);
3429     scaleRight.setState(true);
3430     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3431     scaleRight.addItemListener(this);
3432     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3433     viewBoxesMenuItem.setState(true);
3434     viewBoxesMenuItem.addItemListener(this);
3435     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3436     viewTextMenuItem.setState(true);
3437     viewTextMenuItem.addItemListener(this);
3438     colourTextMenuItem.setLabel(MessageManager
3439             .getString("label.colour_text"));
3440     colourTextMenuItem.addItemListener(this);
3441     displayNonconservedMenuItem.setLabel(MessageManager
3442             .getString("label.show_non_conserved"));
3443     displayNonconservedMenuItem.addItemListener(this);
3444     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3445     wrapMenuItem.addItemListener(this);
3446     renderGapsMenuItem.setLabel(MessageManager
3447             .getString("action.show_gaps"));
3448     renderGapsMenuItem.setState(true);
3449     renderGapsMenuItem.addItemListener(this);
3450     centreColumnLabelFlag.setLabel(MessageManager
3451             .getString("label.centre_column_labels"));
3452     centreColumnLabelFlag.addItemListener(this);
3453     seqLimits.setState(true);
3454     seqLimits.setLabel(MessageManager
3455             .getString("label.show_sequence_limits"));
3456     seqLimits.addItemListener(this);
3457
3458     /*
3459      * Configure Colour menu items and actions
3460      */
3461     applyToAllGroups.setLabel(MessageManager
3462             .getString("label.apply_colour_to_all_groups"));
3463     applyToAllGroups.setState(true);
3464     applyToAllGroups.addItemListener(this);
3465     clustalColour.setLabel(MessageManager
3466             .getString("label.colourScheme_clustal"));
3467     clustalColour.addActionListener(this);
3468     zappoColour.setLabel(MessageManager
3469             .getString("label.colourScheme_zappo"));
3470     zappoColour.addActionListener(this);
3471     taylorColour.setLabel(MessageManager
3472             .getString("label.colourScheme_taylor"));
3473     taylorColour.addActionListener(this);
3474     hydrophobicityColour.setLabel(MessageManager
3475             .getString("label.colourScheme_hydrophobic"));
3476     hydrophobicityColour.addActionListener(this);
3477     helixColour.setLabel(MessageManager
3478             .getString("label.colourScheme_helix_propensity"));
3479     helixColour.addActionListener(this);
3480     strandColour.setLabel(MessageManager
3481             .getString("label.colourScheme_strand_propensity"));
3482     strandColour.addActionListener(this);
3483     turnColour.setLabel(MessageManager
3484             .getString("label.colourScheme_turn_propensity"));
3485     turnColour.addActionListener(this);
3486     buriedColour.setLabel(MessageManager
3487             .getString("label.colourScheme_buried_index"));
3488     buriedColour.addActionListener(this);
3489     purinePyrimidineColour.setLabel(MessageManager
3490             .getString("label.colourScheme_purine/pyrimidine"));
3491     purinePyrimidineColour.addActionListener(this);
3492     // RNAInteractionColour.setLabel(MessageManager
3493     // .getString("label.rna_interaction"));
3494     // RNAInteractionColour.addActionListener(this);
3495     RNAHelixColour.setLabel(MessageManager
3496             .getString("label.colourScheme_rna_helices"));
3497     RNAHelixColour.addActionListener(this);
3498     userDefinedColour.setLabel(MessageManager
3499             .getString("action.user_defined"));
3500     userDefinedColour.addActionListener(this);
3501     PIDColour.setLabel(MessageManager
3502             .getString("label.colourScheme_%_identity"));
3503     PIDColour.addActionListener(this);
3504     BLOSUM62Colour.setLabel(MessageManager
3505             .getString("label.colourScheme_blosum62"));
3506     BLOSUM62Colour.addActionListener(this);
3507     tcoffeeColour.setLabel(MessageManager
3508             .getString("label.colourScheme_t-coffee_scores"));
3509     // it will be enabled only if a score file is provided
3510     tcoffeeColour.setEnabled(false);
3511     tcoffeeColour.addActionListener(this);
3512     conservationMenuItem.setLabel(MessageManager
3513             .getString("action.by_conservation"));
3514     conservationMenuItem.addItemListener(this);
3515     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3516     noColourmenuItem.addActionListener(this);
3517     abovePIDThreshold.setLabel(MessageManager
3518             .getString("label.above_identity_threshold"));
3519     abovePIDThreshold.addItemListener(this);
3520     nucleotideColour.setLabel(MessageManager
3521             .getString("label.colourScheme_nucleotide"));
3522     nucleotideColour.addActionListener(this);
3523     modifyPID.setLabel(MessageManager
3524             .getString("label.modify_identity_threshold"));
3525     modifyPID.addActionListener(this);
3526     modifyConservation.setLabel(MessageManager
3527             .getString("label.modify_conservation_threshold"));
3528     modifyConservation.addActionListener(this);
3529     annotationColour.setLabel(MessageManager
3530             .getString("action.by_annotation"));
3531     annotationColour.addActionListener(this);
3532
3533     /*
3534      * Configure Calculate menu items and actions
3535      */
3536     sortPairwiseMenuItem.setLabel(MessageManager
3537             .getString("action.by_pairwise_id"));
3538     sortPairwiseMenuItem.addActionListener(this);
3539     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3540     sortIDMenuItem.addActionListener(this);
3541     sortLengthMenuItem.setLabel(MessageManager
3542             .getString("action.by_length"));
3543     sortLengthMenuItem.addActionListener(this);
3544     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3545     sortGroupMenuItem.addActionListener(this);
3546     pairwiseAlignmentMenuItem.setLabel(MessageManager
3547             .getString("action.pairwise_alignment"));
3548     pairwiseAlignmentMenuItem.addActionListener(this);
3549     PCAMenuItem.setLabel(MessageManager
3550             .getString("label.principal_component_analysis"));
3551     PCAMenuItem.addActionListener(this);
3552     autoCalculate = new CheckboxMenuItem(
3553             MessageManager.getString("label.autocalculate_consensus"), true);
3554     averageDistanceTreeMenuItem.setLabel(MessageManager
3555             .getString("label.average_distance_identity"));
3556     averageDistanceTreeMenuItem.addActionListener(this);
3557     neighbourTreeMenuItem.setLabel(MessageManager
3558             .getString("label.neighbour_joining_identity"));
3559     neighbourTreeMenuItem.addActionListener(this);
3560     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3561             .getString("label.average_distance_blosum62"));
3562     avDistanceTreeBlosumMenuItem.addActionListener(this);
3563     njTreeBlosumMenuItem.setLabel(MessageManager
3564             .getString("label.neighbour_blosum62"));
3565     njTreeBlosumMenuItem.addActionListener(this);
3566     sortByTreeMenu.setLabel(MessageManager
3567             .getString("action.by_tree_order"));
3568     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3569     Menu calculateTreeMenu = new Menu(
3570             MessageManager.getString("action.calculate_tree"));
3571     autoCalculate.addItemListener(this);
3572     sortByTree.addItemListener(this);
3573
3574     /*
3575      * Configure Help menu items and actions
3576      */
3577     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3578     documentation.setLabel(MessageManager.getString("label.documentation"));
3579     documentation.addActionListener(this);
3580     about.setLabel(MessageManager.getString("label.about"));
3581     about.addActionListener(this);
3582
3583     /*
3584      * Add top level menus to frame
3585      */
3586     alignFrameMenuBar.add(fileMenu);
3587     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3588     alignFrameMenuBar.add(editMenu);
3589     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3590     alignFrameMenuBar.add(selectMenu);
3591     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3592     alignFrameMenuBar.add(viewMenu);
3593     Menu annotationsMenu = new Menu(
3594             MessageManager.getString("action.annotations"));
3595     alignFrameMenuBar.add(annotationsMenu);
3596     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3597     alignFrameMenuBar.add(formatMenu);
3598     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3599     alignFrameMenuBar.add(colourMenu);
3600     Menu calculateMenu = new Menu(
3601             MessageManager.getString("action.calculate"));
3602     alignFrameMenuBar.add(calculateMenu);
3603     alignFrameMenuBar.add(helpMenu);
3604
3605     /*
3606      * File menu
3607      */
3608     fileMenu.add(inputText);
3609     fileMenu.add(loadTree);
3610     fileMenu.add(loadAnnotations);
3611     fileMenu.addSeparator();
3612     fileMenu.add(outputTextboxMenu);
3613     fileMenu.add(outputFeatures);
3614     fileMenu.add(outputAnnotations);
3615     if (jalviewServletURL != null)
3616     {
3617       fileMenu.add(loadApplication);
3618     }
3619     fileMenu.addSeparator();
3620     fileMenu.add(closeMenuItem);
3621
3622     /*
3623      * Edit menu
3624      */
3625     editMenu.add(undoMenuItem);
3626     editMenu.add(redoMenuItem);
3627     editMenu.add(cut);
3628     editMenu.add(copy);
3629     pasteMenu.add(pasteNew);
3630     pasteMenu.add(pasteThis);
3631     editMenu.add(pasteMenu);
3632     editMenu.add(delete);
3633     editMenu.addSeparator();
3634     editMenu.add(remove2LeftMenuItem);
3635     editMenu.add(remove2RightMenuItem);
3636     editMenu.add(removeGappedColumnMenuItem);
3637     editMenu.add(removeAllGapsMenuItem);
3638     editMenu.add(removeRedundancyMenuItem);
3639
3640     /*
3641      * Select menu
3642      */
3643     selectMenu.add(findMenuItem);
3644     selectMenu.addSeparator();
3645     selectMenu.add(selectAllSequenceMenuItem);
3646     selectMenu.add(deselectAllSequenceMenuItem);
3647     selectMenu.add(invertSequenceMenuItem);
3648     selectMenu.add(invertColSel);
3649     selectMenu.add(createGroup);
3650     selectMenu.add(unGroup);
3651     selectMenu.add(grpsFromSelection);
3652     selectMenu.add(deleteGroups);
3653     selectMenu.add(annotationColumnSelection);
3654
3655     /*
3656      * View menu
3657      */
3658     viewMenu.add(newView);
3659     viewMenu.addSeparator();
3660     showMenu.add(showColumns);
3661     showMenu.add(showSeqs);
3662     showMenu.add(showAllHidden);
3663     viewMenu.add(showMenu);
3664     hideMenu.add(hideColumns);
3665     hideMenu.add(hideSequences);
3666     hideMenu.add(hideAllSelection);
3667     hideMenu.add(hideAllButSelection);
3668     viewMenu.add(hideMenu);
3669     viewMenu.addSeparator();
3670     viewMenu.add(followMouseOverFlag);
3671     viewMenu.addSeparator();
3672     viewMenu.add(sequenceFeatures);
3673     viewMenu.add(featureSettings);
3674     viewMenu.addSeparator();
3675     viewMenu.add(alProperties);
3676     viewMenu.addSeparator();
3677     viewMenu.add(overviewMenuItem);
3678
3679     /*
3680      * Annotations menu
3681      */
3682     annotationsMenu.add(annotationPanelMenuItem);
3683     annotationsMenu.addSeparator();
3684     annotationsMenu.add(showAlignmentAnnotations);
3685     annotationsMenu.add(showSequenceAnnotations);
3686     annotationsMenu.add(sortAnnBySequence);
3687     annotationsMenu.add(sortAnnByLabel);
3688     annotationsMenu.addSeparator();
3689     autoAnnMenu.add(showAutoFirst);
3690     autoAnnMenu.add(showAutoLast);
3691     autoAnnMenu.addSeparator();
3692     autoAnnMenu.add(applyAutoAnnotationSettings);
3693     autoAnnMenu.add(showConsensusHistogram);
3694     autoAnnMenu.add(showSequenceLogo);
3695     autoAnnMenu.add(normSequenceLogo);
3696     autoAnnMenu.addSeparator();
3697     autoAnnMenu.add(showGroupConservation);
3698     autoAnnMenu.add(showGroupConsensus);
3699     annotationsMenu.add(autoAnnMenu);
3700
3701     /*
3702      * Format menu
3703      */
3704     formatMenu.add(font);
3705     formatMenu.add(seqLimits);
3706     formatMenu.add(wrapMenuItem);
3707     formatMenu.add(scaleAbove);
3708     formatMenu.add(scaleLeft);
3709     formatMenu.add(scaleRight);
3710     formatMenu.add(viewBoxesMenuItem);
3711     formatMenu.add(viewTextMenuItem);
3712     formatMenu.add(colourTextMenuItem);
3713     formatMenu.add(displayNonconservedMenuItem);
3714     formatMenu.add(renderGapsMenuItem);
3715     formatMenu.add(centreColumnLabelFlag);
3716
3717     /*
3718      * Colour menu
3719      */
3720     colourMenu.add(applyToAllGroups);
3721     colourMenu.addSeparator();
3722     colourMenu.add(noColourmenuItem);
3723     colourMenu.add(clustalColour);
3724     colourMenu.add(BLOSUM62Colour);
3725     colourMenu.add(PIDColour);
3726     colourMenu.add(zappoColour);
3727     colourMenu.add(taylorColour);
3728     colourMenu.add(hydrophobicityColour);
3729     colourMenu.add(helixColour);
3730     colourMenu.add(strandColour);
3731     colourMenu.add(turnColour);
3732     colourMenu.add(buriedColour);
3733     colourMenu.add(nucleotideColour);
3734     colourMenu.add(purinePyrimidineColour);
3735     // colourMenu.add(RNAInteractionColour);
3736     colourMenu.add(tcoffeeColour);
3737     colourMenu.add(userDefinedColour);
3738     colourMenu.addSeparator();
3739     colourMenu.add(conservationMenuItem);
3740     colourMenu.add(modifyConservation);
3741     colourMenu.add(abovePIDThreshold);
3742     colourMenu.add(modifyPID);
3743     colourMenu.add(annotationColour);
3744     colourMenu.add(RNAHelixColour);
3745
3746     /*
3747      * Calculate menu
3748      */
3749     sortMenu.add(sortIDMenuItem);
3750     sortMenu.add(sortLengthMenuItem);
3751     sortMenu.add(sortByTreeMenu);
3752     sortMenu.add(sortGroupMenuItem);
3753     sortMenu.add(sortPairwiseMenuItem);
3754     calculateMenu.add(sortMenu);
3755     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3756     calculateTreeMenu.add(neighbourTreeMenuItem);
3757     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3758     calculateTreeMenu.add(njTreeBlosumMenuItem);
3759     calculateMenu.add(calculateTreeMenu);
3760     calculateMenu.addSeparator();
3761     calculateMenu.add(pairwiseAlignmentMenuItem);
3762     calculateMenu.add(PCAMenuItem);
3763     calculateMenu.add(autoCalculate);
3764     calculateMenu.add(sortByTree);
3765
3766     /*
3767      * Help menu
3768      */
3769     helpMenu.add(documentation);
3770     helpMenu.add(about);
3771
3772     /*
3773      * Status bar
3774      */
3775     statusBar.setBackground(Color.white);
3776     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3777     statusBar.setText(MessageManager.getString("label.status_bar"));
3778     this.add(statusBar, BorderLayout.SOUTH);
3779   }
3780
3781   @Override
3782   public void setStatus(String string)
3783   {
3784     statusBar.setText(string);
3785   };
3786
3787   MenuItem featureSettings = new MenuItem();
3788
3789   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3790
3791   MenuItem annotationColour = new MenuItem();
3792
3793   MenuItem annotationColumnSelection = new MenuItem();
3794
3795   MenuItem invertColSel = new MenuItem();
3796
3797   MenuItem showColumns = new MenuItem();
3798
3799   MenuItem showSeqs = new MenuItem();
3800
3801   MenuItem hideColumns = new MenuItem();
3802
3803   MenuItem hideSequences = new MenuItem();
3804
3805   MenuItem hideAllButSelection = new MenuItem();
3806
3807   MenuItem hideAllSelection = new MenuItem();
3808
3809   MenuItem showAllHidden = new MenuItem();
3810
3811   MenuItem newView = new MenuItem();
3812
3813   private CheckboxMenuItem showAlignmentAnnotations;
3814
3815   private CheckboxMenuItem showSequenceAnnotations;
3816
3817   private CheckboxMenuItem sortAnnBySequence;
3818
3819   private CheckboxMenuItem sortAnnByLabel;
3820
3821   private CheckboxMenuItem showAutoFirst;
3822
3823   private CheckboxMenuItem showAutoLast;
3824
3825   private SplitFrame splitFrame;
3826
3827   /**
3828    * Attach the alignFrame panels after embedding menus, if necessary. This used
3829    * to be called setEmbedded, but is now creates the dropdown menus in a
3830    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3831    *
3832    * @param reallyEmbedded
3833    *          true to attach the view to the applet area on the page rather than
3834    *          in a new window
3835    */
3836   public void createAlignFrameWindow(boolean reallyEmbedded)
3837   {
3838     if (reallyEmbedded)
3839     {
3840       embedAlignFrameInApplet(viewport.applet);
3841     }
3842     else
3843     {
3844       // //////
3845       // test and embed menu bar if necessary.
3846       //
3847       if (embedMenuIfNeeded(alignPanel))
3848       {
3849         /*
3850          * adjust for status bar height too. ? pointless as overridden by layout
3851          * manager
3852          */
3853         alignPanel.setSize(getSize().width,
3854                 getSize().height - statusBar.getHeight());
3855       }
3856       add(statusBar, BorderLayout.SOUTH);
3857       add(alignPanel, BorderLayout.CENTER);
3858       // and register with the applet so it can pass external API calls to us
3859       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3860               frameHeight);
3861     }
3862   }
3863
3864   /**
3865    * Add the components of this AlignFrame to the applet container.
3866    *
3867    * @param theApplet
3868    */
3869   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3870   {
3871     // ////
3872     // Explicitly build the embedded menu panel for the on-page applet
3873     //
3874     // view cannot be closed if its actually on the page
3875     fileMenu.remove(closeMenuItem);
3876     fileMenu.remove(3); // Remove Separator
3877     // construct embedded menu, using default font
3878     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3879     // and actually add the components to the applet area
3880     theApplet.setLayout(new BorderLayout());
3881     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3882     theApplet.add(statusBar, BorderLayout.SOUTH);
3883     // TODO should size be left to the layout manager?
3884     alignPanel.setSize(theApplet.getSize().width,
3885             theApplet.getSize().height - embeddedMenu.getHeight()
3886                     - statusBar.getHeight());
3887     theApplet.add(alignPanel, BorderLayout.CENTER);
3888     final AlignFrame me = this;
3889     theApplet.addFocusListener(new FocusListener()
3890     {
3891
3892       @Override
3893       public void focusLost(FocusEvent e)
3894       {
3895         if (theApplet.currentAlignFrame == me)
3896         {
3897           theApplet.currentAlignFrame = null;
3898         }
3899       }
3900
3901       @Override
3902       public void focusGained(FocusEvent e)
3903       {
3904         theApplet.currentAlignFrame = me;
3905       }
3906     });
3907     theApplet.validate();
3908   }
3909
3910   /**
3911    * create a new binding between structures in an existing jmol viewer instance
3912    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3913    * this does not open a new Jmol window, or modify the display of the
3914    * structures in the original jmol window. Note This method doesn't work
3915    * without an additional javascript library to exchange messages between the
3916    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3917    *
3918    * @param viewer
3919    *          JmolViewer instance
3920    * @param sequenceIds
3921    *          - sequence Ids to search for associations
3922    */
3923   public SequenceStructureBinding addStructureViewInstance(
3924           Object jmolviewer, String[] sequenceIds)
3925   {
3926     Viewer viewer = null;
3927     try
3928     {
3929       viewer = (Viewer) jmolviewer;
3930     } catch (ClassCastException ex)
3931     {
3932       System.err.println("Unsupported viewer object :"
3933               + jmolviewer.getClass());
3934     }
3935     if (viewer == null)
3936     {
3937       System.err.println("Can't use this object as a structure viewer:"
3938               + jmolviewer.getClass());
3939       return null;
3940     }
3941     SequenceI[] seqs = null;
3942     if (sequenceIds == null || sequenceIds.length == 0)
3943     {
3944       seqs = viewport.getAlignment().getSequencesArray();
3945     }
3946     else
3947     {
3948       Vector sqi = new Vector();
3949       AlignmentI al = viewport.getAlignment();
3950       for (int sid = 0; sid < sequenceIds.length; sid++)
3951       {
3952         SequenceI sq = al.findName(sequenceIds[sid]);
3953         if (sq != null)
3954         {
3955           sqi.addElement(sq);
3956         }
3957       }
3958       if (sqi.size() > 0)
3959       {
3960         seqs = new SequenceI[sqi.size()];
3961         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3962         {
3963           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3964         }
3965       }
3966       else
3967       {
3968         return null;
3969       }
3970     }
3971     AAStructureBindingModel jmv = null;
3972     // TODO: search for a jmv that involves viewer
3973     if (jmv == null)
3974     { // create a new viewer/jalview binding.
3975       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3976     }
3977     return jmv;
3978
3979   }
3980
3981   /**
3982    * bind a pdb file to a sequence in the current view
3983    *
3984    * @param sequenceId
3985    *          - sequenceId within the dataset.
3986    * @param pdbEntryString
3987    *          - the short name for the PDB file
3988    * @param pdbFile
3989    *          - pdb file - either a URL or a valid PDB file.
3990    * @return true if binding was as success TODO: consider making an exception
3991    *         structure for indicating when PDB parsing or sequenceId location
3992    *         fails.
3993    */
3994   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3995           String pdbFile)
3996   {
3997     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3998     boolean needtoadd = false;
3999     if (toaddpdb != null)
4000     {
4001       Vector pdbe = toaddpdb.getAllPDBEntries();
4002       PDBEntry pdbentry = null;
4003       if (pdbe != null && pdbe.size() > 0)
4004       {
4005         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4006         {
4007           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4008           if (!pdbentry.getId().equals(pdbEntryString)
4009                   && !pdbentry.getFile().equals(pdbFile))
4010           {
4011             pdbentry = null;
4012           }
4013           else
4014           {
4015             continue;
4016           }
4017         }
4018       }
4019       if (pdbentry == null)
4020       {
4021         pdbentry = new PDBEntry();
4022         pdbentry.setId(pdbEntryString);
4023         pdbentry.setFile(pdbFile);
4024         needtoadd = true; // add this new entry to sequence.
4025       }
4026       // resolve data source
4027       // TODO: this code should be a refactored to an io package
4028       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4029               pdbFile, FileFormat.PDB);
4030       if (protocol == null)
4031       {
4032         return false;
4033       }
4034       if (needtoadd)
4035       {
4036         pdbentry.setProperty("protocol", protocol);
4037         toaddpdb.addPDBId(pdbentry);
4038         alignPanel.getStructureSelectionManager()
4039                 .registerPDBEntry(pdbentry);
4040       }
4041     }
4042     return true;
4043   }
4044
4045   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4046   {
4047     if (seqs != null)
4048     {
4049       Vector sequences = new Vector();
4050       for (int i = 0; i < seqs.length; i++)
4051       {
4052         if (seqs[i] != null)
4053         {
4054           sequences.addElement(new Object[] { seqs[i],
4055               (chains != null) ? chains[i] : null });
4056         }
4057       }
4058       seqs = new SequenceI[sequences.size()];
4059       chains = new String[sequences.size()];
4060       for (int i = 0, isize = sequences.size(); i < isize; i++)
4061       {
4062         Object[] oj = (Object[]) sequences.elementAt(i);
4063
4064         seqs[i] = (SequenceI) oj[0];
4065         chains[i] = (String) oj[1];
4066       }
4067     }
4068     return new Object[] { seqs, chains };
4069
4070   }
4071
4072   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4073           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4074   {
4075     // Scrub any null sequences from the array
4076     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4077     seqs = (SequenceI[]) sqch[0];
4078     chains = (String[]) sqch[1];
4079     if (seqs == null || seqs.length == 0)
4080     {
4081       System.err
4082               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4083     }
4084     if (protocol == null)
4085     {
4086       String sourceType = (String) pdb.getProperty("protocol");
4087       try
4088       {
4089         protocol = DataSourceType.valueOf(sourceType);
4090       } catch (IllegalArgumentException e)
4091       {
4092         // ignore
4093       }
4094       if (protocol == null)
4095       {
4096         System.err.println("Couldn't work out protocol to open structure: "
4097                 + pdb.getId());
4098         return;
4099       }
4100     }
4101     if (applet.useXtrnalSviewer)
4102     {
4103       // register the association(s) and quit, don't create any windows.
4104       if (StructureSelectionManager.getStructureSelectionManager(applet)
4105               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4106       {
4107         System.err.println("Failed to map " + pdb.getFile() + " ("
4108                 + protocol + ") to any sequences");
4109       }
4110       return;
4111     }
4112     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4113     {
4114       // can only do alignments with Jmol
4115       // find the last jmol window assigned to this alignment
4116       AppletJmol ajm = null, tajm;
4117       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4118       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4119       {
4120         tajm = (AppletJmol) jmols.elementAt(i);
4121         if (tajm.ap.alignFrame == this)
4122         {
4123           ajm = tajm;
4124           break;
4125         }
4126       }
4127       if (ajm != null)
4128       {
4129         System.err
4130                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4131         // try and add the pdb structure
4132         // ajm.addS
4133         ajm = null;
4134       }
4135     }
4136     // otherwise, create a new window
4137     if (applet.jmolAvailable)
4138     {
4139       new AppletJmol(pdb, seqs, chains, alignPanel,
4140               protocol);
4141       applet.lastFrameX += 40;
4142       applet.lastFrameY += 40;
4143     }
4144     else
4145     {
4146       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4147     }
4148
4149   }
4150
4151   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4152           SequenceI[][] seqs, String[][] chains, String[] protocols)
4153   {
4154     // TODO Auto-generated method stub
4155     System.err.println("Aligned Structure View: Not yet implemented.");
4156   }
4157
4158   /**
4159    * modify the current selection, providing the user has not made a selection
4160    * already.
4161    *
4162    * @param sel
4163    *          - sequences from this alignment
4164    * @param csel
4165    *          - columns to be selected on the alignment
4166    */
4167   public void select(SequenceGroup sel, ColumnSelection csel)
4168   {
4169     alignPanel.seqPanel.selection(sel, csel, null);
4170   }
4171
4172   public void scrollTo(int row, int column)
4173   {
4174     alignPanel.seqPanel.scrollTo(row, column);
4175   }
4176
4177   public void scrollToRow(int row)
4178   {
4179     alignPanel.seqPanel.scrollToRow(row);
4180   }
4181
4182   public void scrollToColumn(int column)
4183   {
4184     alignPanel.seqPanel.scrollToColumn(column);
4185   }
4186
4187   /**
4188    * @return the alignments unique ID.
4189    */
4190   public String getSequenceSetId()
4191   {
4192     return viewport.getSequenceSetId();
4193   }
4194
4195   /**
4196    * Load the (T-Coffee) score file from the specified url
4197    *
4198    * @param source
4199    *          File/URL/T-COFFEE score file contents
4200    * @throws IOException
4201    * @return true if alignment was annotated with data from source
4202    */
4203   public boolean loadScoreFile(String source) throws IOException
4204   {
4205
4206     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4207             AppletFormatAdapter.checkProtocol(source));
4208     if (!file.isValid())
4209     {
4210       // TODO: raise dialog for gui
4211       System.err.println("Problems parsing T-Coffee scores: "
4212               + file.getWarningMessage());
4213       System.err.println("Origin was:\n" + source);
4214       return false;
4215     }
4216
4217     /*
4218      * check that the score matrix matches the alignment dimensions
4219      */
4220     AlignmentI aln;
4221     if ((aln = viewport.getAlignment()) != null
4222             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4223                     .getWidth()))
4224     {
4225       // TODO: raise a dialog box here rather than bomb out.
4226       System.err
4227               .println("The scores matrix does not match the alignment dimensions");
4228
4229     }
4230
4231     // TODO add parameter to indicate if matching should be done
4232     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4233     {
4234       alignPanel.fontChanged();
4235       tcoffeeColour.setEnabled(true);
4236       // switch to this color
4237       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4238       return true;
4239     }
4240     else
4241     {
4242       System.err.println("Problems resolving T-Coffee scores:");
4243       if (file.getWarningMessage() != null)
4244       {
4245         System.err.println(file.getWarningMessage());
4246       }
4247     }
4248     return false;
4249   }
4250
4251   public SplitFrame getSplitFrame()
4252   {
4253     return this.splitFrame;
4254   }
4255
4256   public void setSplitFrame(SplitFrame sf)
4257   {
4258     this.splitFrame = sf;
4259   }
4260
4261   // may not need this
4262   @Override
4263   public void setShowSeqFeatures(boolean b)
4264   {
4265     // showSeqFeatures.setSelected(b);
4266     viewport.setShowSequenceFeatures(b);
4267
4268   }
4269
4270   @Override
4271   public void setMenusForViewport()
4272   {
4273     // setMenusFromViewport(viewport);
4274
4275   }
4276
4277   @Override
4278   public void refreshFeatureUI(boolean enableIfNecessary)
4279   {
4280     if (enableIfNecessary)
4281     {
4282       sequenceFeatures.setState(true);
4283       alignPanel.av.setShowSequenceFeatures(true);
4284     }
4285   }
4286
4287   @Override
4288   public FeatureSettingsControllerI getFeatureSettingsUI()
4289   {
4290     return alignPanel.av.featureSettings;
4291   }
4292
4293 }