src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.TCoffeeScoreFile;
  56 import jalview.schemes.Blosum62ColourScheme;
  57 import jalview.schemes.BuriedColourScheme;
  58 import jalview.schemes.ClustalxColourScheme;
  59 import jalview.schemes.ColourSchemeI;
  60 import jalview.schemes.HelixColourScheme;
  61 import jalview.schemes.HydrophobicColourScheme;
  62 import jalview.schemes.NucleotideColourScheme;
  63 import jalview.schemes.PIDColourScheme;
  64 import jalview.schemes.PurinePyrimidineColourScheme;
  65 import jalview.schemes.RNAHelicesColour;
  66 import jalview.schemes.StrandColourScheme;
  67 import jalview.schemes.TCoffeeColourScheme;
  68 import jalview.schemes.TaylorColourScheme;
  69 import jalview.schemes.TurnColourScheme;
  70 import jalview.schemes.ZappoColourScheme;
  71 import jalview.structure.StructureSelectionManager;
  72 import jalview.structures.models.AAStructureBindingModel;
  73 import jalview.util.MappingUtils;
  74 import jalview.util.MessageManager;
  75 import jalview.viewmodel.AlignmentViewport;
  76
  77 import java.awt.BorderLayout;
  78 import java.awt.Canvas;
  79 import java.awt.CheckboxMenuItem;
  80 import java.awt.Color;
  81 import java.awt.FlowLayout;
  82 import java.awt.Font;
  83 import java.awt.FontMetrics;
  84 import java.awt.Frame;
  85 import java.awt.Graphics;
  86 import java.awt.Label;
  87 import java.awt.Menu;
  88 import java.awt.MenuBar;
  89 import java.awt.MenuItem;
  90 import java.awt.Panel;
  91 import java.awt.event.ActionEvent;
  92 import java.awt.event.ActionListener;
  93 import java.awt.event.FocusEvent;
  94 import java.awt.event.FocusListener;
  95 import java.awt.event.ItemEvent;
  96 import java.awt.event.ItemListener;
  97 import java.awt.event.KeyEvent;
  98 import java.awt.event.KeyListener;
  99 import java.awt.event.WindowAdapter;
 100 import java.awt.event.WindowEvent;
 101 import java.io.IOException;
 102 import java.net.URL;
 103 import java.net.URLEncoder;
 104 import java.util.Arrays;
 105 import java.util.Deque;
 106 import java.util.HashMap;
 107 import java.util.List;
 108 import java.util.Map;
 109 import java.util.StringTokenizer;
 110 import java.util.Vector;
 111
 112 import org.jmol.viewer.Viewer;
 113
 114 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 115         ItemListener, KeyListener, AlignViewControllerGuiI
 116 {
 117   public AlignViewControllerI avc;
 118
 119   public AlignmentPanel alignPanel;
 120
 121   public AlignViewport viewport;
 122
 123   // width and height may be overridden by applet parameters
 124   int frameWidth = 700;
 125
 126   int frameHeight = 500;
 127
 128   String jalviewServletURL;
 129
 130   /*
 131    * Flag for showing autocalculated consensus above or below other consensus
 132    * rows
 133    */
 134   private boolean showAutoCalculatedAbove;
 135
 136   private SequenceAnnotationOrder annotationSortOrder;
 137
 138   /**
 139    * Constructor that creates the frame and adds it to the display.
 140    *
 141    * @param al
 142    * @param applet
 143    * @param title
 144    * @param embedded
 145    */
 146   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 147           boolean embedded)
 148   {
 149     this(al, applet, title, embedded, true);
 150   }
 151
 152   /**
 153    * Constructor that optionally allows the frame to be displayed or only
 154    * created.
 155    *
 156    * @param al
 157    * @param applet
 158    * @param title
 159    * @param embedded
 160    * @param addToDisplay
 161    */
 162   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 163           boolean embedded, boolean addToDisplay)
 164   {
 165     this(al, null, null, applet, title, embedded, addToDisplay);
 166   }
 167
 168   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 169           ColumnSelection columnSelection, JalviewLite applet,
 170           String title, boolean embedded)
 171   {
 172     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           ColumnSelection columnSelection, JalviewLite applet,
 177           String title, boolean embedded, boolean addToDisplay)
 178   {
 179     if (applet != null)
 180     {
 181       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception ex)
 188     {
 189       ex.printStackTrace();
 190     }
 191     // need to get window geometry before we calculate alignment layout
 192     if (applet != null)
 193     {
 194       String param;
 195       try
 196       {
 197         param = applet.getParameter("windowWidth");
 198         if (param != null)
 199         {
 200           int width = Integer.parseInt(param);
 201           frameWidth = width;
 202         }
 203         param = applet.getParameter("windowHeight");
 204         if (param != null)
 205         {
 206           int height = Integer.parseInt(param);
 207           frameHeight = height;
 208         }
 209       } catch (Exception ex)
 210       {
 211       }
 212     }
 213     viewport = new AlignViewport(al, applet);
 214
 215     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 216     {
 217       viewport.hideSequence(hiddenSeqs);
 218     }
 219     if (columnSelection != null)
 220     {
 221       viewport.setColumnSelection(columnSelection);
 222     }
 223     viewport.setScaleAboveWrapped(scaleAbove.getState());
 224
 225     alignPanel = new AlignmentPanel(this, viewport);
 226     avc = new jalview.controller.AlignViewController(this, viewport,
 227             alignPanel);
 228     viewport.updateConservation(alignPanel);
 229     viewport.updateConsensus(alignPanel);
 230
 231     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 232     followMouseOverFlag.setState(viewport.isFollowHighlight());
 233     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 234     showGroupConservation.setState(viewport.isShowGroupConservation());
 235     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 236     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 237     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 238     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 239     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 240     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 242     showAlignmentAnnotations.setState(true);
 243     showSequenceAnnotations.setState(false);
 244
 245     seqLimits.setState(viewport.getShowJVSuffix());
 246
 247     if (applet != null)
 248     {
 249       String param = applet.getParameter("sortBy");
 250       if (param != null)
 251       {
 252         if (param.equalsIgnoreCase("Id"))
 253         {
 254           sortIDMenuItem_actionPerformed();
 255         }
 256         else if (param.equalsIgnoreCase("Pairwise Identity"))
 257         {
 258           sortPairwiseMenuItem_actionPerformed();
 259         }
 260         else if (param.equalsIgnoreCase("Length"))
 261         {
 262           sortLengthMenuItem_actionPerformed();
 263         }
 264       }
 265
 266       param = applet.getParameter("wrap");
 267       if (param != null)
 268       {
 269         if (param.equalsIgnoreCase("true"))
 270         {
 271           wrapMenuItem.setState(true);
 272           wrapMenuItem_actionPerformed();
 273         }
 274       }
 275       param = applet.getParameter("centrecolumnlabels");
 276       if (param != null)
 277       {
 278         centreColumnLabelFlag.setState(true);
 279         centreColumnLabelFlag_stateChanged();
 280       }
 281
 282     }
 283     if (viewport.getAlignment().isNucleotide())
 284     {
 285       viewport.updateStrucConsensus(alignPanel);
 286       if (viewport.getAlignment().hasRNAStructure())
 287       {
 288         RNAHelixColour.setEnabled(true);
 289       }
 290       else
 291       {
 292         RNAHelixColour.setEnabled(false);
 293       }
 294     }
 295     else
 296     {
 297       RNAHelixColour.setEnabled(false);
 298       purinePyrimidineColour.setEnabled(false);
 299       nucleotideColour.setEnabled(false);
 300     }
 301     // Some JVMS send keyevents to Top frame or lowest panel,
 302     // Havent worked out why yet. So add to both this frame and seqCanvas for
 303     // now
 304     this.addKeyListener(this);
 305     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 306     alignPanel.idPanel.idCanvas.addKeyListener(this);
 307     alignPanel.scalePanel.addKeyListener(this);
 308     alignPanel.annotationPanel.addKeyListener(this);
 309     alignPanel.annotationPanelHolder.addKeyListener(this);
 310     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 311     alignPanel.alabels.addKeyListener(this);
 312
 313     setAnnotationsVisibility();
 314
 315     if (addToDisplay)
 316     {
 317       addToDisplay(embedded);
 318     }
 319   }
 320
 321   /**
 322    * @param embedded
 323    */
 324   public void addToDisplay(boolean embedded)
 325   {
 326     createAlignFrameWindow(embedded);
 327     validate();
 328     alignPanel.adjustAnnotationHeight();
 329     alignPanel.paintAlignment(true);
 330   }
 331
 332   public AlignViewport getAlignViewport()
 333   {
 334     return viewport;
 335   }
 336
 337   public SeqCanvas getSeqcanvas()
 338   {
 339     return alignPanel.seqPanel.seqCanvas;
 340   }
 341
 342   /**
 343    * Load a features file onto the alignment
 344    *
 345    * @param file
 346    *          file URL, content, or other resolvable path
 347    * @param type
 348    *          is protocol for accessing data referred to by file
 349    */
 350
 351   public boolean parseFeaturesFile(String file, DataSourceType type)
 352   {
 353     return parseFeaturesFile(file, type, true);
 354   }
 355
 356   /**
 357    * Load a features file onto the alignment
 358    *
 359    * @param file
 360    *          file URL, content, or other resolvable path
 361    * @param sourceType
 362    *          is protocol for accessing data referred to by file
 363    * @param autoenabledisplay
 364    *          when true, display features flag will be automatically enabled if
 365    *          features are loaded
 366    * @return true if data parsed as a features file
 367    */
 368   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 369           boolean autoenabledisplay)
 370   {
 371     boolean featuresFile = false;
 372     try
 373     {
 374       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 375               .getFeatureRenderer().getFeatureColours();
 376       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 377               "relaxedidmatch", false);
 378       featuresFile = new FeaturesFile(file, sourceType).parse(
 379               viewport.getAlignment(), colours, true, relaxedIdMatching);
 380     } catch (Exception ex)
 381     {
 382       ex.printStackTrace();
 383     }
 384
 385     if (featuresFile)
 386     {
 387       if (autoenabledisplay)
 388       {
 389         viewport.setShowSequenceFeatures(true);
 390         sequenceFeatures.setState(true);
 391       }
 392       if (alignPanel.seqPanel.seqCanvas.fr != null)
 393       {
 394         // update the min/max ranges where necessary
 395         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 396       }
 397       if (viewport.featureSettings != null)
 398       {
 399         viewport.featureSettings.refreshTable();
 400       }
 401       alignPanel.paintAlignment(true);
 402       statusBar.setText(MessageManager
 403               .getString("label.successfully_added_features_alignment"));
 404     }
 405     return featuresFile;
 406   }
 407
 408   @Override
 409   public void keyPressed(KeyEvent evt)
 410   {
 411     if (viewport.cursorMode
 412             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 413                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 414                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 415             && Character.isDigit(evt.getKeyChar()))
 416     {
 417       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 418     }
 419
 420     switch (evt.getKeyCode())
 421     {
 422     case 27: // escape key
 423       deselectAllSequenceMenuItem_actionPerformed();
 424
 425       alignPanel.alabels.cancelDrag();
 426       break;
 427     case KeyEvent.VK_X:
 428       if (evt.isControlDown() || evt.isMetaDown())
 429       {
 430         cut_actionPerformed();
 431       }
 432       break;
 433     case KeyEvent.VK_C:
 434       if (viewport.cursorMode && !evt.isControlDown())
 435       {
 436         alignPanel.seqPanel.setCursorColumn();
 437       }
 438       if (evt.isControlDown() || evt.isMetaDown())
 439       {
 440         copy_actionPerformed();
 441       }
 442       break;
 443     case KeyEvent.VK_V:
 444       if (evt.isControlDown())
 445       {
 446         paste(evt.isShiftDown());
 447       }
 448       break;
 449     case KeyEvent.VK_A:
 450       if (evt.isControlDown() || evt.isMetaDown())
 451       {
 452         selectAllSequenceMenuItem_actionPerformed();
 453       }
 454       break;
 455     case KeyEvent.VK_DOWN:
 456       if (viewport.cursorMode)
 457       {
 458         alignPanel.seqPanel.moveCursor(0, 1);
 459       }
 460       else
 461       {
 462         moveSelectedSequences(false);
 463       }
 464       break;
 465
 466     case KeyEvent.VK_UP:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.moveCursor(0, -1);
 470       }
 471       else
 472       {
 473         moveSelectedSequences(true);
 474       }
 475       break;
 476
 477     case KeyEvent.VK_LEFT:
 478       if (evt.isAltDown() || !viewport.cursorMode)
 479       {
 480         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 481       }
 482       else
 483       {
 484         alignPanel.seqPanel.moveCursor(-1, 0);
 485       }
 486       break;
 487
 488     case KeyEvent.VK_RIGHT:
 489       if (evt.isAltDown() || !viewport.cursorMode)
 490       {
 491         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 492       }
 493       else
 494       {
 495         alignPanel.seqPanel.moveCursor(1, 0);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_SPACE:
 500       if (viewport.cursorMode)
 501       {
 502         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 503                 || evt.isShiftDown() || evt.isAltDown());
 504       }
 505       break;
 506
 507     case KeyEvent.VK_DELETE:
 508     case KeyEvent.VK_BACK_SPACE:
 509       if (viewport.cursorMode)
 510       {
 511         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 512                 || evt.isShiftDown() || evt.isAltDown());
 513       }
 514       else
 515       {
 516         cut_actionPerformed();
 517         alignPanel.seqPanel.seqCanvas.repaint();
 518       }
 519       break;
 520
 521     case KeyEvent.VK_S:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.setCursorRow();
 525       }
 526       break;
 527     case KeyEvent.VK_P:
 528       if (viewport.cursorMode)
 529       {
 530         alignPanel.seqPanel.setCursorPosition();
 531       }
 532       break;
 533
 534     case KeyEvent.VK_ENTER:
 535     case KeyEvent.VK_COMMA:
 536       if (viewport.cursorMode)
 537       {
 538         alignPanel.seqPanel.setCursorRowAndColumn();
 539       }
 540       break;
 541
 542     case KeyEvent.VK_Q:
 543       if (viewport.cursorMode)
 544       {
 545         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 546       }
 547       break;
 548     case KeyEvent.VK_M:
 549       if (viewport.cursorMode)
 550       {
 551         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 552       }
 553       break;
 554
 555     case KeyEvent.VK_F2:
 556       viewport.cursorMode = !viewport.cursorMode;
 557       statusBar.setText(MessageManager.formatMessage(
 558               "label.keyboard_editing_mode",
 559               new String[] { (viewport.cursorMode ? "on" : "off") }));
 560       if (viewport.cursorMode)
 561       {
 562         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 563         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 564       }
 565       break;
 566
 567     case KeyEvent.VK_F:
 568       if (evt.isControlDown())
 569       {
 570         findMenuItem_actionPerformed();
 571       }
 572       break;
 573
 574     case KeyEvent.VK_H:
 575     {
 576       boolean toggleSeqs = !evt.isControlDown();
 577       boolean toggleCols = !evt.isShiftDown();
 578       toggleHiddenRegions(toggleSeqs, toggleCols);
 579       break;
 580     }
 581
 582     case KeyEvent.VK_PAGE_UP:
 583       if (viewport.getWrapAlignment())
 584       {
 585         alignPanel.scrollUp(true);
 586       }
 587       else
 588       {
 589         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 590                 - viewport.endSeq + viewport.startSeq);
 591       }
 592       break;
 593
 594     case KeyEvent.VK_PAGE_DOWN:
 595       if (viewport.getWrapAlignment())
 596       {
 597         alignPanel.scrollUp(false);
 598       }
 599       else
 600       {
 601         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 602                 + viewport.endSeq - viewport.startSeq);
 603       }
 604       break;
 605
 606     case KeyEvent.VK_Z:
 607       if (evt.isControlDown())
 608       {
 609         undoMenuItem_actionPerformed();
 610       }
 611       break;
 612
 613     case KeyEvent.VK_Y:
 614       if (evt.isControlDown())
 615       {
 616         redoMenuItem_actionPerformed();
 617       }
 618       break;
 619
 620     case KeyEvent.VK_L:
 621       if (evt.isControlDown())
 622       {
 623         trimAlignment(true);
 624       }
 625       break;
 626
 627     case KeyEvent.VK_R:
 628       if (evt.isControlDown())
 629       {
 630         trimAlignment(false);
 631       }
 632       break;
 633
 634     case KeyEvent.VK_E:
 635       if (evt.isControlDown())
 636       {
 637         if (evt.isShiftDown())
 638         {
 639           this.removeAllGapsMenuItem_actionPerformed();
 640         }
 641         else
 642         {
 643           removeGappedColumnMenuItem_actionPerformed();
 644         }
 645       }
 646       break;
 647     case KeyEvent.VK_I:
 648       if (evt.isControlDown())
 649       {
 650         if (evt.isAltDown())
 651         {
 652           invertColSel_actionPerformed();
 653         }
 654         else
 655         {
 656           invertSequenceMenuItem_actionPerformed();
 657         }
 658       }
 659       break;
 660
 661     case KeyEvent.VK_G:
 662       if (evt.isControlDown())
 663       {
 664         if (evt.isShiftDown())
 665         {
 666           this.unGroup_actionPerformed();
 667         }
 668         else
 669         {
 670           this.createGroup_actionPerformed();
 671         }
 672       }
 673       break;
 674
 675     case KeyEvent.VK_U:
 676       if (evt.isControlDown())
 677       {
 678         this.deleteGroups_actionPerformed();
 679       }
 680       break;
 681
 682     case KeyEvent.VK_T:
 683       if (evt.isControlDown())
 684       {
 685         newView(null);
 686       }
 687       break;
 688
 689     }
 690     alignPanel.paintAlignment(true);
 691   }
 692
 693   /**
 694    * called by key handler and the hide all/show all menu items
 695    *
 696    * @param toggleSeqs
 697    * @param toggleCols
 698    */
 699   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 700   {
 701     boolean hide = false;
 702     SequenceGroup sg = viewport.getSelectionGroup();
 703     if (!toggleSeqs && !toggleCols)
 704     {
 705       // Hide everything by the current selection - this is a hack - we do the
 706       // invert and then hide
 707       // first check that there will be visible columns after the invert.
 708       if (viewport.hasSelectedColumns()
 709               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 710                       .getEndRes()))
 711       {
 712         // now invert the sequence set, if required - empty selection implies
 713         // that no hiding is required.
 714         if (sg != null)
 715         {
 716           invertSequenceMenuItem_actionPerformed();
 717           sg = viewport.getSelectionGroup();
 718           toggleSeqs = true;
 719
 720         }
 721         viewport.expandColSelection(sg, true);
 722         // finally invert the column selection and get the new sequence
 723         // selection and indicate it should be hidden.
 724         invertColSel_actionPerformed();
 725         toggleCols = true;
 726       }
 727     }
 728
 729     if (toggleSeqs)
 730     {
 731       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 732       {
 733         hide = true;
 734         viewport.hideAllSelectedSeqs();
 735       }
 736       else if (!(toggleCols && viewport.hasSelectedColumns()))
 737       {
 738         viewport.showAllHiddenSeqs();
 739       }
 740     }
 741
 742     if (toggleCols)
 743     {
 744       if (viewport.hasSelectedColumns())
 745       {
 746         viewport.hideSelectedColumns();
 747         if (!toggleSeqs)
 748         {
 749           viewport.setSelectionGroup(sg);
 750         }
 751       }
 752       else if (!hide)
 753       {
 754         viewport.showAllHiddenColumns();
 755       }
 756       viewport.sendSelection();
 757     }
 758   }
 759
 760   @Override
 761   public void keyReleased(KeyEvent evt)
 762   {
 763   }
 764
 765   @Override
 766   public void keyTyped(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void itemStateChanged(ItemEvent evt)
 772   {
 773     final Object source = evt.getSource();
 774     if (source == displayNonconservedMenuItem)
 775     {
 776       displayNonconservedMenuItem_actionPerformed();
 777     }
 778     else if (source == colourTextMenuItem)
 779     {
 780       colourTextMenuItem_actionPerformed();
 781     }
 782     else if (source == wrapMenuItem)
 783     {
 784       wrapMenuItem_actionPerformed();
 785     }
 786     else if (source == scaleAbove)
 787     {
 788       viewport.setScaleAboveWrapped(scaleAbove.getState());
 789     }
 790     else if (source == scaleLeft)
 791     {
 792       viewport.setScaleLeftWrapped(scaleLeft.getState());
 793     }
 794     else if (source == scaleRight)
 795     {
 796       viewport.setScaleRightWrapped(scaleRight.getState());
 797     }
 798     else if (source == seqLimits)
 799     {
 800       seqLimits_itemStateChanged();
 801     }
 802     else if (source == viewBoxesMenuItem)
 803     {
 804       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 805     }
 806     else if (source == viewTextMenuItem)
 807     {
 808       viewport.setShowText(viewTextMenuItem.getState());
 809     }
 810     else if (source == renderGapsMenuItem)
 811     {
 812       viewport.setRenderGaps(renderGapsMenuItem.getState());
 813     }
 814     else if (source == annotationPanelMenuItem)
 815     {
 816       boolean showAnnotations = annotationPanelMenuItem.getState();
 817       showAlignmentAnnotations.setEnabled(showAnnotations);
 818       showSequenceAnnotations.setEnabled(showAnnotations);
 819       viewport.setShowAnnotation(showAnnotations);
 820       alignPanel.setAnnotationVisible(showAnnotations);
 821     }
 822     else if (source == sequenceFeatures)
 823     {
 824       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 825       alignPanel.seqPanel.seqCanvas.repaint();
 826     }
 827     else if (source == showAlignmentAnnotations)
 828     {
 829       setAnnotationsVisibility();
 830     }
 831     else if (source == showSequenceAnnotations)
 832     {
 833       setAnnotationsVisibility();
 834     }
 835     else if (source == sortAnnBySequence)
 836     {
 837       boolean newState = sortAnnBySequence.getState();
 838       sortAnnByLabel.setState(false);
 839       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 840               : SequenceAnnotationOrder.NONE);
 841       setViewportAnnotationOrder();
 842     }
 843     else if (source == sortAnnByLabel)
 844     {
 845       boolean newState = sortAnnByLabel.getState();
 846       sortAnnBySequence.setState(false);
 847       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 848               : SequenceAnnotationOrder.NONE);
 849       setViewportAnnotationOrder();
 850     }
 851     else if (source == showAutoFirst)
 852     {
 853       showAutoLast.setState(!showAutoFirst.getState());
 854       setShowAutoCalculatedAbove(showAutoFirst.getState());
 855       setViewportAnnotationOrder();
 856     }
 857     else if (source == showAutoLast)
 858     {
 859       showAutoFirst.setState(!showAutoLast.getState());
 860       setShowAutoCalculatedAbove(showAutoFirst.getState());
 861       setViewportAnnotationOrder();
 862     }
 863     else if (source == conservationMenuItem)
 864     {
 865       conservationMenuItem_actionPerformed();
 866     }
 867     else if (source == abovePIDThreshold)
 868     {
 869       abovePIDThreshold_actionPerformed();
 870     }
 871     else if (source == applyToAllGroups)
 872     {
 873       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 874     }
 875     else if (source == autoCalculate)
 876     {
 877       viewport.autoCalculateConsensus = autoCalculate.getState();
 878     }
 879     else if (source == sortByTree)
 880     {
 881       viewport.sortByTree = sortByTree.getState();
 882     }
 883     else if (source == this.centreColumnLabelFlag)
 884     {
 885       centreColumnLabelFlag_stateChanged();
 886     }
 887     else if (source == this.followMouseOverFlag)
 888     {
 889       mouseOverFlag_stateChanged();
 890     }
 891     else if (source == showGroupConsensus)
 892     {
 893       showGroupConsensus_actionPerformed();
 894     }
 895     else if (source == showGroupConservation)
 896     {
 897       showGroupConservation_actionPerformed();
 898     }
 899     else if (source == showSequenceLogo)
 900     {
 901       showSequenceLogo_actionPerformed();
 902     }
 903     else if (source == normSequenceLogo)
 904     {
 905       normSequenceLogo_actionPerformed();
 906     }
 907     else if (source == showConsensusHistogram)
 908     {
 909       showConsensusHistogram_actionPerformed();
 910     }
 911     else if (source == applyAutoAnnotationSettings)
 912     {
 913       applyAutoAnnotationSettings_actionPerformed();
 914     }
 915     alignPanel.paintAlignment(true);
 916   }
 917
 918   /**
 919    * Set the visibility state of sequence-related and/or alignment-related
 920    * annotations depending on checkbox selections, and repaint.
 921    *
 922    * @param visible
 923    */
 924   private void setAnnotationsVisibility()
 925   {
 926     boolean showForAlignment = showAlignmentAnnotations.getState();
 927     boolean showForSequences = showSequenceAnnotations.getState();
 928     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 929     {
 930       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 931               .getAlignmentAnnotation())
 932       {
 933         boolean visible = (aa.sequenceRef == null ? showForAlignment
 934                 : showForSequences);
 935         aa.visible = visible;
 936       }
 937     }
 938     alignPanel.validateAnnotationDimensions(true);
 939     validate();
 940     repaint();
 941   }
 942
 943   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 944   {
 945     this.annotationSortOrder = order;
 946   }
 947
 948   /**
 949    * Set flags on the viewport that control annotation ordering
 950    */
 951   private void setViewportAnnotationOrder()
 952   {
 953     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 954     this.alignPanel.av
 955             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 956   }
 957
 958   private void setShowAutoCalculatedAbove(boolean showAbove)
 959   {
 960     this.showAutoCalculatedAbove = showAbove;
 961   }
 962
 963   private void mouseOverFlag_stateChanged()
 964   {
 965     viewport.setFollowHighlight(followMouseOverFlag.getState());
 966     // TODO: could kick the scrollTo mechanism to reset view for current
 967     // searchresults.
 968   }
 969
 970   private void centreColumnLabelFlag_stateChanged()
 971   {
 972     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 973     this.alignPanel.annotationPanel.repaint();
 974   }
 975
 976   @Override
 977   public void actionPerformed(ActionEvent evt)
 978   {
 979     viewport.applet.currentAlignFrame = this;
 980
 981     Object source = evt.getSource();
 982
 983     if (source == inputText)
 984     {
 985       inputText_actionPerformed();
 986     }
 987     else if (source == loadTree)
 988     {
 989       loadTree_actionPerformed();
 990     }
 991     else if (source == loadApplication)
 992     {
 993       launchFullApplication();
 994     }
 995     else if (source == loadAnnotations)
 996     {
 997       loadAnnotations();
 998     }
 999     else if (source == outputAnnotations)
1000     {
1001       outputAnnotations(true);
1002     }
1003     else if (source == outputFeatures)
1004     {
1005       outputFeatures(true, "Jalview");
1006     }
1007     else if (source == closeMenuItem)
1008     {
1009       closeMenuItem_actionPerformed();
1010     }
1011     else if (source == copy)
1012     {
1013       copy_actionPerformed();
1014     }
1015     else if (source == undoMenuItem)
1016     {
1017       undoMenuItem_actionPerformed();
1018     }
1019     else if (source == redoMenuItem)
1020     {
1021       redoMenuItem_actionPerformed();
1022     }
1023     else if (source == inputText)
1024     {
1025       inputText_actionPerformed();
1026     }
1027     else if (source == closeMenuItem)
1028     {
1029       closeMenuItem_actionPerformed();
1030     }
1031     else if (source == undoMenuItem)
1032     {
1033       undoMenuItem_actionPerformed();
1034     }
1035     else if (source == redoMenuItem)
1036     {
1037       redoMenuItem_actionPerformed();
1038     }
1039     else if (source == copy)
1040     {
1041       copy_actionPerformed();
1042     }
1043     else if (source == pasteNew)
1044     {
1045       pasteNew_actionPerformed();
1046     }
1047     else if (source == pasteThis)
1048     {
1049       pasteThis_actionPerformed();
1050     }
1051     else if (source == cut)
1052     {
1053       cut_actionPerformed();
1054     }
1055     else if (source == delete)
1056     {
1057       delete_actionPerformed();
1058     }
1059     else if (source == grpsFromSelection)
1060     {
1061       makeGrpsFromSelection_actionPerformed();
1062     }
1063     else if (source == deleteGroups)
1064     {
1065       deleteGroups_actionPerformed();
1066     }
1067     else if (source == selectAllSequenceMenuItem)
1068     {
1069       selectAllSequenceMenuItem_actionPerformed();
1070     }
1071     else if (source == deselectAllSequenceMenuItem)
1072     {
1073       deselectAllSequenceMenuItem_actionPerformed();
1074     }
1075     else if (source == invertSequenceMenuItem)
1076     {
1077       invertSequenceMenuItem_actionPerformed();
1078       // uncomment to slave sequence selections in split frame
1079       // viewport.sendSelection();
1080     }
1081     else if (source == invertColSel)
1082     {
1083       viewport.invertColumnSelection();
1084       alignPanel.paintAlignment(true);
1085       viewport.sendSelection();
1086     }
1087     else if (source == remove2LeftMenuItem)
1088     {
1089       trimAlignment(true);
1090     }
1091     else if (source == remove2RightMenuItem)
1092     {
1093       trimAlignment(false);
1094     }
1095     else if (source == removeGappedColumnMenuItem)
1096     {
1097       removeGappedColumnMenuItem_actionPerformed();
1098     }
1099     else if (source == removeAllGapsMenuItem)
1100     {
1101       removeAllGapsMenuItem_actionPerformed();
1102     }
1103     else if (source == findMenuItem)
1104     {
1105       findMenuItem_actionPerformed();
1106     }
1107     else if (source == font)
1108     {
1109       new FontChooser(alignPanel);
1110     }
1111     else if (source == newView)
1112     {
1113       newView(null);
1114     }
1115     else if (source == showColumns)
1116     {
1117       viewport.showAllHiddenColumns();
1118       alignPanel.paintAlignment(true);
1119       viewport.sendSelection();
1120     }
1121     else if (source == showSeqs)
1122     {
1123       viewport.showAllHiddenSeqs();
1124       alignPanel.paintAlignment(true);
1125       // uncomment if we want to slave sequence selections in split frame
1126       // viewport.sendSelection();
1127     }
1128     else if (source == hideColumns)
1129     {
1130       viewport.hideSelectedColumns();
1131       alignPanel.paintAlignment(true);
1132       viewport.sendSelection();
1133     }
1134     else if (source == hideSequences
1135             && viewport.getSelectionGroup() != null)
1136     {
1137       viewport.hideAllSelectedSeqs();
1138       alignPanel.paintAlignment(true);
1139       // uncomment if we want to slave sequence selections in split frame
1140       // viewport.sendSelection();
1141     }
1142     else if (source == hideAllButSelection)
1143     {
1144       toggleHiddenRegions(false, false);
1145       alignPanel.paintAlignment(true);
1146       viewport.sendSelection();
1147     }
1148     else if (source == hideAllSelection)
1149     {
1150       SequenceGroup sg = viewport.getSelectionGroup();
1151       viewport.expandColSelection(sg, false);
1152       viewport.hideAllSelectedSeqs();
1153       viewport.hideSelectedColumns();
1154       alignPanel.paintAlignment(true);
1155       viewport.sendSelection();
1156     }
1157     else if (source == showAllHidden)
1158     {
1159       viewport.showAllHiddenColumns();
1160       viewport.showAllHiddenSeqs();
1161       alignPanel.paintAlignment(true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == showGroupConsensus)
1165     {
1166       showGroupConsensus_actionPerformed();
1167     }
1168     else if (source == showGroupConservation)
1169     {
1170       showGroupConservation_actionPerformed();
1171     }
1172     else if (source == showSequenceLogo)
1173     {
1174       showSequenceLogo_actionPerformed();
1175     }
1176     else if (source == normSequenceLogo)
1177     {
1178       normSequenceLogo_actionPerformed();
1179     }
1180     else if (source == showConsensusHistogram)
1181     {
1182       showConsensusHistogram_actionPerformed();
1183     }
1184     else if (source == applyAutoAnnotationSettings)
1185     {
1186       applyAutoAnnotationSettings_actionPerformed();
1187     }
1188     else if (source == featureSettings)
1189     {
1190       new FeatureSettings(alignPanel);
1191     }
1192     else if (source == alProperties)
1193     {
1194       StringBuffer contents = new jalview.io.AlignmentProperties(
1195               viewport.getAlignment()).formatAsString();
1196       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1197       cap.setText(contents.toString());
1198       Frame frame = new Frame();
1199       frame.add(cap);
1200       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1201               "label.alignment_properties", new String[] { getTitle() }),
1202               400, 250);
1203     }
1204     else if (source == overviewMenuItem)
1205     {
1206       overviewMenuItem_actionPerformed();
1207     }
1208     else if (source == noColourmenuItem)
1209     {
1210       changeColour(null);
1211     }
1212     else if (source == clustalColour)
1213     {
1214       abovePIDThreshold.setState(false);
1215       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1216     }
1217     else if (source == zappoColour)
1218     {
1219       changeColour(new ZappoColourScheme());
1220     }
1221     else if (source == taylorColour)
1222     {
1223       changeColour(new TaylorColourScheme());
1224     }
1225     else if (source == hydrophobicityColour)
1226     {
1227       changeColour(new HydrophobicColourScheme());
1228     }
1229     else if (source == helixColour)
1230     {
1231       changeColour(new HelixColourScheme());
1232     }
1233     else if (source == strandColour)
1234     {
1235       changeColour(new StrandColourScheme());
1236     }
1237     else if (source == turnColour)
1238     {
1239       changeColour(new TurnColourScheme());
1240     }
1241     else if (source == buriedColour)
1242     {
1243       changeColour(new BuriedColourScheme());
1244     }
1245     else if (source == nucleotideColour)
1246     {
1247       changeColour(new NucleotideColourScheme());
1248     }
1249     else if (source == purinePyrimidineColour)
1250     {
1251       changeColour(new PurinePyrimidineColourScheme());
1252     }
1253     // else if (source == RNAInteractionColour)
1254     // {
1255     // changeColour(new RNAInteractionColourScheme());
1256     // }
1257     else if (source == RNAHelixColour)
1258     {
1259       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1260       // new RNAHelicesColourChooser(viewport, alignPanel);
1261     }
1262     else if (source == modifyPID)
1263     {
1264       modifyPID_actionPerformed();
1265     }
1266     else if (source == modifyConservation)
1267     {
1268       modifyConservation_actionPerformed();
1269     }
1270     else if (source == userDefinedColour)
1271     {
1272       new UserDefinedColours(alignPanel, null);
1273     }
1274     else if (source == PIDColour)
1275     {
1276       changeColour(new PIDColourScheme());
1277     }
1278     else if (source == BLOSUM62Colour)
1279     {
1280       changeColour(new Blosum62ColourScheme());
1281     }
1282     else if (source == tcoffeeColour)
1283     {
1284       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1285     }
1286     else if (source == annotationColour)
1287     {
1288       new AnnotationColourChooser(viewport, alignPanel);
1289     }
1290     else if (source == annotationColumnSelection)
1291     {
1292       new AnnotationColumnChooser(viewport, alignPanel);
1293     }
1294     else if (source == sortPairwiseMenuItem)
1295     {
1296       sortPairwiseMenuItem_actionPerformed();
1297     }
1298     else if (source == sortIDMenuItem)
1299     {
1300       sortIDMenuItem_actionPerformed();
1301     }
1302     else if (source == sortLengthMenuItem)
1303     {
1304       sortLengthMenuItem_actionPerformed();
1305     }
1306     else if (source == sortGroupMenuItem)
1307     {
1308       sortGroupMenuItem_actionPerformed();
1309     }
1310     else if (source == removeRedundancyMenuItem)
1311     {
1312       removeRedundancyMenuItem_actionPerformed();
1313     }
1314     else if (source == pairwiseAlignmentMenuItem)
1315     {
1316       pairwiseAlignmentMenuItem_actionPerformed();
1317     }
1318     else if (source == PCAMenuItem)
1319     {
1320       PCAMenuItem_actionPerformed();
1321     }
1322     else if (source == averageDistanceTreeMenuItem)
1323     {
1324       averageDistanceTreeMenuItem_actionPerformed();
1325     }
1326     else if (source == neighbourTreeMenuItem)
1327     {
1328       neighbourTreeMenuItem_actionPerformed();
1329     }
1330     else if (source == njTreeBlosumMenuItem)
1331     {
1332       njTreeBlosumMenuItem_actionPerformed();
1333     }
1334     else if (source == avDistanceTreeBlosumMenuItem)
1335     {
1336       avTreeBlosumMenuItem_actionPerformed();
1337     }
1338     else if (source == documentation)
1339     {
1340       documentation_actionPerformed();
1341     }
1342     else if (source == about)
1343     {
1344       about_actionPerformed();
1345     }
1346
1347   }
1348
1349   public void inputText_actionPerformed()
1350   {
1351     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352     Frame frame = new Frame();
1353     frame.add(cap);
1354     jalview.bin.JalviewLite.addFrame(frame,
1355             MessageManager.getString("label.input_cut_paste"), 500, 500);
1356   }
1357
1358   protected void outputText_actionPerformed(ActionEvent e)
1359   {
1360     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1361     Frame frame = new Frame();
1362     frame.add(cap);
1363     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1364             "label.alignment_output_command",
1365             new Object[] { e.getActionCommand() }), 600, 500);
1366
1367     FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1368     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1369             fileFormat, viewport.getAlignment(),
1370             viewport.getShowJVSuffix()));
1371   }
1372
1373   public void loadAnnotations()
1374   {
1375     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376     cap.setText(MessageManager
1377             .getString("label.paste_features_annotations_Tcoffee_here"));
1378     cap.setAnnotationImport();
1379     Frame frame = new Frame();
1380     frame.add(cap);
1381     jalview.bin.JalviewLite.addFrame(frame,
1382             MessageManager.getString("action.paste_annotations"), 400, 300);
1383
1384   }
1385
1386   public String outputAnnotations(boolean displayTextbox)
1387   {
1388     String annotation = new AnnotationFile()
1389             .printAnnotationsForView(viewport);
1390
1391     if (displayTextbox)
1392     {
1393       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1394       Frame frame = new Frame();
1395       frame.add(cap);
1396       jalview.bin.JalviewLite.addFrame(frame,
1397               MessageManager.getString("label.annotations"), 600, 500);
1398       cap.setText(annotation);
1399     }
1400
1401     return annotation;
1402   }
1403
1404   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1405   {
1406     if (alignPanel.getFeatureRenderer() != null
1407             && viewport.getFeaturesDisplayed() != null)
1408     {
1409       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1410
1411     }
1412     return null;
1413   }
1414
1415   public String outputFeatures(boolean displayTextbox, String format)
1416   {
1417     String features;
1418     FeaturesFile formatter = new FeaturesFile();
1419     if (format.equalsIgnoreCase("Jalview"))
1420     {
1421       features = formatter.printJalviewFormat(viewport.getAlignment()
1422               .getSequencesArray(), getDisplayedFeatureCols());
1423     }
1424     else
1425     {
1426       features = formatter.printGffFormat(viewport.getAlignment()
1427               .getSequencesArray(), getDisplayedFeatureCols());
1428     }
1429
1430     if (displayTextbox)
1431     {
1432       boolean frimport = false;
1433       if (features == null || features.equals("No Features Visible"))
1434       {
1435         features = "# No features visible - paste some and import them here.";
1436         frimport = true;
1437       }
1438
1439       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1440       if (frimport)
1441       {
1442         cap.setAnnotationImport();
1443       }
1444       Frame frame = new Frame();
1445       frame.add(cap);
1446       jalview.bin.JalviewLite.addFrame(frame,
1447               MessageManager.getString("label.features"), 600, 500);
1448       cap.setText(features);
1449     }
1450     else
1451     {
1452       if (features == null)
1453       {
1454         features = "";
1455       }
1456     }
1457
1458     return features;
1459   }
1460
1461   void launchFullApplication()
1462   {
1463     StringBuffer url = new StringBuffer(jalviewServletURL);
1464
1465     // allow servlet parameters to be passed in applet parameter
1466     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1467             : "?";
1468     url.append(firstSep);
1469
1470     url.append("open="
1471             + appendProtocol(viewport.applet.getParameter("file")));
1472
1473     if (viewport.applet.getParameter("features") != null)
1474     {
1475       url.append("&features=");
1476       url.append(appendProtocol(viewport.applet.getParameter("features")));
1477     }
1478
1479     if (viewport.applet.getParameter("annotations") != null)
1480     {
1481       url.append("&annotations=");
1482       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1483     }
1484
1485     if (viewport.applet.getParameter("jnetfile") != null)
1486     {
1487       url.append("&annotations=");
1488       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1489     }
1490
1491     if (viewport.applet.getParameter("defaultColour") != null)
1492     {
1493       url.append("&colour="
1494               + removeWhiteSpace(viewport.applet
1495                       .getParameter("defaultColour")));
1496     }
1497
1498     if (viewport.applet.getParameter("userDefinedColour") != null)
1499     {
1500       url.append("&colour="
1501               + removeWhiteSpace(viewport.applet
1502                       .getParameter("userDefinedColour")));
1503     }
1504     if (viewport.applet.getParameter("tree") != null)
1505     {
1506       url.append("&tree="
1507               + appendProtocol(viewport.applet.getParameter("tree")));
1508     }
1509     if (viewport.applet.getParameter("treeFile") != null)
1510     {
1511       url.append("&tree="
1512               + appendProtocol(viewport.applet.getParameter("treeFile")));
1513     }
1514
1515     showURL(url.toString(), "FULL_APP");
1516   }
1517
1518   String removeWhiteSpace(String colour)
1519   {
1520     StringBuffer sb = new StringBuffer();
1521     for (int i = 0; i < colour.length(); i++)
1522     {
1523       if (Character.isWhitespace(colour.charAt(i)))
1524       {
1525         sb.append("%20");
1526       }
1527       else
1528       {
1529         sb.append(colour.charAt(i));
1530       }
1531     }
1532
1533     return sb.toString();
1534   }
1535
1536   String appendProtocol(String url)
1537   {
1538     try
1539     {
1540       new URL(url);
1541       url = URLEncoder.encode(url);
1542     }
1543     /*
1544      * When we finally deprecate 1.1 compatibility, we can start to use
1545      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1546      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1547      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1548      * ex.printStackTrace(); }
1549      */
1550     catch (java.net.MalformedURLException ex)
1551     {
1552       url = viewport.applet.getCodeBase() + url;
1553     }
1554     return url;
1555   }
1556
1557   public void closeMenuItem_actionPerformed()
1558   {
1559     PaintRefresher.RemoveComponent(alignPanel);
1560     if (alignPanel.seqPanel != null
1561             && alignPanel.seqPanel.seqCanvas != null)
1562     {
1563       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1564     }
1565     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1566     {
1567       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1568     }
1569
1570     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1571     {
1572       System.exit(0);
1573     }
1574     else
1575     {
1576     }
1577     viewport = null;
1578     alignPanel = null;
1579     this.dispose();
1580   }
1581
1582   /**
1583    * TODO: JAL-1104
1584    */
1585   void updateEditMenuBar()
1586   {
1587
1588     if (viewport.getHistoryList().size() > 0)
1589     {
1590       undoMenuItem.setEnabled(true);
1591       CommandI command = viewport.getHistoryList().peek();
1592       undoMenuItem.setLabel(MessageManager.formatMessage(
1593               "label.undo_command",
1594               new Object[] { command.getDescription() }));
1595     }
1596     else
1597     {
1598       undoMenuItem.setEnabled(false);
1599       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1600     }
1601
1602     if (viewport.getRedoList().size() > 0)
1603     {
1604       redoMenuItem.setEnabled(true);
1605
1606       CommandI command = viewport.getRedoList().peek();
1607       redoMenuItem.setLabel(MessageManager.formatMessage(
1608               "label.redo_command",
1609               new Object[] { command.getDescription() }));
1610     }
1611     else
1612     {
1613       redoMenuItem.setEnabled(false);
1614       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1615     }
1616   }
1617
1618   /**
1619    * TODO: JAL-1104
1620    */
1621   @Override
1622   public void addHistoryItem(CommandI command)
1623   {
1624     if (command.getSize() > 0)
1625     {
1626       viewport.addToHistoryList(command);
1627       viewport.clearRedoList();
1628       updateEditMenuBar();
1629       viewport.updateHiddenColumns();
1630     }
1631   }
1632
1633   /**
1634    * TODO: JAL-1104 DOCUMENT ME!
1635    *
1636    * @param e
1637    *          DOCUMENT ME!
1638    */
1639   protected void undoMenuItem_actionPerformed()
1640   {
1641     if (viewport.getHistoryList().isEmpty())
1642     {
1643       return;
1644     }
1645
1646     CommandI command = viewport.getHistoryList().pop();
1647     viewport.addToRedoList(command);
1648     command.undoCommand(null);
1649
1650     AlignmentViewport originalSource = getOriginatingSource(command);
1651     // JBPNote Test
1652     if (originalSource != viewport)
1653     {
1654       System.err
1655               .println("Warning: Viewport object mismatch whilst undoing");
1656     }
1657     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1658                                           // viewport.getColumnSelection().getHiddenColumns()
1659                                           // != null;
1660     updateEditMenuBar();
1661     originalSource.firePropertyChange("alignment", null, originalSource
1662             .getAlignment().getSequences());
1663   }
1664
1665   /**
1666    * TODO: JAL-1104 DOCUMENT ME!
1667    *
1668    * @param e
1669    *          DOCUMENT ME!
1670    */
1671   protected void redoMenuItem_actionPerformed()
1672   {
1673     if (viewport.getRedoList().isEmpty())
1674     {
1675       return;
1676     }
1677
1678     CommandI command = viewport.getRedoList().pop();
1679     viewport.addToHistoryList(command);
1680     command.doCommand(null);
1681
1682     AlignmentViewport originalSource = getOriginatingSource(command);
1683     // JBPNote Test
1684     if (originalSource != viewport)
1685     {
1686       System.err
1687               .println("Warning: Viewport object mismatch whilst re-doing");
1688     }
1689     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1690                                           // viewport.getColumnSelection().getHiddenColumns()
1691                                           // != null;
1692
1693     updateEditMenuBar();
1694     originalSource.firePropertyChange("alignment", null, originalSource
1695             .getAlignment().getSequences());
1696   }
1697
1698   AlignmentViewport getOriginatingSource(CommandI command)
1699   {
1700     AlignmentViewport originalSource = null;
1701     // For sequence removal and addition, we need to fire
1702     // the property change event FROM the viewport where the
1703     // original alignment was altered
1704     AlignmentI al = null;
1705     if (command instanceof EditCommand)
1706     {
1707       EditCommand editCommand = (EditCommand) command;
1708       al = editCommand.getAlignment();
1709       Vector comps = (Vector) PaintRefresher.components.get(viewport
1710               .getSequenceSetId());
1711       for (int i = 0; i < comps.size(); i++)
1712       {
1713         if (comps.elementAt(i) instanceof AlignmentPanel)
1714         {
1715           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1716           {
1717             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1718             break;
1719           }
1720         }
1721       }
1722     }
1723
1724     if (originalSource == null)
1725     {
1726       // The original view is closed, we must validate
1727       // the current view against the closed view first
1728       if (al != null)
1729       {
1730         PaintRefresher.validateSequences(al, viewport.getAlignment());
1731       }
1732
1733       originalSource = viewport;
1734     }
1735
1736     return originalSource;
1737   }
1738
1739   /**
1740    * Move the currently selected sequences up or down one position in the
1741    * alignment
1742    *
1743    * @param up
1744    */
1745   public void moveSelectedSequences(boolean up)
1746   {
1747     SequenceGroup sg = viewport.getSelectionGroup();
1748     if (sg == null)
1749     {
1750       return;
1751     }
1752     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753             up ? null : viewport.getHiddenRepSequences(), up);
1754     alignPanel.paintAlignment(true);
1755
1756     /*
1757      * Also move cDNA/protein complement sequences
1758      */
1759     AlignViewportI complement = viewport.getCodingComplement();
1760     if (complement != null)
1761     {
1762       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1763               viewport, complement);
1764       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1765               up ? null : complement.getHiddenRepSequences(), up);
1766       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1767     }
1768   }
1769
1770   synchronized void slideSequences(boolean right, int size)
1771   {
1772     List<SequenceI> sg = new Vector<SequenceI>();
1773     if (viewport.cursorMode)
1774     {
1775       sg.add(viewport.getAlignment().getSequenceAt(
1776               alignPanel.seqPanel.seqCanvas.cursorY));
1777     }
1778     else if (viewport.getSelectionGroup() != null
1779             && viewport.getSelectionGroup().getSize() != viewport
1780                     .getAlignment().getHeight())
1781     {
1782       sg = viewport.getSelectionGroup().getSequences(
1783               viewport.getHiddenRepSequences());
1784     }
1785
1786     if (sg.size() < 1)
1787     {
1788       return;
1789     }
1790
1791     Vector<SequenceI> invertGroup = new Vector();
1792
1793     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1794     {
1795       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1796       {
1797         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1798       }
1799     }
1800
1801     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1802
1803     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1804             .size()]);
1805     for (int i = 0; i < invertGroup.size(); i++)
1806     {
1807       seqs2[i] = invertGroup.elementAt(i);
1808     }
1809
1810     SlideSequencesCommand ssc;
1811     if (right)
1812     {
1813       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1814               size, viewport.getGapCharacter());
1815     }
1816     else
1817     {
1818       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1819               size, viewport.getGapCharacter());
1820     }
1821
1822     int groupAdjustment = 0;
1823     if (ssc.getGapsInsertedBegin() && right)
1824     {
1825       if (viewport.cursorMode)
1826       {
1827         alignPanel.seqPanel.moveCursor(size, 0);
1828       }
1829       else
1830       {
1831         groupAdjustment = size;
1832       }
1833     }
1834     else if (!ssc.getGapsInsertedBegin() && !right)
1835     {
1836       if (viewport.cursorMode)
1837       {
1838         alignPanel.seqPanel.moveCursor(-size, 0);
1839       }
1840       else
1841       {
1842         groupAdjustment = -size;
1843       }
1844     }
1845
1846     if (groupAdjustment != 0)
1847     {
1848       viewport.getSelectionGroup().setStartRes(
1849               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1850       viewport.getSelectionGroup().setEndRes(
1851               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1852     }
1853
1854     boolean appendHistoryItem = false;
1855     Deque<CommandI> historyList = viewport.getHistoryList();
1856     if (historyList != null && historyList.size() > 0
1857             && historyList.peek() instanceof SlideSequencesCommand)
1858     {
1859       appendHistoryItem = ssc
1860               .appendSlideCommand((SlideSequencesCommand) historyList
1861                       .peek());
1862     }
1863
1864     if (!appendHistoryItem)
1865     {
1866       addHistoryItem(ssc);
1867     }
1868
1869     repaint();
1870   }
1871
1872   static StringBuffer copiedSequences;
1873
1874   static Vector copiedHiddenColumns;
1875
1876   protected void copy_actionPerformed()
1877   {
1878     if (viewport.getSelectionGroup() == null)
1879     {
1880       return;
1881     }
1882
1883     SequenceGroup sg = viewport.getSelectionGroup();
1884     copiedSequences = new StringBuffer();
1885     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1886     for (int i = 0; i < sg.getSize(); i++)
1887     {
1888       SequenceI seq = sg.getSequenceAt(i);
1889       int index = viewport.getAlignment().findIndex(seq);
1890       orderedSeqs.put(index, seq);
1891     }
1892
1893     int index = 0, startRes, endRes;
1894     char ch;
1895
1896     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1897     {
1898       copiedHiddenColumns = new Vector();
1899       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1900       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1901       {
1902         copiedHiddenColumns.addElement(new int[] {
1903             region[0] - hiddenOffset, region[1] - hiddenOffset });
1904       }
1905     }
1906     else
1907     {
1908       copiedHiddenColumns = null;
1909     }
1910
1911     for (int i = 0; i < sg.getSize(); i++)
1912     {
1913       SequenceI seq = null;
1914
1915       while (seq == null)
1916       {
1917         if (orderedSeqs.containsKey(index))
1918         {
1919           seq = orderedSeqs.get(index);
1920           index++;
1921           break;
1922         }
1923         else
1924         {
1925           index++;
1926         }
1927       }
1928
1929       // FIND START RES
1930       // Returns residue following index if gap
1931       startRes = seq.findPosition(sg.getStartRes());
1932
1933       // FIND END RES
1934       // Need to find the residue preceeding index if gap
1935       endRes = 0;
1936
1937       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1938       {
1939         ch = seq.getCharAt(j);
1940         if (!jalview.util.Comparison.isGap((ch)))
1941         {
1942           endRes++;
1943         }
1944       }
1945
1946       if (endRes > 0)
1947       {
1948         endRes += seq.getStart() - 1;
1949       }
1950
1951       copiedSequences.append(seq.getName()
1952               + "\t"
1953               + startRes
1954               + "\t"
1955               + endRes
1956               + "\t"
1957               + seq.getSequenceAsString(sg.getStartRes(),
1958                       sg.getEndRes() + 1) + "\n");
1959     }
1960
1961   }
1962
1963   protected void pasteNew_actionPerformed()
1964   {
1965     paste(true);
1966   }
1967
1968   protected void pasteThis_actionPerformed()
1969   {
1970     paste(false);
1971   }
1972
1973   void paste(boolean newAlignment)
1974   {
1975     try
1976     {
1977
1978       if (copiedSequences == null)
1979       {
1980         return;
1981       }
1982
1983       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1984       Vector seqs = new Vector();
1985       while (st.hasMoreElements())
1986       {
1987         String name = st.nextToken();
1988         int start = Integer.parseInt(st.nextToken());
1989         int end = Integer.parseInt(st.nextToken());
1990         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1991       }
1992       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1993       for (int i = 0; i < seqs.size(); i++)
1994       {
1995         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1996       }
1997
1998       if (newAlignment)
1999       {
2000         String newtitle = MessageManager
2001                 .getString("label.copied_sequences");
2002         if (getTitle().startsWith(
2003                 MessageManager.getString("label.copied_sequences")))
2004         {
2005           newtitle = getTitle();
2006         }
2007         else
2008         {
2009           newtitle = newtitle.concat(MessageManager.formatMessage(
2010                   "label.from_msname", new String[] { getTitle() }));
2011         }
2012         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2013                 viewport.applet, newtitle, false);
2014         if (copiedHiddenColumns != null)
2015         {
2016           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2017           {
2018             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2019             af.viewport.hideColumns(region[0], region[1]);
2020           }
2021         }
2022
2023         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2024                 frameHeight);
2025       }
2026       else
2027       {
2028         addSequences(newSeqs);
2029       }
2030
2031     } catch (Exception ex)
2032     {
2033     } // could be anything being pasted in here
2034
2035   }
2036
2037   void addSequences(SequenceI[] seqs)
2038   {
2039     for (int i = 0; i < seqs.length; i++)
2040     {
2041       viewport.getAlignment().addSequence(seqs[i]);
2042     }
2043
2044     // !newAlignment
2045     addHistoryItem(new EditCommand(
2046             MessageManager.getString("label.add_sequences"), Action.PASTE,
2047             seqs, 0, viewport.getAlignment().getWidth(),
2048             viewport.getAlignment()));
2049
2050     viewport.setEndSeq(viewport.getAlignment().getHeight());
2051     viewport.getAlignment().getWidth();
2052     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2053             .getSequences());
2054
2055   }
2056
2057   protected void cut_actionPerformed()
2058   {
2059     copy_actionPerformed();
2060     delete_actionPerformed();
2061   }
2062
2063   protected void delete_actionPerformed()
2064   {
2065
2066     SequenceGroup sg = viewport.getSelectionGroup();
2067     if (sg == null)
2068     {
2069       return;
2070     }
2071
2072     Vector seqs = new Vector();
2073     SequenceI seq;
2074     for (int i = 0; i < sg.getSize(); i++)
2075     {
2076       seq = sg.getSequenceAt(i);
2077       seqs.addElement(seq);
2078     }
2079
2080     /*
2081      * If the cut affects all sequences, warn, remove highlighted columns
2082      */
2083     if (sg.getSize() == viewport.getAlignment().getHeight())
2084     {
2085       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2086               .getAlignment().getWidth()) ? true : false;
2087       if (isEntireAlignWidth)
2088       {
2089         String title = MessageManager.getString("label.delete_all");
2090         Panel infoPanel = new Panel();
2091         infoPanel.setLayout(new FlowLayout());
2092         infoPanel
2093                 .add(new Label(MessageManager.getString("warn.delete_all")));
2094
2095         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2096         dialog.setMainPanel(infoPanel);
2097         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2098         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2099         dialog.setVisible(true);
2100
2101         if (!dialog.accept)
2102         {
2103           return;
2104         }
2105       }
2106       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2107               sg.getEndRes() + 1);
2108     }
2109
2110     SequenceI[] cut = new SequenceI[seqs.size()];
2111     for (int i = 0; i < seqs.size(); i++)
2112     {
2113       cut[i] = (SequenceI) seqs.elementAt(i);
2114     }
2115
2116     /*
2117      * //ADD HISTORY ITEM
2118      */
2119     addHistoryItem(new EditCommand(
2120             MessageManager.getString("label.cut_sequences"), Action.CUT,
2121             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2122             viewport.getAlignment()));
2123
2124     viewport.setSelectionGroup(null);
2125     viewport.getAlignment().deleteGroup(sg);
2126
2127     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2128             .getSequences());
2129
2130     if (viewport.getAlignment().getHeight() < 1)
2131     {
2132       this.setVisible(false);
2133     }
2134     viewport.sendSelection();
2135   }
2136
2137   /**
2138    * group consensus toggled
2139    *
2140    */
2141   protected void showGroupConsensus_actionPerformed()
2142   {
2143     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2144     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145
2146   }
2147
2148   /**
2149    * group conservation toggled.
2150    */
2151   protected void showGroupConservation_actionPerformed()
2152   {
2153     viewport.setShowGroupConservation(showGroupConservation.getState());
2154     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2155   }
2156
2157   /*
2158    * (non-Javadoc)
2159    *
2160    * @see
2161    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2162    * .event.ActionEvent)
2163    */
2164   protected void showConsensusHistogram_actionPerformed()
2165   {
2166     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2167     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2168   }
2169
2170   /*
2171    * (non-Javadoc)
2172    *
2173    * @see
2174    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2175    * .event.ActionEvent)
2176    */
2177   protected void showSequenceLogo_actionPerformed()
2178   {
2179     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2180     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181   }
2182
2183   protected void normSequenceLogo_actionPerformed()
2184   {
2185     showSequenceLogo.setState(true);
2186     viewport.setShowSequenceLogo(true);
2187     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2188     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2189   }
2190
2191   protected void applyAutoAnnotationSettings_actionPerformed()
2192   {
2193     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2194   }
2195
2196   protected void makeGrpsFromSelection_actionPerformed()
2197   {
2198     if (avc.makeGroupsFromSelection())
2199     {
2200       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2201       alignPanel.updateAnnotation();
2202       alignPanel.paintAlignment(true);
2203     }
2204   }
2205
2206   protected void createGroup_actionPerformed()
2207   {
2208     avc.createGroup();
2209   }
2210
2211   protected void unGroup_actionPerformed()
2212   {
2213     if (avc.unGroup())
2214     {
2215       alignPanel.alignmentChanged();
2216     }
2217   }
2218
2219   protected void deleteGroups_actionPerformed()
2220   {
2221     if (avc.deleteGroups())
2222     {
2223       alignPanel.alignmentChanged();
2224     }
2225   }
2226
2227   public void selectAllSequenceMenuItem_actionPerformed()
2228   {
2229     SequenceGroup sg = new SequenceGroup();
2230     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2231     {
2232       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2233     }
2234     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2235     viewport.setSelectionGroup(sg);
2236     // JAL-2034 - should delegate to
2237     // alignPanel to decide if overview needs
2238     // updating.
2239     alignPanel.paintAlignment(false);
2240     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2241     viewport.sendSelection();
2242   }
2243
2244   public void deselectAllSequenceMenuItem_actionPerformed()
2245   {
2246     if (viewport.cursorMode)
2247     {
2248       alignPanel.seqPanel.keyboardNo1 = null;
2249       alignPanel.seqPanel.keyboardNo2 = null;
2250     }
2251     viewport.setSelectionGroup(null);
2252     viewport.getColumnSelection().clear();
2253     viewport.setSelectionGroup(null);
2254     alignPanel.idPanel.idCanvas.searchResults = null;
2255     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2256     // JAL-2034 - should delegate to
2257     // alignPanel to decide if overview needs
2258     // updating.
2259     alignPanel.paintAlignment(false);
2260     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2261     viewport.sendSelection();
2262   }
2263
2264   public void invertSequenceMenuItem_actionPerformed()
2265   {
2266     SequenceGroup sg = viewport.getSelectionGroup();
2267     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2268     {
2269       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2270     }
2271
2272     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273     viewport.sendSelection();
2274   }
2275
2276   public void invertColSel_actionPerformed()
2277   {
2278     viewport.invertColumnSelection();
2279     alignPanel.paintAlignment(true);
2280     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281     viewport.sendSelection();
2282   }
2283
2284   void trimAlignment(boolean trimLeft)
2285   {
2286     ColumnSelection colSel = viewport.getColumnSelection();
2287     int column;
2288
2289     if (!colSel.isEmpty())
2290     {
2291       if (trimLeft)
2292       {
2293         column = colSel.getMin();
2294       }
2295       else
2296       {
2297         column = colSel.getMax();
2298       }
2299
2300       SequenceI[] seqs;
2301       if (viewport.getSelectionGroup() != null)
2302       {
2303         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2304                 viewport.getHiddenRepSequences());
2305       }
2306       else
2307       {
2308         seqs = viewport.getAlignment().getSequencesArray();
2309       }
2310
2311       TrimRegionCommand trimRegion;
2312       if (trimLeft)
2313       {
2314         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2315                 column, viewport.getAlignment());
2316         viewport.setStartRes(0);
2317       }
2318       else
2319       {
2320         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2321                 column, viewport.getAlignment());
2322       }
2323
2324       statusBar.setText(MessageManager.formatMessage(
2325               "label.removed_columns",
2326               new String[] { Integer.valueOf(trimRegion.getSize())
2327                       .toString() }));
2328       addHistoryItem(trimRegion);
2329
2330       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2331       {
2332         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2333                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2334         {
2335           viewport.getAlignment().deleteGroup(sg);
2336         }
2337       }
2338
2339       viewport.firePropertyChange("alignment", null, viewport
2340               .getAlignment().getSequences());
2341     }
2342   }
2343
2344   public void removeGappedColumnMenuItem_actionPerformed()
2345   {
2346     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2347
2348     SequenceI[] seqs;
2349     if (viewport.getSelectionGroup() != null)
2350     {
2351       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2352               viewport.getHiddenRepSequences());
2353       start = viewport.getSelectionGroup().getStartRes();
2354       end = viewport.getSelectionGroup().getEndRes();
2355     }
2356     else
2357     {
2358       seqs = viewport.getAlignment().getSequencesArray();
2359     }
2360
2361     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2362             "Remove Gapped Columns", seqs, start, end,
2363             viewport.getAlignment());
2364
2365     addHistoryItem(removeGapCols);
2366
2367     statusBar.setText(MessageManager.formatMessage(
2368             "label.removed_empty_columns",
2369             new String[] { Integer.valueOf(removeGapCols.getSize())
2370                     .toString() }));
2371
2372     // This is to maintain viewport position on first residue
2373     // of first sequence
2374     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2375     int startRes = seq.findPosition(viewport.startRes);
2376     // ShiftList shifts;
2377     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2378     // edit.alColumnChanges=shifts.getInverse();
2379     // if (viewport.hasHiddenColumns)
2380     // viewport.getColumnSelection().compensateForEdits(shifts);
2381     viewport.setStartRes(seq.findIndex(startRes) - 1);
2382     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2383             .getSequences());
2384
2385   }
2386
2387   public void removeAllGapsMenuItem_actionPerformed()
2388   {
2389     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2390
2391     SequenceI[] seqs;
2392     if (viewport.getSelectionGroup() != null)
2393     {
2394       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2395               viewport.getHiddenRepSequences());
2396       start = viewport.getSelectionGroup().getStartRes();
2397       end = viewport.getSelectionGroup().getEndRes();
2398     }
2399     else
2400     {
2401       seqs = viewport.getAlignment().getSequencesArray();
2402     }
2403
2404     // This is to maintain viewport position on first residue
2405     // of first sequence
2406     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2407     int startRes = seq.findPosition(viewport.startRes);
2408
2409     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2410             viewport.getAlignment()));
2411
2412     viewport.setStartRes(seq.findIndex(startRes) - 1);
2413
2414     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2415             .getSequences());
2416
2417   }
2418
2419   public void findMenuItem_actionPerformed()
2420   {
2421     new Finder(alignPanel);
2422   }
2423
2424   /**
2425    * create a new view derived from the current view
2426    *
2427    * @param viewtitle
2428    * @return frame for the new view
2429    */
2430   public AlignFrame newView(String viewtitle)
2431   {
2432     AlignmentI newal;
2433     if (viewport.hasHiddenRows())
2434     {
2435       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2436               .getFullAlignment().getSequencesArray());
2437     }
2438     else
2439     {
2440       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2441     }
2442
2443     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2444     {
2445       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2446       {
2447         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2448         {
2449           newal.addAnnotation(viewport.getAlignment()
2450                   .getAlignmentAnnotation()[i]);
2451         }
2452       }
2453     }
2454
2455     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2456
2457     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2458     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2459     PaintRefresher.Register(newaf.alignPanel,
2460             newaf.alignPanel.av.getSequenceSetId());
2461
2462     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2463             newaf.alignPanel.av.getSequenceSetId());
2464     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2465             newaf.alignPanel.av.getSequenceSetId());
2466
2467     Vector comps = (Vector) PaintRefresher.components.get(viewport
2468             .getSequenceSetId());
2469     int viewSize = -1;
2470     for (int i = 0; i < comps.size(); i++)
2471     {
2472       if (comps.elementAt(i) instanceof AlignmentPanel)
2473       {
2474         viewSize++;
2475       }
2476     }
2477
2478     String title = new String(this.getTitle());
2479     if (viewtitle != null)
2480     {
2481       title = viewtitle + " ( " + title + ")";
2482     }
2483     else
2484     {
2485       if (title.indexOf("(View") > -1)
2486       {
2487         title = title.substring(0, title.indexOf("(View"));
2488       }
2489       title += "(View " + viewSize + ")";
2490     }
2491
2492     newaf.setTitle(title.toString());
2493
2494     newaf.viewport.setHistoryList(viewport.getHistoryList());
2495     newaf.viewport.setRedoList(viewport.getRedoList());
2496     return newaf;
2497   }
2498
2499   /**
2500    *
2501    * @return list of feature groups on the view
2502    */
2503   public String[] getFeatureGroups()
2504   {
2505     FeatureRenderer fr = null;
2506     if (alignPanel != null
2507             && (fr = alignPanel.getFeatureRenderer()) != null)
2508     {
2509       List<String> gps = fr.getFeatureGroups();
2510       String[] _gps = gps.toArray(new String[gps.size()]);
2511       return _gps;
2512     }
2513     return null;
2514   }
2515
2516   /**
2517    * get sequence feature groups that are hidden or shown
2518    *
2519    * @param visible
2520    *          true is visible
2521    * @return list
2522    */
2523   public String[] getFeatureGroupsOfState(boolean visible)
2524   {
2525     FeatureRenderer fr = null;
2526     if (alignPanel != null
2527             && (fr = alignPanel.getFeatureRenderer()) != null)
2528     {
2529       List<String> gps = fr.getGroups(visible);
2530       String[] _gps = gps.toArray(new String[gps.size()]);
2531       return _gps;
2532     }
2533     return null;
2534   }
2535
2536   /**
2537    * Change the display state for the given feature groups
2538    *
2539    * @param groups
2540    *          list of group strings
2541    * @param state
2542    *          visible or invisible
2543    */
2544   public void setFeatureGroupState(String[] groups, boolean state)
2545   {
2546     FeatureRenderer fr = null;
2547     this.sequenceFeatures.setState(true);
2548     viewport.setShowSequenceFeatures(true);
2549     if (alignPanel != null
2550             && (fr = alignPanel.getFeatureRenderer()) != null)
2551     {
2552
2553       fr.setGroupVisibility(Arrays.asList(groups), state);
2554       alignPanel.seqPanel.seqCanvas.repaint();
2555       if (alignPanel.overviewPanel != null)
2556       {
2557         alignPanel.overviewPanel.updateOverviewImage();
2558       }
2559     }
2560   }
2561
2562   public void seqLimits_itemStateChanged()
2563   {
2564     viewport.setShowJVSuffix(seqLimits.getState());
2565     alignPanel.fontChanged();
2566     alignPanel.paintAlignment(true);
2567   }
2568
2569   protected void colourTextMenuItem_actionPerformed()
2570   {
2571     viewport.setColourText(colourTextMenuItem.getState());
2572     alignPanel.paintAlignment(true);
2573   }
2574
2575   protected void displayNonconservedMenuItem_actionPerformed()
2576   {
2577     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2578     alignPanel.paintAlignment(true);
2579   }
2580
2581   protected void wrapMenuItem_actionPerformed()
2582   {
2583     viewport.setWrapAlignment(wrapMenuItem.getState());
2584     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2585     scaleAbove.setEnabled(wrapMenuItem.getState());
2586     scaleLeft.setEnabled(wrapMenuItem.getState());
2587     scaleRight.setEnabled(wrapMenuItem.getState());
2588     alignPanel.paintAlignment(true);
2589   }
2590
2591   public void overviewMenuItem_actionPerformed()
2592   {
2593     if (alignPanel.overviewPanel != null)
2594     {
2595       return;
2596     }
2597
2598     Frame frame = new Frame();
2599     OverviewPanel overview = new OverviewPanel(alignPanel);
2600     frame.add(overview);
2601     // +50 must allow for applet frame window
2602     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2603             "label.overview_params", new String[] { this.getTitle() }),
2604             overview.getPreferredSize().width,
2605             overview.getPreferredSize().height + 50);
2606
2607     frame.pack();
2608     final AlignmentPanel ap = alignPanel;
2609     frame.addWindowListener(new WindowAdapter()
2610     {
2611       @Override
2612       public void windowClosing(WindowEvent e)
2613       {
2614         if (ap != null)
2615         {
2616           ap.setOverviewPanel(null);
2617         }
2618       };
2619     });
2620
2621     alignPanel.setOverviewPanel(overview);
2622
2623   }
2624
2625   @Override
2626   public void changeColour(ColourSchemeI cs)
2627   {
2628     // FIXME threshold, conservation, increment belong inside
2629     // AlignmentColourScheme and/or ViewStyleI, not ColourSchemeI
2630     if (cs != null)
2631     {
2632       if (viewport.getAbovePIDThreshold())
2633       {
2634         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2635                 viewport.getViewportColourScheme(), "Background"));
2636       }
2637
2638       if (viewport.getConservationSelected())
2639       {
2640         // cs.setConservationApplied(true);
2641         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2642                 viewport.getViewportColourScheme(), "Background"));
2643       }
2644       // else
2645       // {
2646       // cs.setConservationApplied(false);
2647       // }
2648     }
2649     viewport.setGlobalColourScheme(cs);
2650     viewport.getViewportColourScheme().setConservationApplied(
2651             viewport.getConservationSelected());
2652
2653     alignPanel.paintAlignment(true);
2654   }
2655
2656   protected void modifyPID_actionPerformed()
2657   {
2658     if (viewport.getAbovePIDThreshold()
2659             && viewport.getGlobalColourScheme() != null)
2660     {
2661       SliderPanel.setPIDSliderSource(alignPanel,
2662               viewport.getViewportColourScheme(), "Background");
2663       SliderPanel.showPIDSlider();
2664     }
2665   }
2666
2667   protected void modifyConservation_actionPerformed()
2668   {
2669     if (viewport.getConservationSelected()
2670             && viewport.getGlobalColourScheme() != null)
2671     {
2672       SliderPanel.setConservationSlider(alignPanel,
2673               viewport.getViewportColourScheme(), "Background");
2674       SliderPanel.showConservationSlider();
2675     }
2676   }
2677
2678   protected void conservationMenuItem_actionPerformed()
2679   {
2680     viewport.setConservationSelected(conservationMenuItem.getState());
2681
2682     viewport.setAbovePIDThreshold(false);
2683     abovePIDThreshold.setState(false);
2684
2685     changeColour(viewport.getGlobalColourScheme());
2686
2687     modifyConservation_actionPerformed();
2688   }
2689
2690   public void abovePIDThreshold_actionPerformed()
2691   {
2692     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2693
2694     conservationMenuItem.setState(false);
2695     viewport.setConservationSelected(false);
2696
2697     changeColour(viewport.getGlobalColourScheme());
2698
2699     modifyPID_actionPerformed();
2700   }
2701
2702   public void sortPairwiseMenuItem_actionPerformed()
2703   {
2704     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2705     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2706             .getAlignment().getSequenceAt(0), null);
2707
2708     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2709             viewport.getAlignment()));
2710     alignPanel.paintAlignment(true);
2711   }
2712
2713   public void sortIDMenuItem_actionPerformed()
2714   {
2715     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2716     AlignmentSorter.sortByID(viewport.getAlignment());
2717     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2718             viewport.getAlignment()));
2719     alignPanel.paintAlignment(true);
2720   }
2721
2722   public void sortLengthMenuItem_actionPerformed()
2723   {
2724     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2725     AlignmentSorter.sortByLength(viewport.getAlignment());
2726     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2727             viewport.getAlignment()));
2728     alignPanel.paintAlignment(true);
2729   }
2730
2731   public void sortGroupMenuItem_actionPerformed()
2732   {
2733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734     AlignmentSorter.sortByGroup(viewport.getAlignment());
2735     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2736             viewport.getAlignment()));
2737     alignPanel.paintAlignment(true);
2738
2739   }
2740
2741   public void removeRedundancyMenuItem_actionPerformed()
2742   {
2743     new RedundancyPanel(alignPanel);
2744   }
2745
2746   public void pairwiseAlignmentMenuItem_actionPerformed()
2747   {
2748     if (viewport.getSelectionGroup() != null
2749             && viewport.getSelectionGroup().getSize() > 1)
2750     {
2751       Frame frame = new Frame();
2752       frame.add(new PairwiseAlignPanel(alignPanel));
2753       jalview.bin.JalviewLite.addFrame(frame,
2754               MessageManager.getString("action.pairwise_alignment"), 600,
2755               500);
2756     }
2757   }
2758
2759   public void PCAMenuItem_actionPerformed()
2760   {
2761     // are the sequences aligned?
2762     if (!viewport.getAlignment().isAligned(false))
2763     {
2764       SequenceI current;
2765       int Width = viewport.getAlignment().getWidth();
2766
2767       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2768       {
2769         current = viewport.getAlignment().getSequenceAt(i);
2770
2771         if (current.getLength() < Width)
2772         {
2773           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2774         }
2775       }
2776       alignPanel.paintAlignment(true);
2777     }
2778
2779     if ((viewport.getSelectionGroup() != null
2780             && viewport.getSelectionGroup().getSize() < 4 && viewport
2781             .getSelectionGroup().getSize() > 0)
2782             || viewport.getAlignment().getHeight() < 4)
2783     {
2784       return;
2785     }
2786
2787     try
2788     {
2789       new PCAPanel(viewport);
2790     } catch (java.lang.OutOfMemoryError ex)
2791     {
2792     }
2793
2794   }
2795
2796   public void averageDistanceTreeMenuItem_actionPerformed()
2797   {
2798     NewTreePanel("AV", "PID", "Average distance tree using PID");
2799   }
2800
2801   public void neighbourTreeMenuItem_actionPerformed()
2802   {
2803     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2804   }
2805
2806   protected void njTreeBlosumMenuItem_actionPerformed()
2807   {
2808     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2809   }
2810
2811   protected void avTreeBlosumMenuItem_actionPerformed()
2812   {
2813     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2814   }
2815
2816   void NewTreePanel(String type, String pwType, String title)
2817   {
2818     // are the sequences aligned?
2819     if (!viewport.getAlignment().isAligned(false))
2820     {
2821       SequenceI current;
2822       int Width = viewport.getAlignment().getWidth();
2823
2824       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2825       {
2826         current = viewport.getAlignment().getSequenceAt(i);
2827
2828         if (current.getLength() < Width)
2829         {
2830           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2831         }
2832       }
2833       alignPanel.paintAlignment(true);
2834
2835     }
2836
2837     if ((viewport.getSelectionGroup() != null && viewport
2838             .getSelectionGroup().getSize() > 1)
2839             || (viewport.getAlignment().getHeight() > 1))
2840     {
2841       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2842
2843       addTreeMenuItem(tp, title);
2844
2845       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2846     }
2847   }
2848
2849   void loadTree_actionPerformed()
2850   {
2851     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2852     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2853     cap.setTreeImport();
2854     Frame frame = new Frame();
2855     frame.add(cap);
2856     jalview.bin.JalviewLite.addFrame(frame,
2857             MessageManager.getString("label.paste_newick_file"), 400, 300);
2858   }
2859
2860   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2861   {
2862     TreePanel tp = new TreePanel(alignPanel, treeFile,
2863             MessageManager.getString("label.load_tree_from_file"), tree);
2864     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2865     addTreeMenuItem(tp, treeFile);
2866   }
2867
2868   /**
2869    * sort the alignment using the given treePanel
2870    *
2871    * @param treePanel
2872    *          tree used to sort view
2873    * @param title
2874    *          string used for undo event name
2875    */
2876   public void sortByTree(TreePanel treePanel, String title)
2877   {
2878     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2879     AlignmentSorter
2880             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2881     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2882     // HistoryItem.SORT));
2883     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2884             "label.order_by_params", new String[] { title }), oldOrder,
2885             viewport.getAlignment()));
2886     alignPanel.paintAlignment(true);
2887   }
2888
2889   /**
2890    * Do any automatic reordering of the alignment and add the necessary bits to
2891    * the menu structure for the new tree
2892    *
2893    * @param treePanel
2894    * @param title
2895    */
2896   protected void addTreeMenuItem(final TreePanel treePanel,
2897           final String title)
2898   {
2899     final MenuItem item = new MenuItem(title);
2900     sortByTreeMenu.add(item);
2901     item.addActionListener(new java.awt.event.ActionListener()
2902     {
2903       @Override
2904       public void actionPerformed(ActionEvent evt)
2905       {
2906         sortByTree(treePanel, title); // treePanel.getTitle());
2907       }
2908     });
2909
2910     treePanel.addWindowListener(new WindowAdapter()
2911     {
2912       @Override
2913       public void windowOpened(WindowEvent e)
2914       {
2915         if (viewport.sortByTree)
2916         {
2917           sortByTree(treePanel, title);
2918         }
2919         super.windowOpened(e);
2920       }
2921
2922       @Override
2923       public void windowClosing(WindowEvent e)
2924       {
2925         sortByTreeMenu.remove(item);
2926       };
2927     });
2928   }
2929
2930   public boolean sortBy(AlignmentOrder alorder, String undoname)
2931   {
2932     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2933     if (viewport.applet.debug)
2934     {
2935       System.err.println("Sorting " + alorder.getOrder().size()
2936               + " in alignment '" + getTitle() + "'");
2937     }
2938     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2939     if (undoname != null)
2940     {
2941       addHistoryItem(new OrderCommand(undoname, oldOrder,
2942               viewport.getAlignment()));
2943     }
2944     alignPanel.paintAlignment(true);
2945     return true;
2946   }
2947
2948   protected void documentation_actionPerformed()
2949   {
2950     alignPanel.av.applet.openJalviewHelpUrl();
2951   }
2952
2953   protected void about_actionPerformed()
2954   {
2955
2956     class AboutPanel extends Canvas
2957     {
2958       String version;
2959
2960       String builddate;
2961
2962       public AboutPanel(String version, String builddate)
2963       {
2964         this.version = version;
2965         this.builddate = builddate;
2966       }
2967
2968       @Override
2969       public void paint(Graphics g)
2970       {
2971         g.setColor(Color.white);
2972         g.fillRect(0, 0, getSize().width, getSize().height);
2973         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2974         FontMetrics fm = g.getFontMetrics();
2975         int fh = fm.getHeight();
2976         int y = 5, x = 7;
2977         g.setColor(Color.black);
2978         // TODO: update this text for each release or centrally store it for
2979         // lite and application
2980         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2981         g.drawString(MessageManager.formatMessage(
2982                 "label.jalviewLite_release", new String[] { version }), x,
2983                 y += fh);
2984         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2985         g.drawString(MessageManager.formatMessage(
2986                 "label.jaview_build_date", new String[] { builddate }), x,
2987                 y += fh);
2988         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2989         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2990                 x, y += fh * 1.5);
2991         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2992                 x + 50, y += fh + 8);
2993         g.drawString(
2994                 MessageManager.getString("label.jalview_dev_managers"), x,
2995                 y += fh);
2996         g.drawString(MessageManager
2997                 .getString("label.jalview_distribution_lists"), x, y += fh);
2998         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2999                 x, y += fh + 8);
3000         g.drawString(
3001                 MessageManager.getString("label.jalview_cite_1_authors"),
3002                 x, y += fh);
3003         g.drawString(
3004                 MessageManager.getString("label.jalview_cite_1_title"), x,
3005                 y += fh);
3006         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3007                 x, y += fh);
3008       }
3009     }
3010
3011     Frame frame = new Frame();
3012     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3013             .getBuildDate()));
3014     jalview.bin.JalviewLite.addFrame(frame,
3015             MessageManager.getString("label.jalview"), 580, 220);
3016
3017   }
3018
3019   public void showURL(String url, String target)
3020   {
3021     if (viewport.applet == null)
3022     {
3023       System.out.println("Not running as applet - no browser available.");
3024     }
3025     else
3026     {
3027       viewport.applet.showURL(url, target);
3028     }
3029   }
3030
3031   // ////////////////////////////////////////////////////////////////////////////////
3032   // JBuilder Graphics here
3033
3034   MenuBar alignFrameMenuBar = new MenuBar();
3035
3036   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3037
3038   MenuItem loadApplication = new MenuItem(
3039           MessageManager.getString("label.view_full_application"));
3040
3041   MenuItem loadTree = new MenuItem(
3042           MessageManager.getString("label.load_associated_tree"));
3043
3044   MenuItem loadAnnotations = new MenuItem(
3045           MessageManager.getString("label.load_features_annotations"));
3046
3047   MenuItem outputFeatures = new MenuItem(
3048           MessageManager.getString("label.export_features"));
3049
3050   MenuItem outputAnnotations = new MenuItem(
3051           MessageManager.getString("label.export_annotations"));
3052
3053   MenuItem closeMenuItem = new MenuItem(
3054           MessageManager.getString("action.close"));
3055
3056   MenuItem selectAllSequenceMenuItem = new MenuItem(
3057           MessageManager.getString("action.select_all"));
3058
3059   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3060           MessageManager.getString("action.deselect_all"));
3061
3062   MenuItem invertSequenceMenuItem = new MenuItem(
3063           MessageManager.getString("action.invert_selection"));
3064
3065   MenuItem remove2LeftMenuItem = new MenuItem();
3066
3067   MenuItem remove2RightMenuItem = new MenuItem();
3068
3069   MenuItem removeGappedColumnMenuItem = new MenuItem();
3070
3071   MenuItem removeAllGapsMenuItem = new MenuItem();
3072
3073   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3074
3075   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3076
3077   MenuItem sortPairwiseMenuItem = new MenuItem();
3078
3079   MenuItem sortIDMenuItem = new MenuItem();
3080
3081   MenuItem sortLengthMenuItem = new MenuItem();
3082
3083   MenuItem sortGroupMenuItem = new MenuItem();
3084
3085   MenuItem removeRedundancyMenuItem = new MenuItem();
3086
3087   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3088
3089   MenuItem PCAMenuItem = new MenuItem();
3090
3091   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3092
3093   MenuItem neighbourTreeMenuItem = new MenuItem();
3094
3095   BorderLayout borderLayout1 = new BorderLayout();
3096
3097   public Label statusBar = new Label();
3098
3099   MenuItem clustalColour = new MenuItem();
3100
3101   MenuItem zappoColour = new MenuItem();
3102
3103   MenuItem taylorColour = new MenuItem();
3104
3105   MenuItem hydrophobicityColour = new MenuItem();
3106
3107   MenuItem helixColour = new MenuItem();
3108
3109   MenuItem strandColour = new MenuItem();
3110
3111   MenuItem turnColour = new MenuItem();
3112
3113   MenuItem buriedColour = new MenuItem();
3114
3115   MenuItem purinePyrimidineColour = new MenuItem();
3116
3117   // MenuItem RNAInteractionColour = new MenuItem();
3118
3119   MenuItem RNAHelixColour = new MenuItem();
3120
3121   MenuItem userDefinedColour = new MenuItem();
3122
3123   MenuItem PIDColour = new MenuItem();
3124
3125   MenuItem BLOSUM62Colour = new MenuItem();
3126
3127   MenuItem tcoffeeColour = new MenuItem();
3128
3129   MenuItem njTreeBlosumMenuItem = new MenuItem();
3130
3131   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3132
3133   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3134
3135   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3136
3137   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3138
3139   MenuItem alProperties = new MenuItem(
3140           MessageManager.getString("label.alignment_props"));
3141
3142   MenuItem overviewMenuItem = new MenuItem();
3143
3144   MenuItem undoMenuItem = new MenuItem();
3145
3146   MenuItem redoMenuItem = new MenuItem();
3147
3148   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3149
3150   MenuItem noColourmenuItem = new MenuItem();
3151
3152   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3153
3154   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3155
3156   MenuItem findMenuItem = new MenuItem();
3157
3158   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3159
3160   MenuItem nucleotideColour = new MenuItem();
3161
3162   MenuItem deleteGroups = new MenuItem();
3163
3164   MenuItem grpsFromSelection = new MenuItem();
3165
3166   MenuItem createGroup = new MenuItem();
3167
3168   MenuItem unGroup = new MenuItem();
3169
3170   MenuItem delete = new MenuItem();
3171
3172   MenuItem copy = new MenuItem();
3173
3174   MenuItem cut = new MenuItem();
3175
3176   Menu pasteMenu = new Menu();
3177
3178   MenuItem pasteNew = new MenuItem();
3179
3180   MenuItem pasteThis = new MenuItem();
3181
3182   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3183
3184   MenuItem font = new MenuItem();
3185
3186   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3187
3188   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3189
3190   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3191
3192   MenuItem modifyPID = new MenuItem();
3193
3194   MenuItem modifyConservation = new MenuItem();
3195
3196   CheckboxMenuItem autoCalculate = null;
3197
3198   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3199           "Sort Alignment With New Tree", true);
3200
3201   Menu sortByTreeMenu = new Menu();
3202
3203   MenuItem inputText = new MenuItem();
3204
3205   MenuItem documentation = new MenuItem();
3206
3207   MenuItem about = new MenuItem();
3208
3209   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3210
3211   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3216
3217   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3218
3219   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3220
3221   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3222
3223   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3224
3225   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3226
3227   /**
3228    * Initialise menus and other items
3229    *
3230    * @throws Exception
3231    */
3232   private void jbInit() throws Exception
3233   {
3234     setMenuBar(alignFrameMenuBar);
3235
3236     /*
3237      * Configure File menu items and actions
3238      */
3239     inputText
3240             .setLabel(MessageManager.getString("label.input_from_textbox"));
3241     inputText.addActionListener(this);
3242     Menu outputTextboxMenu = new Menu(
3243             MessageManager.getString("label.out_to_textbox"));
3244     for (String ff : FileFormat.getWritableFormats(true))
3245     {
3246       MenuItem item = new MenuItem(ff);
3247
3248       item.addActionListener(new java.awt.event.ActionListener()
3249       {
3250         @Override
3251         public void actionPerformed(ActionEvent e)
3252         {
3253           outputText_actionPerformed(e);
3254         }
3255       });
3256
3257       outputTextboxMenu.add(item);
3258     }
3259     closeMenuItem.addActionListener(this);
3260     loadApplication.addActionListener(this);
3261     loadTree.addActionListener(this);
3262     loadAnnotations.addActionListener(this);
3263     outputFeatures.addActionListener(this);
3264     outputAnnotations.addActionListener(this);
3265
3266     /*
3267      * Configure Edit menu items and actions
3268      */
3269     undoMenuItem.setEnabled(false);
3270     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3271     undoMenuItem.addActionListener(this);
3272     redoMenuItem.setEnabled(false);
3273     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3274     redoMenuItem.addActionListener(this);
3275     copy.setLabel(MessageManager.getString("action.copy"));
3276     copy.addActionListener(this);
3277     cut.setLabel(MessageManager.getString("action.cut"));
3278     cut.addActionListener(this);
3279     delete.setLabel(MessageManager.getString("action.delete"));
3280     delete.addActionListener(this);
3281     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3282     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3283     pasteNew.addActionListener(this);
3284     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3285     pasteThis.addActionListener(this);
3286     remove2LeftMenuItem.setLabel(MessageManager
3287             .getString("action.remove_left"));
3288     remove2LeftMenuItem.addActionListener(this);
3289     remove2RightMenuItem.setLabel(MessageManager
3290             .getString("action.remove_right"));
3291     remove2RightMenuItem.addActionListener(this);
3292     removeGappedColumnMenuItem.setLabel(MessageManager
3293             .getString("action.remove_empty_columns"));
3294     removeGappedColumnMenuItem.addActionListener(this);
3295     removeAllGapsMenuItem.setLabel(MessageManager
3296             .getString("action.remove_all_gaps"));
3297     removeAllGapsMenuItem.addActionListener(this);
3298     removeRedundancyMenuItem.setLabel(MessageManager
3299             .getString("action.remove_redundancy"));
3300     removeRedundancyMenuItem.addActionListener(this);
3301
3302     /*
3303      * Configure Select menu items and actions
3304      */
3305     findMenuItem.setLabel(MessageManager.getString("action.find"));
3306     findMenuItem.addActionListener(this);
3307     selectAllSequenceMenuItem.addActionListener(this);
3308     deselectAllSequenceMenuItem.addActionListener(this);
3309     invertSequenceMenuItem.setLabel(MessageManager
3310             .getString("action.invert_sequence_selection"));
3311     invertSequenceMenuItem.addActionListener(this);
3312     invertColSel.setLabel(MessageManager
3313             .getString("action.invert_column_selection"));
3314     invertColSel.addActionListener(this);
3315     deleteGroups.setLabel(MessageManager
3316             .getString("action.undefine_groups"));
3317     deleteGroups.addActionListener(this);
3318     grpsFromSelection.setLabel(MessageManager
3319             .getString("action.make_groups_selection"));
3320     grpsFromSelection.addActionListener(this);
3321     createGroup.setLabel(MessageManager.getString("action.create_group"));
3322     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3323     annotationColumnSelection.setLabel(MessageManager
3324             .getString("action.select_by_annotation"));
3325     annotationColumnSelection.addActionListener(this);
3326
3327     /*
3328      * Configure View menu items and actions
3329      */
3330     newView.setLabel(MessageManager.getString("action.new_view"));
3331     newView.addActionListener(this);
3332     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3333     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3334     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3335     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3336     hideColumns
3337             .setLabel(MessageManager.getString("label.selected_columns"));
3338     hideSequences.setLabel(MessageManager
3339             .getString("label.selected_sequences"));
3340     hideAllButSelection.setLabel(MessageManager
3341             .getString("label.all_but_selected_region"));
3342     hideAllSelection.setLabel(MessageManager
3343             .getString("label.selected_region"));
3344     showAllHidden.setLabel(MessageManager
3345             .getString("label.all_sequences_columns"));
3346     showColumns.addActionListener(this);
3347     showSeqs.addActionListener(this);
3348     hideColumns.addActionListener(this);
3349     hideSequences.addActionListener(this);
3350     hideAllButSelection.addActionListener(this);
3351     hideAllSelection.addActionListener(this);
3352     showAllHidden.addActionListener(this);
3353     featureSettings.setLabel(MessageManager
3354             .getString("action.feature_settings"));
3355     featureSettings.addActionListener(this);
3356     sequenceFeatures.setLabel(MessageManager
3357             .getString("label.show_sequence_features"));
3358     sequenceFeatures.addItemListener(this);
3359     sequenceFeatures.setState(false);
3360     followMouseOverFlag.setLabel(MessageManager
3361             .getString("label.automatic_scrolling"));
3362     followMouseOverFlag.addItemListener(this);
3363     alProperties.addActionListener(this);
3364     overviewMenuItem.setLabel(MessageManager
3365             .getString("label.overview_window"));
3366     overviewMenuItem.addActionListener(this);
3367
3368     /*
3369      * Configure Annotations menu items and actions
3370      */
3371     annotationPanelMenuItem.setLabel(MessageManager
3372             .getString("label.show_annotations"));
3373     annotationPanelMenuItem.addItemListener(this);
3374     showGroupConsensus.setLabel(MessageManager
3375             .getString("label.group_consensus"));
3376     showGroupConservation.setLabel(MessageManager
3377             .getString("label.group_conservation"));
3378     showConsensusHistogram.setLabel(MessageManager
3379             .getString("label.show_consensus_histogram"));
3380     showSequenceLogo.setLabel(MessageManager
3381             .getString("label.show_consensus_logo"));
3382     normSequenceLogo.setLabel(MessageManager
3383             .getString("label.norm_consensus_logo"));
3384     applyAutoAnnotationSettings.setLabel(MessageManager
3385             .getString("label.apply_all_groups"));
3386     applyAutoAnnotationSettings.setState(true);
3387     Menu autoAnnMenu = new Menu(
3388             MessageManager.getString("label.autocalculated_annotation"));
3389     showGroupConsensus.addItemListener(this);
3390     showGroupConservation.addItemListener(this);
3391     showConsensusHistogram.addItemListener(this);
3392     showSequenceLogo.addItemListener(this);
3393     normSequenceLogo.addItemListener(this);
3394     applyAutoAnnotationSettings.addItemListener(this);
3395     showAlignmentAnnotations = new CheckboxMenuItem(
3396             MessageManager.getString("label.show_all_al_annotations"));
3397     showSequenceAnnotations = new CheckboxMenuItem(
3398             MessageManager.getString("label.show_all_seq_annotations"));
3399     sortAnnBySequence = new CheckboxMenuItem(
3400             MessageManager.getString("label.sort_annotations_by_sequence"));
3401     sortAnnByLabel = new CheckboxMenuItem(
3402             MessageManager.getString("label.sort_annotations_by_label"));
3403     showAutoFirst = new CheckboxMenuItem(
3404             MessageManager.getString("label.show_first"));
3405     showAutoFirst.setState(false); // pending applet parameter
3406     setShowAutoCalculatedAbove(showAutoFirst.getState());
3407     showAutoLast = new CheckboxMenuItem(
3408             MessageManager.getString("label.show_last"));
3409     showAutoLast.setState(!showAutoFirst.getState());
3410     showAlignmentAnnotations.addItemListener(this);
3411     showSequenceAnnotations.addItemListener(this);
3412     sortAnnBySequence.addItemListener(this);
3413     sortAnnByLabel.addItemListener(this);
3414     showAutoFirst.addItemListener(this);
3415     showAutoLast.addItemListener(this);
3416
3417     /*
3418      * Configure Format menu items and actions
3419      */
3420     font.setLabel(MessageManager.getString("action.font"));
3421     font.addActionListener(this);
3422     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3423     scaleAbove.setState(true);
3424     scaleAbove.setEnabled(false);
3425     scaleAbove.addItemListener(this);
3426     scaleLeft.setEnabled(false);
3427     scaleLeft.setState(true);
3428     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3429     scaleLeft.addItemListener(this);
3430     scaleRight.setEnabled(false);
3431     scaleRight.setState(true);
3432     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3433     scaleRight.addItemListener(this);
3434     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3435     viewBoxesMenuItem.setState(true);
3436     viewBoxesMenuItem.addItemListener(this);
3437     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3438     viewTextMenuItem.setState(true);
3439     viewTextMenuItem.addItemListener(this);
3440     colourTextMenuItem.setLabel(MessageManager
3441             .getString("label.colour_text"));
3442     colourTextMenuItem.addItemListener(this);
3443     displayNonconservedMenuItem.setLabel(MessageManager
3444             .getString("label.show_non_conserved"));
3445     displayNonconservedMenuItem.addItemListener(this);
3446     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3447     wrapMenuItem.addItemListener(this);
3448     renderGapsMenuItem.setLabel(MessageManager
3449             .getString("action.show_gaps"));
3450     renderGapsMenuItem.setState(true);
3451     renderGapsMenuItem.addItemListener(this);
3452     centreColumnLabelFlag.setLabel(MessageManager
3453             .getString("label.centre_column_labels"));
3454     centreColumnLabelFlag.addItemListener(this);
3455     seqLimits.setState(true);
3456     seqLimits.setLabel(MessageManager
3457             .getString("label.show_sequence_limits"));
3458     seqLimits.addItemListener(this);
3459
3460     /*
3461      * Configure Colour menu items and actions
3462      */
3463     applyToAllGroups.setLabel(MessageManager
3464             .getString("label.apply_colour_to_all_groups"));
3465     applyToAllGroups.setState(true);
3466     applyToAllGroups.addItemListener(this);
3467     clustalColour.setLabel(MessageManager
3468             .getString("label.colourScheme_clustal"));
3469     clustalColour.addActionListener(this);
3470     zappoColour.setLabel(MessageManager
3471             .getString("label.colourScheme_zappo"));
3472     zappoColour.addActionListener(this);
3473     taylorColour.setLabel(MessageManager
3474             .getString("label.colourScheme_taylor"));
3475     taylorColour.addActionListener(this);
3476     hydrophobicityColour.setLabel(MessageManager
3477             .getString("label.colourScheme_hydrophobic"));
3478     hydrophobicityColour.addActionListener(this);
3479     helixColour.setLabel(MessageManager
3480             .getString("label.colourScheme_helix_propensity"));
3481     helixColour.addActionListener(this);
3482     strandColour.setLabel(MessageManager
3483             .getString("label.colourScheme_strand_propensity"));
3484     strandColour.addActionListener(this);
3485     turnColour.setLabel(MessageManager
3486             .getString("label.colourScheme_turn_propensity"));
3487     turnColour.addActionListener(this);
3488     buriedColour.setLabel(MessageManager
3489             .getString("label.colourScheme_buried_index"));
3490     buriedColour.addActionListener(this);
3491     purinePyrimidineColour.setLabel(MessageManager
3492             .getString("label.colourScheme_purine/pyrimidine"));
3493     purinePyrimidineColour.addActionListener(this);
3494     // RNAInteractionColour.setLabel(MessageManager
3495     // .getString("label.rna_interaction"));
3496     // RNAInteractionColour.addActionListener(this);
3497     RNAHelixColour.setLabel(MessageManager
3498             .getString("label.colourScheme_rna_helices"));
3499     RNAHelixColour.addActionListener(this);
3500     userDefinedColour.setLabel(MessageManager
3501             .getString("action.user_defined"));
3502     userDefinedColour.addActionListener(this);
3503     PIDColour.setLabel(MessageManager
3504             .getString("label.colourScheme_%_identity"));
3505     PIDColour.addActionListener(this);
3506     BLOSUM62Colour.setLabel(MessageManager
3507             .getString("label.colourScheme_blosum62"));
3508     BLOSUM62Colour.addActionListener(this);
3509     tcoffeeColour.setLabel(MessageManager
3510             .getString("label.colourScheme_t-coffee_scores"));
3511     // it will be enabled only if a score file is provided
3512     tcoffeeColour.setEnabled(false);
3513     tcoffeeColour.addActionListener(this);
3514     conservationMenuItem.setLabel(MessageManager
3515             .getString("action.by_conservation"));
3516     conservationMenuItem.addItemListener(this);
3517     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3518     noColourmenuItem.addActionListener(this);
3519     abovePIDThreshold.setLabel(MessageManager
3520             .getString("label.above_identity_threshold"));
3521     abovePIDThreshold.addItemListener(this);
3522     nucleotideColour.setLabel(MessageManager
3523             .getString("label.colourScheme_nucleotide"));
3524     nucleotideColour.addActionListener(this);
3525     modifyPID.setLabel(MessageManager
3526             .getString("label.modify_identity_threshold"));
3527     modifyPID.addActionListener(this);
3528     modifyConservation.setLabel(MessageManager
3529             .getString("label.modify_conservation_threshold"));
3530     modifyConservation.addActionListener(this);
3531     annotationColour.setLabel(MessageManager
3532             .getString("action.by_annotation"));
3533     annotationColour.addActionListener(this);
3534
3535     /*
3536      * Configure Calculate menu items and actions
3537      */
3538     sortPairwiseMenuItem.setLabel(MessageManager
3539             .getString("action.by_pairwise_id"));
3540     sortPairwiseMenuItem.addActionListener(this);
3541     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3542     sortIDMenuItem.addActionListener(this);
3543     sortLengthMenuItem.setLabel(MessageManager
3544             .getString("action.by_length"));
3545     sortLengthMenuItem.addActionListener(this);
3546     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3547     sortGroupMenuItem.addActionListener(this);
3548     pairwiseAlignmentMenuItem.setLabel(MessageManager
3549             .getString("action.pairwise_alignment"));
3550     pairwiseAlignmentMenuItem.addActionListener(this);
3551     PCAMenuItem.setLabel(MessageManager
3552             .getString("label.principal_component_analysis"));
3553     PCAMenuItem.addActionListener(this);
3554     autoCalculate = new CheckboxMenuItem(
3555             MessageManager.getString("label.autocalculate_consensus"), true);
3556     averageDistanceTreeMenuItem.setLabel(MessageManager
3557             .getString("label.average_distance_identity"));
3558     averageDistanceTreeMenuItem.addActionListener(this);
3559     neighbourTreeMenuItem.setLabel(MessageManager
3560             .getString("label.neighbour_joining_identity"));
3561     neighbourTreeMenuItem.addActionListener(this);
3562     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3563             .getString("label.average_distance_blosum62"));
3564     avDistanceTreeBlosumMenuItem.addActionListener(this);
3565     njTreeBlosumMenuItem.setLabel(MessageManager
3566             .getString("label.neighbour_blosum62"));
3567     njTreeBlosumMenuItem.addActionListener(this);
3568     sortByTreeMenu.setLabel(MessageManager
3569             .getString("action.by_tree_order"));
3570     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3571     Menu calculateTreeMenu = new Menu(
3572             MessageManager.getString("action.calculate_tree"));
3573     autoCalculate.addItemListener(this);
3574     sortByTree.addItemListener(this);
3575
3576     /*
3577      * Configure Help menu items and actions
3578      */
3579     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3580     documentation.setLabel(MessageManager.getString("label.documentation"));
3581     documentation.addActionListener(this);
3582     about.setLabel(MessageManager.getString("label.about"));
3583     about.addActionListener(this);
3584
3585     /*
3586      * Add top level menus to frame
3587      */
3588     alignFrameMenuBar.add(fileMenu);
3589     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3590     alignFrameMenuBar.add(editMenu);
3591     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3592     alignFrameMenuBar.add(selectMenu);
3593     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3594     alignFrameMenuBar.add(viewMenu);
3595     Menu annotationsMenu = new Menu(
3596             MessageManager.getString("action.annotations"));
3597     alignFrameMenuBar.add(annotationsMenu);
3598     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3599     alignFrameMenuBar.add(formatMenu);
3600     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3601     alignFrameMenuBar.add(colourMenu);
3602     Menu calculateMenu = new Menu(
3603             MessageManager.getString("action.calculate"));
3604     alignFrameMenuBar.add(calculateMenu);
3605     alignFrameMenuBar.add(helpMenu);
3606
3607     /*
3608      * File menu
3609      */
3610     fileMenu.add(inputText);
3611     fileMenu.add(loadTree);
3612     fileMenu.add(loadAnnotations);
3613     fileMenu.addSeparator();
3614     fileMenu.add(outputTextboxMenu);
3615     fileMenu.add(outputFeatures);
3616     fileMenu.add(outputAnnotations);
3617     if (jalviewServletURL != null)
3618     {
3619       fileMenu.add(loadApplication);
3620     }
3621     fileMenu.addSeparator();
3622     fileMenu.add(closeMenuItem);
3623
3624     /*
3625      * Edit menu
3626      */
3627     editMenu.add(undoMenuItem);
3628     editMenu.add(redoMenuItem);
3629     editMenu.add(cut);
3630     editMenu.add(copy);
3631     pasteMenu.add(pasteNew);
3632     pasteMenu.add(pasteThis);
3633     editMenu.add(pasteMenu);
3634     editMenu.add(delete);
3635     editMenu.addSeparator();
3636     editMenu.add(remove2LeftMenuItem);
3637     editMenu.add(remove2RightMenuItem);
3638     editMenu.add(removeGappedColumnMenuItem);
3639     editMenu.add(removeAllGapsMenuItem);
3640     editMenu.add(removeRedundancyMenuItem);
3641
3642     /*
3643      * Select menu
3644      */
3645     selectMenu.add(findMenuItem);
3646     selectMenu.addSeparator();
3647     selectMenu.add(selectAllSequenceMenuItem);
3648     selectMenu.add(deselectAllSequenceMenuItem);
3649     selectMenu.add(invertSequenceMenuItem);
3650     selectMenu.add(invertColSel);
3651     selectMenu.add(createGroup);
3652     selectMenu.add(unGroup);
3653     selectMenu.add(grpsFromSelection);
3654     selectMenu.add(deleteGroups);
3655     selectMenu.add(annotationColumnSelection);
3656
3657     /*
3658      * View menu
3659      */
3660     viewMenu.add(newView);
3661     viewMenu.addSeparator();
3662     showMenu.add(showColumns);
3663     showMenu.add(showSeqs);
3664     showMenu.add(showAllHidden);
3665     viewMenu.add(showMenu);
3666     hideMenu.add(hideColumns);
3667     hideMenu.add(hideSequences);
3668     hideMenu.add(hideAllSelection);
3669     hideMenu.add(hideAllButSelection);
3670     viewMenu.add(hideMenu);
3671     viewMenu.addSeparator();
3672     viewMenu.add(followMouseOverFlag);
3673     viewMenu.addSeparator();
3674     viewMenu.add(sequenceFeatures);
3675     viewMenu.add(featureSettings);
3676     viewMenu.addSeparator();
3677     viewMenu.add(alProperties);
3678     viewMenu.addSeparator();
3679     viewMenu.add(overviewMenuItem);
3680
3681     /*
3682      * Annotations menu
3683      */
3684     annotationsMenu.add(annotationPanelMenuItem);
3685     annotationsMenu.addSeparator();
3686     annotationsMenu.add(showAlignmentAnnotations);
3687     annotationsMenu.add(showSequenceAnnotations);
3688     annotationsMenu.add(sortAnnBySequence);
3689     annotationsMenu.add(sortAnnByLabel);
3690     annotationsMenu.addSeparator();
3691     autoAnnMenu.add(showAutoFirst);
3692     autoAnnMenu.add(showAutoLast);
3693     autoAnnMenu.addSeparator();
3694     autoAnnMenu.add(applyAutoAnnotationSettings);
3695     autoAnnMenu.add(showConsensusHistogram);
3696     autoAnnMenu.add(showSequenceLogo);
3697     autoAnnMenu.add(normSequenceLogo);
3698     autoAnnMenu.addSeparator();
3699     autoAnnMenu.add(showGroupConservation);
3700     autoAnnMenu.add(showGroupConsensus);
3701     annotationsMenu.add(autoAnnMenu);
3702
3703     /*
3704      * Format menu
3705      */
3706     formatMenu.add(font);
3707     formatMenu.add(seqLimits);
3708     formatMenu.add(wrapMenuItem);
3709     formatMenu.add(scaleAbove);
3710     formatMenu.add(scaleLeft);
3711     formatMenu.add(scaleRight);
3712     formatMenu.add(viewBoxesMenuItem);
3713     formatMenu.add(viewTextMenuItem);
3714     formatMenu.add(colourTextMenuItem);
3715     formatMenu.add(displayNonconservedMenuItem);
3716     formatMenu.add(renderGapsMenuItem);
3717     formatMenu.add(centreColumnLabelFlag);
3718
3719     /*
3720      * Colour menu
3721      */
3722     colourMenu.add(applyToAllGroups);
3723     colourMenu.addSeparator();
3724     colourMenu.add(noColourmenuItem);
3725     colourMenu.add(clustalColour);
3726     colourMenu.add(BLOSUM62Colour);
3727     colourMenu.add(PIDColour);
3728     colourMenu.add(zappoColour);
3729     colourMenu.add(taylorColour);
3730     colourMenu.add(hydrophobicityColour);
3731     colourMenu.add(helixColour);
3732     colourMenu.add(strandColour);
3733     colourMenu.add(turnColour);
3734     colourMenu.add(buriedColour);
3735     colourMenu.add(nucleotideColour);
3736     colourMenu.add(purinePyrimidineColour);
3737     // colourMenu.add(RNAInteractionColour);
3738     colourMenu.add(tcoffeeColour);
3739     colourMenu.add(userDefinedColour);
3740     colourMenu.addSeparator();
3741     colourMenu.add(conservationMenuItem);
3742     colourMenu.add(modifyConservation);
3743     colourMenu.add(abovePIDThreshold);
3744     colourMenu.add(modifyPID);
3745     colourMenu.add(annotationColour);
3746     colourMenu.add(RNAHelixColour);
3747
3748     /*
3749      * Calculate menu
3750      */
3751     sortMenu.add(sortIDMenuItem);
3752     sortMenu.add(sortLengthMenuItem);
3753     sortMenu.add(sortByTreeMenu);
3754     sortMenu.add(sortGroupMenuItem);
3755     sortMenu.add(sortPairwiseMenuItem);
3756     calculateMenu.add(sortMenu);
3757     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3758     calculateTreeMenu.add(neighbourTreeMenuItem);
3759     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3760     calculateTreeMenu.add(njTreeBlosumMenuItem);
3761     calculateMenu.add(calculateTreeMenu);
3762     calculateMenu.addSeparator();
3763     calculateMenu.add(pairwiseAlignmentMenuItem);
3764     calculateMenu.add(PCAMenuItem);
3765     calculateMenu.add(autoCalculate);
3766     calculateMenu.add(sortByTree);
3767
3768     /*
3769      * Help menu
3770      */
3771     helpMenu.add(documentation);
3772     helpMenu.add(about);
3773
3774     /*
3775      * Status bar
3776      */
3777     statusBar.setBackground(Color.white);
3778     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3779     statusBar.setText(MessageManager.getString("label.status_bar"));
3780     this.add(statusBar, BorderLayout.SOUTH);
3781   }
3782
3783   @Override
3784   public void setStatus(String string)
3785   {
3786     statusBar.setText(string);
3787   };
3788
3789   MenuItem featureSettings = new MenuItem();
3790
3791   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3792
3793   MenuItem annotationColour = new MenuItem();
3794
3795   MenuItem annotationColumnSelection = new MenuItem();
3796
3797   MenuItem invertColSel = new MenuItem();
3798
3799   MenuItem showColumns = new MenuItem();
3800
3801   MenuItem showSeqs = new MenuItem();
3802
3803   MenuItem hideColumns = new MenuItem();
3804
3805   MenuItem hideSequences = new MenuItem();
3806
3807   MenuItem hideAllButSelection = new MenuItem();
3808
3809   MenuItem hideAllSelection = new MenuItem();
3810
3811   MenuItem showAllHidden = new MenuItem();
3812
3813   MenuItem newView = new MenuItem();
3814
3815   private CheckboxMenuItem showAlignmentAnnotations;
3816
3817   private CheckboxMenuItem showSequenceAnnotations;
3818
3819   private CheckboxMenuItem sortAnnBySequence;
3820
3821   private CheckboxMenuItem sortAnnByLabel;
3822
3823   private CheckboxMenuItem showAutoFirst;
3824
3825   private CheckboxMenuItem showAutoLast;
3826
3827   private SplitFrame splitFrame;
3828
3829   /**
3830    * Attach the alignFrame panels after embedding menus, if necessary. This used
3831    * to be called setEmbedded, but is now creates the dropdown menus in a
3832    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3833    *
3834    * @param reallyEmbedded
3835    *          true to attach the view to the applet area on the page rather than
3836    *          in a new window
3837    */
3838   public void createAlignFrameWindow(boolean reallyEmbedded)
3839   {
3840     if (reallyEmbedded)
3841     {
3842       embedAlignFrameInApplet(viewport.applet);
3843     }
3844     else
3845     {
3846       // //////
3847       // test and embed menu bar if necessary.
3848       //
3849       if (embedMenuIfNeeded(alignPanel))
3850       {
3851         /*
3852          * adjust for status bar height too. ? pointless as overridden by layout
3853          * manager
3854          */
3855         alignPanel.setSize(getSize().width,
3856                 getSize().height - statusBar.getHeight());
3857       }
3858       add(statusBar, BorderLayout.SOUTH);
3859       add(alignPanel, BorderLayout.CENTER);
3860       // and register with the applet so it can pass external API calls to us
3861       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3862               frameHeight);
3863     }
3864   }
3865
3866   /**
3867    * Add the components of this AlignFrame to the applet container.
3868    *
3869    * @param theApplet
3870    */
3871   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3872   {
3873     // ////
3874     // Explicitly build the embedded menu panel for the on-page applet
3875     //
3876     // view cannot be closed if its actually on the page
3877     fileMenu.remove(closeMenuItem);
3878     fileMenu.remove(3); // Remove Separator
3879     // construct embedded menu, using default font
3880     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3881     // and actually add the components to the applet area
3882     theApplet.setLayout(new BorderLayout());
3883     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3884     theApplet.add(statusBar, BorderLayout.SOUTH);
3885     // TODO should size be left to the layout manager?
3886     alignPanel.setSize(theApplet.getSize().width,
3887             theApplet.getSize().height - embeddedMenu.getHeight()
3888                     - statusBar.getHeight());
3889     theApplet.add(alignPanel, BorderLayout.CENTER);
3890     final AlignFrame me = this;
3891     theApplet.addFocusListener(new FocusListener()
3892     {
3893
3894       @Override
3895       public void focusLost(FocusEvent e)
3896       {
3897         if (theApplet.currentAlignFrame == me)
3898         {
3899           theApplet.currentAlignFrame = null;
3900         }
3901       }
3902
3903       @Override
3904       public void focusGained(FocusEvent e)
3905       {
3906         theApplet.currentAlignFrame = me;
3907       }
3908     });
3909     theApplet.validate();
3910   }
3911
3912   /**
3913    * create a new binding between structures in an existing jmol viewer instance
3914    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3915    * this does not open a new Jmol window, or modify the display of the
3916    * structures in the original jmol window. Note This method doesn't work
3917    * without an additional javascript library to exchange messages between the
3918    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3919    *
3920    * @param viewer
3921    *          JmolViewer instance
3922    * @param sequenceIds
3923    *          - sequence Ids to search for associations
3924    */
3925   public SequenceStructureBinding addStructureViewInstance(
3926           Object jmolviewer, String[] sequenceIds)
3927   {
3928     Viewer viewer = null;
3929     try
3930     {
3931       viewer = (Viewer) jmolviewer;
3932     } catch (ClassCastException ex)
3933     {
3934       System.err.println("Unsupported viewer object :"
3935               + jmolviewer.getClass());
3936     }
3937     if (viewer == null)
3938     {
3939       System.err.println("Can't use this object as a structure viewer:"
3940               + jmolviewer.getClass());
3941       return null;
3942     }
3943     SequenceI[] seqs = null;
3944     if (sequenceIds == null || sequenceIds.length == 0)
3945     {
3946       seqs = viewport.getAlignment().getSequencesArray();
3947     }
3948     else
3949     {
3950       Vector sqi = new Vector();
3951       AlignmentI al = viewport.getAlignment();
3952       for (int sid = 0; sid < sequenceIds.length; sid++)
3953       {
3954         SequenceI sq = al.findName(sequenceIds[sid]);
3955         if (sq != null)
3956         {
3957           sqi.addElement(sq);
3958         }
3959       }
3960       if (sqi.size() > 0)
3961       {
3962         seqs = new SequenceI[sqi.size()];
3963         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3964         {
3965           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3966         }
3967       }
3968       else
3969       {
3970         return null;
3971       }
3972     }
3973     AAStructureBindingModel jmv = null;
3974     // TODO: search for a jmv that involves viewer
3975     if (jmv == null)
3976     { // create a new viewer/jalview binding.
3977       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3978     }
3979     return jmv;
3980
3981   }
3982
3983   /**
3984    * bind a pdb file to a sequence in the current view
3985    *
3986    * @param sequenceId
3987    *          - sequenceId within the dataset.
3988    * @param pdbEntryString
3989    *          - the short name for the PDB file
3990    * @param pdbFile
3991    *          - pdb file - either a URL or a valid PDB file.
3992    * @return true if binding was as success TODO: consider making an exception
3993    *         structure for indicating when PDB parsing or sequenceId location
3994    *         fails.
3995    */
3996   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3997           String pdbFile)
3998   {
3999     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4000     boolean needtoadd = false;
4001     if (toaddpdb != null)
4002     {
4003       Vector pdbe = toaddpdb.getAllPDBEntries();
4004       PDBEntry pdbentry = null;
4005       if (pdbe != null && pdbe.size() > 0)
4006       {
4007         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4008         {
4009           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4010           if (!pdbentry.getId().equals(pdbEntryString)
4011                   && !pdbentry.getFile().equals(pdbFile))
4012           {
4013             pdbentry = null;
4014           }
4015           else
4016           {
4017             continue;
4018           }
4019         }
4020       }
4021       if (pdbentry == null)
4022       {
4023         pdbentry = new PDBEntry();
4024         pdbentry.setId(pdbEntryString);
4025         pdbentry.setFile(pdbFile);
4026         needtoadd = true; // add this new entry to sequence.
4027       }
4028       // resolve data source
4029       // TODO: this code should be a refactored to an io package
4030       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4031               pdbFile, FileFormat.PDB);
4032       if (protocol == null)
4033       {
4034         return false;
4035       }
4036       if (needtoadd)
4037       {
4038         pdbentry.setProperty("protocol", protocol);
4039         toaddpdb.addPDBId(pdbentry);
4040         alignPanel.getStructureSelectionManager()
4041                 .registerPDBEntry(pdbentry);
4042       }
4043     }
4044     return true;
4045   }
4046
4047   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4048   {
4049     if (seqs != null)
4050     {
4051       Vector sequences = new Vector();
4052       for (int i = 0; i < seqs.length; i++)
4053       {
4054         if (seqs[i] != null)
4055         {
4056           sequences.addElement(new Object[] { seqs[i],
4057               (chains != null) ? chains[i] : null });
4058         }
4059       }
4060       seqs = new SequenceI[sequences.size()];
4061       chains = new String[sequences.size()];
4062       for (int i = 0, isize = sequences.size(); i < isize; i++)
4063       {
4064         Object[] oj = (Object[]) sequences.elementAt(i);
4065
4066         seqs[i] = (SequenceI) oj[0];
4067         chains[i] = (String) oj[1];
4068       }
4069     }
4070     return new Object[] { seqs, chains };
4071
4072   }
4073
4074   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4075           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4076   {
4077     // Scrub any null sequences from the array
4078     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4079     seqs = (SequenceI[]) sqch[0];
4080     chains = (String[]) sqch[1];
4081     if (seqs == null || seqs.length == 0)
4082     {
4083       System.err
4084               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4085     }
4086     if (protocol == null)
4087     {
4088       String sourceType = (String) pdb.getProperty("protocol");
4089       try
4090       {
4091         protocol = DataSourceType.valueOf(sourceType);
4092       } catch (IllegalArgumentException e)
4093       {
4094         // ignore
4095       }
4096       if (protocol == null)
4097       {
4098         System.err.println("Couldn't work out protocol to open structure: "
4099                 + pdb.getId());
4100         return;
4101       }
4102     }
4103     if (applet.useXtrnalSviewer)
4104     {
4105       // register the association(s) and quit, don't create any windows.
4106       if (StructureSelectionManager.getStructureSelectionManager(applet)
4107               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4108       {
4109         System.err.println("Failed to map " + pdb.getFile() + " ("
4110                 + protocol + ") to any sequences");
4111       }
4112       return;
4113     }
4114     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4115     {
4116       // can only do alignments with Jmol
4117       // find the last jmol window assigned to this alignment
4118       AppletJmol ajm = null, tajm;
4119       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4120       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4121       {
4122         tajm = (AppletJmol) jmols.elementAt(i);
4123         if (tajm.ap.alignFrame == this)
4124         {
4125           ajm = tajm;
4126           break;
4127         }
4128       }
4129       if (ajm != null)
4130       {
4131         System.err
4132                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4133         // try and add the pdb structure
4134         // ajm.addS
4135         ajm = null;
4136       }
4137     }
4138     // otherwise, create a new window
4139     if (applet.jmolAvailable)
4140     {
4141       new AppletJmol(pdb, seqs, chains, alignPanel,
4142               protocol);
4143       applet.lastFrameX += 40;
4144       applet.lastFrameY += 40;
4145     }
4146     else
4147     {
4148       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4149     }
4150
4151   }
4152
4153   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4154           SequenceI[][] seqs, String[][] chains, String[] protocols)
4155   {
4156     // TODO Auto-generated method stub
4157     System.err.println("Aligned Structure View: Not yet implemented.");
4158   }
4159
4160   /**
4161    * modify the current selection, providing the user has not made a selection
4162    * already.
4163    *
4164    * @param sel
4165    *          - sequences from this alignment
4166    * @param csel
4167    *          - columns to be selected on the alignment
4168    */
4169   public void select(SequenceGroup sel, ColumnSelection csel)
4170   {
4171     alignPanel.seqPanel.selection(sel, csel, null);
4172   }
4173
4174   public void scrollTo(int row, int column)
4175   {
4176     alignPanel.seqPanel.scrollTo(row, column);
4177   }
4178
4179   public void scrollToRow(int row)
4180   {
4181     alignPanel.seqPanel.scrollToRow(row);
4182   }
4183
4184   public void scrollToColumn(int column)
4185   {
4186     alignPanel.seqPanel.scrollToColumn(column);
4187   }
4188
4189   /**
4190    * @return the alignments unique ID.
4191    */
4192   public String getSequenceSetId()
4193   {
4194     return viewport.getSequenceSetId();
4195   }
4196
4197   /**
4198    * Load the (T-Coffee) score file from the specified url
4199    *
4200    * @param source
4201    *          File/URL/T-COFFEE score file contents
4202    * @throws IOException
4203    * @return true if alignment was annotated with data from source
4204    */
4205   public boolean loadScoreFile(String source) throws IOException
4206   {
4207
4208     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4209             AppletFormatAdapter.checkProtocol(source));
4210     if (!file.isValid())
4211     {
4212       // TODO: raise dialog for gui
4213       System.err.println("Problems parsing T-Coffee scores: "
4214               + file.getWarningMessage());
4215       System.err.println("Origin was:\n" + source);
4216       return false;
4217     }
4218
4219     /*
4220      * check that the score matrix matches the alignment dimensions
4221      */
4222     AlignmentI aln;
4223     if ((aln = viewport.getAlignment()) != null
4224             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4225                     .getWidth()))
4226     {
4227       // TODO: raise a dialog box here rather than bomb out.
4228       System.err
4229               .println("The scores matrix does not match the alignment dimensions");
4230
4231     }
4232
4233     // TODO add parameter to indicate if matching should be done
4234     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4235     {
4236       alignPanel.fontChanged();
4237       tcoffeeColour.setEnabled(true);
4238       // switch to this color
4239       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4240       return true;
4241     }
4242     else
4243     {
4244       System.err.println("Problems resolving T-Coffee scores:");
4245       if (file.getWarningMessage() != null)
4246       {
4247         System.err.println(file.getWarningMessage());
4248       }
4249     }
4250     return false;
4251   }
4252
4253   public SplitFrame getSplitFrame()
4254   {
4255     return this.splitFrame;
4256   }
4257
4258   public void setSplitFrame(SplitFrame sf)
4259   {
4260     this.splitFrame = sf;
4261   }
4262
4263   // may not need this
4264   @Override
4265   public void setShowSeqFeatures(boolean b)
4266   {
4267     // showSeqFeatures.setSelected(b);
4268     viewport.setShowSequenceFeatures(b);
4269
4270   }
4271
4272   @Override
4273   public void setMenusForViewport()
4274   {
4275     // setMenusFromViewport(viewport);
4276
4277   }
4278
4279   @Override
4280   public void refreshFeatureUI(boolean enableIfNecessary)
4281   {
4282     if (enableIfNecessary)
4283     {
4284       sequenceFeatures.setState(true);
4285       alignPanel.av.setShowSequenceFeatures(true);
4286     }
4287   }
4288
4289   @Override
4290   public FeatureSettingsControllerI getFeatureSettingsUI()
4291   {
4292     return alignPanel.av.featureSettings;
4293   }
4294
4295 }