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.List;
 108 import java.util.Map;
 109 import java.util.StringTokenizer;
 110 import java.util.Vector;
 111
 112 import org.jmol.viewer.Viewer;
 113
 114 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 115         ItemListener, KeyListener, AlignViewControllerGuiI
 116 {
 117   public AlignViewControllerI avc;
 118
 119   public AlignmentPanel alignPanel;
 120
 121   public AlignViewport viewport;
 122
 123   // width and height may be overridden by applet parameters
 124   int frameWidth = 700;
 125
 126   int frameHeight = 500;
 127
 128   String jalviewServletURL;
 129
 130   /*
 131    * Flag for showing autocalculated consensus above or below other consensus
 132    * rows
 133    */
 134   private boolean showAutoCalculatedAbove;
 135
 136   private SequenceAnnotationOrder annotationSortOrder;
 137
 138   /**
 139    * Constructor that creates the frame and adds it to the display.
 140    *
 141    * @param al
 142    * @param applet
 143    * @param title
 144    * @param embedded
 145    */
 146   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 147           boolean embedded)
 148   {
 149     this(al, applet, title, embedded, true);
 150   }
 151
 152   /**
 153    * Constructor that optionally allows the frame to be displayed or only
 154    * created.
 155    *
 156    * @param al
 157    * @param applet
 158    * @param title
 159    * @param embedded
 160    * @param addToDisplay
 161    */
 162   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 163           boolean embedded, boolean addToDisplay)
 164   {
 165     this(al, null, null, applet, title, embedded, addToDisplay);
 166   }
 167
 168   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 169           ColumnSelection columnSelection, JalviewLite applet,
 170           String title, boolean embedded)
 171   {
 172     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           ColumnSelection columnSelection, JalviewLite applet,
 177           String title, boolean embedded, boolean addToDisplay)
 178   {
 179     if (applet != null)
 180     {
 181       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception ex)
 188     {
 189       ex.printStackTrace();
 190     }
 191     // need to get window geometry before we calculate alignment layout
 192     if (applet != null)
 193     {
 194       String param;
 195       try
 196       {
 197         param = applet.getParameter("windowWidth");
 198         if (param != null)
 199         {
 200           int width = Integer.parseInt(param);
 201           frameWidth = width;
 202         }
 203         param = applet.getParameter("windowHeight");
 204         if (param != null)
 205         {
 206           int height = Integer.parseInt(param);
 207           frameHeight = height;
 208         }
 209       } catch (Exception ex)
 210       {
 211       }
 212     }
 213     viewport = new AlignViewport(al, applet);
 214
 215     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 216     {
 217       viewport.hideSequence(hiddenSeqs);
 218     }
 219     if (columnSelection != null)
 220     {
 221       viewport.setColumnSelection(columnSelection);
 222     }
 223     viewport.setScaleAboveWrapped(scaleAbove.getState());
 224
 225     alignPanel = new AlignmentPanel(this, viewport);
 226     avc = new jalview.controller.AlignViewController(this, viewport,
 227             alignPanel);
 228     viewport.updateConservation(alignPanel);
 229     viewport.updateConsensus(alignPanel);
 230
 231     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 232     followMouseOverFlag.setState(viewport.isFollowHighlight());
 233     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 234     showGroupConservation.setState(viewport.isShowGroupConservation());
 235     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 236     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 237     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 238     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 239     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 240     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 242     showAlignmentAnnotations.setState(true);
 243     showSequenceAnnotations.setState(false);
 244
 245     seqLimits.setState(viewport.getShowJVSuffix());
 246
 247     if (applet != null)
 248     {
 249       String param = applet.getParameter("sortBy");
 250       if (param != null)
 251       {
 252         if (param.equalsIgnoreCase("Id"))
 253         {
 254           sortIDMenuItem_actionPerformed();
 255         }
 256         else if (param.equalsIgnoreCase("Pairwise Identity"))
 257         {
 258           sortPairwiseMenuItem_actionPerformed();
 259         }
 260         else if (param.equalsIgnoreCase("Length"))
 261         {
 262           sortLengthMenuItem_actionPerformed();
 263         }
 264       }
 265
 266       param = applet.getParameter("wrap");
 267       if (param != null)
 268       {
 269         if (param.equalsIgnoreCase("true"))
 270         {
 271           wrapMenuItem.setState(true);
 272           wrapMenuItem_actionPerformed();
 273         }
 274       }
 275       param = applet.getParameter("centrecolumnlabels");
 276       if (param != null)
 277       {
 278         centreColumnLabelFlag.setState(true);
 279         centreColumnLabelFlag_stateChanged();
 280       }
 281
 282     }
 283     if (viewport.getAlignment().isNucleotide())
 284     {
 285       viewport.updateStrucConsensus(alignPanel);
 286       if (viewport.getAlignment().hasRNAStructure())
 287       {
 288         RNAHelixColour.setEnabled(true);
 289       }
 290       else
 291       {
 292         RNAHelixColour.setEnabled(false);
 293       }
 294     }
 295     else
 296     {
 297       RNAHelixColour.setEnabled(false);
 298       purinePyrimidineColour.setEnabled(false);
 299       nucleotideColour.setEnabled(false);
 300     }
 301     // Some JVMS send keyevents to Top frame or lowest panel,
 302     // Havent worked out why yet. So add to both this frame and seqCanvas for
 303     // now
 304     this.addKeyListener(this);
 305     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 306     alignPanel.idPanel.idCanvas.addKeyListener(this);
 307     alignPanel.scalePanel.addKeyListener(this);
 308     alignPanel.annotationPanel.addKeyListener(this);
 309     alignPanel.annotationPanelHolder.addKeyListener(this);
 310     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 311     alignPanel.alabels.addKeyListener(this);
 312
 313     setAnnotationsVisibility();
 314
 315     if (addToDisplay)
 316     {
 317       addToDisplay(embedded);
 318     }
 319   }
 320
 321   /**
 322    * @param embedded
 323    */
 324   public void addToDisplay(boolean embedded)
 325   {
 326     createAlignFrameWindow(embedded);
 327     validate();
 328     alignPanel.adjustAnnotationHeight();
 329     alignPanel.paintAlignment(true);
 330   }
 331
 332   public AlignViewport getAlignViewport()
 333   {
 334     return viewport;
 335   }
 336
 337   public SeqCanvas getSeqcanvas()
 338   {
 339     return alignPanel.seqPanel.seqCanvas;
 340   }
 341
 342   /**
 343    * Load a features file onto the alignment
 344    *
 345    * @param file
 346    *          file URL, content, or other resolvable path
 347    * @param type
 348    *          is protocol for accessing data referred to by file
 349    */
 350
 351   public boolean parseFeaturesFile(String file, DataSourceType type)
 352   {
 353     return parseFeaturesFile(file, type, true);
 354   }
 355
 356   /**
 357    * Load a features file onto the alignment
 358    *
 359    * @param file
 360    *          file URL, content, or other resolvable path
 361    * @param sourceType
 362    *          is protocol for accessing data referred to by file
 363    * @param autoenabledisplay
 364    *          when true, display features flag will be automatically enabled if
 365    *          features are loaded
 366    * @return true if data parsed as a features file
 367    */
 368   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 369           boolean autoenabledisplay)
 370   {
 371     boolean featuresFile = false;
 372     try
 373     {
 374       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 375               .getFeatureRenderer().getFeatureColours();
 376       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 377               "relaxedidmatch", false);
 378       featuresFile = new FeaturesFile(file, sourceType).parse(
 379               viewport.getAlignment(), colours, true, relaxedIdMatching);
 380     } catch (Exception ex)
 381     {
 382       ex.printStackTrace();
 383     }
 384
 385     if (featuresFile)
 386     {
 387       if (autoenabledisplay)
 388       {
 389         viewport.setShowSequenceFeatures(true);
 390         sequenceFeatures.setState(true);
 391       }
 392       if (alignPanel.seqPanel.seqCanvas.fr != null)
 393       {
 394         // update the min/max ranges where necessary
 395         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 396       }
 397       if (viewport.featureSettings != null)
 398       {
 399         viewport.featureSettings.refreshTable();
 400       }
 401       alignPanel.paintAlignment(true);
 402       statusBar.setText(MessageManager
 403               .getString("label.successfully_added_features_alignment"));
 404     }
 405     return featuresFile;
 406   }
 407
 408   @Override
 409   public void keyPressed(KeyEvent evt)
 410   {
 411     if (viewport.cursorMode
 412             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 413                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 414                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 415             && Character.isDigit(evt.getKeyChar()))
 416     {
 417       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 418     }
 419
 420     switch (evt.getKeyCode())
 421     {
 422     case 27: // escape key
 423       deselectAllSequenceMenuItem_actionPerformed();
 424
 425       alignPanel.alabels.cancelDrag();
 426       break;
 427     case KeyEvent.VK_X:
 428       if (evt.isControlDown() || evt.isMetaDown())
 429       {
 430         cut_actionPerformed();
 431       }
 432       break;
 433     case KeyEvent.VK_C:
 434       if (viewport.cursorMode && !evt.isControlDown())
 435       {
 436         alignPanel.seqPanel.setCursorColumn();
 437       }
 438       if (evt.isControlDown() || evt.isMetaDown())
 439       {
 440         copy_actionPerformed();
 441       }
 442       break;
 443     case KeyEvent.VK_V:
 444       if (evt.isControlDown())
 445       {
 446         paste(evt.isShiftDown());
 447       }
 448       break;
 449     case KeyEvent.VK_A:
 450       if (evt.isControlDown() || evt.isMetaDown())
 451       {
 452         selectAllSequenceMenuItem_actionPerformed();
 453       }
 454       break;
 455     case KeyEvent.VK_DOWN:
 456       if (viewport.cursorMode)
 457       {
 458         alignPanel.seqPanel.moveCursor(0, 1);
 459       }
 460       else
 461       {
 462         moveSelectedSequences(false);
 463       }
 464       break;
 465
 466     case KeyEvent.VK_UP:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.moveCursor(0, -1);
 470       }
 471       else
 472       {
 473         moveSelectedSequences(true);
 474       }
 475       break;
 476
 477     case KeyEvent.VK_LEFT:
 478       if (evt.isAltDown() || !viewport.cursorMode)
 479       {
 480         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 481       }
 482       else
 483       {
 484         alignPanel.seqPanel.moveCursor(-1, 0);
 485       }
 486       break;
 487
 488     case KeyEvent.VK_RIGHT:
 489       if (evt.isAltDown() || !viewport.cursorMode)
 490       {
 491         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 492       }
 493       else
 494       {
 495         alignPanel.seqPanel.moveCursor(1, 0);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_SPACE:
 500       if (viewport.cursorMode)
 501       {
 502         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 503                 || evt.isShiftDown() || evt.isAltDown());
 504       }
 505       break;
 506
 507     case KeyEvent.VK_DELETE:
 508     case KeyEvent.VK_BACK_SPACE:
 509       if (viewport.cursorMode)
 510       {
 511         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 512                 || evt.isShiftDown() || evt.isAltDown());
 513       }
 514       else
 515       {
 516         cut_actionPerformed();
 517         alignPanel.seqPanel.seqCanvas.repaint();
 518       }
 519       break;
 520
 521     case KeyEvent.VK_S:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.setCursorRow();
 525       }
 526       break;
 527     case KeyEvent.VK_P:
 528       if (viewport.cursorMode)
 529       {
 530         alignPanel.seqPanel.setCursorPosition();
 531       }
 532       break;
 533
 534     case KeyEvent.VK_ENTER:
 535     case KeyEvent.VK_COMMA:
 536       if (viewport.cursorMode)
 537       {
 538         alignPanel.seqPanel.setCursorRowAndColumn();
 539       }
 540       break;
 541
 542     case KeyEvent.VK_Q:
 543       if (viewport.cursorMode)
 544       {
 545         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 546       }
 547       break;
 548     case KeyEvent.VK_M:
 549       if (viewport.cursorMode)
 550       {
 551         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 552       }
 553       break;
 554
 555     case KeyEvent.VK_F2:
 556       viewport.cursorMode = !viewport.cursorMode;
 557       statusBar.setText(MessageManager.formatMessage(
 558               "label.keyboard_editing_mode",
 559               new String[] { (viewport.cursorMode ? "on" : "off") }));
 560       if (viewport.cursorMode)
 561       {
 562         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 563         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 564       }
 565       break;
 566
 567     case KeyEvent.VK_F:
 568       if (evt.isControlDown())
 569       {
 570         findMenuItem_actionPerformed();
 571       }
 572       break;
 573
 574     case KeyEvent.VK_H:
 575     {
 576       boolean toggleSeqs = !evt.isControlDown();
 577       boolean toggleCols = !evt.isShiftDown();
 578       toggleHiddenRegions(toggleSeqs, toggleCols);
 579       break;
 580     }
 581
 582     case KeyEvent.VK_PAGE_UP:
 583       if (viewport.getWrapAlignment())
 584       {
 585         alignPanel.scrollUp(true);
 586       }
 587       else
 588       {
 589         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 590                 - viewport.endSeq + viewport.startSeq);
 591       }
 592       break;
 593
 594     case KeyEvent.VK_PAGE_DOWN:
 595       if (viewport.getWrapAlignment())
 596       {
 597         alignPanel.scrollUp(false);
 598       }
 599       else
 600       {
 601         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 602                 + viewport.endSeq - viewport.startSeq);
 603       }
 604       break;
 605
 606     case KeyEvent.VK_Z:
 607       if (evt.isControlDown())
 608       {
 609         undoMenuItem_actionPerformed();
 610       }
 611       break;
 612
 613     case KeyEvent.VK_Y:
 614       if (evt.isControlDown())
 615       {
 616         redoMenuItem_actionPerformed();
 617       }
 618       break;
 619
 620     case KeyEvent.VK_L:
 621       if (evt.isControlDown())
 622       {
 623         trimAlignment(true);
 624       }
 625       break;
 626
 627     case KeyEvent.VK_R:
 628       if (evt.isControlDown())
 629       {
 630         trimAlignment(false);
 631       }
 632       break;
 633
 634     case KeyEvent.VK_E:
 635       if (evt.isControlDown())
 636       {
 637         if (evt.isShiftDown())
 638         {
 639           this.removeAllGapsMenuItem_actionPerformed();
 640         }
 641         else
 642         {
 643           removeGappedColumnMenuItem_actionPerformed();
 644         }
 645       }
 646       break;
 647     case KeyEvent.VK_I:
 648       if (evt.isControlDown())
 649       {
 650         if (evt.isAltDown())
 651         {
 652           invertColSel_actionPerformed();
 653         }
 654         else
 655         {
 656           invertSequenceMenuItem_actionPerformed();
 657         }
 658       }
 659       break;
 660
 661     case KeyEvent.VK_G:
 662       if (evt.isControlDown())
 663       {
 664         if (evt.isShiftDown())
 665         {
 666           this.unGroup_actionPerformed();
 667         }
 668         else
 669         {
 670           this.createGroup_actionPerformed();
 671         }
 672       }
 673       break;
 674
 675     case KeyEvent.VK_U:
 676       if (evt.isControlDown())
 677       {
 678         this.deleteGroups_actionPerformed();
 679       }
 680       break;
 681
 682     case KeyEvent.VK_T:
 683       if (evt.isControlDown())
 684       {
 685         newView(null);
 686       }
 687       break;
 688
 689     }
 690     alignPanel.paintAlignment(true);
 691   }
 692
 693   /**
 694    * called by key handler and the hide all/show all menu items
 695    *
 696    * @param toggleSeqs
 697    * @param toggleCols
 698    */
 699   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 700   {
 701     boolean hide = false;
 702     SequenceGroup sg = viewport.getSelectionGroup();
 703     if (!toggleSeqs && !toggleCols)
 704     {
 705       // Hide everything by the current selection - this is a hack - we do the
 706       // invert and then hide
 707       // first check that there will be visible columns after the invert.
 708       if (viewport.hasSelectedColumns()
 709               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 710                       .getEndRes()))
 711       {
 712         // now invert the sequence set, if required - empty selection implies
 713         // that no hiding is required.
 714         if (sg != null)
 715         {
 716           invertSequenceMenuItem_actionPerformed();
 717           sg = viewport.getSelectionGroup();
 718           toggleSeqs = true;
 719
 720         }
 721         viewport.expandColSelection(sg, true);
 722         // finally invert the column selection and get the new sequence
 723         // selection and indicate it should be hidden.
 724         invertColSel_actionPerformed();
 725         toggleCols = true;
 726       }
 727     }
 728
 729     if (toggleSeqs)
 730     {
 731       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 732       {
 733         hide = true;
 734         viewport.hideAllSelectedSeqs();
 735       }
 736       else if (!(toggleCols && viewport.hasSelectedColumns()))
 737       {
 738         viewport.showAllHiddenSeqs();
 739       }
 740     }
 741
 742     if (toggleCols)
 743     {
 744       if (viewport.hasSelectedColumns())
 745       {
 746         viewport.hideSelectedColumns();
 747         if (!toggleSeqs)
 748         {
 749           viewport.setSelectionGroup(sg);
 750         }
 751       }
 752       else if (!hide)
 753       {
 754         viewport.showAllHiddenColumns();
 755       }
 756       viewport.sendSelection();
 757     }
 758   }
 759
 760   @Override
 761   public void keyReleased(KeyEvent evt)
 762   {
 763   }
 764
 765   @Override
 766   public void keyTyped(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void itemStateChanged(ItemEvent evt)
 772   {
 773     final Object source = evt.getSource();
 774     if (source == displayNonconservedMenuItem)
 775     {
 776       displayNonconservedMenuItem_actionPerformed();
 777     }
 778     else if (source == colourTextMenuItem)
 779     {
 780       colourTextMenuItem_actionPerformed();
 781     }
 782     else if (source == wrapMenuItem)
 783     {
 784       wrapMenuItem_actionPerformed();
 785     }
 786     else if (source == scaleAbove)
 787     {
 788       viewport.setScaleAboveWrapped(scaleAbove.getState());
 789     }
 790     else if (source == scaleLeft)
 791     {
 792       viewport.setScaleLeftWrapped(scaleLeft.getState());
 793     }
 794     else if (source == scaleRight)
 795     {
 796       viewport.setScaleRightWrapped(scaleRight.getState());
 797     }
 798     else if (source == seqLimits)
 799     {
 800       seqLimits_itemStateChanged();
 801     }
 802     else if (source == viewBoxesMenuItem)
 803     {
 804       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 805     }
 806     else if (source == viewTextMenuItem)
 807     {
 808       viewport.setShowText(viewTextMenuItem.getState());
 809     }
 810     else if (source == renderGapsMenuItem)
 811     {
 812       viewport.setRenderGaps(renderGapsMenuItem.getState());
 813     }
 814     else if (source == annotationPanelMenuItem)
 815     {
 816       boolean showAnnotations = annotationPanelMenuItem.getState();
 817       showAlignmentAnnotations.setEnabled(showAnnotations);
 818       showSequenceAnnotations.setEnabled(showAnnotations);
 819       viewport.setShowAnnotation(showAnnotations);
 820       alignPanel.setAnnotationVisible(showAnnotations);
 821     }
 822     else if (source == sequenceFeatures)
 823     {
 824       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 825       alignPanel.seqPanel.seqCanvas.repaint();
 826     }
 827     else if (source == showAlignmentAnnotations)
 828     {
 829       setAnnotationsVisibility();
 830     }
 831     else if (source == showSequenceAnnotations)
 832     {
 833       setAnnotationsVisibility();
 834     }
 835     else if (source == sortAnnBySequence)
 836     {
 837       boolean newState = sortAnnBySequence.getState();
 838       sortAnnByLabel.setState(false);
 839       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 840               : SequenceAnnotationOrder.NONE);
 841       setViewportAnnotationOrder();
 842     }
 843     else if (source == sortAnnByLabel)
 844     {
 845       boolean newState = sortAnnByLabel.getState();
 846       sortAnnBySequence.setState(false);
 847       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 848               : SequenceAnnotationOrder.NONE);
 849       setViewportAnnotationOrder();
 850     }
 851     else if (source == showAutoFirst)
 852     {
 853       showAutoLast.setState(!showAutoFirst.getState());
 854       setShowAutoCalculatedAbove(showAutoFirst.getState());
 855       setViewportAnnotationOrder();
 856     }
 857     else if (source == showAutoLast)
 858     {
 859       showAutoFirst.setState(!showAutoLast.getState());
 860       setShowAutoCalculatedAbove(showAutoFirst.getState());
 861       setViewportAnnotationOrder();
 862     }
 863     else if (source == conservationMenuItem)
 864     {
 865       conservationMenuItem_actionPerformed();
 866     }
 867     else if (source == abovePIDThreshold)
 868     {
 869       abovePIDThreshold_actionPerformed();
 870     }
 871     else if (source == applyToAllGroups)
 872     {
 873       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 874     }
 875     else if (source == autoCalculate)
 876     {
 877       viewport.autoCalculateConsensus = autoCalculate.getState();
 878     }
 879     else if (source == sortByTree)
 880     {
 881       viewport.sortByTree = sortByTree.getState();
 882     }
 883     else if (source == this.centreColumnLabelFlag)
 884     {
 885       centreColumnLabelFlag_stateChanged();
 886     }
 887     else if (source == this.followMouseOverFlag)
 888     {
 889       mouseOverFlag_stateChanged();
 890     }
 891     else if (source == showGroupConsensus)
 892     {
 893       showGroupConsensus_actionPerformed();
 894     }
 895     else if (source == showGroupConservation)
 896     {
 897       showGroupConservation_actionPerformed();
 898     }
 899     else if (source == showSequenceLogo)
 900     {
 901       showSequenceLogo_actionPerformed();
 902     }
 903     else if (source == normSequenceLogo)
 904     {
 905       normSequenceLogo_actionPerformed();
 906     }
 907     else if (source == showConsensusHistogram)
 908     {
 909       showConsensusHistogram_actionPerformed();
 910     }
 911     else if (source == applyAutoAnnotationSettings)
 912     {
 913       applyAutoAnnotationSettings_actionPerformed();
 914     }
 915     alignPanel.paintAlignment(true);
 916   }
 917
 918   /**
 919    * Set the visibility state of sequence-related and/or alignment-related
 920    * annotations depending on checkbox selections, and repaint.
 921    *
 922    * @param visible
 923    */
 924   private void setAnnotationsVisibility()
 925   {
 926     boolean showForAlignment = showAlignmentAnnotations.getState();
 927     boolean showForSequences = showSequenceAnnotations.getState();
 928     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 929     {
 930       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 931               .getAlignmentAnnotation())
 932       {
 933         boolean visible = (aa.sequenceRef == null ? showForAlignment
 934                 : showForSequences);
 935         aa.visible = visible;
 936       }
 937     }
 938     alignPanel.validateAnnotationDimensions(true);
 939     validate();
 940     repaint();
 941   }
 942
 943   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 944   {
 945     this.annotationSortOrder = order;
 946   }
 947
 948   /**
 949    * Set flags on the viewport that control annotation ordering
 950    */
 951   private void setViewportAnnotationOrder()
 952   {
 953     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 954     this.alignPanel.av
 955             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 956   }
 957
 958   private void setShowAutoCalculatedAbove(boolean showAbove)
 959   {
 960     this.showAutoCalculatedAbove = showAbove;
 961   }
 962
 963   private void mouseOverFlag_stateChanged()
 964   {
 965     viewport.setFollowHighlight(followMouseOverFlag.getState());
 966     // TODO: could kick the scrollTo mechanism to reset view for current
 967     // searchresults.
 968   }
 969
 970   private void centreColumnLabelFlag_stateChanged()
 971   {
 972     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 973     this.alignPanel.annotationPanel.repaint();
 974   }
 975
 976   @Override
 977   public void actionPerformed(ActionEvent evt)
 978   {
 979     viewport.applet.currentAlignFrame = this;
 980
 981     Object source = evt.getSource();
 982
 983     if (source == inputText)
 984     {
 985       inputText_actionPerformed();
 986     }
 987     else if (source == loadTree)
 988     {
 989       loadTree_actionPerformed();
 990     }
 991     else if (source == loadApplication)
 992     {
 993       launchFullApplication();
 994     }
 995     else if (source == loadAnnotations)
 996     {
 997       loadAnnotations();
 998     }
 999     else if (source == outputAnnotations)
1000     {
1001       outputAnnotations(true);
1002     }
1003     else if (source == outputFeatures)
1004     {
1005       outputFeatures(true, "Jalview");
1006     }
1007     else if (source == closeMenuItem)
1008     {
1009       closeMenuItem_actionPerformed();
1010     }
1011     else if (source == copy)
1012     {
1013       copy_actionPerformed();
1014     }
1015     else if (source == undoMenuItem)
1016     {
1017       undoMenuItem_actionPerformed();
1018     }
1019     else if (source == redoMenuItem)
1020     {
1021       redoMenuItem_actionPerformed();
1022     }
1023     else if (source == inputText)
1024     {
1025       inputText_actionPerformed();
1026     }
1027     else if (source == closeMenuItem)
1028     {
1029       closeMenuItem_actionPerformed();
1030     }
1031     else if (source == undoMenuItem)
1032     {
1033       undoMenuItem_actionPerformed();
1034     }
1035     else if (source == redoMenuItem)
1036     {
1037       redoMenuItem_actionPerformed();
1038     }
1039     else if (source == copy)
1040     {
1041       copy_actionPerformed();
1042     }
1043     else if (source == pasteNew)
1044     {
1045       pasteNew_actionPerformed();
1046     }
1047     else if (source == pasteThis)
1048     {
1049       pasteThis_actionPerformed();
1050     }
1051     else if (source == cut)
1052     {
1053       cut_actionPerformed();
1054     }
1055     else if (source == delete)
1056     {
1057       delete_actionPerformed();
1058     }
1059     else if (source == grpsFromSelection)
1060     {
1061       makeGrpsFromSelection_actionPerformed();
1062     }
1063     else if (source == deleteGroups)
1064     {
1065       deleteGroups_actionPerformed();
1066     }
1067     else if (source == selectAllSequenceMenuItem)
1068     {
1069       selectAllSequenceMenuItem_actionPerformed();
1070     }
1071     else if (source == deselectAllSequenceMenuItem)
1072     {
1073       deselectAllSequenceMenuItem_actionPerformed();
1074     }
1075     else if (source == invertSequenceMenuItem)
1076     {
1077       invertSequenceMenuItem_actionPerformed();
1078       // uncomment to slave sequence selections in split frame
1079       // viewport.sendSelection();
1080     }
1081     else if (source == invertColSel)
1082     {
1083       viewport.invertColumnSelection();
1084       alignPanel.paintAlignment(true);
1085       viewport.sendSelection();
1086     }
1087     else if (source == remove2LeftMenuItem)
1088     {
1089       trimAlignment(true);
1090     }
1091     else if (source == remove2RightMenuItem)
1092     {
1093       trimAlignment(false);
1094     }
1095     else if (source == removeGappedColumnMenuItem)
1096     {
1097       removeGappedColumnMenuItem_actionPerformed();
1098     }
1099     else if (source == removeAllGapsMenuItem)
1100     {
1101       removeAllGapsMenuItem_actionPerformed();
1102     }
1103     else if (source == findMenuItem)
1104     {
1105       findMenuItem_actionPerformed();
1106     }
1107     else if (source == font)
1108     {
1109       new FontChooser(alignPanel);
1110     }
1111     else if (source == newView)
1112     {
1113       newView(null);
1114     }
1115     else if (source == showColumns)
1116     {
1117       viewport.showAllHiddenColumns();
1118       alignPanel.paintAlignment(true);
1119       viewport.sendSelection();
1120     }
1121     else if (source == showSeqs)
1122     {
1123       viewport.showAllHiddenSeqs();
1124       alignPanel.paintAlignment(true);
1125       // uncomment if we want to slave sequence selections in split frame
1126       // viewport.sendSelection();
1127     }
1128     else if (source == hideColumns)
1129     {
1130       viewport.hideSelectedColumns();
1131       alignPanel.paintAlignment(true);
1132       viewport.sendSelection();
1133     }
1134     else if (source == hideSequences
1135             && viewport.getSelectionGroup() != null)
1136     {
1137       viewport.hideAllSelectedSeqs();
1138       alignPanel.paintAlignment(true);
1139       // uncomment if we want to slave sequence selections in split frame
1140       // viewport.sendSelection();
1141     }
1142     else if (source == hideAllButSelection)
1143     {
1144       toggleHiddenRegions(false, false);
1145       alignPanel.paintAlignment(true);
1146       viewport.sendSelection();
1147     }
1148     else if (source == hideAllSelection)
1149     {
1150       SequenceGroup sg = viewport.getSelectionGroup();
1151       viewport.expandColSelection(sg, false);
1152       viewport.hideAllSelectedSeqs();
1153       viewport.hideSelectedColumns();
1154       alignPanel.paintAlignment(true);
1155       viewport.sendSelection();
1156     }
1157     else if (source == showAllHidden)
1158     {
1159       viewport.showAllHiddenColumns();
1160       viewport.showAllHiddenSeqs();
1161       alignPanel.paintAlignment(true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == showGroupConsensus)
1165     {
1166       showGroupConsensus_actionPerformed();
1167     }
1168     else if (source == showGroupConservation)
1169     {
1170       showGroupConservation_actionPerformed();
1171     }
1172     else if (source == showSequenceLogo)
1173     {
1174       showSequenceLogo_actionPerformed();
1175     }
1176     else if (source == normSequenceLogo)
1177     {
1178       normSequenceLogo_actionPerformed();
1179     }
1180     else if (source == showConsensusHistogram)
1181     {
1182       showConsensusHistogram_actionPerformed();
1183     }
1184     else if (source == applyAutoAnnotationSettings)
1185     {
1186       applyAutoAnnotationSettings_actionPerformed();
1187     }
1188     else if (source == featureSettings)
1189     {
1190       new FeatureSettings(alignPanel);
1191     }
1192     else if (source == alProperties)
1193     {
1194       StringBuffer contents = new jalview.io.AlignmentProperties(
1195               viewport.getAlignment()).formatAsString();
1196       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1197       cap.setText(contents.toString());
1198       Frame frame = new Frame();
1199       frame.add(cap);
1200       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1201               "label.alignment_properties", new String[] { getTitle() }),
1202               400, 250);
1203     }
1204     else if (source == overviewMenuItem)
1205     {
1206       overviewMenuItem_actionPerformed();
1207     }
1208     else if (source == noColourmenuItem)
1209     {
1210       changeColour(null);
1211     }
1212     else if (source == clustalColour)
1213     {
1214       abovePIDThreshold.setState(false);
1215       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1216     }
1217     else if (source == zappoColour)
1218     {
1219       changeColour(new ZappoColourScheme());
1220     }
1221     else if (source == taylorColour)
1222     {
1223       changeColour(new TaylorColourScheme());
1224     }
1225     else if (source == hydrophobicityColour)
1226     {
1227       changeColour(new HydrophobicColourScheme());
1228     }
1229     else if (source == helixColour)
1230     {
1231       changeColour(new HelixColourScheme());
1232     }
1233     else if (source == strandColour)
1234     {
1235       changeColour(new StrandColourScheme());
1236     }
1237     else if (source == turnColour)
1238     {
1239       changeColour(new TurnColourScheme());
1240     }
1241     else if (source == buriedColour)
1242     {
1243       changeColour(new BuriedColourScheme());
1244     }
1245     else if (source == nucleotideColour)
1246     {
1247       changeColour(new NucleotideColourScheme());
1248     }
1249     else if (source == purinePyrimidineColour)
1250     {
1251       changeColour(new PurinePyrimidineColourScheme());
1252     }
1253     // else if (source == RNAInteractionColour)
1254     // {
1255     // changeColour(new RNAInteractionColourScheme());
1256     // }
1257     else if (source == RNAHelixColour)
1258     {
1259       new RNAHelicesColourChooser(viewport, alignPanel);
1260     }
1261     else if (source == modifyPID)
1262     {
1263       modifyPID_actionPerformed();
1264     }
1265     else if (source == modifyConservation)
1266     {
1267       modifyConservation_actionPerformed();
1268     }
1269     else if (source == userDefinedColour)
1270     {
1271       new UserDefinedColours(alignPanel, null);
1272     }
1273     else if (source == PIDColour)
1274     {
1275       changeColour(new PIDColourScheme());
1276     }
1277     else if (source == BLOSUM62Colour)
1278     {
1279       changeColour(new Blosum62ColourScheme());
1280     }
1281     else if (source == tcoffeeColour)
1282     {
1283       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1284     }
1285     else if (source == annotationColour)
1286     {
1287       new AnnotationColourChooser(viewport, alignPanel);
1288     }
1289     else if (source == annotationColumnSelection)
1290     {
1291       new AnnotationColumnChooser(viewport, alignPanel);
1292     }
1293     else if (source == sortPairwiseMenuItem)
1294     {
1295       sortPairwiseMenuItem_actionPerformed();
1296     }
1297     else if (source == sortIDMenuItem)
1298     {
1299       sortIDMenuItem_actionPerformed();
1300     }
1301     else if (source == sortLengthMenuItem)
1302     {
1303       sortLengthMenuItem_actionPerformed();
1304     }
1305     else if (source == sortGroupMenuItem)
1306     {
1307       sortGroupMenuItem_actionPerformed();
1308     }
1309     else if (source == removeRedundancyMenuItem)
1310     {
1311       removeRedundancyMenuItem_actionPerformed();
1312     }
1313     else if (source == pairwiseAlignmentMenuItem)
1314     {
1315       pairwiseAlignmentMenuItem_actionPerformed();
1316     }
1317     else if (source == PCAMenuItem)
1318     {
1319       PCAMenuItem_actionPerformed();
1320     }
1321     else if (source == averageDistanceTreeMenuItem)
1322     {
1323       averageDistanceTreeMenuItem_actionPerformed();
1324     }
1325     else if (source == neighbourTreeMenuItem)
1326     {
1327       neighbourTreeMenuItem_actionPerformed();
1328     }
1329     else if (source == njTreeBlosumMenuItem)
1330     {
1331       njTreeBlosumMenuItem_actionPerformed();
1332     }
1333     else if (source == avDistanceTreeBlosumMenuItem)
1334     {
1335       avTreeBlosumMenuItem_actionPerformed();
1336     }
1337     else if (source == documentation)
1338     {
1339       documentation_actionPerformed();
1340     }
1341     else if (source == about)
1342     {
1343       about_actionPerformed();
1344     }
1345
1346   }
1347
1348   public void inputText_actionPerformed()
1349   {
1350     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1351     Frame frame = new Frame();
1352     frame.add(cap);
1353     jalview.bin.JalviewLite.addFrame(frame,
1354             MessageManager.getString("label.input_cut_paste"), 500, 500);
1355   }
1356
1357   protected void outputText_actionPerformed(ActionEvent e)
1358   {
1359     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1360     Frame frame = new Frame();
1361     frame.add(cap);
1362     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1363             "label.alignment_output_command",
1364             new Object[] { e.getActionCommand() }), 600, 500);
1365
1366     FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1367     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1368             fileFormat, viewport.getAlignment(),
1369             viewport.getShowJVSuffix()));
1370   }
1371
1372   public void loadAnnotations()
1373   {
1374     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1375     cap.setText(MessageManager
1376             .getString("label.paste_features_annotations_Tcoffee_here"));
1377     cap.setAnnotationImport();
1378     Frame frame = new Frame();
1379     frame.add(cap);
1380     jalview.bin.JalviewLite.addFrame(frame,
1381             MessageManager.getString("action.paste_annotations"), 400, 300);
1382
1383   }
1384
1385   public String outputAnnotations(boolean displayTextbox)
1386   {
1387     String annotation = new AnnotationFile()
1388             .printAnnotationsForView(viewport);
1389
1390     if (displayTextbox)
1391     {
1392       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1393       Frame frame = new Frame();
1394       frame.add(cap);
1395       jalview.bin.JalviewLite.addFrame(frame,
1396               MessageManager.getString("label.annotations"), 600, 500);
1397       cap.setText(annotation);
1398     }
1399
1400     return annotation;
1401   }
1402
1403   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1404   {
1405     if (alignPanel.getFeatureRenderer() != null
1406             && viewport.getFeaturesDisplayed() != null)
1407     {
1408       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1409
1410     }
1411     return null;
1412   }
1413
1414   public String outputFeatures(boolean displayTextbox, String format)
1415   {
1416     String features;
1417     FeaturesFile formatter = new FeaturesFile();
1418     if (format.equalsIgnoreCase("Jalview"))
1419     {
1420       features = formatter.printJalviewFormat(viewport.getAlignment()
1421               .getSequencesArray(), getDisplayedFeatureCols());
1422     }
1423     else
1424     {
1425       features = formatter.printGffFormat(viewport.getAlignment()
1426               .getSequencesArray(), getDisplayedFeatureCols());
1427     }
1428
1429     if (displayTextbox)
1430     {
1431       boolean frimport = false;
1432       if (features == null || features.equals("No Features Visible"))
1433       {
1434         features = "# No features visible - paste some and import them here.";
1435         frimport = true;
1436       }
1437
1438       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1439       if (frimport)
1440       {
1441         cap.setAnnotationImport();
1442       }
1443       Frame frame = new Frame();
1444       frame.add(cap);
1445       jalview.bin.JalviewLite.addFrame(frame,
1446               MessageManager.getString("label.features"), 600, 500);
1447       cap.setText(features);
1448     }
1449     else
1450     {
1451       if (features == null)
1452       {
1453         features = "";
1454       }
1455     }
1456
1457     return features;
1458   }
1459
1460   void launchFullApplication()
1461   {
1462     StringBuffer url = new StringBuffer(jalviewServletURL);
1463
1464     // allow servlet parameters to be passed in applet parameter
1465     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1466             : "?";
1467     url.append(firstSep);
1468
1469     url.append("open="
1470             + appendProtocol(viewport.applet.getParameter("file")));
1471
1472     if (viewport.applet.getParameter("features") != null)
1473     {
1474       url.append("&features=");
1475       url.append(appendProtocol(viewport.applet.getParameter("features")));
1476     }
1477
1478     if (viewport.applet.getParameter("annotations") != null)
1479     {
1480       url.append("&annotations=");
1481       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1482     }
1483
1484     if (viewport.applet.getParameter("jnetfile") != null)
1485     {
1486       url.append("&annotations=");
1487       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1488     }
1489
1490     if (viewport.applet.getParameter("defaultColour") != null)
1491     {
1492       url.append("&colour="
1493               + removeWhiteSpace(viewport.applet
1494                       .getParameter("defaultColour")));
1495     }
1496
1497     if (viewport.applet.getParameter("userDefinedColour") != null)
1498     {
1499       url.append("&colour="
1500               + removeWhiteSpace(viewport.applet
1501                       .getParameter("userDefinedColour")));
1502     }
1503     if (viewport.applet.getParameter("tree") != null)
1504     {
1505       url.append("&tree="
1506               + appendProtocol(viewport.applet.getParameter("tree")));
1507     }
1508     if (viewport.applet.getParameter("treeFile") != null)
1509     {
1510       url.append("&tree="
1511               + appendProtocol(viewport.applet.getParameter("treeFile")));
1512     }
1513
1514     showURL(url.toString(), "FULL_APP");
1515   }
1516
1517   String removeWhiteSpace(String colour)
1518   {
1519     StringBuffer sb = new StringBuffer();
1520     for (int i = 0; i < colour.length(); i++)
1521     {
1522       if (Character.isWhitespace(colour.charAt(i)))
1523       {
1524         sb.append("%20");
1525       }
1526       else
1527       {
1528         sb.append(colour.charAt(i));
1529       }
1530     }
1531
1532     return sb.toString();
1533   }
1534
1535   String appendProtocol(String url)
1536   {
1537     try
1538     {
1539       new URL(url);
1540       url = URLEncoder.encode(url);
1541     }
1542     /*
1543      * When we finally deprecate 1.1 compatibility, we can start to use
1544      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1545      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1546      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1547      * ex.printStackTrace(); }
1548      */
1549     catch (java.net.MalformedURLException ex)
1550     {
1551       url = viewport.applet.getCodeBase() + url;
1552     }
1553     return url;
1554   }
1555
1556   public void closeMenuItem_actionPerformed()
1557   {
1558     PaintRefresher.RemoveComponent(alignPanel);
1559     if (alignPanel.seqPanel != null
1560             && alignPanel.seqPanel.seqCanvas != null)
1561     {
1562       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1563     }
1564     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1565     {
1566       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1567     }
1568
1569     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1570     {
1571       System.exit(0);
1572     }
1573     else
1574     {
1575     }
1576     viewport = null;
1577     alignPanel = null;
1578     this.dispose();
1579   }
1580
1581   /**
1582    * TODO: JAL-1104
1583    */
1584   void updateEditMenuBar()
1585   {
1586
1587     if (viewport.getHistoryList().size() > 0)
1588     {
1589       undoMenuItem.setEnabled(true);
1590       CommandI command = viewport.getHistoryList().peek();
1591       undoMenuItem.setLabel(MessageManager.formatMessage(
1592               "label.undo_command",
1593               new Object[] { command.getDescription() }));
1594     }
1595     else
1596     {
1597       undoMenuItem.setEnabled(false);
1598       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1599     }
1600
1601     if (viewport.getRedoList().size() > 0)
1602     {
1603       redoMenuItem.setEnabled(true);
1604
1605       CommandI command = viewport.getRedoList().peek();
1606       redoMenuItem.setLabel(MessageManager.formatMessage(
1607               "label.redo_command",
1608               new Object[] { command.getDescription() }));
1609     }
1610     else
1611     {
1612       redoMenuItem.setEnabled(false);
1613       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1614     }
1615   }
1616
1617   /**
1618    * TODO: JAL-1104
1619    */
1620   @Override
1621   public void addHistoryItem(CommandI command)
1622   {
1623     if (command.getSize() > 0)
1624     {
1625       viewport.addToHistoryList(command);
1626       viewport.clearRedoList();
1627       updateEditMenuBar();
1628       viewport.updateHiddenColumns();
1629     }
1630   }
1631
1632   /**
1633    * TODO: JAL-1104 DOCUMENT ME!
1634    *
1635    * @param e
1636    *          DOCUMENT ME!
1637    */
1638   protected void undoMenuItem_actionPerformed()
1639   {
1640     if (viewport.getHistoryList().isEmpty())
1641     {
1642       return;
1643     }
1644
1645     CommandI command = viewport.getHistoryList().pop();
1646     viewport.addToRedoList(command);
1647     command.undoCommand(null);
1648
1649     AlignmentViewport originalSource = getOriginatingSource(command);
1650     // JBPNote Test
1651     if (originalSource != viewport)
1652     {
1653       System.err
1654               .println("Warning: Viewport object mismatch whilst undoing");
1655     }
1656     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1657                                           // viewport.getColumnSelection().getHiddenColumns()
1658                                           // != null;
1659     updateEditMenuBar();
1660     originalSource.firePropertyChange("alignment", null, originalSource
1661             .getAlignment().getSequences());
1662   }
1663
1664   /**
1665    * TODO: JAL-1104 DOCUMENT ME!
1666    *
1667    * @param e
1668    *          DOCUMENT ME!
1669    */
1670   protected void redoMenuItem_actionPerformed()
1671   {
1672     if (viewport.getRedoList().isEmpty())
1673     {
1674       return;
1675     }
1676
1677     CommandI command = viewport.getRedoList().pop();
1678     viewport.addToHistoryList(command);
1679     command.doCommand(null);
1680
1681     AlignmentViewport originalSource = getOriginatingSource(command);
1682     // JBPNote Test
1683     if (originalSource != viewport)
1684     {
1685       System.err
1686               .println("Warning: Viewport object mismatch whilst re-doing");
1687     }
1688     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1689                                           // viewport.getColumnSelection().getHiddenColumns()
1690                                           // != null;
1691
1692     updateEditMenuBar();
1693     originalSource.firePropertyChange("alignment", null, originalSource
1694             .getAlignment().getSequences());
1695   }
1696
1697   AlignmentViewport getOriginatingSource(CommandI command)
1698   {
1699     AlignmentViewport originalSource = null;
1700     // For sequence removal and addition, we need to fire
1701     // the property change event FROM the viewport where the
1702     // original alignment was altered
1703     AlignmentI al = null;
1704     if (command instanceof EditCommand)
1705     {
1706       EditCommand editCommand = (EditCommand) command;
1707       al = editCommand.getAlignment();
1708       Vector comps = (Vector) PaintRefresher.components.get(viewport
1709               .getSequenceSetId());
1710       for (int i = 0; i < comps.size(); i++)
1711       {
1712         if (comps.elementAt(i) instanceof AlignmentPanel)
1713         {
1714           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1715           {
1716             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1717             break;
1718           }
1719         }
1720       }
1721     }
1722
1723     if (originalSource == null)
1724     {
1725       // The original view is closed, we must validate
1726       // the current view against the closed view first
1727       if (al != null)
1728       {
1729         PaintRefresher.validateSequences(al, viewport.getAlignment());
1730       }
1731
1732       originalSource = viewport;
1733     }
1734
1735     return originalSource;
1736   }
1737
1738   /**
1739    * Move the currently selected sequences up or down one position in the
1740    * alignment
1741    *
1742    * @param up
1743    */
1744   public void moveSelectedSequences(boolean up)
1745   {
1746     SequenceGroup sg = viewport.getSelectionGroup();
1747     if (sg == null)
1748     {
1749       return;
1750     }
1751     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1752             up ? null : viewport.getHiddenRepSequences(), up);
1753     alignPanel.paintAlignment(true);
1754
1755     /*
1756      * Also move cDNA/protein complement sequences
1757      */
1758     AlignViewportI complement = viewport.getCodingComplement();
1759     if (complement != null)
1760     {
1761       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1762               viewport, complement);
1763       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1764               up ? null : complement.getHiddenRepSequences(), up);
1765       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1766     }
1767   }
1768
1769   synchronized void slideSequences(boolean right, int size)
1770   {
1771     List<SequenceI> sg = new Vector<SequenceI>();
1772     if (viewport.cursorMode)
1773     {
1774       sg.add(viewport.getAlignment().getSequenceAt(
1775               alignPanel.seqPanel.seqCanvas.cursorY));
1776     }
1777     else if (viewport.getSelectionGroup() != null
1778             && viewport.getSelectionGroup().getSize() != viewport
1779                     .getAlignment().getHeight())
1780     {
1781       sg = viewport.getSelectionGroup().getSequences(
1782               viewport.getHiddenRepSequences());
1783     }
1784
1785     if (sg.size() < 1)
1786     {
1787       return;
1788     }
1789
1790     Vector<SequenceI> invertGroup = new Vector();
1791
1792     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1793     {
1794       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1795       {
1796         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1797       }
1798     }
1799
1800     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1801
1802     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1803             .size()]);
1804     for (int i = 0; i < invertGroup.size(); i++)
1805     {
1806       seqs2[i] = invertGroup.elementAt(i);
1807     }
1808
1809     SlideSequencesCommand ssc;
1810     if (right)
1811     {
1812       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1813               size, viewport.getGapCharacter());
1814     }
1815     else
1816     {
1817       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1818               size, viewport.getGapCharacter());
1819     }
1820
1821     int groupAdjustment = 0;
1822     if (ssc.getGapsInsertedBegin() && right)
1823     {
1824       if (viewport.cursorMode)
1825       {
1826         alignPanel.seqPanel.moveCursor(size, 0);
1827       }
1828       else
1829       {
1830         groupAdjustment = size;
1831       }
1832     }
1833     else if (!ssc.getGapsInsertedBegin() && !right)
1834     {
1835       if (viewport.cursorMode)
1836       {
1837         alignPanel.seqPanel.moveCursor(-size, 0);
1838       }
1839       else
1840       {
1841         groupAdjustment = -size;
1842       }
1843     }
1844
1845     if (groupAdjustment != 0)
1846     {
1847       viewport.getSelectionGroup().setStartRes(
1848               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1849       viewport.getSelectionGroup().setEndRes(
1850               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1851     }
1852
1853     boolean appendHistoryItem = false;
1854     Deque<CommandI> historyList = viewport.getHistoryList();
1855     if (historyList != null && historyList.size() > 0
1856             && historyList.peek() instanceof SlideSequencesCommand)
1857     {
1858       appendHistoryItem = ssc
1859               .appendSlideCommand((SlideSequencesCommand) historyList
1860                       .peek());
1861     }
1862
1863     if (!appendHistoryItem)
1864     {
1865       addHistoryItem(ssc);
1866     }
1867
1868     repaint();
1869   }
1870
1871   static StringBuffer copiedSequences;
1872
1873   static Vector copiedHiddenColumns;
1874
1875   protected void copy_actionPerformed()
1876   {
1877     if (viewport.getSelectionGroup() == null)
1878     {
1879       return;
1880     }
1881
1882     SequenceGroup sg = viewport.getSelectionGroup();
1883     copiedSequences = new StringBuffer();
1884     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1885     for (int i = 0; i < sg.getSize(); i++)
1886     {
1887       SequenceI seq = sg.getSequenceAt(i);
1888       int index = viewport.getAlignment().findIndex(seq);
1889       orderedSeqs.put(index, seq);
1890     }
1891
1892     int index = 0, startRes, endRes;
1893     char ch;
1894
1895     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1896     {
1897       copiedHiddenColumns = new Vector();
1898       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1899       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1900       {
1901         copiedHiddenColumns.addElement(new int[] {
1902             region[0] - hiddenOffset, region[1] - hiddenOffset });
1903       }
1904     }
1905     else
1906     {
1907       copiedHiddenColumns = null;
1908     }
1909
1910     for (int i = 0; i < sg.getSize(); i++)
1911     {
1912       SequenceI seq = null;
1913
1914       while (seq == null)
1915       {
1916         if (orderedSeqs.containsKey(index))
1917         {
1918           seq = orderedSeqs.get(index);
1919           index++;
1920           break;
1921         }
1922         else
1923         {
1924           index++;
1925         }
1926       }
1927
1928       // FIND START RES
1929       // Returns residue following index if gap
1930       startRes = seq.findPosition(sg.getStartRes());
1931
1932       // FIND END RES
1933       // Need to find the residue preceeding index if gap
1934       endRes = 0;
1935
1936       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1937       {
1938         ch = seq.getCharAt(j);
1939         if (!jalview.util.Comparison.isGap((ch)))
1940         {
1941           endRes++;
1942         }
1943       }
1944
1945       if (endRes > 0)
1946       {
1947         endRes += seq.getStart() - 1;
1948       }
1949
1950       copiedSequences.append(seq.getName()
1951               + "\t"
1952               + startRes
1953               + "\t"
1954               + endRes
1955               + "\t"
1956               + seq.getSequenceAsString(sg.getStartRes(),
1957                       sg.getEndRes() + 1) + "\n");
1958     }
1959
1960   }
1961
1962   protected void pasteNew_actionPerformed()
1963   {
1964     paste(true);
1965   }
1966
1967   protected void pasteThis_actionPerformed()
1968   {
1969     paste(false);
1970   }
1971
1972   void paste(boolean newAlignment)
1973   {
1974     try
1975     {
1976
1977       if (copiedSequences == null)
1978       {
1979         return;
1980       }
1981
1982       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1983       Vector seqs = new Vector();
1984       while (st.hasMoreElements())
1985       {
1986         String name = st.nextToken();
1987         int start = Integer.parseInt(st.nextToken());
1988         int end = Integer.parseInt(st.nextToken());
1989         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1990       }
1991       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1992       for (int i = 0; i < seqs.size(); i++)
1993       {
1994         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1995       }
1996
1997       if (newAlignment)
1998       {
1999         String newtitle = MessageManager
2000                 .getString("label.copied_sequences");
2001         if (getTitle().startsWith(
2002                 MessageManager.getString("label.copied_sequences")))
2003         {
2004           newtitle = getTitle();
2005         }
2006         else
2007         {
2008           newtitle = newtitle.concat(MessageManager.formatMessage(
2009                   "label.from_msname", new String[] { getTitle() }));
2010         }
2011         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2012                 viewport.applet, newtitle, false);
2013         if (copiedHiddenColumns != null)
2014         {
2015           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2016           {
2017             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2018             af.viewport.hideColumns(region[0], region[1]);
2019           }
2020         }
2021
2022         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2023                 frameHeight);
2024       }
2025       else
2026       {
2027         addSequences(newSeqs);
2028       }
2029
2030     } catch (Exception ex)
2031     {
2032     } // could be anything being pasted in here
2033
2034   }
2035
2036   void addSequences(SequenceI[] seqs)
2037   {
2038     for (int i = 0; i < seqs.length; i++)
2039     {
2040       viewport.getAlignment().addSequence(seqs[i]);
2041     }
2042
2043     // !newAlignment
2044     addHistoryItem(new EditCommand(
2045             MessageManager.getString("label.add_sequences"), Action.PASTE,
2046             seqs, 0, viewport.getAlignment().getWidth(),
2047             viewport.getAlignment()));
2048
2049     viewport.setEndSeq(viewport.getAlignment().getHeight());
2050     viewport.getAlignment().getWidth();
2051     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2052             .getSequences());
2053
2054   }
2055
2056   protected void cut_actionPerformed()
2057   {
2058     copy_actionPerformed();
2059     delete_actionPerformed();
2060   }
2061
2062   protected void delete_actionPerformed()
2063   {
2064
2065     SequenceGroup sg = viewport.getSelectionGroup();
2066     if (sg == null)
2067     {
2068       return;
2069     }
2070
2071     Vector seqs = new Vector();
2072     SequenceI seq;
2073     for (int i = 0; i < sg.getSize(); i++)
2074     {
2075       seq = sg.getSequenceAt(i);
2076       seqs.addElement(seq);
2077     }
2078
2079     /*
2080      * If the cut affects all sequences, warn, remove highlighted columns
2081      */
2082     if (sg.getSize() == viewport.getAlignment().getHeight())
2083     {
2084       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2085               .getAlignment().getWidth()) ? true : false;
2086       if (isEntireAlignWidth)
2087       {
2088         String title = MessageManager.getString("label.delete_all");
2089         Panel infoPanel = new Panel();
2090         infoPanel.setLayout(new FlowLayout());
2091         infoPanel
2092                 .add(new Label(MessageManager.getString("warn.delete_all")));
2093
2094         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2095         dialog.setMainPanel(infoPanel);
2096         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2097         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2098         dialog.setVisible(true);
2099
2100         if (!dialog.accept)
2101         {
2102           return;
2103         }
2104       }
2105       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2106               sg.getEndRes() + 1);
2107     }
2108
2109     SequenceI[] cut = new SequenceI[seqs.size()];
2110     for (int i = 0; i < seqs.size(); i++)
2111     {
2112       cut[i] = (SequenceI) seqs.elementAt(i);
2113     }
2114
2115     /*
2116      * //ADD HISTORY ITEM
2117      */
2118     addHistoryItem(new EditCommand(
2119             MessageManager.getString("label.cut_sequences"), Action.CUT,
2120             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2121             viewport.getAlignment()));
2122
2123     viewport.setSelectionGroup(null);
2124     viewport.getAlignment().deleteGroup(sg);
2125
2126     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2127             .getSequences());
2128
2129     if (viewport.getAlignment().getHeight() < 1)
2130     {
2131       this.setVisible(false);
2132     }
2133     viewport.sendSelection();
2134   }
2135
2136   /**
2137    * group consensus toggled
2138    *
2139    */
2140   protected void showGroupConsensus_actionPerformed()
2141   {
2142     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2143     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2144
2145   }
2146
2147   /**
2148    * group conservation toggled.
2149    */
2150   protected void showGroupConservation_actionPerformed()
2151   {
2152     viewport.setShowGroupConservation(showGroupConservation.getState());
2153     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2154   }
2155
2156   /*
2157    * (non-Javadoc)
2158    *
2159    * @see
2160    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2161    * .event.ActionEvent)
2162    */
2163   protected void showConsensusHistogram_actionPerformed()
2164   {
2165     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2166     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2167   }
2168
2169   /*
2170    * (non-Javadoc)
2171    *
2172    * @see
2173    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2174    * .event.ActionEvent)
2175    */
2176   protected void showSequenceLogo_actionPerformed()
2177   {
2178     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2179     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180   }
2181
2182   protected void normSequenceLogo_actionPerformed()
2183   {
2184     showSequenceLogo.setState(true);
2185     viewport.setShowSequenceLogo(true);
2186     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2187     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2188   }
2189
2190   protected void applyAutoAnnotationSettings_actionPerformed()
2191   {
2192     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2193   }
2194
2195   protected void makeGrpsFromSelection_actionPerformed()
2196   {
2197     if (avc.makeGroupsFromSelection())
2198     {
2199       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2200       alignPanel.updateAnnotation();
2201       alignPanel.paintAlignment(true);
2202     }
2203   }
2204
2205   protected void createGroup_actionPerformed()
2206   {
2207     avc.createGroup();
2208   }
2209
2210   protected void unGroup_actionPerformed()
2211   {
2212     if (avc.unGroup())
2213     {
2214       alignPanel.alignmentChanged();
2215     }
2216   }
2217
2218   protected void deleteGroups_actionPerformed()
2219   {
2220     if (avc.deleteGroups())
2221     {
2222       alignPanel.alignmentChanged();
2223     }
2224   }
2225
2226   public void selectAllSequenceMenuItem_actionPerformed()
2227   {
2228     SequenceGroup sg = new SequenceGroup();
2229     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2230     {
2231       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2232     }
2233     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2234     viewport.setSelectionGroup(sg);
2235     // JAL-2034 - should delegate to
2236     // alignPanel to decide if overview needs
2237     // updating.
2238     alignPanel.paintAlignment(false);
2239     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2240     viewport.sendSelection();
2241   }
2242
2243   public void deselectAllSequenceMenuItem_actionPerformed()
2244   {
2245     if (viewport.cursorMode)
2246     {
2247       alignPanel.seqPanel.keyboardNo1 = null;
2248       alignPanel.seqPanel.keyboardNo2 = null;
2249     }
2250     viewport.setSelectionGroup(null);
2251     viewport.getColumnSelection().clear();
2252     viewport.setSelectionGroup(null);
2253     alignPanel.idPanel.idCanvas.searchResults = null;
2254     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2255     // JAL-2034 - should delegate to
2256     // alignPanel to decide if overview needs
2257     // updating.
2258     alignPanel.paintAlignment(false);
2259     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2260     viewport.sendSelection();
2261   }
2262
2263   public void invertSequenceMenuItem_actionPerformed()
2264   {
2265     SequenceGroup sg = viewport.getSelectionGroup();
2266     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2267     {
2268       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2269     }
2270
2271     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2272     viewport.sendSelection();
2273   }
2274
2275   public void invertColSel_actionPerformed()
2276   {
2277     viewport.invertColumnSelection();
2278     alignPanel.paintAlignment(true);
2279     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2280     viewport.sendSelection();
2281   }
2282
2283   void trimAlignment(boolean trimLeft)
2284   {
2285     ColumnSelection colSel = viewport.getColumnSelection();
2286     int column;
2287
2288     if (!colSel.isEmpty())
2289     {
2290       if (trimLeft)
2291       {
2292         column = colSel.getMin();
2293       }
2294       else
2295       {
2296         column = colSel.getMax();
2297       }
2298
2299       SequenceI[] seqs;
2300       if (viewport.getSelectionGroup() != null)
2301       {
2302         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2303                 viewport.getHiddenRepSequences());
2304       }
2305       else
2306       {
2307         seqs = viewport.getAlignment().getSequencesArray();
2308       }
2309
2310       TrimRegionCommand trimRegion;
2311       if (trimLeft)
2312       {
2313         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2314                 column, viewport.getAlignment());
2315         viewport.setStartRes(0);
2316       }
2317       else
2318       {
2319         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2320                 column, viewport.getAlignment());
2321       }
2322
2323       statusBar.setText(MessageManager.formatMessage(
2324               "label.removed_columns",
2325               new String[] { Integer.valueOf(trimRegion.getSize())
2326                       .toString() }));
2327       addHistoryItem(trimRegion);
2328
2329       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2330       {
2331         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2332                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2333         {
2334           viewport.getAlignment().deleteGroup(sg);
2335         }
2336       }
2337
2338       viewport.firePropertyChange("alignment", null, viewport
2339               .getAlignment().getSequences());
2340     }
2341   }
2342
2343   public void removeGappedColumnMenuItem_actionPerformed()
2344   {
2345     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2346
2347     SequenceI[] seqs;
2348     if (viewport.getSelectionGroup() != null)
2349     {
2350       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2351               viewport.getHiddenRepSequences());
2352       start = viewport.getSelectionGroup().getStartRes();
2353       end = viewport.getSelectionGroup().getEndRes();
2354     }
2355     else
2356     {
2357       seqs = viewport.getAlignment().getSequencesArray();
2358     }
2359
2360     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2361             "Remove Gapped Columns", seqs, start, end,
2362             viewport.getAlignment());
2363
2364     addHistoryItem(removeGapCols);
2365
2366     statusBar.setText(MessageManager.formatMessage(
2367             "label.removed_empty_columns",
2368             new String[] { Integer.valueOf(removeGapCols.getSize())
2369                     .toString() }));
2370
2371     // This is to maintain viewport position on first residue
2372     // of first sequence
2373     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2374     int startRes = seq.findPosition(viewport.startRes);
2375     // ShiftList shifts;
2376     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2377     // edit.alColumnChanges=shifts.getInverse();
2378     // if (viewport.hasHiddenColumns)
2379     // viewport.getColumnSelection().compensateForEdits(shifts);
2380     viewport.setStartRes(seq.findIndex(startRes) - 1);
2381     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2382             .getSequences());
2383
2384   }
2385
2386   public void removeAllGapsMenuItem_actionPerformed()
2387   {
2388     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2389
2390     SequenceI[] seqs;
2391     if (viewport.getSelectionGroup() != null)
2392     {
2393       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2394               viewport.getHiddenRepSequences());
2395       start = viewport.getSelectionGroup().getStartRes();
2396       end = viewport.getSelectionGroup().getEndRes();
2397     }
2398     else
2399     {
2400       seqs = viewport.getAlignment().getSequencesArray();
2401     }
2402
2403     // This is to maintain viewport position on first residue
2404     // of first sequence
2405     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2406     int startRes = seq.findPosition(viewport.startRes);
2407
2408     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2409             viewport.getAlignment()));
2410
2411     viewport.setStartRes(seq.findIndex(startRes) - 1);
2412
2413     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2414             .getSequences());
2415
2416   }
2417
2418   public void findMenuItem_actionPerformed()
2419   {
2420     new Finder(alignPanel);
2421   }
2422
2423   /**
2424    * create a new view derived from the current view
2425    *
2426    * @param viewtitle
2427    * @return frame for the new view
2428    */
2429   public AlignFrame newView(String viewtitle)
2430   {
2431     AlignmentI newal;
2432     if (viewport.hasHiddenRows())
2433     {
2434       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2435               .getFullAlignment().getSequencesArray());
2436     }
2437     else
2438     {
2439       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2440     }
2441
2442     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2443     {
2444       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2445       {
2446         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2447         {
2448           newal.addAnnotation(viewport.getAlignment()
2449                   .getAlignmentAnnotation()[i]);
2450         }
2451       }
2452     }
2453
2454     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2455
2456     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2457     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2458     PaintRefresher.Register(newaf.alignPanel,
2459             newaf.alignPanel.av.getSequenceSetId());
2460
2461     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2462             newaf.alignPanel.av.getSequenceSetId());
2463     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2464             newaf.alignPanel.av.getSequenceSetId());
2465
2466     Vector comps = (Vector) PaintRefresher.components.get(viewport
2467             .getSequenceSetId());
2468     int viewSize = -1;
2469     for (int i = 0; i < comps.size(); i++)
2470     {
2471       if (comps.elementAt(i) instanceof AlignmentPanel)
2472       {
2473         viewSize++;
2474       }
2475     }
2476
2477     String title = new String(this.getTitle());
2478     if (viewtitle != null)
2479     {
2480       title = viewtitle + " ( " + title + ")";
2481     }
2482     else
2483     {
2484       if (title.indexOf("(View") > -1)
2485       {
2486         title = title.substring(0, title.indexOf("(View"));
2487       }
2488       title += "(View " + viewSize + ")";
2489     }
2490
2491     newaf.setTitle(title.toString());
2492
2493     newaf.viewport.setHistoryList(viewport.getHistoryList());
2494     newaf.viewport.setRedoList(viewport.getRedoList());
2495     return newaf;
2496   }
2497
2498   /**
2499    *
2500    * @return list of feature groups on the view
2501    */
2502   public String[] getFeatureGroups()
2503   {
2504     FeatureRenderer fr = null;
2505     if (alignPanel != null
2506             && (fr = alignPanel.getFeatureRenderer()) != null)
2507     {
2508       List<String> gps = fr.getFeatureGroups();
2509       String[] _gps = gps.toArray(new String[gps.size()]);
2510       return _gps;
2511     }
2512     return null;
2513   }
2514
2515   /**
2516    * get sequence feature groups that are hidden or shown
2517    *
2518    * @param visible
2519    *          true is visible
2520    * @return list
2521    */
2522   public String[] getFeatureGroupsOfState(boolean visible)
2523   {
2524     FeatureRenderer fr = null;
2525     if (alignPanel != null
2526             && (fr = alignPanel.getFeatureRenderer()) != null)
2527     {
2528       List<String> gps = fr.getGroups(visible);
2529       String[] _gps = gps.toArray(new String[gps.size()]);
2530       return _gps;
2531     }
2532     return null;
2533   }
2534
2535   /**
2536    * Change the display state for the given feature groups
2537    *
2538    * @param groups
2539    *          list of group strings
2540    * @param state
2541    *          visible or invisible
2542    */
2543   public void setFeatureGroupState(String[] groups, boolean state)
2544   {
2545     FeatureRenderer fr = null;
2546     this.sequenceFeatures.setState(true);
2547     viewport.setShowSequenceFeatures(true);
2548     if (alignPanel != null
2549             && (fr = alignPanel.getFeatureRenderer()) != null)
2550     {
2551
2552       fr.setGroupVisibility(Arrays.asList(groups), state);
2553       alignPanel.seqPanel.seqCanvas.repaint();
2554       if (alignPanel.overviewPanel != null)
2555       {
2556         alignPanel.overviewPanel.updateOverviewImage();
2557       }
2558     }
2559   }
2560
2561   public void seqLimits_itemStateChanged()
2562   {
2563     viewport.setShowJVSuffix(seqLimits.getState());
2564     alignPanel.fontChanged();
2565     alignPanel.paintAlignment(true);
2566   }
2567
2568   protected void colourTextMenuItem_actionPerformed()
2569   {
2570     viewport.setColourText(colourTextMenuItem.getState());
2571     alignPanel.paintAlignment(true);
2572   }
2573
2574   protected void displayNonconservedMenuItem_actionPerformed()
2575   {
2576     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2577     alignPanel.paintAlignment(true);
2578   }
2579
2580   protected void wrapMenuItem_actionPerformed()
2581   {
2582     viewport.setWrapAlignment(wrapMenuItem.getState());
2583     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2584     scaleAbove.setEnabled(wrapMenuItem.getState());
2585     scaleLeft.setEnabled(wrapMenuItem.getState());
2586     scaleRight.setEnabled(wrapMenuItem.getState());
2587     alignPanel.paintAlignment(true);
2588   }
2589
2590   public void overviewMenuItem_actionPerformed()
2591   {
2592     if (alignPanel.overviewPanel != null)
2593     {
2594       return;
2595     }
2596
2597     Frame frame = new Frame();
2598     OverviewPanel overview = new OverviewPanel(alignPanel);
2599     frame.add(overview);
2600     // +50 must allow for applet frame window
2601     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2602             "label.overview_params", new String[] { this.getTitle() }),
2603             overview.getPreferredSize().width,
2604             overview.getPreferredSize().height + 50);
2605
2606     frame.pack();
2607     final AlignmentPanel ap = alignPanel;
2608     frame.addWindowListener(new WindowAdapter()
2609     {
2610       @Override
2611       public void windowClosing(WindowEvent e)
2612       {
2613         if (ap != null)
2614         {
2615           ap.setOverviewPanel(null);
2616         }
2617       };
2618     });
2619
2620     alignPanel.setOverviewPanel(overview);
2621
2622   }
2623
2624   @Override
2625   public void changeColour(ColourSchemeI cs)
2626   {
2627
2628     if (cs != null)
2629     {
2630       if (viewport.getAbovePIDThreshold())
2631       {
2632         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2633                 cs, "Background"));
2634       }
2635
2636       if (viewport.getConservationSelected())
2637       {
2638         cs.setConservationApplied(true);
2639         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2640                 cs, "Background"));
2641       }
2642       else
2643       {
2644         cs.setConservationApplied(false);
2645       }
2646     }
2647     viewport.setGlobalColourScheme(cs);
2648
2649     alignPanel.paintAlignment(true);
2650   }
2651
2652   protected void modifyPID_actionPerformed()
2653   {
2654     if (viewport.getAbovePIDThreshold()
2655             && viewport.getGlobalColourScheme() != null)
2656     {
2657       SliderPanel.setPIDSliderSource(alignPanel,
2658               viewport.getGlobalColourScheme(), "Background");
2659       SliderPanel.showPIDSlider();
2660     }
2661   }
2662
2663   protected void modifyConservation_actionPerformed()
2664   {
2665     if (viewport.getConservationSelected()
2666             && viewport.getGlobalColourScheme() != null)
2667     {
2668       SliderPanel.setConservationSlider(alignPanel,
2669               viewport.getGlobalColourScheme(), "Background");
2670       SliderPanel.showConservationSlider();
2671     }
2672   }
2673
2674   protected void conservationMenuItem_actionPerformed()
2675   {
2676     viewport.setConservationSelected(conservationMenuItem.getState());
2677
2678     viewport.setAbovePIDThreshold(false);
2679     abovePIDThreshold.setState(false);
2680
2681     changeColour(viewport.getGlobalColourScheme());
2682
2683     modifyConservation_actionPerformed();
2684   }
2685
2686   public void abovePIDThreshold_actionPerformed()
2687   {
2688     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2689
2690     conservationMenuItem.setState(false);
2691     viewport.setConservationSelected(false);
2692
2693     changeColour(viewport.getGlobalColourScheme());
2694
2695     modifyPID_actionPerformed();
2696   }
2697
2698   public void sortPairwiseMenuItem_actionPerformed()
2699   {
2700     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2701     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2702             .getAlignment().getSequenceAt(0), null);
2703
2704     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2705             viewport.getAlignment()));
2706     alignPanel.paintAlignment(true);
2707   }
2708
2709   public void sortIDMenuItem_actionPerformed()
2710   {
2711     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2712     AlignmentSorter.sortByID(viewport.getAlignment());
2713     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2714             viewport.getAlignment()));
2715     alignPanel.paintAlignment(true);
2716   }
2717
2718   public void sortLengthMenuItem_actionPerformed()
2719   {
2720     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2721     AlignmentSorter.sortByLength(viewport.getAlignment());
2722     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2723             viewport.getAlignment()));
2724     alignPanel.paintAlignment(true);
2725   }
2726
2727   public void sortGroupMenuItem_actionPerformed()
2728   {
2729     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2730     AlignmentSorter.sortByGroup(viewport.getAlignment());
2731     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2732             viewport.getAlignment()));
2733     alignPanel.paintAlignment(true);
2734
2735   }
2736
2737   public void removeRedundancyMenuItem_actionPerformed()
2738   {
2739     new RedundancyPanel(alignPanel);
2740   }
2741
2742   public void pairwiseAlignmentMenuItem_actionPerformed()
2743   {
2744     if (viewport.getSelectionGroup() != null
2745             && viewport.getSelectionGroup().getSize() > 1)
2746     {
2747       Frame frame = new Frame();
2748       frame.add(new PairwiseAlignPanel(alignPanel));
2749       jalview.bin.JalviewLite.addFrame(frame,
2750               MessageManager.getString("action.pairwise_alignment"), 600,
2751               500);
2752     }
2753   }
2754
2755   public void PCAMenuItem_actionPerformed()
2756   {
2757     // are the sequences aligned?
2758     if (!viewport.getAlignment().isAligned(false))
2759     {
2760       SequenceI current;
2761       int Width = viewport.getAlignment().getWidth();
2762
2763       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2764       {
2765         current = viewport.getAlignment().getSequenceAt(i);
2766
2767         if (current.getLength() < Width)
2768         {
2769           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2770         }
2771       }
2772       alignPanel.paintAlignment(true);
2773     }
2774
2775     if ((viewport.getSelectionGroup() != null
2776             && viewport.getSelectionGroup().getSize() < 4 && viewport
2777             .getSelectionGroup().getSize() > 0)
2778             || viewport.getAlignment().getHeight() < 4)
2779     {
2780       return;
2781     }
2782
2783     try
2784     {
2785       new PCAPanel(viewport);
2786     } catch (java.lang.OutOfMemoryError ex)
2787     {
2788     }
2789
2790   }
2791
2792   public void averageDistanceTreeMenuItem_actionPerformed()
2793   {
2794     NewTreePanel("AV", "PID", "Average distance tree using PID");
2795   }
2796
2797   public void neighbourTreeMenuItem_actionPerformed()
2798   {
2799     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2800   }
2801
2802   protected void njTreeBlosumMenuItem_actionPerformed()
2803   {
2804     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2805   }
2806
2807   protected void avTreeBlosumMenuItem_actionPerformed()
2808   {
2809     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2810   }
2811
2812   void NewTreePanel(String type, String pwType, String title)
2813   {
2814     // are the sequences aligned?
2815     if (!viewport.getAlignment().isAligned(false))
2816     {
2817       SequenceI current;
2818       int Width = viewport.getAlignment().getWidth();
2819
2820       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2821       {
2822         current = viewport.getAlignment().getSequenceAt(i);
2823
2824         if (current.getLength() < Width)
2825         {
2826           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2827         }
2828       }
2829       alignPanel.paintAlignment(true);
2830
2831     }
2832
2833     if ((viewport.getSelectionGroup() != null && viewport
2834             .getSelectionGroup().getSize() > 1)
2835             || (viewport.getAlignment().getHeight() > 1))
2836     {
2837       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2838
2839       addTreeMenuItem(tp, title);
2840
2841       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2842     }
2843   }
2844
2845   void loadTree_actionPerformed()
2846   {
2847     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2848     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2849     cap.setTreeImport();
2850     Frame frame = new Frame();
2851     frame.add(cap);
2852     jalview.bin.JalviewLite.addFrame(frame,
2853             MessageManager.getString("label.paste_newick_file"), 400, 300);
2854   }
2855
2856   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2857   {
2858     TreePanel tp = new TreePanel(alignPanel, treeFile,
2859             MessageManager.getString("label.load_tree_from_file"), tree);
2860     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2861     addTreeMenuItem(tp, treeFile);
2862   }
2863
2864   /**
2865    * sort the alignment using the given treePanel
2866    *
2867    * @param treePanel
2868    *          tree used to sort view
2869    * @param title
2870    *          string used for undo event name
2871    */
2872   public void sortByTree(TreePanel treePanel, String title)
2873   {
2874     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2875     AlignmentSorter
2876             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2877     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2878     // HistoryItem.SORT));
2879     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2880             "label.order_by_params", new String[] { title }), oldOrder,
2881             viewport.getAlignment()));
2882     alignPanel.paintAlignment(true);
2883   }
2884
2885   /**
2886    * Do any automatic reordering of the alignment and add the necessary bits to
2887    * the menu structure for the new tree
2888    *
2889    * @param treePanel
2890    * @param title
2891    */
2892   protected void addTreeMenuItem(final TreePanel treePanel,
2893           final String title)
2894   {
2895     final MenuItem item = new MenuItem(title);
2896     sortByTreeMenu.add(item);
2897     item.addActionListener(new java.awt.event.ActionListener()
2898     {
2899       @Override
2900       public void actionPerformed(ActionEvent evt)
2901       {
2902         sortByTree(treePanel, title); // treePanel.getTitle());
2903       }
2904     });
2905
2906     treePanel.addWindowListener(new WindowAdapter()
2907     {
2908       @Override
2909       public void windowOpened(WindowEvent e)
2910       {
2911         if (viewport.sortByTree)
2912         {
2913           sortByTree(treePanel, title);
2914         }
2915         super.windowOpened(e);
2916       }
2917
2918       @Override
2919       public void windowClosing(WindowEvent e)
2920       {
2921         sortByTreeMenu.remove(item);
2922       };
2923     });
2924   }
2925
2926   public boolean sortBy(AlignmentOrder alorder, String undoname)
2927   {
2928     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2929     if (viewport.applet.debug)
2930     {
2931       System.err.println("Sorting " + alorder.getOrder().size()
2932               + " in alignment '" + getTitle() + "'");
2933     }
2934     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2935     if (undoname != null)
2936     {
2937       addHistoryItem(new OrderCommand(undoname, oldOrder,
2938               viewport.getAlignment()));
2939     }
2940     alignPanel.paintAlignment(true);
2941     return true;
2942   }
2943
2944   protected void documentation_actionPerformed()
2945   {
2946     alignPanel.av.applet.openJalviewHelpUrl();
2947   }
2948
2949   protected void about_actionPerformed()
2950   {
2951
2952     class AboutPanel extends Canvas
2953     {
2954       String version;
2955
2956       String builddate;
2957
2958       public AboutPanel(String version, String builddate)
2959       {
2960         this.version = version;
2961         this.builddate = builddate;
2962       }
2963
2964       @Override
2965       public void paint(Graphics g)
2966       {
2967         g.setColor(Color.white);
2968         g.fillRect(0, 0, getSize().width, getSize().height);
2969         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2970         FontMetrics fm = g.getFontMetrics();
2971         int fh = fm.getHeight();
2972         int y = 5, x = 7;
2973         g.setColor(Color.black);
2974         // TODO: update this text for each release or centrally store it for
2975         // lite and application
2976         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2977         g.drawString(MessageManager.formatMessage(
2978                 "label.jalviewLite_release", new String[] { version }), x,
2979                 y += fh);
2980         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2981         g.drawString(MessageManager.formatMessage(
2982                 "label.jaview_build_date", new String[] { builddate }), x,
2983                 y += fh);
2984         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2985         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2986                 x, y += fh * 1.5);
2987         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2988                 x + 50, y += fh + 8);
2989         g.drawString(
2990                 MessageManager.getString("label.jalview_dev_managers"), x,
2991                 y += fh);
2992         g.drawString(MessageManager
2993                 .getString("label.jalview_distribution_lists"), x, y += fh);
2994         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2995                 x, y += fh + 8);
2996         g.drawString(
2997                 MessageManager.getString("label.jalview_cite_1_authors"),
2998                 x, y += fh);
2999         g.drawString(
3000                 MessageManager.getString("label.jalview_cite_1_title"), x,
3001                 y += fh);
3002         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3003                 x, y += fh);
3004       }
3005     }
3006
3007     Frame frame = new Frame();
3008     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3009             .getBuildDate()));
3010     jalview.bin.JalviewLite.addFrame(frame,
3011             MessageManager.getString("label.jalview"), 580, 220);
3012
3013   }
3014
3015   public void showURL(String url, String target)
3016   {
3017     if (viewport.applet == null)
3018     {
3019       System.out.println("Not running as applet - no browser available.");
3020     }
3021     else
3022     {
3023       viewport.applet.showURL(url, target);
3024     }
3025   }
3026
3027   // ////////////////////////////////////////////////////////////////////////////////
3028   // JBuilder Graphics here
3029
3030   MenuBar alignFrameMenuBar = new MenuBar();
3031
3032   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3033
3034   MenuItem loadApplication = new MenuItem(
3035           MessageManager.getString("label.view_full_application"));
3036
3037   MenuItem loadTree = new MenuItem(
3038           MessageManager.getString("label.load_associated_tree"));
3039
3040   MenuItem loadAnnotations = new MenuItem(
3041           MessageManager.getString("label.load_features_annotations"));
3042
3043   MenuItem outputFeatures = new MenuItem(
3044           MessageManager.getString("label.export_features"));
3045
3046   MenuItem outputAnnotations = new MenuItem(
3047           MessageManager.getString("label.export_annotations"));
3048
3049   MenuItem closeMenuItem = new MenuItem(
3050           MessageManager.getString("action.close"));
3051
3052   MenuItem selectAllSequenceMenuItem = new MenuItem(
3053           MessageManager.getString("action.select_all"));
3054
3055   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3056           MessageManager.getString("action.deselect_all"));
3057
3058   MenuItem invertSequenceMenuItem = new MenuItem(
3059           MessageManager.getString("action.invert_selection"));
3060
3061   MenuItem remove2LeftMenuItem = new MenuItem();
3062
3063   MenuItem remove2RightMenuItem = new MenuItem();
3064
3065   MenuItem removeGappedColumnMenuItem = new MenuItem();
3066
3067   MenuItem removeAllGapsMenuItem = new MenuItem();
3068
3069   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3070
3071   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3072
3073   MenuItem sortPairwiseMenuItem = new MenuItem();
3074
3075   MenuItem sortIDMenuItem = new MenuItem();
3076
3077   MenuItem sortLengthMenuItem = new MenuItem();
3078
3079   MenuItem sortGroupMenuItem = new MenuItem();
3080
3081   MenuItem removeRedundancyMenuItem = new MenuItem();
3082
3083   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3084
3085   MenuItem PCAMenuItem = new MenuItem();
3086
3087   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3088
3089   MenuItem neighbourTreeMenuItem = new MenuItem();
3090
3091   BorderLayout borderLayout1 = new BorderLayout();
3092
3093   public Label statusBar = new Label();
3094
3095   MenuItem clustalColour = new MenuItem();
3096
3097   MenuItem zappoColour = new MenuItem();
3098
3099   MenuItem taylorColour = new MenuItem();
3100
3101   MenuItem hydrophobicityColour = new MenuItem();
3102
3103   MenuItem helixColour = new MenuItem();
3104
3105   MenuItem strandColour = new MenuItem();
3106
3107   MenuItem turnColour = new MenuItem();
3108
3109   MenuItem buriedColour = new MenuItem();
3110
3111   MenuItem purinePyrimidineColour = new MenuItem();
3112
3113   // MenuItem RNAInteractionColour = new MenuItem();
3114
3115   MenuItem RNAHelixColour = new MenuItem();
3116
3117   MenuItem userDefinedColour = new MenuItem();
3118
3119   MenuItem PIDColour = new MenuItem();
3120
3121   MenuItem BLOSUM62Colour = new MenuItem();
3122
3123   MenuItem tcoffeeColour = new MenuItem();
3124
3125   MenuItem njTreeBlosumMenuItem = new MenuItem();
3126
3127   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3128
3129   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3130
3131   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3132
3133   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3134
3135   MenuItem alProperties = new MenuItem(
3136           MessageManager.getString("label.alignment_props"));
3137
3138   MenuItem overviewMenuItem = new MenuItem();
3139
3140   MenuItem undoMenuItem = new MenuItem();
3141
3142   MenuItem redoMenuItem = new MenuItem();
3143
3144   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3145
3146   MenuItem noColourmenuItem = new MenuItem();
3147
3148   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3149
3150   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3151
3152   MenuItem findMenuItem = new MenuItem();
3153
3154   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3155
3156   MenuItem nucleotideColour = new MenuItem();
3157
3158   MenuItem deleteGroups = new MenuItem();
3159
3160   MenuItem grpsFromSelection = new MenuItem();
3161
3162   MenuItem createGroup = new MenuItem();
3163
3164   MenuItem unGroup = new MenuItem();
3165
3166   MenuItem delete = new MenuItem();
3167
3168   MenuItem copy = new MenuItem();
3169
3170   MenuItem cut = new MenuItem();
3171
3172   Menu pasteMenu = new Menu();
3173
3174   MenuItem pasteNew = new MenuItem();
3175
3176   MenuItem pasteThis = new MenuItem();
3177
3178   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3179
3180   MenuItem font = new MenuItem();
3181
3182   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3183
3184   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3185
3186   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3187
3188   MenuItem modifyPID = new MenuItem();
3189
3190   MenuItem modifyConservation = new MenuItem();
3191
3192   CheckboxMenuItem autoCalculate = null;
3193
3194   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3195           "Sort Alignment With New Tree", true);
3196
3197   Menu sortByTreeMenu = new Menu();
3198
3199   MenuItem inputText = new MenuItem();
3200
3201   MenuItem documentation = new MenuItem();
3202
3203   MenuItem about = new MenuItem();
3204
3205   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3206
3207   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3208
3209   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3222
3223   /**
3224    * Initialise menus and other items
3225    *
3226    * @throws Exception
3227    */
3228   private void jbInit() throws Exception
3229   {
3230     setMenuBar(alignFrameMenuBar);
3231
3232     /*
3233      * Configure File menu items and actions
3234      */
3235     inputText
3236             .setLabel(MessageManager.getString("label.input_from_textbox"));
3237     inputText.addActionListener(this);
3238     Menu outputTextboxMenu = new Menu(
3239             MessageManager.getString("label.out_to_textbox"));
3240     for (String ff : FileFormat.getWritableFormats(true))
3241     {
3242       MenuItem item = new MenuItem(ff);
3243
3244       item.addActionListener(new java.awt.event.ActionListener()
3245       {
3246         @Override
3247         public void actionPerformed(ActionEvent e)
3248         {
3249           outputText_actionPerformed(e);
3250         }
3251       });
3252
3253       outputTextboxMenu.add(item);
3254     }
3255     closeMenuItem.addActionListener(this);
3256     loadApplication.addActionListener(this);
3257     loadTree.addActionListener(this);
3258     loadAnnotations.addActionListener(this);
3259     outputFeatures.addActionListener(this);
3260     outputAnnotations.addActionListener(this);
3261
3262     /*
3263      * Configure Edit menu items and actions
3264      */
3265     undoMenuItem.setEnabled(false);
3266     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3267     undoMenuItem.addActionListener(this);
3268     redoMenuItem.setEnabled(false);
3269     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3270     redoMenuItem.addActionListener(this);
3271     copy.setLabel(MessageManager.getString("action.copy"));
3272     copy.addActionListener(this);
3273     cut.setLabel(MessageManager.getString("action.cut"));
3274     cut.addActionListener(this);
3275     delete.setLabel(MessageManager.getString("action.delete"));
3276     delete.addActionListener(this);
3277     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3278     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3279     pasteNew.addActionListener(this);
3280     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3281     pasteThis.addActionListener(this);
3282     remove2LeftMenuItem.setLabel(MessageManager
3283             .getString("action.remove_left"));
3284     remove2LeftMenuItem.addActionListener(this);
3285     remove2RightMenuItem.setLabel(MessageManager
3286             .getString("action.remove_right"));
3287     remove2RightMenuItem.addActionListener(this);
3288     removeGappedColumnMenuItem.setLabel(MessageManager
3289             .getString("action.remove_empty_columns"));
3290     removeGappedColumnMenuItem.addActionListener(this);
3291     removeAllGapsMenuItem.setLabel(MessageManager
3292             .getString("action.remove_all_gaps"));
3293     removeAllGapsMenuItem.addActionListener(this);
3294     removeRedundancyMenuItem.setLabel(MessageManager
3295             .getString("action.remove_redundancy"));
3296     removeRedundancyMenuItem.addActionListener(this);
3297
3298     /*
3299      * Configure Select menu items and actions
3300      */
3301     findMenuItem.setLabel(MessageManager.getString("action.find"));
3302     findMenuItem.addActionListener(this);
3303     selectAllSequenceMenuItem.addActionListener(this);
3304     deselectAllSequenceMenuItem.addActionListener(this);
3305     invertSequenceMenuItem.setLabel(MessageManager
3306             .getString("action.invert_sequence_selection"));
3307     invertSequenceMenuItem.addActionListener(this);
3308     invertColSel.setLabel(MessageManager
3309             .getString("action.invert_column_selection"));
3310     invertColSel.addActionListener(this);
3311     deleteGroups.setLabel(MessageManager
3312             .getString("action.undefine_groups"));
3313     deleteGroups.addActionListener(this);
3314     grpsFromSelection.setLabel(MessageManager
3315             .getString("action.make_groups_selection"));
3316     grpsFromSelection.addActionListener(this);
3317     createGroup.setLabel(MessageManager.getString("action.create_group"));
3318     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3319     annotationColumnSelection.setLabel(MessageManager
3320             .getString("action.select_by_annotation"));
3321     annotationColumnSelection.addActionListener(this);
3322
3323     /*
3324      * Configure View menu items and actions
3325      */
3326     newView.setLabel(MessageManager.getString("action.new_view"));
3327     newView.addActionListener(this);
3328     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3329     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3330     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3331     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3332     hideColumns
3333             .setLabel(MessageManager.getString("label.selected_columns"));
3334     hideSequences.setLabel(MessageManager
3335             .getString("label.selected_sequences"));
3336     hideAllButSelection.setLabel(MessageManager
3337             .getString("label.all_but_selected_region"));
3338     hideAllSelection.setLabel(MessageManager
3339             .getString("label.selected_region"));
3340     showAllHidden.setLabel(MessageManager
3341             .getString("label.all_sequences_columns"));
3342     showColumns.addActionListener(this);
3343     showSeqs.addActionListener(this);
3344     hideColumns.addActionListener(this);
3345     hideSequences.addActionListener(this);
3346     hideAllButSelection.addActionListener(this);
3347     hideAllSelection.addActionListener(this);
3348     showAllHidden.addActionListener(this);
3349     featureSettings.setLabel(MessageManager
3350             .getString("action.feature_settings"));
3351     featureSettings.addActionListener(this);
3352     sequenceFeatures.setLabel(MessageManager
3353             .getString("label.show_sequence_features"));
3354     sequenceFeatures.addItemListener(this);
3355     sequenceFeatures.setState(false);
3356     followMouseOverFlag.setLabel(MessageManager
3357             .getString("label.automatic_scrolling"));
3358     followMouseOverFlag.addItemListener(this);
3359     alProperties.addActionListener(this);
3360     overviewMenuItem.setLabel(MessageManager
3361             .getString("label.overview_window"));
3362     overviewMenuItem.addActionListener(this);
3363
3364     /*
3365      * Configure Annotations menu items and actions
3366      */
3367     annotationPanelMenuItem.setLabel(MessageManager
3368             .getString("label.show_annotations"));
3369     annotationPanelMenuItem.addItemListener(this);
3370     showGroupConsensus.setLabel(MessageManager
3371             .getString("label.group_consensus"));
3372     showGroupConservation.setLabel(MessageManager
3373             .getString("label.group_conservation"));
3374     showConsensusHistogram.setLabel(MessageManager
3375             .getString("label.show_consensus_histogram"));
3376     showSequenceLogo.setLabel(MessageManager
3377             .getString("label.show_consensus_logo"));
3378     normSequenceLogo.setLabel(MessageManager
3379             .getString("label.norm_consensus_logo"));
3380     applyAutoAnnotationSettings.setLabel(MessageManager
3381             .getString("label.apply_all_groups"));
3382     applyAutoAnnotationSettings.setState(true);
3383     Menu autoAnnMenu = new Menu(
3384             MessageManager.getString("label.autocalculated_annotation"));
3385     showGroupConsensus.addItemListener(this);
3386     showGroupConservation.addItemListener(this);
3387     showConsensusHistogram.addItemListener(this);
3388     showSequenceLogo.addItemListener(this);
3389     normSequenceLogo.addItemListener(this);
3390     applyAutoAnnotationSettings.addItemListener(this);
3391     showAlignmentAnnotations = new CheckboxMenuItem(
3392             MessageManager.getString("label.show_all_al_annotations"));
3393     showSequenceAnnotations = new CheckboxMenuItem(
3394             MessageManager.getString("label.show_all_seq_annotations"));
3395     sortAnnBySequence = new CheckboxMenuItem(
3396             MessageManager.getString("label.sort_annotations_by_sequence"));
3397     sortAnnByLabel = new CheckboxMenuItem(
3398             MessageManager.getString("label.sort_annotations_by_label"));
3399     showAutoFirst = new CheckboxMenuItem(
3400             MessageManager.getString("label.show_first"));
3401     showAutoFirst.setState(false); // pending applet parameter
3402     setShowAutoCalculatedAbove(showAutoFirst.getState());
3403     showAutoLast = new CheckboxMenuItem(
3404             MessageManager.getString("label.show_last"));
3405     showAutoLast.setState(!showAutoFirst.getState());
3406     showAlignmentAnnotations.addItemListener(this);
3407     showSequenceAnnotations.addItemListener(this);
3408     sortAnnBySequence.addItemListener(this);
3409     sortAnnByLabel.addItemListener(this);
3410     showAutoFirst.addItemListener(this);
3411     showAutoLast.addItemListener(this);
3412
3413     /*
3414      * Configure Format menu items and actions
3415      */
3416     font.setLabel(MessageManager.getString("action.font"));
3417     font.addActionListener(this);
3418     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3419     scaleAbove.setState(true);
3420     scaleAbove.setEnabled(false);
3421     scaleAbove.addItemListener(this);
3422     scaleLeft.setEnabled(false);
3423     scaleLeft.setState(true);
3424     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3425     scaleLeft.addItemListener(this);
3426     scaleRight.setEnabled(false);
3427     scaleRight.setState(true);
3428     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3429     scaleRight.addItemListener(this);
3430     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3431     viewBoxesMenuItem.setState(true);
3432     viewBoxesMenuItem.addItemListener(this);
3433     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3434     viewTextMenuItem.setState(true);
3435     viewTextMenuItem.addItemListener(this);
3436     colourTextMenuItem.setLabel(MessageManager
3437             .getString("label.colour_text"));
3438     colourTextMenuItem.addItemListener(this);
3439     displayNonconservedMenuItem.setLabel(MessageManager
3440             .getString("label.show_non_conserved"));
3441     displayNonconservedMenuItem.addItemListener(this);
3442     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3443     wrapMenuItem.addItemListener(this);
3444     renderGapsMenuItem.setLabel(MessageManager
3445             .getString("action.show_gaps"));
3446     renderGapsMenuItem.setState(true);
3447     renderGapsMenuItem.addItemListener(this);
3448     centreColumnLabelFlag.setLabel(MessageManager
3449             .getString("label.centre_column_labels"));
3450     centreColumnLabelFlag.addItemListener(this);
3451     seqLimits.setState(true);
3452     seqLimits.setLabel(MessageManager
3453             .getString("label.show_sequence_limits"));
3454     seqLimits.addItemListener(this);
3455
3456     /*
3457      * Configure Colour menu items and actions
3458      */
3459     applyToAllGroups.setLabel(MessageManager
3460             .getString("label.apply_colour_to_all_groups"));
3461     applyToAllGroups.setState(true);
3462     applyToAllGroups.addItemListener(this);
3463     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3464     clustalColour.addActionListener(this);
3465     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3466     zappoColour.addActionListener(this);
3467     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3468     taylorColour.addActionListener(this);
3469     hydrophobicityColour.setLabel(MessageManager
3470             .getString("label.hydrophobicity"));
3471     hydrophobicityColour.addActionListener(this);
3472     helixColour
3473             .setLabel(MessageManager.getString("label.helix_propensity"));
3474     helixColour.addActionListener(this);
3475     strandColour.setLabel(MessageManager
3476             .getString("label.strand_propensity"));
3477     strandColour.addActionListener(this);
3478     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3479     turnColour.addActionListener(this);
3480     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3481     buriedColour.addActionListener(this);
3482     purinePyrimidineColour.setLabel(MessageManager
3483             .getString("label.purine_pyrimidine"));
3484     purinePyrimidineColour.addActionListener(this);
3485     // RNAInteractionColour.setLabel(MessageManager
3486     // .getString("label.rna_interaction"));
3487     // RNAInteractionColour.addActionListener(this);
3488     RNAHelixColour.setLabel(MessageManager
3489             .getString("action.by_rna_helixes"));
3490     RNAHelixColour.addActionListener(this);
3491     userDefinedColour.setLabel(MessageManager
3492             .getString("action.user_defined"));
3493     userDefinedColour.addActionListener(this);
3494     PIDColour.setLabel(MessageManager
3495             .getString("label.percentage_identity"));
3496     PIDColour.addActionListener(this);
3497     BLOSUM62Colour.setLabel(MessageManager
3498             .getString("label.blosum62_score"));
3499     BLOSUM62Colour.addActionListener(this);
3500     tcoffeeColour
3501             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3502     // it will be enabled only if a score file is provided
3503     tcoffeeColour.setEnabled(false);
3504     tcoffeeColour.addActionListener(this);
3505     conservationMenuItem.setLabel(MessageManager
3506             .getString("action.by_conservation"));
3507     conservationMenuItem.addItemListener(this);
3508     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3509     noColourmenuItem.addActionListener(this);
3510     abovePIDThreshold.setLabel(MessageManager
3511             .getString("label.above_identity_threshold"));
3512     abovePIDThreshold.addItemListener(this);
3513     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3514     nucleotideColour.addActionListener(this);
3515     modifyPID.setLabel(MessageManager
3516             .getString("label.modify_identity_threshold"));
3517     modifyPID.addActionListener(this);
3518     modifyConservation.setLabel(MessageManager
3519             .getString("label.modify_conservation_threshold"));
3520     modifyConservation.addActionListener(this);
3521     annotationColour.setLabel(MessageManager
3522             .getString("action.by_annotation"));
3523     annotationColour.addActionListener(this);
3524
3525     /*
3526      * Configure Calculate menu items and actions
3527      */
3528     sortPairwiseMenuItem.setLabel(MessageManager
3529             .getString("action.by_pairwise_id"));
3530     sortPairwiseMenuItem.addActionListener(this);
3531     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3532     sortIDMenuItem.addActionListener(this);
3533     sortLengthMenuItem.setLabel(MessageManager
3534             .getString("action.by_length"));
3535     sortLengthMenuItem.addActionListener(this);
3536     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3537     sortGroupMenuItem.addActionListener(this);
3538     pairwiseAlignmentMenuItem.setLabel(MessageManager
3539             .getString("action.pairwise_alignment"));
3540     pairwiseAlignmentMenuItem.addActionListener(this);
3541     PCAMenuItem.setLabel(MessageManager
3542             .getString("label.principal_component_analysis"));
3543     PCAMenuItem.addActionListener(this);
3544     autoCalculate = new CheckboxMenuItem(
3545             MessageManager.getString("label.autocalculate_consensus"), true);
3546     averageDistanceTreeMenuItem.setLabel(MessageManager
3547             .getString("label.average_distance_identity"));
3548     averageDistanceTreeMenuItem.addActionListener(this);
3549     neighbourTreeMenuItem.setLabel(MessageManager
3550             .getString("label.neighbour_joining_identity"));
3551     neighbourTreeMenuItem.addActionListener(this);
3552     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3553             .getString("label.average_distance_bloslum62"));
3554     avDistanceTreeBlosumMenuItem.addActionListener(this);
3555     njTreeBlosumMenuItem.setLabel(MessageManager
3556             .getString("label.neighbour_blosum62"));
3557     njTreeBlosumMenuItem.addActionListener(this);
3558     sortByTreeMenu.setLabel(MessageManager
3559             .getString("action.by_tree_order"));
3560     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3561     Menu calculateTreeMenu = new Menu(
3562             MessageManager.getString("action.calculate_tree"));
3563     autoCalculate.addItemListener(this);
3564     sortByTree.addItemListener(this);
3565
3566     /*
3567      * Configure Help menu items and actions
3568      */
3569     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3570     documentation.setLabel(MessageManager.getString("label.documentation"));
3571     documentation.addActionListener(this);
3572     about.setLabel(MessageManager.getString("label.about"));
3573     about.addActionListener(this);
3574
3575     /*
3576      * Add top level menus to frame
3577      */
3578     alignFrameMenuBar.add(fileMenu);
3579     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3580     alignFrameMenuBar.add(editMenu);
3581     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3582     alignFrameMenuBar.add(selectMenu);
3583     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3584     alignFrameMenuBar.add(viewMenu);
3585     Menu annotationsMenu = new Menu(
3586             MessageManager.getString("action.annotations"));
3587     alignFrameMenuBar.add(annotationsMenu);
3588     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3589     alignFrameMenuBar.add(formatMenu);
3590     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3591     alignFrameMenuBar.add(colourMenu);
3592     Menu calculateMenu = new Menu(
3593             MessageManager.getString("action.calculate"));
3594     alignFrameMenuBar.add(calculateMenu);
3595     alignFrameMenuBar.add(helpMenu);
3596
3597     /*
3598      * File menu
3599      */
3600     fileMenu.add(inputText);
3601     fileMenu.add(loadTree);
3602     fileMenu.add(loadAnnotations);
3603     fileMenu.addSeparator();
3604     fileMenu.add(outputTextboxMenu);
3605     fileMenu.add(outputFeatures);
3606     fileMenu.add(outputAnnotations);
3607     if (jalviewServletURL != null)
3608     {
3609       fileMenu.add(loadApplication);
3610     }
3611     fileMenu.addSeparator();
3612     fileMenu.add(closeMenuItem);
3613
3614     /*
3615      * Edit menu
3616      */
3617     editMenu.add(undoMenuItem);
3618     editMenu.add(redoMenuItem);
3619     editMenu.add(cut);
3620     editMenu.add(copy);
3621     pasteMenu.add(pasteNew);
3622     pasteMenu.add(pasteThis);
3623     editMenu.add(pasteMenu);
3624     editMenu.add(delete);
3625     editMenu.addSeparator();
3626     editMenu.add(remove2LeftMenuItem);
3627     editMenu.add(remove2RightMenuItem);
3628     editMenu.add(removeGappedColumnMenuItem);
3629     editMenu.add(removeAllGapsMenuItem);
3630     editMenu.add(removeRedundancyMenuItem);
3631
3632     /*
3633      * Select menu
3634      */
3635     selectMenu.add(findMenuItem);
3636     selectMenu.addSeparator();
3637     selectMenu.add(selectAllSequenceMenuItem);
3638     selectMenu.add(deselectAllSequenceMenuItem);
3639     selectMenu.add(invertSequenceMenuItem);
3640     selectMenu.add(invertColSel);
3641     selectMenu.add(createGroup);
3642     selectMenu.add(unGroup);
3643     selectMenu.add(grpsFromSelection);
3644     selectMenu.add(deleteGroups);
3645     selectMenu.add(annotationColumnSelection);
3646
3647     /*
3648      * View menu
3649      */
3650     viewMenu.add(newView);
3651     viewMenu.addSeparator();
3652     showMenu.add(showColumns);
3653     showMenu.add(showSeqs);
3654     showMenu.add(showAllHidden);
3655     viewMenu.add(showMenu);
3656     hideMenu.add(hideColumns);
3657     hideMenu.add(hideSequences);
3658     hideMenu.add(hideAllSelection);
3659     hideMenu.add(hideAllButSelection);
3660     viewMenu.add(hideMenu);
3661     viewMenu.addSeparator();
3662     viewMenu.add(followMouseOverFlag);
3663     viewMenu.addSeparator();
3664     viewMenu.add(sequenceFeatures);
3665     viewMenu.add(featureSettings);
3666     viewMenu.addSeparator();
3667     viewMenu.add(alProperties);
3668     viewMenu.addSeparator();
3669     viewMenu.add(overviewMenuItem);
3670
3671     /*
3672      * Annotations menu
3673      */
3674     annotationsMenu.add(annotationPanelMenuItem);
3675     annotationsMenu.addSeparator();
3676     annotationsMenu.add(showAlignmentAnnotations);
3677     annotationsMenu.add(showSequenceAnnotations);
3678     annotationsMenu.add(sortAnnBySequence);
3679     annotationsMenu.add(sortAnnByLabel);
3680     annotationsMenu.addSeparator();
3681     autoAnnMenu.add(showAutoFirst);
3682     autoAnnMenu.add(showAutoLast);
3683     autoAnnMenu.addSeparator();
3684     autoAnnMenu.add(applyAutoAnnotationSettings);
3685     autoAnnMenu.add(showConsensusHistogram);
3686     autoAnnMenu.add(showSequenceLogo);
3687     autoAnnMenu.add(normSequenceLogo);
3688     autoAnnMenu.addSeparator();
3689     autoAnnMenu.add(showGroupConservation);
3690     autoAnnMenu.add(showGroupConsensus);
3691     annotationsMenu.add(autoAnnMenu);
3692
3693     /*
3694      * Format menu
3695      */
3696     formatMenu.add(font);
3697     formatMenu.add(seqLimits);
3698     formatMenu.add(wrapMenuItem);
3699     formatMenu.add(scaleAbove);
3700     formatMenu.add(scaleLeft);
3701     formatMenu.add(scaleRight);
3702     formatMenu.add(viewBoxesMenuItem);
3703     formatMenu.add(viewTextMenuItem);
3704     formatMenu.add(colourTextMenuItem);
3705     formatMenu.add(displayNonconservedMenuItem);
3706     formatMenu.add(renderGapsMenuItem);
3707     formatMenu.add(centreColumnLabelFlag);
3708
3709     /*
3710      * Colour menu
3711      */
3712     colourMenu.add(applyToAllGroups);
3713     colourMenu.addSeparator();
3714     colourMenu.add(noColourmenuItem);
3715     colourMenu.add(clustalColour);
3716     colourMenu.add(BLOSUM62Colour);
3717     colourMenu.add(PIDColour);
3718     colourMenu.add(zappoColour);
3719     colourMenu.add(taylorColour);
3720     colourMenu.add(hydrophobicityColour);
3721     colourMenu.add(helixColour);
3722     colourMenu.add(strandColour);
3723     colourMenu.add(turnColour);
3724     colourMenu.add(buriedColour);
3725     colourMenu.add(nucleotideColour);
3726     colourMenu.add(purinePyrimidineColour);
3727     // colourMenu.add(RNAInteractionColour);
3728     colourMenu.add(tcoffeeColour);
3729     colourMenu.add(userDefinedColour);
3730     colourMenu.addSeparator();
3731     colourMenu.add(conservationMenuItem);
3732     colourMenu.add(modifyConservation);
3733     colourMenu.add(abovePIDThreshold);
3734     colourMenu.add(modifyPID);
3735     colourMenu.add(annotationColour);
3736     colourMenu.add(RNAHelixColour);
3737
3738     /*
3739      * Calculate menu
3740      */
3741     sortMenu.add(sortIDMenuItem);
3742     sortMenu.add(sortLengthMenuItem);
3743     sortMenu.add(sortByTreeMenu);
3744     sortMenu.add(sortGroupMenuItem);
3745     sortMenu.add(sortPairwiseMenuItem);
3746     calculateMenu.add(sortMenu);
3747     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3748     calculateTreeMenu.add(neighbourTreeMenuItem);
3749     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3750     calculateTreeMenu.add(njTreeBlosumMenuItem);
3751     calculateMenu.add(calculateTreeMenu);
3752     calculateMenu.addSeparator();
3753     calculateMenu.add(pairwiseAlignmentMenuItem);
3754     calculateMenu.add(PCAMenuItem);
3755     calculateMenu.add(autoCalculate);
3756     calculateMenu.add(sortByTree);
3757
3758     /*
3759      * Help menu
3760      */
3761     helpMenu.add(documentation);
3762     helpMenu.add(about);
3763
3764     /*
3765      * Status bar
3766      */
3767     statusBar.setBackground(Color.white);
3768     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3769     statusBar.setText(MessageManager.getString("label.status_bar"));
3770     this.add(statusBar, BorderLayout.SOUTH);
3771   }
3772
3773   @Override
3774   public void setStatus(String string)
3775   {
3776     statusBar.setText(string);
3777   };
3778
3779   MenuItem featureSettings = new MenuItem();
3780
3781   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3782
3783   MenuItem annotationColour = new MenuItem();
3784
3785   MenuItem annotationColumnSelection = new MenuItem();
3786
3787   MenuItem invertColSel = new MenuItem();
3788
3789   MenuItem showColumns = new MenuItem();
3790
3791   MenuItem showSeqs = new MenuItem();
3792
3793   MenuItem hideColumns = new MenuItem();
3794
3795   MenuItem hideSequences = new MenuItem();
3796
3797   MenuItem hideAllButSelection = new MenuItem();
3798
3799   MenuItem hideAllSelection = new MenuItem();
3800
3801   MenuItem showAllHidden = new MenuItem();
3802
3803   MenuItem newView = new MenuItem();
3804
3805   private CheckboxMenuItem showAlignmentAnnotations;
3806
3807   private CheckboxMenuItem showSequenceAnnotations;
3808
3809   private CheckboxMenuItem sortAnnBySequence;
3810
3811   private CheckboxMenuItem sortAnnByLabel;
3812
3813   private CheckboxMenuItem showAutoFirst;
3814
3815   private CheckboxMenuItem showAutoLast;
3816
3817   private SplitFrame splitFrame;
3818
3819   /**
3820    * Attach the alignFrame panels after embedding menus, if necessary. This used
3821    * to be called setEmbedded, but is now creates the dropdown menus in a
3822    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3823    *
3824    * @param reallyEmbedded
3825    *          true to attach the view to the applet area on the page rather than
3826    *          in a new window
3827    */
3828   public void createAlignFrameWindow(boolean reallyEmbedded)
3829   {
3830     if (reallyEmbedded)
3831     {
3832       embedAlignFrameInApplet(viewport.applet);
3833     }
3834     else
3835     {
3836       // //////
3837       // test and embed menu bar if necessary.
3838       //
3839       if (embedMenuIfNeeded(alignPanel))
3840       {
3841         /*
3842          * adjust for status bar height too. ? pointless as overridden by layout
3843          * manager
3844          */
3845         alignPanel.setSize(getSize().width,
3846                 getSize().height - statusBar.getHeight());
3847       }
3848       add(statusBar, BorderLayout.SOUTH);
3849       add(alignPanel, BorderLayout.CENTER);
3850       // and register with the applet so it can pass external API calls to us
3851       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3852               frameHeight);
3853     }
3854   }
3855
3856   /**
3857    * Add the components of this AlignFrame to the applet container.
3858    *
3859    * @param theApplet
3860    */
3861   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3862   {
3863     // ////
3864     // Explicitly build the embedded menu panel for the on-page applet
3865     //
3866     // view cannot be closed if its actually on the page
3867     fileMenu.remove(closeMenuItem);
3868     fileMenu.remove(3); // Remove Separator
3869     // construct embedded menu, using default font
3870     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3871     // and actually add the components to the applet area
3872     theApplet.setLayout(new BorderLayout());
3873     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3874     theApplet.add(statusBar, BorderLayout.SOUTH);
3875     // TODO should size be left to the layout manager?
3876     alignPanel.setSize(theApplet.getSize().width,
3877             theApplet.getSize().height - embeddedMenu.getHeight()
3878                     - statusBar.getHeight());
3879     theApplet.add(alignPanel, BorderLayout.CENTER);
3880     final AlignFrame me = this;
3881     theApplet.addFocusListener(new FocusListener()
3882     {
3883
3884       @Override
3885       public void focusLost(FocusEvent e)
3886       {
3887         if (theApplet.currentAlignFrame == me)
3888         {
3889           theApplet.currentAlignFrame = null;
3890         }
3891       }
3892
3893       @Override
3894       public void focusGained(FocusEvent e)
3895       {
3896         theApplet.currentAlignFrame = me;
3897       }
3898     });
3899     theApplet.validate();
3900   }
3901
3902   /**
3903    * create a new binding between structures in an existing jmol viewer instance
3904    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3905    * this does not open a new Jmol window, or modify the display of the
3906    * structures in the original jmol window. Note This method doesn't work
3907    * without an additional javascript library to exchange messages between the
3908    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3909    *
3910    * @param viewer
3911    *          JmolViewer instance
3912    * @param sequenceIds
3913    *          - sequence Ids to search for associations
3914    */
3915   public SequenceStructureBinding addStructureViewInstance(
3916           Object jmolviewer, String[] sequenceIds)
3917   {
3918     Viewer viewer = null;
3919     try
3920     {
3921       viewer = (Viewer) jmolviewer;
3922     } catch (ClassCastException ex)
3923     {
3924       System.err.println("Unsupported viewer object :"
3925               + jmolviewer.getClass());
3926     }
3927     if (viewer == null)
3928     {
3929       System.err.println("Can't use this object as a structure viewer:"
3930               + jmolviewer.getClass());
3931       return null;
3932     }
3933     SequenceI[] seqs = null;
3934     if (sequenceIds == null || sequenceIds.length == 0)
3935     {
3936       seqs = viewport.getAlignment().getSequencesArray();
3937     }
3938     else
3939     {
3940       Vector sqi = new Vector();
3941       AlignmentI al = viewport.getAlignment();
3942       for (int sid = 0; sid < sequenceIds.length; sid++)
3943       {
3944         SequenceI sq = al.findName(sequenceIds[sid]);
3945         if (sq != null)
3946         {
3947           sqi.addElement(sq);
3948         }
3949       }
3950       if (sqi.size() > 0)
3951       {
3952         seqs = new SequenceI[sqi.size()];
3953         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3954         {
3955           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3956         }
3957       }
3958       else
3959       {
3960         return null;
3961       }
3962     }
3963     AAStructureBindingModel jmv = null;
3964     // TODO: search for a jmv that involves viewer
3965     if (jmv == null)
3966     { // create a new viewer/jalview binding.
3967       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3968     }
3969     return jmv;
3970
3971   }
3972
3973   /**
3974    * bind a pdb file to a sequence in the current view
3975    *
3976    * @param sequenceId
3977    *          - sequenceId within the dataset.
3978    * @param pdbEntryString
3979    *          - the short name for the PDB file
3980    * @param pdbFile
3981    *          - pdb file - either a URL or a valid PDB file.
3982    * @return true if binding was as success TODO: consider making an exception
3983    *         structure for indicating when PDB parsing or sequenceId location
3984    *         fails.
3985    */
3986   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3987           String pdbFile)
3988   {
3989     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3990     boolean needtoadd = false;
3991     if (toaddpdb != null)
3992     {
3993       Vector pdbe = toaddpdb.getAllPDBEntries();
3994       PDBEntry pdbentry = null;
3995       if (pdbe != null && pdbe.size() > 0)
3996       {
3997         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3998         {
3999           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4000           if (!pdbentry.getId().equals(pdbEntryString)
4001                   && !pdbentry.getFile().equals(pdbFile))
4002           {
4003             pdbentry = null;
4004           }
4005           else
4006           {
4007             continue;
4008           }
4009         }
4010       }
4011       if (pdbentry == null)
4012       {
4013         pdbentry = new PDBEntry();
4014         pdbentry.setId(pdbEntryString);
4015         pdbentry.setFile(pdbFile);
4016         needtoadd = true; // add this new entry to sequence.
4017       }
4018       // resolve data source
4019       // TODO: this code should be a refactored to an io package
4020       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4021               pdbFile, FileFormat.PDB);
4022       if (protocol == null)
4023       {
4024         return false;
4025       }
4026       if (needtoadd)
4027       {
4028         pdbentry.setProperty("protocol", protocol);
4029         toaddpdb.addPDBId(pdbentry);
4030         alignPanel.getStructureSelectionManager()
4031                 .registerPDBEntry(pdbentry);
4032       }
4033     }
4034     return true;
4035   }
4036
4037   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4038   {
4039     if (seqs != null)
4040     {
4041       Vector sequences = new Vector();
4042       for (int i = 0; i < seqs.length; i++)
4043       {
4044         if (seqs[i] != null)
4045         {
4046           sequences.addElement(new Object[] { seqs[i],
4047               (chains != null) ? chains[i] : null });
4048         }
4049       }
4050       seqs = new SequenceI[sequences.size()];
4051       chains = new String[sequences.size()];
4052       for (int i = 0, isize = sequences.size(); i < isize; i++)
4053       {
4054         Object[] oj = (Object[]) sequences.elementAt(i);
4055
4056         seqs[i] = (SequenceI) oj[0];
4057         chains[i] = (String) oj[1];
4058       }
4059     }
4060     return new Object[] { seqs, chains };
4061
4062   }
4063
4064   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4065           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4066   {
4067     // Scrub any null sequences from the array
4068     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4069     seqs = (SequenceI[]) sqch[0];
4070     chains = (String[]) sqch[1];
4071     if (seqs == null || seqs.length == 0)
4072     {
4073       System.err
4074               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4075     }
4076     if (protocol == null)
4077     {
4078       String sourceType = (String) pdb.getProperty("protocol");
4079       try
4080       {
4081         protocol = DataSourceType.valueOf(sourceType);
4082       } catch (IllegalArgumentException e)
4083       {
4084         // ignore
4085       }
4086       if (protocol == null)
4087       {
4088         System.err.println("Couldn't work out protocol to open structure: "
4089                 + pdb.getId());
4090         return;
4091       }
4092     }
4093     if (applet.useXtrnalSviewer)
4094     {
4095       // register the association(s) and quit, don't create any windows.
4096       if (StructureSelectionManager.getStructureSelectionManager(applet)
4097               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4098       {
4099         System.err.println("Failed to map " + pdb.getFile() + " ("
4100                 + protocol + ") to any sequences");
4101       }
4102       return;
4103     }
4104     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4105     {
4106       // can only do alignments with Jmol
4107       // find the last jmol window assigned to this alignment
4108       AppletJmol ajm = null, tajm;
4109       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4110       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4111       {
4112         tajm = (AppletJmol) jmols.elementAt(i);
4113         if (tajm.ap.alignFrame == this)
4114         {
4115           ajm = tajm;
4116           break;
4117         }
4118       }
4119       if (ajm != null)
4120       {
4121         System.err
4122                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4123         // try and add the pdb structure
4124         // ajm.addS
4125         ajm = null;
4126       }
4127     }
4128     // otherwise, create a new window
4129     if (applet.jmolAvailable)
4130     {
4131       new AppletJmol(pdb, seqs, chains, alignPanel,
4132               protocol);
4133       applet.lastFrameX += 40;
4134       applet.lastFrameY += 40;
4135     }
4136     else
4137     {
4138       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4139     }
4140
4141   }
4142
4143   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4144           SequenceI[][] seqs, String[][] chains, String[] protocols)
4145   {
4146     // TODO Auto-generated method stub
4147     System.err.println("Aligned Structure View: Not yet implemented.");
4148   }
4149
4150   /**
4151    * modify the current selection, providing the user has not made a selection
4152    * already.
4153    *
4154    * @param sel
4155    *          - sequences from this alignment
4156    * @param csel
4157    *          - columns to be selected on the alignment
4158    */
4159   public void select(SequenceGroup sel, ColumnSelection csel)
4160   {
4161     alignPanel.seqPanel.selection(sel, csel, null);
4162   }
4163
4164   public void scrollTo(int row, int column)
4165   {
4166     alignPanel.seqPanel.scrollTo(row, column);
4167   }
4168
4169   public void scrollToRow(int row)
4170   {
4171     alignPanel.seqPanel.scrollToRow(row);
4172   }
4173
4174   public void scrollToColumn(int column)
4175   {
4176     alignPanel.seqPanel.scrollToColumn(column);
4177   }
4178
4179   /**
4180    * @return the alignments unique ID.
4181    */
4182   public String getSequenceSetId()
4183   {
4184     return viewport.getSequenceSetId();
4185   }
4186
4187   /**
4188    * Load the (T-Coffee) score file from the specified url
4189    *
4190    * @param source
4191    *          File/URL/T-COFFEE score file contents
4192    * @throws IOException
4193    * @return true if alignment was annotated with data from source
4194    */
4195   public boolean loadScoreFile(String source) throws IOException
4196   {
4197
4198     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4199             AppletFormatAdapter.checkProtocol(source));
4200     if (!file.isValid())
4201     {
4202       // TODO: raise dialog for gui
4203       System.err.println("Problems parsing T-Coffee scores: "
4204               + file.getWarningMessage());
4205       System.err.println("Origin was:\n" + source);
4206       return false;
4207     }
4208
4209     /*
4210      * check that the score matrix matches the alignment dimensions
4211      */
4212     AlignmentI aln;
4213     if ((aln = viewport.getAlignment()) != null
4214             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4215                     .getWidth()))
4216     {
4217       // TODO: raise a dialog box here rather than bomb out.
4218       System.err
4219               .println("The scores matrix does not match the alignment dimensions");
4220
4221     }
4222
4223     // TODO add parameter to indicate if matching should be done
4224     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4225     {
4226       alignPanel.fontChanged();
4227       tcoffeeColour.setEnabled(true);
4228       // switch to this color
4229       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4230       return true;
4231     }
4232     else
4233     {
4234       System.err.println("Problems resolving T-Coffee scores:");
4235       if (file.getWarningMessage() != null)
4236       {
4237         System.err.println(file.getWarningMessage());
4238       }
4239     }
4240     return false;
4241   }
4242
4243   public SplitFrame getSplitFrame()
4244   {
4245     return this.splitFrame;
4246   }
4247
4248   public void setSplitFrame(SplitFrame sf)
4249   {
4250     this.splitFrame = sf;
4251   }
4252
4253   // may not need this
4254   @Override
4255   public void setShowSeqFeatures(boolean b)
4256   {
4257     // showSeqFeatures.setSelected(b);
4258     viewport.setShowSequenceFeatures(b);
4259
4260   }
4261
4262   @Override
4263   public void setMenusForViewport()
4264   {
4265     // setMenusFromViewport(viewport);
4266
4267   }
4268
4269   @Override
4270   public void refreshFeatureUI(boolean enableIfNecessary)
4271   {
4272     if (enableIfNecessary)
4273     {
4274       sequenceFeatures.setState(true);
4275       alignPanel.av.setShowSequenceFeatures(true);
4276     }
4277   }
4278
4279   @Override
4280   public FeatureSettingsControllerI getFeatureSettingsUI()
4281   {
4282     return alignPanel.av.featureSettings;
4283   }
4284
4285 }