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.analysis.TreeBuilder;
  26 import jalview.analysis.scoremodels.PIDModel;
  27 import jalview.analysis.scoremodels.ScoreModels;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.FeatureColourI;
  32 import jalview.api.FeatureRenderer;
  33 import jalview.api.FeatureSettingsControllerI;
  34 import jalview.api.SequenceStructureBinding;
  35 import jalview.bin.JalviewLite;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentAnnotation;
  46 import jalview.datamodel.AlignmentI;
  47 import jalview.datamodel.AlignmentOrder;
  48 import jalview.datamodel.ColumnSelection;
  49 import jalview.datamodel.HiddenColumns;
  50 import jalview.datamodel.PDBEntry;
  51 import jalview.datamodel.Sequence;
  52 import jalview.datamodel.SequenceGroup;
  53 import jalview.datamodel.SequenceI;
  54 import jalview.io.AnnotationFile;
  55 import jalview.io.AppletFormatAdapter;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FeaturesFile;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileFormatI;
  60 import jalview.io.FileFormats;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColour;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.ZappoColourScheme;
  77 import jalview.structure.StructureSelectionManager;
  78 import jalview.structures.models.AAStructureBindingModel;
  79 import jalview.util.MappingUtils;
  80 import jalview.util.MessageManager;
  81 import jalview.viewmodel.AlignmentViewport;
  82 import jalview.viewmodel.ViewportRanges;
  83
  84 import java.awt.BorderLayout;
  85 import java.awt.Canvas;
  86 import java.awt.CheckboxMenuItem;
  87 import java.awt.Color;
  88 import java.awt.FlowLayout;
  89 import java.awt.Font;
  90 import java.awt.FontMetrics;
  91 import java.awt.Frame;
  92 import java.awt.Graphics;
  93 import java.awt.Label;
  94 import java.awt.Menu;
  95 import java.awt.MenuBar;
  96 import java.awt.MenuItem;
  97 import java.awt.Panel;
  98 import java.awt.event.ActionEvent;
  99 import java.awt.event.ActionListener;
 100 import java.awt.event.FocusEvent;
 101 import java.awt.event.FocusListener;
 102 import java.awt.event.ItemEvent;
 103 import java.awt.event.ItemListener;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.KeyListener;
 106 import java.awt.event.WindowAdapter;
 107 import java.awt.event.WindowEvent;
 108 import java.io.IOException;
 109 import java.io.UnsupportedEncodingException;
 110 import java.net.URL;
 111 import java.net.URLEncoder;
 112 import java.util.Arrays;
 113 import java.util.Deque;
 114 import java.util.HashMap;
 115 import java.util.List;
 116 import java.util.Map;
 117 import java.util.StringTokenizer;
 118 import java.util.Vector;
 119
 120 import org.jmol.viewer.Viewer;
 121
 122 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 123         ItemListener, KeyListener, AlignViewControllerGuiI
 124 {
 125   public AlignViewControllerI avc;
 126
 127   public AlignmentPanel alignPanel;
 128
 129   public AlignViewport viewport;
 130
 131   // width and height may be overridden by applet parameters
 132   int frameWidth = 700;
 133
 134   int frameHeight = 500;
 135
 136   String jalviewServletURL;
 137
 138   /*
 139    * Flag for showing autocalculated consensus above or below other consensus
 140    * rows
 141    */
 142   private boolean showAutoCalculatedAbove;
 143
 144   private SequenceAnnotationOrder annotationSortOrder;
 145
 146   /**
 147    * Constructor that creates the frame and adds it to the display.
 148    *
 149    * @param al
 150    * @param applet
 151    * @param title
 152    * @param embedded
 153    */
 154   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 155           boolean embedded)
 156   {
 157     this(al, applet, title, embedded, true);
 158   }
 159
 160   /**
 161    * Constructor that optionally allows the frame to be displayed or only
 162    * created.
 163    *
 164    * @param al
 165    * @param applet
 166    * @param title
 167    * @param embedded
 168    * @param addToDisplay
 169    */
 170   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 171           boolean embedded, boolean addToDisplay)
 172   {
 173     this(al, null, null, applet, title, embedded, addToDisplay);
 174   }
 175
 176   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 177           HiddenColumns hidden, JalviewLite applet, String title,
 178           boolean embedded)
 179   {
 180     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 181   }
 182
 183   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 184           HiddenColumns hidden, JalviewLite applet, String title,
 185           boolean embedded, boolean addToDisplay)
 186   {
 187     if (applet != null)
 188     {
 189       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 190     }
 191
 192     try
 193     {
 194       jbInit();
 195     } catch (Exception ex)
 196     {
 197       ex.printStackTrace();
 198     }
 199     // need to get window geometry before we calculate alignment layout
 200     if (applet != null)
 201     {
 202       String param;
 203       try
 204       {
 205         param = applet.getParameter("windowWidth");
 206         if (param != null)
 207         {
 208           int width = Integer.parseInt(param);
 209           frameWidth = width;
 210         }
 211         param = applet.getParameter("windowHeight");
 212         if (param != null)
 213         {
 214           int height = Integer.parseInt(param);
 215           frameHeight = height;
 216         }
 217       } catch (Exception ex)
 218       {
 219       }
 220     }
 221     viewport = new AlignViewport(al, applet);
 222
 223     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 224     {
 225       viewport.hideSequence(hiddenSeqs);
 226     }
 227     if (hidden != null)
 228     {
 229       viewport.getAlignment().setHiddenColumns(hidden);
 230     }
 231     viewport.setScaleAboveWrapped(scaleAbove.getState());
 232
 233     alignPanel = new AlignmentPanel(this, viewport);
 234     avc = new jalview.controller.AlignViewController(this, viewport,
 235             alignPanel);
 236     viewport.updateConservation(alignPanel);
 237     viewport.updateConsensus(alignPanel);
 238
 239     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 240     followMouseOverFlag.setState(viewport.isFollowHighlight());
 241     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 242     showGroupConservation.setState(viewport.isShowGroupConservation());
 243     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 244     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 245     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 246     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 247     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 248     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 250     showAlignmentAnnotations.setState(true);
 251     showSequenceAnnotations.setState(false);
 252
 253     seqLimits.setState(viewport.getShowJVSuffix());
 254
 255     if (applet != null)
 256     {
 257       String param = applet.getParameter("sortBy");
 258       if (param != null)
 259       {
 260         if (param.equalsIgnoreCase("Id"))
 261         {
 262           sortIDMenuItem_actionPerformed();
 263         }
 264         else if (param.equalsIgnoreCase("Pairwise Identity"))
 265         {
 266           sortPairwiseMenuItem_actionPerformed();
 267         }
 268         else if (param.equalsIgnoreCase("Length"))
 269         {
 270           sortLengthMenuItem_actionPerformed();
 271         }
 272       }
 273
 274       param = applet.getParameter("wrap");
 275       if (param != null)
 276       {
 277         if (param.equalsIgnoreCase("true"))
 278         {
 279           wrapMenuItem.setState(true);
 280           wrapMenuItem_actionPerformed();
 281         }
 282       }
 283       param = applet.getParameter("centrecolumnlabels");
 284       if (param != null)
 285       {
 286         centreColumnLabelFlag.setState(true);
 287         centreColumnLabelFlag_stateChanged();
 288       }
 289
 290     }
 291     if (viewport.getAlignment().isNucleotide())
 292     {
 293       conservationMenuItem.setEnabled(false);
 294       clustalColour.setEnabled(false);
 295       BLOSUM62Colour.setEnabled(false);
 296       zappoColour.setEnabled(false);
 297       taylorColour.setEnabled(false);
 298       hydrophobicityColour.setEnabled(false);
 299       helixColour.setEnabled(false);
 300       strandColour.setEnabled(false);
 301       turnColour.setEnabled(false);
 302       buriedColour.setEnabled(false);
 303       viewport.updateStrucConsensus(alignPanel);
 304       if (viewport.getAlignment().hasRNAStructure())
 305       {
 306         RNAHelixColour.setEnabled(true);
 307       }
 308       else
 309       {
 310         RNAHelixColour.setEnabled(false);
 311       }
 312     }
 313     else
 314     {
 315       RNAHelixColour.setEnabled(false);
 316       purinePyrimidineColour.setEnabled(false);
 317       nucleotideColour.setEnabled(false);
 318     }
 319     // Some JVMS send keyevents to Top frame or lowest panel,
 320     // Havent worked out why yet. So add to both this frame and seqCanvas for
 321     // now
 322     this.addKeyListener(this);
 323     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 324     alignPanel.idPanel.idCanvas.addKeyListener(this);
 325     alignPanel.scalePanel.addKeyListener(this);
 326     alignPanel.annotationPanel.addKeyListener(this);
 327     alignPanel.annotationPanelHolder.addKeyListener(this);
 328     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 329     alignPanel.alabels.addKeyListener(this);
 330
 331     setAnnotationsVisibility();
 332
 333     if (addToDisplay)
 334     {
 335       addToDisplay(embedded);
 336     }
 337   }
 338
 339   /**
 340    * @param embedded
 341    */
 342   public void addToDisplay(boolean embedded)
 343   {
 344     createAlignFrameWindow(embedded);
 345     validate();
 346     alignPanel.adjustAnnotationHeight();
 347     alignPanel.paintAlignment(true, true);
 348   }
 349
 350   public AlignViewport getAlignViewport()
 351   {
 352     return viewport;
 353   }
 354
 355   public SeqCanvas getSeqcanvas()
 356   {
 357     return alignPanel.seqPanel.seqCanvas;
 358   }
 359
 360   /**
 361    * Load a features file onto the alignment
 362    *
 363    * @param file
 364    *          file URL, content, or other resolvable path
 365    * @param type
 366    *          is protocol for accessing data referred to by file
 367    */
 368
 369   public boolean parseFeaturesFile(String file, DataSourceType type)
 370   {
 371     return parseFeaturesFile(file, type, true);
 372   }
 373
 374   /**
 375    * Load a features file onto the alignment
 376    *
 377    * @param file
 378    *          file URL, content, or other resolvable path
 379    * @param sourceType
 380    *          is protocol for accessing data referred to by file
 381    * @param autoenabledisplay
 382    *          when true, display features flag will be automatically enabled if
 383    *          features are loaded
 384    * @return true if data parsed as a features file
 385    */
 386   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 387           boolean autoenabledisplay)
 388   {
 389     boolean featuresFile = false;
 390     try
 391     {
 392       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 393               .getFeatureRenderer().getFeatureColours();
 394       boolean relaxedIdMatching = viewport.applet
 395               .getDefaultParameter("relaxedidmatch", false);
 396       featuresFile = new FeaturesFile(file, sourceType).parse(
 397               viewport.getAlignment(), colours, true, relaxedIdMatching);
 398     } catch (Exception ex)
 399     {
 400       ex.printStackTrace();
 401     }
 402
 403     if (featuresFile)
 404     {
 405       if (autoenabledisplay)
 406       {
 407         viewport.setShowSequenceFeatures(true);
 408         sequenceFeatures.setState(true);
 409       }
 410       if (alignPanel.seqPanel.seqCanvas.fr != null)
 411       {
 412         // update the min/max ranges where necessary
 413         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 414       }
 415       if (viewport.featureSettings != null)
 416       {
 417         viewport.featureSettings.refreshTable();
 418       }
 419       alignPanel.paintAlignment(true, true);
 420       statusBar.setText(MessageManager
 421               .getString("label.successfully_added_features_alignment"));
 422     }
 423     return featuresFile;
 424   }
 425
 426   @Override
 427   public void keyPressed(KeyEvent evt)
 428   {
 429     ViewportRanges ranges = viewport.getRanges();
 430
 431     if (viewport.cursorMode
 432             && ((evt.getKeyCode() >= KeyEvent.VK_0
 433                     && evt.getKeyCode() <= KeyEvent.VK_9)
 434                     || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 435                             && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 436             && Character.isDigit(evt.getKeyChar()))
 437     {
 438       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 439     }
 440
 441     switch (evt.getKeyCode())
 442     {
 443     case 27: // escape key
 444       deselectAllSequenceMenuItem_actionPerformed();
 445
 446       alignPanel.alabels.cancelDrag();
 447       break;
 448     case KeyEvent.VK_X:
 449       if (evt.isControlDown() || evt.isMetaDown())
 450       {
 451         cut_actionPerformed();
 452       }
 453       break;
 454     case KeyEvent.VK_C:
 455       if (viewport.cursorMode && !evt.isControlDown())
 456       {
 457         alignPanel.seqPanel.setCursorColumn();
 458       }
 459       if (evt.isControlDown() || evt.isMetaDown())
 460       {
 461         copy_actionPerformed();
 462       }
 463       break;
 464     case KeyEvent.VK_V:
 465       if (evt.isControlDown())
 466       {
 467         paste(evt.isShiftDown());
 468       }
 469       break;
 470     case KeyEvent.VK_A:
 471       if (evt.isControlDown() || evt.isMetaDown())
 472       {
 473         selectAllSequenceMenuItem_actionPerformed();
 474       }
 475       break;
 476     case KeyEvent.VK_DOWN:
 477       if (viewport.cursorMode)
 478       {
 479         alignPanel.seqPanel.moveCursor(0, 1);
 480       }
 481       else
 482       {
 483         moveSelectedSequences(false);
 484       }
 485       break;
 486
 487     case KeyEvent.VK_UP:
 488       if (viewport.cursorMode)
 489       {
 490         alignPanel.seqPanel.moveCursor(0, -1);
 491       }
 492       else
 493       {
 494         moveSelectedSequences(true);
 495       }
 496       break;
 497
 498     case KeyEvent.VK_LEFT:
 499       if (evt.isAltDown() || !viewport.cursorMode)
 500       {
 501         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 502       }
 503       else
 504       {
 505         alignPanel.seqPanel.moveCursor(-1, 0);
 506       }
 507       break;
 508
 509     case KeyEvent.VK_RIGHT:
 510       if (evt.isAltDown() || !viewport.cursorMode)
 511       {
 512         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 513       }
 514       else
 515       {
 516         alignPanel.seqPanel.moveCursor(1, 0);
 517       }
 518       break;
 519
 520     case KeyEvent.VK_SPACE:
 521       if (viewport.cursorMode)
 522       {
 523         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 524                 || evt.isShiftDown() || evt.isAltDown());
 525       }
 526       break;
 527
 528     case KeyEvent.VK_DELETE:
 529     case KeyEvent.VK_BACK_SPACE:
 530       if (viewport.cursorMode)
 531       {
 532         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 533                 || evt.isShiftDown() || evt.isAltDown());
 534       }
 535       else
 536       {
 537         cut_actionPerformed();
 538         alignPanel.seqPanel.seqCanvas.repaint();
 539       }
 540       break;
 541
 542     case KeyEvent.VK_S:
 543       if (viewport.cursorMode)
 544       {
 545         alignPanel.seqPanel.setCursorRow();
 546       }
 547       break;
 548     case KeyEvent.VK_P:
 549       if (viewport.cursorMode)
 550       {
 551         alignPanel.seqPanel.setCursorPosition();
 552       }
 553       break;
 554
 555     case KeyEvent.VK_ENTER:
 556     case KeyEvent.VK_COMMA:
 557       if (viewport.cursorMode)
 558       {
 559         alignPanel.seqPanel.setCursorRowAndColumn();
 560       }
 561       break;
 562
 563     case KeyEvent.VK_Q:
 564       if (viewport.cursorMode)
 565       {
 566         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 567       }
 568       break;
 569     case KeyEvent.VK_M:
 570       if (viewport.cursorMode)
 571       {
 572         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 573       }
 574       break;
 575
 576     case KeyEvent.VK_F2:
 577       viewport.cursorMode = !viewport.cursorMode;
 578       statusBar.setText(MessageManager
 579               .formatMessage("label.keyboard_editing_mode", new String[]
 580               { (viewport.cursorMode ? "on" : "off") }));
 581       if (viewport.cursorMode)
 582       {
 583         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 584         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 585       }
 586       break;
 587
 588     case KeyEvent.VK_F:
 589       if (evt.isControlDown())
 590       {
 591         findMenuItem_actionPerformed();
 592       }
 593       break;
 594
 595     case KeyEvent.VK_H:
 596     {
 597       boolean toggleSeqs = !evt.isControlDown();
 598       boolean toggleCols = !evt.isShiftDown();
 599       toggleHiddenRegions(toggleSeqs, toggleCols);
 600       break;
 601     }
 602
 603     case KeyEvent.VK_PAGE_UP:
 604       ranges.pageUp();
 605       break;
 606
 607     case KeyEvent.VK_PAGE_DOWN:
 608       ranges.pageDown();
 609       break;
 610
 611     case KeyEvent.VK_Z:
 612       if (evt.isControlDown())
 613       {
 614         undoMenuItem_actionPerformed();
 615       }
 616       break;
 617
 618     case KeyEvent.VK_Y:
 619       if (evt.isControlDown())
 620       {
 621         redoMenuItem_actionPerformed();
 622       }
 623       break;
 624
 625     case KeyEvent.VK_L:
 626       if (evt.isControlDown())
 627       {
 628         trimAlignment(true);
 629       }
 630       break;
 631
 632     case KeyEvent.VK_R:
 633       if (evt.isControlDown())
 634       {
 635         trimAlignment(false);
 636       }
 637       break;
 638
 639     case KeyEvent.VK_E:
 640       if (evt.isControlDown())
 641       {
 642         if (evt.isShiftDown())
 643         {
 644           this.removeAllGapsMenuItem_actionPerformed();
 645         }
 646         else
 647         {
 648           removeGappedColumnMenuItem_actionPerformed();
 649         }
 650       }
 651       break;
 652     case KeyEvent.VK_I:
 653       if (evt.isControlDown())
 654       {
 655         if (evt.isAltDown())
 656         {
 657           invertColSel_actionPerformed();
 658         }
 659         else
 660         {
 661           invertSequenceMenuItem_actionPerformed();
 662         }
 663       }
 664       break;
 665
 666     case KeyEvent.VK_G:
 667       if (evt.isControlDown())
 668       {
 669         if (evt.isShiftDown())
 670         {
 671           this.unGroup_actionPerformed();
 672         }
 673         else
 674         {
 675           this.createGroup_actionPerformed();
 676         }
 677       }
 678       break;
 679
 680     case KeyEvent.VK_U:
 681       if (evt.isControlDown())
 682       {
 683         this.deleteGroups_actionPerformed();
 684       }
 685       break;
 686
 687     case KeyEvent.VK_T:
 688       if (evt.isControlDown())
 689       {
 690         newView(null);
 691       }
 692       break;
 693
 694     }
 695     // TODO: repaint flags set only if the keystroke warrants it
 696     alignPanel.paintAlignment(true, true);
 697   }
 698
 699   /**
 700    * called by key handler and the hide all/show all menu items
 701    *
 702    * @param toggleSeqs
 703    * @param toggleCols
 704    */
 705   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 706   {
 707     boolean hide = false;
 708     SequenceGroup sg = viewport.getSelectionGroup();
 709     if (!toggleSeqs && !toggleCols)
 710     {
 711       // Hide everything by the current selection - this is a hack - we do the
 712       // invert and then hide
 713       // first check that there will be visible columns after the invert.
 714       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 715               && sg.getStartRes() <= sg.getEndRes()))
 716       {
 717         // now invert the sequence set, if required - empty selection implies
 718         // that no hiding is required.
 719         if (sg != null)
 720         {
 721           invertSequenceMenuItem_actionPerformed();
 722           sg = viewport.getSelectionGroup();
 723           toggleSeqs = true;
 724
 725         }
 726         viewport.expandColSelection(sg, true);
 727         // finally invert the column selection and get the new sequence
 728         // selection and indicate it should be hidden.
 729         invertColSel_actionPerformed();
 730         toggleCols = true;
 731       }
 732     }
 733
 734     if (toggleSeqs)
 735     {
 736       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 737       {
 738         hide = true;
 739         viewport.hideAllSelectedSeqs();
 740       }
 741       else if (!(toggleCols && viewport.hasSelectedColumns()))
 742       {
 743         viewport.showAllHiddenSeqs();
 744       }
 745     }
 746
 747     if (toggleCols)
 748     {
 749       if (viewport.hasSelectedColumns())
 750       {
 751         viewport.hideSelectedColumns();
 752         if (!toggleSeqs)
 753         {
 754           viewport.setSelectionGroup(sg);
 755         }
 756       }
 757       else if (!hide)
 758       {
 759         viewport.showAllHiddenColumns();
 760       }
 761       viewport.sendSelection();
 762     }
 763   }
 764
 765   @Override
 766   public void keyReleased(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void keyTyped(KeyEvent evt)
 772   {
 773   }
 774
 775   @Override
 776   public void itemStateChanged(ItemEvent evt)
 777   {
 778     final Object source = evt.getSource();
 779     if (source == displayNonconservedMenuItem)
 780     {
 781       displayNonconservedMenuItem_actionPerformed();
 782     }
 783     else if (source == colourTextMenuItem)
 784     {
 785       colourTextMenuItem_actionPerformed();
 786     }
 787     else if (source == wrapMenuItem)
 788     {
 789       wrapMenuItem_actionPerformed();
 790     }
 791     else if (source == scaleAbove)
 792     {
 793       viewport.setScaleAboveWrapped(scaleAbove.getState());
 794     }
 795     else if (source == scaleLeft)
 796     {
 797       viewport.setScaleLeftWrapped(scaleLeft.getState());
 798     }
 799     else if (source == scaleRight)
 800     {
 801       viewport.setScaleRightWrapped(scaleRight.getState());
 802     }
 803     else if (source == seqLimits)
 804     {
 805       seqLimits_itemStateChanged();
 806     }
 807     else if (source == viewBoxesMenuItem)
 808     {
 809       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 810     }
 811     else if (source == viewTextMenuItem)
 812     {
 813       viewport.setShowText(viewTextMenuItem.getState());
 814     }
 815     else if (source == renderGapsMenuItem)
 816     {
 817       viewport.setRenderGaps(renderGapsMenuItem.getState());
 818     }
 819     else if (source == annotationPanelMenuItem)
 820     {
 821       boolean showAnnotations = annotationPanelMenuItem.getState();
 822       showAlignmentAnnotations.setEnabled(showAnnotations);
 823       showSequenceAnnotations.setEnabled(showAnnotations);
 824       viewport.setShowAnnotation(showAnnotations);
 825       alignPanel.setAnnotationVisible(showAnnotations);
 826     }
 827     else if (source == sequenceFeatures)
 828     {
 829       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 830       alignPanel.seqPanel.seqCanvas.repaint();
 831     }
 832     else if (source == showAlignmentAnnotations)
 833     {
 834       setAnnotationsVisibility();
 835     }
 836     else if (source == showSequenceAnnotations)
 837     {
 838       setAnnotationsVisibility();
 839     }
 840     else if (source == sortAnnBySequence)
 841     {
 842       boolean newState = sortAnnBySequence.getState();
 843       sortAnnByLabel.setState(false);
 844       setAnnotationSortOrder(
 845               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 846                       : SequenceAnnotationOrder.NONE);
 847       setViewportAnnotationOrder();
 848     }
 849     else if (source == sortAnnByLabel)
 850     {
 851       boolean newState = sortAnnByLabel.getState();
 852       sortAnnBySequence.setState(false);
 853       setAnnotationSortOrder(
 854               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 855                       : SequenceAnnotationOrder.NONE);
 856       setViewportAnnotationOrder();
 857     }
 858     else if (source == showAutoFirst)
 859     {
 860       showAutoLast.setState(!showAutoFirst.getState());
 861       setShowAutoCalculatedAbove(showAutoFirst.getState());
 862       setViewportAnnotationOrder();
 863     }
 864     else if (source == showAutoLast)
 865     {
 866       showAutoFirst.setState(!showAutoLast.getState());
 867       setShowAutoCalculatedAbove(showAutoFirst.getState());
 868       setViewportAnnotationOrder();
 869     }
 870     else if (source == conservationMenuItem)
 871     {
 872       conservationMenuItem_actionPerformed();
 873     }
 874     else if (source == abovePIDThreshold)
 875     {
 876       abovePIDThreshold_actionPerformed();
 877     }
 878     else if (source == applyToAllGroups)
 879     {
 880       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 881     }
 882     else if (source == autoCalculate)
 883     {
 884       viewport.autoCalculateConsensus = autoCalculate.getState();
 885     }
 886     else if (source == sortByTree)
 887     {
 888       viewport.sortByTree = sortByTree.getState();
 889     }
 890     else if (source == this.centreColumnLabelFlag)
 891     {
 892       centreColumnLabelFlag_stateChanged();
 893     }
 894     else if (source == this.followMouseOverFlag)
 895     {
 896       mouseOverFlag_stateChanged();
 897     }
 898     else if (source == showGroupConsensus)
 899     {
 900       showGroupConsensus_actionPerformed();
 901     }
 902     else if (source == showGroupConservation)
 903     {
 904       showGroupConservation_actionPerformed();
 905     }
 906     else if (source == showSequenceLogo)
 907     {
 908       showSequenceLogo_actionPerformed();
 909     }
 910     else if (source == normSequenceLogo)
 911     {
 912       normSequenceLogo_actionPerformed();
 913     }
 914     else if (source == showConsensusHistogram)
 915     {
 916       showConsensusHistogram_actionPerformed();
 917     }
 918     else if (source == applyAutoAnnotationSettings)
 919     {
 920       applyAutoAnnotationSettings_actionPerformed();
 921     }
 922     // TODO: repaint flags set only if warranted
 923     alignPanel.paintAlignment(true, true);
 924   }
 925
 926   /**
 927    * Set the visibility state of sequence-related and/or alignment-related
 928    * annotations depending on checkbox selections, and repaint.
 929    *
 930    * @param visible
 931    */
 932   private void setAnnotationsVisibility()
 933   {
 934     boolean showForAlignment = showAlignmentAnnotations.getState();
 935     boolean showForSequences = showSequenceAnnotations.getState();
 936     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 937     {
 938       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 939               .getAlignmentAnnotation())
 940       {
 941         boolean visible = (aa.sequenceRef == null ? showForAlignment
 942                 : showForSequences);
 943         aa.visible = visible;
 944       }
 945     }
 946     alignPanel.validateAnnotationDimensions(true);
 947     validate();
 948     repaint();
 949   }
 950
 951   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 952   {
 953     this.annotationSortOrder = order;
 954   }
 955
 956   /**
 957    * Set flags on the viewport that control annotation ordering
 958    */
 959   private void setViewportAnnotationOrder()
 960   {
 961     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 962     this.alignPanel.av
 963             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 964   }
 965
 966   private void setShowAutoCalculatedAbove(boolean showAbove)
 967   {
 968     this.showAutoCalculatedAbove = showAbove;
 969   }
 970
 971   private void mouseOverFlag_stateChanged()
 972   {
 973     viewport.setFollowHighlight(followMouseOverFlag.getState());
 974     // TODO: could kick the scrollTo mechanism to reset view for current
 975     // searchresults.
 976   }
 977
 978   private void centreColumnLabelFlag_stateChanged()
 979   {
 980     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 981     this.alignPanel.annotationPanel.repaint();
 982   }
 983
 984   @Override
 985   public void actionPerformed(ActionEvent evt)
 986   {
 987     viewport.applet.currentAlignFrame = this;
 988
 989     Object source = evt.getSource();
 990
 991     if (source == inputText)
 992     {
 993       inputText_actionPerformed();
 994     }
 995     else if (source == loadTree)
 996     {
 997       loadTree_actionPerformed();
 998     }
 999     else if (source == loadApplication)
1000     {
1001       launchFullApplication();
1002     }
1003     else if (source == loadAnnotations)
1004     {
1005       loadAnnotations();
1006     }
1007     else if (source == outputAnnotations)
1008     {
1009       outputAnnotations(true);
1010     }
1011     else if (source == outputFeatures)
1012     {
1013       outputFeatures(true, "Jalview");
1014     }
1015     else if (source == closeMenuItem)
1016     {
1017       closeMenuItem_actionPerformed();
1018     }
1019     else if (source == copy)
1020     {
1021       copy_actionPerformed();
1022     }
1023     else if (source == undoMenuItem)
1024     {
1025       undoMenuItem_actionPerformed();
1026     }
1027     else if (source == redoMenuItem)
1028     {
1029       redoMenuItem_actionPerformed();
1030     }
1031     else if (source == inputText)
1032     {
1033       inputText_actionPerformed();
1034     }
1035     else if (source == closeMenuItem)
1036     {
1037       closeMenuItem_actionPerformed();
1038     }
1039     else if (source == undoMenuItem)
1040     {
1041       undoMenuItem_actionPerformed();
1042     }
1043     else if (source == redoMenuItem)
1044     {
1045       redoMenuItem_actionPerformed();
1046     }
1047     else if (source == copy)
1048     {
1049       copy_actionPerformed();
1050     }
1051     else if (source == pasteNew)
1052     {
1053       pasteNew_actionPerformed();
1054     }
1055     else if (source == pasteThis)
1056     {
1057       pasteThis_actionPerformed();
1058     }
1059     else if (source == cut)
1060     {
1061       cut_actionPerformed();
1062     }
1063     else if (source == delete)
1064     {
1065       delete_actionPerformed();
1066     }
1067     else if (source == createGroup)
1068     {
1069       createGroup_actionPerformed();
1070     }
1071     else if (source == unGroup)
1072     {
1073       unGroup_actionPerformed();
1074     }
1075     else if (source == grpsFromSelection)
1076     {
1077       makeGrpsFromSelection_actionPerformed();
1078     }
1079     else if (source == deleteGroups)
1080     {
1081       deleteGroups_actionPerformed();
1082     }
1083     else if (source == selectAllSequenceMenuItem)
1084     {
1085       selectAllSequenceMenuItem_actionPerformed();
1086     }
1087     else if (source == deselectAllSequenceMenuItem)
1088     {
1089       deselectAllSequenceMenuItem_actionPerformed();
1090     }
1091     else if (source == invertSequenceMenuItem)
1092     {
1093       invertSequenceMenuItem_actionPerformed();
1094       // uncomment to slave sequence selections in split frame
1095       // viewport.sendSelection();
1096     }
1097     else if (source == invertColSel)
1098     {
1099       viewport.invertColumnSelection();
1100       alignPanel.paintAlignment(false, false);
1101       viewport.sendSelection();
1102     }
1103     else if (source == remove2LeftMenuItem)
1104     {
1105       trimAlignment(true);
1106     }
1107     else if (source == remove2RightMenuItem)
1108     {
1109       trimAlignment(false);
1110     }
1111     else if (source == removeGappedColumnMenuItem)
1112     {
1113       removeGappedColumnMenuItem_actionPerformed();
1114     }
1115     else if (source == removeAllGapsMenuItem)
1116     {
1117       removeAllGapsMenuItem_actionPerformed();
1118     }
1119     else if (source == findMenuItem)
1120     {
1121       findMenuItem_actionPerformed();
1122     }
1123     else if (source == font)
1124     {
1125       new FontChooser(alignPanel);
1126     }
1127     else if (source == newView)
1128     {
1129       newView(null);
1130     }
1131     else if (source == showColumns)
1132     {
1133       viewport.showAllHiddenColumns();
1134       alignPanel.paintAlignment(true, true);
1135       viewport.sendSelection();
1136     }
1137     else if (source == showSeqs)
1138     {
1139       viewport.showAllHiddenSeqs();
1140       alignPanel.paintAlignment(true, true);
1141       // uncomment if we want to slave sequence selections in split frame
1142       // viewport.sendSelection();
1143     }
1144     else if (source == hideColumns)
1145     {
1146       viewport.hideSelectedColumns();
1147       alignPanel.paintAlignment(true, true);
1148       viewport.sendSelection();
1149     }
1150     else if (source == hideSequences
1151             && viewport.getSelectionGroup() != null)
1152     {
1153       viewport.hideAllSelectedSeqs();
1154       alignPanel.paintAlignment(true, true);
1155       // uncomment if we want to slave sequence selections in split frame
1156       // viewport.sendSelection();
1157     }
1158     else if (source == hideAllButSelection)
1159     {
1160       toggleHiddenRegions(false, false);
1161       alignPanel.paintAlignment(true, true);
1162       viewport.sendSelection();
1163     }
1164     else if (source == hideAllSelection)
1165     {
1166       SequenceGroup sg = viewport.getSelectionGroup();
1167       viewport.expandColSelection(sg, false);
1168       viewport.hideAllSelectedSeqs();
1169       viewport.hideSelectedColumns();
1170       alignPanel.paintAlignment(true, true);
1171       viewport.sendSelection();
1172     }
1173     else if (source == showAllHidden)
1174     {
1175       viewport.showAllHiddenColumns();
1176       viewport.showAllHiddenSeqs();
1177       alignPanel.paintAlignment(true, true);
1178       viewport.sendSelection();
1179     }
1180     else if (source == showGroupConsensus)
1181     {
1182       showGroupConsensus_actionPerformed();
1183     }
1184     else if (source == showGroupConservation)
1185     {
1186       showGroupConservation_actionPerformed();
1187     }
1188     else if (source == showSequenceLogo)
1189     {
1190       showSequenceLogo_actionPerformed();
1191     }
1192     else if (source == normSequenceLogo)
1193     {
1194       normSequenceLogo_actionPerformed();
1195     }
1196     else if (source == showConsensusHistogram)
1197     {
1198       showConsensusHistogram_actionPerformed();
1199     }
1200     else if (source == applyAutoAnnotationSettings)
1201     {
1202       applyAutoAnnotationSettings_actionPerformed();
1203     }
1204     else if (source == featureSettings)
1205     {
1206       new FeatureSettings(alignPanel);
1207     }
1208     else if (source == alProperties)
1209     {
1210       StringBuffer contents = new jalview.io.AlignmentProperties(
1211               viewport.getAlignment()).formatAsString();
1212       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1213       cap.setText(contents.toString());
1214       Frame frame = new Frame();
1215       frame.add(cap);
1216       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1217               .formatMessage("label.alignment_properties", new String[]
1218               { getTitle() }), 400, 250);
1219     }
1220     else if (source == overviewMenuItem)
1221     {
1222       overviewMenuItem_actionPerformed();
1223     }
1224     else if (source == noColourmenuItem)
1225     {
1226       changeColour(null);
1227     }
1228     else if (source == clustalColour)
1229     {
1230       abovePIDThreshold.setState(false);
1231       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1232     }
1233     else if (source == zappoColour)
1234     {
1235       changeColour(new ZappoColourScheme());
1236     }
1237     else if (source == taylorColour)
1238     {
1239       changeColour(new TaylorColourScheme());
1240     }
1241     else if (source == hydrophobicityColour)
1242     {
1243       changeColour(new HydrophobicColourScheme());
1244     }
1245     else if (source == helixColour)
1246     {
1247       changeColour(new HelixColourScheme());
1248     }
1249     else if (source == strandColour)
1250     {
1251       changeColour(new StrandColourScheme());
1252     }
1253     else if (source == turnColour)
1254     {
1255       changeColour(new TurnColourScheme());
1256     }
1257     else if (source == buriedColour)
1258     {
1259       changeColour(new BuriedColourScheme());
1260     }
1261     else if (source == nucleotideColour)
1262     {
1263       changeColour(new NucleotideColourScheme());
1264     }
1265     else if (source == purinePyrimidineColour)
1266     {
1267       changeColour(new PurinePyrimidineColourScheme());
1268     }
1269     // else if (source == RNAInteractionColour)
1270     // {
1271     // changeColour(new RNAInteractionColourScheme());
1272     // }
1273     else if (source == RNAHelixColour)
1274     {
1275       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1276       // new RNAHelicesColourChooser(viewport, alignPanel);
1277     }
1278     else if (source == modifyPID)
1279     {
1280       modifyPID_actionPerformed();
1281     }
1282     else if (source == modifyConservation)
1283     {
1284       modifyConservation_actionPerformed();
1285     }
1286     else if (source == userDefinedColour)
1287     {
1288       new UserDefinedColours(alignPanel, null);
1289     }
1290     else if (source == PIDColour)
1291     {
1292       changeColour(new PIDColourScheme());
1293     }
1294     else if (source == BLOSUM62Colour)
1295     {
1296       changeColour(new Blosum62ColourScheme());
1297     }
1298     else if (source == tcoffeeColour)
1299     {
1300       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1301     }
1302     else if (source == annotationColour)
1303     {
1304       new AnnotationColourChooser(viewport, alignPanel);
1305     }
1306     else if (source == annotationColumnSelection)
1307     {
1308       new AnnotationColumnChooser(viewport, alignPanel);
1309     }
1310     else if (source == sortPairwiseMenuItem)
1311     {
1312       sortPairwiseMenuItem_actionPerformed();
1313     }
1314     else if (source == sortIDMenuItem)
1315     {
1316       sortIDMenuItem_actionPerformed();
1317     }
1318     else if (source == sortLengthMenuItem)
1319     {
1320       sortLengthMenuItem_actionPerformed();
1321     }
1322     else if (source == sortGroupMenuItem)
1323     {
1324       sortGroupMenuItem_actionPerformed();
1325     }
1326     else if (source == removeRedundancyMenuItem)
1327     {
1328       removeRedundancyMenuItem_actionPerformed();
1329     }
1330     else if (source == pairwiseAlignmentMenuItem)
1331     {
1332       pairwiseAlignmentMenuItem_actionPerformed();
1333     }
1334     else if (source == PCAMenuItem)
1335     {
1336       PCAMenuItem_actionPerformed();
1337     }
1338     else if (source == averageDistanceTreeMenuItem)
1339     {
1340       averageDistanceTreeMenuItem_actionPerformed();
1341     }
1342     else if (source == neighbourTreeMenuItem)
1343     {
1344       neighbourTreeMenuItem_actionPerformed();
1345     }
1346     else if (source == njTreeBlosumMenuItem)
1347     {
1348       njTreeBlosumMenuItem_actionPerformed();
1349     }
1350     else if (source == avDistanceTreeBlosumMenuItem)
1351     {
1352       avTreeBlosumMenuItem_actionPerformed();
1353     }
1354     else if (source == documentation)
1355     {
1356       documentation_actionPerformed();
1357     }
1358     else if (source == about)
1359     {
1360       about_actionPerformed();
1361     }
1362
1363   }
1364
1365   public void inputText_actionPerformed()
1366   {
1367     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1368     Frame frame = new Frame();
1369     frame.add(cap);
1370     jalview.bin.JalviewLite.addFrame(frame,
1371             MessageManager.getString("label.input_cut_paste"), 500, 500);
1372   }
1373
1374   protected void outputText_actionPerformed(ActionEvent e)
1375   {
1376     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377     Frame frame = new Frame();
1378     frame.add(cap);
1379     JalviewLite.addFrame(frame, MessageManager
1380             .formatMessage("label.alignment_output_command", new Object[]
1381             { e.getActionCommand() }), 600, 500);
1382
1383     FileFormatI fileFormat = FileFormats.getInstance()
1384             .forName(e.getActionCommand());
1385     cap.setText(
1386             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1387                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1388   }
1389
1390   public void loadAnnotations()
1391   {
1392     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1393     cap.setText(MessageManager
1394             .getString("label.paste_features_annotations_Tcoffee_here"));
1395     cap.setAnnotationImport();
1396     Frame frame = new Frame();
1397     frame.add(cap);
1398     jalview.bin.JalviewLite.addFrame(frame,
1399             MessageManager.getString("action.paste_annotations"), 400, 300);
1400
1401   }
1402
1403   public String outputAnnotations(boolean displayTextbox)
1404   {
1405     String annotation = new AnnotationFile()
1406             .printAnnotationsForView(viewport);
1407
1408     if (displayTextbox)
1409     {
1410       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1411       Frame frame = new Frame();
1412       frame.add(cap);
1413       jalview.bin.JalviewLite.addFrame(frame,
1414               MessageManager.getString("label.annotations"), 600, 500);
1415       cap.setText(annotation);
1416     }
1417
1418     return annotation;
1419   }
1420
1421   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1422   {
1423     if (alignPanel.getFeatureRenderer() != null
1424             && viewport.getFeaturesDisplayed() != null)
1425     {
1426       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1427
1428     }
1429     return null;
1430   }
1431
1432   private List<String> getDisplayedFeatureGroups()
1433   {
1434     if (alignPanel.getFeatureRenderer() != null
1435             && viewport.getFeaturesDisplayed() != null)
1436     {
1437       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1438
1439     }
1440     return null;
1441   }
1442
1443   public String outputFeatures(boolean displayTextbox, String format)
1444   {
1445     String features;
1446     FeaturesFile formatter = new FeaturesFile();
1447     if (format.equalsIgnoreCase("Jalview"))
1448     {
1449       features = formatter.printJalviewFormat(
1450               viewport.getAlignment().getSequencesArray(),
1451               alignPanel.getFeatureRenderer(), true);
1452     }
1453     else
1454     {
1455       features = formatter.printGffFormat(viewport.getAlignment()
1456               .getSequencesArray(), alignPanel.getFeatureRenderer(), true);
1457     }
1458
1459     if (displayTextbox)
1460     {
1461       boolean frimport = false;
1462       if (features == null || features.equals("No Features Visible"))
1463       {
1464         features = "# No features visible - paste some and import them here.";
1465         frimport = true;
1466       }
1467
1468       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1469       if (frimport)
1470       {
1471         cap.setAnnotationImport();
1472       }
1473       Frame frame = new Frame();
1474       frame.add(cap);
1475       jalview.bin.JalviewLite.addFrame(frame,
1476               MessageManager.getString("label.features"), 600, 500);
1477       cap.setText(features);
1478     }
1479     else
1480     {
1481       if (features == null)
1482       {
1483         features = "";
1484       }
1485     }
1486
1487     return features;
1488   }
1489
1490   void launchFullApplication()
1491   {
1492     StringBuffer url = new StringBuffer(jalviewServletURL);
1493
1494     // allow servlet parameters to be passed in applet parameter
1495     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1496             : "?";
1497     url.append(firstSep);
1498
1499     url.append(
1500             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1501
1502     if (viewport.applet.getParameter("features") != null)
1503     {
1504       url.append("&features=");
1505       url.append(appendProtocol(viewport.applet.getParameter("features")));
1506     }
1507
1508     if (viewport.applet.getParameter("annotations") != null)
1509     {
1510       url.append("&annotations=");
1511       url.append(
1512               appendProtocol(viewport.applet.getParameter("annotations")));
1513     }
1514
1515     if (viewport.applet.getParameter("jnetfile") != null
1516             || viewport.applet.getParameter("jpredfile") != null)
1517     {
1518       url.append("&annotations=");
1519       url.append(appendProtocol(
1520               viewport.applet.getParameter("jnetfile") != null
1521                       ? viewport.applet.getParameter("jnetfile")
1522                       : viewport.applet.getParameter("jpredfile")));
1523     }
1524
1525     if (viewport.applet.getParameter("defaultColour") != null)
1526     {
1527       url.append("&colour=" + removeWhiteSpace(
1528               viewport.applet.getParameter("defaultColour")));
1529     }
1530
1531     if (viewport.applet.getParameter("userDefinedColour") != null)
1532     {
1533       url.append("&colour=" + removeWhiteSpace(
1534               viewport.applet.getParameter("userDefinedColour")));
1535     }
1536     if (viewport.applet.getParameter("tree") != null)
1537     {
1538       url.append("&tree="
1539               + appendProtocol(viewport.applet.getParameter("tree")));
1540     }
1541     if (viewport.applet.getParameter("treeFile") != null)
1542     {
1543       url.append("&tree="
1544               + appendProtocol(viewport.applet.getParameter("treeFile")));
1545     }
1546
1547     showURL(url.toString(), "FULL_APP");
1548   }
1549
1550   String removeWhiteSpace(String colour)
1551   {
1552     StringBuffer sb = new StringBuffer();
1553     for (int i = 0; i < colour.length(); i++)
1554     {
1555       if (Character.isWhitespace(colour.charAt(i)))
1556       {
1557         sb.append("%20");
1558       }
1559       else
1560       {
1561         sb.append(colour.charAt(i));
1562       }
1563     }
1564
1565     return sb.toString();
1566   }
1567
1568   String appendProtocol(String url)
1569   {
1570     try
1571     {
1572       new URL(url);
1573       url = URLEncoder.encode(url, "UTF-8");
1574     }
1575     /*
1576      * When we finally deprecate 1.1 compatibility, we can start to use
1577      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1578      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1579      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1580      * ex.printStackTrace(); }
1581      */
1582     catch (java.net.MalformedURLException ex)
1583     {
1584       url = viewport.applet.getCodeBase() + url;
1585     }
1586     catch (UnsupportedEncodingException ex)
1587     {
1588       System.err.println(
1589               "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1590                       + url);
1591       ex.printStackTrace();
1592     }
1593     return url;
1594   }
1595
1596   public void closeMenuItem_actionPerformed()
1597   {
1598     PaintRefresher.RemoveComponent(alignPanel);
1599     if (alignPanel.seqPanel != null
1600             && alignPanel.seqPanel.seqCanvas != null)
1601     {
1602       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1603     }
1604     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1605     {
1606       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1607     }
1608
1609     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1610     {
1611       System.exit(0);
1612     }
1613
1614     viewport = null;
1615     if (alignPanel != null && alignPanel.overviewPanel != null)
1616     {
1617       alignPanel.overviewPanel.dispose();
1618     }
1619     alignPanel = null;
1620     this.dispose();
1621   }
1622
1623   /**
1624    * TODO: JAL-1104
1625    */
1626   void updateEditMenuBar()
1627   {
1628
1629     if (viewport.getHistoryList().size() > 0)
1630     {
1631       undoMenuItem.setEnabled(true);
1632       CommandI command = viewport.getHistoryList().peek();
1633       undoMenuItem.setLabel(MessageManager
1634               .formatMessage("label.undo_command", new Object[]
1635               { command.getDescription() }));
1636     }
1637     else
1638     {
1639       undoMenuItem.setEnabled(false);
1640       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1641     }
1642
1643     if (viewport.getRedoList().size() > 0)
1644     {
1645       redoMenuItem.setEnabled(true);
1646
1647       CommandI command = viewport.getRedoList().peek();
1648       redoMenuItem.setLabel(MessageManager
1649               .formatMessage("label.redo_command", new Object[]
1650               { command.getDescription() }));
1651     }
1652     else
1653     {
1654       redoMenuItem.setEnabled(false);
1655       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1656     }
1657   }
1658
1659   /**
1660    * TODO: JAL-1104
1661    */
1662   @Override
1663   public void addHistoryItem(CommandI command)
1664   {
1665     if (command.getSize() > 0)
1666     {
1667       viewport.addToHistoryList(command);
1668       viewport.clearRedoList();
1669       updateEditMenuBar();
1670       viewport.updateHiddenColumns();
1671     }
1672   }
1673
1674   /**
1675    * TODO: JAL-1104 DOCUMENT ME!
1676    *
1677    * @param e
1678    *          DOCUMENT ME!
1679    */
1680   protected void undoMenuItem_actionPerformed()
1681   {
1682     if (viewport.getHistoryList().isEmpty())
1683     {
1684       return;
1685     }
1686
1687     CommandI command = viewport.getHistoryList().pop();
1688     viewport.addToRedoList(command);
1689     command.undoCommand(null);
1690
1691     AlignmentViewport originalSource = getOriginatingSource(command);
1692     // JBPNote Test
1693     if (originalSource != viewport)
1694     {
1695       System.err
1696               .println("Warning: Viewport object mismatch whilst undoing");
1697     }
1698     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1699                                           // viewport.getColumnSelection().getHiddenColumns()
1700                                           // != null;
1701     updateEditMenuBar();
1702     originalSource.firePropertyChange("alignment", null,
1703             originalSource.getAlignment().getSequences());
1704   }
1705
1706   /**
1707    * TODO: JAL-1104 DOCUMENT ME!
1708    *
1709    * @param e
1710    *          DOCUMENT ME!
1711    */
1712   protected void redoMenuItem_actionPerformed()
1713   {
1714     if (viewport.getRedoList().isEmpty())
1715     {
1716       return;
1717     }
1718
1719     CommandI command = viewport.getRedoList().pop();
1720     viewport.addToHistoryList(command);
1721     command.doCommand(null);
1722
1723     AlignmentViewport originalSource = getOriginatingSource(command);
1724     // JBPNote Test
1725     if (originalSource != viewport)
1726     {
1727       System.err
1728               .println("Warning: Viewport object mismatch whilst re-doing");
1729     }
1730     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1731                                           // viewport.getColumnSelection().getHiddenColumns()
1732                                           // != null;
1733
1734     updateEditMenuBar();
1735     originalSource.firePropertyChange("alignment", null,
1736             originalSource.getAlignment().getSequences());
1737   }
1738
1739   AlignmentViewport getOriginatingSource(CommandI command)
1740   {
1741     AlignmentViewport originalSource = null;
1742     // For sequence removal and addition, we need to fire
1743     // the property change event FROM the viewport where the
1744     // original alignment was altered
1745     AlignmentI al = null;
1746     if (command instanceof EditCommand)
1747     {
1748       EditCommand editCommand = (EditCommand) command;
1749       al = editCommand.getAlignment();
1750       Vector comps = PaintRefresher.components
1751               .get(viewport.getSequenceSetId());
1752       for (int i = 0; i < comps.size(); i++)
1753       {
1754         if (comps.elementAt(i) instanceof AlignmentPanel)
1755         {
1756           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1757           {
1758             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1759             break;
1760           }
1761         }
1762       }
1763     }
1764
1765     if (originalSource == null)
1766     {
1767       // The original view is closed, we must validate
1768       // the current view against the closed view first
1769       if (al != null)
1770       {
1771         PaintRefresher.validateSequences(al, viewport.getAlignment());
1772       }
1773
1774       originalSource = viewport;
1775     }
1776
1777     return originalSource;
1778   }
1779
1780   /**
1781    * Move the currently selected sequences up or down one position in the
1782    * alignment
1783    *
1784    * @param up
1785    */
1786   public void moveSelectedSequences(boolean up)
1787   {
1788     SequenceGroup sg = viewport.getSelectionGroup();
1789     if (sg == null)
1790     {
1791       return;
1792     }
1793     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1794             up ? null : viewport.getHiddenRepSequences(), up);
1795     alignPanel.paintAlignment(true, false);
1796
1797     /*
1798      * Also move cDNA/protein complement sequences
1799      */
1800     AlignViewportI complement = viewport.getCodingComplement();
1801     if (complement != null)
1802     {
1803       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1804               viewport, complement);
1805       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1806               up ? null : complement.getHiddenRepSequences(), up);
1807       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1808               false);
1809     }
1810   }
1811
1812   synchronized void slideSequences(boolean right, int size)
1813   {
1814     List<SequenceI> sg = new Vector<>();
1815     if (viewport.cursorMode)
1816     {
1817       sg.add(viewport.getAlignment()
1818               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1819     }
1820     else if (viewport.getSelectionGroup() != null
1821             && viewport.getSelectionGroup().getSize() != viewport
1822                     .getAlignment().getHeight())
1823     {
1824       sg = viewport.getSelectionGroup()
1825               .getSequences(viewport.getHiddenRepSequences());
1826     }
1827
1828     if (sg.size() < 1)
1829     {
1830       return;
1831     }
1832
1833     Vector<SequenceI> invertGroup = new Vector();
1834
1835     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1836     {
1837       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1838       {
1839         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1840       }
1841     }
1842
1843     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1844
1845     SequenceI[] seqs2 = invertGroup
1846             .toArray(new SequenceI[invertGroup.size()]);
1847     for (int i = 0; i < invertGroup.size(); i++)
1848     {
1849       seqs2[i] = invertGroup.elementAt(i);
1850     }
1851
1852     SlideSequencesCommand ssc;
1853     if (right)
1854     {
1855       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1856               viewport.getGapCharacter());
1857     }
1858     else
1859     {
1860       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1861               viewport.getGapCharacter());
1862     }
1863
1864     int groupAdjustment = 0;
1865     if (ssc.getGapsInsertedBegin() && right)
1866     {
1867       if (viewport.cursorMode)
1868       {
1869         alignPanel.seqPanel.moveCursor(size, 0);
1870       }
1871       else
1872       {
1873         groupAdjustment = size;
1874       }
1875     }
1876     else if (!ssc.getGapsInsertedBegin() && !right)
1877     {
1878       if (viewport.cursorMode)
1879       {
1880         alignPanel.seqPanel.moveCursor(-size, 0);
1881       }
1882       else
1883       {
1884         groupAdjustment = -size;
1885       }
1886     }
1887
1888     if (groupAdjustment != 0)
1889     {
1890       viewport.getSelectionGroup().setStartRes(
1891               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1892       viewport.getSelectionGroup().setEndRes(
1893               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1894     }
1895
1896     boolean appendHistoryItem = false;
1897     Deque<CommandI> historyList = viewport.getHistoryList();
1898     if (historyList != null && historyList.size() > 0
1899             && historyList.peek() instanceof SlideSequencesCommand)
1900     {
1901       appendHistoryItem = ssc.appendSlideCommand(
1902               (SlideSequencesCommand) historyList.peek());
1903     }
1904
1905     if (!appendHistoryItem)
1906     {
1907       addHistoryItem(ssc);
1908     }
1909
1910     repaint();
1911   }
1912
1913   static StringBuffer copiedSequences;
1914
1915   static HiddenColumns copiedHiddenColumns;
1916
1917   protected void copy_actionPerformed()
1918   {
1919     if (viewport.getSelectionGroup() == null)
1920     {
1921       return;
1922     }
1923
1924     SequenceGroup sg = viewport.getSelectionGroup();
1925     copiedSequences = new StringBuffer();
1926     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1927     for (int i = 0; i < sg.getSize(); i++)
1928     {
1929       SequenceI seq = sg.getSequenceAt(i);
1930       int index = viewport.getAlignment().findIndex(seq);
1931       orderedSeqs.put(index, seq);
1932     }
1933
1934     int index = 0, startRes, endRes;
1935     char ch;
1936
1937     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1938     {
1939       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1940       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1941
1942       // create new HiddenColumns object with copy of hidden regions
1943       // between startRes and endRes, offset by startRes
1944       copiedHiddenColumns = new HiddenColumns(
1945               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1946               hiddenCutoff, hiddenOffset);
1947     }
1948     else
1949     {
1950       copiedHiddenColumns = null;
1951     }
1952
1953     for (int i = 0; i < sg.getSize(); i++)
1954     {
1955       SequenceI seq = null;
1956
1957       while (seq == null)
1958       {
1959         if (orderedSeqs.containsKey(index))
1960         {
1961           seq = orderedSeqs.get(index);
1962           index++;
1963           break;
1964         }
1965         else
1966         {
1967           index++;
1968         }
1969       }
1970
1971       // FIND START RES
1972       // Returns residue following index if gap
1973       startRes = seq.findPosition(sg.getStartRes());
1974
1975       // FIND END RES
1976       // Need to find the residue preceeding index if gap
1977       endRes = 0;
1978
1979       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1980       {
1981         ch = seq.getCharAt(j);
1982         if (!jalview.util.Comparison.isGap((ch)))
1983         {
1984           endRes++;
1985         }
1986       }
1987
1988       if (endRes > 0)
1989       {
1990         endRes += seq.getStart() - 1;
1991       }
1992
1993       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1994               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1995                       sg.getEndRes() + 1)
1996               + "\n");
1997     }
1998
1999   }
2000
2001   protected void pasteNew_actionPerformed()
2002   {
2003     paste(true);
2004   }
2005
2006   protected void pasteThis_actionPerformed()
2007   {
2008     paste(false);
2009   }
2010
2011   void paste(boolean newAlignment)
2012   {
2013     try
2014     {
2015       if (copiedSequences == null)
2016       {
2017         return;
2018       }
2019
2020       StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2021               "\t");
2022       Vector seqs = new Vector();
2023       while (st.hasMoreElements())
2024       {
2025         String name = st.nextToken();
2026         int start = Integer.parseInt(st.nextToken());
2027         int end = Integer.parseInt(st.nextToken());
2028         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2029       }
2030       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2031       for (int i = 0; i < seqs.size(); i++)
2032       {
2033         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2034       }
2035
2036       if (newAlignment)
2037       {
2038         String newtitle = MessageManager
2039                 .getString("label.copied_sequences");
2040         if (getTitle().startsWith(
2041                 MessageManager.getString("label.copied_sequences")))
2042         {
2043           newtitle = getTitle();
2044         }
2045         else
2046         {
2047           newtitle = newtitle.concat(MessageManager
2048                   .formatMessage("label.from_msname", new String[]
2049                   { getTitle() }));
2050         }
2051         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2052                 viewport.applet, newtitle, false);
2053         af.viewport.setHiddenColumns(copiedHiddenColumns);
2054
2055         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2056                 frameHeight);
2057       }
2058       else
2059       {
2060         addSequences(newSeqs);
2061       }
2062
2063     } catch (Exception ex)
2064     {
2065     } // could be anything being pasted in here
2066
2067   }
2068
2069   void addSequences(SequenceI[] seqs)
2070   {
2071     for (int i = 0; i < seqs.length; i++)
2072     {
2073       viewport.getAlignment().addSequence(seqs[i]);
2074     }
2075
2076     // !newAlignment
2077     addHistoryItem(new EditCommand(
2078             MessageManager.getString("label.add_sequences"), Action.PASTE,
2079             seqs, 0, viewport.getAlignment().getWidth(),
2080             viewport.getAlignment()));
2081
2082     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2083     viewport.getAlignment().getWidth();
2084     viewport.firePropertyChange("alignment", null,
2085             viewport.getAlignment().getSequences());
2086
2087   }
2088
2089   protected void cut_actionPerformed()
2090   {
2091     copy_actionPerformed();
2092     delete_actionPerformed();
2093   }
2094
2095   protected void delete_actionPerformed()
2096   {
2097
2098     SequenceGroup sg = viewport.getSelectionGroup();
2099     if (sg == null)
2100     {
2101       return;
2102     }
2103
2104     Vector seqs = new Vector();
2105     SequenceI seq;
2106     for (int i = 0; i < sg.getSize(); i++)
2107     {
2108       seq = sg.getSequenceAt(i);
2109       seqs.addElement(seq);
2110     }
2111
2112     /*
2113      * If the cut affects all sequences, warn, remove highlighted columns
2114      */
2115     if (sg.getSize() == viewport.getAlignment().getHeight())
2116     {
2117       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2118               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2119       if (isEntireAlignWidth)
2120       {
2121         String title = MessageManager.getString("label.delete_all");
2122         Panel infoPanel = new Panel();
2123         infoPanel.setLayout(new FlowLayout());
2124         infoPanel.add(
2125                 new Label(MessageManager.getString("warn.delete_all")));
2126
2127         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2128         dialog.setMainPanel(infoPanel);
2129         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2130         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2131         dialog.setVisible(true);
2132
2133         if (!dialog.accept)
2134         {
2135           return;
2136         }
2137       }
2138       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2139               sg.getEndRes() + 1);
2140     }
2141
2142     SequenceI[] cut = new SequenceI[seqs.size()];
2143     for (int i = 0; i < seqs.size(); i++)
2144     {
2145       cut[i] = (SequenceI) seqs.elementAt(i);
2146     }
2147
2148     /*
2149      * //ADD HISTORY ITEM
2150      */
2151     addHistoryItem(new EditCommand(
2152             MessageManager.getString("label.cut_sequences"), Action.CUT,
2153             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2154             viewport.getAlignment()));
2155
2156     viewport.setSelectionGroup(null);
2157     viewport.getAlignment().deleteGroup(sg);
2158
2159     viewport.firePropertyChange("alignment", null,
2160             viewport.getAlignment().getSequences());
2161
2162     if (viewport.getAlignment().getHeight() < 1)
2163     {
2164       this.setVisible(false);
2165     }
2166     viewport.sendSelection();
2167   }
2168
2169   /**
2170    * group consensus toggled
2171    *
2172    */
2173   protected void showGroupConsensus_actionPerformed()
2174   {
2175     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2176     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2177
2178   }
2179
2180   /**
2181    * group conservation toggled.
2182    */
2183   protected void showGroupConservation_actionPerformed()
2184   {
2185     viewport.setShowGroupConservation(showGroupConservation.getState());
2186     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2187   }
2188
2189   /*
2190    * (non-Javadoc)
2191    *
2192    * @see
2193    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2194    * .event.ActionEvent)
2195    */
2196   protected void showConsensusHistogram_actionPerformed()
2197   {
2198     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2199     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2200   }
2201
2202   /*
2203    * (non-Javadoc)
2204    *
2205    * @see
2206    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2207    * .event.ActionEvent)
2208    */
2209   protected void showSequenceLogo_actionPerformed()
2210   {
2211     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2212     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2213   }
2214
2215   protected void normSequenceLogo_actionPerformed()
2216   {
2217     showSequenceLogo.setState(true);
2218     viewport.setShowSequenceLogo(true);
2219     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2220     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2221   }
2222
2223   protected void applyAutoAnnotationSettings_actionPerformed()
2224   {
2225     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2226   }
2227
2228   protected void makeGrpsFromSelection_actionPerformed()
2229   {
2230     if (avc.makeGroupsFromSelection())
2231     {
2232       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2233       alignPanel.updateAnnotation();
2234       alignPanel.paintAlignment(true, true);
2235     }
2236   }
2237
2238   protected void createGroup_actionPerformed()
2239   {
2240     avc.createGroup();
2241   }
2242
2243   protected void unGroup_actionPerformed()
2244   {
2245     if (avc.unGroup())
2246     {
2247       alignPanel.alignmentChanged();
2248     }
2249   }
2250
2251   protected void deleteGroups_actionPerformed()
2252   {
2253     if (avc.deleteGroups())
2254     {
2255       alignPanel.alignmentChanged();
2256     }
2257   }
2258
2259   public void selectAllSequenceMenuItem_actionPerformed()
2260   {
2261     SequenceGroup sg = new SequenceGroup();
2262     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2263     {
2264       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2265     }
2266     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2267     viewport.setSelectionGroup(sg);
2268     // JAL-2034 - should delegate to
2269     // alignPanel to decide if overview needs
2270     // updating.
2271     alignPanel.paintAlignment(false, false);
2272     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273     viewport.sendSelection();
2274   }
2275
2276   public void deselectAllSequenceMenuItem_actionPerformed()
2277   {
2278     if (viewport.cursorMode)
2279     {
2280       alignPanel.seqPanel.keyboardNo1 = null;
2281       alignPanel.seqPanel.keyboardNo2 = null;
2282     }
2283     viewport.setSelectionGroup(null);
2284     viewport.getColumnSelection().clear();
2285     viewport.setSelectionGroup(null);
2286     alignPanel.idPanel.idCanvas.searchResults = null;
2287     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2288     // JAL-2034 - should delegate to
2289     // alignPanel to decide if overview needs
2290     // updating.
2291     alignPanel.paintAlignment(false, false);
2292     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2293     viewport.sendSelection();
2294   }
2295
2296   public void invertSequenceMenuItem_actionPerformed()
2297   {
2298     SequenceGroup sg = viewport.getSelectionGroup();
2299     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2300     {
2301       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2302     }
2303
2304     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2305     viewport.sendSelection();
2306   }
2307
2308   public void invertColSel_actionPerformed()
2309   {
2310     viewport.invertColumnSelection();
2311     alignPanel.paintAlignment(true, false);
2312     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2313     viewport.sendSelection();
2314   }
2315
2316   void trimAlignment(boolean trimLeft)
2317   {
2318     AlignmentI al = viewport.getAlignment();
2319     ViewportRanges ranges = viewport.getRanges();
2320     ColumnSelection colSel = viewport.getColumnSelection();
2321     int column;
2322
2323     if (!colSel.isEmpty())
2324     {
2325       if (trimLeft)
2326       {
2327         column = colSel.getMin();
2328       }
2329       else
2330       {
2331         column = colSel.getMax();
2332       }
2333
2334       SequenceI[] seqs;
2335       if (viewport.getSelectionGroup() != null)
2336       {
2337         seqs = viewport.getSelectionGroup()
2338                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2339       }
2340       else
2341       {
2342         seqs = al.getSequencesArray();
2343       }
2344
2345       TrimRegionCommand trimRegion;
2346       if (trimLeft)
2347       {
2348         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2349                 column, al);
2350         ranges.setStartRes(0);
2351       }
2352       else
2353       {
2354         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2355                 column, al);
2356       }
2357
2358       statusBar.setText(MessageManager
2359               .formatMessage("label.removed_columns", new String[]
2360               { Integer.valueOf(trimRegion.getSize()).toString() }));
2361       addHistoryItem(trimRegion);
2362
2363       for (SequenceGroup sg : al.getGroups())
2364       {
2365         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2366                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2367         {
2368           al.deleteGroup(sg);
2369         }
2370       }
2371
2372       viewport.firePropertyChange("alignment", null, al.getSequences());
2373     }
2374   }
2375
2376   public void removeGappedColumnMenuItem_actionPerformed()
2377   {
2378     AlignmentI al = viewport.getAlignment();
2379     ViewportRanges ranges = viewport.getRanges();
2380     int start = 0;
2381     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2382
2383     SequenceI[] seqs;
2384     if (viewport.getSelectionGroup() != null)
2385     {
2386       seqs = viewport.getSelectionGroup()
2387               .getSequencesAsArray(viewport.getHiddenRepSequences());
2388       start = viewport.getSelectionGroup().getStartRes();
2389       end = viewport.getSelectionGroup().getEndRes();
2390     }
2391     else
2392     {
2393       seqs = viewport.getAlignment().getSequencesArray();
2394     }
2395
2396     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2397             "Remove Gapped Columns", seqs, start, end,
2398             viewport.getAlignment());
2399
2400     addHistoryItem(removeGapCols);
2401
2402     statusBar.setText(MessageManager
2403             .formatMessage("label.removed_empty_columns", new String[]
2404             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2405
2406     // This is to maintain viewport position on first residue
2407     // of first sequence
2408     SequenceI seq = al.getSequenceAt(0);
2409     int startRes = seq.findPosition(ranges.getStartRes());
2410     // ShiftList shifts;
2411     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2412     // edit.alColumnChanges=shifts.getInverse();
2413     // if (viewport.hasHiddenColumns)
2414     // viewport.getColumnSelection().compensateForEdits(shifts);
2415     ranges.setStartRes(seq.findIndex(startRes) - 1);
2416     viewport.firePropertyChange("alignment", null, al.getSequences());
2417
2418   }
2419
2420   public void removeAllGapsMenuItem_actionPerformed()
2421   {
2422     AlignmentI al = viewport.getAlignment();
2423     ViewportRanges ranges = viewport.getRanges();
2424     int start = 0;
2425     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2426
2427     SequenceI[] seqs;
2428     if (viewport.getSelectionGroup() != null)
2429     {
2430       seqs = viewport.getSelectionGroup()
2431               .getSequencesAsArray(viewport.getHiddenRepSequences());
2432       start = viewport.getSelectionGroup().getStartRes();
2433       end = viewport.getSelectionGroup().getEndRes();
2434     }
2435     else
2436     {
2437       seqs = viewport.getAlignment().getSequencesArray();
2438     }
2439
2440     // This is to maintain viewport position on first residue
2441     // of first sequence
2442     SequenceI seq = al.getSequenceAt(0);
2443     int startRes = seq.findPosition(ranges.getStartRes());
2444
2445     addHistoryItem(
2446             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2447
2448     ranges.setStartRes(seq.findIndex(startRes) - 1);
2449
2450     viewport.firePropertyChange("alignment", null, al.getSequences());
2451
2452   }
2453
2454   public void findMenuItem_actionPerformed()
2455   {
2456     new Finder(alignPanel);
2457   }
2458
2459   /**
2460    * create a new view derived from the current view
2461    *
2462    * @param viewtitle
2463    * @return frame for the new view
2464    */
2465   public AlignFrame newView(String viewtitle)
2466   {
2467     AlignmentI newal;
2468     if (viewport.hasHiddenRows())
2469     {
2470       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2471               .getFullAlignment().getSequencesArray());
2472     }
2473     else
2474     {
2475       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2476     }
2477
2478     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2479     {
2480       for (int i = 0; i < viewport.getAlignment()
2481               .getAlignmentAnnotation().length; i++)
2482       {
2483         if (!viewport.getAlignment()
2484                 .getAlignmentAnnotation()[i].autoCalculated)
2485         {
2486           newal.addAnnotation(
2487                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2488         }
2489       }
2490     }
2491
2492     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2493
2494     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2495     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2496     PaintRefresher.Register(newaf.alignPanel,
2497             newaf.alignPanel.av.getSequenceSetId());
2498
2499     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2500             newaf.alignPanel.av.getSequenceSetId());
2501     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2502             newaf.alignPanel.av.getSequenceSetId());
2503
2504     Vector comps = PaintRefresher.components
2505             .get(viewport.getSequenceSetId());
2506     int viewSize = -1;
2507     for (int i = 0; i < comps.size(); i++)
2508     {
2509       if (comps.elementAt(i) instanceof AlignmentPanel)
2510       {
2511         viewSize++;
2512       }
2513     }
2514
2515     String title = new String(this.getTitle());
2516     if (viewtitle != null)
2517     {
2518       title = viewtitle + " ( " + title + ")";
2519     }
2520     else
2521     {
2522       if (title.indexOf("(View") > -1)
2523       {
2524         title = title.substring(0, title.indexOf("(View"));
2525       }
2526       title += "(View " + viewSize + ")";
2527     }
2528
2529     newaf.setTitle(title.toString());
2530
2531     newaf.viewport.setHistoryList(viewport.getHistoryList());
2532     newaf.viewport.setRedoList(viewport.getRedoList());
2533     return newaf;
2534   }
2535
2536   /**
2537    *
2538    * @return list of feature groups on the view
2539    */
2540   public String[] getFeatureGroups()
2541   {
2542     FeatureRenderer fr = null;
2543     if (alignPanel != null
2544             && (fr = alignPanel.getFeatureRenderer()) != null)
2545     {
2546       List<String> gps = fr.getFeatureGroups();
2547       String[] _gps = gps.toArray(new String[gps.size()]);
2548       return _gps;
2549     }
2550     return null;
2551   }
2552
2553   /**
2554    * get sequence feature groups that are hidden or shown
2555    *
2556    * @param visible
2557    *          true is visible
2558    * @return list
2559    */
2560   public String[] getFeatureGroupsOfState(boolean visible)
2561   {
2562     FeatureRenderer fr = null;
2563     if (alignPanel != null
2564             && (fr = alignPanel.getFeatureRenderer()) != null)
2565     {
2566       List<String> gps = fr.getGroups(visible);
2567       String[] _gps = gps.toArray(new String[gps.size()]);
2568       return _gps;
2569     }
2570     return null;
2571   }
2572
2573   /**
2574    * Change the display state for the given feature groups
2575    *
2576    * @param groups
2577    *          list of group strings
2578    * @param state
2579    *          visible or invisible
2580    */
2581   public void setFeatureGroupState(String[] groups, boolean state)
2582   {
2583     FeatureRenderer fr = null;
2584     this.sequenceFeatures.setState(true);
2585     viewport.setShowSequenceFeatures(true);
2586     if (alignPanel != null
2587             && (fr = alignPanel.getFeatureRenderer()) != null)
2588     {
2589
2590       fr.setGroupVisibility(Arrays.asList(groups), state);
2591       alignPanel.seqPanel.seqCanvas.repaint();
2592       if (alignPanel.overviewPanel != null)
2593       {
2594         alignPanel.overviewPanel.updateOverviewImage();
2595       }
2596     }
2597   }
2598
2599   public void seqLimits_itemStateChanged()
2600   {
2601     viewport.setShowJVSuffix(seqLimits.getState());
2602     alignPanel.fontChanged();
2603     alignPanel.paintAlignment(true, false);
2604   }
2605
2606   protected void colourTextMenuItem_actionPerformed()
2607   {
2608     viewport.setColourText(colourTextMenuItem.getState());
2609     alignPanel.paintAlignment(false, false);
2610   }
2611
2612   protected void displayNonconservedMenuItem_actionPerformed()
2613   {
2614     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2615     alignPanel.paintAlignment(false, false);
2616   }
2617
2618   protected void wrapMenuItem_actionPerformed()
2619   {
2620     viewport.setWrapAlignment(wrapMenuItem.getState());
2621     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2622     scaleAbove.setEnabled(wrapMenuItem.getState());
2623     scaleLeft.setEnabled(wrapMenuItem.getState());
2624     scaleRight.setEnabled(wrapMenuItem.getState());
2625     alignPanel.paintAlignment(true, false);
2626   }
2627
2628   public void overviewMenuItem_actionPerformed()
2629   {
2630     if (alignPanel.overviewPanel != null)
2631     {
2632       return;
2633     }
2634
2635     Frame frame = new Frame();
2636     final OverviewPanel overview = new OverviewPanel(alignPanel);
2637     frame.add(overview);
2638     // +50 must allow for applet frame window
2639     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2640             .formatMessage("label.overview_params", new String[]
2641             { this.getTitle() }), overview.getPreferredSize().width,
2642             overview.getPreferredSize().height + 50);
2643
2644     frame.pack();
2645     final AlignmentPanel ap = alignPanel;
2646     frame.addWindowListener(new WindowAdapter()
2647     {
2648       @Override
2649       public void windowClosing(WindowEvent e)
2650       {
2651         overview.dispose();
2652         if (ap != null)
2653         {
2654           ap.setOverviewPanel(null);
2655         }
2656       };
2657     });
2658
2659     alignPanel.setOverviewPanel(overview);
2660
2661   }
2662
2663   @Override
2664   public void changeColour(ColourSchemeI cs)
2665   {
2666     viewport.setGlobalColourScheme(cs);
2667
2668     alignPanel.paintAlignment(true, true);
2669   }
2670
2671   protected void modifyPID_actionPerformed()
2672   {
2673     if (viewport.getAbovePIDThreshold()
2674             && viewport.getGlobalColourScheme() != null)
2675     {
2676       SliderPanel.setPIDSliderSource(alignPanel,
2677               viewport.getResidueShading(), alignPanel.getViewName());
2678       SliderPanel.showPIDSlider();
2679     }
2680   }
2681
2682   protected void modifyConservation_actionPerformed()
2683   {
2684     if (viewport.getConservationSelected()
2685             && viewport.getGlobalColourScheme() != null)
2686     {
2687       SliderPanel.setConservationSlider(alignPanel,
2688               viewport.getResidueShading(), alignPanel.getViewName());
2689       SliderPanel.showConservationSlider();
2690     }
2691   }
2692
2693   protected void conservationMenuItem_actionPerformed()
2694   {
2695     boolean selected = conservationMenuItem.getState();
2696     modifyConservation.setEnabled(selected);
2697     viewport.setConservationSelected(selected);
2698     viewport.getResidueShading().setConservationApplied(selected);
2699
2700     changeColour(viewport.getGlobalColourScheme());
2701
2702     if (selected)
2703     {
2704       modifyConservation_actionPerformed();
2705     }
2706     else
2707     {
2708       SliderPanel.hideConservationSlider();
2709     }
2710   }
2711
2712   public void abovePIDThreshold_actionPerformed()
2713   {
2714     boolean selected = abovePIDThreshold.getState();
2715     modifyPID.setEnabled(selected);
2716     viewport.setAbovePIDThreshold(selected);
2717     if (!selected)
2718     {
2719       viewport.getResidueShading().setThreshold(0,
2720               viewport.isIgnoreGapsConsensus());
2721     }
2722
2723     changeColour(viewport.getGlobalColourScheme());
2724
2725     if (selected)
2726     {
2727       modifyPID_actionPerformed();
2728     }
2729     else
2730     {
2731       SliderPanel.hidePIDSlider();
2732     }
2733   }
2734
2735   public void sortPairwiseMenuItem_actionPerformed()
2736   {
2737     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2738     AlignmentSorter.sortByPID(viewport.getAlignment(),
2739             viewport.getAlignment().getSequenceAt(0));
2740
2741     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2742             viewport.getAlignment()));
2743     alignPanel.paintAlignment(true, false);
2744   }
2745
2746   public void sortIDMenuItem_actionPerformed()
2747   {
2748     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2749     AlignmentSorter.sortByID(viewport.getAlignment());
2750     addHistoryItem(
2751             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2752     alignPanel.paintAlignment(true, false);
2753   }
2754
2755   public void sortLengthMenuItem_actionPerformed()
2756   {
2757     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2758     AlignmentSorter.sortByLength(viewport.getAlignment());
2759     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2760             viewport.getAlignment()));
2761     alignPanel.paintAlignment(true, false);
2762   }
2763
2764   public void sortGroupMenuItem_actionPerformed()
2765   {
2766     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2767     AlignmentSorter.sortByGroup(viewport.getAlignment());
2768     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2769             viewport.getAlignment()));
2770     alignPanel.paintAlignment(true, false);
2771
2772   }
2773
2774   public void removeRedundancyMenuItem_actionPerformed()
2775   {
2776     new RedundancyPanel(alignPanel);
2777   }
2778
2779   public void pairwiseAlignmentMenuItem_actionPerformed()
2780   {
2781     if (viewport.getSelectionGroup() != null
2782             && viewport.getSelectionGroup().getSize() > 1)
2783     {
2784       Frame frame = new Frame();
2785       frame.add(new PairwiseAlignPanel(alignPanel));
2786       jalview.bin.JalviewLite.addFrame(frame,
2787               MessageManager.getString("action.pairwise_alignment"), 600,
2788               500);
2789     }
2790   }
2791
2792   public void PCAMenuItem_actionPerformed()
2793   {
2794     // are the sequences aligned?
2795     if (!viewport.getAlignment().isAligned(false))
2796     {
2797       SequenceI current;
2798       int Width = viewport.getAlignment().getWidth();
2799
2800       for (int i = 0; i < viewport.getAlignment().getSequences()
2801               .size(); i++)
2802       {
2803         current = viewport.getAlignment().getSequenceAt(i);
2804
2805         if (current.getLength() < Width)
2806         {
2807           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2808         }
2809       }
2810       alignPanel.paintAlignment(false, false);
2811     }
2812
2813     if ((viewport.getSelectionGroup() != null
2814             && viewport.getSelectionGroup().getSize() < 4
2815             && viewport.getSelectionGroup().getSize() > 0)
2816             || viewport.getAlignment().getHeight() < 4)
2817     {
2818       return;
2819     }
2820
2821     try
2822     {
2823       new PCAPanel(viewport);
2824     } catch (java.lang.OutOfMemoryError ex)
2825     {
2826     }
2827
2828   }
2829
2830   public void averageDistanceTreeMenuItem_actionPerformed()
2831   {
2832     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2833             "Average distance tree using PID");
2834   }
2835
2836   public void neighbourTreeMenuItem_actionPerformed()
2837   {
2838     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2839             "Neighbour joining tree using PID");
2840   }
2841
2842   protected void njTreeBlosumMenuItem_actionPerformed()
2843   {
2844     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2845             ScoreModels.getInstance().getBlosum62().getName(),
2846             "Neighbour joining tree using BLOSUM62");
2847   }
2848
2849   protected void avTreeBlosumMenuItem_actionPerformed()
2850   {
2851     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2852             ScoreModels.getInstance().getBlosum62().getName(),
2853             "Average distance tree using BLOSUM62");
2854   }
2855
2856   void newTreePanel(String type, String pwType, String title)
2857   {
2858     // are the sequences aligned?
2859     if (!viewport.getAlignment().isAligned(false))
2860     {
2861       SequenceI current;
2862       int Width = viewport.getAlignment().getWidth();
2863
2864       for (int i = 0; i < viewport.getAlignment().getSequences()
2865               .size(); i++)
2866       {
2867         current = viewport.getAlignment().getSequenceAt(i);
2868
2869         if (current.getLength() < Width)
2870         {
2871           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2872         }
2873       }
2874       alignPanel.paintAlignment(false, false);
2875
2876     }
2877
2878     if ((viewport.getSelectionGroup() != null
2879             && viewport.getSelectionGroup().getSize() > 1)
2880             || (viewport.getAlignment().getHeight() > 1))
2881     {
2882       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2883
2884       addTreeMenuItem(tp, title);
2885
2886       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2887     }
2888   }
2889
2890   void loadTree_actionPerformed()
2891   {
2892     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2893     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2894     cap.setTreeImport();
2895     Frame frame = new Frame();
2896     frame.add(cap);
2897     jalview.bin.JalviewLite.addFrame(frame,
2898             MessageManager.getString("label.paste_newick_file"), 400, 300);
2899   }
2900
2901   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2902   {
2903     TreePanel tp = new TreePanel(alignPanel, treeFile,
2904             MessageManager.getString("label.load_tree_from_file"), tree);
2905     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2906     addTreeMenuItem(tp, treeFile);
2907   }
2908
2909   /**
2910    * sort the alignment using the given treePanel
2911    *
2912    * @param treePanel
2913    *          tree used to sort view
2914    * @param title
2915    *          string used for undo event name
2916    */
2917   public void sortByTree(TreePanel treePanel, String title)
2918   {
2919     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2920     AlignmentSorter.sortByTree(viewport.getAlignment(),
2921             treePanel.getTree());
2922     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2923     // HistoryItem.SORT));
2924     addHistoryItem(new OrderCommand(MessageManager
2925             .formatMessage("label.order_by_params", new String[]
2926             { title }), oldOrder, viewport.getAlignment()));
2927     alignPanel.paintAlignment(true, false);
2928   }
2929
2930   /**
2931    * Do any automatic reordering of the alignment and add the necessary bits to
2932    * the menu structure for the new tree
2933    *
2934    * @param treePanel
2935    * @param title
2936    */
2937   protected void addTreeMenuItem(final TreePanel treePanel,
2938           final String title)
2939   {
2940     final MenuItem item = new MenuItem(title);
2941     sortByTreeMenu.add(item);
2942     item.addActionListener(new java.awt.event.ActionListener()
2943     {
2944       @Override
2945       public void actionPerformed(ActionEvent evt)
2946       {
2947         sortByTree(treePanel, title); // treePanel.getTitle());
2948       }
2949     });
2950
2951     treePanel.addWindowListener(new WindowAdapter()
2952     {
2953       @Override
2954       public void windowOpened(WindowEvent e)
2955       {
2956         if (viewport.sortByTree)
2957         {
2958           sortByTree(treePanel, title);
2959         }
2960         super.windowOpened(e);
2961       }
2962
2963       @Override
2964       public void windowClosing(WindowEvent e)
2965       {
2966         sortByTreeMenu.remove(item);
2967       };
2968     });
2969   }
2970
2971   public boolean sortBy(AlignmentOrder alorder, String undoname)
2972   {
2973     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2974     if (viewport.applet.debug)
2975     {
2976       System.err.println("Sorting " + alorder.getOrder().size()
2977               + " in alignment '" + getTitle() + "'");
2978     }
2979     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2980     if (undoname != null)
2981     {
2982       addHistoryItem(new OrderCommand(undoname, oldOrder,
2983               viewport.getAlignment()));
2984     }
2985     alignPanel.paintAlignment(true, false);
2986     return true;
2987   }
2988
2989   protected void documentation_actionPerformed()
2990   {
2991     alignPanel.av.applet.openJalviewHelpUrl();
2992   }
2993
2994   protected void about_actionPerformed()
2995   {
2996
2997     class AboutPanel extends Canvas
2998     {
2999       String version;
3000
3001       String builddate;
3002
3003       public AboutPanel(String version, String builddate)
3004       {
3005         this.version = version;
3006         this.builddate = builddate;
3007       }
3008
3009       @Override
3010       public void paint(Graphics g)
3011       {
3012         g.setColor(Color.white);
3013         g.fillRect(0, 0, getSize().width, getSize().height);
3014         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3015         FontMetrics fm = g.getFontMetrics();
3016         int fh = fm.getHeight();
3017         int y = 5, x = 7;
3018         g.setColor(Color.black);
3019         // TODO: update this text for each release or centrally store it for
3020         // lite and application
3021         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3022         g.drawString(MessageManager
3023                 .formatMessage("label.jalviewLite_release", new String[]
3024                 { version }), x, y += fh);
3025         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3026         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3027                 new String[]
3028                 { builddate }), x, y += fh);
3029         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3030         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3031                 y += fh * 1.5);
3032         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3033                 x + 50, y += fh + 8);
3034         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3035                 x, y += fh);
3036         g.drawString(MessageManager
3037                 .getString("label.jalview_distribution_lists"), x, y += fh);
3038         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3039                 x, y += fh + 8);
3040         g.drawString(
3041                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3042                 y += fh);
3043         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3044                 x, y += fh);
3045         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3046                 x, y += fh);
3047       }
3048     }
3049
3050     Frame frame = new Frame();
3051     frame.add(new AboutPanel(JalviewLite.getVersion(),
3052             JalviewLite.getBuildDate()));
3053     jalview.bin.JalviewLite.addFrame(frame,
3054             MessageManager.getString("label.jalview"), 580, 220);
3055
3056   }
3057
3058   public void showURL(String url, String target)
3059   {
3060     if (viewport.applet == null)
3061     {
3062       System.out.println("Not running as applet - no browser available.");
3063     }
3064     else
3065     {
3066       viewport.applet.showURL(url, target);
3067     }
3068   }
3069
3070   // ////////////////////////////////////////////////////////////////////////////////
3071   // JBuilder Graphics here
3072
3073   MenuBar alignFrameMenuBar = new MenuBar();
3074
3075   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3076
3077   MenuItem loadApplication = new MenuItem(
3078           MessageManager.getString("label.view_full_application"));
3079
3080   MenuItem loadTree = new MenuItem(
3081           MessageManager.getString("label.load_associated_tree"));
3082
3083   MenuItem loadAnnotations = new MenuItem(
3084           MessageManager.getString("label.load_features_annotations"));
3085
3086   MenuItem outputFeatures = new MenuItem(
3087           MessageManager.getString("label.export_features"));
3088
3089   MenuItem outputAnnotations = new MenuItem(
3090           MessageManager.getString("label.export_annotations"));
3091
3092   MenuItem closeMenuItem = new MenuItem(
3093           MessageManager.getString("action.close"));
3094
3095   MenuItem selectAllSequenceMenuItem = new MenuItem(
3096           MessageManager.getString("action.select_all"));
3097
3098   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3099           MessageManager.getString("action.deselect_all"));
3100
3101   MenuItem invertSequenceMenuItem = new MenuItem(
3102           MessageManager.getString("action.invert_selection"));
3103
3104   MenuItem remove2LeftMenuItem = new MenuItem();
3105
3106   MenuItem remove2RightMenuItem = new MenuItem();
3107
3108   MenuItem removeGappedColumnMenuItem = new MenuItem();
3109
3110   MenuItem removeAllGapsMenuItem = new MenuItem();
3111
3112   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3113
3114   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3115
3116   MenuItem sortPairwiseMenuItem = new MenuItem();
3117
3118   MenuItem sortIDMenuItem = new MenuItem();
3119
3120   MenuItem sortLengthMenuItem = new MenuItem();
3121
3122   MenuItem sortGroupMenuItem = new MenuItem();
3123
3124   MenuItem removeRedundancyMenuItem = new MenuItem();
3125
3126   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3127
3128   MenuItem PCAMenuItem = new MenuItem();
3129
3130   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3131
3132   MenuItem neighbourTreeMenuItem = new MenuItem();
3133
3134   BorderLayout borderLayout1 = new BorderLayout();
3135
3136   public Label statusBar = new Label();
3137
3138   MenuItem clustalColour = new MenuItem();
3139
3140   MenuItem zappoColour = new MenuItem();
3141
3142   MenuItem taylorColour = new MenuItem();
3143
3144   MenuItem hydrophobicityColour = new MenuItem();
3145
3146   MenuItem helixColour = new MenuItem();
3147
3148   MenuItem strandColour = new MenuItem();
3149
3150   MenuItem turnColour = new MenuItem();
3151
3152   MenuItem buriedColour = new MenuItem();
3153
3154   MenuItem purinePyrimidineColour = new MenuItem();
3155
3156   // MenuItem RNAInteractionColour = new MenuItem();
3157
3158   MenuItem RNAHelixColour = new MenuItem();
3159
3160   MenuItem userDefinedColour = new MenuItem();
3161
3162   MenuItem PIDColour = new MenuItem();
3163
3164   MenuItem BLOSUM62Colour = new MenuItem();
3165
3166   MenuItem tcoffeeColour = new MenuItem();
3167
3168   MenuItem njTreeBlosumMenuItem = new MenuItem();
3169
3170   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3171
3172   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3173
3174   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3175
3176   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3177
3178   MenuItem alProperties = new MenuItem(
3179           MessageManager.getString("label.alignment_props"));
3180
3181   MenuItem overviewMenuItem = new MenuItem();
3182
3183   MenuItem undoMenuItem = new MenuItem();
3184
3185   MenuItem redoMenuItem = new MenuItem();
3186
3187   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3188
3189   MenuItem noColourmenuItem = new MenuItem();
3190
3191   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3192
3193   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3194
3195   MenuItem findMenuItem = new MenuItem();
3196
3197   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3198
3199   MenuItem nucleotideColour = new MenuItem();
3200
3201   MenuItem deleteGroups = new MenuItem();
3202
3203   MenuItem grpsFromSelection = new MenuItem();
3204
3205   MenuItem createGroup = new MenuItem();
3206
3207   MenuItem unGroup = new MenuItem();
3208
3209   MenuItem delete = new MenuItem();
3210
3211   MenuItem copy = new MenuItem();
3212
3213   MenuItem cut = new MenuItem();
3214
3215   Menu pasteMenu = new Menu();
3216
3217   MenuItem pasteNew = new MenuItem();
3218
3219   MenuItem pasteThis = new MenuItem();
3220
3221   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3222
3223   MenuItem font = new MenuItem();
3224
3225   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3226
3227   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3228
3229   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3230
3231   MenuItem modifyPID = new MenuItem();
3232
3233   MenuItem modifyConservation = new MenuItem();
3234
3235   CheckboxMenuItem autoCalculate = null;
3236
3237   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3238           "Sort Alignment With New Tree", true);
3239
3240   Menu sortByTreeMenu = new Menu();
3241
3242   MenuItem inputText = new MenuItem();
3243
3244   MenuItem documentation = new MenuItem();
3245
3246   MenuItem about = new MenuItem();
3247
3248   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3253
3254   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3255
3256   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3257
3258   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3259
3260   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3261
3262   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3263
3264   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3265
3266   /**
3267    * Initialise menus and other items
3268    *
3269    * @throws Exception
3270    */
3271   private void jbInit() throws Exception
3272   {
3273     setMenuBar(alignFrameMenuBar);
3274
3275     /*
3276      * Configure File menu items and actions
3277      */
3278     inputText
3279             .setLabel(MessageManager.getString("label.input_from_textbox"));
3280     inputText.addActionListener(this);
3281     Menu outputTextboxMenu = new Menu(
3282             MessageManager.getString("label.out_to_textbox"));
3283     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3284     {
3285       MenuItem item = new MenuItem(ff);
3286
3287       item.addActionListener(new java.awt.event.ActionListener()
3288       {
3289         @Override
3290         public void actionPerformed(ActionEvent e)
3291         {
3292           outputText_actionPerformed(e);
3293         }
3294       });
3295
3296       outputTextboxMenu.add(item);
3297     }
3298     closeMenuItem.addActionListener(this);
3299     loadApplication.addActionListener(this);
3300     loadTree.addActionListener(this);
3301     loadAnnotations.addActionListener(this);
3302     outputFeatures.addActionListener(this);
3303     outputAnnotations.addActionListener(this);
3304
3305     /*
3306      * Configure Edit menu items and actions
3307      */
3308     undoMenuItem.setEnabled(false);
3309     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3310     undoMenuItem.addActionListener(this);
3311     redoMenuItem.setEnabled(false);
3312     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3313     redoMenuItem.addActionListener(this);
3314     copy.setLabel(MessageManager.getString("action.copy"));
3315     copy.addActionListener(this);
3316     cut.setLabel(MessageManager.getString("action.cut"));
3317     cut.addActionListener(this);
3318     delete.setLabel(MessageManager.getString("action.delete"));
3319     delete.addActionListener(this);
3320     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3321     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3322     pasteNew.addActionListener(this);
3323     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3324     pasteThis.addActionListener(this);
3325     remove2LeftMenuItem
3326             .setLabel(MessageManager.getString("action.remove_left"));
3327     remove2LeftMenuItem.addActionListener(this);
3328     remove2RightMenuItem
3329             .setLabel(MessageManager.getString("action.remove_right"));
3330     remove2RightMenuItem.addActionListener(this);
3331     removeGappedColumnMenuItem.setLabel(
3332             MessageManager.getString("action.remove_empty_columns"));
3333     removeGappedColumnMenuItem.addActionListener(this);
3334     removeAllGapsMenuItem
3335             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3336     removeAllGapsMenuItem.addActionListener(this);
3337     removeRedundancyMenuItem
3338             .setLabel(MessageManager.getString("action.remove_redundancy"));
3339     removeRedundancyMenuItem.addActionListener(this);
3340
3341     /*
3342      * Configure Select menu items and actions
3343      */
3344     findMenuItem.setLabel(MessageManager.getString("action.find"));
3345     findMenuItem.addActionListener(this);
3346     selectAllSequenceMenuItem.addActionListener(this);
3347     deselectAllSequenceMenuItem.addActionListener(this);
3348     invertSequenceMenuItem.setLabel(
3349             MessageManager.getString("action.invert_sequence_selection"));
3350     invertSequenceMenuItem.addActionListener(this);
3351     invertColSel.setLabel(
3352             MessageManager.getString("action.invert_column_selection"));
3353     invertColSel.addActionListener(this);
3354     deleteGroups
3355             .setLabel(MessageManager.getString("action.undefine_groups"));
3356     deleteGroups.addActionListener(this);
3357     grpsFromSelection.setLabel(
3358             MessageManager.getString("action.make_groups_selection"));
3359     grpsFromSelection.addActionListener(this);
3360     createGroup.setLabel(MessageManager.getString("action.create_group"));
3361     createGroup.addActionListener(this);
3362     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3363     unGroup.addActionListener(this);
3364
3365     annotationColumnSelection.setLabel(
3366             MessageManager.getString("action.select_by_annotation"));
3367     annotationColumnSelection.addActionListener(this);
3368
3369     /*
3370      * Configure View menu items and actions
3371      */
3372     newView.setLabel(MessageManager.getString("action.new_view"));
3373     newView.addActionListener(this);
3374     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3375     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3376     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3377     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3378     hideColumns
3379             .setLabel(MessageManager.getString("label.selected_columns"));
3380     hideSequences
3381             .setLabel(MessageManager.getString("label.selected_sequences"));
3382     hideAllButSelection.setLabel(
3383             MessageManager.getString("label.all_but_selected_region"));
3384     hideAllSelection
3385             .setLabel(MessageManager.getString("label.selected_region"));
3386     showAllHidden.setLabel(
3387             MessageManager.getString("label.all_sequences_columns"));
3388     showColumns.addActionListener(this);
3389     showSeqs.addActionListener(this);
3390     hideColumns.addActionListener(this);
3391     hideSequences.addActionListener(this);
3392     hideAllButSelection.addActionListener(this);
3393     hideAllSelection.addActionListener(this);
3394     showAllHidden.addActionListener(this);
3395     featureSettings
3396             .setLabel(MessageManager.getString("action.feature_settings"));
3397     featureSettings.addActionListener(this);
3398     sequenceFeatures.setLabel(
3399             MessageManager.getString("label.show_sequence_features"));
3400     sequenceFeatures.addItemListener(this);
3401     sequenceFeatures.setState(false);
3402     followMouseOverFlag.setLabel(
3403             MessageManager.getString("label.automatic_scrolling"));
3404     followMouseOverFlag.addItemListener(this);
3405     alProperties.addActionListener(this);
3406     overviewMenuItem
3407             .setLabel(MessageManager.getString("label.overview_window"));
3408     overviewMenuItem.addActionListener(this);
3409
3410     /*
3411      * Configure Annotations menu items and actions
3412      */
3413     annotationPanelMenuItem
3414             .setLabel(MessageManager.getString("label.show_annotations"));
3415     annotationPanelMenuItem.addItemListener(this);
3416     showGroupConsensus
3417             .setLabel(MessageManager.getString("label.group_consensus"));
3418     showGroupConservation
3419             .setLabel(MessageManager.getString("label.group_conservation"));
3420     showConsensusHistogram.setLabel(
3421             MessageManager.getString("label.show_consensus_histogram"));
3422     showSequenceLogo.setLabel(
3423             MessageManager.getString("label.show_consensus_logo"));
3424     normSequenceLogo.setLabel(
3425             MessageManager.getString("label.norm_consensus_logo"));
3426     applyAutoAnnotationSettings
3427             .setLabel(MessageManager.getString("label.apply_all_groups"));
3428     applyAutoAnnotationSettings.setState(true);
3429     Menu autoAnnMenu = new Menu(
3430             MessageManager.getString("label.autocalculated_annotation"));
3431     showGroupConsensus.addItemListener(this);
3432     showGroupConservation.addItemListener(this);
3433     showConsensusHistogram.addItemListener(this);
3434     showSequenceLogo.addItemListener(this);
3435     normSequenceLogo.addItemListener(this);
3436     applyAutoAnnotationSettings.addItemListener(this);
3437     showAlignmentAnnotations = new CheckboxMenuItem(
3438             MessageManager.getString("label.show_all_al_annotations"));
3439     showSequenceAnnotations = new CheckboxMenuItem(
3440             MessageManager.getString("label.show_all_seq_annotations"));
3441     sortAnnBySequence = new CheckboxMenuItem(
3442             MessageManager.getString("label.sort_annotations_by_sequence"));
3443     sortAnnByLabel = new CheckboxMenuItem(
3444             MessageManager.getString("label.sort_annotations_by_label"));
3445     showAutoFirst = new CheckboxMenuItem(
3446             MessageManager.getString("label.show_first"));
3447     showAutoFirst.setState(false); // pending applet parameter
3448     setShowAutoCalculatedAbove(showAutoFirst.getState());
3449     showAutoLast = new CheckboxMenuItem(
3450             MessageManager.getString("label.show_last"));
3451     showAutoLast.setState(!showAutoFirst.getState());
3452     showAlignmentAnnotations.addItemListener(this);
3453     showSequenceAnnotations.addItemListener(this);
3454     sortAnnBySequence.addItemListener(this);
3455     sortAnnByLabel.addItemListener(this);
3456     showAutoFirst.addItemListener(this);
3457     showAutoLast.addItemListener(this);
3458
3459     /*
3460      * Configure Format menu items and actions
3461      */
3462     font.setLabel(MessageManager.getString("action.font"));
3463     font.addActionListener(this);
3464     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3465     scaleAbove.setState(true);
3466     scaleAbove.setEnabled(false);
3467     scaleAbove.addItemListener(this);
3468     scaleLeft.setEnabled(false);
3469     scaleLeft.setState(true);
3470     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3471     scaleLeft.addItemListener(this);
3472     scaleRight.setEnabled(false);
3473     scaleRight.setState(true);
3474     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3475     scaleRight.addItemListener(this);
3476     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3477     viewBoxesMenuItem.setState(true);
3478     viewBoxesMenuItem.addItemListener(this);
3479     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3480     viewTextMenuItem.setState(true);
3481     viewTextMenuItem.addItemListener(this);
3482     colourTextMenuItem
3483             .setLabel(MessageManager.getString("label.colour_text"));
3484     colourTextMenuItem.addItemListener(this);
3485     displayNonconservedMenuItem
3486             .setLabel(MessageManager.getString("label.show_non_conserved"));
3487     displayNonconservedMenuItem.addItemListener(this);
3488     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3489     wrapMenuItem.addItemListener(this);
3490     renderGapsMenuItem
3491             .setLabel(MessageManager.getString("action.show_gaps"));
3492     renderGapsMenuItem.setState(true);
3493     renderGapsMenuItem.addItemListener(this);
3494     centreColumnLabelFlag.setLabel(
3495             MessageManager.getString("label.centre_column_labels"));
3496     centreColumnLabelFlag.addItemListener(this);
3497     seqLimits.setState(true);
3498     seqLimits.setLabel(
3499             MessageManager.getString("label.show_sequence_limits"));
3500     seqLimits.addItemListener(this);
3501
3502     /*
3503      * Configure Colour menu items and actions
3504      */
3505     applyToAllGroups.setLabel(
3506             MessageManager.getString("label.apply_colour_to_all_groups"));
3507     applyToAllGroups.setState(true);
3508     applyToAllGroups.addItemListener(this);
3509     clustalColour.setLabel(
3510             MessageManager.getString("label.colourScheme_clustal"));
3511     clustalColour.addActionListener(this);
3512     zappoColour
3513             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3514     zappoColour.addActionListener(this);
3515     taylorColour.setLabel(
3516             MessageManager.getString("label.colourScheme_taylor"));
3517     taylorColour.addActionListener(this);
3518     hydrophobicityColour.setLabel(
3519             MessageManager.getString("label.colourScheme_hydrophobic"));
3520     hydrophobicityColour.addActionListener(this);
3521     helixColour.setLabel(MessageManager
3522             .getString("label.colourScheme_helix_propensity"));
3523     helixColour.addActionListener(this);
3524     strandColour.setLabel(MessageManager
3525             .getString("label.colourScheme_strand_propensity"));
3526     strandColour.addActionListener(this);
3527     turnColour.setLabel(
3528             MessageManager.getString("label.colourScheme_turn_propensity"));
3529     turnColour.addActionListener(this);
3530     buriedColour.setLabel(
3531             MessageManager.getString("label.colourScheme_buried_index"));
3532     buriedColour.addActionListener(this);
3533     purinePyrimidineColour.setLabel(MessageManager
3534             .getString("label.colourScheme_purine/pyrimidine"));
3535     purinePyrimidineColour.addActionListener(this);
3536     // RNAInteractionColour.setLabel(MessageManager
3537     // .getString("label.rna_interaction"));
3538     // RNAInteractionColour.addActionListener(this);
3539     RNAHelixColour.setLabel(
3540             MessageManager.getString("label.colourScheme_rna_helices"));
3541     RNAHelixColour.addActionListener(this);
3542     userDefinedColour
3543             .setLabel(MessageManager.getString("action.user_defined"));
3544     userDefinedColour.addActionListener(this);
3545     PIDColour.setLabel(
3546             MessageManager.getString("label.colourScheme_%_identity"));
3547     PIDColour.addActionListener(this);
3548     BLOSUM62Colour.setLabel(
3549             MessageManager.getString("label.colourScheme_blosum62"));
3550     BLOSUM62Colour.addActionListener(this);
3551     tcoffeeColour.setLabel(
3552             MessageManager.getString("label.colourScheme_t-coffee_scores"));
3553     // it will be enabled only if a score file is provided
3554     tcoffeeColour.setEnabled(false);
3555     tcoffeeColour.addActionListener(this);
3556     conservationMenuItem
3557             .setLabel(MessageManager.getString("action.by_conservation"));
3558     conservationMenuItem.addItemListener(this);
3559     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3560     noColourmenuItem.addActionListener(this);
3561     abovePIDThreshold.setLabel(
3562             MessageManager.getString("label.above_identity_threshold"));
3563     abovePIDThreshold.addItemListener(this);
3564     nucleotideColour.setLabel(
3565             MessageManager.getString("label.colourScheme_nucleotide"));
3566     nucleotideColour.addActionListener(this);
3567     modifyPID.setLabel(
3568             MessageManager.getString("label.modify_identity_threshold"));
3569     modifyPID.setEnabled(abovePIDThreshold.getState());
3570     modifyPID.addActionListener(this);
3571     modifyConservation.setLabel(MessageManager
3572             .getString("label.modify_conservation_threshold"));
3573     modifyConservation.setEnabled(conservationMenuItem.getState());
3574     modifyConservation.addActionListener(this);
3575     annotationColour
3576             .setLabel(MessageManager.getString("action.by_annotation"));
3577     annotationColour.addActionListener(this);
3578
3579     /*
3580      * Configure Calculate menu items and actions
3581      */
3582     sortPairwiseMenuItem
3583             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3584     sortPairwiseMenuItem.addActionListener(this);
3585     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3586     sortIDMenuItem.addActionListener(this);
3587     sortLengthMenuItem
3588             .setLabel(MessageManager.getString("action.by_length"));
3589     sortLengthMenuItem.addActionListener(this);
3590     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3591     sortGroupMenuItem.addActionListener(this);
3592     pairwiseAlignmentMenuItem.setLabel(
3593             MessageManager.getString("action.pairwise_alignment"));
3594     pairwiseAlignmentMenuItem.addActionListener(this);
3595     PCAMenuItem.setLabel(
3596             MessageManager.getString("label.principal_component_analysis"));
3597     PCAMenuItem.addActionListener(this);
3598     autoCalculate = new CheckboxMenuItem(
3599             MessageManager.getString("label.autocalculate_consensus"),
3600             true);
3601     averageDistanceTreeMenuItem.setLabel(
3602             MessageManager.getString("label.average_distance_identity"));
3603     averageDistanceTreeMenuItem.addActionListener(this);
3604     neighbourTreeMenuItem.setLabel(
3605             MessageManager.getString("label.neighbour_joining_identity"));
3606     neighbourTreeMenuItem.addActionListener(this);
3607     avDistanceTreeBlosumMenuItem.setLabel(
3608             MessageManager.getString("label.average_distance_blosum62"));
3609     avDistanceTreeBlosumMenuItem.addActionListener(this);
3610     njTreeBlosumMenuItem
3611             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3612     njTreeBlosumMenuItem.addActionListener(this);
3613     sortByTreeMenu
3614             .setLabel(MessageManager.getString("action.by_tree_order"));
3615     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3616     Menu calculateTreeMenu = new Menu(
3617             MessageManager.getString("action.calculate_tree"));
3618     autoCalculate.addItemListener(this);
3619     sortByTree.addItemListener(this);
3620
3621     /*
3622      * Configure Help menu items and actions
3623      */
3624     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3625     documentation.setLabel(MessageManager.getString("label.documentation"));
3626     documentation.addActionListener(this);
3627     about.setLabel(MessageManager.getString("label.about"));
3628     about.addActionListener(this);
3629
3630     /*
3631      * Add top level menus to frame
3632      */
3633     alignFrameMenuBar.add(fileMenu);
3634     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3635     alignFrameMenuBar.add(editMenu);
3636     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3637     alignFrameMenuBar.add(selectMenu);
3638     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3639     alignFrameMenuBar.add(viewMenu);
3640     Menu annotationsMenu = new Menu(
3641             MessageManager.getString("action.annotations"));
3642     alignFrameMenuBar.add(annotationsMenu);
3643     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3644     alignFrameMenuBar.add(formatMenu);
3645     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3646     alignFrameMenuBar.add(colourMenu);
3647     Menu calculateMenu = new Menu(
3648             MessageManager.getString("action.calculate"));
3649     alignFrameMenuBar.add(calculateMenu);
3650     alignFrameMenuBar.add(helpMenu);
3651
3652     /*
3653      * File menu
3654      */
3655     fileMenu.add(inputText);
3656     fileMenu.add(loadTree);
3657     fileMenu.add(loadAnnotations);
3658     fileMenu.addSeparator();
3659     fileMenu.add(outputTextboxMenu);
3660     fileMenu.add(outputFeatures);
3661     fileMenu.add(outputAnnotations);
3662     if (jalviewServletURL != null)
3663     {
3664       fileMenu.add(loadApplication);
3665     }
3666     fileMenu.addSeparator();
3667     fileMenu.add(closeMenuItem);
3668
3669     /*
3670      * Edit menu
3671      */
3672     editMenu.add(undoMenuItem);
3673     editMenu.add(redoMenuItem);
3674     editMenu.add(cut);
3675     editMenu.add(copy);
3676     pasteMenu.add(pasteNew);
3677     pasteMenu.add(pasteThis);
3678     editMenu.add(pasteMenu);
3679     editMenu.add(delete);
3680     editMenu.addSeparator();
3681     editMenu.add(remove2LeftMenuItem);
3682     editMenu.add(remove2RightMenuItem);
3683     editMenu.add(removeGappedColumnMenuItem);
3684     editMenu.add(removeAllGapsMenuItem);
3685     editMenu.add(removeRedundancyMenuItem);
3686
3687     /*
3688      * Select menu
3689      */
3690     selectMenu.add(findMenuItem);
3691     selectMenu.addSeparator();
3692     selectMenu.add(selectAllSequenceMenuItem);
3693     selectMenu.add(deselectAllSequenceMenuItem);
3694     selectMenu.add(invertSequenceMenuItem);
3695     selectMenu.add(invertColSel);
3696     selectMenu.add(createGroup);
3697     selectMenu.add(unGroup);
3698     selectMenu.add(grpsFromSelection);
3699     selectMenu.add(deleteGroups);
3700     selectMenu.add(annotationColumnSelection);
3701
3702     /*
3703      * View menu
3704      */
3705     viewMenu.add(newView);
3706     viewMenu.addSeparator();
3707     showMenu.add(showColumns);
3708     showMenu.add(showSeqs);
3709     showMenu.add(showAllHidden);
3710     viewMenu.add(showMenu);
3711     hideMenu.add(hideColumns);
3712     hideMenu.add(hideSequences);
3713     hideMenu.add(hideAllSelection);
3714     hideMenu.add(hideAllButSelection);
3715     viewMenu.add(hideMenu);
3716     viewMenu.addSeparator();
3717     viewMenu.add(followMouseOverFlag);
3718     viewMenu.addSeparator();
3719     viewMenu.add(sequenceFeatures);
3720     viewMenu.add(featureSettings);
3721     viewMenu.addSeparator();
3722     viewMenu.add(alProperties);
3723     viewMenu.addSeparator();
3724     viewMenu.add(overviewMenuItem);
3725
3726     /*
3727      * Annotations menu
3728      */
3729     annotationsMenu.add(annotationPanelMenuItem);
3730     annotationsMenu.addSeparator();
3731     annotationsMenu.add(showAlignmentAnnotations);
3732     annotationsMenu.add(showSequenceAnnotations);
3733     annotationsMenu.add(sortAnnBySequence);
3734     annotationsMenu.add(sortAnnByLabel);
3735     annotationsMenu.addSeparator();
3736     autoAnnMenu.add(showAutoFirst);
3737     autoAnnMenu.add(showAutoLast);
3738     autoAnnMenu.addSeparator();
3739     autoAnnMenu.add(applyAutoAnnotationSettings);
3740     autoAnnMenu.add(showConsensusHistogram);
3741     autoAnnMenu.add(showSequenceLogo);
3742     autoAnnMenu.add(normSequenceLogo);
3743     autoAnnMenu.addSeparator();
3744     autoAnnMenu.add(showGroupConservation);
3745     autoAnnMenu.add(showGroupConsensus);
3746     annotationsMenu.add(autoAnnMenu);
3747
3748     /*
3749      * Format menu
3750      */
3751     formatMenu.add(font);
3752     formatMenu.add(seqLimits);
3753     formatMenu.add(wrapMenuItem);
3754     formatMenu.add(scaleAbove);
3755     formatMenu.add(scaleLeft);
3756     formatMenu.add(scaleRight);
3757     formatMenu.add(viewBoxesMenuItem);
3758     formatMenu.add(viewTextMenuItem);
3759     formatMenu.add(colourTextMenuItem);
3760     formatMenu.add(displayNonconservedMenuItem);
3761     formatMenu.add(renderGapsMenuItem);
3762     formatMenu.add(centreColumnLabelFlag);
3763
3764     /*
3765      * Colour menu
3766      */
3767     colourMenu.add(applyToAllGroups);
3768     colourMenu.addSeparator();
3769     colourMenu.add(noColourmenuItem);
3770     colourMenu.add(clustalColour);
3771     colourMenu.add(BLOSUM62Colour);
3772     colourMenu.add(PIDColour);
3773     colourMenu.add(zappoColour);
3774     colourMenu.add(taylorColour);
3775     colourMenu.add(hydrophobicityColour);
3776     colourMenu.add(helixColour);
3777     colourMenu.add(strandColour);
3778     colourMenu.add(turnColour);
3779     colourMenu.add(buriedColour);
3780     colourMenu.add(nucleotideColour);
3781     colourMenu.add(purinePyrimidineColour);
3782     // colourMenu.add(RNAInteractionColour);
3783     colourMenu.add(tcoffeeColour);
3784     colourMenu.add(userDefinedColour);
3785     colourMenu.addSeparator();
3786     colourMenu.add(conservationMenuItem);
3787     colourMenu.add(modifyConservation);
3788     colourMenu.add(abovePIDThreshold);
3789     colourMenu.add(modifyPID);
3790     colourMenu.add(annotationColour);
3791     colourMenu.add(RNAHelixColour);
3792
3793     /*
3794      * Calculate menu
3795      */
3796     sortMenu.add(sortIDMenuItem);
3797     sortMenu.add(sortLengthMenuItem);
3798     sortMenu.add(sortByTreeMenu);
3799     sortMenu.add(sortGroupMenuItem);
3800     sortMenu.add(sortPairwiseMenuItem);
3801     calculateMenu.add(sortMenu);
3802     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3803     calculateTreeMenu.add(neighbourTreeMenuItem);
3804     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3805     calculateTreeMenu.add(njTreeBlosumMenuItem);
3806     calculateMenu.add(calculateTreeMenu);
3807     calculateMenu.addSeparator();
3808     calculateMenu.add(pairwiseAlignmentMenuItem);
3809     calculateMenu.add(PCAMenuItem);
3810     calculateMenu.add(autoCalculate);
3811     calculateMenu.add(sortByTree);
3812
3813     /*
3814      * Help menu
3815      */
3816     helpMenu.add(documentation);
3817     helpMenu.add(about);
3818
3819     /*
3820      * Status bar
3821      */
3822     statusBar.setBackground(Color.white);
3823     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3824     statusBar.setText(MessageManager.getString("label.status_bar"));
3825     this.add(statusBar, BorderLayout.SOUTH);
3826   }
3827
3828   @Override
3829   public void setStatus(String string)
3830   {
3831     statusBar.setText(string);
3832   };
3833
3834   MenuItem featureSettings = new MenuItem();
3835
3836   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3837
3838   MenuItem annotationColour = new MenuItem();
3839
3840   MenuItem annotationColumnSelection = new MenuItem();
3841
3842   MenuItem invertColSel = new MenuItem();
3843
3844   MenuItem showColumns = new MenuItem();
3845
3846   MenuItem showSeqs = new MenuItem();
3847
3848   MenuItem hideColumns = new MenuItem();
3849
3850   MenuItem hideSequences = new MenuItem();
3851
3852   MenuItem hideAllButSelection = new MenuItem();
3853
3854   MenuItem hideAllSelection = new MenuItem();
3855
3856   MenuItem showAllHidden = new MenuItem();
3857
3858   MenuItem newView = new MenuItem();
3859
3860   private CheckboxMenuItem showAlignmentAnnotations;
3861
3862   private CheckboxMenuItem showSequenceAnnotations;
3863
3864   private CheckboxMenuItem sortAnnBySequence;
3865
3866   private CheckboxMenuItem sortAnnByLabel;
3867
3868   private CheckboxMenuItem showAutoFirst;
3869
3870   private CheckboxMenuItem showAutoLast;
3871
3872   private SplitFrame splitFrame;
3873
3874   /**
3875    * Attach the alignFrame panels after embedding menus, if necessary. This used
3876    * to be called setEmbedded, but is now creates the dropdown menus in a
3877    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3878    *
3879    * @param reallyEmbedded
3880    *          true to attach the view to the applet area on the page rather than
3881    *          in a new window
3882    */
3883   public void createAlignFrameWindow(boolean reallyEmbedded)
3884   {
3885     if (reallyEmbedded)
3886     {
3887       embedAlignFrameInApplet(viewport.applet);
3888     }
3889     else
3890     {
3891       // //////
3892       // test and embed menu bar if necessary.
3893       //
3894       if (embedMenuIfNeeded(alignPanel))
3895       {
3896         /*
3897          * adjust for status bar height too. ? pointless as overridden by layout
3898          * manager
3899          */
3900         alignPanel.setSize(getSize().width,
3901                 getSize().height - statusBar.getHeight());
3902       }
3903       add(statusBar, BorderLayout.SOUTH);
3904       add(alignPanel, BorderLayout.CENTER);
3905       // and register with the applet so it can pass external API calls to us
3906       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3907               frameHeight);
3908     }
3909   }
3910
3911   /**
3912    * Add the components of this AlignFrame to the applet container.
3913    *
3914    * @param theApplet
3915    */
3916   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3917   {
3918     // ////
3919     // Explicitly build the embedded menu panel for the on-page applet
3920     //
3921     // view cannot be closed if its actually on the page
3922     fileMenu.remove(closeMenuItem);
3923     fileMenu.remove(3); // Remove Separator
3924     // construct embedded menu, using default font
3925     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3926     // and actually add the components to the applet area
3927     theApplet.setLayout(new BorderLayout());
3928     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3929     theApplet.add(statusBar, BorderLayout.SOUTH);
3930     // TODO should size be left to the layout manager?
3931     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3932             - embeddedMenu.getHeight() - statusBar.getHeight());
3933     theApplet.add(alignPanel, BorderLayout.CENTER);
3934     final AlignFrame me = this;
3935     theApplet.addFocusListener(new FocusListener()
3936     {
3937
3938       @Override
3939       public void focusLost(FocusEvent e)
3940       {
3941         if (theApplet.currentAlignFrame == me)
3942         {
3943           theApplet.currentAlignFrame = null;
3944         }
3945       }
3946
3947       @Override
3948       public void focusGained(FocusEvent e)
3949       {
3950         theApplet.currentAlignFrame = me;
3951       }
3952     });
3953     theApplet.validate();
3954   }
3955
3956   /**
3957    * create a new binding between structures in an existing jmol viewer instance
3958    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3959    * this does not open a new Jmol window, or modify the display of the
3960    * structures in the original jmol window. Note This method doesn't work
3961    * without an additional javascript library to exchange messages between the
3962    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3963    *
3964    * @param viewer
3965    *          JmolViewer instance
3966    * @param sequenceIds
3967    *          - sequence Ids to search for associations
3968    */
3969   public SequenceStructureBinding addStructureViewInstance(
3970           Object jmolviewer, String[] sequenceIds)
3971   {
3972     Viewer viewer = null;
3973     try
3974     {
3975       viewer = (Viewer) jmolviewer;
3976     } catch (ClassCastException ex)
3977     {
3978       System.err.println(
3979               "Unsupported viewer object :" + jmolviewer.getClass());
3980     }
3981     if (viewer == null)
3982     {
3983       System.err.println("Can't use this object as a structure viewer:"
3984               + jmolviewer.getClass());
3985       return null;
3986     }
3987     SequenceI[] seqs = null;
3988     if (sequenceIds == null || sequenceIds.length == 0)
3989     {
3990       seqs = viewport.getAlignment().getSequencesArray();
3991     }
3992     else
3993     {
3994       Vector sqi = new Vector();
3995       AlignmentI al = viewport.getAlignment();
3996       for (int sid = 0; sid < sequenceIds.length; sid++)
3997       {
3998         SequenceI sq = al.findName(sequenceIds[sid]);
3999         if (sq != null)
4000         {
4001           sqi.addElement(sq);
4002         }
4003       }
4004       if (sqi.size() > 0)
4005       {
4006         seqs = new SequenceI[sqi.size()];
4007         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4008         {
4009           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4010         }
4011       }
4012       else
4013       {
4014         return null;
4015       }
4016     }
4017     AAStructureBindingModel jmv = null;
4018     // TODO: search for a jmv that involves viewer
4019     if (jmv == null)
4020     { // create a new viewer/jalview binding.
4021       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4022     }
4023     return jmv;
4024
4025   }
4026
4027   /**
4028    * bind a pdb file to a sequence in the current view
4029    *
4030    * @param sequenceId
4031    *          - sequenceId within the dataset.
4032    * @param pdbEntryString
4033    *          - the short name for the PDB file
4034    * @param pdbFile
4035    *          - pdb file - either a URL or a valid PDB file.
4036    * @return true if binding was as success TODO: consider making an exception
4037    *         structure for indicating when PDB parsing or sequenceId location
4038    *         fails.
4039    */
4040   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4041           String pdbFile)
4042   {
4043     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4044     boolean needtoadd = false;
4045     if (toaddpdb != null)
4046     {
4047       Vector pdbe = toaddpdb.getAllPDBEntries();
4048       PDBEntry pdbentry = null;
4049       if (pdbe != null && pdbe.size() > 0)
4050       {
4051         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4052         {
4053           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4054           if (!pdbentry.getId().equals(pdbEntryString)
4055                   && !pdbentry.getFile().equals(pdbFile))
4056           {
4057             pdbentry = null;
4058           }
4059           else
4060           {
4061             continue;
4062           }
4063         }
4064       }
4065       if (pdbentry == null)
4066       {
4067         pdbentry = new PDBEntry();
4068         pdbentry.setId(pdbEntryString);
4069         pdbentry.setFile(pdbFile);
4070         needtoadd = true; // add this new entry to sequence.
4071       }
4072       // resolve data source
4073       // TODO: this code should be a refactored to an io package
4074       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4075               FileFormat.PDB);
4076       if (protocol == null)
4077       {
4078         return false;
4079       }
4080       if (needtoadd)
4081       {
4082         pdbentry.setProperty("protocol", protocol);
4083         toaddpdb.addPDBId(pdbentry);
4084         alignPanel.getStructureSelectionManager()
4085                 .registerPDBEntry(pdbentry);
4086       }
4087     }
4088     return true;
4089   }
4090
4091   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4092   {
4093     if (seqs != null)
4094     {
4095       Vector sequences = new Vector();
4096       for (int i = 0; i < seqs.length; i++)
4097       {
4098         if (seqs[i] != null)
4099         {
4100           sequences
4101                   .addElement(new Object[]
4102                   { seqs[i], (chains != null) ? chains[i] : null });
4103         }
4104       }
4105       seqs = new SequenceI[sequences.size()];
4106       chains = new String[sequences.size()];
4107       for (int i = 0, isize = sequences.size(); i < isize; i++)
4108       {
4109         Object[] oj = (Object[]) sequences.elementAt(i);
4110
4111         seqs[i] = (SequenceI) oj[0];
4112         chains[i] = (String) oj[1];
4113       }
4114     }
4115     return new Object[] { seqs, chains };
4116
4117   }
4118
4119   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4120           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4121   {
4122     // Scrub any null sequences from the array
4123     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4124     seqs = (SequenceI[]) sqch[0];
4125     chains = (String[]) sqch[1];
4126     if (seqs == null || seqs.length == 0)
4127     {
4128       System.err.println(
4129               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4130     }
4131     if (protocol == null)
4132     {
4133       String sourceType = (String) pdb.getProperty("protocol");
4134       try
4135       {
4136         protocol = DataSourceType.valueOf(sourceType);
4137       } catch (IllegalArgumentException e)
4138       {
4139         // ignore
4140       }
4141       if (protocol == null)
4142       {
4143         System.err.println("Couldn't work out protocol to open structure: "
4144                 + pdb.getId());
4145         return;
4146       }
4147     }
4148     if (applet.useXtrnalSviewer)
4149     {
4150       // register the association(s) and quit, don't create any windows.
4151       if (StructureSelectionManager.getStructureSelectionManager(applet)
4152               .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4153       {
4154         System.err.println("Failed to map " + pdb.getFile() + " ("
4155                 + protocol + ") to any sequences");
4156       }
4157       return;
4158     }
4159     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4160     {
4161       // can only do alignments with Jmol
4162       // find the last jmol window assigned to this alignment
4163       AppletJmol ajm = null, tajm;
4164       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4165       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4166       {
4167         tajm = (AppletJmol) jmols.elementAt(i);
4168         if (tajm.ap.alignFrame == this)
4169         {
4170           ajm = tajm;
4171           break;
4172         }
4173       }
4174       if (ajm != null)
4175       {
4176         System.err.println(
4177                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4178         // try and add the pdb structure
4179         // ajm.addS
4180         ajm = null;
4181       }
4182     }
4183     // otherwise, create a new window
4184     if (applet.jmolAvailable)
4185     {
4186       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4187       applet.lastFrameX += 40;
4188       applet.lastFrameY += 40;
4189     }
4190     else
4191     {
4192       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4193     }
4194
4195   }
4196
4197   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4198           SequenceI[][] seqs, String[][] chains, String[] protocols)
4199   {
4200     // TODO Auto-generated method stub
4201     System.err.println("Aligned Structure View: Not yet implemented.");
4202   }
4203
4204   /**
4205    * modify the current selection, providing the user has not made a selection
4206    * already.
4207    *
4208    * @param sel
4209    *          - sequences from this alignment
4210    * @param csel
4211    *          - columns to be selected on the alignment
4212    */
4213   public void select(SequenceGroup sel, ColumnSelection csel,
4214           HiddenColumns hidden)
4215   {
4216     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4217   }
4218
4219   public void scrollTo(int row, int column)
4220   {
4221     alignPanel.seqPanel.scrollTo(row, column);
4222   }
4223
4224   public void scrollToRow(int row)
4225   {
4226     alignPanel.seqPanel.scrollToRow(row);
4227   }
4228
4229   public void scrollToColumn(int column)
4230   {
4231     alignPanel.seqPanel.scrollToColumn(column);
4232   }
4233
4234   /**
4235    * @return the alignments unique ID.
4236    */
4237   public String getSequenceSetId()
4238   {
4239     return viewport.getSequenceSetId();
4240   }
4241
4242   /**
4243    * Load the (T-Coffee) score file from the specified url
4244    *
4245    * @param source
4246    *          File/URL/T-COFFEE score file contents
4247    * @throws IOException
4248    * @return true if alignment was annotated with data from source
4249    */
4250   public boolean loadScoreFile(String source) throws IOException
4251   {
4252
4253     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4254             AppletFormatAdapter.checkProtocol(source));
4255     if (!file.isValid())
4256     {
4257       // TODO: raise dialog for gui
4258       System.err.println("Problems parsing T-Coffee scores: "
4259               + file.getWarningMessage());
4260       System.err.println("Origin was:\n" + source);
4261       return false;
4262     }
4263
4264     /*
4265      * check that the score matrix matches the alignment dimensions
4266      */
4267     AlignmentI aln;
4268     if ((aln = viewport.getAlignment()) != null
4269             && (aln.getHeight() != file.getHeight()
4270                     || aln.getWidth() != file.getWidth()))
4271     {
4272       // TODO: raise a dialog box here rather than bomb out.
4273       System.err.println(
4274               "The scores matrix does not match the alignment dimensions");
4275
4276     }
4277
4278     // TODO add parameter to indicate if matching should be done
4279     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4280     {
4281       alignPanel.fontChanged();
4282       tcoffeeColour.setEnabled(true);
4283       // switch to this color
4284       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4285       return true;
4286     }
4287     else
4288     {
4289       System.err.println("Problems resolving T-Coffee scores:");
4290       if (file.getWarningMessage() != null)
4291       {
4292         System.err.println(file.getWarningMessage());
4293       }
4294     }
4295     return false;
4296   }
4297
4298   public SplitFrame getSplitFrame()
4299   {
4300     return this.splitFrame;
4301   }
4302
4303   public void setSplitFrame(SplitFrame sf)
4304   {
4305     this.splitFrame = sf;
4306   }
4307
4308   // may not need this
4309   @Override
4310   public void setShowSeqFeatures(boolean b)
4311   {
4312     // showSeqFeatures.setSelected(b);
4313     viewport.setShowSequenceFeatures(b);
4314
4315   }
4316
4317   @Override
4318   public void setMenusForViewport()
4319   {
4320     // setMenusFromViewport(viewport);
4321
4322   }
4323
4324   @Override
4325   public void refreshFeatureUI(boolean enableIfNecessary)
4326   {
4327     if (enableIfNecessary)
4328     {
4329       sequenceFeatures.setState(true);
4330       alignPanel.av.setShowSequenceFeatures(true);
4331     }
4332   }
4333
4334   @Override
4335   public FeatureSettingsControllerI getFeatureSettingsUI()
4336   {
4337     return alignPanel.av.featureSettings;
4338   }
4339
4340 }