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.FeatureRenderer;
  29 import jalview.api.FeatureSettingsControllerI;
  30 import jalview.api.SequenceStructureBinding;
  31 import jalview.bin.JalviewLite;
  32 import jalview.commands.CommandI;
  33 import jalview.commands.EditCommand;
  34 import jalview.commands.EditCommand.Action;
  35 import jalview.commands.OrderCommand;
  36 import jalview.commands.RemoveGapColCommand;
  37 import jalview.commands.RemoveGapsCommand;
  38 import jalview.commands.SlideSequencesCommand;
  39 import jalview.commands.TrimRegionCommand;
  40 import jalview.datamodel.Alignment;
  41 import jalview.datamodel.AlignmentAnnotation;
  42 import jalview.datamodel.AlignmentI;
  43 import jalview.datamodel.AlignmentOrder;
  44 import jalview.datamodel.ColumnSelection;
  45 import jalview.datamodel.PDBEntry;
  46 import jalview.datamodel.Sequence;
  47 import jalview.datamodel.SequenceGroup;
  48 import jalview.datamodel.SequenceI;
  49 import jalview.io.AnnotationFile;
  50 import jalview.io.AppletFormatAdapter;
  51 import jalview.io.FeaturesFile;
  52 import jalview.io.TCoffeeScoreFile;
  53 import jalview.schemes.Blosum62ColourScheme;
  54 import jalview.schemes.BuriedColourScheme;
  55 import jalview.schemes.ClustalxColourScheme;
  56 import jalview.schemes.ColourSchemeI;
  57 import jalview.schemes.HelixColourScheme;
  58 import jalview.schemes.HydrophobicColourScheme;
  59 import jalview.schemes.NucleotideColourScheme;
  60 import jalview.schemes.PIDColourScheme;
  61 import jalview.schemes.PurinePyrimidineColourScheme;
  62 import jalview.schemes.RNAHelicesColourChooser;
  63 import jalview.schemes.StrandColourScheme;
  64 import jalview.schemes.TCoffeeColourScheme;
  65 import jalview.schemes.TaylorColourScheme;
  66 import jalview.schemes.TurnColourScheme;
  67 import jalview.schemes.ZappoColourScheme;
  68 import jalview.structure.StructureSelectionManager;
  69 import jalview.structures.models.AAStructureBindingModel;
  70 import jalview.util.MappingUtils;
  71 import jalview.util.MessageManager;
  72 import jalview.viewmodel.AlignmentViewport;
  73
  74 import java.awt.BorderLayout;
  75 import java.awt.Canvas;
  76 import java.awt.CheckboxMenuItem;
  77 import java.awt.Color;
  78 import java.awt.FlowLayout;
  79 import java.awt.Font;
  80 import java.awt.FontMetrics;
  81 import java.awt.Frame;
  82 import java.awt.Graphics;
  83 import java.awt.Label;
  84 import java.awt.Menu;
  85 import java.awt.MenuBar;
  86 import java.awt.MenuItem;
  87 import java.awt.Panel;
  88 import java.awt.event.ActionEvent;
  89 import java.awt.event.ActionListener;
  90 import java.awt.event.FocusEvent;
  91 import java.awt.event.FocusListener;
  92 import java.awt.event.ItemEvent;
  93 import java.awt.event.ItemListener;
  94 import java.awt.event.KeyEvent;
  95 import java.awt.event.KeyListener;
  96 import java.awt.event.WindowAdapter;
  97 import java.awt.event.WindowEvent;
  98 import java.io.IOException;
  99 import java.net.URL;
 100 import java.net.URLEncoder;
 101 import java.util.Arrays;
 102 import java.util.Deque;
 103 import java.util.HashMap;
 104 import java.util.Hashtable;
 105 import java.util.List;
 106 import java.util.Map;
 107 import java.util.StringTokenizer;
 108 import java.util.Vector;
 109
 110 import org.jmol.viewer.Viewer;
 111
 112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 113         ItemListener, KeyListener, AlignViewControllerGuiI
 114 {
 115   public AlignViewControllerI avc;
 116
 117   public AlignmentPanel alignPanel;
 118
 119   public AlignViewport viewport;
 120
 121   // width and height may be overridden by applet parameters
 122   int frameWidth = 700;
 123
 124   int frameHeight = 500;
 125
 126   String jalviewServletURL;
 127
 128   /*
 129    * Flag for showing autocalculated consensus above or below other consensus
 130    * rows
 131    */
 132   private boolean showAutoCalculatedAbove;
 133
 134   private SequenceAnnotationOrder annotationSortOrder;
 135
 136   /**
 137    * Constructor that creates the frame and adds it to the display.
 138    *
 139    * @param al
 140    * @param applet
 141    * @param title
 142    * @param embedded
 143    */
 144   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 145           boolean embedded)
 146   {
 147     this(al, applet, title, embedded, true);
 148   }
 149
 150   /**
 151    * Constructor that optionally allows the frame to be displayed or only
 152    * created.
 153    *
 154    * @param al
 155    * @param applet
 156    * @param title
 157    * @param embedded
 158    * @param addToDisplay
 159    */
 160   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 161           boolean embedded, boolean addToDisplay)
 162   {
 163     this(al, null, null, applet, title, embedded, addToDisplay);
 164   }
 165
 166   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 167           ColumnSelection columnSelection, JalviewLite applet,
 168           String title, boolean embedded)
 169   {
 170     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 171   }
 172
 173   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 174           ColumnSelection columnSelection, JalviewLite applet,
 175           String title, boolean embedded, boolean addToDisplay)
 176   {
 177     if (applet != null)
 178     {
 179       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 180     }
 181
 182     try
 183     {
 184       jbInit();
 185     } catch (Exception ex)
 186     {
 187       ex.printStackTrace();
 188     }
 189     // need to get window geometry before we calculate alignment layout
 190     if (applet != null)
 191     {
 192       String param;
 193       try
 194       {
 195         param = applet.getParameter("windowWidth");
 196         if (param != null)
 197         {
 198           int width = Integer.parseInt(param);
 199           frameWidth = width;
 200         }
 201         param = applet.getParameter("windowHeight");
 202         if (param != null)
 203         {
 204           int height = Integer.parseInt(param);
 205           frameHeight = height;
 206         }
 207       } catch (Exception ex)
 208       {
 209       }
 210     }
 211     viewport = new AlignViewport(al, applet);
 212
 213     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 214     {
 215       viewport.hideSequence(hiddenSeqs);
 216     }
 217     if (columnSelection != null)
 218     {
 219       viewport.setColumnSelection(columnSelection);
 220     }
 221
 222     alignPanel = new AlignmentPanel(this, viewport);
 223     avc = new jalview.controller.AlignViewController(this, viewport,
 224             alignPanel);
 225     viewport.updateConservation(alignPanel);
 226     viewport.updateConsensus(alignPanel);
 227
 228     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 229     followMouseOverFlag.setState(viewport.isFollowHighlight());
 230     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 231     showGroupConservation.setState(viewport.isShowGroupConservation());
 232     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 233     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 234     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 235     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 236     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 237     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 238     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 239     showAlignmentAnnotations.setState(true);
 240     showSequenceAnnotations.setState(false);
 241
 242     seqLimits.setState(viewport.getShowJVSuffix());
 243
 244     if (applet != null)
 245     {
 246       String param = applet.getParameter("sortBy");
 247       if (param != null)
 248       {
 249         if (param.equalsIgnoreCase("Id"))
 250         {
 251           sortIDMenuItem_actionPerformed();
 252         }
 253         else if (param.equalsIgnoreCase("Pairwise Identity"))
 254         {
 255           sortPairwiseMenuItem_actionPerformed();
 256         }
 257         else if (param.equalsIgnoreCase("Length"))
 258         {
 259           sortLengthMenuItem_actionPerformed();
 260         }
 261       }
 262
 263       param = applet.getParameter("wrap");
 264       if (param != null)
 265       {
 266         if (param.equalsIgnoreCase("true"))
 267         {
 268           wrapMenuItem.setState(true);
 269           wrapMenuItem_actionPerformed();
 270         }
 271       }
 272       param = applet.getParameter("centrecolumnlabels");
 273       if (param != null)
 274       {
 275         centreColumnLabelFlag.setState(true);
 276         centreColumnLabelFlag_stateChanged();
 277       }
 278
 279     }
 280     if (viewport.getAlignment().isNucleotide())
 281     {
 282       viewport.updateStrucConsensus(alignPanel);
 283       if (viewport.getAlignment().hasRNAStructure())
 284       {
 285         RNAHelixColour.setEnabled(true);
 286       }
 287       else
 288       {
 289         RNAHelixColour.setEnabled(false);
 290       }
 291     }
 292     else
 293     {
 294       RNAHelixColour.setEnabled(false);
 295       purinePyrimidineColour.setEnabled(false);
 296     }
 297     // Some JVMS send keyevents to Top frame or lowest panel,
 298     // Havent worked out why yet. So add to both this frame and seqCanvas for
 299     // now
 300     this.addKeyListener(this);
 301     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 302     alignPanel.idPanel.idCanvas.addKeyListener(this);
 303     alignPanel.scalePanel.addKeyListener(this);
 304     alignPanel.annotationPanel.addKeyListener(this);
 305     alignPanel.annotationPanelHolder.addKeyListener(this);
 306     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 307     alignPanel.alabels.addKeyListener(this);
 308
 309     setAnnotationsVisibility();
 310
 311     if (addToDisplay)
 312     {
 313       addToDisplay(embedded);
 314     }
 315   }
 316
 317   /**
 318    * @param embedded
 319    */
 320   public void addToDisplay(boolean embedded)
 321   {
 322     createAlignFrameWindow(embedded);
 323     validate();
 324     alignPanel.adjustAnnotationHeight();
 325     alignPanel.paintAlignment(true);
 326   }
 327
 328   public AlignViewport getAlignViewport()
 329   {
 330     return viewport;
 331   }
 332
 333   public SeqCanvas getSeqcanvas()
 334   {
 335     return alignPanel.seqPanel.seqCanvas;
 336   }
 337
 338   /**
 339    * Load a features file onto the alignment
 340    *
 341    * @param file
 342    *          file URL, content, or other resolvable path
 343    * @param type
 344    *          is protocol for accessing data referred to by file
 345    */
 346
 347   public boolean parseFeaturesFile(String file, String type)
 348   {
 349     return parseFeaturesFile(file, type, true);
 350   }
 351
 352   /**
 353    * Load a features file onto the alignment
 354    *
 355    * @param file
 356    *          file URL, content, or other resolvable path
 357    * @param type
 358    *          is protocol for accessing data referred to by file
 359    * @param autoenabledisplay
 360    *          when true, display features flag will be automatically enabled if
 361    *          features are loaded
 362    * @return true if data parsed as a features file
 363    */
 364   public boolean parseFeaturesFile(String file, String type,
 365           boolean autoenabledisplay)
 366   {
 367     // TODO: test if importing a features file onto an alignment which already
 368     // has features with links overwrites the original links.
 369
 370     Hashtable featureLinks = new Hashtable();
 371     boolean featuresFile = false;
 372     try
 373     {
 374       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
 375               .getAlignment(), alignPanel.seqPanel.seqCanvas
 376               .getFeatureRenderer().getFeatureColours(), featureLinks,
 377               true, viewport.applet.getDefaultParameter("relaxedidmatch",
 378                       false));
 379     } catch (Exception ex)
 380     {
 381       ex.printStackTrace();
 382     }
 383
 384     if (featuresFile)
 385     {
 386       if (featureLinks.size() > 0)
 387       {
 388         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 389       }
 390       if (autoenabledisplay)
 391       {
 392         viewport.setShowSequenceFeatures(true);
 393         sequenceFeatures.setState(true);
 394       }
 395       if (alignPanel.seqPanel.seqCanvas.fr != null)
 396       {
 397         // update the min/max ranges where necessary
 398         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 399       }
 400       if (viewport.featureSettings != null)
 401       {
 402         viewport.featureSettings.refreshTable();
 403       }
 404       alignPanel.paintAlignment(true);
 405       statusBar.setText(MessageManager
 406               .getString("label.successfully_added_features_alignment"));
 407     }
 408     return featuresFile;
 409   }
 410
 411   @Override
 412   public void keyPressed(KeyEvent evt)
 413   {
 414     if (viewport.cursorMode
 415             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 416                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 417                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 418             && Character.isDigit(evt.getKeyChar()))
 419     {
 420       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 421     }
 422
 423     switch (evt.getKeyCode())
 424     {
 425     case 27: // escape key
 426       deselectAllSequenceMenuItem_actionPerformed();
 427
 428       alignPanel.alabels.cancelDrag();
 429       break;
 430     case KeyEvent.VK_X:
 431       if (evt.isControlDown() || evt.isMetaDown())
 432       {
 433         cut_actionPerformed();
 434       }
 435       break;
 436     case KeyEvent.VK_C:
 437       if (viewport.cursorMode && !evt.isControlDown())
 438       {
 439         alignPanel.seqPanel.setCursorColumn();
 440       }
 441       if (evt.isControlDown() || evt.isMetaDown())
 442       {
 443         copy_actionPerformed();
 444       }
 445       break;
 446     case KeyEvent.VK_V:
 447       if (evt.isControlDown())
 448       {
 449         paste(evt.isShiftDown());
 450       }
 451       break;
 452     case KeyEvent.VK_A:
 453       if (evt.isControlDown() || evt.isMetaDown())
 454       {
 455         selectAllSequenceMenuItem_actionPerformed();
 456       }
 457       break;
 458     case KeyEvent.VK_DOWN:
 459       if (viewport.cursorMode)
 460       {
 461         alignPanel.seqPanel.moveCursor(0, 1);
 462       }
 463       else
 464       {
 465         moveSelectedSequences(false);
 466       }
 467       break;
 468
 469     case KeyEvent.VK_UP:
 470       if (viewport.cursorMode)
 471       {
 472         alignPanel.seqPanel.moveCursor(0, -1);
 473       }
 474       else
 475       {
 476         moveSelectedSequences(true);
 477       }
 478       break;
 479
 480     case KeyEvent.VK_LEFT:
 481       if (evt.isAltDown() || !viewport.cursorMode)
 482       {
 483         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 484       }
 485       else
 486       {
 487         alignPanel.seqPanel.moveCursor(-1, 0);
 488       }
 489       break;
 490
 491     case KeyEvent.VK_RIGHT:
 492       if (evt.isAltDown() || !viewport.cursorMode)
 493       {
 494         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 495       }
 496       else
 497       {
 498         alignPanel.seqPanel.moveCursor(1, 0);
 499       }
 500       break;
 501
 502     case KeyEvent.VK_SPACE:
 503       if (viewport.cursorMode)
 504       {
 505         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 506                 || evt.isShiftDown() || evt.isAltDown());
 507       }
 508       break;
 509
 510     case KeyEvent.VK_DELETE:
 511     case KeyEvent.VK_BACK_SPACE:
 512       if (viewport.cursorMode)
 513       {
 514         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 515                 || evt.isShiftDown() || evt.isAltDown());
 516       }
 517       else
 518       {
 519         cut_actionPerformed();
 520         alignPanel.seqPanel.seqCanvas.repaint();
 521       }
 522       break;
 523
 524     case KeyEvent.VK_S:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorRow();
 528       }
 529       break;
 530     case KeyEvent.VK_P:
 531       if (viewport.cursorMode)
 532       {
 533         alignPanel.seqPanel.setCursorPosition();
 534       }
 535       break;
 536
 537     case KeyEvent.VK_ENTER:
 538     case KeyEvent.VK_COMMA:
 539       if (viewport.cursorMode)
 540       {
 541         alignPanel.seqPanel.setCursorRowAndColumn();
 542       }
 543       break;
 544
 545     case KeyEvent.VK_Q:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 549       }
 550       break;
 551     case KeyEvent.VK_M:
 552       if (viewport.cursorMode)
 553       {
 554         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 555       }
 556       break;
 557
 558     case KeyEvent.VK_F2:
 559       viewport.cursorMode = !viewport.cursorMode;
 560       statusBar.setText(MessageManager.formatMessage(
 561               "label.keyboard_editing_mode",
 562               new String[] { (viewport.cursorMode ? "on" : "off") }));
 563       if (viewport.cursorMode)
 564       {
 565         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 566         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 567       }
 568       break;
 569
 570     case KeyEvent.VK_F:
 571       if (evt.isControlDown())
 572       {
 573         findMenuItem_actionPerformed();
 574       }
 575       break;
 576
 577     case KeyEvent.VK_H:
 578     {
 579       boolean toggleSeqs = !evt.isControlDown();
 580       boolean toggleCols = !evt.isShiftDown();
 581       toggleHiddenRegions(toggleSeqs, toggleCols);
 582       break;
 583     }
 584
 585     case KeyEvent.VK_PAGE_UP:
 586       if (viewport.getWrapAlignment())
 587       {
 588         alignPanel.scrollUp(true);
 589       }
 590       else
 591       {
 592         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 593                 - viewport.endSeq + viewport.startSeq);
 594       }
 595       break;
 596
 597     case KeyEvent.VK_PAGE_DOWN:
 598       if (viewport.getWrapAlignment())
 599       {
 600         alignPanel.scrollUp(false);
 601       }
 602       else
 603       {
 604         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 605                 + viewport.endSeq - viewport.startSeq);
 606       }
 607       break;
 608
 609     case KeyEvent.VK_Z:
 610       if (evt.isControlDown())
 611       {
 612         undoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_Y:
 617       if (evt.isControlDown())
 618       {
 619         redoMenuItem_actionPerformed();
 620       }
 621       break;
 622
 623     case KeyEvent.VK_L:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(true);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_R:
 631       if (evt.isControlDown())
 632       {
 633         trimAlignment(false);
 634       }
 635       break;
 636
 637     case KeyEvent.VK_E:
 638       if (evt.isControlDown())
 639       {
 640         if (evt.isShiftDown())
 641         {
 642           this.removeAllGapsMenuItem_actionPerformed();
 643         }
 644         else
 645         {
 646           removeGappedColumnMenuItem_actionPerformed();
 647         }
 648       }
 649       break;
 650     case KeyEvent.VK_I:
 651       if (evt.isControlDown())
 652       {
 653         if (evt.isAltDown())
 654         {
 655           invertColSel_actionPerformed();
 656         }
 657         else
 658         {
 659           invertSequenceMenuItem_actionPerformed();
 660         }
 661       }
 662       break;
 663
 664     case KeyEvent.VK_G:
 665       if (evt.isControlDown())
 666       {
 667         if (evt.isShiftDown())
 668         {
 669           this.unGroup_actionPerformed();
 670         }
 671         else
 672         {
 673           this.createGroup_actionPerformed();
 674         }
 675       }
 676       break;
 677
 678     case KeyEvent.VK_U:
 679       if (evt.isControlDown())
 680       {
 681         this.deleteGroups_actionPerformed();
 682       }
 683       break;
 684
 685     case KeyEvent.VK_T:
 686       if (evt.isControlDown())
 687       {
 688         newView(null);
 689       }
 690       break;
 691
 692     }
 693     alignPanel.paintAlignment(true);
 694   }
 695
 696   /**
 697    * called by key handler and the hide all/show all menu items
 698    *
 699    * @param toggleSeqs
 700    * @param toggleCols
 701    */
 702   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 703   {
 704     boolean hide = false;
 705     SequenceGroup sg = viewport.getSelectionGroup();
 706     if (!toggleSeqs && !toggleCols)
 707     {
 708       // Hide everything by the current selection - this is a hack - we do the
 709       // invert and then hide
 710       // first check that there will be visible columns after the invert.
 711       if ((viewport.getColumnSelection() != null
 712               && viewport.getColumnSelection().getSelected() != null && viewport
 713               .getColumnSelection().getSelected().size() > 0)
 714               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 715                       .getEndRes()))
 716       {
 717         // now invert the sequence set, if required - empty selection implies
 718         // that no hiding is required.
 719         if (sg != null)
 720         {
 721           invertSequenceMenuItem_actionPerformed();
 722           sg = viewport.getSelectionGroup();
 723           toggleSeqs = true;
 724
 725         }
 726         viewport.expandColSelection(sg, true);
 727         // finally invert the column selection and get the new sequence
 728         // selection and indicate it should be hidden.
 729         invertColSel_actionPerformed();
 730         toggleCols = true;
 731       }
 732     }
 733
 734     if (toggleSeqs)
 735     {
 736       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 737       {
 738         hide = true;
 739         viewport.hideAllSelectedSeqs();
 740       }
 741       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 742               .size() > 0))
 743       {
 744         viewport.showAllHiddenSeqs();
 745       }
 746     }
 747
 748     if (toggleCols)
 749     {
 750       if (viewport.getColumnSelection().getSelected().size() > 0)
 751       {
 752         viewport.hideSelectedColumns();
 753         if (!toggleSeqs)
 754         {
 755           viewport.setSelectionGroup(sg);
 756         }
 757       }
 758       else if (!hide)
 759       {
 760         viewport.showAllHiddenColumns();
 761       }
 762     }
 763   }
 764
 765   @Override
 766   public void keyReleased(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void keyTyped(KeyEvent evt)
 772   {
 773   }
 774
 775   @Override
 776   public void itemStateChanged(ItemEvent evt)
 777   {
 778     final Object source = evt.getSource();
 779     if (source == displayNonconservedMenuItem)
 780     {
 781       displayNonconservedMenuItem_actionPerformed();
 782     }
 783     else if (source == colourTextMenuItem)
 784     {
 785       colourTextMenuItem_actionPerformed();
 786     }
 787     else if (source == wrapMenuItem)
 788     {
 789       wrapMenuItem_actionPerformed();
 790     }
 791     else if (source == scaleAbove)
 792     {
 793       viewport.setScaleAboveWrapped(scaleAbove.getState());
 794     }
 795     else if (source == scaleLeft)
 796     {
 797       viewport.setScaleLeftWrapped(scaleLeft.getState());
 798     }
 799     else if (source == scaleRight)
 800     {
 801       viewport.setScaleRightWrapped(scaleRight.getState());
 802     }
 803     else if (source == seqLimits)
 804     {
 805       seqLimits_itemStateChanged();
 806     }
 807     else if (source == viewBoxesMenuItem)
 808     {
 809       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 810     }
 811     else if (source == viewTextMenuItem)
 812     {
 813       viewport.setShowText(viewTextMenuItem.getState());
 814     }
 815     else if (source == renderGapsMenuItem)
 816     {
 817       viewport.setRenderGaps(renderGapsMenuItem.getState());
 818     }
 819     else if (source == annotationPanelMenuItem)
 820     {
 821       boolean showAnnotations = annotationPanelMenuItem.getState();
 822       showAlignmentAnnotations.setEnabled(showAnnotations);
 823       showSequenceAnnotations.setEnabled(showAnnotations);
 824       viewport.setShowAnnotation(showAnnotations);
 825       alignPanel.setAnnotationVisible(showAnnotations);
 826     }
 827     else if (source == sequenceFeatures)
 828     {
 829       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 830       alignPanel.seqPanel.seqCanvas.repaint();
 831     }
 832     else if (source == showAlignmentAnnotations)
 833     {
 834       setAnnotationsVisibility();
 835     }
 836     else if (source == showSequenceAnnotations)
 837     {
 838       setAnnotationsVisibility();
 839     }
 840     else if (source == sortAnnBySequence)
 841     {
 842       boolean newState = sortAnnBySequence.getState();
 843       sortAnnByLabel.setState(false);
 844       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 845               : SequenceAnnotationOrder.NONE);
 846       setViewportAnnotationOrder();
 847     }
 848     else if (source == sortAnnByLabel)
 849     {
 850       boolean newState = sortAnnByLabel.getState();
 851       sortAnnBySequence.setState(false);
 852       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 853               : SequenceAnnotationOrder.NONE);
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == showAutoFirst)
 857     {
 858       showAutoLast.setState(!showAutoFirst.getState());
 859       setShowAutoCalculatedAbove(showAutoFirst.getState());
 860       setViewportAnnotationOrder();
 861     }
 862     else if (source == showAutoLast)
 863     {
 864       showAutoFirst.setState(!showAutoLast.getState());
 865       setShowAutoCalculatedAbove(showAutoFirst.getState());
 866       setViewportAnnotationOrder();
 867     }
 868     else if (source == conservationMenuItem)
 869     {
 870       conservationMenuItem_actionPerformed();
 871     }
 872     else if (source == abovePIDThreshold)
 873     {
 874       abovePIDThreshold_actionPerformed();
 875     }
 876     else if (source == applyToAllGroups)
 877     {
 878       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 879     }
 880     else if (source == autoCalculate)
 881     {
 882       viewport.autoCalculateConsensus = autoCalculate.getState();
 883     }
 884     else if (source == sortByTree)
 885     {
 886       viewport.sortByTree = sortByTree.getState();
 887     }
 888     else if (source == this.centreColumnLabelFlag)
 889     {
 890       centreColumnLabelFlag_stateChanged();
 891     }
 892     else if (source == this.followMouseOverFlag)
 893     {
 894       mouseOverFlag_stateChanged();
 895     }
 896     else if (source == showGroupConsensus)
 897     {
 898       showGroupConsensus_actionPerformed();
 899     }
 900     else if (source == showGroupConservation)
 901     {
 902       showGroupConservation_actionPerformed();
 903     }
 904     else if (source == showSequenceLogo)
 905     {
 906       showSequenceLogo_actionPerformed();
 907     }
 908     else if (source == normSequenceLogo)
 909     {
 910       normSequenceLogo_actionPerformed();
 911     }
 912     else if (source == showConsensusHistogram)
 913     {
 914       showConsensusHistogram_actionPerformed();
 915     }
 916     else if (source == applyAutoAnnotationSettings)
 917     {
 918       applyAutoAnnotationSettings_actionPerformed();
 919     }
 920     alignPanel.paintAlignment(true);
 921   }
 922
 923   /**
 924    * Set the visibility state of sequence-related and/or alignment-related
 925    * annotations depending on checkbox selections, and repaint.
 926    *
 927    * @param visible
 928    */
 929   private void setAnnotationsVisibility()
 930   {
 931     boolean showForAlignment = showAlignmentAnnotations.getState();
 932     boolean showForSequences = showSequenceAnnotations.getState();
 933     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 934     {
 935       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 936             .getAlignmentAnnotation())
 937     {
 938       boolean visible = (aa.sequenceRef == null ? showForAlignment
 939               : showForSequences);
 940       aa.visible = visible;
 941       }
 942     }
 943     alignPanel.validateAnnotationDimensions(true);
 944     validate();
 945     repaint();
 946   }
 947
 948   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 949   {
 950     this.annotationSortOrder = order;
 951   }
 952
 953   /**
 954    * Set flags on the viewport that control annotation ordering
 955    */
 956   private void setViewportAnnotationOrder()
 957   {
 958     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 959     this.alignPanel.av
 960             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 961   }
 962
 963   private void setShowAutoCalculatedAbove(boolean showAbove)
 964   {
 965     this.showAutoCalculatedAbove = showAbove;
 966   }
 967
 968   private void mouseOverFlag_stateChanged()
 969   {
 970     viewport.setFollowHighlight(followMouseOverFlag.getState());
 971     // TODO: could kick the scrollTo mechanism to reset view for current
 972     // searchresults.
 973   }
 974
 975   private void centreColumnLabelFlag_stateChanged()
 976   {
 977     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 978     this.alignPanel.annotationPanel.repaint();
 979   }
 980
 981   @Override
 982   public void actionPerformed(ActionEvent evt)
 983   {
 984     viewport.applet.currentAlignFrame = this;
 985
 986     Object source = evt.getSource();
 987
 988     if (source == inputText)
 989     {
 990       inputText_actionPerformed();
 991     }
 992     else if (source == loadTree)
 993     {
 994       loadTree_actionPerformed();
 995     }
 996     else if (source == loadApplication)
 997     {
 998       launchFullApplication();
 999     }
1000     else if (source == loadAnnotations)
1001     {
1002       loadAnnotations();
1003     }
1004     else if (source == outputAnnotations)
1005     {
1006       outputAnnotations(true);
1007     }
1008     else if (source == outputFeatures)
1009     {
1010       outputFeatures(true, "Jalview");
1011     }
1012     else if (source == closeMenuItem)
1013     {
1014       closeMenuItem_actionPerformed();
1015     }
1016     else if (source == copy)
1017     {
1018       copy_actionPerformed();
1019     }
1020     else if (source == undoMenuItem)
1021     {
1022       undoMenuItem_actionPerformed();
1023     }
1024     else if (source == redoMenuItem)
1025     {
1026       redoMenuItem_actionPerformed();
1027     }
1028     else if (source == inputText)
1029     {
1030       inputText_actionPerformed();
1031     }
1032     else if (source == closeMenuItem)
1033     {
1034       closeMenuItem_actionPerformed();
1035     }
1036     else if (source == undoMenuItem)
1037     {
1038       undoMenuItem_actionPerformed();
1039     }
1040     else if (source == redoMenuItem)
1041     {
1042       redoMenuItem_actionPerformed();
1043     }
1044     else if (source == copy)
1045     {
1046       copy_actionPerformed();
1047     }
1048     else if (source == pasteNew)
1049     {
1050       pasteNew_actionPerformed();
1051     }
1052     else if (source == pasteThis)
1053     {
1054       pasteThis_actionPerformed();
1055     }
1056     else if (source == cut)
1057     {
1058       cut_actionPerformed();
1059     }
1060     else if (source == delete)
1061     {
1062       delete_actionPerformed();
1063     }
1064     else if (source == grpsFromSelection)
1065     {
1066       makeGrpsFromSelection_actionPerformed();
1067     }
1068     else if (source == deleteGroups)
1069     {
1070       deleteGroups_actionPerformed();
1071     }
1072     else if (source == selectAllSequenceMenuItem)
1073     {
1074       selectAllSequenceMenuItem_actionPerformed();
1075     }
1076     else if (source == deselectAllSequenceMenuItem)
1077     {
1078       deselectAllSequenceMenuItem_actionPerformed();
1079     }
1080     else if (source == invertSequenceMenuItem)
1081     {
1082       invertSequenceMenuItem_actionPerformed();
1083     }
1084     else if (source == invertColSel)
1085     {
1086       viewport.invertColumnSelection();
1087       alignPanel.paintAlignment(true);
1088     }
1089     else if (source == remove2LeftMenuItem)
1090     {
1091       trimAlignment(true);
1092     }
1093     else if (source == remove2RightMenuItem)
1094     {
1095       trimAlignment(false);
1096     }
1097     else if (source == removeGappedColumnMenuItem)
1098     {
1099       removeGappedColumnMenuItem_actionPerformed();
1100     }
1101     else if (source == removeAllGapsMenuItem)
1102     {
1103       removeAllGapsMenuItem_actionPerformed();
1104     }
1105     else if (source == findMenuItem)
1106     {
1107       findMenuItem_actionPerformed();
1108     }
1109     else if (source == font)
1110     {
1111       new FontChooser(alignPanel);
1112     }
1113     else if (source == newView)
1114     {
1115       newView(null);
1116     }
1117     else if (source == showColumns)
1118     {
1119       viewport.showAllHiddenColumns();
1120       alignPanel.paintAlignment(true);
1121     }
1122     else if (source == showSeqs)
1123     {
1124       viewport.showAllHiddenSeqs();
1125       alignPanel.paintAlignment(true);
1126     }
1127     else if (source == hideColumns)
1128     {
1129       viewport.hideSelectedColumns();
1130       alignPanel.paintAlignment(true);
1131     }
1132     else if (source == hideSequences
1133             && viewport.getSelectionGroup() != null)
1134     {
1135       viewport.hideAllSelectedSeqs();
1136       alignPanel.paintAlignment(true);
1137     }
1138     else if (source == hideAllButSelection)
1139     {
1140       toggleHiddenRegions(false, false);
1141       alignPanel.paintAlignment(true);
1142     }
1143     else if (source == hideAllSelection)
1144     {
1145       SequenceGroup sg = viewport.getSelectionGroup();
1146       viewport.expandColSelection(sg, false);
1147       viewport.hideAllSelectedSeqs();
1148       viewport.hideSelectedColumns();
1149       alignPanel.paintAlignment(true);
1150     }
1151     else if (source == showAllHidden)
1152     {
1153       viewport.showAllHiddenColumns();
1154       viewport.showAllHiddenSeqs();
1155       alignPanel.paintAlignment(true);
1156     }
1157     else if (source == showGroupConsensus)
1158     {
1159       showGroupConsensus_actionPerformed();
1160     }
1161     else if (source == showGroupConservation)
1162     {
1163       showGroupConservation_actionPerformed();
1164     }
1165     else if (source == showSequenceLogo)
1166     {
1167       showSequenceLogo_actionPerformed();
1168     }
1169     else if (source == normSequenceLogo)
1170     {
1171       normSequenceLogo_actionPerformed();
1172     }
1173     else if (source == showConsensusHistogram)
1174     {
1175       showConsensusHistogram_actionPerformed();
1176     }
1177     else if (source == applyAutoAnnotationSettings)
1178     {
1179       applyAutoAnnotationSettings_actionPerformed();
1180     }
1181     else if (source == featureSettings)
1182     {
1183       new FeatureSettings(alignPanel);
1184     }
1185     else if (source == alProperties)
1186     {
1187       StringBuffer contents = new jalview.io.AlignmentProperties(
1188               viewport.getAlignment()).formatAsString();
1189       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1190       cap.setText(contents.toString());
1191       Frame frame = new Frame();
1192       frame.add(cap);
1193       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1194               "label.alignment_properties", new String[] { getTitle() }),
1195               400, 250);
1196     }
1197     else if (source == overviewMenuItem)
1198     {
1199       overviewMenuItem_actionPerformed();
1200     }
1201     else if (source == noColourmenuItem)
1202     {
1203       changeColour(null);
1204     }
1205     else if (source == clustalColour)
1206     {
1207       abovePIDThreshold.setState(false);
1208       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1209     }
1210     else if (source == zappoColour)
1211     {
1212       changeColour(new ZappoColourScheme());
1213     }
1214     else if (source == taylorColour)
1215     {
1216       changeColour(new TaylorColourScheme());
1217     }
1218     else if (source == hydrophobicityColour)
1219     {
1220       changeColour(new HydrophobicColourScheme());
1221     }
1222     else if (source == helixColour)
1223     {
1224       changeColour(new HelixColourScheme());
1225     }
1226     else if (source == strandColour)
1227     {
1228       changeColour(new StrandColourScheme());
1229     }
1230     else if (source == turnColour)
1231     {
1232       changeColour(new TurnColourScheme());
1233     }
1234     else if (source == buriedColour)
1235     {
1236       changeColour(new BuriedColourScheme());
1237     }
1238     else if (source == nucleotideColour)
1239     {
1240       changeColour(new NucleotideColourScheme());
1241     }
1242     else if (source == purinePyrimidineColour)
1243     {
1244       changeColour(new PurinePyrimidineColourScheme());
1245     }
1246     // else if (source == RNAInteractionColour)
1247     // {
1248     // changeColour(new RNAInteractionColourScheme());
1249     // }
1250     else if (source == RNAHelixColour)
1251     {
1252       new RNAHelicesColourChooser(viewport, alignPanel);
1253     }
1254     else if (source == modifyPID)
1255     {
1256       modifyPID_actionPerformed();
1257     }
1258     else if (source == modifyConservation)
1259     {
1260       modifyConservation_actionPerformed();
1261     }
1262     else if (source == userDefinedColour)
1263     {
1264       new UserDefinedColours(alignPanel, null);
1265     }
1266     else if (source == PIDColour)
1267     {
1268       changeColour(new PIDColourScheme());
1269     }
1270     else if (source == BLOSUM62Colour)
1271     {
1272       changeColour(new Blosum62ColourScheme());
1273     }
1274     else if (source == tcoffeeColour)
1275     {
1276       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1277     }
1278     else if (source == annotationColour)
1279     {
1280       new AnnotationColourChooser(viewport, alignPanel);
1281     }
1282     else if (source == annotationColumnSelection)
1283     {
1284       new AnnotationColumnChooser(viewport, alignPanel);
1285     }
1286     else if (source == sortPairwiseMenuItem)
1287     {
1288       sortPairwiseMenuItem_actionPerformed();
1289     }
1290     else if (source == sortIDMenuItem)
1291     {
1292       sortIDMenuItem_actionPerformed();
1293     }
1294     else if (source == sortLengthMenuItem)
1295     {
1296       sortLengthMenuItem_actionPerformed();
1297     }
1298     else if (source == sortGroupMenuItem)
1299     {
1300       sortGroupMenuItem_actionPerformed();
1301     }
1302     else if (source == removeRedundancyMenuItem)
1303     {
1304       removeRedundancyMenuItem_actionPerformed();
1305     }
1306     else if (source == pairwiseAlignmentMenuItem)
1307     {
1308       pairwiseAlignmentMenuItem_actionPerformed();
1309     }
1310     else if (source == PCAMenuItem)
1311     {
1312       PCAMenuItem_actionPerformed();
1313     }
1314     else if (source == averageDistanceTreeMenuItem)
1315     {
1316       averageDistanceTreeMenuItem_actionPerformed();
1317     }
1318     else if (source == neighbourTreeMenuItem)
1319     {
1320       neighbourTreeMenuItem_actionPerformed();
1321     }
1322     else if (source == njTreeBlosumMenuItem)
1323     {
1324       njTreeBlosumMenuItem_actionPerformed();
1325     }
1326     else if (source == avDistanceTreeBlosumMenuItem)
1327     {
1328       avTreeBlosumMenuItem_actionPerformed();
1329     }
1330     else if (source == documentation)
1331     {
1332       documentation_actionPerformed();
1333     }
1334     else if (source == about)
1335     {
1336       about_actionPerformed();
1337     }
1338
1339   }
1340
1341   public void inputText_actionPerformed()
1342   {
1343     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1344     Frame frame = new Frame();
1345     frame.add(cap);
1346     jalview.bin.JalviewLite.addFrame(frame,
1347             MessageManager.getString("label.input_cut_paste"), 500, 500);
1348   }
1349
1350   protected void outputText_actionPerformed(ActionEvent e)
1351   {
1352     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1353     Frame frame = new Frame();
1354     frame.add(cap);
1355     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1356             "label.alignment_output_command",
1357             new Object[] { e.getActionCommand() }), 600, 500);
1358
1359     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1360     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1361             e.getActionCommand(), viewport.getAlignment(),
1362             viewport.getShowJVSuffix()));
1363   }
1364
1365   public void loadAnnotations()
1366   {
1367     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1368     cap.setText(MessageManager
1369             .getString("label.paste_features_annotations_Tcoffee_here"));
1370     cap.setAnnotationImport();
1371     Frame frame = new Frame();
1372     frame.add(cap);
1373     jalview.bin.JalviewLite.addFrame(frame,
1374             MessageManager.getString("action.paste_annotations"), 400, 300);
1375
1376   }
1377
1378   public String outputAnnotations(boolean displayTextbox)
1379   {
1380     String annotation = new AnnotationFile()
1381             .printAnnotationsForView(viewport);
1382
1383     if (displayTextbox)
1384     {
1385       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1386       Frame frame = new Frame();
1387       frame.add(cap);
1388       jalview.bin.JalviewLite.addFrame(frame,
1389               MessageManager.getString("label.annotations"), 600, 500);
1390       cap.setText(annotation);
1391     }
1392
1393     return annotation;
1394   }
1395
1396   private Map<String, Object> getDisplayedFeatureCols()
1397   {
1398     if (alignPanel.getFeatureRenderer() != null
1399             && viewport.getFeaturesDisplayed() != null)
1400     {
1401       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1402
1403     }
1404     return null;
1405   }
1406
1407   public String outputFeatures(boolean displayTextbox, String format)
1408   {
1409     String features;
1410     if (format.equalsIgnoreCase("Jalview"))
1411     {
1412       features = new FeaturesFile().printJalviewFormat(viewport
1413               .getAlignment().getSequencesArray(),
1414               getDisplayedFeatureCols());
1415     }
1416     else
1417     {
1418       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1419               .getSequencesArray(), getDisplayedFeatureCols());
1420     }
1421
1422     if (displayTextbox)
1423     {
1424       boolean frimport = false;
1425       if (features == null || features.equals("No Features Visible"))
1426       {
1427         features = "# No features visible - paste some and import them here.";
1428         frimport = true;
1429       }
1430
1431       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1432       if (frimport)
1433       {
1434         cap.setAnnotationImport();
1435       }
1436       Frame frame = new Frame();
1437       frame.add(cap);
1438       jalview.bin.JalviewLite.addFrame(frame,
1439               MessageManager.getString("label.features"), 600, 500);
1440       cap.setText(features);
1441     }
1442     else
1443     {
1444       if (features == null)
1445       {
1446         features = "";
1447       }
1448     }
1449
1450     return features;
1451   }
1452
1453   void launchFullApplication()
1454   {
1455     StringBuffer url = new StringBuffer(jalviewServletURL);
1456
1457     // allow servlet parameters to be passed in applet parameter
1458     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1459             : "?";
1460     url.append(firstSep);
1461
1462     url.append("open="
1463             + appendProtocol(viewport.applet.getParameter("file")));
1464
1465     if (viewport.applet.getParameter("features") != null)
1466     {
1467       url.append("&features=");
1468       url.append(appendProtocol(viewport.applet.getParameter("features")));
1469     }
1470
1471     if (viewport.applet.getParameter("annotations") != null)
1472     {
1473       url.append("&annotations=");
1474       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1475     }
1476
1477     if (viewport.applet.getParameter("jnetfile") != null)
1478     {
1479       url.append("&annotations=");
1480       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1481     }
1482
1483     if (viewport.applet.getParameter("defaultColour") != null)
1484     {
1485       url.append("&colour="
1486               + removeWhiteSpace(viewport.applet
1487                       .getParameter("defaultColour")));
1488     }
1489
1490     if (viewport.applet.getParameter("userDefinedColour") != null)
1491     {
1492       url.append("&colour="
1493               + removeWhiteSpace(viewport.applet
1494                       .getParameter("userDefinedColour")));
1495     }
1496     if (viewport.applet.getParameter("tree") != null)
1497     {
1498       url.append("&tree="
1499               + appendProtocol(viewport.applet.getParameter("tree")));
1500     }
1501     if (viewport.applet.getParameter("treeFile") != null)
1502     {
1503       url.append("&tree="
1504               + appendProtocol(viewport.applet.getParameter("treeFile")));
1505     }
1506
1507     showURL(url.toString(), "FULL_APP");
1508   }
1509
1510   String removeWhiteSpace(String colour)
1511   {
1512     StringBuffer sb = new StringBuffer();
1513     for (int i = 0; i < colour.length(); i++)
1514     {
1515       if (Character.isWhitespace(colour.charAt(i)))
1516       {
1517         sb.append("%20");
1518       }
1519       else
1520       {
1521         sb.append(colour.charAt(i));
1522       }
1523     }
1524
1525     return sb.toString();
1526   }
1527
1528   String appendProtocol(String url)
1529   {
1530     try
1531     {
1532       new URL(url);
1533       url = URLEncoder.encode(url);
1534     }
1535     /*
1536      * When we finally deprecate 1.1 compatibility, we can start to use
1537      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1538      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1539      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1540      * ex.printStackTrace(); }
1541      */
1542     catch (java.net.MalformedURLException ex)
1543     {
1544       url = viewport.applet.getCodeBase() + url;
1545     }
1546     return url;
1547   }
1548
1549   public void closeMenuItem_actionPerformed()
1550   {
1551     PaintRefresher.RemoveComponent(alignPanel);
1552     if (alignPanel.seqPanel != null
1553             && alignPanel.seqPanel.seqCanvas != null)
1554     {
1555       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1556     }
1557     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1558     {
1559       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1560     }
1561
1562     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1563     {
1564       System.exit(0);
1565     }
1566     else
1567     {
1568     }
1569     viewport = null;
1570     alignPanel = null;
1571     this.dispose();
1572   }
1573
1574   /**
1575    * TODO: JAL-1104
1576    */
1577   void updateEditMenuBar()
1578   {
1579
1580     if (viewport.getHistoryList().size() > 0)
1581     {
1582       undoMenuItem.setEnabled(true);
1583       CommandI command = viewport.getHistoryList().peek();
1584       undoMenuItem.setLabel(MessageManager.formatMessage(
1585               "label.undo_command",
1586               new Object[] { command.getDescription() }));
1587     }
1588     else
1589     {
1590       undoMenuItem.setEnabled(false);
1591       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1592     }
1593
1594     if (viewport.getRedoList().size() > 0)
1595     {
1596       redoMenuItem.setEnabled(true);
1597
1598       CommandI command = viewport.getRedoList().peek();
1599       redoMenuItem.setLabel(MessageManager.formatMessage(
1600               "label.redo_command",
1601               new Object[] { command.getDescription() }));
1602     }
1603     else
1604     {
1605       redoMenuItem.setEnabled(false);
1606       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1607     }
1608   }
1609
1610   /**
1611    * TODO: JAL-1104
1612    */
1613   @Override
1614   public void addHistoryItem(CommandI command)
1615   {
1616     if (command.getSize() > 0)
1617     {
1618       viewport.addToHistoryList(command);
1619       viewport.clearRedoList();
1620       updateEditMenuBar();
1621       viewport.updateHiddenColumns();
1622     }
1623   }
1624
1625   /**
1626    * TODO: JAL-1104 DOCUMENT ME!
1627    *
1628    * @param e
1629    *          DOCUMENT ME!
1630    */
1631   protected void undoMenuItem_actionPerformed()
1632   {
1633     if (viewport.getHistoryList().isEmpty())
1634     {
1635       return;
1636     }
1637
1638     CommandI command = viewport.getHistoryList().pop();
1639     viewport.addToRedoList(command);
1640     command.undoCommand(null);
1641
1642     AlignmentViewport originalSource = getOriginatingSource(command);
1643     // JBPNote Test
1644     if (originalSource != viewport)
1645     {
1646       System.err
1647               .println("Warning: Viewport object mismatch whilst undoing");
1648     }
1649     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1650                                           // viewport.getColumnSelection().getHiddenColumns()
1651                                           // != null;
1652     updateEditMenuBar();
1653     originalSource.firePropertyChange("alignment", null, originalSource
1654             .getAlignment().getSequences());
1655   }
1656
1657   /**
1658    * TODO: JAL-1104 DOCUMENT ME!
1659    *
1660    * @param e
1661    *          DOCUMENT ME!
1662    */
1663   protected void redoMenuItem_actionPerformed()
1664   {
1665     if (viewport.getRedoList().isEmpty())
1666     {
1667       return;
1668     }
1669
1670     CommandI command = viewport.getRedoList().pop();
1671     viewport.addToHistoryList(command);
1672     command.doCommand(null);
1673
1674     AlignmentViewport originalSource = getOriginatingSource(command);
1675     // JBPNote Test
1676     if (originalSource != viewport)
1677     {
1678       System.err
1679               .println("Warning: Viewport object mismatch whilst re-doing");
1680     }
1681     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1682                                           // viewport.getColumnSelection().getHiddenColumns()
1683                                           // != null;
1684
1685     updateEditMenuBar();
1686     originalSource.firePropertyChange("alignment", null, originalSource
1687             .getAlignment().getSequences());
1688   }
1689
1690   AlignmentViewport getOriginatingSource(CommandI command)
1691   {
1692     AlignmentViewport originalSource = null;
1693     // For sequence removal and addition, we need to fire
1694     // the property change event FROM the viewport where the
1695     // original alignment was altered
1696     AlignmentI al = null;
1697     if (command instanceof EditCommand)
1698     {
1699       EditCommand editCommand = (EditCommand) command;
1700       al = editCommand.getAlignment();
1701       Vector comps = (Vector) PaintRefresher.components.get(viewport
1702               .getSequenceSetId());
1703       for (int i = 0; i < comps.size(); i++)
1704       {
1705         if (comps.elementAt(i) instanceof AlignmentPanel)
1706         {
1707           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1708           {
1709             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1710             break;
1711           }
1712         }
1713       }
1714     }
1715
1716     if (originalSource == null)
1717     {
1718       // The original view is closed, we must validate
1719       // the current view against the closed view first
1720       if (al != null)
1721       {
1722         PaintRefresher.validateSequences(al, viewport.getAlignment());
1723       }
1724
1725       originalSource = viewport;
1726     }
1727
1728     return originalSource;
1729   }
1730
1731   /**
1732    * Move the currently selected sequences up or down one position in the
1733    * alignment
1734    *
1735    * @param up
1736    */
1737   public void moveSelectedSequences(boolean up)
1738   {
1739     SequenceGroup sg = viewport.getSelectionGroup();
1740     if (sg == null)
1741     {
1742       return;
1743     }
1744     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1745             up ? null : viewport.getHiddenRepSequences(), up);
1746     alignPanel.paintAlignment(true);
1747
1748     /*
1749      * Also move cDNA/protein complement sequences
1750      */
1751     AlignViewportI complement = viewport.getCodingComplement();
1752     if (complement != null)
1753     {
1754       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1755               viewport, complement);
1756       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1757               up ? null : complement.getHiddenRepSequences(), up);
1758       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1759     }
1760   }
1761
1762   synchronized void slideSequences(boolean right, int size)
1763   {
1764     List<SequenceI> sg = new Vector<SequenceI>();
1765     if (viewport.cursorMode)
1766     {
1767       sg.add(viewport.getAlignment().getSequenceAt(
1768               alignPanel.seqPanel.seqCanvas.cursorY));
1769     }
1770     else if (viewport.getSelectionGroup() != null
1771             && viewport.getSelectionGroup().getSize() != viewport
1772                     .getAlignment().getHeight())
1773     {
1774       sg = viewport.getSelectionGroup().getSequences(
1775               viewport.getHiddenRepSequences());
1776     }
1777
1778     if (sg.size() < 1)
1779     {
1780       return;
1781     }
1782
1783     Vector<SequenceI> invertGroup = new Vector();
1784
1785     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1786     {
1787       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1788       {
1789         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1790       }
1791     }
1792
1793     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1794
1795     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1796             .size()]);
1797     for (int i = 0; i < invertGroup.size(); i++)
1798     {
1799       seqs2[i] = invertGroup.elementAt(i);
1800     }
1801
1802     SlideSequencesCommand ssc;
1803     if (right)
1804     {
1805       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1806               size, viewport.getGapCharacter());
1807     }
1808     else
1809     {
1810       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1811               size, viewport.getGapCharacter());
1812     }
1813
1814     int groupAdjustment = 0;
1815     if (ssc.getGapsInsertedBegin() && right)
1816     {
1817       if (viewport.cursorMode)
1818       {
1819         alignPanel.seqPanel.moveCursor(size, 0);
1820       }
1821       else
1822       {
1823         groupAdjustment = size;
1824       }
1825     }
1826     else if (!ssc.getGapsInsertedBegin() && !right)
1827     {
1828       if (viewport.cursorMode)
1829       {
1830         alignPanel.seqPanel.moveCursor(-size, 0);
1831       }
1832       else
1833       {
1834         groupAdjustment = -size;
1835       }
1836     }
1837
1838     if (groupAdjustment != 0)
1839     {
1840       viewport.getSelectionGroup().setStartRes(
1841               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1842       viewport.getSelectionGroup().setEndRes(
1843               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1844     }
1845
1846     boolean appendHistoryItem = false;
1847     Deque<CommandI> historyList = viewport.getHistoryList();
1848     if (historyList != null && historyList.size() > 0
1849             && historyList.peek() instanceof SlideSequencesCommand)
1850     {
1851       appendHistoryItem = ssc
1852               .appendSlideCommand((SlideSequencesCommand) historyList
1853                       .peek());
1854     }
1855
1856     if (!appendHistoryItem)
1857     {
1858       addHistoryItem(ssc);
1859     }
1860
1861     repaint();
1862   }
1863
1864   static StringBuffer copiedSequences;
1865
1866   static Vector copiedHiddenColumns;
1867
1868   protected void copy_actionPerformed()
1869   {
1870     if (viewport.getSelectionGroup() == null)
1871     {
1872       return;
1873     }
1874
1875     SequenceGroup sg = viewport.getSelectionGroup();
1876     copiedSequences = new StringBuffer();
1877     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1878     for (int i = 0; i < sg.getSize(); i++)
1879     {
1880       SequenceI seq = sg.getSequenceAt(i);
1881       int index = viewport.getAlignment().findIndex(seq);
1882       orderedSeqs.put(index, seq);
1883     }
1884
1885     int index = 0, startRes, endRes;
1886     char ch;
1887
1888     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1889     {
1890       copiedHiddenColumns = new Vector();
1891       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1892       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1893       {
1894         copiedHiddenColumns.addElement(new int[] {
1895             region[0] - hiddenOffset, region[1] - hiddenOffset });
1896       }
1897     }
1898     else
1899     {
1900       copiedHiddenColumns = null;
1901     }
1902
1903     for (int i = 0; i < sg.getSize(); i++)
1904     {
1905       SequenceI seq = null;
1906
1907       while (seq == null)
1908       {
1909         if (orderedSeqs.containsKey(index))
1910         {
1911           seq = orderedSeqs.get(index);
1912           index++;
1913           break;
1914         }
1915         else
1916         {
1917           index++;
1918         }
1919       }
1920
1921       // FIND START RES
1922       // Returns residue following index if gap
1923       startRes = seq.findPosition(sg.getStartRes());
1924
1925       // FIND END RES
1926       // Need to find the residue preceeding index if gap
1927       endRes = 0;
1928
1929       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1930       {
1931         ch = seq.getCharAt(j);
1932         if (!jalview.util.Comparison.isGap((ch)))
1933         {
1934           endRes++;
1935         }
1936       }
1937
1938       if (endRes > 0)
1939       {
1940         endRes += seq.getStart() - 1;
1941       }
1942
1943       copiedSequences.append(seq.getName()
1944               + "\t"
1945               + startRes
1946               + "\t"
1947               + endRes
1948               + "\t"
1949               + seq.getSequenceAsString(sg.getStartRes(),
1950                       sg.getEndRes() + 1) + "\n");
1951     }
1952
1953   }
1954
1955   protected void pasteNew_actionPerformed()
1956   {
1957     paste(true);
1958   }
1959
1960   protected void pasteThis_actionPerformed()
1961   {
1962     paste(false);
1963   }
1964
1965   void paste(boolean newAlignment)
1966   {
1967     try
1968     {
1969
1970       if (copiedSequences == null)
1971       {
1972         return;
1973       }
1974
1975       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1976       Vector seqs = new Vector();
1977       while (st.hasMoreElements())
1978       {
1979         String name = st.nextToken();
1980         int start = Integer.parseInt(st.nextToken());
1981         int end = Integer.parseInt(st.nextToken());
1982         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1983       }
1984       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1985       for (int i = 0; i < seqs.size(); i++)
1986       {
1987         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1988       }
1989
1990       if (newAlignment)
1991       {
1992         String newtitle = MessageManager
1993                 .getString("label.copied_sequences");
1994         if (getTitle().startsWith(
1995                 MessageManager.getString("label.copied_sequences")))
1996         {
1997           newtitle = getTitle();
1998         }
1999         else
2000         {
2001           newtitle = newtitle.concat(MessageManager.formatMessage(
2002                   "label.from_msname", new String[] { getTitle() }));
2003         }
2004         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2005                 viewport.applet, newtitle, false);
2006         if (copiedHiddenColumns != null)
2007         {
2008           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2009           {
2010             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2011             af.viewport.hideColumns(region[0], region[1]);
2012           }
2013         }
2014
2015         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2016                 frameHeight);
2017       }
2018       else
2019       {
2020         addSequences(newSeqs);
2021       }
2022
2023     } catch (Exception ex)
2024     {
2025     } // could be anything being pasted in here
2026
2027   }
2028
2029   void addSequences(SequenceI[] seqs)
2030   {
2031     for (int i = 0; i < seqs.length; i++)
2032     {
2033       viewport.getAlignment().addSequence(seqs[i]);
2034     }
2035
2036     // !newAlignment
2037     addHistoryItem(new EditCommand(
2038             MessageManager.getString("label.add_sequences"), Action.PASTE,
2039             seqs, 0, viewport.getAlignment().getWidth(),
2040             viewport.getAlignment()));
2041
2042     viewport.setEndSeq(viewport.getAlignment().getHeight());
2043     viewport.getAlignment().getWidth();
2044     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2045             .getSequences());
2046
2047   }
2048
2049   protected void cut_actionPerformed()
2050   {
2051     copy_actionPerformed();
2052     delete_actionPerformed();
2053   }
2054
2055   protected void delete_actionPerformed()
2056   {
2057
2058     SequenceGroup sg = viewport.getSelectionGroup();
2059     if (sg == null)
2060     {
2061       return;
2062     }
2063
2064     Vector seqs = new Vector();
2065     SequenceI seq;
2066     for (int i = 0; i < sg.getSize(); i++)
2067     {
2068       seq = sg.getSequenceAt(i);
2069       seqs.addElement(seq);
2070     }
2071
2072     /*
2073      * If the cut affects all sequences, warn, remove highlighted columns
2074      */
2075     if (sg.getSize() == viewport.getAlignment().getHeight())
2076     {
2077       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2078               .getAlignment().getWidth()) ? true : false;
2079       if (isEntireAlignWidth)
2080       {
2081         String title = MessageManager.getString("label.delete_all");
2082         Panel infoPanel = new Panel();
2083         infoPanel.setLayout(new FlowLayout());
2084         infoPanel
2085                 .add(new Label(MessageManager.getString("warn.delete_all")));
2086
2087         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2088         dialog.setMainPanel(infoPanel);
2089         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2090         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2091         dialog.setVisible(true);
2092
2093         if (!dialog.accept)
2094         {
2095           return;
2096         }
2097       }
2098       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2099               sg.getEndRes() + 1);
2100     }
2101
2102     SequenceI[] cut = new SequenceI[seqs.size()];
2103     for (int i = 0; i < seqs.size(); i++)
2104     {
2105       cut[i] = (SequenceI) seqs.elementAt(i);
2106     }
2107
2108     /*
2109      * //ADD HISTORY ITEM
2110      */
2111     addHistoryItem(new EditCommand(
2112             MessageManager.getString("label.cut_sequences"), Action.CUT,
2113             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2114             viewport.getAlignment()));
2115
2116     viewport.setSelectionGroup(null);
2117     viewport.getAlignment().deleteGroup(sg);
2118
2119     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2120             .getSequences());
2121
2122     if (viewport.getAlignment().getHeight() < 1)
2123     {
2124       this.setVisible(false);
2125     }
2126     viewport.sendSelection();
2127   }
2128
2129   /**
2130    * group consensus toggled
2131    *
2132    */
2133   protected void showGroupConsensus_actionPerformed()
2134   {
2135     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2136     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2137
2138   }
2139
2140   /**
2141    * group conservation toggled.
2142    */
2143   protected void showGroupConservation_actionPerformed()
2144   {
2145     viewport.setShowGroupConservation(showGroupConservation.getState());
2146     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2147   }
2148
2149   /*
2150    * (non-Javadoc)
2151    *
2152    * @see
2153    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2154    * .event.ActionEvent)
2155    */
2156   protected void showConsensusHistogram_actionPerformed()
2157   {
2158     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2159     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2160   }
2161
2162   /*
2163    * (non-Javadoc)
2164    *
2165    * @see
2166    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2167    * .event.ActionEvent)
2168    */
2169   protected void showSequenceLogo_actionPerformed()
2170   {
2171     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2172     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2173   }
2174
2175   protected void normSequenceLogo_actionPerformed()
2176   {
2177     showSequenceLogo.setState(true);
2178     viewport.setShowSequenceLogo(true);
2179     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2180     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181   }
2182
2183   protected void applyAutoAnnotationSettings_actionPerformed()
2184   {
2185     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2186   }
2187
2188   protected void makeGrpsFromSelection_actionPerformed()
2189   {
2190     if (avc.makeGroupsFromSelection())
2191     {
2192       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2193       alignPanel.updateAnnotation();
2194       alignPanel.paintAlignment(true);
2195     }
2196   }
2197
2198   protected void createGroup_actionPerformed()
2199   {
2200     avc.createGroup();
2201   }
2202
2203   protected void unGroup_actionPerformed()
2204   {
2205     if (avc.unGroup())
2206     {
2207       alignPanel.alignmentChanged();
2208     }
2209   }
2210
2211   protected void deleteGroups_actionPerformed()
2212   {
2213     if (avc.deleteGroups())
2214     {
2215       alignPanel.alignmentChanged();
2216     }
2217   }
2218
2219   public void selectAllSequenceMenuItem_actionPerformed()
2220   {
2221     SequenceGroup sg = new SequenceGroup();
2222     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2223     {
2224       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2225     }
2226     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2227     viewport.setSelectionGroup(sg);
2228     alignPanel.paintAlignment(true);
2229     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2230     viewport.sendSelection();
2231   }
2232
2233   public void deselectAllSequenceMenuItem_actionPerformed()
2234   {
2235     if (viewport.cursorMode)
2236     {
2237       alignPanel.seqPanel.keyboardNo1 = null;
2238       alignPanel.seqPanel.keyboardNo2 = null;
2239     }
2240     viewport.setSelectionGroup(null);
2241     viewport.getColumnSelection().clear();
2242     viewport.setSelectionGroup(null);
2243     alignPanel.idPanel.idCanvas.searchResults = null;
2244     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2245     alignPanel.paintAlignment(true);
2246     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2247     viewport.sendSelection();
2248   }
2249
2250   public void invertSequenceMenuItem_actionPerformed()
2251   {
2252     SequenceGroup sg = viewport.getSelectionGroup();
2253     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2254     {
2255       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2256     }
2257
2258     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2259     viewport.sendSelection();
2260   }
2261
2262   public void invertColSel_actionPerformed()
2263   {
2264     viewport.invertColumnSelection();
2265     alignPanel.paintAlignment(true);
2266     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2267     viewport.sendSelection();
2268   }
2269
2270   void trimAlignment(boolean trimLeft)
2271   {
2272     ColumnSelection colSel = viewport.getColumnSelection();
2273     int column;
2274
2275     if (!colSel.isEmpty())
2276     {
2277       if (trimLeft)
2278       {
2279         column = colSel.getMin();
2280       }
2281       else
2282       {
2283         column = colSel.getMax();
2284       }
2285
2286       SequenceI[] seqs;
2287       if (viewport.getSelectionGroup() != null)
2288       {
2289         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2290                 viewport.getHiddenRepSequences());
2291       }
2292       else
2293       {
2294         seqs = viewport.getAlignment().getSequencesArray();
2295       }
2296
2297       TrimRegionCommand trimRegion;
2298       if (trimLeft)
2299       {
2300         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2301                 column, viewport.getAlignment());
2302         viewport.setStartRes(0);
2303       }
2304       else
2305       {
2306         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2307                 column, viewport.getAlignment());
2308       }
2309
2310       statusBar.setText(MessageManager.formatMessage(
2311               "label.removed_columns",
2312               new String[] { Integer.valueOf(trimRegion.getSize())
2313                       .toString() }));
2314       addHistoryItem(trimRegion);
2315
2316       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2317       {
2318         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2319                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2320         {
2321           viewport.getAlignment().deleteGroup(sg);
2322         }
2323       }
2324
2325       viewport.firePropertyChange("alignment", null, viewport
2326               .getAlignment().getSequences());
2327     }
2328   }
2329
2330   public void removeGappedColumnMenuItem_actionPerformed()
2331   {
2332     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2333
2334     SequenceI[] seqs;
2335     if (viewport.getSelectionGroup() != null)
2336     {
2337       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2338               viewport.getHiddenRepSequences());
2339       start = viewport.getSelectionGroup().getStartRes();
2340       end = viewport.getSelectionGroup().getEndRes();
2341     }
2342     else
2343     {
2344       seqs = viewport.getAlignment().getSequencesArray();
2345     }
2346
2347     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2348             "Remove Gapped Columns", seqs, start, end,
2349             viewport.getAlignment());
2350
2351     addHistoryItem(removeGapCols);
2352
2353     statusBar.setText(MessageManager.formatMessage(
2354             "label.removed_empty_columns",
2355             new String[] { Integer.valueOf(removeGapCols.getSize())
2356                     .toString() }));
2357
2358     // This is to maintain viewport position on first residue
2359     // of first sequence
2360     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2361     int startRes = seq.findPosition(viewport.startRes);
2362     // ShiftList shifts;
2363     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2364     // edit.alColumnChanges=shifts.getInverse();
2365     // if (viewport.hasHiddenColumns)
2366     // viewport.getColumnSelection().compensateForEdits(shifts);
2367     viewport.setStartRes(seq.findIndex(startRes) - 1);
2368     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2369             .getSequences());
2370
2371   }
2372
2373   public void removeAllGapsMenuItem_actionPerformed()
2374   {
2375     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2376
2377     SequenceI[] seqs;
2378     if (viewport.getSelectionGroup() != null)
2379     {
2380       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2381               viewport.getHiddenRepSequences());
2382       start = viewport.getSelectionGroup().getStartRes();
2383       end = viewport.getSelectionGroup().getEndRes();
2384     }
2385     else
2386     {
2387       seqs = viewport.getAlignment().getSequencesArray();
2388     }
2389
2390     // This is to maintain viewport position on first residue
2391     // of first sequence
2392     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2393     int startRes = seq.findPosition(viewport.startRes);
2394
2395     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2396             viewport.getAlignment()));
2397
2398     viewport.setStartRes(seq.findIndex(startRes) - 1);
2399
2400     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2401             .getSequences());
2402
2403   }
2404
2405   public void findMenuItem_actionPerformed()
2406   {
2407     new Finder(alignPanel);
2408   }
2409
2410   /**
2411    * create a new view derived from the current view
2412    *
2413    * @param viewtitle
2414    * @return frame for the new view
2415    */
2416   public AlignFrame newView(String viewtitle)
2417   {
2418     AlignmentI newal;
2419     if (viewport.hasHiddenRows())
2420     {
2421       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2422               .getFullAlignment().getSequencesArray());
2423     }
2424     else
2425     {
2426       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2427     }
2428
2429     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2430     {
2431       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2432       {
2433         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2434         {
2435           newal.addAnnotation(viewport.getAlignment()
2436                   .getAlignmentAnnotation()[i]);
2437         }
2438       }
2439     }
2440
2441     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2442
2443     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2444     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2445     PaintRefresher.Register(newaf.alignPanel,
2446             newaf.alignPanel.av.getSequenceSetId());
2447
2448     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2449             newaf.alignPanel.av.getSequenceSetId());
2450     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2451             newaf.alignPanel.av.getSequenceSetId());
2452
2453     Vector comps = (Vector) PaintRefresher.components.get(viewport
2454             .getSequenceSetId());
2455     int viewSize = -1;
2456     for (int i = 0; i < comps.size(); i++)
2457     {
2458       if (comps.elementAt(i) instanceof AlignmentPanel)
2459       {
2460         viewSize++;
2461       }
2462     }
2463
2464     String title = new String(this.getTitle());
2465     if (viewtitle != null)
2466     {
2467       title = viewtitle + " ( " + title + ")";
2468     }
2469     else
2470     {
2471       if (title.indexOf("(View") > -1)
2472       {
2473         title = title.substring(0, title.indexOf("(View"));
2474       }
2475       title += "(View " + viewSize + ")";
2476     }
2477
2478     newaf.setTitle(title.toString());
2479
2480     newaf.viewport.setHistoryList(viewport.getHistoryList());
2481     newaf.viewport.setRedoList(viewport.getRedoList());
2482     return newaf;
2483   }
2484
2485   /**
2486    *
2487    * @return list of feature groups on the view
2488    */
2489   public String[] getFeatureGroups()
2490   {
2491     FeatureRenderer fr = null;
2492     if (alignPanel != null
2493             && (fr = alignPanel.getFeatureRenderer()) != null)
2494     {
2495       List<String> gps = fr.getFeatureGroups();
2496       String[] _gps = gps.toArray(new String[gps.size()]);
2497       return _gps;
2498     }
2499     return null;
2500   }
2501
2502   /**
2503    * get sequence feature groups that are hidden or shown
2504    *
2505    * @param visible
2506    *          true is visible
2507    * @return list
2508    */
2509   public String[] getFeatureGroupsOfState(boolean visible)
2510   {
2511     FeatureRenderer fr = null;
2512     if (alignPanel != null
2513             && (fr = alignPanel.getFeatureRenderer()) != null)
2514     {
2515       List<String> gps = fr.getGroups(visible);
2516       String[] _gps = gps.toArray(new String[gps.size()]);
2517       return _gps;
2518     }
2519     return null;
2520   }
2521
2522   /**
2523    * Change the display state for the given feature groups
2524    *
2525    * @param groups
2526    *          list of group strings
2527    * @param state
2528    *          visible or invisible
2529    */
2530   public void setFeatureGroupState(String[] groups, boolean state)
2531   {
2532     FeatureRenderer fr = null;
2533     this.sequenceFeatures.setState(true);
2534     viewport.setShowSequenceFeatures(true);
2535     if (alignPanel != null
2536             && (fr = alignPanel.getFeatureRenderer()) != null)
2537     {
2538
2539       fr.setGroupVisibility(Arrays.asList(groups), state);
2540       alignPanel.seqPanel.seqCanvas.repaint();
2541       if (alignPanel.overviewPanel != null)
2542       {
2543         alignPanel.overviewPanel.updateOverviewImage();
2544       }
2545     }
2546   }
2547
2548   public void seqLimits_itemStateChanged()
2549   {
2550     viewport.setShowJVSuffix(seqLimits.getState());
2551     alignPanel.fontChanged();
2552     alignPanel.paintAlignment(true);
2553   }
2554
2555   protected void colourTextMenuItem_actionPerformed()
2556   {
2557     viewport.setColourText(colourTextMenuItem.getState());
2558     alignPanel.paintAlignment(true);
2559   }
2560
2561   protected void displayNonconservedMenuItem_actionPerformed()
2562   {
2563     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2564     alignPanel.paintAlignment(true);
2565   }
2566
2567   protected void wrapMenuItem_actionPerformed()
2568   {
2569     viewport.setWrapAlignment(wrapMenuItem.getState());
2570     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2571     scaleAbove.setEnabled(wrapMenuItem.getState());
2572     scaleLeft.setEnabled(wrapMenuItem.getState());
2573     scaleRight.setEnabled(wrapMenuItem.getState());
2574     alignPanel.paintAlignment(true);
2575   }
2576
2577   public void overviewMenuItem_actionPerformed()
2578   {
2579     if (alignPanel.overviewPanel != null)
2580     {
2581       return;
2582     }
2583
2584     Frame frame = new Frame();
2585     OverviewPanel overview = new OverviewPanel(alignPanel);
2586     frame.add(overview);
2587     // +50 must allow for applet frame window
2588     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2589             "label.overview_params", new String[] { this.getTitle() }),
2590             overview.getPreferredSize().width,
2591             overview.getPreferredSize().height + 50);
2592
2593     frame.pack();
2594     final AlignmentPanel ap = alignPanel;
2595     frame.addWindowListener(new WindowAdapter()
2596     {
2597       @Override
2598       public void windowClosing(WindowEvent e)
2599       {
2600         if (ap != null)
2601         {
2602           ap.setOverviewPanel(null);
2603         }
2604       };
2605     });
2606
2607     alignPanel.setOverviewPanel(overview);
2608
2609   }
2610
2611   @Override
2612   public void changeColour(ColourSchemeI cs)
2613   {
2614
2615     if (cs != null)
2616     {
2617       if (viewport.getAbovePIDThreshold())
2618       {
2619         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2620                 cs, "Background"));
2621       }
2622
2623       if (viewport.getConservationSelected())
2624       {
2625         cs.setConservationApplied(true);
2626         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2627                 cs, "Background"));
2628       }
2629       else
2630       {
2631         cs.setConservationApplied(false);
2632       }
2633     }
2634     viewport.setGlobalColourScheme(cs);
2635
2636     alignPanel.paintAlignment(true);
2637   }
2638
2639   protected void modifyPID_actionPerformed()
2640   {
2641     if (viewport.getAbovePIDThreshold()
2642             && viewport.getGlobalColourScheme() != null)
2643     {
2644       SliderPanel.setPIDSliderSource(alignPanel,
2645               viewport.getGlobalColourScheme(), "Background");
2646       SliderPanel.showPIDSlider();
2647     }
2648   }
2649
2650   protected void modifyConservation_actionPerformed()
2651   {
2652     if (viewport.getConservationSelected()
2653             && viewport.getGlobalColourScheme() != null)
2654     {
2655       SliderPanel.setConservationSlider(alignPanel,
2656               viewport.getGlobalColourScheme(), "Background");
2657       SliderPanel.showConservationSlider();
2658     }
2659   }
2660
2661   protected void conservationMenuItem_actionPerformed()
2662   {
2663     viewport.setConservationSelected(conservationMenuItem.getState());
2664
2665     viewport.setAbovePIDThreshold(false);
2666     abovePIDThreshold.setState(false);
2667
2668     changeColour(viewport.getGlobalColourScheme());
2669
2670     modifyConservation_actionPerformed();
2671   }
2672
2673   public void abovePIDThreshold_actionPerformed()
2674   {
2675     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2676
2677     conservationMenuItem.setState(false);
2678     viewport.setConservationSelected(false);
2679
2680     changeColour(viewport.getGlobalColourScheme());
2681
2682     modifyPID_actionPerformed();
2683   }
2684
2685   public void sortPairwiseMenuItem_actionPerformed()
2686   {
2687     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2688     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2689             .getAlignment().getSequenceAt(0), null);
2690
2691     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2692             viewport.getAlignment()));
2693     alignPanel.paintAlignment(true);
2694   }
2695
2696   public void sortIDMenuItem_actionPerformed()
2697   {
2698     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2699     AlignmentSorter.sortByID(viewport.getAlignment());
2700     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2701             viewport.getAlignment()));
2702     alignPanel.paintAlignment(true);
2703   }
2704
2705   public void sortLengthMenuItem_actionPerformed()
2706   {
2707     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2708     AlignmentSorter.sortByLength(viewport.getAlignment());
2709     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2710             viewport.getAlignment()));
2711     alignPanel.paintAlignment(true);
2712   }
2713
2714   public void sortGroupMenuItem_actionPerformed()
2715   {
2716     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2717     AlignmentSorter.sortByGroup(viewport.getAlignment());
2718     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2719             viewport.getAlignment()));
2720     alignPanel.paintAlignment(true);
2721
2722   }
2723
2724   public void removeRedundancyMenuItem_actionPerformed()
2725   {
2726     new RedundancyPanel(alignPanel);
2727   }
2728
2729   public void pairwiseAlignmentMenuItem_actionPerformed()
2730   {
2731     if (viewport.getSelectionGroup() != null
2732             && viewport.getSelectionGroup().getSize() > 1)
2733     {
2734       Frame frame = new Frame();
2735       frame.add(new PairwiseAlignPanel(alignPanel));
2736       jalview.bin.JalviewLite.addFrame(frame,
2737               MessageManager.getString("action.pairwise_alignment"), 600,
2738               500);
2739     }
2740   }
2741
2742   public void PCAMenuItem_actionPerformed()
2743   {
2744     // are the sequences aligned?
2745     if (!viewport.getAlignment().isAligned(false))
2746     {
2747       SequenceI current;
2748       int Width = viewport.getAlignment().getWidth();
2749
2750       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2751       {
2752         current = viewport.getAlignment().getSequenceAt(i);
2753
2754         if (current.getLength() < Width)
2755         {
2756           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2757         }
2758       }
2759       alignPanel.paintAlignment(true);
2760     }
2761
2762     if ((viewport.getSelectionGroup() != null
2763             && viewport.getSelectionGroup().getSize() < 4 && viewport
2764             .getSelectionGroup().getSize() > 0)
2765             || viewport.getAlignment().getHeight() < 4)
2766     {
2767       return;
2768     }
2769
2770     try
2771     {
2772       new PCAPanel(viewport);
2773     } catch (java.lang.OutOfMemoryError ex)
2774     {
2775     }
2776
2777   }
2778
2779   public void averageDistanceTreeMenuItem_actionPerformed()
2780   {
2781     NewTreePanel("AV", "PID", "Average distance tree using PID");
2782   }
2783
2784   public void neighbourTreeMenuItem_actionPerformed()
2785   {
2786     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2787   }
2788
2789   protected void njTreeBlosumMenuItem_actionPerformed()
2790   {
2791     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2792   }
2793
2794   protected void avTreeBlosumMenuItem_actionPerformed()
2795   {
2796     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2797   }
2798
2799   void NewTreePanel(String type, String pwType, String title)
2800   {
2801     // are the sequences aligned?
2802     if (!viewport.getAlignment().isAligned(false))
2803     {
2804       SequenceI current;
2805       int Width = viewport.getAlignment().getWidth();
2806
2807       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2808       {
2809         current = viewport.getAlignment().getSequenceAt(i);
2810
2811         if (current.getLength() < Width)
2812         {
2813           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2814         }
2815       }
2816       alignPanel.paintAlignment(true);
2817
2818     }
2819
2820     if ((viewport.getSelectionGroup() != null && viewport
2821             .getSelectionGroup().getSize() > 1)
2822             || (viewport.getAlignment().getHeight() > 1))
2823     {
2824       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2825
2826       addTreeMenuItem(tp, title);
2827
2828       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2829     }
2830   }
2831
2832   void loadTree_actionPerformed()
2833   {
2834     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2835     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2836     cap.setTreeImport();
2837     Frame frame = new Frame();
2838     frame.add(cap);
2839     jalview.bin.JalviewLite.addFrame(frame,
2840             MessageManager.getString("label.paste_newick_file"), 400, 300);
2841   }
2842
2843   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2844   {
2845     TreePanel tp = new TreePanel(alignPanel, treeFile,
2846             MessageManager.getString("label.load_tree_from_file"), tree);
2847     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2848     addTreeMenuItem(tp, treeFile);
2849   }
2850
2851   /**
2852    * sort the alignment using the given treePanel
2853    *
2854    * @param treePanel
2855    *          tree used to sort view
2856    * @param title
2857    *          string used for undo event name
2858    */
2859   public void sortByTree(TreePanel treePanel, String title)
2860   {
2861     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2862     AlignmentSorter
2863             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2864     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2865     // HistoryItem.SORT));
2866     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2867             "label.order_by_params", new String[] { title }), oldOrder,
2868             viewport.getAlignment()));
2869     alignPanel.paintAlignment(true);
2870   }
2871
2872   /**
2873    * Do any automatic reordering of the alignment and add the necessary bits to
2874    * the menu structure for the new tree
2875    *
2876    * @param treePanel
2877    * @param title
2878    */
2879   protected void addTreeMenuItem(final TreePanel treePanel,
2880           final String title)
2881   {
2882     final MenuItem item = new MenuItem(title);
2883     sortByTreeMenu.add(item);
2884     item.addActionListener(new java.awt.event.ActionListener()
2885     {
2886       @Override
2887       public void actionPerformed(ActionEvent evt)
2888       {
2889         sortByTree(treePanel, title); // treePanel.getTitle());
2890       }
2891     });
2892
2893     treePanel.addWindowListener(new WindowAdapter()
2894     {
2895       @Override
2896       public void windowOpened(WindowEvent e)
2897       {
2898         if (viewport.sortByTree)
2899         {
2900           sortByTree(treePanel, title);
2901         }
2902         super.windowOpened(e);
2903       }
2904
2905       @Override
2906       public void windowClosing(WindowEvent e)
2907       {
2908         sortByTreeMenu.remove(item);
2909       };
2910     });
2911   }
2912
2913   public boolean sortBy(AlignmentOrder alorder, String undoname)
2914   {
2915     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2916     if (viewport.applet.debug)
2917     {
2918       System.err.println("Sorting " + alorder.getOrder().size()
2919               + " in alignment '" + getTitle() + "'");
2920     }
2921     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2922     if (undoname != null)
2923     {
2924       addHistoryItem(new OrderCommand(undoname, oldOrder,
2925               viewport.getAlignment()));
2926     }
2927     alignPanel.paintAlignment(true);
2928     return true;
2929   }
2930
2931   protected void documentation_actionPerformed()
2932   {
2933     alignPanel.av.applet.openJalviewHelpUrl();
2934   }
2935
2936   protected void about_actionPerformed()
2937   {
2938
2939     class AboutPanel extends Canvas
2940     {
2941       String version;
2942
2943       String builddate;
2944
2945       public AboutPanel(String version, String builddate)
2946       {
2947         this.version = version;
2948         this.builddate = builddate;
2949       }
2950
2951       @Override
2952       public void paint(Graphics g)
2953       {
2954         g.setColor(Color.white);
2955         g.fillRect(0, 0, getSize().width, getSize().height);
2956         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2957         FontMetrics fm = g.getFontMetrics();
2958         int fh = fm.getHeight();
2959         int y = 5, x = 7;
2960         g.setColor(Color.black);
2961         // TODO: update this text for each release or centrally store it for
2962         // lite and application
2963         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2964         g.drawString(MessageManager.formatMessage(
2965                 "label.jalviewLite_release", new String[] { version }), x,
2966                 y += fh);
2967         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2968         g.drawString(MessageManager.formatMessage(
2969                 "label.jaview_build_date", new String[] { builddate }), x,
2970                 y += fh);
2971         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2972         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2973                 x, y += fh * 1.5);
2974         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2975                 x + 50, y += fh + 8);
2976         g.drawString(
2977                 MessageManager.getString("label.jalview_dev_managers"), x,
2978                 y += fh);
2979         g.drawString(MessageManager
2980                 .getString("label.jalview_distribution_lists"), x, y += fh);
2981         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2982                 x, y += fh + 8);
2983         g.drawString(
2984                 MessageManager.getString("label.jalview_cite_1_authors"),
2985                 x, y += fh);
2986         g.drawString(
2987                 MessageManager.getString("label.jalview_cite_1_title"), x,
2988                 y += fh);
2989         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2990                 x, y += fh);
2991       }
2992     }
2993
2994     Frame frame = new Frame();
2995     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2996             .getBuildDate()));
2997     jalview.bin.JalviewLite.addFrame(frame,
2998             MessageManager.getString("label.jalview"), 580, 220);
2999
3000   }
3001
3002   public void showURL(String url, String target)
3003   {
3004     if (viewport.applet == null)
3005     {
3006       System.out.println("Not running as applet - no browser available.");
3007     }
3008     else
3009     {
3010       viewport.applet.showURL(url, target);
3011     }
3012   }
3013
3014   // ////////////////////////////////////////////////////////////////////////////////
3015   // JBuilder Graphics here
3016
3017   MenuBar alignFrameMenuBar = new MenuBar();
3018
3019   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3020
3021   MenuItem loadApplication = new MenuItem(
3022           MessageManager.getString("label.view_full_application"));
3023
3024   MenuItem loadTree = new MenuItem(
3025           MessageManager.getString("label.load_associated_tree"));
3026
3027   MenuItem loadAnnotations = new MenuItem(
3028           MessageManager.getString("label.load_features_annotations"));
3029
3030   MenuItem outputFeatures = new MenuItem(
3031           MessageManager.getString("label.export_features"));
3032
3033   MenuItem outputAnnotations = new MenuItem(
3034           MessageManager.getString("label.export_annotations"));
3035
3036   MenuItem closeMenuItem = new MenuItem(
3037           MessageManager.getString("action.close"));
3038
3039   MenuItem selectAllSequenceMenuItem = new MenuItem(
3040           MessageManager.getString("action.select_all"));
3041
3042   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3043           MessageManager.getString("action.deselect_all"));
3044
3045   MenuItem invertSequenceMenuItem = new MenuItem(
3046           MessageManager.getString("action.invert_selection"));
3047
3048   MenuItem remove2LeftMenuItem = new MenuItem();
3049
3050   MenuItem remove2RightMenuItem = new MenuItem();
3051
3052   MenuItem removeGappedColumnMenuItem = new MenuItem();
3053
3054   MenuItem removeAllGapsMenuItem = new MenuItem();
3055
3056   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3057
3058   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3059
3060   MenuItem sortPairwiseMenuItem = new MenuItem();
3061
3062   MenuItem sortIDMenuItem = new MenuItem();
3063
3064   MenuItem sortLengthMenuItem = new MenuItem();
3065
3066   MenuItem sortGroupMenuItem = new MenuItem();
3067
3068   MenuItem removeRedundancyMenuItem = new MenuItem();
3069
3070   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3071
3072   MenuItem PCAMenuItem = new MenuItem();
3073
3074   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3075
3076   MenuItem neighbourTreeMenuItem = new MenuItem();
3077
3078   BorderLayout borderLayout1 = new BorderLayout();
3079
3080   public Label statusBar = new Label();
3081
3082   MenuItem clustalColour = new MenuItem();
3083
3084   MenuItem zappoColour = new MenuItem();
3085
3086   MenuItem taylorColour = new MenuItem();
3087
3088   MenuItem hydrophobicityColour = new MenuItem();
3089
3090   MenuItem helixColour = new MenuItem();
3091
3092   MenuItem strandColour = new MenuItem();
3093
3094   MenuItem turnColour = new MenuItem();
3095
3096   MenuItem buriedColour = new MenuItem();
3097
3098   MenuItem purinePyrimidineColour = new MenuItem();
3099
3100   // MenuItem RNAInteractionColour = new MenuItem();
3101
3102   MenuItem RNAHelixColour = new MenuItem();
3103
3104   MenuItem userDefinedColour = new MenuItem();
3105
3106   MenuItem PIDColour = new MenuItem();
3107
3108   MenuItem BLOSUM62Colour = new MenuItem();
3109
3110   MenuItem tcoffeeColour = new MenuItem();
3111
3112   MenuItem njTreeBlosumMenuItem = new MenuItem();
3113
3114   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3115
3116   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3117
3118   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3119
3120   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3121
3122   MenuItem alProperties = new MenuItem(
3123           MessageManager.getString("label.alignment_props"));
3124
3125   MenuItem overviewMenuItem = new MenuItem();
3126
3127   MenuItem undoMenuItem = new MenuItem();
3128
3129   MenuItem redoMenuItem = new MenuItem();
3130
3131   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3132
3133   MenuItem noColourmenuItem = new MenuItem();
3134
3135   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3136
3137   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3138
3139   MenuItem findMenuItem = new MenuItem();
3140
3141   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3142
3143   MenuItem nucleotideColour = new MenuItem();
3144
3145   MenuItem deleteGroups = new MenuItem();
3146
3147   MenuItem grpsFromSelection = new MenuItem();
3148
3149   MenuItem createGroup = new MenuItem();
3150
3151   MenuItem unGroup = new MenuItem();
3152
3153   MenuItem delete = new MenuItem();
3154
3155   MenuItem copy = new MenuItem();
3156
3157   MenuItem cut = new MenuItem();
3158
3159   Menu pasteMenu = new Menu();
3160
3161   MenuItem pasteNew = new MenuItem();
3162
3163   MenuItem pasteThis = new MenuItem();
3164
3165   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3166
3167   MenuItem font = new MenuItem();
3168
3169   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3170
3171   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3174
3175   MenuItem modifyPID = new MenuItem();
3176
3177   MenuItem modifyConservation = new MenuItem();
3178
3179   CheckboxMenuItem autoCalculate = null;
3180
3181   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3182           "Sort Alignment With New Tree", true);
3183
3184   Menu sortByTreeMenu = new Menu();
3185
3186   MenuItem inputText = new MenuItem();
3187
3188   MenuItem documentation = new MenuItem();
3189
3190   MenuItem about = new MenuItem();
3191
3192   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3193
3194   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3195
3196   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3197
3198   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3199
3200   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3201
3202   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3203
3204   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3205
3206   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3209
3210   /**
3211    * Initialise menus and other items
3212    *
3213    * @throws Exception
3214    */
3215   private void jbInit() throws Exception
3216   {
3217     setMenuBar(alignFrameMenuBar);
3218
3219     /*
3220      * Configure File menu items and actions
3221      */
3222     inputText
3223             .setLabel(MessageManager.getString("label.input_from_textbox"));
3224     inputText.addActionListener(this);
3225     Menu outputTextboxMenu = new Menu(
3226             MessageManager.getString("label.out_to_textbox"));
3227     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3228     {
3229
3230       MenuItem item = new MenuItem(
3231               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3232
3233       item.addActionListener(new java.awt.event.ActionListener()
3234       {
3235         @Override
3236         public void actionPerformed(ActionEvent e)
3237         {
3238           outputText_actionPerformed(e);
3239         }
3240       });
3241
3242       outputTextboxMenu.add(item);
3243     }
3244     closeMenuItem.addActionListener(this);
3245     loadApplication.addActionListener(this);
3246     loadTree.addActionListener(this);
3247     loadAnnotations.addActionListener(this);
3248     outputFeatures.addActionListener(this);
3249     outputAnnotations.addActionListener(this);
3250
3251     /*
3252      * Configure Edit menu items and actions
3253      */
3254     undoMenuItem.setEnabled(false);
3255     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3256     undoMenuItem.addActionListener(this);
3257     redoMenuItem.setEnabled(false);
3258     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3259     redoMenuItem.addActionListener(this);
3260     copy.setLabel(MessageManager.getString("action.copy"));
3261     copy.addActionListener(this);
3262     cut.setLabel(MessageManager.getString("action.cut"));
3263     cut.addActionListener(this);
3264     delete.setLabel(MessageManager.getString("action.delete"));
3265     delete.addActionListener(this);
3266     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3267     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3268     pasteNew.addActionListener(this);
3269     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3270     pasteThis.addActionListener(this);
3271     remove2LeftMenuItem.setLabel(MessageManager
3272             .getString("action.remove_left"));
3273     remove2LeftMenuItem.addActionListener(this);
3274     remove2RightMenuItem.setLabel(MessageManager
3275             .getString("action.remove_right"));
3276     remove2RightMenuItem.addActionListener(this);
3277     removeGappedColumnMenuItem.setLabel(MessageManager
3278             .getString("action.remove_empty_columns"));
3279     removeGappedColumnMenuItem.addActionListener(this);
3280     removeAllGapsMenuItem.setLabel(MessageManager
3281             .getString("action.remove_all_gaps"));
3282     removeAllGapsMenuItem.addActionListener(this);
3283     removeRedundancyMenuItem.setLabel(MessageManager
3284             .getString("action.remove_redundancy"));
3285     removeRedundancyMenuItem.addActionListener(this);
3286
3287     /*
3288      * Configure Select menu items and actions
3289      */
3290     findMenuItem.setLabel(MessageManager.getString("action.find"));
3291     findMenuItem.addActionListener(this);
3292     selectAllSequenceMenuItem.addActionListener(this);
3293     deselectAllSequenceMenuItem.addActionListener(this);
3294     invertSequenceMenuItem.setLabel(MessageManager
3295             .getString("action.invert_sequence_selection"));
3296     invertSequenceMenuItem.addActionListener(this);
3297     invertColSel.setLabel(MessageManager
3298             .getString("action.invert_column_selection"));
3299     invertColSel.addActionListener(this);
3300     deleteGroups.setLabel(MessageManager
3301             .getString("action.undefine_groups"));
3302     deleteGroups.addActionListener(this);
3303     grpsFromSelection.setLabel(MessageManager
3304             .getString("action.make_groups_selection"));
3305     grpsFromSelection.addActionListener(this);
3306     createGroup.setLabel(MessageManager.getString("action.create_group"));
3307     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3308     annotationColumnSelection.setLabel(MessageManager
3309             .getString("action.select_by_annotation"));
3310     annotationColumnSelection.addActionListener(this);
3311
3312     /*
3313      * Configure View menu items and actions
3314      */
3315     newView.setLabel(MessageManager.getString("action.new_view"));
3316     newView.addActionListener(this);
3317     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3318     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3319     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3320     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3321     hideColumns
3322             .setLabel(MessageManager.getString("label.selected_columns"));
3323     hideSequences.setLabel(MessageManager
3324             .getString("label.selected_sequences"));
3325     hideAllButSelection.setLabel(MessageManager
3326             .getString("label.all_but_selected_region"));
3327     hideAllSelection.setLabel(MessageManager
3328             .getString("label.selected_region"));
3329     showAllHidden.setLabel(MessageManager
3330             .getString("label.all_sequences_columns"));
3331     showColumns.addActionListener(this);
3332     showSeqs.addActionListener(this);
3333     hideColumns.addActionListener(this);
3334     hideSequences.addActionListener(this);
3335     hideAllButSelection.addActionListener(this);
3336     hideAllSelection.addActionListener(this);
3337     showAllHidden.addActionListener(this);
3338     featureSettings.setLabel(MessageManager
3339             .getString("action.feature_settings"));
3340     featureSettings.addActionListener(this);
3341     sequenceFeatures.setLabel(MessageManager
3342             .getString("label.show_sequence_features"));
3343     sequenceFeatures.addItemListener(this);
3344     sequenceFeatures.setState(false);
3345     followMouseOverFlag.setLabel(MessageManager
3346             .getString("label.automatic_scrolling"));
3347     followMouseOverFlag.addItemListener(this);
3348     alProperties.addActionListener(this);
3349     overviewMenuItem.setLabel(MessageManager
3350             .getString("label.overview_window"));
3351     overviewMenuItem.addActionListener(this);
3352
3353     /*
3354      * Configure Annotations menu items and actions
3355      */
3356     annotationPanelMenuItem.setLabel(MessageManager
3357             .getString("label.show_annotations"));
3358     annotationPanelMenuItem.addItemListener(this);
3359     showGroupConsensus.setLabel(MessageManager
3360             .getString("label.group_consensus"));
3361     showGroupConservation.setLabel(MessageManager
3362             .getString("label.group_conservation"));
3363     showConsensusHistogram.setLabel(MessageManager
3364             .getString("label.show_consensus_histogram"));
3365     showSequenceLogo.setLabel(MessageManager
3366             .getString("label.show_consensus_logo"));
3367     normSequenceLogo.setLabel(MessageManager
3368             .getString("label.norm_consensus_logo"));
3369     applyAutoAnnotationSettings.setLabel(MessageManager
3370             .getString("label.apply_all_groups"));
3371     applyAutoAnnotationSettings.setState(true);
3372     Menu autoAnnMenu = new Menu(
3373             MessageManager.getString("label.autocalculated_annotation"));
3374     showGroupConsensus.addItemListener(this);
3375     showGroupConservation.addItemListener(this);
3376     showConsensusHistogram.addItemListener(this);
3377     showSequenceLogo.addItemListener(this);
3378     normSequenceLogo.addItemListener(this);
3379     applyAutoAnnotationSettings.addItemListener(this);
3380     showAlignmentAnnotations = new CheckboxMenuItem(
3381             MessageManager.getString("label.show_all_al_annotations"));
3382     showSequenceAnnotations = new CheckboxMenuItem(
3383             MessageManager.getString("label.show_all_seq_annotations"));
3384     sortAnnBySequence = new CheckboxMenuItem(
3385             MessageManager.getString("label.sort_annotations_by_sequence"));
3386     sortAnnByLabel = new CheckboxMenuItem(
3387             MessageManager.getString("label.sort_annotations_by_label"));
3388     showAutoFirst = new CheckboxMenuItem(
3389             MessageManager.getString("label.show_first"));
3390     showAutoFirst.setState(false); // pending applet parameter
3391     setShowAutoCalculatedAbove(showAutoFirst.getState());
3392     showAutoLast = new CheckboxMenuItem(
3393             MessageManager.getString("label.show_last"));
3394     showAutoLast.setState(!showAutoFirst.getState());
3395     showAlignmentAnnotations.addItemListener(this);
3396     showSequenceAnnotations.addItemListener(this);
3397     sortAnnBySequence.addItemListener(this);
3398     sortAnnByLabel.addItemListener(this);
3399     showAutoFirst.addItemListener(this);
3400     showAutoLast.addItemListener(this);
3401
3402     /*
3403      * Configure Format menu items and actions
3404      */
3405     font.setLabel(MessageManager.getString("action.font"));
3406     font.addActionListener(this);
3407     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3408     scaleAbove.setState(true);
3409     scaleAbove.setEnabled(false);
3410     scaleAbove.addItemListener(this);
3411     scaleLeft.setEnabled(false);
3412     scaleLeft.setState(true);
3413     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3414     scaleLeft.addItemListener(this);
3415     scaleRight.setEnabled(false);
3416     scaleRight.setState(true);
3417     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3418     scaleRight.addItemListener(this);
3419     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3420     viewBoxesMenuItem.setState(true);
3421     viewBoxesMenuItem.addItemListener(this);
3422     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3423     viewTextMenuItem.setState(true);
3424     viewTextMenuItem.addItemListener(this);
3425     colourTextMenuItem.setLabel(MessageManager
3426             .getString("label.colour_text"));
3427     colourTextMenuItem.addItemListener(this);
3428     displayNonconservedMenuItem.setLabel(MessageManager
3429             .getString("label.show_non_conversed"));
3430     displayNonconservedMenuItem.addItemListener(this);
3431     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3432     wrapMenuItem.addItemListener(this);
3433     renderGapsMenuItem.setLabel(MessageManager
3434             .getString("action.show_gaps"));
3435     renderGapsMenuItem.setState(true);
3436     renderGapsMenuItem.addItemListener(this);
3437     centreColumnLabelFlag.setLabel(MessageManager
3438             .getString("label.centre_column_labels"));
3439     centreColumnLabelFlag.addItemListener(this);
3440     seqLimits.setState(true);
3441     seqLimits.setLabel(MessageManager
3442             .getString("label.show_sequence_limits"));
3443     seqLimits.addItemListener(this);
3444
3445     /*
3446      * Configure Colour menu items and actions
3447      */
3448     applyToAllGroups.setLabel(MessageManager
3449             .getString("label.apply_colour_to_all_groups"));
3450     applyToAllGroups.setState(true);
3451     applyToAllGroups.addItemListener(this);
3452     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3453     clustalColour.addActionListener(this);
3454     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3455     zappoColour.addActionListener(this);
3456     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3457     taylorColour.addActionListener(this);
3458     hydrophobicityColour.setLabel(MessageManager
3459             .getString("label.hydrophobicity"));
3460     hydrophobicityColour.addActionListener(this);
3461     helixColour
3462             .setLabel(MessageManager.getString("label.helix_propensity"));
3463     helixColour.addActionListener(this);
3464     strandColour.setLabel(MessageManager
3465             .getString("label.strand_propensity"));
3466     strandColour.addActionListener(this);
3467     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3468     turnColour.addActionListener(this);
3469     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3470     buriedColour.addActionListener(this);
3471     purinePyrimidineColour.setLabel(MessageManager
3472             .getString("label.purine_pyrimidine"));
3473     purinePyrimidineColour.addActionListener(this);
3474     // RNAInteractionColour.setLabel(MessageManager
3475     // .getString("label.rna_interaction"));
3476     // RNAInteractionColour.addActionListener(this);
3477     RNAHelixColour.setLabel(MessageManager
3478             .getString("action.by_rna_helixes"));
3479     RNAHelixColour.addActionListener(this);
3480     userDefinedColour.setLabel(MessageManager
3481             .getString("action.user_defined"));
3482     userDefinedColour.addActionListener(this);
3483     PIDColour.setLabel(MessageManager
3484             .getString("label.percentage_identity"));
3485     PIDColour.addActionListener(this);
3486     BLOSUM62Colour.setLabel(MessageManager
3487             .getString("label.blosum62_score"));
3488     BLOSUM62Colour.addActionListener(this);
3489     tcoffeeColour
3490             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3491     // it will be enabled only if a score file is provided
3492     tcoffeeColour.setEnabled(false);
3493     tcoffeeColour.addActionListener(this);
3494     conservationMenuItem.setLabel(MessageManager
3495             .getString("action.by_conservation"));
3496     conservationMenuItem.addItemListener(this);
3497     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3498     noColourmenuItem.addActionListener(this);
3499     abovePIDThreshold.setLabel(MessageManager
3500             .getString("label.above_identity_threshold"));
3501     abovePIDThreshold.addItemListener(this);
3502     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3503     nucleotideColour.addActionListener(this);
3504     modifyPID.setLabel(MessageManager
3505             .getString("label.modify_identity_thereshold"));
3506     modifyPID.addActionListener(this);
3507     modifyConservation.setLabel(MessageManager
3508             .getString("label.modify_conservation_thereshold"));
3509     modifyConservation.addActionListener(this);
3510     annotationColour.setLabel(MessageManager
3511             .getString("action.by_annotation"));
3512     annotationColour.addActionListener(this);
3513
3514     /*
3515      * Configure Calculate menu items and actions
3516      */
3517     sortPairwiseMenuItem.setLabel(MessageManager
3518             .getString("action.by_pairwise_id"));
3519     sortPairwiseMenuItem.addActionListener(this);
3520     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3521     sortIDMenuItem.addActionListener(this);
3522     sortLengthMenuItem.setLabel(MessageManager
3523             .getString("action.by_length"));
3524     sortLengthMenuItem.addActionListener(this);
3525     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3526     sortGroupMenuItem.addActionListener(this);
3527     pairwiseAlignmentMenuItem.setLabel(MessageManager
3528             .getString("action.pairwise_alignment"));
3529     pairwiseAlignmentMenuItem.addActionListener(this);
3530     PCAMenuItem.setLabel(MessageManager
3531             .getString("label.principal_component_analysis"));
3532     PCAMenuItem.addActionListener(this);
3533     autoCalculate = new CheckboxMenuItem(
3534             MessageManager.getString("label.autocalculate_consensus"), true);
3535     averageDistanceTreeMenuItem.setLabel(MessageManager
3536             .getString("label.average_distance_identity"));
3537     averageDistanceTreeMenuItem.addActionListener(this);
3538     neighbourTreeMenuItem.setLabel(MessageManager
3539             .getString("label.neighbour_joining_identity"));
3540     neighbourTreeMenuItem.addActionListener(this);
3541     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3542             .getString("label.average_distance_bloslum62"));
3543     avDistanceTreeBlosumMenuItem.addActionListener(this);
3544     njTreeBlosumMenuItem.setLabel(MessageManager
3545             .getString("label.neighbour_blosum62"));
3546     njTreeBlosumMenuItem.addActionListener(this);
3547     sortByTreeMenu.setLabel(MessageManager
3548             .getString("action.by_tree_order"));
3549     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3550     Menu calculateTreeMenu = new Menu(
3551             MessageManager.getString("action.calculate_tree"));
3552     autoCalculate.addItemListener(this);
3553     sortByTree.addItemListener(this);
3554
3555     /*
3556      * Configure Help menu items and actions
3557      */
3558     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3559     documentation.setLabel(MessageManager.getString("label.documentation"));
3560     documentation.addActionListener(this);
3561     about.setLabel(MessageManager.getString("label.about"));
3562     about.addActionListener(this);
3563
3564     /*
3565      * Add top level menus to frame
3566      */
3567     alignFrameMenuBar.add(fileMenu);
3568     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3569     alignFrameMenuBar.add(editMenu);
3570     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3571     alignFrameMenuBar.add(selectMenu);
3572     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3573     alignFrameMenuBar.add(viewMenu);
3574     Menu annotationsMenu = new Menu(
3575             MessageManager.getString("action.annotations"));
3576     alignFrameMenuBar.add(annotationsMenu);
3577     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3578     alignFrameMenuBar.add(formatMenu);
3579     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3580     alignFrameMenuBar.add(colourMenu);
3581     Menu calculateMenu = new Menu(
3582             MessageManager.getString("action.calculate"));
3583     alignFrameMenuBar.add(calculateMenu);
3584     alignFrameMenuBar.add(helpMenu);
3585
3586     /*
3587      * File menu
3588      */
3589     fileMenu.add(inputText);
3590     fileMenu.add(loadTree);
3591     fileMenu.add(loadAnnotations);
3592     fileMenu.addSeparator();
3593     fileMenu.add(outputTextboxMenu);
3594     fileMenu.add(outputFeatures);
3595     fileMenu.add(outputAnnotations);
3596     if (jalviewServletURL != null)
3597     {
3598       fileMenu.add(loadApplication);
3599     }
3600     fileMenu.addSeparator();
3601     fileMenu.add(closeMenuItem);
3602
3603     /*
3604      * Edit menu
3605      */
3606     editMenu.add(undoMenuItem);
3607     editMenu.add(redoMenuItem);
3608     editMenu.add(cut);
3609     editMenu.add(copy);
3610     pasteMenu.add(pasteNew);
3611     pasteMenu.add(pasteThis);
3612     editMenu.add(pasteMenu);
3613     editMenu.add(delete);
3614     editMenu.addSeparator();
3615     editMenu.add(remove2LeftMenuItem);
3616     editMenu.add(remove2RightMenuItem);
3617     editMenu.add(removeGappedColumnMenuItem);
3618     editMenu.add(removeAllGapsMenuItem);
3619     editMenu.add(removeRedundancyMenuItem);
3620
3621     /*
3622      * Select menu
3623      */
3624     selectMenu.add(findMenuItem);
3625     selectMenu.addSeparator();
3626     selectMenu.add(selectAllSequenceMenuItem);
3627     selectMenu.add(deselectAllSequenceMenuItem);
3628     selectMenu.add(invertSequenceMenuItem);
3629     selectMenu.add(invertColSel);
3630     selectMenu.add(createGroup);
3631     selectMenu.add(unGroup);
3632     selectMenu.add(grpsFromSelection);
3633     selectMenu.add(deleteGroups);
3634     selectMenu.add(annotationColumnSelection);
3635
3636     /*
3637      * View menu
3638      */
3639     viewMenu.add(newView);
3640     viewMenu.addSeparator();
3641     showMenu.add(showColumns);
3642     showMenu.add(showSeqs);
3643     showMenu.add(showAllHidden);
3644     viewMenu.add(showMenu);
3645     hideMenu.add(hideColumns);
3646     hideMenu.add(hideSequences);
3647     hideMenu.add(hideAllSelection);
3648     hideMenu.add(hideAllButSelection);
3649     viewMenu.add(hideMenu);
3650     viewMenu.addSeparator();
3651     viewMenu.add(followMouseOverFlag);
3652     viewMenu.addSeparator();
3653     viewMenu.add(sequenceFeatures);
3654     viewMenu.add(featureSettings);
3655     viewMenu.addSeparator();
3656     viewMenu.add(alProperties);
3657     viewMenu.addSeparator();
3658     viewMenu.add(overviewMenuItem);
3659
3660     /*
3661      * Annotations menu
3662      */
3663     annotationsMenu.add(annotationPanelMenuItem);
3664     annotationsMenu.addSeparator();
3665     annotationsMenu.add(showAlignmentAnnotations);
3666     annotationsMenu.add(showSequenceAnnotations);
3667     annotationsMenu.add(sortAnnBySequence);
3668     annotationsMenu.add(sortAnnByLabel);
3669     annotationsMenu.addSeparator();
3670     autoAnnMenu.add(showAutoFirst);
3671     autoAnnMenu.add(showAutoLast);
3672     autoAnnMenu.addSeparator();
3673     autoAnnMenu.add(applyAutoAnnotationSettings);
3674     autoAnnMenu.add(showConsensusHistogram);
3675     autoAnnMenu.add(showSequenceLogo);
3676     autoAnnMenu.add(normSequenceLogo);
3677     autoAnnMenu.addSeparator();
3678     autoAnnMenu.add(showGroupConservation);
3679     autoAnnMenu.add(showGroupConsensus);
3680     annotationsMenu.add(autoAnnMenu);
3681
3682     /*
3683      * Format menu
3684      */
3685     formatMenu.add(font);
3686     formatMenu.add(seqLimits);
3687     formatMenu.add(wrapMenuItem);
3688     formatMenu.add(scaleAbove);
3689     formatMenu.add(scaleLeft);
3690     formatMenu.add(scaleRight);
3691     formatMenu.add(viewBoxesMenuItem);
3692     formatMenu.add(viewTextMenuItem);
3693     formatMenu.add(colourTextMenuItem);
3694     formatMenu.add(displayNonconservedMenuItem);
3695     formatMenu.add(renderGapsMenuItem);
3696     formatMenu.add(centreColumnLabelFlag);
3697
3698     /*
3699      * Colour menu
3700      */
3701     colourMenu.add(applyToAllGroups);
3702     colourMenu.addSeparator();
3703     colourMenu.add(noColourmenuItem);
3704     colourMenu.add(clustalColour);
3705     colourMenu.add(BLOSUM62Colour);
3706     colourMenu.add(PIDColour);
3707     colourMenu.add(zappoColour);
3708     colourMenu.add(taylorColour);
3709     colourMenu.add(hydrophobicityColour);
3710     colourMenu.add(helixColour);
3711     colourMenu.add(strandColour);
3712     colourMenu.add(turnColour);
3713     colourMenu.add(buriedColour);
3714     colourMenu.add(nucleotideColour);
3715     colourMenu.add(purinePyrimidineColour);
3716     // colourMenu.add(RNAInteractionColour);
3717     colourMenu.add(tcoffeeColour);
3718     colourMenu.add(userDefinedColour);
3719     colourMenu.addSeparator();
3720     colourMenu.add(conservationMenuItem);
3721     colourMenu.add(modifyConservation);
3722     colourMenu.add(abovePIDThreshold);
3723     colourMenu.add(modifyPID);
3724     colourMenu.add(annotationColour);
3725     colourMenu.add(RNAHelixColour);
3726
3727     /*
3728      * Calculate menu
3729      */
3730     sortMenu.add(sortIDMenuItem);
3731     sortMenu.add(sortLengthMenuItem);
3732     sortMenu.add(sortByTreeMenu);
3733     sortMenu.add(sortGroupMenuItem);
3734     sortMenu.add(sortPairwiseMenuItem);
3735     calculateMenu.add(sortMenu);
3736     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3737     calculateTreeMenu.add(neighbourTreeMenuItem);
3738     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3739     calculateTreeMenu.add(njTreeBlosumMenuItem);
3740     calculateMenu.add(calculateTreeMenu);
3741     calculateMenu.addSeparator();
3742     calculateMenu.add(pairwiseAlignmentMenuItem);
3743     calculateMenu.add(PCAMenuItem);
3744     calculateMenu.add(autoCalculate);
3745     calculateMenu.add(sortByTree);
3746
3747     /*
3748      * Help menu
3749      */
3750     helpMenu.add(documentation);
3751     helpMenu.add(about);
3752
3753     /*
3754      * Status bar
3755      */
3756     statusBar.setBackground(Color.white);
3757     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3758     statusBar.setText(MessageManager.getString("label.status_bar"));
3759     this.add(statusBar, BorderLayout.SOUTH);
3760   }
3761
3762   @Override
3763   public void setStatus(String string)
3764   {
3765     statusBar.setText(string);
3766   };
3767
3768   MenuItem featureSettings = new MenuItem();
3769
3770   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3771
3772   MenuItem annotationColour = new MenuItem();
3773
3774   MenuItem annotationColumnSelection = new MenuItem();
3775
3776   MenuItem invertColSel = new MenuItem();
3777
3778   MenuItem showColumns = new MenuItem();
3779
3780   MenuItem showSeqs = new MenuItem();
3781
3782   MenuItem hideColumns = new MenuItem();
3783
3784   MenuItem hideSequences = new MenuItem();
3785
3786   MenuItem hideAllButSelection = new MenuItem();
3787
3788   MenuItem hideAllSelection = new MenuItem();
3789
3790   MenuItem showAllHidden = new MenuItem();
3791
3792   MenuItem newView = new MenuItem();
3793
3794   private CheckboxMenuItem showAlignmentAnnotations;
3795
3796   private CheckboxMenuItem showSequenceAnnotations;
3797
3798   private CheckboxMenuItem sortAnnBySequence;
3799
3800   private CheckboxMenuItem sortAnnByLabel;
3801
3802   private CheckboxMenuItem showAutoFirst;
3803
3804   private CheckboxMenuItem showAutoLast;
3805
3806   private SplitFrame splitFrame;
3807
3808   /**
3809    * Attach the alignFrame panels after embedding menus, if necessary. This used
3810    * to be called setEmbedded, but is now creates the dropdown menus in a
3811    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3812    *
3813    * @param reallyEmbedded
3814    *          true to attach the view to the applet area on the page rather than
3815    *          in a new window
3816    */
3817   public void createAlignFrameWindow(boolean reallyEmbedded)
3818   {
3819     if (reallyEmbedded)
3820     {
3821       embedAlignFrameInApplet(viewport.applet);
3822     }
3823     else
3824     {
3825       // //////
3826       // test and embed menu bar if necessary.
3827       //
3828       if (embedMenuIfNeeded(alignPanel))
3829       {
3830         /*
3831          * adjust for status bar height too. ? pointless as overridden by layout
3832          * manager
3833          */
3834         alignPanel.setSize(getSize().width,
3835                 getSize().height - statusBar.getHeight());
3836       }
3837       add(statusBar, BorderLayout.SOUTH);
3838       add(alignPanel, BorderLayout.CENTER);
3839       // and register with the applet so it can pass external API calls to us
3840       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3841               frameHeight);
3842     }
3843   }
3844
3845   /**
3846    * Add the components of this AlignFrame to the applet container.
3847    *
3848    * @param theApplet
3849    */
3850   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3851   {
3852     // ////
3853     // Explicitly build the embedded menu panel for the on-page applet
3854     //
3855     // view cannot be closed if its actually on the page
3856     fileMenu.remove(closeMenuItem);
3857     fileMenu.remove(3); // Remove Separator
3858     // construct embedded menu, using default font
3859     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3860     // and actually add the components to the applet area
3861     theApplet.setLayout(new BorderLayout());
3862     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3863     theApplet.add(statusBar, BorderLayout.SOUTH);
3864     // TODO should size be left to the layout manager?
3865     alignPanel.setSize(theApplet.getSize().width,
3866             theApplet.getSize().height - embeddedMenu.getHeight()
3867                     - statusBar.getHeight());
3868     theApplet.add(alignPanel, BorderLayout.CENTER);
3869     final AlignFrame me = this;
3870     theApplet.addFocusListener(new FocusListener()
3871     {
3872
3873       @Override
3874       public void focusLost(FocusEvent e)
3875       {
3876         if (theApplet.currentAlignFrame == me)
3877         {
3878           theApplet.currentAlignFrame = null;
3879         }
3880       }
3881
3882       @Override
3883       public void focusGained(FocusEvent e)
3884       {
3885         theApplet.currentAlignFrame = me;
3886       }
3887     });
3888     theApplet.validate();
3889   }
3890
3891   /**
3892    * create a new binding between structures in an existing jmol viewer instance
3893    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3894    * this does not open a new Jmol window, or modify the display of the
3895    * structures in the original jmol window. Note This method doesn't work
3896    * without an additional javascript library to exchange messages between the
3897    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3898    *
3899    * @param viewer
3900    *          JmolViewer instance
3901    * @param sequenceIds
3902    *          - sequence Ids to search for associations
3903    */
3904   public SequenceStructureBinding addStructureViewInstance(
3905           Object jmolviewer, String[] sequenceIds)
3906   {
3907     Viewer viewer = null;
3908     try
3909     {
3910       viewer = (Viewer) jmolviewer;
3911     } catch (ClassCastException ex)
3912     {
3913       System.err.println("Unsupported viewer object :"
3914               + jmolviewer.getClass());
3915     }
3916     if (viewer == null)
3917     {
3918       System.err.println("Can't use this object as a structure viewer:"
3919               + jmolviewer.getClass());
3920       return null;
3921     }
3922     SequenceI[] seqs = null;
3923     if (sequenceIds == null || sequenceIds.length == 0)
3924     {
3925       seqs = viewport.getAlignment().getSequencesArray();
3926     }
3927     else
3928     {
3929       Vector sqi = new Vector();
3930       AlignmentI al = viewport.getAlignment();
3931       for (int sid = 0; sid < sequenceIds.length; sid++)
3932       {
3933         SequenceI sq = al.findName(sequenceIds[sid]);
3934         if (sq != null)
3935         {
3936           sqi.addElement(sq);
3937         }
3938       }
3939       if (sqi.size() > 0)
3940       {
3941         seqs = new SequenceI[sqi.size()];
3942         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3943         {
3944           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3945         }
3946       }
3947       else
3948       {
3949         return null;
3950       }
3951     }
3952     AAStructureBindingModel jmv = null;
3953     // TODO: search for a jmv that involves viewer
3954     if (jmv == null)
3955     { // create a new viewer/jalview binding.
3956       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3957     }
3958     return jmv;
3959
3960   }
3961
3962   /**
3963    * bind a pdb file to a sequence in the current view
3964    *
3965    * @param sequenceId
3966    *          - sequenceId within the dataset.
3967    * @param pdbEntryString
3968    *          - the short name for the PDB file
3969    * @param pdbFile
3970    *          - pdb file - either a URL or a valid PDB file.
3971    * @return true if binding was as success TODO: consider making an exception
3972    *         structure for indicating when PDB parsing or sequenceId location
3973    *         fails.
3974    */
3975   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3976           String pdbFile)
3977   {
3978     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3979     boolean needtoadd = false;
3980     if (toaddpdb != null)
3981     {
3982       Vector pdbe = toaddpdb.getAllPDBEntries();
3983       PDBEntry pdbentry = null;
3984       if (pdbe != null && pdbe.size() > 0)
3985       {
3986         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3987         {
3988           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3989           if (!pdbentry.getId().equals(pdbEntryString)
3990                   && !pdbentry.getFile().equals(pdbFile))
3991           {
3992             pdbentry = null;
3993           }
3994           else
3995           {
3996             continue;
3997           }
3998         }
3999       }
4000       if (pdbentry == null)
4001       {
4002         pdbentry = new PDBEntry();
4003         pdbentry.setId(pdbEntryString);
4004         pdbentry.setFile(pdbFile);
4005         needtoadd = true; // add this new entry to sequence.
4006       }
4007       // resolve data source
4008       // TODO: this code should be a refactored to an io package
4009       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4010       if (protocol == null)
4011       {
4012         return false;
4013       }
4014       if (needtoadd)
4015       {
4016         // make a note of the access mode and add
4017         if (pdbentry.getProperty() == null)
4018         {
4019           pdbentry.setProperty(new Hashtable());
4020         }
4021         pdbentry.getProperty().put("protocol", protocol);
4022         toaddpdb.addPDBId(pdbentry);
4023         alignPanel.getStructureSelectionManager()
4024                 .registerPDBEntry(pdbentry);
4025       }
4026     }
4027     return true;
4028   }
4029
4030   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4031   {
4032     if (seqs != null)
4033     {
4034       Vector sequences = new Vector();
4035       for (int i = 0; i < seqs.length; i++)
4036       {
4037         if (seqs[i] != null)
4038         {
4039           sequences.addElement(new Object[] { seqs[i],
4040               (chains != null) ? chains[i] : null });
4041         }
4042       }
4043       seqs = new SequenceI[sequences.size()];
4044       chains = new String[sequences.size()];
4045       for (int i = 0, isize = sequences.size(); i < isize; i++)
4046       {
4047         Object[] oj = (Object[]) sequences.elementAt(i);
4048
4049         seqs[i] = (SequenceI) oj[0];
4050         chains[i] = (String) oj[1];
4051       }
4052     }
4053     return new Object[] { seqs, chains };
4054
4055   }
4056
4057   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4058           SequenceI[] seqs, String[] chains, String protocol)
4059   {
4060     // Scrub any null sequences from the array
4061     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4062     seqs = (SequenceI[]) sqch[0];
4063     chains = (String[]) sqch[1];
4064     if (seqs == null || seqs.length == 0)
4065     {
4066       System.err
4067               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4068     }
4069     if (protocol == null || protocol.trim().length() == 0
4070             || protocol.equals("null"))
4071     {
4072       protocol = (String) pdb.getProperty().get("protocol");
4073       if (protocol == null)
4074       {
4075         System.err.println("Couldn't work out protocol to open structure: "
4076                 + pdb.getId());
4077         return;
4078       }
4079     }
4080     if (applet.useXtrnalSviewer)
4081     {
4082       // register the association(s) and quit, don't create any windows.
4083       if (StructureSelectionManager.getStructureSelectionManager(applet)
4084               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4085       {
4086         System.err.println("Failed to map " + pdb.getFile() + " ("
4087                 + protocol + ") to any sequences");
4088       }
4089       return;
4090     }
4091     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4092     {
4093       // can only do alignments with Jmol
4094       // find the last jmol window assigned to this alignment
4095       jalview.appletgui.AppletJmol ajm = null, tajm;
4096       Vector jmols = applet
4097               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4098       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4099       {
4100         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4101         if (tajm.ap.alignFrame == this)
4102         {
4103           ajm = tajm;
4104           break;
4105         }
4106       }
4107       if (ajm != null)
4108       {
4109         System.err
4110                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4111         // try and add the pdb structure
4112         // ajm.addS
4113         ajm = null;
4114       }
4115     }
4116     // otherwise, create a new window
4117     if (applet.jmolAvailable)
4118     {
4119       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4120               protocol);
4121       applet.lastFrameX += 40;
4122       applet.lastFrameY += 40;
4123     }
4124     else
4125     {
4126       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4127     }
4128
4129   }
4130
4131   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4132           SequenceI[][] seqs, String[][] chains, String[] protocols)
4133   {
4134     // TODO Auto-generated method stub
4135     System.err.println("Aligned Structure View: Not yet implemented.");
4136   }
4137
4138   /**
4139    * modify the current selection, providing the user has not made a selection
4140    * already.
4141    *
4142    * @param sel
4143    *          - sequences from this alignment
4144    * @param csel
4145    *          - columns to be selected on the alignment
4146    */
4147   public void select(SequenceGroup sel, ColumnSelection csel)
4148   {
4149     alignPanel.seqPanel.selection(sel, csel, null);
4150   }
4151
4152   public void scrollTo(int row, int column)
4153   {
4154     alignPanel.seqPanel.scrollTo(row, column);
4155   }
4156
4157   public void scrollToRow(int row)
4158   {
4159     alignPanel.seqPanel.scrollToRow(row);
4160   }
4161
4162   public void scrollToColumn(int column)
4163   {
4164     alignPanel.seqPanel.scrollToColumn(column);
4165   }
4166
4167   /**
4168    * @return the alignments unique ID.
4169    */
4170   public String getSequenceSetId()
4171   {
4172     return viewport.getSequenceSetId();
4173   }
4174
4175   /**
4176    * Load the (T-Coffee) score file from the specified url
4177    *
4178    * @param source
4179    *          File/URL/T-COFFEE score file contents
4180    * @throws IOException
4181    * @return true if alignment was annotated with data from source
4182    */
4183   public boolean loadScoreFile(String source) throws IOException
4184   {
4185
4186     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4187             AppletFormatAdapter.checkProtocol(source));
4188     if (!file.isValid())
4189     {
4190       // TODO: raise dialog for gui
4191       System.err.println("Problems parsing T-Coffee scores: "
4192               + file.getWarningMessage());
4193       System.err.println("Origin was:\n" + source);
4194       return false;
4195     }
4196
4197     /*
4198      * check that the score matrix matches the alignment dimensions
4199      */
4200     AlignmentI aln;
4201     if ((aln = viewport.getAlignment()) != null
4202             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4203                     .getWidth()))
4204     {
4205       // TODO: raise a dialog box here rather than bomb out.
4206       System.err
4207               .println("The scores matrix does not match the alignment dimensions");
4208
4209     }
4210
4211     // TODO add parameter to indicate if matching should be done
4212     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4213     {
4214       alignPanel.fontChanged();
4215       tcoffeeColour.setEnabled(true);
4216       // switch to this color
4217       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4218       return true;
4219     }
4220     else
4221     {
4222       System.err.println("Problems resolving T-Coffee scores:");
4223       if (file.getWarningMessage() != null)
4224       {
4225         System.err.println(file.getWarningMessage());
4226       }
4227     }
4228     return false;
4229   }
4230
4231   public SplitFrame getSplitFrame()
4232   {
4233     return this.splitFrame;
4234   }
4235
4236   public void setSplitFrame(SplitFrame sf)
4237   {
4238     this.splitFrame = sf;
4239   }
4240
4241   // may not need this
4242   @Override
4243   public void setShowSeqFeatures(boolean b)
4244   {
4245     // showSeqFeatures.setSelected(b);
4246     viewport.setShowSequenceFeatures(b);
4247
4248   }
4249
4250   @Override
4251   public void setMenusForViewport()
4252   {
4253     // setMenusFromViewport(viewport);
4254
4255   }
4256
4257   @Override
4258   public void refreshFeatureUI(boolean enableIfNecessary)
4259   {
4260     if (enableIfNecessary)
4261     {
4262       sequenceFeatures.setState(true);
4263       alignPanel.av.setShowSequenceFeatures(true);
4264     }
4265   }
4266
4267   @Override
4268   public FeatureSettingsControllerI getFeatureSettingsUI()
4269   {
4270     return alignPanel.av.featureSettings;
4271   }
4272
4273 }