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.RNAHelicesColourChooser;
  66 import jalview.schemes.StrandColourScheme;
  67 import jalview.schemes.TCoffeeColourScheme;
  68 import jalview.schemes.TaylorColourScheme;
  69 import jalview.schemes.TurnColourScheme;
  70 import jalview.schemes.ZappoColourScheme;
  71 import jalview.structure.StructureSelectionManager;
  72 import jalview.structures.models.AAStructureBindingModel;
  73 import jalview.util.MappingUtils;
  74 import jalview.util.MessageManager;
  75 import jalview.viewmodel.AlignmentViewport;
  76
  77 import java.awt.BorderLayout;
  78 import java.awt.Canvas;
  79 import java.awt.CheckboxMenuItem;
  80 import java.awt.Color;
  81 import java.awt.FlowLayout;
  82 import java.awt.Font;
  83 import java.awt.FontMetrics;
  84 import java.awt.Frame;
  85 import java.awt.Graphics;
  86 import java.awt.Label;
  87 import java.awt.Menu;
  88 import java.awt.MenuBar;
  89 import java.awt.MenuItem;
  90 import java.awt.Panel;
  91 import java.awt.event.ActionEvent;
  92 import java.awt.event.ActionListener;
  93 import java.awt.event.FocusEvent;
  94 import java.awt.event.FocusListener;
  95 import java.awt.event.ItemEvent;
  96 import java.awt.event.ItemListener;
  97 import java.awt.event.KeyEvent;
  98 import java.awt.event.KeyListener;
  99 import java.awt.event.WindowAdapter;
 100 import java.awt.event.WindowEvent;
 101 import java.io.IOException;
 102 import java.net.URL;
 103 import java.net.URLEncoder;
 104 import java.util.Arrays;
 105 import java.util.Deque;
 106 import java.util.HashMap;
 107 import java.util.Hashtable;
 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     }
 301     // Some JVMS send keyevents to Top frame or lowest panel,
 302     // Havent worked out why yet. So add to both this frame and seqCanvas for
 303     // now
 304     this.addKeyListener(this);
 305     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 306     alignPanel.idPanel.idCanvas.addKeyListener(this);
 307     alignPanel.scalePanel.addKeyListener(this);
 308     alignPanel.annotationPanel.addKeyListener(this);
 309     alignPanel.annotationPanelHolder.addKeyListener(this);
 310     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 311     alignPanel.alabels.addKeyListener(this);
 312
 313     setAnnotationsVisibility();
 314
 315     if (addToDisplay)
 316     {
 317       addToDisplay(embedded);
 318     }
 319   }
 320
 321   /**
 322    * @param embedded
 323    */
 324   public void addToDisplay(boolean embedded)
 325   {
 326     createAlignFrameWindow(embedded);
 327     validate();
 328     alignPanel.adjustAnnotationHeight();
 329     alignPanel.paintAlignment(true);
 330   }
 331
 332   public AlignViewport getAlignViewport()
 333   {
 334     return viewport;
 335   }
 336
 337   public SeqCanvas getSeqcanvas()
 338   {
 339     return alignPanel.seqPanel.seqCanvas;
 340   }
 341
 342   /**
 343    * Load a features file onto the alignment
 344    *
 345    * @param file
 346    *          file URL, content, or other resolvable path
 347    * @param type
 348    *          is protocol for accessing data referred to by file
 349    */
 350
 351   public boolean parseFeaturesFile(String file, DataSourceType type)
 352   {
 353     return parseFeaturesFile(file, type, true);
 354   }
 355
 356   /**
 357    * Load a features file onto the alignment
 358    *
 359    * @param file
 360    *          file URL, content, or other resolvable path
 361    * @param paste
 362    *          is protocol for accessing data referred to by file
 363    * @param autoenabledisplay
 364    *          when true, display features flag will be automatically enabled if
 365    *          features are loaded
 366    * @return true if data parsed as a features file
 367    */
 368   public boolean parseFeaturesFile(String file, DataSourceType paste,
 369           boolean autoenabledisplay)
 370   {
 371     boolean featuresFile = false;
 372     try
 373     {
 374       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 375               .getFeatureRenderer().getFeatureColours();
 376       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 377               "relaxedidmatch", false);
 378       featuresFile = new FeaturesFile(file, paste).parse(
 379               viewport.getAlignment(), colours, true, relaxedIdMatching);
 380     } catch (Exception ex)
 381     {
 382       ex.printStackTrace();
 383     }
 384
 385     if (featuresFile)
 386     {
 387       if (autoenabledisplay)
 388       {
 389         viewport.setShowSequenceFeatures(true);
 390         sequenceFeatures.setState(true);
 391       }
 392       if (alignPanel.seqPanel.seqCanvas.fr != null)
 393       {
 394         // update the min/max ranges where necessary
 395         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 396       }
 397       if (viewport.featureSettings != null)
 398       {
 399         viewport.featureSettings.refreshTable();
 400       }
 401       alignPanel.paintAlignment(true);
 402       statusBar.setText(MessageManager
 403               .getString("label.successfully_added_features_alignment"));
 404     }
 405     return featuresFile;
 406   }
 407
 408   @Override
 409   public void keyPressed(KeyEvent evt)
 410   {
 411     if (viewport.cursorMode
 412             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 413                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 414                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 415             && Character.isDigit(evt.getKeyChar()))
 416     {
 417       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 418     }
 419
 420     switch (evt.getKeyCode())
 421     {
 422     case 27: // escape key
 423       deselectAllSequenceMenuItem_actionPerformed();
 424
 425       alignPanel.alabels.cancelDrag();
 426       break;
 427     case KeyEvent.VK_X:
 428       if (evt.isControlDown() || evt.isMetaDown())
 429       {
 430         cut_actionPerformed();
 431       }
 432       break;
 433     case KeyEvent.VK_C:
 434       if (viewport.cursorMode && !evt.isControlDown())
 435       {
 436         alignPanel.seqPanel.setCursorColumn();
 437       }
 438       if (evt.isControlDown() || evt.isMetaDown())
 439       {
 440         copy_actionPerformed();
 441       }
 442       break;
 443     case KeyEvent.VK_V:
 444       if (evt.isControlDown())
 445       {
 446         paste(evt.isShiftDown());
 447       }
 448       break;
 449     case KeyEvent.VK_A:
 450       if (evt.isControlDown() || evt.isMetaDown())
 451       {
 452         selectAllSequenceMenuItem_actionPerformed();
 453       }
 454       break;
 455     case KeyEvent.VK_DOWN:
 456       if (viewport.cursorMode)
 457       {
 458         alignPanel.seqPanel.moveCursor(0, 1);
 459       }
 460       else
 461       {
 462         moveSelectedSequences(false);
 463       }
 464       break;
 465
 466     case KeyEvent.VK_UP:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.moveCursor(0, -1);
 470       }
 471       else
 472       {
 473         moveSelectedSequences(true);
 474       }
 475       break;
 476
 477     case KeyEvent.VK_LEFT:
 478       if (evt.isAltDown() || !viewport.cursorMode)
 479       {
 480         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 481       }
 482       else
 483       {
 484         alignPanel.seqPanel.moveCursor(-1, 0);
 485       }
 486       break;
 487
 488     case KeyEvent.VK_RIGHT:
 489       if (evt.isAltDown() || !viewport.cursorMode)
 490       {
 491         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 492       }
 493       else
 494       {
 495         alignPanel.seqPanel.moveCursor(1, 0);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_SPACE:
 500       if (viewport.cursorMode)
 501       {
 502         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 503                 || evt.isShiftDown() || evt.isAltDown());
 504       }
 505       break;
 506
 507     case KeyEvent.VK_DELETE:
 508     case KeyEvent.VK_BACK_SPACE:
 509       if (viewport.cursorMode)
 510       {
 511         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 512                 || evt.isShiftDown() || evt.isAltDown());
 513       }
 514       else
 515       {
 516         cut_actionPerformed();
 517         alignPanel.seqPanel.seqCanvas.repaint();
 518       }
 519       break;
 520
 521     case KeyEvent.VK_S:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.setCursorRow();
 525       }
 526       break;
 527     case KeyEvent.VK_P:
 528       if (viewport.cursorMode)
 529       {
 530         alignPanel.seqPanel.setCursorPosition();
 531       }
 532       break;
 533
 534     case KeyEvent.VK_ENTER:
 535     case KeyEvent.VK_COMMA:
 536       if (viewport.cursorMode)
 537       {
 538         alignPanel.seqPanel.setCursorRowAndColumn();
 539       }
 540       break;
 541
 542     case KeyEvent.VK_Q:
 543       if (viewport.cursorMode)
 544       {
 545         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 546       }
 547       break;
 548     case KeyEvent.VK_M:
 549       if (viewport.cursorMode)
 550       {
 551         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 552       }
 553       break;
 554
 555     case KeyEvent.VK_F2:
 556       viewport.cursorMode = !viewport.cursorMode;
 557       statusBar.setText(MessageManager.formatMessage(
 558               "label.keyboard_editing_mode",
 559               new String[] { (viewport.cursorMode ? "on" : "off") }));
 560       if (viewport.cursorMode)
 561       {
 562         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 563         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 564       }
 565       break;
 566
 567     case KeyEvent.VK_F:
 568       if (evt.isControlDown())
 569       {
 570         findMenuItem_actionPerformed();
 571       }
 572       break;
 573
 574     case KeyEvent.VK_H:
 575     {
 576       boolean toggleSeqs = !evt.isControlDown();
 577       boolean toggleCols = !evt.isShiftDown();
 578       toggleHiddenRegions(toggleSeqs, toggleCols);
 579       break;
 580     }
 581
 582     case KeyEvent.VK_PAGE_UP:
 583       if (viewport.getWrapAlignment())
 584       {
 585         alignPanel.scrollUp(true);
 586       }
 587       else
 588       {
 589         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 590                 - viewport.endSeq + viewport.startSeq);
 591       }
 592       break;
 593
 594     case KeyEvent.VK_PAGE_DOWN:
 595       if (viewport.getWrapAlignment())
 596       {
 597         alignPanel.scrollUp(false);
 598       }
 599       else
 600       {
 601         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 602                 + viewport.endSeq - viewport.startSeq);
 603       }
 604       break;
 605
 606     case KeyEvent.VK_Z:
 607       if (evt.isControlDown())
 608       {
 609         undoMenuItem_actionPerformed();
 610       }
 611       break;
 612
 613     case KeyEvent.VK_Y:
 614       if (evt.isControlDown())
 615       {
 616         redoMenuItem_actionPerformed();
 617       }
 618       break;
 619
 620     case KeyEvent.VK_L:
 621       if (evt.isControlDown())
 622       {
 623         trimAlignment(true);
 624       }
 625       break;
 626
 627     case KeyEvent.VK_R:
 628       if (evt.isControlDown())
 629       {
 630         trimAlignment(false);
 631       }
 632       break;
 633
 634     case KeyEvent.VK_E:
 635       if (evt.isControlDown())
 636       {
 637         if (evt.isShiftDown())
 638         {
 639           this.removeAllGapsMenuItem_actionPerformed();
 640         }
 641         else
 642         {
 643           removeGappedColumnMenuItem_actionPerformed();
 644         }
 645       }
 646       break;
 647     case KeyEvent.VK_I:
 648       if (evt.isControlDown())
 649       {
 650         if (evt.isAltDown())
 651         {
 652           invertColSel_actionPerformed();
 653         }
 654         else
 655         {
 656           invertSequenceMenuItem_actionPerformed();
 657         }
 658       }
 659       break;
 660
 661     case KeyEvent.VK_G:
 662       if (evt.isControlDown())
 663       {
 664         if (evt.isShiftDown())
 665         {
 666           this.unGroup_actionPerformed();
 667         }
 668         else
 669         {
 670           this.createGroup_actionPerformed();
 671         }
 672       }
 673       break;
 674
 675     case KeyEvent.VK_U:
 676       if (evt.isControlDown())
 677       {
 678         this.deleteGroups_actionPerformed();
 679       }
 680       break;
 681
 682     case KeyEvent.VK_T:
 683       if (evt.isControlDown())
 684       {
 685         newView(null);
 686       }
 687       break;
 688
 689     }
 690     alignPanel.paintAlignment(true);
 691   }
 692
 693   /**
 694    * called by key handler and the hide all/show all menu items
 695    *
 696    * @param toggleSeqs
 697    * @param toggleCols
 698    */
 699   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 700   {
 701     boolean hide = false;
 702     SequenceGroup sg = viewport.getSelectionGroup();
 703     if (!toggleSeqs && !toggleCols)
 704     {
 705       // Hide everything by the current selection - this is a hack - we do the
 706       // invert and then hide
 707       // first check that there will be visible columns after the invert.
 708       if ((viewport.getColumnSelection() != null
 709               && viewport.getColumnSelection().getSelected() != null && viewport
 710               .getColumnSelection().getSelected().size() > 0)
 711               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 712                       .getEndRes()))
 713       {
 714         // now invert the sequence set, if required - empty selection implies
 715         // that no hiding is required.
 716         if (sg != null)
 717         {
 718           invertSequenceMenuItem_actionPerformed();
 719           sg = viewport.getSelectionGroup();
 720           toggleSeqs = true;
 721
 722         }
 723         viewport.expandColSelection(sg, true);
 724         // finally invert the column selection and get the new sequence
 725         // selection and indicate it should be hidden.
 726         invertColSel_actionPerformed();
 727         toggleCols = true;
 728       }
 729     }
 730
 731     if (toggleSeqs)
 732     {
 733       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 734       {
 735         hide = true;
 736         viewport.hideAllSelectedSeqs();
 737       }
 738       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 739               .size() > 0))
 740       {
 741         viewport.showAllHiddenSeqs();
 742       }
 743     }
 744
 745     if (toggleCols)
 746     {
 747       if (viewport.getColumnSelection().getSelected().size() > 0)
 748       {
 749         viewport.hideSelectedColumns();
 750         if (!toggleSeqs)
 751         {
 752           viewport.setSelectionGroup(sg);
 753         }
 754       }
 755       else if (!hide)
 756       {
 757         viewport.showAllHiddenColumns();
 758       }
 759       viewport.sendSelection();
 760     }
 761   }
 762
 763   @Override
 764   public void keyReleased(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void keyTyped(KeyEvent evt)
 770   {
 771   }
 772
 773   @Override
 774   public void itemStateChanged(ItemEvent evt)
 775   {
 776     final Object source = evt.getSource();
 777     if (source == displayNonconservedMenuItem)
 778     {
 779       displayNonconservedMenuItem_actionPerformed();
 780     }
 781     else if (source == colourTextMenuItem)
 782     {
 783       colourTextMenuItem_actionPerformed();
 784     }
 785     else if (source == wrapMenuItem)
 786     {
 787       wrapMenuItem_actionPerformed();
 788     }
 789     else if (source == scaleAbove)
 790     {
 791       viewport.setScaleAboveWrapped(scaleAbove.getState());
 792     }
 793     else if (source == scaleLeft)
 794     {
 795       viewport.setScaleLeftWrapped(scaleLeft.getState());
 796     }
 797     else if (source == scaleRight)
 798     {
 799       viewport.setScaleRightWrapped(scaleRight.getState());
 800     }
 801     else if (source == seqLimits)
 802     {
 803       seqLimits_itemStateChanged();
 804     }
 805     else if (source == viewBoxesMenuItem)
 806     {
 807       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 808     }
 809     else if (source == viewTextMenuItem)
 810     {
 811       viewport.setShowText(viewTextMenuItem.getState());
 812     }
 813     else if (source == renderGapsMenuItem)
 814     {
 815       viewport.setRenderGaps(renderGapsMenuItem.getState());
 816     }
 817     else if (source == annotationPanelMenuItem)
 818     {
 819       boolean showAnnotations = annotationPanelMenuItem.getState();
 820       showAlignmentAnnotations.setEnabled(showAnnotations);
 821       showSequenceAnnotations.setEnabled(showAnnotations);
 822       viewport.setShowAnnotation(showAnnotations);
 823       alignPanel.setAnnotationVisible(showAnnotations);
 824     }
 825     else if (source == sequenceFeatures)
 826     {
 827       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 828       alignPanel.seqPanel.seqCanvas.repaint();
 829     }
 830     else if (source == showAlignmentAnnotations)
 831     {
 832       setAnnotationsVisibility();
 833     }
 834     else if (source == showSequenceAnnotations)
 835     {
 836       setAnnotationsVisibility();
 837     }
 838     else if (source == sortAnnBySequence)
 839     {
 840       boolean newState = sortAnnBySequence.getState();
 841       sortAnnByLabel.setState(false);
 842       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 843               : SequenceAnnotationOrder.NONE);
 844       setViewportAnnotationOrder();
 845     }
 846     else if (source == sortAnnByLabel)
 847     {
 848       boolean newState = sortAnnByLabel.getState();
 849       sortAnnBySequence.setState(false);
 850       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 851               : SequenceAnnotationOrder.NONE);
 852       setViewportAnnotationOrder();
 853     }
 854     else if (source == showAutoFirst)
 855     {
 856       showAutoLast.setState(!showAutoFirst.getState());
 857       setShowAutoCalculatedAbove(showAutoFirst.getState());
 858       setViewportAnnotationOrder();
 859     }
 860     else if (source == showAutoLast)
 861     {
 862       showAutoFirst.setState(!showAutoLast.getState());
 863       setShowAutoCalculatedAbove(showAutoFirst.getState());
 864       setViewportAnnotationOrder();
 865     }
 866     else if (source == conservationMenuItem)
 867     {
 868       conservationMenuItem_actionPerformed();
 869     }
 870     else if (source == abovePIDThreshold)
 871     {
 872       abovePIDThreshold_actionPerformed();
 873     }
 874     else if (source == applyToAllGroups)
 875     {
 876       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 877     }
 878     else if (source == autoCalculate)
 879     {
 880       viewport.autoCalculateConsensus = autoCalculate.getState();
 881     }
 882     else if (source == sortByTree)
 883     {
 884       viewport.sortByTree = sortByTree.getState();
 885     }
 886     else if (source == this.centreColumnLabelFlag)
 887     {
 888       centreColumnLabelFlag_stateChanged();
 889     }
 890     else if (source == this.followMouseOverFlag)
 891     {
 892       mouseOverFlag_stateChanged();
 893     }
 894     else if (source == showGroupConsensus)
 895     {
 896       showGroupConsensus_actionPerformed();
 897     }
 898     else if (source == showGroupConservation)
 899     {
 900       showGroupConservation_actionPerformed();
 901     }
 902     else if (source == showSequenceLogo)
 903     {
 904       showSequenceLogo_actionPerformed();
 905     }
 906     else if (source == normSequenceLogo)
 907     {
 908       normSequenceLogo_actionPerformed();
 909     }
 910     else if (source == showConsensusHistogram)
 911     {
 912       showConsensusHistogram_actionPerformed();
 913     }
 914     else if (source == applyAutoAnnotationSettings)
 915     {
 916       applyAutoAnnotationSettings_actionPerformed();
 917     }
 918     alignPanel.paintAlignment(true);
 919   }
 920
 921   /**
 922    * Set the visibility state of sequence-related and/or alignment-related
 923    * annotations depending on checkbox selections, and repaint.
 924    *
 925    * @param visible
 926    */
 927   private void setAnnotationsVisibility()
 928   {
 929     boolean showForAlignment = showAlignmentAnnotations.getState();
 930     boolean showForSequences = showSequenceAnnotations.getState();
 931     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 932     {
 933       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 934             .getAlignmentAnnotation())
 935     {
 936       boolean visible = (aa.sequenceRef == null ? showForAlignment
 937               : showForSequences);
 938       aa.visible = visible;
 939       }
 940     }
 941     alignPanel.validateAnnotationDimensions(true);
 942     validate();
 943     repaint();
 944   }
 945
 946   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 947   {
 948     this.annotationSortOrder = order;
 949   }
 950
 951   /**
 952    * Set flags on the viewport that control annotation ordering
 953    */
 954   private void setViewportAnnotationOrder()
 955   {
 956     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 957     this.alignPanel.av
 958             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 959   }
 960
 961   private void setShowAutoCalculatedAbove(boolean showAbove)
 962   {
 963     this.showAutoCalculatedAbove = showAbove;
 964   }
 965
 966   private void mouseOverFlag_stateChanged()
 967   {
 968     viewport.setFollowHighlight(followMouseOverFlag.getState());
 969     // TODO: could kick the scrollTo mechanism to reset view for current
 970     // searchresults.
 971   }
 972
 973   private void centreColumnLabelFlag_stateChanged()
 974   {
 975     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 976     this.alignPanel.annotationPanel.repaint();
 977   }
 978
 979   @Override
 980   public void actionPerformed(ActionEvent evt)
 981   {
 982     viewport.applet.currentAlignFrame = this;
 983
 984     Object source = evt.getSource();
 985
 986     if (source == inputText)
 987     {
 988       inputText_actionPerformed();
 989     }
 990     else if (source == loadTree)
 991     {
 992       loadTree_actionPerformed();
 993     }
 994     else if (source == loadApplication)
 995     {
 996       launchFullApplication();
 997     }
 998     else if (source == loadAnnotations)
 999     {
1000       loadAnnotations();
1001     }
1002     else if (source == outputAnnotations)
1003     {
1004       outputAnnotations(true);
1005     }
1006     else if (source == outputFeatures)
1007     {
1008       outputFeatures(true, "Jalview");
1009     }
1010     else if (source == closeMenuItem)
1011     {
1012       closeMenuItem_actionPerformed();
1013     }
1014     else if (source == copy)
1015     {
1016       copy_actionPerformed();
1017     }
1018     else if (source == undoMenuItem)
1019     {
1020       undoMenuItem_actionPerformed();
1021     }
1022     else if (source == redoMenuItem)
1023     {
1024       redoMenuItem_actionPerformed();
1025     }
1026     else if (source == inputText)
1027     {
1028       inputText_actionPerformed();
1029     }
1030     else if (source == closeMenuItem)
1031     {
1032       closeMenuItem_actionPerformed();
1033     }
1034     else if (source == undoMenuItem)
1035     {
1036       undoMenuItem_actionPerformed();
1037     }
1038     else if (source == redoMenuItem)
1039     {
1040       redoMenuItem_actionPerformed();
1041     }
1042     else if (source == copy)
1043     {
1044       copy_actionPerformed();
1045     }
1046     else if (source == pasteNew)
1047     {
1048       pasteNew_actionPerformed();
1049     }
1050     else if (source == pasteThis)
1051     {
1052       pasteThis_actionPerformed();
1053     }
1054     else if (source == cut)
1055     {
1056       cut_actionPerformed();
1057     }
1058     else if (source == delete)
1059     {
1060       delete_actionPerformed();
1061     }
1062     else if (source == grpsFromSelection)
1063     {
1064       makeGrpsFromSelection_actionPerformed();
1065     }
1066     else if (source == deleteGroups)
1067     {
1068       deleteGroups_actionPerformed();
1069     }
1070     else if (source == selectAllSequenceMenuItem)
1071     {
1072       selectAllSequenceMenuItem_actionPerformed();
1073     }
1074     else if (source == deselectAllSequenceMenuItem)
1075     {
1076       deselectAllSequenceMenuItem_actionPerformed();
1077     }
1078     else if (source == invertSequenceMenuItem)
1079     {
1080       invertSequenceMenuItem_actionPerformed();
1081       // uncomment to slave sequence selections in split frame
1082       // viewport.sendSelection();
1083     }
1084     else if (source == invertColSel)
1085     {
1086       viewport.invertColumnSelection();
1087       alignPanel.paintAlignment(true);
1088       viewport.sendSelection();
1089     }
1090     else if (source == remove2LeftMenuItem)
1091     {
1092       trimAlignment(true);
1093     }
1094     else if (source == remove2RightMenuItem)
1095     {
1096       trimAlignment(false);
1097     }
1098     else if (source == removeGappedColumnMenuItem)
1099     {
1100       removeGappedColumnMenuItem_actionPerformed();
1101     }
1102     else if (source == removeAllGapsMenuItem)
1103     {
1104       removeAllGapsMenuItem_actionPerformed();
1105     }
1106     else if (source == findMenuItem)
1107     {
1108       findMenuItem_actionPerformed();
1109     }
1110     else if (source == font)
1111     {
1112       new FontChooser(alignPanel);
1113     }
1114     else if (source == newView)
1115     {
1116       newView(null);
1117     }
1118     else if (source == showColumns)
1119     {
1120       viewport.showAllHiddenColumns();
1121       alignPanel.paintAlignment(true);
1122       viewport.sendSelection();
1123     }
1124     else if (source == showSeqs)
1125     {
1126       viewport.showAllHiddenSeqs();
1127       alignPanel.paintAlignment(true);
1128       // uncomment if we want to slave sequence selections in split frame
1129       // viewport.sendSelection();
1130     }
1131     else if (source == hideColumns)
1132     {
1133       viewport.hideSelectedColumns();
1134       alignPanel.paintAlignment(true);
1135       viewport.sendSelection();
1136     }
1137     else if (source == hideSequences
1138             && viewport.getSelectionGroup() != null)
1139     {
1140       viewport.hideAllSelectedSeqs();
1141       alignPanel.paintAlignment(true);
1142       // uncomment if we want to slave sequence selections in split frame
1143       // viewport.sendSelection();
1144     }
1145     else if (source == hideAllButSelection)
1146     {
1147       toggleHiddenRegions(false, false);
1148       alignPanel.paintAlignment(true);
1149       viewport.sendSelection();
1150     }
1151     else if (source == hideAllSelection)
1152     {
1153       SequenceGroup sg = viewport.getSelectionGroup();
1154       viewport.expandColSelection(sg, false);
1155       viewport.hideAllSelectedSeqs();
1156       viewport.hideSelectedColumns();
1157       alignPanel.paintAlignment(true);
1158       viewport.sendSelection();
1159     }
1160     else if (source == showAllHidden)
1161     {
1162       viewport.showAllHiddenColumns();
1163       viewport.showAllHiddenSeqs();
1164       alignPanel.paintAlignment(true);
1165       viewport.sendSelection();
1166     }
1167     else if (source == showGroupConsensus)
1168     {
1169       showGroupConsensus_actionPerformed();
1170     }
1171     else if (source == showGroupConservation)
1172     {
1173       showGroupConservation_actionPerformed();
1174     }
1175     else if (source == showSequenceLogo)
1176     {
1177       showSequenceLogo_actionPerformed();
1178     }
1179     else if (source == normSequenceLogo)
1180     {
1181       normSequenceLogo_actionPerformed();
1182     }
1183     else if (source == showConsensusHistogram)
1184     {
1185       showConsensusHistogram_actionPerformed();
1186     }
1187     else if (source == applyAutoAnnotationSettings)
1188     {
1189       applyAutoAnnotationSettings_actionPerformed();
1190     }
1191     else if (source == featureSettings)
1192     {
1193       new FeatureSettings(alignPanel);
1194     }
1195     else if (source == alProperties)
1196     {
1197       StringBuffer contents = new jalview.io.AlignmentProperties(
1198               viewport.getAlignment()).formatAsString();
1199       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1200       cap.setText(contents.toString());
1201       Frame frame = new Frame();
1202       frame.add(cap);
1203       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1204               "label.alignment_properties", new String[] { getTitle() }),
1205               400, 250);
1206     }
1207     else if (source == overviewMenuItem)
1208     {
1209       overviewMenuItem_actionPerformed();
1210     }
1211     else if (source == noColourmenuItem)
1212     {
1213       changeColour(null);
1214     }
1215     else if (source == clustalColour)
1216     {
1217       abovePIDThreshold.setState(false);
1218       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1219     }
1220     else if (source == zappoColour)
1221     {
1222       changeColour(new ZappoColourScheme());
1223     }
1224     else if (source == taylorColour)
1225     {
1226       changeColour(new TaylorColourScheme());
1227     }
1228     else if (source == hydrophobicityColour)
1229     {
1230       changeColour(new HydrophobicColourScheme());
1231     }
1232     else if (source == helixColour)
1233     {
1234       changeColour(new HelixColourScheme());
1235     }
1236     else if (source == strandColour)
1237     {
1238       changeColour(new StrandColourScheme());
1239     }
1240     else if (source == turnColour)
1241     {
1242       changeColour(new TurnColourScheme());
1243     }
1244     else if (source == buriedColour)
1245     {
1246       changeColour(new BuriedColourScheme());
1247     }
1248     else if (source == nucleotideColour)
1249     {
1250       changeColour(new NucleotideColourScheme());
1251     }
1252     else if (source == purinePyrimidineColour)
1253     {
1254       changeColour(new PurinePyrimidineColourScheme());
1255     }
1256     // else if (source == RNAInteractionColour)
1257     // {
1258     // changeColour(new RNAInteractionColourScheme());
1259     // }
1260     else if (source == RNAHelixColour)
1261     {
1262       new RNAHelicesColourChooser(viewport, alignPanel);
1263     }
1264     else if (source == modifyPID)
1265     {
1266       modifyPID_actionPerformed();
1267     }
1268     else if (source == modifyConservation)
1269     {
1270       modifyConservation_actionPerformed();
1271     }
1272     else if (source == userDefinedColour)
1273     {
1274       new UserDefinedColours(alignPanel, null);
1275     }
1276     else if (source == PIDColour)
1277     {
1278       changeColour(new PIDColourScheme());
1279     }
1280     else if (source == BLOSUM62Colour)
1281     {
1282       changeColour(new Blosum62ColourScheme());
1283     }
1284     else if (source == tcoffeeColour)
1285     {
1286       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1287     }
1288     else if (source == annotationColour)
1289     {
1290       new AnnotationColourChooser(viewport, alignPanel);
1291     }
1292     else if (source == annotationColumnSelection)
1293     {
1294       new AnnotationColumnChooser(viewport, alignPanel);
1295     }
1296     else if (source == sortPairwiseMenuItem)
1297     {
1298       sortPairwiseMenuItem_actionPerformed();
1299     }
1300     else if (source == sortIDMenuItem)
1301     {
1302       sortIDMenuItem_actionPerformed();
1303     }
1304     else if (source == sortLengthMenuItem)
1305     {
1306       sortLengthMenuItem_actionPerformed();
1307     }
1308     else if (source == sortGroupMenuItem)
1309     {
1310       sortGroupMenuItem_actionPerformed();
1311     }
1312     else if (source == removeRedundancyMenuItem)
1313     {
1314       removeRedundancyMenuItem_actionPerformed();
1315     }
1316     else if (source == pairwiseAlignmentMenuItem)
1317     {
1318       pairwiseAlignmentMenuItem_actionPerformed();
1319     }
1320     else if (source == PCAMenuItem)
1321     {
1322       PCAMenuItem_actionPerformed();
1323     }
1324     else if (source == averageDistanceTreeMenuItem)
1325     {
1326       averageDistanceTreeMenuItem_actionPerformed();
1327     }
1328     else if (source == neighbourTreeMenuItem)
1329     {
1330       neighbourTreeMenuItem_actionPerformed();
1331     }
1332     else if (source == njTreeBlosumMenuItem)
1333     {
1334       njTreeBlosumMenuItem_actionPerformed();
1335     }
1336     else if (source == avDistanceTreeBlosumMenuItem)
1337     {
1338       avTreeBlosumMenuItem_actionPerformed();
1339     }
1340     else if (source == documentation)
1341     {
1342       documentation_actionPerformed();
1343     }
1344     else if (source == about)
1345     {
1346       about_actionPerformed();
1347     }
1348
1349   }
1350
1351   public void inputText_actionPerformed()
1352   {
1353     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1354     Frame frame = new Frame();
1355     frame.add(cap);
1356     jalview.bin.JalviewLite.addFrame(frame,
1357             MessageManager.getString("label.input_cut_paste"), 500, 500);
1358   }
1359
1360   protected void outputText_actionPerformed(ActionEvent e)
1361   {
1362     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1363     Frame frame = new Frame();
1364     frame.add(cap);
1365     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1366             "label.alignment_output_command",
1367             new Object[] { e.getActionCommand() }), 600, 500);
1368
1369     FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1370     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1371             fileFormat, viewport.getAlignment(),
1372             viewport.getShowJVSuffix()));
1373   }
1374
1375   public void loadAnnotations()
1376   {
1377     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378     cap.setText(MessageManager
1379             .getString("label.paste_features_annotations_Tcoffee_here"));
1380     cap.setAnnotationImport();
1381     Frame frame = new Frame();
1382     frame.add(cap);
1383     jalview.bin.JalviewLite.addFrame(frame,
1384             MessageManager.getString("action.paste_annotations"), 400, 300);
1385
1386   }
1387
1388   public String outputAnnotations(boolean displayTextbox)
1389   {
1390     String annotation = new AnnotationFile()
1391             .printAnnotationsForView(viewport);
1392
1393     if (displayTextbox)
1394     {
1395       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1396       Frame frame = new Frame();
1397       frame.add(cap);
1398       jalview.bin.JalviewLite.addFrame(frame,
1399               MessageManager.getString("label.annotations"), 600, 500);
1400       cap.setText(annotation);
1401     }
1402
1403     return annotation;
1404   }
1405
1406   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1407   {
1408     if (alignPanel.getFeatureRenderer() != null
1409             && viewport.getFeaturesDisplayed() != null)
1410     {
1411       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1412
1413     }
1414     return null;
1415   }
1416
1417   public String outputFeatures(boolean displayTextbox, String format)
1418   {
1419     String features;
1420     FeaturesFile formatter = new FeaturesFile();
1421     if (format.equalsIgnoreCase("Jalview"))
1422     {
1423       features = formatter.printJalviewFormat(viewport
1424               .getAlignment().getSequencesArray(),
1425               getDisplayedFeatureCols());
1426     }
1427     else
1428     {
1429       features = formatter.printGffFormat(viewport.getAlignment()
1430               .getSequencesArray(), getDisplayedFeatureCols());
1431     }
1432
1433     if (displayTextbox)
1434     {
1435       boolean frimport = false;
1436       if (features == null || features.equals("No Features Visible"))
1437       {
1438         features = "# No features visible - paste some and import them here.";
1439         frimport = true;
1440       }
1441
1442       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1443       if (frimport)
1444       {
1445         cap.setAnnotationImport();
1446       }
1447       Frame frame = new Frame();
1448       frame.add(cap);
1449       jalview.bin.JalviewLite.addFrame(frame,
1450               MessageManager.getString("label.features"), 600, 500);
1451       cap.setText(features);
1452     }
1453     else
1454     {
1455       if (features == null)
1456       {
1457         features = "";
1458       }
1459     }
1460
1461     return features;
1462   }
1463
1464   void launchFullApplication()
1465   {
1466     StringBuffer url = new StringBuffer(jalviewServletURL);
1467
1468     // allow servlet parameters to be passed in applet parameter
1469     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1470             : "?";
1471     url.append(firstSep);
1472
1473     url.append("open="
1474             + appendProtocol(viewport.applet.getParameter("file")));
1475
1476     if (viewport.applet.getParameter("features") != null)
1477     {
1478       url.append("&features=");
1479       url.append(appendProtocol(viewport.applet.getParameter("features")));
1480     }
1481
1482     if (viewport.applet.getParameter("annotations") != null)
1483     {
1484       url.append("&annotations=");
1485       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1486     }
1487
1488     if (viewport.applet.getParameter("jnetfile") != null)
1489     {
1490       url.append("&annotations=");
1491       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1492     }
1493
1494     if (viewport.applet.getParameter("defaultColour") != null)
1495     {
1496       url.append("&colour="
1497               + removeWhiteSpace(viewport.applet
1498                       .getParameter("defaultColour")));
1499     }
1500
1501     if (viewport.applet.getParameter("userDefinedColour") != null)
1502     {
1503       url.append("&colour="
1504               + removeWhiteSpace(viewport.applet
1505                       .getParameter("userDefinedColour")));
1506     }
1507     if (viewport.applet.getParameter("tree") != null)
1508     {
1509       url.append("&tree="
1510               + appendProtocol(viewport.applet.getParameter("tree")));
1511     }
1512     if (viewport.applet.getParameter("treeFile") != null)
1513     {
1514       url.append("&tree="
1515               + appendProtocol(viewport.applet.getParameter("treeFile")));
1516     }
1517
1518     showURL(url.toString(), "FULL_APP");
1519   }
1520
1521   String removeWhiteSpace(String colour)
1522   {
1523     StringBuffer sb = new StringBuffer();
1524     for (int i = 0; i < colour.length(); i++)
1525     {
1526       if (Character.isWhitespace(colour.charAt(i)))
1527       {
1528         sb.append("%20");
1529       }
1530       else
1531       {
1532         sb.append(colour.charAt(i));
1533       }
1534     }
1535
1536     return sb.toString();
1537   }
1538
1539   String appendProtocol(String url)
1540   {
1541     try
1542     {
1543       new URL(url);
1544       url = URLEncoder.encode(url);
1545     }
1546     /*
1547      * When we finally deprecate 1.1 compatibility, we can start to use
1548      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1549      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1550      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1551      * ex.printStackTrace(); }
1552      */
1553     catch (java.net.MalformedURLException ex)
1554     {
1555       url = viewport.applet.getCodeBase() + url;
1556     }
1557     return url;
1558   }
1559
1560   public void closeMenuItem_actionPerformed()
1561   {
1562     PaintRefresher.RemoveComponent(alignPanel);
1563     if (alignPanel.seqPanel != null
1564             && alignPanel.seqPanel.seqCanvas != null)
1565     {
1566       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1567     }
1568     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1569     {
1570       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1571     }
1572
1573     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1574     {
1575       System.exit(0);
1576     }
1577     else
1578     {
1579     }
1580     viewport = null;
1581     alignPanel = null;
1582     this.dispose();
1583   }
1584
1585   /**
1586    * TODO: JAL-1104
1587    */
1588   void updateEditMenuBar()
1589   {
1590
1591     if (viewport.getHistoryList().size() > 0)
1592     {
1593       undoMenuItem.setEnabled(true);
1594       CommandI command = viewport.getHistoryList().peek();
1595       undoMenuItem.setLabel(MessageManager.formatMessage(
1596               "label.undo_command",
1597               new Object[] { command.getDescription() }));
1598     }
1599     else
1600     {
1601       undoMenuItem.setEnabled(false);
1602       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1603     }
1604
1605     if (viewport.getRedoList().size() > 0)
1606     {
1607       redoMenuItem.setEnabled(true);
1608
1609       CommandI command = viewport.getRedoList().peek();
1610       redoMenuItem.setLabel(MessageManager.formatMessage(
1611               "label.redo_command",
1612               new Object[] { command.getDescription() }));
1613     }
1614     else
1615     {
1616       redoMenuItem.setEnabled(false);
1617       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1618     }
1619   }
1620
1621   /**
1622    * TODO: JAL-1104
1623    */
1624   @Override
1625   public void addHistoryItem(CommandI command)
1626   {
1627     if (command.getSize() > 0)
1628     {
1629       viewport.addToHistoryList(command);
1630       viewport.clearRedoList();
1631       updateEditMenuBar();
1632       viewport.updateHiddenColumns();
1633     }
1634   }
1635
1636   /**
1637    * TODO: JAL-1104 DOCUMENT ME!
1638    *
1639    * @param e
1640    *          DOCUMENT ME!
1641    */
1642   protected void undoMenuItem_actionPerformed()
1643   {
1644     if (viewport.getHistoryList().isEmpty())
1645     {
1646       return;
1647     }
1648
1649     CommandI command = viewport.getHistoryList().pop();
1650     viewport.addToRedoList(command);
1651     command.undoCommand(null);
1652
1653     AlignmentViewport originalSource = getOriginatingSource(command);
1654     // JBPNote Test
1655     if (originalSource != viewport)
1656     {
1657       System.err
1658               .println("Warning: Viewport object mismatch whilst undoing");
1659     }
1660     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1661                                           // viewport.getColumnSelection().getHiddenColumns()
1662                                           // != null;
1663     updateEditMenuBar();
1664     originalSource.firePropertyChange("alignment", null, originalSource
1665             .getAlignment().getSequences());
1666   }
1667
1668   /**
1669    * TODO: JAL-1104 DOCUMENT ME!
1670    *
1671    * @param e
1672    *          DOCUMENT ME!
1673    */
1674   protected void redoMenuItem_actionPerformed()
1675   {
1676     if (viewport.getRedoList().isEmpty())
1677     {
1678       return;
1679     }
1680
1681     CommandI command = viewport.getRedoList().pop();
1682     viewport.addToHistoryList(command);
1683     command.doCommand(null);
1684
1685     AlignmentViewport originalSource = getOriginatingSource(command);
1686     // JBPNote Test
1687     if (originalSource != viewport)
1688     {
1689       System.err
1690               .println("Warning: Viewport object mismatch whilst re-doing");
1691     }
1692     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1693                                           // viewport.getColumnSelection().getHiddenColumns()
1694                                           // != null;
1695
1696     updateEditMenuBar();
1697     originalSource.firePropertyChange("alignment", null, originalSource
1698             .getAlignment().getSequences());
1699   }
1700
1701   AlignmentViewport getOriginatingSource(CommandI command)
1702   {
1703     AlignmentViewport originalSource = null;
1704     // For sequence removal and addition, we need to fire
1705     // the property change event FROM the viewport where the
1706     // original alignment was altered
1707     AlignmentI al = null;
1708     if (command instanceof EditCommand)
1709     {
1710       EditCommand editCommand = (EditCommand) command;
1711       al = editCommand.getAlignment();
1712       Vector comps = (Vector) PaintRefresher.components.get(viewport
1713               .getSequenceSetId());
1714       for (int i = 0; i < comps.size(); i++)
1715       {
1716         if (comps.elementAt(i) instanceof AlignmentPanel)
1717         {
1718           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1719           {
1720             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1721             break;
1722           }
1723         }
1724       }
1725     }
1726
1727     if (originalSource == null)
1728     {
1729       // The original view is closed, we must validate
1730       // the current view against the closed view first
1731       if (al != null)
1732       {
1733         PaintRefresher.validateSequences(al, viewport.getAlignment());
1734       }
1735
1736       originalSource = viewport;
1737     }
1738
1739     return originalSource;
1740   }
1741
1742   /**
1743    * Move the currently selected sequences up or down one position in the
1744    * alignment
1745    *
1746    * @param up
1747    */
1748   public void moveSelectedSequences(boolean up)
1749   {
1750     SequenceGroup sg = viewport.getSelectionGroup();
1751     if (sg == null)
1752     {
1753       return;
1754     }
1755     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1756             up ? null : viewport.getHiddenRepSequences(), up);
1757     alignPanel.paintAlignment(true);
1758
1759     /*
1760      * Also move cDNA/protein complement sequences
1761      */
1762     AlignViewportI complement = viewport.getCodingComplement();
1763     if (complement != null)
1764     {
1765       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1766               viewport, complement);
1767       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1768               up ? null : complement.getHiddenRepSequences(), up);
1769       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1770     }
1771   }
1772
1773   synchronized void slideSequences(boolean right, int size)
1774   {
1775     List<SequenceI> sg = new Vector<SequenceI>();
1776     if (viewport.cursorMode)
1777     {
1778       sg.add(viewport.getAlignment().getSequenceAt(
1779               alignPanel.seqPanel.seqCanvas.cursorY));
1780     }
1781     else if (viewport.getSelectionGroup() != null
1782             && viewport.getSelectionGroup().getSize() != viewport
1783                     .getAlignment().getHeight())
1784     {
1785       sg = viewport.getSelectionGroup().getSequences(
1786               viewport.getHiddenRepSequences());
1787     }
1788
1789     if (sg.size() < 1)
1790     {
1791       return;
1792     }
1793
1794     Vector<SequenceI> invertGroup = new Vector();
1795
1796     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1797     {
1798       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1799       {
1800         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1801       }
1802     }
1803
1804     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1805
1806     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1807             .size()]);
1808     for (int i = 0; i < invertGroup.size(); i++)
1809     {
1810       seqs2[i] = invertGroup.elementAt(i);
1811     }
1812
1813     SlideSequencesCommand ssc;
1814     if (right)
1815     {
1816       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1817               size, viewport.getGapCharacter());
1818     }
1819     else
1820     {
1821       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1822               size, viewport.getGapCharacter());
1823     }
1824
1825     int groupAdjustment = 0;
1826     if (ssc.getGapsInsertedBegin() && right)
1827     {
1828       if (viewport.cursorMode)
1829       {
1830         alignPanel.seqPanel.moveCursor(size, 0);
1831       }
1832       else
1833       {
1834         groupAdjustment = size;
1835       }
1836     }
1837     else if (!ssc.getGapsInsertedBegin() && !right)
1838     {
1839       if (viewport.cursorMode)
1840       {
1841         alignPanel.seqPanel.moveCursor(-size, 0);
1842       }
1843       else
1844       {
1845         groupAdjustment = -size;
1846       }
1847     }
1848
1849     if (groupAdjustment != 0)
1850     {
1851       viewport.getSelectionGroup().setStartRes(
1852               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1853       viewport.getSelectionGroup().setEndRes(
1854               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1855     }
1856
1857     boolean appendHistoryItem = false;
1858     Deque<CommandI> historyList = viewport.getHistoryList();
1859     if (historyList != null && historyList.size() > 0
1860             && historyList.peek() instanceof SlideSequencesCommand)
1861     {
1862       appendHistoryItem = ssc
1863               .appendSlideCommand((SlideSequencesCommand) historyList
1864                       .peek());
1865     }
1866
1867     if (!appendHistoryItem)
1868     {
1869       addHistoryItem(ssc);
1870     }
1871
1872     repaint();
1873   }
1874
1875   static StringBuffer copiedSequences;
1876
1877   static Vector copiedHiddenColumns;
1878
1879   protected void copy_actionPerformed()
1880   {
1881     if (viewport.getSelectionGroup() == null)
1882     {
1883       return;
1884     }
1885
1886     SequenceGroup sg = viewport.getSelectionGroup();
1887     copiedSequences = new StringBuffer();
1888     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1889     for (int i = 0; i < sg.getSize(); i++)
1890     {
1891       SequenceI seq = sg.getSequenceAt(i);
1892       int index = viewport.getAlignment().findIndex(seq);
1893       orderedSeqs.put(index, seq);
1894     }
1895
1896     int index = 0, startRes, endRes;
1897     char ch;
1898
1899     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1900     {
1901       copiedHiddenColumns = new Vector();
1902       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1903       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1904       {
1905         copiedHiddenColumns.addElement(new int[] {
1906             region[0] - hiddenOffset, region[1] - hiddenOffset });
1907       }
1908     }
1909     else
1910     {
1911       copiedHiddenColumns = null;
1912     }
1913
1914     for (int i = 0; i < sg.getSize(); i++)
1915     {
1916       SequenceI seq = null;
1917
1918       while (seq == null)
1919       {
1920         if (orderedSeqs.containsKey(index))
1921         {
1922           seq = orderedSeqs.get(index);
1923           index++;
1924           break;
1925         }
1926         else
1927         {
1928           index++;
1929         }
1930       }
1931
1932       // FIND START RES
1933       // Returns residue following index if gap
1934       startRes = seq.findPosition(sg.getStartRes());
1935
1936       // FIND END RES
1937       // Need to find the residue preceeding index if gap
1938       endRes = 0;
1939
1940       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1941       {
1942         ch = seq.getCharAt(j);
1943         if (!jalview.util.Comparison.isGap((ch)))
1944         {
1945           endRes++;
1946         }
1947       }
1948
1949       if (endRes > 0)
1950       {
1951         endRes += seq.getStart() - 1;
1952       }
1953
1954       copiedSequences.append(seq.getName()
1955               + "\t"
1956               + startRes
1957               + "\t"
1958               + endRes
1959               + "\t"
1960               + seq.getSequenceAsString(sg.getStartRes(),
1961                       sg.getEndRes() + 1) + "\n");
1962     }
1963
1964   }
1965
1966   protected void pasteNew_actionPerformed()
1967   {
1968     paste(true);
1969   }
1970
1971   protected void pasteThis_actionPerformed()
1972   {
1973     paste(false);
1974   }
1975
1976   void paste(boolean newAlignment)
1977   {
1978     try
1979     {
1980
1981       if (copiedSequences == null)
1982       {
1983         return;
1984       }
1985
1986       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1987       Vector seqs = new Vector();
1988       while (st.hasMoreElements())
1989       {
1990         String name = st.nextToken();
1991         int start = Integer.parseInt(st.nextToken());
1992         int end = Integer.parseInt(st.nextToken());
1993         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1994       }
1995       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1996       for (int i = 0; i < seqs.size(); i++)
1997       {
1998         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1999       }
2000
2001       if (newAlignment)
2002       {
2003         String newtitle = MessageManager
2004                 .getString("label.copied_sequences");
2005         if (getTitle().startsWith(
2006                 MessageManager.getString("label.copied_sequences")))
2007         {
2008           newtitle = getTitle();
2009         }
2010         else
2011         {
2012           newtitle = newtitle.concat(MessageManager.formatMessage(
2013                   "label.from_msname", new String[] { getTitle() }));
2014         }
2015         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2016                 viewport.applet, newtitle, false);
2017         if (copiedHiddenColumns != null)
2018         {
2019           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2020           {
2021             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2022             af.viewport.hideColumns(region[0], region[1]);
2023           }
2024         }
2025
2026         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2027                 frameHeight);
2028       }
2029       else
2030       {
2031         addSequences(newSeqs);
2032       }
2033
2034     } catch (Exception ex)
2035     {
2036     } // could be anything being pasted in here
2037
2038   }
2039
2040   void addSequences(SequenceI[] seqs)
2041   {
2042     for (int i = 0; i < seqs.length; i++)
2043     {
2044       viewport.getAlignment().addSequence(seqs[i]);
2045     }
2046
2047     // !newAlignment
2048     addHistoryItem(new EditCommand(
2049             MessageManager.getString("label.add_sequences"), Action.PASTE,
2050             seqs, 0, viewport.getAlignment().getWidth(),
2051             viewport.getAlignment()));
2052
2053     viewport.setEndSeq(viewport.getAlignment().getHeight());
2054     viewport.getAlignment().getWidth();
2055     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2056             .getSequences());
2057
2058   }
2059
2060   protected void cut_actionPerformed()
2061   {
2062     copy_actionPerformed();
2063     delete_actionPerformed();
2064   }
2065
2066   protected void delete_actionPerformed()
2067   {
2068
2069     SequenceGroup sg = viewport.getSelectionGroup();
2070     if (sg == null)
2071     {
2072       return;
2073     }
2074
2075     Vector seqs = new Vector();
2076     SequenceI seq;
2077     for (int i = 0; i < sg.getSize(); i++)
2078     {
2079       seq = sg.getSequenceAt(i);
2080       seqs.addElement(seq);
2081     }
2082
2083     /*
2084      * If the cut affects all sequences, warn, remove highlighted columns
2085      */
2086     if (sg.getSize() == viewport.getAlignment().getHeight())
2087     {
2088       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2089               .getAlignment().getWidth()) ? true : false;
2090       if (isEntireAlignWidth)
2091       {
2092         String title = MessageManager.getString("label.delete_all");
2093         Panel infoPanel = new Panel();
2094         infoPanel.setLayout(new FlowLayout());
2095         infoPanel
2096                 .add(new Label(MessageManager.getString("warn.delete_all")));
2097
2098         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2099         dialog.setMainPanel(infoPanel);
2100         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2101         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2102         dialog.setVisible(true);
2103
2104         if (!dialog.accept)
2105         {
2106           return;
2107         }
2108       }
2109       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2110               sg.getEndRes() + 1);
2111     }
2112
2113     SequenceI[] cut = new SequenceI[seqs.size()];
2114     for (int i = 0; i < seqs.size(); i++)
2115     {
2116       cut[i] = (SequenceI) seqs.elementAt(i);
2117     }
2118
2119     /*
2120      * //ADD HISTORY ITEM
2121      */
2122     addHistoryItem(new EditCommand(
2123             MessageManager.getString("label.cut_sequences"), Action.CUT,
2124             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2125             viewport.getAlignment()));
2126
2127     viewport.setSelectionGroup(null);
2128     viewport.getAlignment().deleteGroup(sg);
2129
2130     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2131             .getSequences());
2132
2133     if (viewport.getAlignment().getHeight() < 1)
2134     {
2135       this.setVisible(false);
2136     }
2137     viewport.sendSelection();
2138   }
2139
2140   /**
2141    * group consensus toggled
2142    *
2143    */
2144   protected void showGroupConsensus_actionPerformed()
2145   {
2146     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2147     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2148
2149   }
2150
2151   /**
2152    * group conservation toggled.
2153    */
2154   protected void showGroupConservation_actionPerformed()
2155   {
2156     viewport.setShowGroupConservation(showGroupConservation.getState());
2157     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2158   }
2159
2160   /*
2161    * (non-Javadoc)
2162    *
2163    * @see
2164    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2165    * .event.ActionEvent)
2166    */
2167   protected void showConsensusHistogram_actionPerformed()
2168   {
2169     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2170     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2171   }
2172
2173   /*
2174    * (non-Javadoc)
2175    *
2176    * @see
2177    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2178    * .event.ActionEvent)
2179    */
2180   protected void showSequenceLogo_actionPerformed()
2181   {
2182     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2183     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184   }
2185
2186   protected void normSequenceLogo_actionPerformed()
2187   {
2188     showSequenceLogo.setState(true);
2189     viewport.setShowSequenceLogo(true);
2190     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2191     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192   }
2193
2194   protected void applyAutoAnnotationSettings_actionPerformed()
2195   {
2196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197   }
2198
2199   protected void makeGrpsFromSelection_actionPerformed()
2200   {
2201     if (avc.makeGroupsFromSelection())
2202     {
2203       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2204       alignPanel.updateAnnotation();
2205       alignPanel.paintAlignment(true);
2206     }
2207   }
2208
2209   protected void createGroup_actionPerformed()
2210   {
2211     avc.createGroup();
2212   }
2213
2214   protected void unGroup_actionPerformed()
2215   {
2216     if (avc.unGroup())
2217     {
2218       alignPanel.alignmentChanged();
2219     }
2220   }
2221
2222   protected void deleteGroups_actionPerformed()
2223   {
2224     if (avc.deleteGroups())
2225     {
2226       alignPanel.alignmentChanged();
2227     }
2228   }
2229
2230   public void selectAllSequenceMenuItem_actionPerformed()
2231   {
2232     SequenceGroup sg = new SequenceGroup();
2233     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2234     {
2235       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2236     }
2237     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2238     viewport.setSelectionGroup(sg);
2239     // JAL-2034 - should delegate to
2240     // alignPanel to decide if overview needs
2241     // updating.
2242     alignPanel.paintAlignment(false);
2243     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2244     viewport.sendSelection();
2245   }
2246
2247   public void deselectAllSequenceMenuItem_actionPerformed()
2248   {
2249     if (viewport.cursorMode)
2250     {
2251       alignPanel.seqPanel.keyboardNo1 = null;
2252       alignPanel.seqPanel.keyboardNo2 = null;
2253     }
2254     viewport.setSelectionGroup(null);
2255     viewport.getColumnSelection().clear();
2256     viewport.setSelectionGroup(null);
2257     alignPanel.idPanel.idCanvas.searchResults = null;
2258     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2259     // JAL-2034 - should delegate to
2260     // alignPanel to decide if overview needs
2261     // updating.
2262     alignPanel.paintAlignment(false);
2263     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2264     viewport.sendSelection();
2265   }
2266
2267   public void invertSequenceMenuItem_actionPerformed()
2268   {
2269     SequenceGroup sg = viewport.getSelectionGroup();
2270     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2271     {
2272       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2273     }
2274
2275     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2276     viewport.sendSelection();
2277   }
2278
2279   public void invertColSel_actionPerformed()
2280   {
2281     viewport.invertColumnSelection();
2282     alignPanel.paintAlignment(true);
2283     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2284     viewport.sendSelection();
2285   }
2286
2287   void trimAlignment(boolean trimLeft)
2288   {
2289     ColumnSelection colSel = viewport.getColumnSelection();
2290     int column;
2291
2292     if (!colSel.isEmpty())
2293     {
2294       if (trimLeft)
2295       {
2296         column = colSel.getMin();
2297       }
2298       else
2299       {
2300         column = colSel.getMax();
2301       }
2302
2303       SequenceI[] seqs;
2304       if (viewport.getSelectionGroup() != null)
2305       {
2306         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2307                 viewport.getHiddenRepSequences());
2308       }
2309       else
2310       {
2311         seqs = viewport.getAlignment().getSequencesArray();
2312       }
2313
2314       TrimRegionCommand trimRegion;
2315       if (trimLeft)
2316       {
2317         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2318                 column, viewport.getAlignment());
2319         viewport.setStartRes(0);
2320       }
2321       else
2322       {
2323         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2324                 column, viewport.getAlignment());
2325       }
2326
2327       statusBar.setText(MessageManager.formatMessage(
2328               "label.removed_columns",
2329               new String[] { Integer.valueOf(trimRegion.getSize())
2330                       .toString() }));
2331       addHistoryItem(trimRegion);
2332
2333       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2334       {
2335         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2336                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2337         {
2338           viewport.getAlignment().deleteGroup(sg);
2339         }
2340       }
2341
2342       viewport.firePropertyChange("alignment", null, viewport
2343               .getAlignment().getSequences());
2344     }
2345   }
2346
2347   public void removeGappedColumnMenuItem_actionPerformed()
2348   {
2349     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2350
2351     SequenceI[] seqs;
2352     if (viewport.getSelectionGroup() != null)
2353     {
2354       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2355               viewport.getHiddenRepSequences());
2356       start = viewport.getSelectionGroup().getStartRes();
2357       end = viewport.getSelectionGroup().getEndRes();
2358     }
2359     else
2360     {
2361       seqs = viewport.getAlignment().getSequencesArray();
2362     }
2363
2364     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2365             "Remove Gapped Columns", seqs, start, end,
2366             viewport.getAlignment());
2367
2368     addHistoryItem(removeGapCols);
2369
2370     statusBar.setText(MessageManager.formatMessage(
2371             "label.removed_empty_columns",
2372             new String[] { Integer.valueOf(removeGapCols.getSize())
2373                     .toString() }));
2374
2375     // This is to maintain viewport position on first residue
2376     // of first sequence
2377     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2378     int startRes = seq.findPosition(viewport.startRes);
2379     // ShiftList shifts;
2380     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2381     // edit.alColumnChanges=shifts.getInverse();
2382     // if (viewport.hasHiddenColumns)
2383     // viewport.getColumnSelection().compensateForEdits(shifts);
2384     viewport.setStartRes(seq.findIndex(startRes) - 1);
2385     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2386             .getSequences());
2387
2388   }
2389
2390   public void removeAllGapsMenuItem_actionPerformed()
2391   {
2392     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2393
2394     SequenceI[] seqs;
2395     if (viewport.getSelectionGroup() != null)
2396     {
2397       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2398               viewport.getHiddenRepSequences());
2399       start = viewport.getSelectionGroup().getStartRes();
2400       end = viewport.getSelectionGroup().getEndRes();
2401     }
2402     else
2403     {
2404       seqs = viewport.getAlignment().getSequencesArray();
2405     }
2406
2407     // This is to maintain viewport position on first residue
2408     // of first sequence
2409     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2410     int startRes = seq.findPosition(viewport.startRes);
2411
2412     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2413             viewport.getAlignment()));
2414
2415     viewport.setStartRes(seq.findIndex(startRes) - 1);
2416
2417     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2418             .getSequences());
2419
2420   }
2421
2422   public void findMenuItem_actionPerformed()
2423   {
2424     new Finder(alignPanel);
2425   }
2426
2427   /**
2428    * create a new view derived from the current view
2429    *
2430    * @param viewtitle
2431    * @return frame for the new view
2432    */
2433   public AlignFrame newView(String viewtitle)
2434   {
2435     AlignmentI newal;
2436     if (viewport.hasHiddenRows())
2437     {
2438       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2439               .getFullAlignment().getSequencesArray());
2440     }
2441     else
2442     {
2443       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2444     }
2445
2446     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2447     {
2448       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2449       {
2450         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2451         {
2452           newal.addAnnotation(viewport.getAlignment()
2453                   .getAlignmentAnnotation()[i]);
2454         }
2455       }
2456     }
2457
2458     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2459
2460     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2461     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2462     PaintRefresher.Register(newaf.alignPanel,
2463             newaf.alignPanel.av.getSequenceSetId());
2464
2465     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2466             newaf.alignPanel.av.getSequenceSetId());
2467     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2468             newaf.alignPanel.av.getSequenceSetId());
2469
2470     Vector comps = (Vector) PaintRefresher.components.get(viewport
2471             .getSequenceSetId());
2472     int viewSize = -1;
2473     for (int i = 0; i < comps.size(); i++)
2474     {
2475       if (comps.elementAt(i) instanceof AlignmentPanel)
2476       {
2477         viewSize++;
2478       }
2479     }
2480
2481     String title = new String(this.getTitle());
2482     if (viewtitle != null)
2483     {
2484       title = viewtitle + " ( " + title + ")";
2485     }
2486     else
2487     {
2488       if (title.indexOf("(View") > -1)
2489       {
2490         title = title.substring(0, title.indexOf("(View"));
2491       }
2492       title += "(View " + viewSize + ")";
2493     }
2494
2495     newaf.setTitle(title.toString());
2496
2497     newaf.viewport.setHistoryList(viewport.getHistoryList());
2498     newaf.viewport.setRedoList(viewport.getRedoList());
2499     return newaf;
2500   }
2501
2502   /**
2503    *
2504    * @return list of feature groups on the view
2505    */
2506   public String[] getFeatureGroups()
2507   {
2508     FeatureRenderer fr = null;
2509     if (alignPanel != null
2510             && (fr = alignPanel.getFeatureRenderer()) != null)
2511     {
2512       List<String> gps = fr.getFeatureGroups();
2513       String[] _gps = gps.toArray(new String[gps.size()]);
2514       return _gps;
2515     }
2516     return null;
2517   }
2518
2519   /**
2520    * get sequence feature groups that are hidden or shown
2521    *
2522    * @param visible
2523    *          true is visible
2524    * @return list
2525    */
2526   public String[] getFeatureGroupsOfState(boolean visible)
2527   {
2528     FeatureRenderer fr = null;
2529     if (alignPanel != null
2530             && (fr = alignPanel.getFeatureRenderer()) != null)
2531     {
2532       List<String> gps = fr.getGroups(visible);
2533       String[] _gps = gps.toArray(new String[gps.size()]);
2534       return _gps;
2535     }
2536     return null;
2537   }
2538
2539   /**
2540    * Change the display state for the given feature groups
2541    *
2542    * @param groups
2543    *          list of group strings
2544    * @param state
2545    *          visible or invisible
2546    */
2547   public void setFeatureGroupState(String[] groups, boolean state)
2548   {
2549     FeatureRenderer fr = null;
2550     this.sequenceFeatures.setState(true);
2551     viewport.setShowSequenceFeatures(true);
2552     if (alignPanel != null
2553             && (fr = alignPanel.getFeatureRenderer()) != null)
2554     {
2555
2556       fr.setGroupVisibility(Arrays.asList(groups), state);
2557       alignPanel.seqPanel.seqCanvas.repaint();
2558       if (alignPanel.overviewPanel != null)
2559       {
2560         alignPanel.overviewPanel.updateOverviewImage();
2561       }
2562     }
2563   }
2564
2565   public void seqLimits_itemStateChanged()
2566   {
2567     viewport.setShowJVSuffix(seqLimits.getState());
2568     alignPanel.fontChanged();
2569     alignPanel.paintAlignment(true);
2570   }
2571
2572   protected void colourTextMenuItem_actionPerformed()
2573   {
2574     viewport.setColourText(colourTextMenuItem.getState());
2575     alignPanel.paintAlignment(true);
2576   }
2577
2578   protected void displayNonconservedMenuItem_actionPerformed()
2579   {
2580     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2581     alignPanel.paintAlignment(true);
2582   }
2583
2584   protected void wrapMenuItem_actionPerformed()
2585   {
2586     viewport.setWrapAlignment(wrapMenuItem.getState());
2587     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2588     scaleAbove.setEnabled(wrapMenuItem.getState());
2589     scaleLeft.setEnabled(wrapMenuItem.getState());
2590     scaleRight.setEnabled(wrapMenuItem.getState());
2591     alignPanel.paintAlignment(true);
2592   }
2593
2594   public void overviewMenuItem_actionPerformed()
2595   {
2596     if (alignPanel.overviewPanel != null)
2597     {
2598       return;
2599     }
2600
2601     Frame frame = new Frame();
2602     OverviewPanel overview = new OverviewPanel(alignPanel);
2603     frame.add(overview);
2604     // +50 must allow for applet frame window
2605     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2606             "label.overview_params", new String[] { this.getTitle() }),
2607             overview.getPreferredSize().width,
2608             overview.getPreferredSize().height + 50);
2609
2610     frame.pack();
2611     final AlignmentPanel ap = alignPanel;
2612     frame.addWindowListener(new WindowAdapter()
2613     {
2614       @Override
2615       public void windowClosing(WindowEvent e)
2616       {
2617         if (ap != null)
2618         {
2619           ap.setOverviewPanel(null);
2620         }
2621       };
2622     });
2623
2624     alignPanel.setOverviewPanel(overview);
2625
2626   }
2627
2628   @Override
2629   public void changeColour(ColourSchemeI cs)
2630   {
2631
2632     if (cs != null)
2633     {
2634       if (viewport.getAbovePIDThreshold())
2635       {
2636         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2637                 cs, "Background"));
2638       }
2639
2640       if (viewport.getConservationSelected())
2641       {
2642         cs.setConservationApplied(true);
2643         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2644                 cs, "Background"));
2645       }
2646       else
2647       {
2648         cs.setConservationApplied(false);
2649       }
2650     }
2651     viewport.setGlobalColourScheme(cs);
2652
2653     alignPanel.paintAlignment(true);
2654   }
2655
2656   protected void modifyPID_actionPerformed()
2657   {
2658     if (viewport.getAbovePIDThreshold()
2659             && viewport.getGlobalColourScheme() != null)
2660     {
2661       SliderPanel.setPIDSliderSource(alignPanel,
2662               viewport.getGlobalColourScheme(), "Background");
2663       SliderPanel.showPIDSlider();
2664     }
2665   }
2666
2667   protected void modifyConservation_actionPerformed()
2668   {
2669     if (viewport.getConservationSelected()
2670             && viewport.getGlobalColourScheme() != null)
2671     {
2672       SliderPanel.setConservationSlider(alignPanel,
2673               viewport.getGlobalColourScheme(), "Background");
2674       SliderPanel.showConservationSlider();
2675     }
2676   }
2677
2678   protected void conservationMenuItem_actionPerformed()
2679   {
2680     viewport.setConservationSelected(conservationMenuItem.getState());
2681
2682     viewport.setAbovePIDThreshold(false);
2683     abovePIDThreshold.setState(false);
2684
2685     changeColour(viewport.getGlobalColourScheme());
2686
2687     modifyConservation_actionPerformed();
2688   }
2689
2690   public void abovePIDThreshold_actionPerformed()
2691   {
2692     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2693
2694     conservationMenuItem.setState(false);
2695     viewport.setConservationSelected(false);
2696
2697     changeColour(viewport.getGlobalColourScheme());
2698
2699     modifyPID_actionPerformed();
2700   }
2701
2702   public void sortPairwiseMenuItem_actionPerformed()
2703   {
2704     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2705     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2706             .getAlignment().getSequenceAt(0), null);
2707
2708     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2709             viewport.getAlignment()));
2710     alignPanel.paintAlignment(true);
2711   }
2712
2713   public void sortIDMenuItem_actionPerformed()
2714   {
2715     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2716     AlignmentSorter.sortByID(viewport.getAlignment());
2717     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2718             viewport.getAlignment()));
2719     alignPanel.paintAlignment(true);
2720   }
2721
2722   public void sortLengthMenuItem_actionPerformed()
2723   {
2724     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2725     AlignmentSorter.sortByLength(viewport.getAlignment());
2726     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2727             viewport.getAlignment()));
2728     alignPanel.paintAlignment(true);
2729   }
2730
2731   public void sortGroupMenuItem_actionPerformed()
2732   {
2733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734     AlignmentSorter.sortByGroup(viewport.getAlignment());
2735     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2736             viewport.getAlignment()));
2737     alignPanel.paintAlignment(true);
2738
2739   }
2740
2741   public void removeRedundancyMenuItem_actionPerformed()
2742   {
2743     new RedundancyPanel(alignPanel);
2744   }
2745
2746   public void pairwiseAlignmentMenuItem_actionPerformed()
2747   {
2748     if (viewport.getSelectionGroup() != null
2749             && viewport.getSelectionGroup().getSize() > 1)
2750     {
2751       Frame frame = new Frame();
2752       frame.add(new PairwiseAlignPanel(alignPanel));
2753       jalview.bin.JalviewLite.addFrame(frame,
2754               MessageManager.getString("action.pairwise_alignment"), 600,
2755               500);
2756     }
2757   }
2758
2759   public void PCAMenuItem_actionPerformed()
2760   {
2761     // are the sequences aligned?
2762     if (!viewport.getAlignment().isAligned(false))
2763     {
2764       SequenceI current;
2765       int Width = viewport.getAlignment().getWidth();
2766
2767       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2768       {
2769         current = viewport.getAlignment().getSequenceAt(i);
2770
2771         if (current.getLength() < Width)
2772         {
2773           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2774         }
2775       }
2776       alignPanel.paintAlignment(true);
2777     }
2778
2779     if ((viewport.getSelectionGroup() != null
2780             && viewport.getSelectionGroup().getSize() < 4 && viewport
2781             .getSelectionGroup().getSize() > 0)
2782             || viewport.getAlignment().getHeight() < 4)
2783     {
2784       return;
2785     }
2786
2787     try
2788     {
2789       new PCAPanel(viewport);
2790     } catch (java.lang.OutOfMemoryError ex)
2791     {
2792     }
2793
2794   }
2795
2796   public void averageDistanceTreeMenuItem_actionPerformed()
2797   {
2798     NewTreePanel("AV", "PID", "Average distance tree using PID");
2799   }
2800
2801   public void neighbourTreeMenuItem_actionPerformed()
2802   {
2803     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2804   }
2805
2806   protected void njTreeBlosumMenuItem_actionPerformed()
2807   {
2808     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2809   }
2810
2811   protected void avTreeBlosumMenuItem_actionPerformed()
2812   {
2813     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2814   }
2815
2816   void NewTreePanel(String type, String pwType, String title)
2817   {
2818     // are the sequences aligned?
2819     if (!viewport.getAlignment().isAligned(false))
2820     {
2821       SequenceI current;
2822       int Width = viewport.getAlignment().getWidth();
2823
2824       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2825       {
2826         current = viewport.getAlignment().getSequenceAt(i);
2827
2828         if (current.getLength() < Width)
2829         {
2830           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2831         }
2832       }
2833       alignPanel.paintAlignment(true);
2834
2835     }
2836
2837     if ((viewport.getSelectionGroup() != null && viewport
2838             .getSelectionGroup().getSize() > 1)
2839             || (viewport.getAlignment().getHeight() > 1))
2840     {
2841       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2842
2843       addTreeMenuItem(tp, title);
2844
2845       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2846     }
2847   }
2848
2849   void loadTree_actionPerformed()
2850   {
2851     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2852     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2853     cap.setTreeImport();
2854     Frame frame = new Frame();
2855     frame.add(cap);
2856     jalview.bin.JalviewLite.addFrame(frame,
2857             MessageManager.getString("label.paste_newick_file"), 400, 300);
2858   }
2859
2860   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2861   {
2862     TreePanel tp = new TreePanel(alignPanel, treeFile,
2863             MessageManager.getString("label.load_tree_from_file"), tree);
2864     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2865     addTreeMenuItem(tp, treeFile);
2866   }
2867
2868   /**
2869    * sort the alignment using the given treePanel
2870    *
2871    * @param treePanel
2872    *          tree used to sort view
2873    * @param title
2874    *          string used for undo event name
2875    */
2876   public void sortByTree(TreePanel treePanel, String title)
2877   {
2878     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2879     AlignmentSorter
2880             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2881     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2882     // HistoryItem.SORT));
2883     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2884             "label.order_by_params", new String[] { title }), oldOrder,
2885             viewport.getAlignment()));
2886     alignPanel.paintAlignment(true);
2887   }
2888
2889   /**
2890    * Do any automatic reordering of the alignment and add the necessary bits to
2891    * the menu structure for the new tree
2892    *
2893    * @param treePanel
2894    * @param title
2895    */
2896   protected void addTreeMenuItem(final TreePanel treePanel,
2897           final String title)
2898   {
2899     final MenuItem item = new MenuItem(title);
2900     sortByTreeMenu.add(item);
2901     item.addActionListener(new java.awt.event.ActionListener()
2902     {
2903       @Override
2904       public void actionPerformed(ActionEvent evt)
2905       {
2906         sortByTree(treePanel, title); // treePanel.getTitle());
2907       }
2908     });
2909
2910     treePanel.addWindowListener(new WindowAdapter()
2911     {
2912       @Override
2913       public void windowOpened(WindowEvent e)
2914       {
2915         if (viewport.sortByTree)
2916         {
2917           sortByTree(treePanel, title);
2918         }
2919         super.windowOpened(e);
2920       }
2921
2922       @Override
2923       public void windowClosing(WindowEvent e)
2924       {
2925         sortByTreeMenu.remove(item);
2926       };
2927     });
2928   }
2929
2930   public boolean sortBy(AlignmentOrder alorder, String undoname)
2931   {
2932     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2933     if (viewport.applet.debug)
2934     {
2935       System.err.println("Sorting " + alorder.getOrder().size()
2936               + " in alignment '" + getTitle() + "'");
2937     }
2938     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2939     if (undoname != null)
2940     {
2941       addHistoryItem(new OrderCommand(undoname, oldOrder,
2942               viewport.getAlignment()));
2943     }
2944     alignPanel.paintAlignment(true);
2945     return true;
2946   }
2947
2948   protected void documentation_actionPerformed()
2949   {
2950     alignPanel.av.applet.openJalviewHelpUrl();
2951   }
2952
2953   protected void about_actionPerformed()
2954   {
2955
2956     class AboutPanel extends Canvas
2957     {
2958       String version;
2959
2960       String builddate;
2961
2962       public AboutPanel(String version, String builddate)
2963       {
2964         this.version = version;
2965         this.builddate = builddate;
2966       }
2967
2968       @Override
2969       public void paint(Graphics g)
2970       {
2971         g.setColor(Color.white);
2972         g.fillRect(0, 0, getSize().width, getSize().height);
2973         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2974         FontMetrics fm = g.getFontMetrics();
2975         int fh = fm.getHeight();
2976         int y = 5, x = 7;
2977         g.setColor(Color.black);
2978         // TODO: update this text for each release or centrally store it for
2979         // lite and application
2980         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2981         g.drawString(MessageManager.formatMessage(
2982                 "label.jalviewLite_release", new String[] { version }), x,
2983                 y += fh);
2984         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2985         g.drawString(MessageManager.formatMessage(
2986                 "label.jaview_build_date", new String[] { builddate }), x,
2987                 y += fh);
2988         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2989         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2990                 x, y += fh * 1.5);
2991         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2992                 x + 50, y += fh + 8);
2993         g.drawString(
2994                 MessageManager.getString("label.jalview_dev_managers"), x,
2995                 y += fh);
2996         g.drawString(MessageManager
2997                 .getString("label.jalview_distribution_lists"), x, y += fh);
2998         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2999                 x, y += fh + 8);
3000         g.drawString(
3001                 MessageManager.getString("label.jalview_cite_1_authors"),
3002                 x, y += fh);
3003         g.drawString(
3004                 MessageManager.getString("label.jalview_cite_1_title"), x,
3005                 y += fh);
3006         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3007                 x, y += fh);
3008       }
3009     }
3010
3011     Frame frame = new Frame();
3012     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3013             .getBuildDate()));
3014     jalview.bin.JalviewLite.addFrame(frame,
3015             MessageManager.getString("label.jalview"), 580, 220);
3016
3017   }
3018
3019   public void showURL(String url, String target)
3020   {
3021     if (viewport.applet == null)
3022     {
3023       System.out.println("Not running as applet - no browser available.");
3024     }
3025     else
3026     {
3027       viewport.applet.showURL(url, target);
3028     }
3029   }
3030
3031   // ////////////////////////////////////////////////////////////////////////////////
3032   // JBuilder Graphics here
3033
3034   MenuBar alignFrameMenuBar = new MenuBar();
3035
3036   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3037
3038   MenuItem loadApplication = new MenuItem(
3039           MessageManager.getString("label.view_full_application"));
3040
3041   MenuItem loadTree = new MenuItem(
3042           MessageManager.getString("label.load_associated_tree"));
3043
3044   MenuItem loadAnnotations = new MenuItem(
3045           MessageManager.getString("label.load_features_annotations"));
3046
3047   MenuItem outputFeatures = new MenuItem(
3048           MessageManager.getString("label.export_features"));
3049
3050   MenuItem outputAnnotations = new MenuItem(
3051           MessageManager.getString("label.export_annotations"));
3052
3053   MenuItem closeMenuItem = new MenuItem(
3054           MessageManager.getString("action.close"));
3055
3056   MenuItem selectAllSequenceMenuItem = new MenuItem(
3057           MessageManager.getString("action.select_all"));
3058
3059   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3060           MessageManager.getString("action.deselect_all"));
3061
3062   MenuItem invertSequenceMenuItem = new MenuItem(
3063           MessageManager.getString("action.invert_selection"));
3064
3065   MenuItem remove2LeftMenuItem = new MenuItem();
3066
3067   MenuItem remove2RightMenuItem = new MenuItem();
3068
3069   MenuItem removeGappedColumnMenuItem = new MenuItem();
3070
3071   MenuItem removeAllGapsMenuItem = new MenuItem();
3072
3073   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3074
3075   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3076
3077   MenuItem sortPairwiseMenuItem = new MenuItem();
3078
3079   MenuItem sortIDMenuItem = new MenuItem();
3080
3081   MenuItem sortLengthMenuItem = new MenuItem();
3082
3083   MenuItem sortGroupMenuItem = new MenuItem();
3084
3085   MenuItem removeRedundancyMenuItem = new MenuItem();
3086
3087   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3088
3089   MenuItem PCAMenuItem = new MenuItem();
3090
3091   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3092
3093   MenuItem neighbourTreeMenuItem = new MenuItem();
3094
3095   BorderLayout borderLayout1 = new BorderLayout();
3096
3097   public Label statusBar = new Label();
3098
3099   MenuItem clustalColour = new MenuItem();
3100
3101   MenuItem zappoColour = new MenuItem();
3102
3103   MenuItem taylorColour = new MenuItem();
3104
3105   MenuItem hydrophobicityColour = new MenuItem();
3106
3107   MenuItem helixColour = new MenuItem();
3108
3109   MenuItem strandColour = new MenuItem();
3110
3111   MenuItem turnColour = new MenuItem();
3112
3113   MenuItem buriedColour = new MenuItem();
3114
3115   MenuItem purinePyrimidineColour = new MenuItem();
3116
3117   // MenuItem RNAInteractionColour = new MenuItem();
3118
3119   MenuItem RNAHelixColour = new MenuItem();
3120
3121   MenuItem userDefinedColour = new MenuItem();
3122
3123   MenuItem PIDColour = new MenuItem();
3124
3125   MenuItem BLOSUM62Colour = new MenuItem();
3126
3127   MenuItem tcoffeeColour = new MenuItem();
3128
3129   MenuItem njTreeBlosumMenuItem = new MenuItem();
3130
3131   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3132
3133   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3134
3135   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3136
3137   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3138
3139   MenuItem alProperties = new MenuItem(
3140           MessageManager.getString("label.alignment_props"));
3141
3142   MenuItem overviewMenuItem = new MenuItem();
3143
3144   MenuItem undoMenuItem = new MenuItem();
3145
3146   MenuItem redoMenuItem = new MenuItem();
3147
3148   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3149
3150   MenuItem noColourmenuItem = new MenuItem();
3151
3152   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3153
3154   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3155
3156   MenuItem findMenuItem = new MenuItem();
3157
3158   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3159
3160   MenuItem nucleotideColour = new MenuItem();
3161
3162   MenuItem deleteGroups = new MenuItem();
3163
3164   MenuItem grpsFromSelection = new MenuItem();
3165
3166   MenuItem createGroup = new MenuItem();
3167
3168   MenuItem unGroup = new MenuItem();
3169
3170   MenuItem delete = new MenuItem();
3171
3172   MenuItem copy = new MenuItem();
3173
3174   MenuItem cut = new MenuItem();
3175
3176   Menu pasteMenu = new Menu();
3177
3178   MenuItem pasteNew = new MenuItem();
3179
3180   MenuItem pasteThis = new MenuItem();
3181
3182   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3183
3184   MenuItem font = new MenuItem();
3185
3186   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3187
3188   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3189
3190   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3191
3192   MenuItem modifyPID = new MenuItem();
3193
3194   MenuItem modifyConservation = new MenuItem();
3195
3196   CheckboxMenuItem autoCalculate = null;
3197
3198   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3199           "Sort Alignment With New Tree", true);
3200
3201   Menu sortByTreeMenu = new Menu();
3202
3203   MenuItem inputText = new MenuItem();
3204
3205   MenuItem documentation = new MenuItem();
3206
3207   MenuItem about = new MenuItem();
3208
3209   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3222
3223   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3224
3225   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3226
3227   /**
3228    * Initialise menus and other items
3229    *
3230    * @throws Exception
3231    */
3232   private void jbInit() throws Exception
3233   {
3234     setMenuBar(alignFrameMenuBar);
3235
3236     /*
3237      * Configure File menu items and actions
3238      */
3239     inputText
3240             .setLabel(MessageManager.getString("label.input_from_textbox"));
3241     inputText.addActionListener(this);
3242     Menu outputTextboxMenu = new Menu(
3243             MessageManager.getString("label.out_to_textbox"));
3244     for (String ff : FileFormat.getWritableFormats())
3245     {
3246       MenuItem item = new MenuItem(ff);
3247
3248       item.addActionListener(new java.awt.event.ActionListener()
3249       {
3250         @Override
3251         public void actionPerformed(ActionEvent e)
3252         {
3253           outputText_actionPerformed(e);
3254         }
3255       });
3256
3257       outputTextboxMenu.add(item);
3258     }
3259     closeMenuItem.addActionListener(this);
3260     loadApplication.addActionListener(this);
3261     loadTree.addActionListener(this);
3262     loadAnnotations.addActionListener(this);
3263     outputFeatures.addActionListener(this);
3264     outputAnnotations.addActionListener(this);
3265
3266     /*
3267      * Configure Edit menu items and actions
3268      */
3269     undoMenuItem.setEnabled(false);
3270     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3271     undoMenuItem.addActionListener(this);
3272     redoMenuItem.setEnabled(false);
3273     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3274     redoMenuItem.addActionListener(this);
3275     copy.setLabel(MessageManager.getString("action.copy"));
3276     copy.addActionListener(this);
3277     cut.setLabel(MessageManager.getString("action.cut"));
3278     cut.addActionListener(this);
3279     delete.setLabel(MessageManager.getString("action.delete"));
3280     delete.addActionListener(this);
3281     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3282     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3283     pasteNew.addActionListener(this);
3284     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3285     pasteThis.addActionListener(this);
3286     remove2LeftMenuItem.setLabel(MessageManager
3287             .getString("action.remove_left"));
3288     remove2LeftMenuItem.addActionListener(this);
3289     remove2RightMenuItem.setLabel(MessageManager
3290             .getString("action.remove_right"));
3291     remove2RightMenuItem.addActionListener(this);
3292     removeGappedColumnMenuItem.setLabel(MessageManager
3293             .getString("action.remove_empty_columns"));
3294     removeGappedColumnMenuItem.addActionListener(this);
3295     removeAllGapsMenuItem.setLabel(MessageManager
3296             .getString("action.remove_all_gaps"));
3297     removeAllGapsMenuItem.addActionListener(this);
3298     removeRedundancyMenuItem.setLabel(MessageManager
3299             .getString("action.remove_redundancy"));
3300     removeRedundancyMenuItem.addActionListener(this);
3301
3302     /*
3303      * Configure Select menu items and actions
3304      */
3305     findMenuItem.setLabel(MessageManager.getString("action.find"));
3306     findMenuItem.addActionListener(this);
3307     selectAllSequenceMenuItem.addActionListener(this);
3308     deselectAllSequenceMenuItem.addActionListener(this);
3309     invertSequenceMenuItem.setLabel(MessageManager
3310             .getString("action.invert_sequence_selection"));
3311     invertSequenceMenuItem.addActionListener(this);
3312     invertColSel.setLabel(MessageManager
3313             .getString("action.invert_column_selection"));
3314     invertColSel.addActionListener(this);
3315     deleteGroups.setLabel(MessageManager
3316             .getString("action.undefine_groups"));
3317     deleteGroups.addActionListener(this);
3318     grpsFromSelection.setLabel(MessageManager
3319             .getString("action.make_groups_selection"));
3320     grpsFromSelection.addActionListener(this);
3321     createGroup.setLabel(MessageManager.getString("action.create_group"));
3322     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3323     annotationColumnSelection.setLabel(MessageManager
3324             .getString("action.select_by_annotation"));
3325     annotationColumnSelection.addActionListener(this);
3326
3327     /*
3328      * Configure View menu items and actions
3329      */
3330     newView.setLabel(MessageManager.getString("action.new_view"));
3331     newView.addActionListener(this);
3332     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3333     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3334     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3335     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3336     hideColumns
3337             .setLabel(MessageManager.getString("label.selected_columns"));
3338     hideSequences.setLabel(MessageManager
3339             .getString("label.selected_sequences"));
3340     hideAllButSelection.setLabel(MessageManager
3341             .getString("label.all_but_selected_region"));
3342     hideAllSelection.setLabel(MessageManager
3343             .getString("label.selected_region"));
3344     showAllHidden.setLabel(MessageManager
3345             .getString("label.all_sequences_columns"));
3346     showColumns.addActionListener(this);
3347     showSeqs.addActionListener(this);
3348     hideColumns.addActionListener(this);
3349     hideSequences.addActionListener(this);
3350     hideAllButSelection.addActionListener(this);
3351     hideAllSelection.addActionListener(this);
3352     showAllHidden.addActionListener(this);
3353     featureSettings.setLabel(MessageManager
3354             .getString("action.feature_settings"));
3355     featureSettings.addActionListener(this);
3356     sequenceFeatures.setLabel(MessageManager
3357             .getString("label.show_sequence_features"));
3358     sequenceFeatures.addItemListener(this);
3359     sequenceFeatures.setState(false);
3360     followMouseOverFlag.setLabel(MessageManager
3361             .getString("label.automatic_scrolling"));
3362     followMouseOverFlag.addItemListener(this);
3363     alProperties.addActionListener(this);
3364     overviewMenuItem.setLabel(MessageManager
3365             .getString("label.overview_window"));
3366     overviewMenuItem.addActionListener(this);
3367
3368     /*
3369      * Configure Annotations menu items and actions
3370      */
3371     annotationPanelMenuItem.setLabel(MessageManager
3372             .getString("label.show_annotations"));
3373     annotationPanelMenuItem.addItemListener(this);
3374     showGroupConsensus.setLabel(MessageManager
3375             .getString("label.group_consensus"));
3376     showGroupConservation.setLabel(MessageManager
3377             .getString("label.group_conservation"));
3378     showConsensusHistogram.setLabel(MessageManager
3379             .getString("label.show_consensus_histogram"));
3380     showSequenceLogo.setLabel(MessageManager
3381             .getString("label.show_consensus_logo"));
3382     normSequenceLogo.setLabel(MessageManager
3383             .getString("label.norm_consensus_logo"));
3384     applyAutoAnnotationSettings.setLabel(MessageManager
3385             .getString("label.apply_all_groups"));
3386     applyAutoAnnotationSettings.setState(true);
3387     Menu autoAnnMenu = new Menu(
3388             MessageManager.getString("label.autocalculated_annotation"));
3389     showGroupConsensus.addItemListener(this);
3390     showGroupConservation.addItemListener(this);
3391     showConsensusHistogram.addItemListener(this);
3392     showSequenceLogo.addItemListener(this);
3393     normSequenceLogo.addItemListener(this);
3394     applyAutoAnnotationSettings.addItemListener(this);
3395     showAlignmentAnnotations = new CheckboxMenuItem(
3396             MessageManager.getString("label.show_all_al_annotations"));
3397     showSequenceAnnotations = new CheckboxMenuItem(
3398             MessageManager.getString("label.show_all_seq_annotations"));
3399     sortAnnBySequence = new CheckboxMenuItem(
3400             MessageManager.getString("label.sort_annotations_by_sequence"));
3401     sortAnnByLabel = new CheckboxMenuItem(
3402             MessageManager.getString("label.sort_annotations_by_label"));
3403     showAutoFirst = new CheckboxMenuItem(
3404             MessageManager.getString("label.show_first"));
3405     showAutoFirst.setState(false); // pending applet parameter
3406     setShowAutoCalculatedAbove(showAutoFirst.getState());
3407     showAutoLast = new CheckboxMenuItem(
3408             MessageManager.getString("label.show_last"));
3409     showAutoLast.setState(!showAutoFirst.getState());
3410     showAlignmentAnnotations.addItemListener(this);
3411     showSequenceAnnotations.addItemListener(this);
3412     sortAnnBySequence.addItemListener(this);
3413     sortAnnByLabel.addItemListener(this);
3414     showAutoFirst.addItemListener(this);
3415     showAutoLast.addItemListener(this);
3416
3417     /*
3418      * Configure Format menu items and actions
3419      */
3420     font.setLabel(MessageManager.getString("action.font"));
3421     font.addActionListener(this);
3422     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3423     scaleAbove.setState(true);
3424     scaleAbove.setEnabled(false);
3425     scaleAbove.addItemListener(this);
3426     scaleLeft.setEnabled(false);
3427     scaleLeft.setState(true);
3428     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3429     scaleLeft.addItemListener(this);
3430     scaleRight.setEnabled(false);
3431     scaleRight.setState(true);
3432     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3433     scaleRight.addItemListener(this);
3434     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3435     viewBoxesMenuItem.setState(true);
3436     viewBoxesMenuItem.addItemListener(this);
3437     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3438     viewTextMenuItem.setState(true);
3439     viewTextMenuItem.addItemListener(this);
3440     colourTextMenuItem.setLabel(MessageManager
3441             .getString("label.colour_text"));
3442     colourTextMenuItem.addItemListener(this);
3443     displayNonconservedMenuItem.setLabel(MessageManager
3444             .getString("label.show_non_conversed"));
3445     displayNonconservedMenuItem.addItemListener(this);
3446     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3447     wrapMenuItem.addItemListener(this);
3448     renderGapsMenuItem.setLabel(MessageManager
3449             .getString("action.show_gaps"));
3450     renderGapsMenuItem.setState(true);
3451     renderGapsMenuItem.addItemListener(this);
3452     centreColumnLabelFlag.setLabel(MessageManager
3453             .getString("label.centre_column_labels"));
3454     centreColumnLabelFlag.addItemListener(this);
3455     seqLimits.setState(true);
3456     seqLimits.setLabel(MessageManager
3457             .getString("label.show_sequence_limits"));
3458     seqLimits.addItemListener(this);
3459
3460     /*
3461      * Configure Colour menu items and actions
3462      */
3463     applyToAllGroups.setLabel(MessageManager
3464             .getString("label.apply_colour_to_all_groups"));
3465     applyToAllGroups.setState(true);
3466     applyToAllGroups.addItemListener(this);
3467     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3468     clustalColour.addActionListener(this);
3469     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3470     zappoColour.addActionListener(this);
3471     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3472     taylorColour.addActionListener(this);
3473     hydrophobicityColour.setLabel(MessageManager
3474             .getString("label.hydrophobicity"));
3475     hydrophobicityColour.addActionListener(this);
3476     helixColour
3477             .setLabel(MessageManager.getString("label.helix_propensity"));
3478     helixColour.addActionListener(this);
3479     strandColour.setLabel(MessageManager
3480             .getString("label.strand_propensity"));
3481     strandColour.addActionListener(this);
3482     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3483     turnColour.addActionListener(this);
3484     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3485     buriedColour.addActionListener(this);
3486     purinePyrimidineColour.setLabel(MessageManager
3487             .getString("label.purine_pyrimidine"));
3488     purinePyrimidineColour.addActionListener(this);
3489     // RNAInteractionColour.setLabel(MessageManager
3490     // .getString("label.rna_interaction"));
3491     // RNAInteractionColour.addActionListener(this);
3492     RNAHelixColour.setLabel(MessageManager
3493             .getString("action.by_rna_helixes"));
3494     RNAHelixColour.addActionListener(this);
3495     userDefinedColour.setLabel(MessageManager
3496             .getString("action.user_defined"));
3497     userDefinedColour.addActionListener(this);
3498     PIDColour.setLabel(MessageManager
3499             .getString("label.percentage_identity"));
3500     PIDColour.addActionListener(this);
3501     BLOSUM62Colour.setLabel(MessageManager
3502             .getString("label.blosum62_score"));
3503     BLOSUM62Colour.addActionListener(this);
3504     tcoffeeColour
3505             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3506     // it will be enabled only if a score file is provided
3507     tcoffeeColour.setEnabled(false);
3508     tcoffeeColour.addActionListener(this);
3509     conservationMenuItem.setLabel(MessageManager
3510             .getString("action.by_conservation"));
3511     conservationMenuItem.addItemListener(this);
3512     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3513     noColourmenuItem.addActionListener(this);
3514     abovePIDThreshold.setLabel(MessageManager
3515             .getString("label.above_identity_threshold"));
3516     abovePIDThreshold.addItemListener(this);
3517     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3518     nucleotideColour.addActionListener(this);
3519     modifyPID.setLabel(MessageManager
3520             .getString("label.modify_identity_threshold"));
3521     modifyPID.addActionListener(this);
3522     modifyConservation.setLabel(MessageManager
3523             .getString("label.modify_conservation_threshold"));
3524     modifyConservation.addActionListener(this);
3525     annotationColour.setLabel(MessageManager
3526             .getString("action.by_annotation"));
3527     annotationColour.addActionListener(this);
3528
3529     /*
3530      * Configure Calculate menu items and actions
3531      */
3532     sortPairwiseMenuItem.setLabel(MessageManager
3533             .getString("action.by_pairwise_id"));
3534     sortPairwiseMenuItem.addActionListener(this);
3535     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3536     sortIDMenuItem.addActionListener(this);
3537     sortLengthMenuItem.setLabel(MessageManager
3538             .getString("action.by_length"));
3539     sortLengthMenuItem.addActionListener(this);
3540     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3541     sortGroupMenuItem.addActionListener(this);
3542     pairwiseAlignmentMenuItem.setLabel(MessageManager
3543             .getString("action.pairwise_alignment"));
3544     pairwiseAlignmentMenuItem.addActionListener(this);
3545     PCAMenuItem.setLabel(MessageManager
3546             .getString("label.principal_component_analysis"));
3547     PCAMenuItem.addActionListener(this);
3548     autoCalculate = new CheckboxMenuItem(
3549             MessageManager.getString("label.autocalculate_consensus"), true);
3550     averageDistanceTreeMenuItem.setLabel(MessageManager
3551             .getString("label.average_distance_identity"));
3552     averageDistanceTreeMenuItem.addActionListener(this);
3553     neighbourTreeMenuItem.setLabel(MessageManager
3554             .getString("label.neighbour_joining_identity"));
3555     neighbourTreeMenuItem.addActionListener(this);
3556     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3557             .getString("label.average_distance_bloslum62"));
3558     avDistanceTreeBlosumMenuItem.addActionListener(this);
3559     njTreeBlosumMenuItem.setLabel(MessageManager
3560             .getString("label.neighbour_blosum62"));
3561     njTreeBlosumMenuItem.addActionListener(this);
3562     sortByTreeMenu.setLabel(MessageManager
3563             .getString("action.by_tree_order"));
3564     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3565     Menu calculateTreeMenu = new Menu(
3566             MessageManager.getString("action.calculate_tree"));
3567     autoCalculate.addItemListener(this);
3568     sortByTree.addItemListener(this);
3569
3570     /*
3571      * Configure Help menu items and actions
3572      */
3573     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3574     documentation.setLabel(MessageManager.getString("label.documentation"));
3575     documentation.addActionListener(this);
3576     about.setLabel(MessageManager.getString("label.about"));
3577     about.addActionListener(this);
3578
3579     /*
3580      * Add top level menus to frame
3581      */
3582     alignFrameMenuBar.add(fileMenu);
3583     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3584     alignFrameMenuBar.add(editMenu);
3585     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3586     alignFrameMenuBar.add(selectMenu);
3587     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3588     alignFrameMenuBar.add(viewMenu);
3589     Menu annotationsMenu = new Menu(
3590             MessageManager.getString("action.annotations"));
3591     alignFrameMenuBar.add(annotationsMenu);
3592     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3593     alignFrameMenuBar.add(formatMenu);
3594     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3595     alignFrameMenuBar.add(colourMenu);
3596     Menu calculateMenu = new Menu(
3597             MessageManager.getString("action.calculate"));
3598     alignFrameMenuBar.add(calculateMenu);
3599     alignFrameMenuBar.add(helpMenu);
3600
3601     /*
3602      * File menu
3603      */
3604     fileMenu.add(inputText);
3605     fileMenu.add(loadTree);
3606     fileMenu.add(loadAnnotations);
3607     fileMenu.addSeparator();
3608     fileMenu.add(outputTextboxMenu);
3609     fileMenu.add(outputFeatures);
3610     fileMenu.add(outputAnnotations);
3611     if (jalviewServletURL != null)
3612     {
3613       fileMenu.add(loadApplication);
3614     }
3615     fileMenu.addSeparator();
3616     fileMenu.add(closeMenuItem);
3617
3618     /*
3619      * Edit menu
3620      */
3621     editMenu.add(undoMenuItem);
3622     editMenu.add(redoMenuItem);
3623     editMenu.add(cut);
3624     editMenu.add(copy);
3625     pasteMenu.add(pasteNew);
3626     pasteMenu.add(pasteThis);
3627     editMenu.add(pasteMenu);
3628     editMenu.add(delete);
3629     editMenu.addSeparator();
3630     editMenu.add(remove2LeftMenuItem);
3631     editMenu.add(remove2RightMenuItem);
3632     editMenu.add(removeGappedColumnMenuItem);
3633     editMenu.add(removeAllGapsMenuItem);
3634     editMenu.add(removeRedundancyMenuItem);
3635
3636     /*
3637      * Select menu
3638      */
3639     selectMenu.add(findMenuItem);
3640     selectMenu.addSeparator();
3641     selectMenu.add(selectAllSequenceMenuItem);
3642     selectMenu.add(deselectAllSequenceMenuItem);
3643     selectMenu.add(invertSequenceMenuItem);
3644     selectMenu.add(invertColSel);
3645     selectMenu.add(createGroup);
3646     selectMenu.add(unGroup);
3647     selectMenu.add(grpsFromSelection);
3648     selectMenu.add(deleteGroups);
3649     selectMenu.add(annotationColumnSelection);
3650
3651     /*
3652      * View menu
3653      */
3654     viewMenu.add(newView);
3655     viewMenu.addSeparator();
3656     showMenu.add(showColumns);
3657     showMenu.add(showSeqs);
3658     showMenu.add(showAllHidden);
3659     viewMenu.add(showMenu);
3660     hideMenu.add(hideColumns);
3661     hideMenu.add(hideSequences);
3662     hideMenu.add(hideAllSelection);
3663     hideMenu.add(hideAllButSelection);
3664     viewMenu.add(hideMenu);
3665     viewMenu.addSeparator();
3666     viewMenu.add(followMouseOverFlag);
3667     viewMenu.addSeparator();
3668     viewMenu.add(sequenceFeatures);
3669     viewMenu.add(featureSettings);
3670     viewMenu.addSeparator();
3671     viewMenu.add(alProperties);
3672     viewMenu.addSeparator();
3673     viewMenu.add(overviewMenuItem);
3674
3675     /*
3676      * Annotations menu
3677      */
3678     annotationsMenu.add(annotationPanelMenuItem);
3679     annotationsMenu.addSeparator();
3680     annotationsMenu.add(showAlignmentAnnotations);
3681     annotationsMenu.add(showSequenceAnnotations);
3682     annotationsMenu.add(sortAnnBySequence);
3683     annotationsMenu.add(sortAnnByLabel);
3684     annotationsMenu.addSeparator();
3685     autoAnnMenu.add(showAutoFirst);
3686     autoAnnMenu.add(showAutoLast);
3687     autoAnnMenu.addSeparator();
3688     autoAnnMenu.add(applyAutoAnnotationSettings);
3689     autoAnnMenu.add(showConsensusHistogram);
3690     autoAnnMenu.add(showSequenceLogo);
3691     autoAnnMenu.add(normSequenceLogo);
3692     autoAnnMenu.addSeparator();
3693     autoAnnMenu.add(showGroupConservation);
3694     autoAnnMenu.add(showGroupConsensus);
3695     annotationsMenu.add(autoAnnMenu);
3696
3697     /*
3698      * Format menu
3699      */
3700     formatMenu.add(font);
3701     formatMenu.add(seqLimits);
3702     formatMenu.add(wrapMenuItem);
3703     formatMenu.add(scaleAbove);
3704     formatMenu.add(scaleLeft);
3705     formatMenu.add(scaleRight);
3706     formatMenu.add(viewBoxesMenuItem);
3707     formatMenu.add(viewTextMenuItem);
3708     formatMenu.add(colourTextMenuItem);
3709     formatMenu.add(displayNonconservedMenuItem);
3710     formatMenu.add(renderGapsMenuItem);
3711     formatMenu.add(centreColumnLabelFlag);
3712
3713     /*
3714      * Colour menu
3715      */
3716     colourMenu.add(applyToAllGroups);
3717     colourMenu.addSeparator();
3718     colourMenu.add(noColourmenuItem);
3719     colourMenu.add(clustalColour);
3720     colourMenu.add(BLOSUM62Colour);
3721     colourMenu.add(PIDColour);
3722     colourMenu.add(zappoColour);
3723     colourMenu.add(taylorColour);
3724     colourMenu.add(hydrophobicityColour);
3725     colourMenu.add(helixColour);
3726     colourMenu.add(strandColour);
3727     colourMenu.add(turnColour);
3728     colourMenu.add(buriedColour);
3729     colourMenu.add(nucleotideColour);
3730     colourMenu.add(purinePyrimidineColour);
3731     // colourMenu.add(RNAInteractionColour);
3732     colourMenu.add(tcoffeeColour);
3733     colourMenu.add(userDefinedColour);
3734     colourMenu.addSeparator();
3735     colourMenu.add(conservationMenuItem);
3736     colourMenu.add(modifyConservation);
3737     colourMenu.add(abovePIDThreshold);
3738     colourMenu.add(modifyPID);
3739     colourMenu.add(annotationColour);
3740     colourMenu.add(RNAHelixColour);
3741
3742     /*
3743      * Calculate menu
3744      */
3745     sortMenu.add(sortIDMenuItem);
3746     sortMenu.add(sortLengthMenuItem);
3747     sortMenu.add(sortByTreeMenu);
3748     sortMenu.add(sortGroupMenuItem);
3749     sortMenu.add(sortPairwiseMenuItem);
3750     calculateMenu.add(sortMenu);
3751     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3752     calculateTreeMenu.add(neighbourTreeMenuItem);
3753     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3754     calculateTreeMenu.add(njTreeBlosumMenuItem);
3755     calculateMenu.add(calculateTreeMenu);
3756     calculateMenu.addSeparator();
3757     calculateMenu.add(pairwiseAlignmentMenuItem);
3758     calculateMenu.add(PCAMenuItem);
3759     calculateMenu.add(autoCalculate);
3760     calculateMenu.add(sortByTree);
3761
3762     /*
3763      * Help menu
3764      */
3765     helpMenu.add(documentation);
3766     helpMenu.add(about);
3767
3768     /*
3769      * Status bar
3770      */
3771     statusBar.setBackground(Color.white);
3772     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3773     statusBar.setText(MessageManager.getString("label.status_bar"));
3774     this.add(statusBar, BorderLayout.SOUTH);
3775   }
3776
3777   @Override
3778   public void setStatus(String string)
3779   {
3780     statusBar.setText(string);
3781   };
3782
3783   MenuItem featureSettings = new MenuItem();
3784
3785   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3786
3787   MenuItem annotationColour = new MenuItem();
3788
3789   MenuItem annotationColumnSelection = new MenuItem();
3790
3791   MenuItem invertColSel = new MenuItem();
3792
3793   MenuItem showColumns = new MenuItem();
3794
3795   MenuItem showSeqs = new MenuItem();
3796
3797   MenuItem hideColumns = new MenuItem();
3798
3799   MenuItem hideSequences = new MenuItem();
3800
3801   MenuItem hideAllButSelection = new MenuItem();
3802
3803   MenuItem hideAllSelection = new MenuItem();
3804
3805   MenuItem showAllHidden = new MenuItem();
3806
3807   MenuItem newView = new MenuItem();
3808
3809   private CheckboxMenuItem showAlignmentAnnotations;
3810
3811   private CheckboxMenuItem showSequenceAnnotations;
3812
3813   private CheckboxMenuItem sortAnnBySequence;
3814
3815   private CheckboxMenuItem sortAnnByLabel;
3816
3817   private CheckboxMenuItem showAutoFirst;
3818
3819   private CheckboxMenuItem showAutoLast;
3820
3821   private SplitFrame splitFrame;
3822
3823   /**
3824    * Attach the alignFrame panels after embedding menus, if necessary. This used
3825    * to be called setEmbedded, but is now creates the dropdown menus in a
3826    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3827    *
3828    * @param reallyEmbedded
3829    *          true to attach the view to the applet area on the page rather than
3830    *          in a new window
3831    */
3832   public void createAlignFrameWindow(boolean reallyEmbedded)
3833   {
3834     if (reallyEmbedded)
3835     {
3836       embedAlignFrameInApplet(viewport.applet);
3837     }
3838     else
3839     {
3840       // //////
3841       // test and embed menu bar if necessary.
3842       //
3843       if (embedMenuIfNeeded(alignPanel))
3844       {
3845         /*
3846          * adjust for status bar height too. ? pointless as overridden by layout
3847          * manager
3848          */
3849         alignPanel.setSize(getSize().width,
3850                 getSize().height - statusBar.getHeight());
3851       }
3852       add(statusBar, BorderLayout.SOUTH);
3853       add(alignPanel, BorderLayout.CENTER);
3854       // and register with the applet so it can pass external API calls to us
3855       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3856               frameHeight);
3857     }
3858   }
3859
3860   /**
3861    * Add the components of this AlignFrame to the applet container.
3862    *
3863    * @param theApplet
3864    */
3865   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3866   {
3867     // ////
3868     // Explicitly build the embedded menu panel for the on-page applet
3869     //
3870     // view cannot be closed if its actually on the page
3871     fileMenu.remove(closeMenuItem);
3872     fileMenu.remove(3); // Remove Separator
3873     // construct embedded menu, using default font
3874     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3875     // and actually add the components to the applet area
3876     theApplet.setLayout(new BorderLayout());
3877     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3878     theApplet.add(statusBar, BorderLayout.SOUTH);
3879     // TODO should size be left to the layout manager?
3880     alignPanel.setSize(theApplet.getSize().width,
3881             theApplet.getSize().height - embeddedMenu.getHeight()
3882                     - statusBar.getHeight());
3883     theApplet.add(alignPanel, BorderLayout.CENTER);
3884     final AlignFrame me = this;
3885     theApplet.addFocusListener(new FocusListener()
3886     {
3887
3888       @Override
3889       public void focusLost(FocusEvent e)
3890       {
3891         if (theApplet.currentAlignFrame == me)
3892         {
3893           theApplet.currentAlignFrame = null;
3894         }
3895       }
3896
3897       @Override
3898       public void focusGained(FocusEvent e)
3899       {
3900         theApplet.currentAlignFrame = me;
3901       }
3902     });
3903     theApplet.validate();
3904   }
3905
3906   /**
3907    * create a new binding between structures in an existing jmol viewer instance
3908    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3909    * this does not open a new Jmol window, or modify the display of the
3910    * structures in the original jmol window. Note This method doesn't work
3911    * without an additional javascript library to exchange messages between the
3912    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3913    *
3914    * @param viewer
3915    *          JmolViewer instance
3916    * @param sequenceIds
3917    *          - sequence Ids to search for associations
3918    */
3919   public SequenceStructureBinding addStructureViewInstance(
3920           Object jmolviewer, String[] sequenceIds)
3921   {
3922     Viewer viewer = null;
3923     try
3924     {
3925       viewer = (Viewer) jmolviewer;
3926     } catch (ClassCastException ex)
3927     {
3928       System.err.println("Unsupported viewer object :"
3929               + jmolviewer.getClass());
3930     }
3931     if (viewer == null)
3932     {
3933       System.err.println("Can't use this object as a structure viewer:"
3934               + jmolviewer.getClass());
3935       return null;
3936     }
3937     SequenceI[] seqs = null;
3938     if (sequenceIds == null || sequenceIds.length == 0)
3939     {
3940       seqs = viewport.getAlignment().getSequencesArray();
3941     }
3942     else
3943     {
3944       Vector sqi = new Vector();
3945       AlignmentI al = viewport.getAlignment();
3946       for (int sid = 0; sid < sequenceIds.length; sid++)
3947       {
3948         SequenceI sq = al.findName(sequenceIds[sid]);
3949         if (sq != null)
3950         {
3951           sqi.addElement(sq);
3952         }
3953       }
3954       if (sqi.size() > 0)
3955       {
3956         seqs = new SequenceI[sqi.size()];
3957         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3958         {
3959           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3960         }
3961       }
3962       else
3963       {
3964         return null;
3965       }
3966     }
3967     AAStructureBindingModel jmv = null;
3968     // TODO: search for a jmv that involves viewer
3969     if (jmv == null)
3970     { // create a new viewer/jalview binding.
3971       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3972     }
3973     return jmv;
3974
3975   }
3976
3977   /**
3978    * bind a pdb file to a sequence in the current view
3979    *
3980    * @param sequenceId
3981    *          - sequenceId within the dataset.
3982    * @param pdbEntryString
3983    *          - the short name for the PDB file
3984    * @param pdbFile
3985    *          - pdb file - either a URL or a valid PDB file.
3986    * @return true if binding was as success TODO: consider making an exception
3987    *         structure for indicating when PDB parsing or sequenceId location
3988    *         fails.
3989    */
3990   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3991           String pdbFile)
3992   {
3993     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3994     boolean needtoadd = false;
3995     if (toaddpdb != null)
3996     {
3997       Vector pdbe = toaddpdb.getAllPDBEntries();
3998       PDBEntry pdbentry = null;
3999       if (pdbe != null && pdbe.size() > 0)
4000       {
4001         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4002         {
4003           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4004           if (!pdbentry.getId().equals(pdbEntryString)
4005                   && !pdbentry.getFile().equals(pdbFile))
4006           {
4007             pdbentry = null;
4008           }
4009           else
4010           {
4011             continue;
4012           }
4013         }
4014       }
4015       if (pdbentry == null)
4016       {
4017         pdbentry = new PDBEntry();
4018         pdbentry.setId(pdbEntryString);
4019         pdbentry.setFile(pdbFile);
4020         needtoadd = true; // add this new entry to sequence.
4021       }
4022       // resolve data source
4023       // TODO: this code should be a refactored to an io package
4024       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4025               pdbFile, FileFormat.PDB);
4026       if (protocol == null)
4027       {
4028         return false;
4029       }
4030       if (needtoadd)
4031       {
4032         // make a note of the access mode and add
4033         if (pdbentry.getProperty() == null)
4034         {
4035           pdbentry.setProperty(new Hashtable<String, String>());
4036         }
4037         pdbentry.getProperty().put("protocol", protocol.toString());
4038         toaddpdb.addPDBId(pdbentry);
4039         alignPanel.getStructureSelectionManager()
4040                 .registerPDBEntry(pdbentry);
4041       }
4042     }
4043     return true;
4044   }
4045
4046   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4047   {
4048     if (seqs != null)
4049     {
4050       Vector sequences = new Vector();
4051       for (int i = 0; i < seqs.length; i++)
4052       {
4053         if (seqs[i] != null)
4054         {
4055           sequences.addElement(new Object[] { seqs[i],
4056               (chains != null) ? chains[i] : null });
4057         }
4058       }
4059       seqs = new SequenceI[sequences.size()];
4060       chains = new String[sequences.size()];
4061       for (int i = 0, isize = sequences.size(); i < isize; i++)
4062       {
4063         Object[] oj = (Object[]) sequences.elementAt(i);
4064
4065         seqs[i] = (SequenceI) oj[0];
4066         chains[i] = (String) oj[1];
4067       }
4068     }
4069     return new Object[] { seqs, chains };
4070
4071   }
4072
4073   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4074           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4075   {
4076     // Scrub any null sequences from the array
4077     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4078     seqs = (SequenceI[]) sqch[0];
4079     chains = (String[]) sqch[1];
4080     if (seqs == null || seqs.length == 0)
4081     {
4082       System.err
4083               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4084     }
4085     if (protocol == null)
4086     {
4087       String sourceType = pdb.getProperty().get("protocol");
4088       try
4089       {
4090         protocol = DataSourceType.valueOf(sourceType);
4091       } catch (IllegalArgumentException e)
4092       {
4093         // ignore
4094       }
4095       if (protocol == null)
4096       {
4097         System.err.println("Couldn't work out protocol to open structure: "
4098                 + pdb.getId());
4099         return;
4100       }
4101     }
4102     if (applet.useXtrnalSviewer)
4103     {
4104       // register the association(s) and quit, don't create any windows.
4105       if (StructureSelectionManager.getStructureSelectionManager(applet)
4106               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4107       {
4108         System.err.println("Failed to map " + pdb.getFile() + " ("
4109                 + protocol + ") to any sequences");
4110       }
4111       return;
4112     }
4113     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4114     {
4115       // can only do alignments with Jmol
4116       // find the last jmol window assigned to this alignment
4117       AppletJmol ajm = null, tajm;
4118       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4119       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4120       {
4121         tajm = (AppletJmol) jmols.elementAt(i);
4122         if (tajm.ap.alignFrame == this)
4123         {
4124           ajm = tajm;
4125           break;
4126         }
4127       }
4128       if (ajm != null)
4129       {
4130         System.err
4131                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4132         // try and add the pdb structure
4133         // ajm.addS
4134         ajm = null;
4135       }
4136     }
4137     // otherwise, create a new window
4138     if (applet.jmolAvailable)
4139     {
4140       new AppletJmol(pdb, seqs, chains, alignPanel,
4141               protocol);
4142       applet.lastFrameX += 40;
4143       applet.lastFrameY += 40;
4144     }
4145     else
4146     {
4147       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4148     }
4149
4150   }
4151
4152   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4153           SequenceI[][] seqs, String[][] chains, String[] protocols)
4154   {
4155     // TODO Auto-generated method stub
4156     System.err.println("Aligned Structure View: Not yet implemented.");
4157   }
4158
4159   /**
4160    * modify the current selection, providing the user has not made a selection
4161    * already.
4162    *
4163    * @param sel
4164    *          - sequences from this alignment
4165    * @param csel
4166    *          - columns to be selected on the alignment
4167    */
4168   public void select(SequenceGroup sel, ColumnSelection csel)
4169   {
4170     alignPanel.seqPanel.selection(sel, csel, null);
4171   }
4172
4173   public void scrollTo(int row, int column)
4174   {
4175     alignPanel.seqPanel.scrollTo(row, column);
4176   }
4177
4178   public void scrollToRow(int row)
4179   {
4180     alignPanel.seqPanel.scrollToRow(row);
4181   }
4182
4183   public void scrollToColumn(int column)
4184   {
4185     alignPanel.seqPanel.scrollToColumn(column);
4186   }
4187
4188   /**
4189    * @return the alignments unique ID.
4190    */
4191   public String getSequenceSetId()
4192   {
4193     return viewport.getSequenceSetId();
4194   }
4195
4196   /**
4197    * Load the (T-Coffee) score file from the specified url
4198    *
4199    * @param source
4200    *          File/URL/T-COFFEE score file contents
4201    * @throws IOException
4202    * @return true if alignment was annotated with data from source
4203    */
4204   public boolean loadScoreFile(String source) throws IOException
4205   {
4206
4207     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4208             AppletFormatAdapter.checkProtocol(source));
4209     if (!file.isValid())
4210     {
4211       // TODO: raise dialog for gui
4212       System.err.println("Problems parsing T-Coffee scores: "
4213               + file.getWarningMessage());
4214       System.err.println("Origin was:\n" + source);
4215       return false;
4216     }
4217
4218     /*
4219      * check that the score matrix matches the alignment dimensions
4220      */
4221     AlignmentI aln;
4222     if ((aln = viewport.getAlignment()) != null
4223             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4224                     .getWidth()))
4225     {
4226       // TODO: raise a dialog box here rather than bomb out.
4227       System.err
4228               .println("The scores matrix does not match the alignment dimensions");
4229
4230     }
4231
4232     // TODO add parameter to indicate if matching should be done
4233     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4234     {
4235       alignPanel.fontChanged();
4236       tcoffeeColour.setEnabled(true);
4237       // switch to this color
4238       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4239       return true;
4240     }
4241     else
4242     {
4243       System.err.println("Problems resolving T-Coffee scores:");
4244       if (file.getWarningMessage() != null)
4245       {
4246         System.err.println(file.getWarningMessage());
4247       }
4248     }
4249     return false;
4250   }
4251
4252   public SplitFrame getSplitFrame()
4253   {
4254     return this.splitFrame;
4255   }
4256
4257   public void setSplitFrame(SplitFrame sf)
4258   {
4259     this.splitFrame = sf;
4260   }
4261
4262   // may not need this
4263   @Override
4264   public void setShowSeqFeatures(boolean b)
4265   {
4266     // showSeqFeatures.setSelected(b);
4267     viewport.setShowSequenceFeatures(b);
4268
4269   }
4270
4271   @Override
4272   public void setMenusForViewport()
4273   {
4274     // setMenusFromViewport(viewport);
4275
4276   }
4277
4278   @Override
4279   public void refreshFeatureUI(boolean enableIfNecessary)
4280   {
4281     if (enableIfNecessary)
4282     {
4283       sequenceFeatures.setState(true);
4284       alignPanel.av.setShowSequenceFeatures(true);
4285     }
4286   }
4287
4288   @Override
4289   public FeatureSettingsControllerI getFeatureSettingsUI()
4290   {
4291     return alignPanel.av.featureSettings;
4292   }
4293
4294 }